title: 10X_Bone_Marrow_Mouse_Normal_2

description:
Normal_WBM_S1_L001_R1_001.fastq.gz
processed data file:
mmu_10X_scRNA_Landscape_of_leukemogenesis_all_counts.csv
mmu_10X_scRNA_Landscape_of_leukemogenesis_all.rds
mmu_10X_scRNA_Landscape_of_leukemogenesis_all_unspliced.rds
mmu_10X_scRNA_Landscape_of_leukemogenesis_counts.csv
mmu_10X_scRNA_Landscape_of_leukemogenesis_Malignant_at_T3_counts.csv
mmu_10X_scRNA_Landscape_of_leukemogenesis_Malignant_at_T3.rds
mmu_10X_scRNA_Landscape_of_leukemogenesis_PLC_counts.csv
mmu_10X_scRNA_Landscape_of_leukemogenesis_PLC.rds
mmu_10X_scRNA_Landscape_of_leukemogenesis.rds
mmu_10X_scRNA_Landscape_of_leukemogenesis_tipping_point_counts.csv
mmu_10X_scRNA_Landscape_of_leukemogenesis_tipping_point.rds
mmu_10X_scRNA_Landscape_of_Malignant_all_counts.csv
mmu_10X_scRNA_Landscape_of_Malignant_all.rds


title: S_asf1ab_1

status: Public on Jan 30 2023

type: SRA

city: Shanghai

first: Chuanwei

last: Yang

address: 2005 Songhu Road, Yangpu District

department: school of life sciences

country: China

institute: Fudan university

library_source: transcriptomic

data_processing:
Raw sequence reads were initially processed by FASTQC for quality control, and then adapter sequences and poor quality reads were removed by using CUTADAPT
Quality filtered reads were then mapped to TAIR10 using STAR
Read counts were calculated by using htseq-count
Differential gene expression analysis was done using R package DESeq2
Genome_build: TAIR10
Supplementary_files_format_and_content: The expression levels (FPKM) of differentially expressed genes after shade treatment.

molecule: total RNA

organism: Arabidopsis thaliana

source_name: 6-day-old white light-grown treated with 1 hr shade seedlings

growth_protocol: 6-day-old white light-grown Col-0 (WT), pif7, asf1ab, and hira seedlings treated with 1 hr shade.

extract_protocol:
Total RNA was extracted from the snap-frozen tissues using TRIzol® Reagent (Invitrogen) according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: With 1 hr shade (R/FR=0.4) treatment

tag: tissue

value: whole seedlings

tag: age

tag: genotype

tag: treatment

value: shade


title: Patient20_Sample4

city: New York

first: Angelica

last: Galianese

state: New York

address: 615 W 164th Street, Apt 21C

country: USA

institute: Columbia University

description: COUNTS_TABLE_RAW3: P20_S4

data_processing:
single end: For producing count tables: We use RTA (Illumina) for base calling and bcl2fastq2 (version 2.17) for converting BCL to fastq format, coupled with adaptor trimming. We map the reads to a reference genome (Human: NCBI/build37.2) using STAR(2.5.2b) and featureCounts(v1.5.0-p3).
paired end: For producing count tables: We use RTA (Illumina) for base calling and bcl2fastq2 (version 2.20) for converting BCL to fastq format, coupled with adaptor trimming. We perform a pseudoalignment to a kallisto index created from transcriptomes (Human: GRCh38) using kallisto (0.44.0).
For producing unmapped reads: Produced with Pandora (Abate et al., 2015; Wang et al). The Pandora workflow takes RNA-seq data as input and produces the annotated microbial reads present in the sample as outputs. The pipeline runs through five main modules: 1) mapping to the human host genome using STAR (Dobin et al., 2013) and bowtie2 (Langmead & Salzberg, 2012); 2) processing of the host-mapped reads with featureCounts (Liao et al., 2014)  to obtain the host gene expression profile; 3) de-novo assembly of host-subtracted short (2x100bp) reads using Trinity (Grabherr et al., 2011) to create long contiguous full-length transcripts (contigs); 4) contigs alignment to curated sets of NCBI sequences from viruses, bacteria, fungi and other eukaryotic parasites with BLAST (Altschul et al., 1990); and 5) filtering and parsing the BLAST results into a report specifying the detected microbial abundances in the sample.
Assembly: single end: NCBI/build37.2
Assembly: paired end: GRCh38
Raw counts provided for all samples

organism: Homo sapiens

source_name: nasopharyngeal samples

extract_protocol:
Nasopharyngeal swabs were collected from each participant using a minitip flock swab (VWR catalog no. 10755-196; Copan Diagnostics) and immediately placed in a 15 mL tube containing 2 mL of DNA/RNA Shield (Product no. R1100-250; Zymo). Samples were separated into two 1 mL aliquots, and stored at −80°C. After thawing, RNA extraction was done using Zymo Quick-RNA™ Microprep Kit RNA extraction kit (ZYMO, R1050) including the recommended on column DNase I treatment step for 15 min. An Agilent Bioanalyzer was used for quality control prior to library creation
For single end samples: RNA RIBOZERO 30M SE100. For paired end samples: RNA RIBOZERO 20M PE100. Then proceed with library construction using Illumina TruSeq  chemistry.

value: nasopharyngeal samples

tag: subject

tag: geographic location

tag: collection date


title: RT2102

city: Stanford

first: Gabor

last: Boross

state: CA

address: 450 Serra Mall

institute: Stanford University

description: barcode region of lentiviral backbones from genomic DNA from bulk tumor-bearing lungs were PCR-amplified and high-throughput DNA sequenced

library_source: other

data_processing:
For genomic barcoded DNA, the sgIDs (specific for given guideRNA and so genotype of the tumor) and barcodes (specific to tumor) were identified from fastq files and tumor size (cell number) was calculated by normalizing the number of reads to  three benchmarks “spike-in” cell lines with custom R and python scripts.
Assembly: mm10
Supplementary files format and content: The oncogene_negative_fitness_landscape_LUAD_tumor_sizes.csv file contains all tumor sizes (number of cells) for all tumors/expansions. The mouse genotype, sample title, guideRNA are shown in comma separated text table.
Library strategy: Ultra-deep sequencing of DNA barcode amplicon

molecule: other

organism: Mus musculus

source_name: Autochthonous lung tumor

growth_protocol: Autochthonous lung tumors were initiated in mice below with Lenti-sgTSTriple-pool/Cre lentiviral pool  and harvested after 3 months.  KrasLSL-G12D;T (KT)  R26LSL-Tomato;H11LSL-Cas9 (TC)  Lkb1f/f;TC  (Lkb1;TC)  Keap1f/f;TC (Keap1;TC)

extract_protocol:
Following homogenization and overnight protease K digestion, genomicDNA was extracted from the lung lysates using standard phenol-chloroform and ethanolprecipitation methods.
Q5 High-Fidelity 2x Master Mix (New England Biolabs, M0494X) was used to amplify the sgID-BC region from 50 ng of DNA from dissected tumors or 32 μg of bulk lung genomic DNA. The unique dual-indexed primers used were Forward: AATGATACGGCGACCACCGAGATCTACAC- 8 nucleotides for i5 index-ACACTCTTTCCCTACACGACGCTCTTCCGATCT-6 to 9 random nucleotides for increasing the diversity-GCGCACGTCTGCCGCGCTG and Reverse: CAAGCAGAAGACGGCATACGAGAT-6 nucleotides for i7 index-GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT-9 to 6 random nucleotides for increasing the diversity-CAGGTTCTTGCGAACCTCAT. The PCR products were purified with Agencourt AMPure XP beads (Beckman Coulter, A63881) using a double size selection protocol. The concentration and quality of the purified libraries were determined using the Agilent High Sensitivity DNA kit (Agilent Technologies, 5067-121791801811821831841851861871881891901911921931941951961974626) on the Agilent 2100 Bioanalyzer (Agilent Technologies, G2939BA). The libraries were pooled based on lung weights to ensure even reading depth, cleaned up again using AMPure XP beads, and sequenced (read length 2x150bp) on the Illumina HiSeq 2500 platform (Admera Health Biopharma Services).

value: Autochthonous lung tumor


title: S_pif7_2


title: S_asf1ab_2


title: 10X_Bone_Marrow_Mouse_AML_T1_2

city: Chengdu, Cihna

first: Xaingyu

last: Pan

state: Sichuan

address: No.17 Renming road section3

department: State Key Laboratory of Biotherapy, West China Hospital, Sihcuan University.

institute: Sichuan University

description:
T1_R_S1_L001_R1_001.fastq.gz
processed data file:
mmu_10X_scRNA_Landscape_of_leukemogenesis_all_counts.csv
mmu_10X_scRNA_Landscape_of_leukemogenesis_all.rds
mmu_10X_scRNA_Landscape_of_leukemogenesis_all_unspliced.rds
mmu_10X_scRNA_Landscape_of_leukemogenesis_counts.csv
mmu_10X_scRNA_Landscape_of_leukemogenesis_Malignant_at_T3_counts.csv
mmu_10X_scRNA_Landscape_of_leukemogenesis_Malignant_at_T3.rds
mmu_10X_scRNA_Landscape_of_leukemogenesis_PLC_counts.csv
mmu_10X_scRNA_Landscape_of_leukemogenesis_PLC.rds
mmu_10X_scRNA_Landscape_of_leukemogenesis.rds
mmu_10X_scRNA_Landscape_of_leukemogenesis_tipping_point_counts.csv
mmu_10X_scRNA_Landscape_of_leukemogenesis_tipping_point.rds
mmu_10X_scRNA_Landscape_of_Malignant_all_counts.csv
mmu_10X_scRNA_Landscape_of_Malignant_all.rds

data_processing:
ScRNA-seq alignment process was completed by cellranger(version 2.1.0)
Seurat V3 workflow
Genome_build: mm10 mouse genome references for mouse and hg19 human genome references
Supplementary_files_format_and_content: txt files with gene counts, rds files with annotation and umap information

molecule: polyA RNA

source_name: AML_BM_T1_10X genomics

extract_protocol:
Preparation: Whole Bone Marrow (WBM) are isolated from mouse tibiae, femora and ilia leg bones by crushing in 2%FBS(PBS) buffer, add 1:1000 DNase1 and then translate into 15mL BD tube, centrifuge at 1200rpm, RT for 3min. Then discard the supernatant and add 3mL 1XACK lysis buffer to resuspend bone marrow pellet on ice for 3~5 min, and then add PBS (more than lysis buffer) to terminate lysis reaction, centrifuge at 1200rpm, RT for 3min. Discard the supernatant and then add 0.04% PBS-BSA buffer to resuspend cell pellet and then filtered through a 40μm cell strainer. More than 80% of the living cells in the sample and the density of living cells ranged from 600 to 1200 cells/μl was preferable. Sample quality is measured using Bio-rad TC20 automated cell counter.
Follwed by v2 protocol of chemistry of the 3’ scRNA-seq 10X genomics platform and modified SMART-seq2 protocol based on published previously (Fuchou Tang, 2010).

tag: strain background

tag: tissue type

value: AML

tag: time point

value: BM

tag: strategy

value: 10X genomics


title: Smartseq2_cells_174_Bone_Marrow_AML

description:
WBH-AMLSC-2-WBH-AMLSC-2-P9_TKR180900407-9.out
processed data file:
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_counts.csv
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis.rds
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_unspliced.rds


title: Monkey

city: xian

first: Cangang

last: Zhang

state: State...

address: Yanta district, xi 'an city, shaanxi province

institute: xian jiaotong university

data_processing:
The 10x Genomics Cell Ranger (3.0.1 version) pipeline was used to demultiplex raw files into FASTQ files, extract barcodes and UMI, filter, and map reads to the corresponding reference genome, and generate a matrix containing UMI counts.
A 10x Genomics Cell Ranger pipeline was used to identify clonotypes by alignment and annotation with the default settings.
Genome_build: Fish:GRCz11, Frog:Xenopus_laevis_v2, Mouse:GRCm38, Rat:Rnor_6.0, Pig:Sscrofa11, Monkey:Mmul_8, Human:GRCh38
Supplementary_files_format_and_content: Supplementary_files_format_and_content: filtered_feature_bc_matrix.tar contains counts matrix (stored in the Market Exchange Format for sparse matrices).

organism: Macaca mulatta

extract_protocol:
Spleen tissues were processed with the flat end of a syringe in a 100 mm culture dish containing 5 ml cold FACS buffer (2% FBS in PBS), then passed through a 70 μm cell strainer into a 15 ml tube. Cells were centrifuged to remove the supernatant. Cell pellets were treated with 1ml ACK (Ammonium-Chloride-Potassium) Lysing Buffer to remove the red blood cells. After washing with 10 ml cold FACS buffer, the remaining cells were stained with 7AAD (Part 76332; Lot B226294 Biolegend) for 30 min at 4 °C, then washed and resuspended in cold FACS buffer for flow cytometric sorting using FACS Aria II Cell Sorter (BD Biosciences). Sorted 7AAD- cells with a viability higher than 90% were used for 10X genomics scRNA-seq. Finally, libraries were sequenced on a NovaSeq 6000 system with NovaSeq 6000 S4 Reagent Kit (300 cycles).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Splenocytes were sorted from the spleens of  seven vertebrate species

tag: cell type

value: Splenocytes


title: S_pif7_1


title: Patient20_Sample3

description: COUNTS_TABLE_RAW3: P20_S3


title: Smartseq2_cells_173_Bone_Marrow_AML

description:
WBH-AMLSC-2-WBH-AMLSC-2-P8_TKR180900407-8.out
processed data file:
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_counts.csv
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis.rds
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_unspliced.rds


title: S_WT_3

value: WT


title: Smartseq2_cells_172_Bone_Marrow_AML

description:
WBH-AMLSC-2-WBH-AMLSC-2-P7_TKR180900407-7.out
processed data file:
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_counts.csv
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis.rds
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_unspliced.rds


title: Patient20_Sample2

description: COUNTS_TABLE_RAW3: P20_S2


title: Patient20_Sample1

description: COUNTS_TABLE_RAW3: P20_S1


title: S_WT_2


title: S_WT_1


title: Patient19_Sample9

description: COUNTS_TABLE_RAW2: P19_S9


title: Smartseq2_cells_170_Bone_Marrow_AML

description:
WBH-AMLSC-2-WBH-AMLSC-2-P78_TKR180900407-SN72.out
processed data file:
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_counts.csv
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis.rds
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_unspliced.rds


title: Smartseq2_cells_169_Bone_Marrow_AML

description:
WBH-AMLSC-2-WBH-AMLSC-2-P77_TKR180900407-SN71.out
processed data file:
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_counts.csv
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis.rds
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_unspliced.rds


title: W_hira_2

source_name: 6-day-old white light-grown seedlings

value: hira

value: control


title: W_hira_3


title: Patient19_Sample5

description: COUNTS_TABLE_RAW2: P19_S5


title: Smartseq2_cells_168_Bone_Marrow_AML

description:
WBH-AMLSC-2-WBH-AMLSC-2-P76_TKR180900407-SN70.out
processed data file:
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_counts.csv
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis.rds
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_unspliced.rds


title: W_asf1ab_3


title: Smartseq2_cells_166_Bone_Marrow_AML

description:
WBH-AMLSC-2-WBH-AMLSC-2-P74_TKR180900407-SN68.out
processed data file:
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_counts.csv
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis.rds
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_unspliced.rds


title: W_asf1ab_2


title: W_asf1ab_1


title: Patient19_Sample6

description: COUNTS_TABLE_RAW2: P19_S6


title: Smartseq2_cells_165_Bone_Marrow_AML

description:
WBH-AMLSC-2-WBH-AMLSC-2-P73_TKR180900407-SN67.out
processed data file:
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_counts.csv
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis.rds
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_unspliced.rds


title: Smartseq2_cells_164_Bone_Marrow_AML

description:
WBH-AMLSC-2-WBH-AMLSC-2-P72_TKR180900407-SN66.out
processed data file:
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_counts.csv
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis.rds
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_unspliced.rds


title: Smartseq2_cells_163_Bone_Marrow_AML

description:
WBH-AMLSC-2-WBH-AMLSC-2-P71_TKR180900407-SN65.out
processed data file:
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_counts.csv
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis.rds
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_unspliced.rds


title: Patient19_Sample8

description: COUNTS_TABLE_RAW2: P19_S8


title: Patient19_Sample7

description: COUNTS_TABLE_RAW2: P19_S7


title: Patient18_Sample10

description: COUNTS_TABLE_RAW2: P18_S10


title: Patient19_Sample3

description: COUNTS_TABLE_RAW2: P19_S3


title: W_pif7_2


title: W_WT_2


title: W_pif7_3


title: Patient18_Sample8

description: COUNTS_TABLE_RAW2: P18_S8


title: W_hira_1


title: Patient19_Sample4

description: COUNTS_TABLE_RAW2: P19_S4


title: Patient19_Sample2

description: COUNTS_TABLE_RAW2: P19_S2


title: W_WT_1


title: Smartseq2_cells_171_Bone_Marrow_AML

description:
WBH-AMLSC-2-WBH-AMLSC-2-P79_TKR180900407-SN76.out
processed data file:
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_counts.csv
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis.rds
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_unspliced.rds


title: Smartseq2_cells_162_Bone_Marrow_AML

description:
WBH-AMLSC-2-WBH-AMLSC-2-P70_TKR180900407-SN64.out
processed data file:
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_counts.csv
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis.rds
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_unspliced.rds


title: W_pif7_1


title: Smartseq2_cells_158_Bone_Marrow_AML

description:
WBH-AMLSC-2-WBH-AMLSC-2-P67_TKR180900407-SN58.out
processed data file:
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_counts.csv
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis.rds
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_unspliced.rds


title: Smartseq2_cells_157_Bone_Marrow_AML

description:
WBH-AMLSC-2-WBH-AMLSC-2-P66_TKR180900407-GH03.out
processed data file:
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_counts.csv
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis.rds
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_unspliced.rds


title: Smartseq2_cells_161_Bone_Marrow_AML

description:
WBH-AMLSC-2-WBH-AMLSC-2-P6_TKR180900407-6.out
processed data file:
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_counts.csv
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis.rds
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_unspliced.rds


title: Patient18_Sample6

description: COUNTS_TABLE_RAW2: P18_S6


title: Patient18_Sample9

description: COUNTS_TABLE_RAW2: P18_S9


title: Smartseq2_cells_156_Bone_Marrow_AML

description:
WBH-AMLSC-2-WBH-AMLSC-2-P65_TKR180900407-SN56.out
processed data file:
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_counts.csv
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis.rds
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_unspliced.rds


title: Patient19_Sample1

description: COUNTS_TABLE_RAW2: P19_S1


title: Smartseq2_cells_160_Bone_Marrow_AML

description:
WBH-AMLSC-2-WBH-AMLSC-2-P69_TKR180900407-SN60.out
processed data file:
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_counts.csv
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis.rds
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_unspliced.rds


title: Smartseq2_cells_159_Bone_Marrow_AML

description:
WBH-AMLSC-2-WBH-AMLSC-2-P68_TKR180900407-SN59.out
processed data file:
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_counts.csv
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis.rds
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_unspliced.rds


title: Smartseq2_cells_167_Bone_Marrow_AML

description:
WBH-AMLSC-2-WBH-AMLSC-2-P75_TKR180900407-SN69.out
processed data file:
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_counts.csv
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis.rds
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_unspliced.rds


title: W_WT_3


title: Patient18_Sample2

description: COUNTS_TABLE_RAW2: P18_S2


title: LIGHT_3H_01 (biol rep 1)

city: Brno

first: Tomas

last: Barta

address: Kamenice 3

department: Faculty of Medicine

country: Czech Republic

institute: Masaryk University

description: microRNA NGS

data_processing:
Removal of very low-quality read ends (Phred<5)
Keeping only reads with a Phred score of 10 over at least 85% of the length
Only reads within 16-27 bp were kept as potential microRNA reads. FASTX-Toolkit  was used for the quality filtering; the rest of the steps were performed by Cutadapt (v2.5) and bash scripting.
The quality of the final preprocessed reads was assessed with Overall mapping rates to the human reference genome (hg38), and the general quality of the preprocessed reads was assessed by Bowtie (v1.3.1).
The raw microRNA expression levels were quantified by seqcluster (v1.2.8) and seqbuster/miraligner (v3.5).

source_name: Retinal organoid

growth_protocol: iPSC derived retinal organoids were cultured in NR medium6 (DMEM/F12 [Gibco, Item No: 21331-020], 1% N-2 supplement [Gibco, Item No: 17502001], 1% GlutaMAX supplement [Gibco, Item No: 35050061], 10% foetal bovine serum [FBS; Biosera, Item No: FB-1101], 0.5 mM retinoic acid [Sigma, Item No: R2625], 0.1 mM Taurine [Sigma, Item No: T8691], 1× Penicillin- Streptomycin Solution [Biosera, Item No: XC-A4122]).

extract_protocol:
Retinal organoids were washed with phosphate-buffered saline (PBS), (pH 7.4) and lysed using RNA Blue reagent (Top-Bio). After 1-bromo-3-chloropropane (Sigma-Aldrich) addition and centrifugation (21.000 × g, 15 minutes, 4 °C), the cell lysates were separated into three layers. The top aqueous layer containing RNA was transferred to a new tube and precipitated by addition of isopropanol, followed by 10 minutes incubation on ice and centrifugation (18.000 × g, 10 minutes, 4 °C). RNA pellets were washed with 70% ethanol (8.500 × g, 10 minutes, 4 °C), air-dried, solubilized in PCR grade water (Top-Bio), and only samples with RINe values ≥ 9 were used for library preparation. .
NEBNext Multiplex Small RNA Library Prep Set for Illumina (#E7300S, #E7580S Set1, 2; New England Biolabs; Ipswich, MA, USA) was used to prepare libraries for further sequencing according to the manufacturer’s instructions. Briefly, 800 ng of total RNA were used to create size selected small RNA libraries (size selection with 6% PAGE gel). The sequencing was performed with 2.0 pM library using the NextSeq® 500/550 High Output Kit v2.5 (#20024906; 75 cycles; Illumina; San Diego, CA, USA).

treatment_protocol: Retinal organoids were photostimulated using 100 lx white light for 1 hour and 3 hours, respectively.

value: Retinal organoid

tag: cell line

value: iPSC Neo5

value: 3 hour 100 lx white light


title: LIGHT_3H_02 (biol rep 2)

description: microRNA NGS


title: LIGHT_1H_01 (biol rep 1)

description: microRNA NGS

value: 1 hour 100 lx white light


title: Smartseq2_cells_153_Bone_Marrow_AML

description:
WBH-AMLSC-2-WBH-AMLSC-2-P62_TKR180900407-SN53.out
processed data file:
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_counts.csv
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis.rds
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_unspliced.rds


title: LIGHT_1H_03 (biol rep 3)

description: microRNA NGS


title: Patient18_Sample5

description: COUNTS_TABLE_RAW2: P18_S5


title: Smartseq2_cells_155_Bone_Marrow_AML

description:
WBH-AMLSC-2-WBH-AMLSC-2-P64_TKR180900407-SN55.out
processed data file:
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_counts.csv
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis.rds
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_unspliced.rds


title: Patient18_Sample1

description: COUNTS_TABLE_RAW2: P18_S1


title: Smartseq2_cells_152_Bone_Marrow_AML

description:
WBH-AMLSC-2-WBH-AMLSC-2-P61_TKR180900407-SN52.out
processed data file:
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_counts.csv
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis.rds
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_unspliced.rds


title: LIGHT_3H_03 (biol rep 3)

description: microRNA NGS


title: Patient18_Sample4

description: COUNTS_TABLE_RAW2: P18_S4


title: Patient18_Sample3

description: COUNTS_TABLE_RAW2: P18_S3


title: Patient17_Sample3

description: COUNTS_TABLE_RAW3: P17_S3


title: Patient17_Sample1

description: COUNTS_TABLE_RAW3: P17_S1


title: Smartseq2_cells_154_Bone_Marrow_AML

description:
WBH-AMLSC-2-WBH-AMLSC-2-P63_TKR180900407-SN54.out
processed data file:
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_counts.csv
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis.rds
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_unspliced.rds


title: Patient15_Sample15

description: COUNTS_TABLE_RAW1: P15_S15


title: DARK_02 (biol rep 2)

description: microRNA NGS

value: Dark


title: Patient17_Sample2

description: COUNTS_TABLE_RAW3: P17_S2


title: LIGHT_1H_02 (biol rep 2)

description: microRNA NGS


title: Smartseq2_cells_150_Bone_Marrow_AML

description:
WBH-AMLSC-2-WBH-AMLSC-2-P5_TKR180900407-5.out
processed data file:
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_counts.csv
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis.rds
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_unspliced.rds


title: DARK_01 (biol rep 1)

description: microRNA NGS


title: Patient18_Sample7

description: COUNTS_TABLE_RAW2: P18_S7


title: Patient15_Sample13

description: COUNTS_TABLE_RAW1: P15_S13


title: Smartseq2_cells_148_Bone_Marrow_AML

description:
WBH-AMLSC-2-WBH-AMLSC-2-P58_TKR180900407-SN46.out
processed data file:
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_counts.csv
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis.rds
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_unspliced.rds


title: Smartseq2_cells_149_Bone_Marrow_AML

description:
WBH-AMLSC-2-WBH-AMLSC-2-P59_TKR180900407-SN47.out
processed data file:
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_counts.csv
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis.rds
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_unspliced.rds


title: Patient15_Sample11

description: COUNTS_TABLE_RAW1: P15_S11


title: DARK_03 (biol rep 3)

description: microRNA NGS


title: Patient15_Sample10

description: COUNTS_TABLE_RAW1: P15_S10


title: Smartseq2_cells_146_Bone_Marrow_AML

description:
WBH-AMLSC-2-WBH-AMLSC-2-P56_TKR180900407-SN44.out
processed data file:
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_counts.csv
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis.rds
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_unspliced.rds


title: Smartseq2_cells_151_Bone_Marrow_AML

description:
WBH-AMLSC-2-WBH-AMLSC-2-P60_TKR180900407-SN48.out
processed data file:
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_counts.csv
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis.rds
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_unspliced.rds


title: Smartseq2_cells_147_Bone_Marrow_AML

description:
WBH-AMLSC-2-WBH-AMLSC-2-P57_TKR180900407-SN45.out
processed data file:
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_counts.csv
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis.rds
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_unspliced.rds


title: Patient15_Sample12

description: COUNTS_TABLE_RAW1: P15_S12


title: Smartseq2_cells_142_Bone_Marrow_AML

description:
WBH-AMLSC-2-WBH-AMLSC-2-P52_TKR180900407-SN40.out
processed data file:
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_counts.csv
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis.rds
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_unspliced.rds


title: Patient15_Sample9

description: COUNTS_TABLE_RAW1: P15_S9


title: Smartseq2_cells_139_Bone_Marrow_AML

description:
WBH-AMLSC-2-WBH-AMLSC-2-P4_TKR180900407-4.out
processed data file:
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_counts.csv
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis.rds
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_unspliced.rds


title: Smartseq2_cells_145_Bone_Marrow_AML

description:
WBH-AMLSC-2-WBH-AMLSC-2-P55_TKR180900407-GG04.out
processed data file:
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_counts.csv
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis.rds
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_unspliced.rds


title: Patient15_Sample16

description: COUNTS_TABLE_RAW1: P15_S16


title: Patient15_Sample14

description: COUNTS_TABLE_RAW1: P15_S14


title: Smartseq2_cells_143_Bone_Marrow_AML

description:
WBH-AMLSC-2-WBH-AMLSC-2-P53_TKR180900407-SN41.out
processed data file:
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_counts.csv
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis.rds
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_unspliced.rds


title: Patient15_Sample6

description: COUNTS_TABLE_RAW1: P15_S6


title: Smartseq2_cells_138_Bone_Marrow_AML

description:
WBH-AMLSC-2-WBH-AMLSC-2-P49_TKR180900407-SN34.out
processed data file:
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_counts.csv
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis.rds
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_unspliced.rds


title: Smartseq2_cells_140_Bone_Marrow_AML

description:
WBH-AMLSC-2-WBH-AMLSC-2-P50_TKR180900407-SN35.out
processed data file:
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_counts.csv
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis.rds
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_unspliced.rds


title: Patient15_Sample7

description: COUNTS_TABLE_RAW1: P15_S7


title: Smartseq2_cells_136_Bone_Marrow_AML

description:
WBH-AMLSC-2-WBH-AMLSC-2-P47_TKR180900407-SN32.out
processed data file:
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_counts.csv
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis.rds
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_unspliced.rds


title: Smartseq2_cells_141_Bone_Marrow_AML

description:
WBH-AMLSC-2-WBH-AMLSC-2-P51_TKR180900407-SN36.out
processed data file:
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_counts.csv
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis.rds
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_unspliced.rds


title: Patient15_Sample4

description: COUNTS_TABLE_RAW1: P15_S4


title: Patient15_Sample1

description: COUNTS_TABLE_RAW1: P15_S1


title: Patient15_Sample8

description: COUNTS_TABLE_RAW1: P15_S8


title: Patient15_Sample5

description: COUNTS_TABLE_RAW1: P15_S5


title: Smartseq2_cells_144_Bone_Marrow_AML

description:
WBH-AMLSC-2-WBH-AMLSC-2-P54_TKR180900407-AK706.out
processed data file:
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_counts.csv
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis.rds
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_unspliced.rds


title: Patient14_Sample5

description: COUNTS_TABLE_RAW5: P14_S5


title: Smartseq2_cells_137_Bone_Marrow_AML

description:
WBH-AMLSC-2-WBH-AMLSC-2-P48_TKR180900407-SN33.out
processed data file:
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_counts.csv
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis.rds
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_unspliced.rds


title: Smartseq2_cells_133_Bone_Marrow_AML

description:
WBH-AMLSC-2-WBH-AMLSC-2-P44_TKR180900407-SN29.out
processed data file:
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_counts.csv
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis.rds
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_unspliced.rds


title: Patient15_Sample2

description: COUNTS_TABLE_RAW1: P15_S2


title: Patient14_Sample7

description: COUNTS_TABLE_RAW5: P14_S7


title: Smartseq2_cells_132_Bone_Marrow_AML

description:
WBH-AMLSC-2-WBH-AMLSC-2-P43_TKR180900407-SN28.out
processed data file:
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_counts.csv
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis.rds
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_unspliced.rds


title: Smartseq2_cells_125_Bone_Marrow_AML

description:
WBH-AMLSC-2-WBH-AMLSC-2-P37_TKR180900407-SN19.out
processed data file:
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_counts.csv
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis.rds
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_unspliced.rds


title: Patient15_Sample3

description: COUNTS_TABLE_RAW1: P15_S3


title: Smartseq2_cells_127_Bone_Marrow_AML

description:
WBH-AMLSC-2-WBH-AMLSC-2-P39_TKR180900407-SN21.out
processed data file:
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_counts.csv
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis.rds
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_unspliced.rds


title: Smartseq2_cells_135_Bone_Marrow_AML

description:
WBH-AMLSC-2-WBH-AMLSC-2-P46_TKR180900407-SN31.out
processed data file:
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_counts.csv
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis.rds
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_unspliced.rds


title: Patient14_Sample8

description: COUNTS_TABLE_RAW5: P14_S8


title: Smartseq2_cells_131_Bone_Marrow_AML

description:
WBH-AMLSC-2-WBH-AMLSC-2-P42_TKR180900407-SN24.out
processed data file:
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_counts.csv
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis.rds
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_unspliced.rds


title: Smartseq2_cells_130_Bone_Marrow_AML

description:
WBH-AMLSC-2-WBH-AMLSC-2-P41_TKR180900407-SN23.out
processed data file:
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_counts.csv
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis.rds
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_unspliced.rds


title: Smartseq2_cells_126_Bone_Marrow_AML

description:
WBH-AMLSC-2-WBH-AMLSC-2-P38_TKR180900407-SN20.out
processed data file:
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_counts.csv
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis.rds
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_unspliced.rds


title: Patient13_Sample15

description: COUNTS_TABLE_RAW2: P13_S15


title: Smartseq2_cells_123_Bone_Marrow_AML

description:
WBH-AMLSC-2-WBH-AMLSC-2-P35_TKR180900407-SN17.out
processed data file:
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_counts.csv
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis.rds
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_unspliced.rds


title: Patient14_Sample4

description: COUNTS_TABLE_RAW5: P14_S4


title: Patient13_Sample16

description: COUNTS_TABLE_RAW2: P13_S16


title: Smartseq2_cells_128_Bone_Marrow_AML

description:
WBH-AMLSC-2-WBH-AMLSC-2-P3_TKR180900407-3.out
processed data file:
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_counts.csv
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis.rds
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_unspliced.rds


title: Patient14_Sample1

description: COUNTS_TABLE_RAW5: P14_S1


title: Patient14_Sample3

description: COUNTS_TABLE_RAW5: P14_S3


title: Smartseq2_cells_134_Bone_Marrow_AML

description:
WBH-AMLSC-2-WBH-AMLSC-2-P45_TKR180900407-SN30.out
processed data file:
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_counts.csv
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis.rds
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_unspliced.rds


title: Patient14_Sample2

description: COUNTS_TABLE_RAW5: P14_S2


title: Patient14_Sample6

description: COUNTS_TABLE_RAW5: P14_S6


title: Smartseq2_cells_129_Bone_Marrow_AML

description:
WBH-AMLSC-2-WBH-AMLSC-2-P40_TKR180900407-AK693.out
processed data file:
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_counts.csv
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis.rds
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_unspliced.rds


title: Smartseq2_cells_120_Bone_Marrow_AML

description:
WBH-AMLSC-2-WBH-AMLSC-2-P32_TKR180900407-SN11.out
processed data file:
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_counts.csv
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis.rds
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_unspliced.rds


title: Smartseq2_cells_121_Bone_Marrow_AML

description:
WBH-AMLSC-2-WBH-AMLSC-2-P33_TKR180900407-SN12.out
processed data file:
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_counts.csv
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis.rds
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_unspliced.rds


title: Smartseq2_cells_122_Bone_Marrow_AML

description:
WBH-AMLSC-2-WBH-AMLSC-2-P34_TKR180900407-SN16.out
processed data file:
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_counts.csv
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis.rds
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_unspliced.rds


title: Smartseq2_cells_119_Bone_Marrow_AML

description:
WBH-AMLSC-2-WBH-AMLSC-2-P31_TKR180900407-SN10.out
processed data file:
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_counts.csv
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis.rds
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_unspliced.rds


title: Patient13_Sample13

description: COUNTS_TABLE_RAW2: P13_S13


title: Smartseq2_cells_118_Bone_Marrow_AML

description:
WBH-AMLSC-2-WBH-AMLSC-2-P30_TKR180900407-SN9.out
processed data file:
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_counts.csv
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis.rds
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_unspliced.rds


title: Patient13_Sample7

description: COUNTS_TABLE_RAW2: P13_S7


title: Smartseq2_cells_115_Bone_Marrow_AML

description:
WBH-AMLSC-2-WBH-AMLSC-2-P28_TKR180900407-SN7.out
processed data file:
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_counts.csv
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis.rds
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_unspliced.rds


title: Patient13_Sample5

description: COUNTS_TABLE_RAW2: P13_S5


title: Patient13_Sample12

description: COUNTS_TABLE_RAW2: P13_S12


title: Smartseq2_cells_114_Bone_Marrow_AML

description:
WBH-AMLSC-2-WBH-AMLSC-2-P27_TKR180900407-SN6.out
processed data file:
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_counts.csv
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis.rds
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_unspliced.rds


title: Patient13_Sample14

description: COUNTS_TABLE_RAW2: P13_S14


title: Smartseq2_cells_112_Bone_Marrow_AML

description:
WBH-AMLSC-2-WBH-AMLSC-2-P25_TKR180900407-AK690.out
processed data file:
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_counts.csv
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis.rds
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_unspliced.rds


title: Smartseq2_cells_113_Bone_Marrow_AML

description:
WBH-AMLSC-2-WBH-AMLSC-2-P26_TKR180900407-SN5.out
processed data file:
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_counts.csv
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis.rds
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_unspliced.rds


title: Patient13_Sample3

description: COUNTS_TABLE_RAW2: P13_S3


title: Patient13_Sample4

description: COUNTS_TABLE_RAW2: P13_S4


title: Smartseq2_cells_124_Bone_Marrow_AML

description:
WBH-AMLSC-2-WBH-AMLSC-2-P36_TKR180900407-AK691.out
processed data file:
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_counts.csv
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis.rds
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_unspliced.rds


title: Smartseq2_cells_109_Bone_Marrow_AML

description:
WBH-AMLSC-2-WBH-AMLSC-2-P22_TKR180900407-23.out
processed data file:
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_counts.csv
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis.rds
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_unspliced.rds


title: Smartseq2_cells_110_Bone_Marrow_AML

description:
WBH-AMLSC-2-WBH-AMLSC-2-P23_TKR180900407-25.out
processed data file:
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_counts.csv
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis.rds
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_unspliced.rds


title: Patient13_Sample2

description: COUNTS_TABLE_RAW2: P13_S2


title: Patient13_Sample9

description: COUNTS_TABLE_RAW2: P13_S9


title: Patient13_Sample11

description: COUNTS_TABLE_RAW2: P13_S11


title: Patient13_Sample6

description: COUNTS_TABLE_RAW2: P13_S6


title: KiPS_RESET_D12_TSCmedium_Rep_2

city: Padua

first: Graziano

last: Martello

address: viale Colombo 3

department: Department of Biology

country: Italy

institute: University of Padua

data_processing:
trimming was performed using BBDuk from BBTools v38.87
alignment was performed with STAR 2.7.6a
quantification was performed with Salmon v1.6.0
Assembly: Human GRCh38.p13 Ensembl release 105
Supplementary files format and content: raw_counts_matrix_2.txt is a txt containing EnsemblID, official gene symbols and raw counts for each condition

source_name: KiPS-chemical resetting

extract_protocol:
Total RNA was isolated using Total RNA Purification kit (Norgen Biotek), according to manufactorer's protocol.
Quant Seq 3' mRNA-seq Library Prep kit (Lexogen) is used for library construction.

value: chemical reset induced pluripotent stem cells

tag: growth protocol

value: Cells were cultured on mitotically inactivated mouse embryonic fibroblasts (MEFs; DR4 ATCC) in PXGL medium3 or in RSeT medium (Stem Cell Technologies 05969 ). The PXGL medium was prepared as follows:N2B27 (DMEM/F12 [Gibco 11320-074], and Neurobasal in 1:1 ratio [Gibco 21103-049], with 1:200 N2 Supplement [Gibco 17502-048], and 1:100 B27 Supplement [Gibco 17504-044], 2 mM L-glutamine [Gibco 25030-024], 0.1 mM 2-mercaptoethanol [Sigma-Aldrich M3148]) supplemented with 1µM PD0325901 (Axon Medchem), 2 μM XAV939 (Axon Medchem), 2 μM Gö6983 (Axon Medchem) and 10 ng/ml human LIF (produced in-house). Human naive PSCs were passaged as single cells every 4 days at split ratio 1:3 or 1:4 following dissociation with TrypLE (Gibco 12563-029) for 10 minutes at room temperature (RT). The ROCK inhibitor (Y27632, Axon Medchem 1683) was added in the naïve medium only for 24h after passaging.

tag: treatment protocol

value: Chemical resetting from primed to naive PSC. Cells were seeded at 10000 cells/cm2 on mitotically inactivated MEFs in E8 medium with 10µM ROCKi (added only for 24 hours). Two days after plating (day 0), medium was changed to PDL/HDACi (N2B27 with 1µM PD0325901, 10ng/ml human LIF and 1mM VPA (HDACi)). Following 3 days in PDL/HDACi, medium was changed to PXGL for a further 10-11 days before passing in PXGL medium on MEFs (see Fig. 1a). For the chemical resetting from primed to ccTSCs, KiPS were seeded at 10000 cells/cm2 on mitotically inactivated MEFs in E8 medium. Two days later (day 0) medium was changed to PDL/HDACi. Following 3 days in PDL/HDACi, medium was changed to PXGL.


title: Patient13_Sample1

description: COUNTS_TABLE_RAW2: P13_S1

value: nasopharyngeal samples


title: Smartseq2_cells_111_Bone_Marrow_AML

description:
WBH-AMLSC-2-WBH-AMLSC-2-P24_TKR180900407-27.out
processed data file:
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_counts.csv
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis.rds
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_unspliced.rds


title: Smartseq2_cells_117_Bone_Marrow_AML

description:
WBH-AMLSC-2-WBH-AMLSC-2-P2_TKR180900407-2.out
processed data file:
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_counts.csv
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis.rds
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_unspliced.rds


title: Patient12_Sample5

description: COUNTS_TABLE_RAW5: P12_S5


title: Patient13_Sample8

description: COUNTS_TABLE_RAW2: P13_S8


title: Smartseq2_cells_108_Bone_Marrow_AML

description:
WBH-AMLSC-2-WBH-AMLSC-2-P21_TKR180900407-22.out
processed data file:
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_counts.csv
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis.rds
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_unspliced.rds


title: KiPS_RESET_D12_TSCmedium_Rep_1


title: Patient12_Sample2

description: COUNTS_TABLE_RAW5: P12_S2


title: Smartseq2_cells_106_Bone_Marrow_AML

description:
WBH-AMLSC-2-WBH-AMLSC-2-P1_TKR180900407-1.out
processed data file:
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_counts.csv
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis.rds
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_unspliced.rds


title: Smartseq2_cells_104_Bone_Marrow_AML

description:
WBH-AMLSC-2-WBH-AMLSC-2-P18_TKR180900407-19.out
processed data file:
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_counts.csv
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis.rds
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_unspliced.rds


title: Smartseq2_cells_103_Bone_Marrow_AML

description:
WBH-AMLSC-2-WBH-AMLSC-2-P17_TKR180900407-18.out
processed data file:
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_counts.csv
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis.rds
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_unspliced.rds


title: Smartseq2_cells_101_Bone_Marrow_AML

description:
WBH-AMLSC-2-WBH-AMLSC-2-P15_TKR180900407-15.out
processed data file:
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_counts.csv
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis.rds
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_unspliced.rds


title: Patient11_Sample4

description: COUNTS_TABLE_RAW1: P11_S4


title: Patient13_Sample10

description: COUNTS_TABLE_RAW2: P13_S10


title: KiPS_RESET_D9_PXGLmedium_Rep_1


title: Smartseq2_cells_102_Bone_Marrow_AML

description:
WBH-AMLSC-2-WBH-AMLSC-2-P16_TKR180900407-16.out
processed data file:
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_counts.csv
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis.rds
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_unspliced.rds


title: Smartseq2_cells_100_Bone_Marrow_AML

description:
WBH-AMLSC-2-WBH-AMLSC-2-P14_TKR180900407-14.out
processed data file:
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_counts.csv
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis.rds
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_unspliced.rds


title: KiPS_RESET_D6_TSCmedium_Rep_2


title: Patient11_Sample3

description: COUNTS_TABLE_RAW1: P11_S3


title: Smartseq2_cells_107_Bone_Marrow_AML

description:
WBH-AMLSC-2-WBH-AMLSC-2-P20_TKR180900407-21.out
processed data file:
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_counts.csv
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis.rds
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_unspliced.rds


title: KiPS_RESET_D12_PXGLmedium_Rep_2


title: Patient11_Sample5

description: COUNTS_TABLE_RAW1: P11_S5


title: KiPS_RESET_D12_PXGLmedium_Rep_1


title: KiPS_RESET_D9_TSCmedium_Rep_1


title: KiPS_RESET_D6_TSCmedium_Rep_1


title: KiPS_RESET_D9_TSCmedium_Rep_2


title: Patient12_Sample3

description: COUNTS_TABLE_RAW5: P12_S3


title: KiPS_RESET_D6_PXGLmedium_Rep_1


title: Patient11_Sample1

description: COUNTS_TABLE_RAW1: P11_S1


title: Patient12_Sample1

description: COUNTS_TABLE_RAW5: P12_S1


title: Patient11_Sample2

description: COUNTS_TABLE_RAW1: P11_S2


title: Patient10_Sample6

description: COUNTS_TABLE_RAW5: P10_S6


title: Patient12_Sample4

description: COUNTS_TABLE_RAW5: P12_S4


title: Smartseq2_cells_105_Bone_Marrow_AML

description:
WBH-AMLSC-2-WBH-AMLSC-2-P19_TKR180900407-20.out
processed data file:
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_counts.csv
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis.rds
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_unspliced.rds


title: Smartseq2_cells_98_Bone_Marrow_AML

description:
WBH-AMLSC-2-WBH-AMLSC-2-P12_TKR180900407-12.out
processed data file:
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_counts.csv
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis.rds
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_unspliced.rds


title: Patient10_Sample8

description: COUNTS_TABLE_RAW5: P10_S8


title: KiPS_RESET_D6_PXGLmedium_Rep_2


title: KiPS_RESET_D9_PXGLmedium_Rep_2


title: Patient10_Sample7

description: COUNTS_TABLE_RAW5: P10_S7


title: Patient10_Sample5

description: COUNTS_TABLE_RAW5: P10_S5


title: Smartseq2_cells_96_Bone_Marrow_AML

description:
WBH-AMLSC-2-WBH-AMLSC-2-P10_TKR180900407-10.out
processed data file:
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_counts.csv
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis.rds
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_unspliced.rds


title: Smartseq2_cells_97_Bone_Marrow_AML

description:
WBH-AMLSC-2-WBH-AMLSC-2-P11_TKR180900407-11.out
processed data file:
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_counts.csv
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis.rds
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_unspliced.rds


title: KiPS_RESET_D5_TSCmedium_Rep_1


title: Smartseq2_cells_99_Bone_Marrow_AML

description:
WBH-AMLSC-2-WBH-AMLSC-2-P13_TKR180900407-13.out
processed data file:
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_counts.csv
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis.rds
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_unspliced.rds


title: KiPS_RESET_D3_Rep_2


title: Patient10_Sample4

description: COUNTS_TABLE_RAW5: P10_S4


title: Patient10_Sample3

description: COUNTS_TABLE_RAW5: P10_S3


title: Smartseq2_cells_92_Bone_Marrow_AML

description:
WBH-AMLSC-1-WBH-AMLSC-1-P93_TKR180900408-SN93.out
processed data file:
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_counts.csv
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis.rds
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_unspliced.rds


title: Patient10_Sample2

description: COUNTS_TABLE_RAW5: P10_S2


title: KiPS_RESET_D5_PXGLmedium_Rep_1


title: Patient10_Sample1

description: COUNTS_TABLE_RAW5: P10_S1


title: Smartseq2_cells_93_Bone_Marrow_AML

description:
WBH-AMLSC-1-WBH-AMLSC-1-P94_TKR180900408-SN94.out
processed data file:
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_counts.csv
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis.rds
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_unspliced.rds


title: KiPS_RESET_D4_TSCmedium_Rep_1


title: Smartseq2_cells_95_Bone_Marrow_AML

description:
WBH-AMLSC-1-WBH-AMLSC-1-P9_TKR180900408-9.out
processed data file:
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_counts.csv
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis.rds
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_unspliced.rds


title: KiPS_RESET_D4_PXGLmedium_Rep_1


title: Patient9_Sample16

description: COUNTS_TABLE_RAW5: P9_S16


title: Smartseq2_cells_94_Bone_Marrow_AML

description:
WBH-AMLSC-1-WBH-AMLSC-1-P95_TKR180900408-SN95.out
processed data file:
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_counts.csv
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis.rds
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_unspliced.rds


title: Patient9_Sample14

description: COUNTS_TABLE_RAW5: P9_S14


title: Smartseq2_cells_116_Bone_Marrow_AML

description:
WBH-AMLSC-2-WBH-AMLSC-2-P29_TKR180900407-GG03.out
processed data file:
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_counts.csv
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis.rds
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_unspliced.rds


title: Smartseq2_cells_91_Bone_Marrow_AML

description:
WBH-AMLSC-1-WBH-AMLSC-1-P92_TKR180900408-SN92.out
processed data file:
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_counts.csv
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis.rds
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_unspliced.rds


title: KiPS_RESET_D0_Rep_1

source_name: KiPS primed-iPSCs

value: primed induced pluripotent stem cells


title: KiPS_RESET_D3_Rep_1


title: KiPS_RESET_D2_Rep_1


title: Smartseq2_cells_89_Bone_Marrow_AML

description:
WBH-AMLSC-1-WBH-AMLSC-1-P90_TKR180900408-SN90.out
processed data file:
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_counts.csv
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis.rds
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_unspliced.rds

value: AML


title: Patient9_Sample12

description: COUNTS_TABLE_RAW5: P9_S12


title: Smartseq2_cells_86_Bone_Marrow_AML

description:
WBH-AMLSC-1-WBH-AMLSC-1-P88_TKR180900408-GH12.out
processed data file:
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_counts.csv
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis.rds
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_unspliced.rds

value: BM


title: Smartseq2_cells_88_Bone_Marrow_AML

description:
WBH-AMLSC-1-WBH-AMLSC-1-P8_TKR180900408-8.out
processed data file:
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_counts.csv
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis.rds
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_unspliced.rds


title: KiPS_Rep_1

value: Cells were cultured in Feeder-free on pre-coated plates with 0.5% growth factor-reduced Matrigel (CORNING 356231) (in PBS with MgCl2/CaCl2, Sigma-Aldrich D8662) in E8 medium (made in-house according to12) at 37°C, 5% CO2, 5% O2. Cells were passaged every 3-4 days at a split ratio of 1:8 following dissociation with 0.5 mM EDTA (Invitrogen AM99260G) in PBS without MgCl2/CaCl2 (Sigma-Aldrich D8662), pH8.


title: Smartseq2_cells_87_Bone_Marrow_AML

description:
WBH-AMLSC-1-WBH-AMLSC-1-P89_TKR180900408-SN89.out
processed data file:
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_counts.csv
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis.rds
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_unspliced.rds


title: Smartseq2_cells_84_Bone_Marrow_AML

description:
WBH-AMLSC-1-WBH-AMLSC-1-P86_TKR180900408-SN83.out
processed data file:
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_counts.csv
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis.rds
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_unspliced.rds


title: Patient9_Sample11

description: COUNTS_TABLE_RAW5: P9_S11


title: KiPS_RESET_D0_Rep_2


title: Patient9_Sample10

description: COUNTS_TABLE_RAW5: P9_S10


title: KiPS_RESET_D2_Rep_2


title: Patient9_Sample15

description: COUNTS_TABLE_RAW5: P9_S15


title: Patient9_Sample13

description: COUNTS_TABLE_RAW5: P9_S13


title: Smartseq2_cells_85_Bone_Marrow_AML

description:
WBH-AMLSC-1-WBH-AMLSC-1-P87_TKR180900408-SN84.out
processed data file:
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_counts.csv
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis.rds
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_unspliced.rds


title: Patient9_Sample9

description: COUNTS_TABLE_RAW5: P9_S9


title: KiPS_Rep_2


title: KiPS_Rep_3


title: HPD06-TSC_Rep_3

source_name: TSC derived from HPD06 naive-iPSCs

value: throphoblast stem cells derived from naive induced pluripotent stem cells

value: hTSCs were cultured in 12-well plate coated with 5 μg/mL Collagen IV (Corning, 354233) at 37°C overnight or on mitotically inactivated mouse embryonic fibroblasts. Cells were cultured in 0.8 mL TS medium [DMEM/F12 supplemented with 0.1 mM 2-mercaptoethanol, 0.2% FBS, 0.5% Penicillin-Streptomycin, 0.3%, BSA (Gibco 15260-037), 1% ITS-X (Gibco, 51500), 1.5 μg/ml L-ascorbic acid (Sigma A4544), 50 ng/ml EGF (peprotech AF-100-15), 2 μM CHIR99021 (Axon Medchem cat. nos 1386 and 1408), 0.5 μM A83-01 (Axon Medchem 1421), 1 μM SB431542 (Axon Medchem 1661), 0.8 mM VPA (HDACi, Sigma, P4543), and 5 μM Y-27632] and in 5% CO2 and 5% O2. Media were changed every 2 days, and cells were passed using TrypLE Express every 3-4 days at a ratio of 1:8.

value: Naive hPSCs did a pre-treatment on MEF with TS medium for 24h, whereupon naive hPSCs were single-cell dissociated by TrypLE Express, and 0.25–0.5 × 106 cells were seeded on a 12-well plate pre-coated with 5 μg/mL Collagen IV or on mitotically inactivated mouse embryonic fibroblasts and cultured in 0.8 mL TS medium. Cells were cultured in 5% CO2 and 5% O2, media was changed every 2 days, and passaged upon 80–100% confluency at a ratio of 1:2 to 1:4. During derivation from naive hPSCs, the cells grew slowly during the initial few passages. Between passage 5 and 10, highly proliferative hTSCs emerged.


title: HPD06-TSC_Rep_1


title: Smartseq2_cells_83_Bone_Marrow_AML

description:
WBH-AMLSC-1-WBH-AMLSC-1-P85_TKR180900408-SN82.out
processed data file:
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_counts.csv
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis.rds
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_unspliced.rds


title: HPD06-TSC_Rep_2


title: Patient9_Sample8

description: COUNTS_TABLE_RAW5: P9_S8


title: Smartseq2_cells_82_Bone_Marrow_AML

description:
WBH-AMLSC-1-WBH-AMLSC-1-P84_TKR180900408-SN81.out
processed data file:
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_counts.csv
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis.rds
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_unspliced.rds


title: Smartseq2_cells_81_Bone_Marrow_AML

description:
WBH-AMLSC-1-WBH-AMLSC-1-P83_TKR180900408-SN80.out
processed data file:
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_counts.csv
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis.rds
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_unspliced.rds


title: Patient9_Sample5

description: COUNTS_TABLE_RAW5: P9_S5


title: Smartseq2_cells_80_Bone_Marrow_AML

description:
WBH-AMLSC-1-WBH-AMLSC-1-P82_TKR180900408-SN79.out
processed data file:
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_counts.csv
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis.rds
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_unspliced.rds


title: Smartseq2_cells_90_Bone_Marrow_AML

description:
WBH-AMLSC-1-WBH-AMLSC-1-P91_TKR180900408-SN91.out
processed data file:
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_counts.csv
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis.rds
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_unspliced.rds


title: Patient9_Sample7

description: COUNTS_TABLE_RAW5: P9_S7


title: H9-TSC_Rep_3

source_name: TSC derived from H9 naive-iPSCs


title: Patient9_Sample6

description: COUNTS_TABLE_RAW5: P9_S6


title: Patient9_Sample4

description: COUNTS_TABLE_RAW5: P9_S4


title: Patient9_Sample3

description: COUNTS_TABLE_RAW5: P9_S3


title: Smartseq2_cells_78_Bone_Marrow_AML

description:
WBH-AMLSC-1-WBH-AMLSC-1-P80_TKR180900408-SN77.out
processed data file:
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_counts.csv
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis.rds
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_unspliced.rds


title: Smartseq2_cells_77_Bone_Marrow_AML

description:
WBH-AMLSC-1-WBH-AMLSC-1-P7_TKR180900408-7.out
processed data file:
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_counts.csv
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis.rds
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_unspliced.rds


title: Smartseq2_cells_75_Bone_Marrow_AML

description:
WBH-AMLSC-1-WBH-AMLSC-1-P78_TKR180900408-SN72.out
processed data file:
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_counts.csv
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis.rds
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_unspliced.rds


title: Patient9_Sample1

description: COUNTS_TABLE_RAW5: P9_S1


title: Patient9_Sample2

description: COUNTS_TABLE_RAW5: P9_S2


title: H9-TSC_Rep_2


title: ccTSC.02_p10_Rep_2

source_name: TSC derived from KiPS primed-iPSCs


title: Patient8_Sample11

description: COUNTS_TABLE_RAW5: P8_S11


title: ccTSC.02_p10_Rep_1


title: Patient8_Sample10

description: COUNTS_TABLE_RAW5: P8_S10


title: ccTSC.02_p10_Rep_3


title: Patient8_Sample9

description: COUNTS_TABLE_RAW5: P8_S9


title: Patient8_Sample7

description: COUNTS_TABLE_RAW5: P8_S7


title: Smartseq2_cells_76_Bone_Marrow_AML

description:
WBH-AMLSC-1-WBH-AMLSC-1-P79_TKR180900408-SN76.out
processed data file:
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_counts.csv
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis.rds
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_unspliced.rds


title: Patient8_Sample4

description: COUNTS_TABLE_RAW5: P8_S4


title: Smartseq2_cells_68_Bone_Marrow_AML

description:
WBH-AMLSC-1-WBH-AMLSC-1-P71_TKR180900408-SN65.out
processed data file:
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_counts.csv
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis.rds
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_unspliced.rds


title: Smartseq2_cells_66_Bone_Marrow_AML

description:
WBH-AMLSC-1-WBH-AMLSC-1-P6_TKR180900408-6.out
processed data file:
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_counts.csv
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis.rds
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_unspliced.rds


title: Patient8_Sample2

description: COUNTS_TABLE_RAW5: P8_S2


title: ccTSC.01_p10_Rep_3

value: human embryonic stem cells


title: Smartseq2_cells_74_Bone_Marrow_AML

description:
WBH-AMLSC-1-WBH-AMLSC-1-P77_TKR180900408-SN71.out
processed data file:
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_counts.csv
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis.rds
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_unspliced.rds


title: ccTSC.01_p10_Rep_2


title: Smartseq2_cells_64_Bone_Marrow_AML

description:
WBH-AMLSC-1-WBH-AMLSC-1-P68_TKR180900408-SN59.out
processed data file:
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_counts.csv
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis.rds
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_unspliced.rds


title: Smartseq2_cells_72_Bone_Marrow_AML

description:
WBH-AMLSC-1-WBH-AMLSC-1-P75_TKR180900408-SN69.out
processed data file:
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_counts.csv
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis.rds
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_unspliced.rds


title: Smartseq2_cells_73_Bone_Marrow_AML

description:
WBH-AMLSC-1-WBH-AMLSC-1-P76_TKR180900408-SN70.out
processed data file:
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_counts.csv
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis.rds
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_unspliced.rds


title: ccTSC.01_p10_Rep_1


title: Smartseq2_cells_71_Bone_Marrow_AML

description:
WBH-AMLSC-1-WBH-AMLSC-1-P74_TKR180900408-SN68.out
processed data file:
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_counts.csv
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis.rds
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_unspliced.rds


title: Smartseq2_cells_79_Bone_Marrow_AML

description:
WBH-AMLSC-1-WBH-AMLSC-1-P81_TKR180900408-SN78.out
processed data file:
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_counts.csv
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis.rds
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_unspliced.rds


title: Smartseq2_cells_69_Bone_Marrow_AML

description:
WBH-AMLSC-1-WBH-AMLSC-1-P72_TKR180900408-SN66.out
processed data file:
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_counts.csv
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis.rds
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_unspliced.rds


title: Patient8_Sample5

description: COUNTS_TABLE_RAW5: P8_S5


title: Patient7_Sample3

description: COUNTS_TABLE_RAW5: P7_S3


title: Smartseq2_cells_62_Bone_Marrow_AML

description:
WBH-AMLSC-1-WBH-AMLSC-1-P66_TKR180900408-GH03.out
processed data file:
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_counts.csv
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis.rds
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_unspliced.rds


title: Smartseq2_cells_63_Bone_Marrow_AML

description:
WBH-AMLSC-1-WBH-AMLSC-1-P67_TKR180900408-SN58.out
processed data file:
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_counts.csv
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis.rds
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_unspliced.rds


title: Smartseq2_cells_70_Bone_Marrow_AML

description:
WBH-AMLSC-1-WBH-AMLSC-1-P73_TKR180900408-SN67.out
processed data file:
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_counts.csv
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis.rds
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_unspliced.rds


title: Patient8_Sample8

description: COUNTS_TABLE_RAW5: P8_S8


title: Smartseq2_cells_67_Bone_Marrow_AML

description:
WBH-AMLSC-1-WBH-AMLSC-1-P70_TKR180900408-SN64.out
processed data file:
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_counts.csv
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis.rds
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_unspliced.rds


title: Patient8_Sample1

description: COUNTS_TABLE_RAW5: P8_S1


title: Smartseq2_cells_59_Bone_Marrow_AML

description:
WBH-AMLSC-1-WBH-AMLSC-1-P63_TKR180900408-SN54.out
processed data file:
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_counts.csv
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis.rds
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_unspliced.rds


title: Smartseq2_cells_60_Bone_Marrow_AML

description:
WBH-AMLSC-1-WBH-AMLSC-1-P64_TKR180900408-SN55.out
processed data file:
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_counts.csv
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis.rds
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_unspliced.rds


title: Smartseq2_cells_57_Bone_Marrow_AML

description:
WBH-AMLSC-1-WBH-AMLSC-1-P61_TKR180900408-SN52.out
processed data file:
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_counts.csv
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis.rds
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_unspliced.rds


title: Patient7_Sample4

description: COUNTS_TABLE_RAW5: P7_S4


title: Patient8_Sample3

description: COUNTS_TABLE_RAW5: P8_S3


title: H9-TSC_Rep_1

value: naive induced pluripotent stem cells


title: Patient6_Sample4

description: COUNTS_TABLE_RAW5: P6_S4


title: Smartseq2_cells_61_Bone_Marrow_AML

description:
WBH-AMLSC-1-WBH-AMLSC-1-P65_TKR180900408-SN56.out
processed data file:
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_counts.csv
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis.rds
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_unspliced.rds


title: Smartseq2_cells_65_Bone_Marrow_AML

description:
WBH-AMLSC-1-WBH-AMLSC-1-P69_TKR180900408-SN60.out
processed data file:
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_counts.csv
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis.rds
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_unspliced.rds


title: Patient6_Sample2

description: COUNTS_TABLE_RAW5: P6_S2


title: Smartseq2_cells_53_Bone_Marrow_AML

description:
WBH-AMLSC-1-WBH-AMLSC-1-P58_TKR180900408-SN46.out
processed data file:
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_counts.csv
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis.rds
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_unspliced.rds


title: Patient8_Sample6

description: COUNTS_TABLE_RAW5: P8_S6


title: Smartseq2_cells_52_Bone_Marrow_AML

description:
WBH-AMLSC-1-WBH-AMLSC-1-P57_TKR180900408-SN45.out
processed data file:
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_counts.csv
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis.rds
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_unspliced.rds


title: Patient7_Sample1

description: COUNTS_TABLE_RAW5: P7_S1


title: Patient5_Sample13

description: COUNTS_TABLE_RAW3: P5_S13


title: Patient5_Sample12

description: COUNTS_TABLE_RAW3: P5_S12


title: Smartseq2_cells_56_Bone_Marrow_AML

description:
WBH-AMLSC-1-WBH-AMLSC-1-P60_TKR180900408-SN48.out
processed data file:
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_counts.csv
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis.rds
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_unspliced.rds


title: Smartseq2_cells_48_Bone_Marrow_AML

description:
WBH-AMLSC-1-WBH-AMLSC-1-P53_TKR180900408-SN41.out
processed data file:
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_counts.csv
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis.rds
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_unspliced.rds


title: Patient5_Sample11

description: COUNTS_TABLE_RAW3: P5_S11


title: Smartseq2_cells_47_Bone_Marrow_AML

description:
WBH-AMLSC-1-WBH-AMLSC-1-P52_TKR180900408-SN40.out
processed data file:
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_counts.csv
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis.rds
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_unspliced.rds


title: Patient5_Sample9

description: COUNTS_TABLE_RAW3: P5_S9


title: Patient5_Sample8

description: COUNTS_TABLE_RAW3: P5_S8


title: Patient6_Sample7

description: COUNTS_TABLE_RAW5: P6_S7


title: Smartseq2_cells_43_Bone_Marrow_AML

description:
WBH-AMLSC-1-WBH-AMLSC-1-P49_TKR180900408-SN34.out
processed data file:
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_counts.csv
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis.rds
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_unspliced.rds


title: Patient5_Sample5

description: COUNTS_TABLE_RAW3: P5_S5


title: Smartseq2_cells_58_Bone_Marrow_AML

description:
WBH-AMLSC-1-WBH-AMLSC-1-P62_TKR180900408-SN53.out
processed data file:
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_counts.csv
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis.rds
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_unspliced.rds


title: Smartseq2_cells_42_Bone_Marrow_AML

description:
WBH-AMLSC-1-WBH-AMLSC-1-P48_TKR180900408-SN33.out
processed data file:
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_counts.csv
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis.rds
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_unspliced.rds


title: Patient7_Sample2

description: COUNTS_TABLE_RAW5: P7_S2


title: Patient5_Sample3

description: COUNTS_TABLE_RAW3: P5_S3


title: Smartseq2_cells_41_Bone_Marrow_AML

description:
WBH-AMLSC-1-WBH-AMLSC-1-P47_TKR180900408-SN32.out
processed data file:
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_counts.csv
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis.rds
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_unspliced.rds


title: Patient6_Sample6

description: COUNTS_TABLE_RAW5: P6_S6


title: Patient5_Sample2

description: COUNTS_TABLE_RAW3: P5_S2


title: Patient6_Sample8

description: COUNTS_TABLE_RAW5: P6_S8


title: Smartseq2_cells_51_Bone_Marrow_AML

description:
WBH-AMLSC-1-WBH-AMLSC-1-P56_TKR180900408-SN44.out
processed data file:
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_counts.csv
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis.rds
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_unspliced.rds


title: Patient6_Sample1

description: COUNTS_TABLE_RAW5: P6_S1


title: Patient5_Sample1

description: COUNTS_TABLE_RAW3: P5_S1


title: Smartseq2_cells_55_Bone_Marrow_AML

description:
WBH-AMLSC-1-WBH-AMLSC-1-P5_TKR180900408-5.out
processed data file:
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_counts.csv
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis.rds
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_unspliced.rds


title: Patient5_Sample10

description: COUNTS_TABLE_RAW3: P5_S10


title: Patient6_Sample3

description: COUNTS_TABLE_RAW5: P6_S3


title: Patient4_Sample3

description: COUNTS_TABLE_RAW5: P4_S3


title: Smartseq2_cells_37_Bone_Marrow_AML

description:
WBH-AMLSC-1-WBH-AMLSC-1-P43_TKR180900408-SN28.out
processed data file:
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_counts.csv
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis.rds
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_unspliced.rds


title: Smartseq2_cells_54_Bone_Marrow_AML

description:
WBH-AMLSC-1-WBH-AMLSC-1-P59_TKR180900408-SN47.out
processed data file:
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_counts.csv
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis.rds
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_unspliced.rds


title: Smartseq2_cells_36_Bone_Marrow_AML

description:
WBH-AMLSC-1-WBH-AMLSC-1-P42_TKR180900408-SN24.out
processed data file:
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_counts.csv
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis.rds
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_unspliced.rds


title: Smartseq2_cells_40_Bone_Marrow_AML

description:
WBH-AMLSC-1-WBH-AMLSC-1-P46_TKR180900408-SN31.out
processed data file:
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_counts.csv
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis.rds
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_unspliced.rds


title: Patient5_Sample14

description: COUNTS_TABLE_RAW3: P5_S14


title: Patient6_Sample5

description: COUNTS_TABLE_RAW5: P6_S5


title: Patient5_Sample7

description: COUNTS_TABLE_RAW3: P5_S7


title: Smartseq2_cells_33_Bone_Marrow_AML

description:
WBH-AMLSC-1-WBH-AMLSC-1-P3_TKR180900408-3.out
processed data file:
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_counts.csv
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis.rds
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_unspliced.rds


title: Smartseq2_cells_31_Bone_Marrow_AML

description:
WBH-AMLSC-1-WBH-AMLSC-1-P38_TKR180900408-SN20.out
processed data file:
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_counts.csv
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis.rds
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_unspliced.rds


title: Smartseq2_cells_46_Bone_Marrow_AML

description:
WBH-AMLSC-1-WBH-AMLSC-1-P51_TKR180900408-SN36.out
processed data file:
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_counts.csv
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis.rds
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_unspliced.rds


title: Smartseq2_cells_49_Bone_Marrow_AML

description:
WBH-AMLSC-1-WBH-AMLSC-1-P54_TKR180900408-AK706.out
processed data file:
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_counts.csv
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis.rds
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_unspliced.rds


title: Patient4_Sample2

description: COUNTS_TABLE_RAW5: P4_S2


title: Patient3_Sample12

description: COUNTS_TABLE_RAW1: P3_S12


title: Smartseq2_cells_29_Bone_Marrow_AML

description:
WBH-AMLSC-1-WBH-AMLSC-1-P36_TKR180900408-AK691.out
processed data file:
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_counts.csv
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis.rds
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_unspliced.rds


title: Smartseq2_cells_50_Bone_Marrow_AML

description:
WBH-AMLSC-1-WBH-AMLSC-1-P55_TKR180900408-GG04.out
processed data file:
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_counts.csv
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis.rds
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_unspliced.rds


title: Patient3_Sample18

description: COUNTS_TABLE_RAW1: P3_S18


title: Patient3_Sample11

description: COUNTS_TABLE_RAW1: P3_S11


title: Patient5_Sample4

description: COUNTS_TABLE_RAW3: P5_S4


title: Smartseq2_cells_45_Bone_Marrow_AML

description:
WBH-AMLSC-1-WBH-AMLSC-1-P50_TKR180900408-SN35.out
processed data file:
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_counts.csv
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis.rds
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_unspliced.rds


title: Smartseq2_cells_28_Bone_Marrow_AML

description:
WBH-AMLSC-1-WBH-AMLSC-1-P35_TKR180900408-SN17.out
processed data file:
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_counts.csv
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis.rds
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_unspliced.rds


title: Patient3_Sample15

description: COUNTS_TABLE_RAW1: P3_S15


title: Smartseq2_cells_26_Bone_Marrow_AML

description:
WBH-AMLSC-1-WBH-AMLSC-1-P33_TKR180900408-SN12.out
processed data file:
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_counts.csv
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis.rds
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_unspliced.rds


title: Patient4_Sample1

description: COUNTS_TABLE_RAW5: P4_S1


title: Patient3_Sample17

description: COUNTS_TABLE_RAW1: P3_S17


title: Patient5_Sample6

description: COUNTS_TABLE_RAW3: P5_S6


title: Smartseq2_cells_39_Bone_Marrow_AML

description:
WBH-AMLSC-1-WBH-AMLSC-1-P45_TKR180900408-SN30.out
processed data file:
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_counts.csv
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis.rds
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_unspliced.rds


title: Patient3_Sample3

description: COUNTS_TABLE_RAW1: P3_S3


title: Patient3_Sample4

description: COUNTS_TABLE_RAW1: P3_S4


title: Smartseq2_cells_27_Bone_Marrow_AML

description:
WBH-AMLSC-1-WBH-AMLSC-1-P34_TKR180900408-SN16.out
processed data file:
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_counts.csv
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis.rds
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_unspliced.rds


title: Smartseq2_cells_34_Bone_Marrow_AML

description:
WBH-AMLSC-1-WBH-AMLSC-1-P40_TKR180900408-AK693.out
processed data file:
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_counts.csv
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis.rds
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_unspliced.rds


title: Smartseq2_cells_44_Bone_Marrow_AML

description:
WBH-AMLSC-1-WBH-AMLSC-1-P4_TKR180900408-4.out
processed data file:
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_counts.csv
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis.rds
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_unspliced.rds


title: Smartseq2_cells_35_Bone_Marrow_AML

description:
WBH-AMLSC-1-WBH-AMLSC-1-P41_TKR180900408-SN23.out
processed data file:
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_counts.csv
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis.rds
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_unspliced.rds


title: Smartseq2_cells_38_Bone_Marrow_AML

description:
WBH-AMLSC-1-WBH-AMLSC-1-P44_TKR180900408-SN29.out
processed data file:
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_counts.csv
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis.rds
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_unspliced.rds


title: Patient1_Sample2

description: COUNTS_TABLE_RAW5: P1_S2


title: Patient1_Sample1

description: COUNTS_TABLE_RAW5: P1_S1


title: Patient3_Sample13

description: COUNTS_TABLE_RAW1: P3_S13


title: Patient3_Sample14

description: COUNTS_TABLE_RAW1: P3_S14


title: Smartseq2_cells_17_Bone_Marrow_AML

description:
WBH-AMLSC-1-WBH-AMLSC-1-P25_TKR180900408-AK690.out
processed data file:
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_counts.csv
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis.rds
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_unspliced.rds


title: Patient3_Sample16

description: COUNTS_TABLE_RAW1: P3_S16


title: H3K27ac, WCM1078, Organoid, Input

city: Boston

first: Himisha

last: Beltran

state: MA

address: 450 Brookline Ave

department: Department of Medical Oncology

institute: Dana Farber Cancer Institute

library_source: genomic

data_processing:
Illumina Casava1.7 software used for basecalling.
Reads were aligned to mm9 using BWA
For peak calling MACS2 was used.
Assembly: hg19
Supplementary files format and content: bw files were generated using MACS2 using the chilin pipeline

molecule: genomic DNA

source_name: Neuroendocrine prostate cancer

growth_protocol: The NEPC organoids were combined with growth factor-reduced Matrigel (Corning) in a 1:2 volume ratio. Six droplets of 50 μl cell suspension/Matrigel mixture was pipetted onto each well of a six-well cell suspension culture plate (Greiner). The 6-well plate was placed into a cell culture incubator at 37 °C and 5% CO2 for 30 min to solidify the droplets before 2.5 ml of prostate-specific culture media was added to each well. The organoids were grown in prostate-specific culture media composed of Advanced DMEM/F12 (Invitrogen) with GlutaMAX (1×, Invitrogen), HEPES Buffer (1M, Invitrogen), 100 U/ml penicillin, 100 μg/ml streptomycin (Gibco), B27 supplement (Gibco), N-Acetylcysteine 1.25 mM (Sigma-Aldrich), Mouse Recombinant protein EGF 50 ng/ml (Peprotech), Human Recombinant FGF-10 20 ng/ml (Peprotech), Recombinant Human FGF-basic 1 ng/ml (Peprotech), A-83-01 500 nM (Tocris), SB202190 10 μM (Sigma-Aldrich), Nicotinaminde 10 mM (Sigma-Aldrich), PGE2 1 μM (Tocris), NRG 100 μl/ml (GenScript), Y-27632-2HC1 10µM (Selleck), Noggin conditioned media (10%) and R-spondin conditioned media (5%). The culture was replenished with fresh media every 3−4 days during organoid growth. Dense cultures with organoids ranging in size from 200 to 500 um were passaged every 10 to 12 days.

extract_protocol: Cells was fixed using 1% formaldehyde and chromatin sheared to 300-500 bp in size using the Covaris E220 ultrasonicator. Resulting chromatin was incubated overnight with indicated antibodies. Purified immunoprecipitates were isolated and quantified by Qubit fluorometer.  DNA sequencing libraries were prepared using the ThruPLEX-FD Prep kit (Rubicon Genomics). Libraries were sequenced using 75-bp reads on the Illumina platform at the Dana-Farber Cancer Institute.

treatment_protocol: Not applicable

value: Neuroendocrine prostate cancer

value: Not applicable

value: NEPC organoid

value: Wild Type


title: Smartseq2_cells_32_Bone_Marrow_AML

description:
WBH-AMLSC-1-WBH-AMLSC-1-P39_TKR180900408-SN21.out
processed data file:
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_counts.csv
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis.rds
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_unspliced.rds


title: Patient3_Sample5

description: COUNTS_TABLE_RAW1: P3_S5


title: H3K27ac, WCM155, Organoid, Input


title: Patient3_Sample6

description: COUNTS_TABLE_RAW1: P3_S6


title: Smartseq2_cells_15_Bone_Marrow_AML

description:
WBH-AMLSC-1-WBH-AMLSC-1-P23_TKR180900408-25.out
processed data file:
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_counts.csv
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis.rds
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_unspliced.rds


title: Patient1_Sample3

description: COUNTS_TABLE_RAW5: P1_S3


title: H3K27ac, WCM154, Organoid, Input


title: Smartseq2_cells_23_Bone_Marrow_AML

description:
WBH-AMLSC-1-WBH-AMLSC-1-P30_TKR180900408-SN9.out
processed data file:
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_counts.csv
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis.rds
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_unspliced.rds


title: Smartseq2_cells_22_Bone_Marrow_AML

description:
WBH-AMLSC-1-WBH-AMLSC-1-P2_TKR180900408-2.out
processed data file:
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_counts.csv
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis.rds
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_unspliced.rds


title: Smartseq2_cells_21_Bone_Marrow_AML

description:
WBH-AMLSC-1-WBH-AMLSC-1-P29_TKR180900408-GG03.out
processed data file:
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_counts.csv
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis.rds
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_unspliced.rds


title: Patient3_Sample1

description: COUNTS_TABLE_RAW1: P3_S1


title: Smartseq2_cells_24_Bone_Marrow_AML

description:
WBH-AMLSC-1-WBH-AMLSC-1-P31_TKR180900408-SN10.out
processed data file:
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_counts.csv
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis.rds
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_unspliced.rds


title: Smartseq2_cells_25_Bone_Marrow_AML

description:
WBH-AMLSC-1-WBH-AMLSC-1-P32_TKR180900408-SN11.out
processed data file:
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_counts.csv
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis.rds
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_unspliced.rds


title: Smartseq2_cells_14_Bone_Marrow_AML

description:
WBH-AMLSC-1-WBH-AMLSC-1-P22_TKR180900408-23.out
processed data file:
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_counts.csv
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis.rds
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_unspliced.rds


title: Smartseq2_cells_20_Bone_Marrow_AML

description:
WBH-AMLSC-1-WBH-AMLSC-1-P28_TKR180900408-SN7.out
processed data file:
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_counts.csv
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis.rds
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_unspliced.rds


title: Smartseq2_cells_18_Bone_Marrow_AML

description:
WBH-AMLSC-1-WBH-AMLSC-1-P26_TKR180900408-SN5.out
processed data file:
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_counts.csv
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis.rds
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_unspliced.rds


title: H3K27ac, WCM1262, Organoid, Input


title: Smartseq2_cells_30_Bone_Marrow_AML

description:
WBH-AMLSC-1-WBH-AMLSC-1-P37_TKR180900408-SN19.out
processed data file:
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_counts.csv
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis.rds
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_unspliced.rds


title: Smartseq2_cells_19_Bone_Marrow_AML

description:
WBH-AMLSC-1-WBH-AMLSC-1-P27_TKR180900408-SN6.out
processed data file:
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_counts.csv
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis.rds
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_unspliced.rds


title: Smartseq2_cells_16_Bone_Marrow_AML

description:
WBH-AMLSC-1-WBH-AMLSC-1-P24_TKR180900408-27.out
processed data file:
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_counts.csv
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis.rds
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_unspliced.rds


title: H3K27ac, 22Rv1_WT, Cell line, Input

source_name: Adenocarcinoma of prostate

value: Adenocarcinoma of prostate

value: CRPC cell line


title: Smartseq2_cells_10_Bone_Marrow_AML

description:
WBH-AMLSC-1-WBH-AMLSC-1-P19_TKR180900408-20.out
processed data file:
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_counts.csv
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis.rds
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_unspliced.rds


title: Patient3_Sample2

description: COUNTS_TABLE_RAW1: P3_S2


title: Smartseq2_cells_11_Bone_Marrow_AML

description:
WBH-AMLSC-1-WBH-AMLSC-1-P1_TKR180900408-1.out
processed data file:
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_counts.csv
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis.rds
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_unspliced.rds


title: H3K27ac, 22Rv1_WT, Cell line, Abcam 4729


title: H3K27ac, WCM1262, Organoid, Abcam 4729


title: Smartseq2_cells_12_Bone_Marrow_AML

description:
WBH-AMLSC-1-WBH-AMLSC-1-P20_TKR180900408-21.out
processed data file:
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_counts.csv
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis.rds
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_unspliced.rds


title: Smartseq2_cells_9_Bone_Marrow_AML

description:
WBH-AMLSC-1-WBH-AMLSC-1-P18_TKR180900408-19.out
processed data file:
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_counts.csv
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis.rds
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_unspliced.rds


title: H3K27ac, WCM155, Organoid, Abcam 4729


title: Smartseq2_cells_13_Bone_Marrow_AML

description:
WBH-AMLSC-1-WBH-AMLSC-1-P21_TKR180900408-22.out
processed data file:
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_counts.csv
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis.rds
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_unspliced.rds


title: H3K27ac, WCM1078, Organoid, Abcam 4729


title: Smartseq2_cells_8_Bone_Marrow_AML

description:
WBH-AMLSC-1-WBH-AMLSC-1-P17_TKR180900408-18.out
processed data file:
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_counts.csv
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis.rds
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_unspliced.rds


title: Smartseq2_cells_7_Bone_Marrow_AML

description:
WBH-AMLSC-1-WBH-AMLSC-1-P16_TKR180900408-16.out
processed data file:
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_counts.csv
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis.rds
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_unspliced.rds


title: Smartseq2_cells_1_Bone_Marrow_AML

description:
WBH-AMLSC-1-WBH-AMLSC-1-P10_TKR180900408-10.out
processed data file:
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_counts.csv
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis.rds
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_unspliced.rds


title: Smartseq2_cells_5_Bone_Marrow_AML

description:
WBH-AMLSC-1-WBH-AMLSC-1-P14_TKR180900408-14.out
processed data file:
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_counts.csv
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis.rds
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_unspliced.rds


title: Smartseq2_cells_3_Bone_Marrow_AML

description:
WBH-AMLSC-1-WBH-AMLSC-1-P12_TKR180900408-12.out
processed data file:
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_counts.csv
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis.rds
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_unspliced.rds


title: bone, 8000µɛ loaded, 0 h post-culture, donor6

city: Amsterdam

first: Chen

address: Meibergdreef 9

country: Netherlands

institute: Amsterdam UMC

data_processing:
Sequence reads were quality trimmed using Sickle (version 1.33).
Trimmed sequence reads were aligned to the GRCh37 reference (grch37_snp_tran) using HiSat2 (version 2.0.4).
Resulting bam files were sorted using samtools (version 1.3), and expression counts were generated by featureCount (version 1.5.0-p3).
Normalization and estimation of dispersion was performed by edgeR (version 3.38.1).
Assembly: GRCh37
Supplementary files format and content: Tab-delimited text files include RPKM values for each sample.

source_name: cortical fibular bone

growth_protocol: Bone explants were cultured for 1 or 2 days in 6-well plates, containing minimal essential medium (MEM) supplemented with 5% fetal bovine serum (FBS), 5% bovine calf serum (BCS), 1% penicillin-streptomycin (10,000 U/mL, and 0.5% amphotericin B solution at 37°C.

extract_protocol:
Bone explants were pulverized using a 6775 Freezer/Mill cryogenic grinder (SPEX SamplePrep, Metuchen, NJ, USA). Explants were grinded (rate: 10 cycles/sec; 20 impacts/sec) for 2 min in liquid nitrogen. After pulverization, the TRIzol/bone powder mixture was incubated for 1 h in a shaking waterbath at 37°C. Isolation and purification of RNA was performed using RNeasy Midi columns (Qiagen, Hilden, Germany) or Zymo-Spin IIICG columns (Direct-zol RNA MiniPrep Plus, Zymo Research, Irvine, CA, USA).
cDNA libraries for RNA-seq were prepared using KAPA mRNA Hyperprep kit (Roche Sequencing Solutions, Indianapolis, IN, USA).

treatment_protocol: Explants were either or not mechanically loaded by three-point bending with a rounded contact point and a span length of 8 mm, at a magnitude of 2000 or 8000 µɛ at 1 Hz frequency for 5 min. In short, mechanical loading was applied using a custom-made loading apparatus, which generated sinusoidal displacement using a computer-driven voice coil linear microactuator (type NCM04-25250-2LVE; H2W Technologies, Valencia, CA, USA). Immediately after mechanical loading, explants were post-cultured (without mechanical loading) for 0, 6 or 24 h in MEM containing 5% FBS, 5% BCS, 1% penicillin-streptomycin, and 0.5% amphotericin B solution.

value: cortical fibular bone

tag: gender

value: female

value: mechanical loading

tag: magnitude of_mechanical_loading

tag: post-culture

value: 0 h


title: bone, 8000µɛ loaded, 6 h post-culture, donor6

tag: tissue

tag: age

value: 6 h


title: bone, 2000µɛ loaded, 0 h post-culture, donor6

tag: treatment


title: bone, 0 µɛ (unloaded), 24 h post-culture, donor6

value: unloaded

value: 0 ue


title: bone, 8000µɛ loaded, 24 h post-culture, donor5

value: male


title: bone, 2000µɛ loaded, 6 h post-culture, donor6


title: Smartseq2_cells_2_Bone_Marrow_AML

description:
WBH-AMLSC-1-WBH-AMLSC-1-P11_TKR180900408-11.out
processed data file:
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_counts.csv
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis.rds
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_unspliced.rds

value: AML

value: BM


title: bone, 0 µɛ (unloaded), 0 h/ 6 h post-culture, donor6


title: RNA_ST_679

city: Seoul

first: Je-Yoel

last: Cho

address: 1, Gwanak-ro, Gwanak-gu

department: Biochemistry

country: South Korea

institute: Seoul National University

data_processing:
Data were filtered and trimmed using Trimmomatic
The sequenced reads aligned to the canine reference genome (canFam3.1 assembly) using STAR
TIN values were calculated using RSeQC
Gene expression value were calculated usin RSEM
Assembly: canFam3.1
Supplementary files format and content: bigWig

organism: Canis lupus familiaris

source_name: Stomach

growth_protocol: One male and two female beagles  were kindly donated by Dr. Jong-Gu Kang from the College of Veterinary Medicine at Chungbuk National University.

extract_protocol:
Total RNA was extracted from each tissue using the RNeasy Mini plus kit (Qiagen, USA). Pulverization for sample homogenization was performed with liquid nitrogen prior to RNA isolation, according to the manufacturer's instruction. The RNA quality was assessed by analysis of 18S and 28S rRNA band integrity on a RNA 6000 Nano Kit (part # 5067-1511) using an Agilent Bioanalyzer (Agilent, USA).
Library was prepared using TruSeq Stranded Total RNA sample preparation kit (RS-122-9007) and sequenced using HiSeq 2500 or NovaSeq 6000 (Illumina) by Theragen Inc (Korea).

treatment_protocol: Three dogs in healthy condition were euthanized by intravenous administration of alfaxalone and KCl. Eleven common tissues (cerebrum [CR], cerebellum [CL], colon [CO], kidney [KI], liver [LI], lung [LU], mammary gland [MG], ovary [OV], pancreas [PA], spleen [SP] and stomach [ST]) were isolated from the three beagles. All tissues were rinsed with ice-cold PBS before being minced. Immediately after mincing, tissues were divided into 4 tubes based on the types of analysis, and frozen with liquid nitrogen

value: Stomach

tag: Sex

value: Female

tag: breed

value: Beagle


title: Smartseq2_cells_6_Bone_Marrow_AML

description:
WBH-AMLSC-1-WBH-AMLSC-1-P15_TKR180900408-15.out
processed data file:
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_counts.csv
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis.rds
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_unspliced.rds


title: bone, 2000µɛ loaded, 24 h post-culture, donor5


title: RNA_SP_jj8

source_name: Spleen

value: Spleen

value: Male


title: Smartseq2_cells_4_Bone_Marrow_AML

description:
WBH-AMLSC-1-WBH-AMLSC-1-P13_TKR180900408-13.out
processed data file:
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_counts.csv
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis.rds
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_unspliced.rds


title: bone, 8000µɛ loaded, 0 h post-culture, donor5


title: H3K27ac, WCM154, Organoid, Abcam 4729

value: Neuroendocrine prostate cancer

value: Not applicable

value: NEPC organoid

tag: genotype

value: Wild Type


title: RNA_PA_244

source_name: Pancreas

value: Pancreas


title: RNA_OV_244

source_name: Ovary

value: Ovary


title: RNA_ST_244


title: bone, 8000µɛ loaded, 24 h post-culture, donor6

value: cortical fibular bone

value: female

value: mechanical loading


title: bone, 0 µɛ (unloaded), 0 h/ 6 h post-culture, donor5

value: male

value: unloaded

value: 0 ue


title: bone, 8000µɛ loaded, 6 h post-culture, donor5

value: 6 h


title: RNA_MG_679

source_name: Mammary gland

value: Mammary gland

value: Female


title: bone, 8000µɛ loaded, 24 h post-culture, donor4


title: RNA_PA_679

value: Beagle


title: bone, 2000µɛ loaded, 6 h post-culture, donor5


title: RNA_OV_679


title: bone, 8000µɛ loaded, 0 h post-culture, donor4

value: 0 h


title: RNA_KI_679

source_name: Kidney

value: Kidney


title: bone, 8000µɛ loaded, 6 h post-culture, donor4


title: bone, 2000µɛ loaded, 0 h post-culture, donor5


title: RNA_CO_679

source_name: Colon

value: Colon


title: RNA_KI_244


title: RNA_CR_jj8

source_name: Cerebrum

value: Cerebrum

value: Male


title: bone, 2000 µɛ loaded, 24 h post-culture, donor3


title: RNA_MG_244


title: bone, 2000µɛ loaded, 24 h post-culture, donor4


title: bone, 2000 µɛ loaded, 24 h post-culture, donor1


title: ChIP_input_PA_679

data_processing:
All of pre-processing steps including trimming, alignment, generation of signal track, peak calling and diverse type of QC were performed using ENCODE ChIP-seq processing pipeline (https://github.com/ENCODE-DCC/chip-seq-pipeline2)
Assembly: canFam3.1
Supplementary files format and content: narrowPeak (except for Input sample)

extract_protocol:
The 11 frozen tissues were thawed on ice and 10 mg of tissue per IP reaction was chopped into ~1 mm3 pieces with two razor blades on the ice. Chopped tissues were washed out with PBS buffer containing Protease K, 10mM PMSF, and 10mM Sodium Butyrate histone deacetylase inhibitor to remove blood from the tissue. Washed tissue was grinded using pestle and mortar. Then prepared cell mass was cross-linked in the PBS buffer with 1.5% Formaldehyde added at room temperature(RT) for 20 minutes. By adding 125 mM Glycine and placing the samples on the rotator for 5 min, cross-linking reactions were stopped. Fixed cell mass was washed twice with PBS buffer containing Protease K, 10mM PMSF, and 10mM Sodium Butyrate.  Fixed cell mass was lysed using buffer A (5 mM PIPES buffer, 85 mM KCl, and 0.5% NP 40). The supernatant was centrifuged out and added to buffer B (50 mM Tris-HCl, 0.5% SDS, and 2.5mM EDTA). All buffers contained Protease K, 10 mM PMSF, and 10 mM Sodium Butyrate histone deacetylase inhibitor. Sonication was then carried out to get 300-500 bp size fragments using Bioruptor Pico (Diagenode). Twenty to fifty cycles of 30 seconds, on and off, were performed at 4 ℃ depending on the tissue. Liver cells were sonicated for only 20 cycles. Chromatin solution was centrifuged to remove the debris and diluted with ChIP IP buffer (16.7 mM Tris-HCl, 0.05% SDS, 1.1% Triton X-100, 1.2 mM EDTA, and 167 mM NaCl). After adding 5 µg of sample to 10 µg of anti-H3K4me1 (ab8895), H3K27Ac (ab4729), H3K4me3 (ab8580), H3K27me3 (ab6002), H3K9me3 (ab8898), and IgG (Sc-2027) per IP reaction, the chromatin solution was incubated overnight at 4 ℃. The cross-linking was reversed and DNA was purified after treatment with protease K and RNase A. ChIPed DNA was quantified using the Qubit fluoro-spectrometer (ThermoFisher Scientific, Waltham, MA, USA) and the enrichment was validated by PCR.
The ChIP library was prepared using the TruSeq ChIP Library Preparation Kit and sequenced in ~500 bp fragments using HiSeq 2500 system (Illumina) by Macrogen (Macrogen, Korea).

value: Pancreas

tag: chip antibody


title: RNA_LU_jj8

source_name: Lung

value: Lung


title: bone, 2000 µɛ loaded, 0 h post-culture, donor4

value: cortical fibular bone


title: RNA_CO_244


title: ChIP_input_OV_679

value: Ovary


title: bone, 8000 µɛ loaded, 0 h post-culture, donor1

value: mechanical loading


title: bone, 0 µɛ (unloaded), 24 h post-culture, donor5

value: male


title: bone, 0 µɛ (unloaded), 0 h/ 6 h/ 24 h post-culture, donor4

value: female

value: unloaded


title: ChIP_input_MG_679


title: ChIP_input_LI_jj8

source_name: Liver

value: Liver


title: bone marrow, R8, 2nd

city: Providence

first: Patrycja

middle: M

last: Dubielecka

state: RI

address: 1 Hoppin St., Coro West, 5th Fl., Suite 5.36

department: Division of Hematology/Oncology, Department of Medicine

institute: Warren Alpert Medical School of Brown University and Rhode Island Hospital

data_processing:
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36.
The trimmed reads were mapped to the Homo sapiens GRCh38 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b. BAM files were generated as a result of this step.
Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2. The hit counts were summarized and reported using the gene_id feature in the annotation file. Only unique reads that fell within exon regions were counted.
Assembly: Homo sapiens GRCh38
Supplementary files format and content: tab-delimited text files show raw hit counts for each Sample

source_name: bone marrow

extract_protocol:
RNA was isolated from patient FFPE core bone marrow biopsies using the Qiagen's Rneasy FFPE Kit (Catalog# 73504)
Library preparation, Illumina, RNA with rRNA depletion

value: F

value: bone marrow

tag: treatment response

value: Responder

tag: time


title: bone marrow, R5, 2nd

value: M


title: ChIP_input_SP_jj8

value: Spleen

value: Beagle


title: bone, 0 µɛ (unloaded), 0 h/ 6 h/ 24 h post-culture, donor1

value: 0 ue


title: bone, 8000 µɛ loaded, 24 h post-culture, donor1


title: RNA_LI_jj8

value: Male


title: bone marrow, R8, 1st


title: ChIP_input_ST_jj8

value: Stomach


title: RNA_CL_jj8

source_name: Cerebellum

value: Cerebellum


title: ChIP_input_CR_jj8

value: Cerebrum


title: ChIP_input_CL_jj8


title: bone marrow, R3, 2nd


title: bone, 2000 µɛ loaded, 6 h post-culture, donor1

value: cortical fibular bone

value: 6 h


title: bone marrow, R14, 2nd


title: ChIP_k9me3_SP_jj8

value: H3K9me3 (Abcam, #ab8898)


title: bone, 8000 µɛ loaded, 6 h post-culture, donor1

value: male

value: mechanical loading


title: ChIP_input_LU_jj8

value: Lung


title: ChIP_k9me3_MG_679

value: Mammary gland

value: Female


title: ChIP_input_CO_jj8

value: Colon


title: bone, 2000 µɛ loaded, 6 h post-culture, donor2

value: female


title: bone marrow, NR9, 2nd

value: M

value: bone marrow

value: Non-Responder


title: bone marrow, R1, 1st

value: Responder


title: bone marrow, R1, 2nd


title: ChIP_k9me3_CO_jj8

value: Male

value: Beagle


title: ChIP_input_KI_679

value: Kidney


title: bone marrow, NR9, 1st


title: bone marrow, R5, 1st

value: F


title: ChIP_k9me3_CL_jj8

value: Cerebellum


title: bone, 2000 µɛ loaded, 0 h post-culture, donor1

value: cortical fibular bone

value: 0 h


title: bone marrow, R3, 1st


title: ChIP_k9me3_LU_jj8

value: H3K9me3 (Abcam, #ab8898)


title: bone marrow, R14, 1st


title: bone marrow, NR3, 2nd


title: ChIP_k9me3_LI_jj8

value: Liver


title: bone marrow, R12, 2nd


title: ChIP_k9me3_PA_679

value: Pancreas


title: ChIP_k9me3_KI_679

value: Female