title: P10_S2_PD

city: Trondheim

first: Kristine

last: Misund

address: Prinsesse Kristinas gate 1

department: Department of Clinical and Molecular Medicine

country: Norway

institute: NTNU

data_processing:
Libraries were either; 1) normalized and pooled to 2.2/2.5 pM (flowcell 1/flowcell2) and subjected to clustering on two NextSeq 500 high output flowcells. Finally paired end read sequencing was performed for 75X2 cycles on a NextSeq 500 instrument (Illumina, Inc. San Diego, CA, USA), according to the manufacturer's instructions. Base calling were done on the NS500 instrument by RTA 2.4.6. or; 2) normalized and pooled to 2.3 pM and subject to clustering by a cBot Cluster Generation System on a HiSeq4000 flowcell (Illumina), according to manufacturers instructions. Finally paired end read sequencing was performed for 75X2 cycles performed on a Illumina HiSeq4000 instrument, in accordance with the manufacturer’s instructions. FASTQ files were created with bcl2fastq 2.17 (Illumina).
Transcript expression values were generated by quasi alignment using salmon (http://salmon.readthedocs.io/en/latest/index.html) and the Ensembl (Hg19) human genome.
Aggregation of transcript to gene expression was performed using tximport (http://bioconductor.org/packages/release/bioc/html/tximport.html) and normalized to transcripts per million (TPM) values.
Genome_build: Hg19
Supplementary_files_format_and_content: tab-delimited text file include gene counts for every gene and every sample
Supplementary_files_format_and_content: tab-delimited text file include TPM values for every gene and every sample

source_name: Multiple myeloma cells (CD138+)

extract_protocol:
CD138-positive tumor cells were isolated using RoboSep (StemCell Technologies, Grenoble, France). Tumor purity was subsequently determined by evaluation of MGG-stained cytopspin slides or by flow cytometry. Only samples with a tumor purity ≥80% were included in the study. Tumor  total RNA were extracted using All-Prep Kit (Qiagen, Hilden, Germany) according to the manufacturer's instructions
RNA Seq libraries were prepared using TruSeq Stranded mRNA kit (Illumina) according to the manufacturer's instructions. Briefly, 500 ng total RNA was used as starting material.

tag: Stage

value: Progressive Disease (PD)

tag: sample


title: P10_S1_NDMM

status: Public on May 01 2022

type: SRA

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

value: Newly Diagnosed symptomatic MM (NDMM)


title: P15_S2_PD


title: P15_S3_PD


title: P20_S2_PD


title: P20_S1_NDMM


title: P15_S1_NDMM


title: P8_S1_PD


title: P4_S2_PD


title: 031_JLat92_IFNB_12h

city: Minneapolis

first: Michael

last: Gale

state: Minnesota

address: 689 23rd Ave SE

department: Microbiology and Immunology

country: USA

institute: University of Minnesota

description: Replicate 1

data_processing:
Read quality for each sample was first assessed with FASTQC
Globin and rRNA reads were filtered out using bowtie2 version 2.3.4
Remaining reads were alligned to the GRCh37 genome using STAR version 2.4.0h1
Gene counts were calculated with HTSeq-count version 0.6.1p1
Genes with counts less than 10 averaged across all samples were filtered out. The filtered count matrix then underwent TMM normalization followed by voom transformation.
Genome_build: GRCh37

molecule: polyA RNA

growth_protocol: Cells were cultured in RPMI supplemented with 10% FBS, 1% L-glutamine, 1% non-essential amino acids, 1% sodium pyrvuate, and 1% antibiotic/antimycotic cocktail. All cells were maintained at 37°C and 5% CO2.

extract_protocol:
Cell lysates were digested in RLT and total cellular RNA extracted using the miRNeasy Micro kit (Qiagen) according to the manufacturer's instructions, and residual genomic DNA removed by DNAse treatment.
mRNA-seq libraries were constructed using Illumina TruSeq® Stranded mRNA HT kit following the manufacturer's recommended protocol.
Libraries were sequenced on an Illumina NextSeq500 sequencer using Illumina NextSeq 500/550 High Output v2 kits (150 cycles) following the manufacturer's protocol for sample handling and loading.

treatment_protocol: Cells were seeded at 5 x 105 cells/ml in complete RPMI in 12-well plates and cultured overnight at 37°C. The following day cells were treated with media containing 100IU/mL human recombinant IFN-β and sampled at 4h, 8h, and 12h.

tag: treatment

value: IFNb Treated 12h

tag: cell type

value: Jlat9.2 CD4+ T Cells


title: 032_JLat92_IFNB_12h

description: Replicate 2


title: 030_JLat92_IFNB_8h

description: Replicate 3

value: IFNb Treated 8h


title: 029_JLat92_IFNB_8h

description: Replicate 2


title: 033_JLat92_IFNB_12h

description: Replicate 3


title: 024_JLat92_Mock_4h

description: Replicate 3

value: Mock 4h


title: 026_JLat92_IFNB_4h

description: Replicate 2

value: IFNb Treated 4h


title: 025_JLat92_IFNB_4h

description: Replicate 1


title: 027_JLat92_IFNB_4h

description: Replicate 3


title: CORL311_Input

city: Cold Spring Harbor

first: Xiaoli

middle: Sky

last: Wu

state: New York

address: 1 Bungtown Road

institute: Cold Spring Harbor Laboratory

library_source: genomic

data_processing:
Sequencing reads were first trimmed and filtered with Trimmomatic (0.39-Java-11) with minimal read length 50 using default settings for ChIP-Seq. For RNA-seq, sequencing reads were mapped onto reference human genome hg38 using Hisat2 2.1.0 with default  setting.
For ChIP-Seq, Reads that passed the quality control were then mapped to hg38 with bowtie2 2.4.2 with very-sensitive setting and 2 mismatches are allowed
For ChIP-Seq, Bam files are then  sorted with Samtools 1.11 with default settings. PCR duplicates were removed with Picard  2.21.6 with default settings and indexed with Samtools. Peaks were called with Macs2 2.2.7.1 with  input as negative control with default settings and a 5% FDR as cutoff.
Bedtools 2.30.0 was used to intersect as well as merge peaks from different experiments to generate high-confidence peaks or all C11orf53-OCT11 occupying sites (54, 55). Homer v4.11 makeTagDirectory and makeUCSCfile were used to generate bigwigs files for visualizing ChIP-Seq tracks on UCSC genome browser. The annotatePeaks was used to annotate peak features for C11orf53-OCT11 occupying peaks as well as  calculating tag counts on C11orf53/OCT11 intensity on all C11orf53-OCT11 binding sites with +/- 250  bp around peak center. MEME SUIT 5.4.1 MEME was used to discover motifs enriched on defined peak  regions.
For scRNA-seq, the Cell Ranger  pipeline (v5.0.0, 10X Genomics) was used to align FASTQ reads to the mouse reference genome (gexmm10-  2020-A, 10X Genomics) and produce digital gene-cell counts matrices. The resulting genebarcode  matrices were fed into Scanpy 1.8.1 for secondary analysis.
For RNA-seq, differentially expressed genes were analyzed using counts from HTSeq-count 0.13.5. Genes  with TPM >= 2 in at least one condition were then fed into DESeq2 with masking structural RNAs and  non-coding RNA for calculating fold change. TPM was quantified with Salmon 1.0.0 with  default settings.
Genome_build: hg38
Supplementary_files_format_and_content: TPM or htseq-count matrix for RNA-Seq, h5ad and h5 files for scRNA-seq. Trimmed fastq file, bigwig, bam/bai and peak files for ChIP-Seq.

molecule: genomic DNA

source_name: small cell lung cancer tuft variant

growth_protocol: Cells were cultured in RPMI with 10% FBS and penicillin.streptomycin except NCIH1048, which was cultured in DMEM:F12 supplemented with 0.005 mg/mL insulin, 0.01 mg/mL transferrin, 30 nM sodium  selenite, 10 nM hydrocortisone, 10 nM β-estradiol, 4.5 mM L-glutamine and 5% FBS.

extract_protocol:
Total RNA was extracted using TRIzol following the standard protocol; cells were fixed with 1% formaldehyde for 10 minutes and quenched with glycine following standard protocol (see method in paper) for ChIP-Seq.
polyA RNA was selected and fragmented with NEBNext Poly (A) mRNA Magnetic isolation  module (NEB #E7350) and the library was prepared with NEBNext Ultra II RNA Library Prep kit for  Illumina (NEB #E7770) with 2 ug RNA according to the manufacturer's protocol. For single cell RNA-seq, cell suspensions were stained for viability with Sytox blue (ThermoFisher S34857) and sorted on a Sony  SH800S (Sony Biotechnology Inc, San Jose, CA) using a 100 μm chip (Catalog #LE-C3110) in “Ultra  Purity” mode. Sorted cells were washed and resuspended in PBS containing 0.04% BSA. An aliquot  was stained with ViaStain AOPI (Nexcelom #CS2-0106-5mL) and counted using a Countess FL II  automated cell. Up to 12,000 cells were loaded per lane on 10X Chromium microfluidic chips. Single  cell capture, barcoding, and library preparation were performed using the 10X Chromium chemistry,  using the NextGEM Single-Cell 3’ Library Kit v3.1 (1000121; 10X Genomics). ChIP-seq library was prepared using the NEBNext Ultra II DNA Library Prep Kit  for Illumina (E7645) following manufacturer's protocol with AMPure XP beads (Beckman, A63881)  with no size selection.

treatment_protocol: see above

tag: cell line

tag: chip antibody


title: 028_JLat92_IFNB_8h

description: Replicate 1


title: 023_JLat92_Mock_4h

description: Replicate 2


title: 011_Jurkat_IFNB_12h

description: Replicate 2

value: Jurkat E6-1 CD4+ T Cells


title: 012_Jurkat_IFNB_12h

description: Replicate 3


title: P8_S2_PD


title: 022_JLat92_Mock_4h

description: Replicate 1


title: 010_Jurkat_IFNB_12h

description: Replicate 1


title: 008_Jurkat_IFNB_8h

description: Replicate 2


title: P4_S1_NDMM


title: 009_Jurkat_IFNB_8h

description: Replicate 3


title: 005_Jurkat_IFNB_4h

description: Replicate 2


title: 001_Jurkat_Mock_4h

description: Replicate 1


title: 003_Jurkat_Mock_4h

description: Replicate 3


title: 007_Jurkat_IFNB_8h

description: Replicate 1


title: 002_Jurkat_Mock_4h

description: Replicate 2


title: 004_Jurkat_IFNB_4h

description: Replicate 1


title: 006_Jurkat_IFNB_4h

description: Replicate 3


title: Severe LAP_04 [P414D7]

city: Groningen

first: Kieu

last: Le

state: Groningen

address: Antonious Deusinglaan 1

department: Genetics

country: Netherlands

institute: University Medical Centre Groningen

data_processing:
Raw RNA-seq reads were aligned to the human genome version 37 using STAR (v2.5.1b)
HTSeq-count package (v0.61) was used to count and normalize the number of reads mapped to each gene
Differential expression was determined using DEseq2 ( v.1.12.4)
Genome_build: version 37
Supplementary_files_format_and_content: csv table containing expression normal counts

source_name: primary monocytes_severe LAP

growth_protocol: Monocytes from sepsis patients (stratified by LAP responses) were isolated from PBMCs using magnetic bead separation with anti-CD14 coated beads (MACS Miltenyi Germany) according to the protocol supplemented by the manufacturer.

extract_protocol:
Monocytes isolated from different groups of sepsis patients stratified by LAP responses were lysed in Trizol reagent and stored at −80°C. Total RNA was extracted from cells using the QIAGEN RNeasy RNA extraction kit, using on-column DNaseI treatment. Ribosomal RNA was removed using the riboZero rRNA removal kit.
All samples had good qualities (RIN score >=8). RNA libraries were prepared to enrich for polyA tail-RNA using Bioscientific NEXTflex-Rapid-Directional mRNA-seq kits. RNA libraries were prepared with the Caliper SciClone system.

treatment_protocol: The monocytes were resuspended in RPMI 1640 culture medium supplemented with Hepes 10 mM, penicillin-streptomycin 1%, l-glutamine 1%, sodium pyruvate 1%, glucose 25 mM and fetal bovine serum 10%.

tag: subject group

value: Severe LAP activity defect

value: primary monocytes


title: Mild LAP_04 [1419D7]

source_name: primary monocytes_mild LAP

value: Mild LAP activity defect


title: Mild LAP_07 [P413D7]


title: Severe LAP_02 [1514cars]


title: Mild LAP_06 [1449D7]


title: Severe LAP_03 [P412D7]


title: Mild LAP_02 [1099CARS]


title: Severe LAP_01 [1415D7]


title: Mild LAP_05 [1431D7]


title: Mild LAP_03 [1391D7]


title: Intact LAP_04 [1315CARS]

source_name: primary monocytes_Intact LAP

value: Intact LAP activity


title: Intact LAP_05 [1329D7]


title: Intact LAP_08 [1568D7]


title: Mild LAP_01 [1076CARS]


title: Intact LAP_06 [1344CARS]


title: Exophytic melanoma mROI 31 (HTA-MELATLAS-1)

city: Boston,

first: Ajit Johnson

last: Nirmal

state: MA

address: 200 Longwood Avenue

department: Harvard Program in Therapeutic Science

institute: Harvard Medical School

data_processing:
The FASTQ files were processed using the bcbio pipeline v.1.2.1 software
The reads were mapped to the GRCh38 human reference genome using HISAT2 and Salmon
Length scaled transcripts per million (TPM) derived from Salmon was used for analysis.
Genome_build: hg38
Supplementary_files_format_and_content: HTA-MELATLAS-1.counts  (Length-scaled transcript per million (TPM) CSV file)

source_name: Exophytic melanoma

extract_protocol:
40 μm regions of interest were extracted using a mechanical picker from 5 μm tissue section. Tissue microregions were deposited with 2 µl PBS into PCR tubes containing 18 µl of lysis buffer: 1:16 mix of Proteinase K solution (QIAGEN) in PKD buffer (QIAGEN), with 0.1% RNasin Plus. After deposit, tubes were immediately placed in dry ice and stored at -80°C until ready for downstream RNA-seq workflow.
PCR tubes containing tissue microregions in the lysis buffer were removed from the freezer, allowed to thaw at room temperature for 5 min, and incubated at 56°C for 1 hr. Tubes were briefly vortexed, spun down, and placed on ice. Dynabeads Oligo(dT)25 beads (ThermoFisher) were washed three times with ice-cold 1X hybridization buffer (NorthernMax buffer (ThermoFisher) with 0.05% Tween 20 and 0.0025% RNasin Plus), and resuspended in original bead volume with ice-cold 2x hybridization buffer (NorthernMax buffer with 0.1% Tween 20 and 0.005% RNasin Plus). A volume of 20 µl of washed beads was added to each lysed sample, mixed by pipette, and incubated at 56°C for 1 min followed by room temperature incubation for 10 min. Samples were placed on a magnet and washed twice with an ice-cold 1X hybridization buffer, then once with ice-cold 1X PBS with 0.0025% RNasin Plus. Supernatant was removed, and the pellet was resuspended in 10.5 µl nuclease-free water. Samples were incubated at 80°C for 2 min and immediately placed on a magnet. Supernatant was transferred to new PCR tubes or plates, and placed on ice for subsequent whole transcriptome amplification or stored at -80°C. Reverse transcription and cDNA amplification were performed using the SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Takara Bio, Kusatsu, Shiga, Japan). Resulting amplified cDNA libraries were assessed for DNA concentration using the Qubit dsDNA HS Assay Kit (ThermoFisher) and for fragment size distribution using the BioAnalyzer 2100 High Sensitivity DNA Kit (Agilent). Melanoma tissue microregion libraries were prepared with ThruPLEX DNA-seq Kit (Takara Bio). Resulting libraries were characterized by using the Qubit dsDNA HS Assay Kit and BioAnalyzer 2100 High Sensitivity DNA Kit, pooled at equimolar ratios, and sequenced using a NextSeq (Illumina) sequencer.

tag: tissue

value: Exophytic melanoma

tag: batch


title: Exophytic melanoma mROI 32 (HTA-MELATLAS-1)


title: Intact LAP_01 [1011CARS]


title: Exophytic melanoma mROI 30 (HTA-MELATLAS-1)


title: Exophytic melanoma mROI 33 (HTA-MELATLAS-1)


title: Intact LAP_07 [1502CARS]


title: Exophytic melanoma mROI 34 (HTA-MELATLAS-1)


title: Exophytic melanoma mROI 27 (HTA-MELATLAS-1)


title: Exophytic melanoma mROI 24 (HTA-MELATLAS-1)


title: Exophytic melanoma mROI 25 (HTA-MELATLAS-1)


title: Exophytic melanoma mROI 23 (HTA-MELATLAS-1)


title: Intact LAP_03 [1314D7]


title: Exophytic melanoma mROI 29 (HTA-MELATLAS-1)


title: Exophytic melanoma mROI 21 (HTA-MELATLAS-1)


title: Exophytic melanoma mROI 19 (HTA-MELATLAS-1)


title: Exophytic melanoma mROI 18 (HTA-MELATLAS-1)


title: Exophytic melanoma mROI 20 (HTA-MELATLAS-1)


title: Intact LAP_02 [1161D7]


title: Exophytic melanoma mROI 28 (HTA-MELATLAS-1)


title: Exophytic melanoma mROI 22 (HTA-MELATLAS-1)


title: ATCC cell line COLO205

city: Montreal

first: Pierre

last: Thibault

state: Quebec

address: 2950 Chem. de Polytechnique

country: Canada

institute: Institute of Research in Immunology and Cancer (IRIC)

description:
title in publication:
COLO205

data_processing:
Sequences were trimmed using Trimmomatic version 0.35 and aligned to the reference human genome version GRCh38 (gene annotation from Gencode version 33, based on Ensembl 99) using STAR version 2.7.1a
Gene expressions were obtained both as read count directly from STAR as well as computed using RSEM to obtain normalized gene and transcript-level expression, in transcript-per-million (TPM) values, for these stranded RNA libraries.
Genome_build: GRCh38 (encode version 33, based on Ensembl 99)
Supplementary_files_format_and_content: tab-separated value files containing TPM values for each sample

source_name: colon

growth_protocol: All cell lines were grown in their respective ATCC-recommended media and maintained at 37°C with 5% CO2

extract_protocol:
TriZol + RNeasy Mini kit (Qiagen) (samples 1-5) or AllPrep DNA/RNA/miRNA Universal kit (Qiagen) (samples 6-17)
KAPA mRNAseq Hyperprep kit (Roche)

value: colon

tag: disease state

value: Dukes' type D, colorectal adenocarcinoma


title: Inflammatory regression mROI 43 (HTA-MELATLAS-1)

source_name: Inflammatory regression

value: Inflammatory regression


title: Inflammatory regression mROI 44 (HTA-MELATLAS-1)


title: Exophytic melanoma mROI 26 (HTA-MELATLAS-1)


title: Inflammatory regression mROI 45 (HTA-MELATLAS-1)


title: hCMEC1_ATAC

city: Houston

first: Manuel

middle: Eliezer

last: Cantu Gutierrez

state: TX

address: 1 Baylor Plaza

institute: Baylor College of Medicine

data_processing:
For ATAC-seq results: Reads were mapped to the GRCh38 version of the human genome using Bowtie2 with default paired-end settings (Langmead and Salzberg, 2012). Mitochondrial reads, reads with a MAPQ < 10, and reads which did not align to the reference genome were removed using Samtools (version 1.13) (Danecek et al., 2021). Duplicated reads were then removed with Picard MarkDuplicates (Institute, 2019). Peak calling was carried out with MACS2 (callpeak  --nomodel –broad) (v2.2.7.1)(Zhang et al., 2008). Diffbind (version 3.2) (Ross-Innes et al., 2012; Stark R, 2011) was used to import peaksets (min.overlap= 0.66) into RStudio Server (version 1.4.1717, https://www.rstudio.com) using R (version 4.1 (Team, 4.1). dba.blacklist function was used to filter out peaks that overlap with the ENCODE blacklist. Consensus peaks were converted to mm10 using the liftOver tool available from the UCSC Genome Browser. A region was considered conserved if a minimum 0.95 ratio of bases remap. Selected regions were also examined using the ECR Browser (Ovcharenko et al., 2004) where the regions were analyzed using rVista 2.0 (Loots and Ovcharenko, 2004) in order to identify conserved transcription factor motifs. The TRANSFAC professional V10.2 vertebrate library was used with default parameters.
For RNA-seq results: Reads were first mapped to the human genome (GRCh38) using Salmon (version 1.5.1) (Patro et al., 2017). Transcript level quantification was then imported using txtimport (version 1.20.0) (Soneson et al., 2015) and analyzed using DESeq2 (Love et al., 2014). Genes were kept and considered actively expressed if they had more than 10 raw counts and >2 log2 fold change normalized expression.
Genome_build: GRCh38
Supplementary_files_format_and_content: Bigwig, bam and peak files for ATAC data. RNA-seq results contain sf abundance quantification file: Plain-text, tab-separated file with a single header line (which names all of the columns) that contains Name, Length, EffectiveLength, TPM and NumReads.

source_name: Brain microvascular cells

growth_protocol: Immortalized hCMEC/D3 (Millipore, SCC066) cells were grown to confluence using endothelial cell medium (ScienCell, #1001) on plates coated with Collagen Type I Rat Tail (Sigma-Aldrich, #C7661). Passages 4-6 were used for experiments.

extract_protocol:
RNA was extracted using Trizol reagent.
ATAC libraries were processed as previously described (Corces et al., 2017). The quality of purified DNA libraries was assessed using the Agilent High Sensitivity DNA kit (Agilent Technologies). Paired end, 2 x 75 bp sequencing was performed on an Illumina Nextseq 500 instrument. RNA from all samples was thawed and following confirmation of integrity and concentration using a Bioanalyzer, 100 ng was used for low-input library preparation using the NEBNext Ultra II RNA Library Prep kit for Illumina. The libraries were then quantified and sequenced using an Illumina NovaSeq 6000 at a depth of 20 million reads per sample.


title: S3-026241T1(3)_N

description:
title in publication:
S2 NAT


title: Inflammatory regression mROI 41 (HTA-MELATLAS-1)


title: Inflammatory regression mROI 40 (HTA-MELATLAS-1)


title: Inflammatory regression mROI 42 (HTA-MELATLAS-1)


title: Inflammatory regression mROI 47 (HTA-MELATLAS-1)


title: Inflammatory regression mROI 39 (HTA-MELATLAS-1)


title: Melanoma in situ mROI 97 (HTA-MELATLAS-1)

source_name: Melanoma in situ

value: Melanoma in situ


title: Inflammatory regression mROI 38 (HTA-MELATLAS-1)


title: Melanoma in situ mROI 95 (HTA-MELATLAS-1)


title: Melanoma in situ mROI 94 (HTA-MELATLAS-1)


title: Inflammatory regression mROI 46 (HTA-MELATLAS-1)


title: Melanoma in situ mROI 88 (HTA-MELATLAS-1)


title: Melanoma in situ mROI 96 (HTA-MELATLAS-1)


title: Melanoma in situ mROI 87 (HTA-MELATLAS-1)


title: Melanoma in situ mROI 86 (HTA-MELATLAS-1)


title: Melanoma in situ mROI 83 (HTA-MELATLAS-1)


title: Melanoma in situ mROI 85 (HTA-MELATLAS-1)


title: Melanoma in situ mROI 82 (HTA-MELATLAS-1)


title: Melanoma in situ mROI 84 (HTA-MELATLAS-1)


title: Melanoma in situ mROI 89 (HTA-MELATLAS-1)


title: Melanoma in situ mROI 80 (HTA-MELATLAS-1)


title: Melanoma in situ mROI 77 (HTA-MELATLAS-1)


title: Melanoma in situ mROI 92 (HTA-MELATLAS-1)


title: Melanoma in situ mROI 73 (HTA-MELATLAS-1)


title: Melanoma in situ mROI 75 (HTA-MELATLAS-1)


title: Melanoma in situ mROI 79 (HTA-MELATLAS-1)


title: Melanoma in situ mROI 72 (HTA-MELATLAS-1)


title: Melanoma in situ mROI 76 (HTA-MELATLAS-1)


title: Melanoma in situ mROI 93 (HTA-MELATLAS-1)


title: Melanoma in situ mROI 68 (HTA-MELATLAS-1)


title: Melanoma in situ mROI 91 (HTA-MELATLAS-1)


title: Melanoma in situ mROI 70 (HTA-MELATLAS-1)


title: Melanoma in situ mROI 74 (HTA-MELATLAS-1)


title: Melanoma in situ mROI 90 (HTA-MELATLAS-1)


title: Melanoma in situ mROI 71 (HTA-MELATLAS-1)


title: Melanoma in situ mROI 61 (HTA-MELATLAS-1)


title: Melanoma in situ mROI 81 (HTA-MELATLAS-1)


title: Melanoma in situ mROI 63 (HTA-MELATLAS-1)


title: Melanoma in situ mROI 60 (HTA-MELATLAS-1)


title: Melanoma in situ mROI 64 (HTA-MELATLAS-1)


title: Melanoma in situ mROI 62 (HTA-MELATLAS-1)


title: Melanoma in situ mROI 58 (HTA-MELATLAS-1)


title: Melanoma in situ mROI 66 (HTA-MELATLAS-1)


title: Melanoma in situ mROI 57 (HTA-MELATLAS-1)


title: Melanoma in situ mROI 78 (HTA-MELATLAS-1)


title: Melanoma in situ mROI 67 (HTA-MELATLAS-1)


title: Melanoma in situ mROI 69 (HTA-MELATLAS-1)


title: Melanoma in situ mROI 56 (HTA-MELATLAS-1)


title: Melanoma in situ mROI 55 (HTA-MELATLAS-1)


title: Melanoma in situ mROI 53 (HTA-MELATLAS-1)


title: Melanoma in situ mROI 65 (HTA-MELATLAS-1)


title: Melanoma in situ mROI 52 (HTA-MELATLAS-1)


title: Melanoma in situ mROI 50 (HTA-MELATLAS-1)


title: Melanoma in situ mROI 49 (HTA-MELATLAS-1)


title: Melanoma in situ mROI 51 (HTA-MELATLAS-1)


title: Melanoma in situ mROI 59 (HTA-MELATLAS-1)


title: Melanoma in situ mROI 47 (HTA-MELATLAS-1)


title: Melanoma in situ mROI 48 (HTA-MELATLAS-1)


title: Melanoma in situ mROI 45 (HTA-MELATLAS-1)


title: Exophytic melanoma mROI 17 (HTA-MELATLAS-1)


title: Melanoma in situ mROI 54 (HTA-MELATLAS-1)


title: Exophytic melanoma mROI 14 (HTA-MELATLAS-1)


title: Exophytic melanoma mROI 15 (HTA-MELATLAS-1)


title: Exophytic melanoma mROI 13 (HTA-MELATLAS-1)


title: Exophytic melanoma mROI 16 (HTA-MELATLAS-1)


title: Melanoma in situ mROI 46 (HTA-MELATLAS-1)


title: Exophytic melanoma mROI 12 (HTA-MELATLAS-1)


title: Exophytic melanoma mROI 9 (HTA-MELATLAS-1)


title: Exophytic melanoma mROI 5 (HTA-MELATLAS-1)


title: Exophytic melanoma mROI 7 (HTA-MELATLAS-1)


title: Exophytic melanoma mROI 8 (HTA-MELATLAS-1)


title: Exophytic melanoma mROI 6 (HTA-MELATLAS-1)


title: Inflammatory regression mROI 33 (HTA-MELATLAS-1)


title: Exophytic melanoma mROI 11 (HTA-MELATLAS-1)


title: Inflammatory regression mROI 29 (HTA-MELATLAS-1)


title: Inflammatory regression mROI 37 (HTA-MELATLAS-1)


title: Inflammatory regression mROI 35 (HTA-MELATLAS-1)


title: Exophytic melanoma mROI 4 (HTA-MELATLAS-1)


title: Exophytic melanoma mROI 10 (HTA-MELATLAS-1)


title: Inflammatory regression mROI 34 (HTA-MELATLAS-1)


title: Inflammatory regression mROI 27 (HTA-MELATLAS-1)


title: Inflammatory regression mROI 24 (HTA-MELATLAS-1)


title: Inflammatory regression mROI 22 (HTA-MELATLAS-1)


title: Inflammatory regression mROI 28 (HTA-MELATLAS-1)


title: Inflammatory regression mROI 20 (HTA-MELATLAS-1)


title: Inflammatory regression mROI 23 (HTA-MELATLAS-1)


title: Inflammatory regression mROI 21 (HTA-MELATLAS-1)


title: Inflammatory regression mROI 25 (HTA-MELATLAS-1)


title: Inflammatory regression mROI 19 (HTA-MELATLAS-1)


title: Inflammatory regression mROI 30 (HTA-MELATLAS-1)


title: Inflammatory regression mROI 32 (HTA-MELATLAS-1)


title: Inflammatory regression mROI 36 (HTA-MELATLAS-1)


title: Melanoma in situ mROI 42 (HTA-MELATLAS-1)


title: Melanoma in situ mROI 40 (HTA-MELATLAS-1)


title: Melanoma in situ mROI 41 (HTA-MELATLAS-1)


title: Melanoma in situ mROI 37 (HTA-MELATLAS-1)


title: Inflammatory regression mROI 31 (HTA-MELATLAS-1)


title: Melanoma in situ mROI 44 (HTA-MELATLAS-1)


title: Melanoma in situ mROI 43 (HTA-MELATLAS-1)


title: Melanoma in situ mROI 38 (HTA-MELATLAS-1)


title: Inflammatory regression mROI 26 (HTA-MELATLAS-1)


title: Melanoma in situ mROI 33 (HTA-MELATLAS-1)


title: Inflammatory regression mROI 18 (HTA-MELATLAS-1)


title: Melanoma in situ mROI 32 (HTA-MELATLAS-1)


title: Melanoma in situ mROI 35 (HTA-MELATLAS-1)


title: Melanoma in situ mROI 29 (HTA-MELATLAS-1)


title: Melanoma in situ mROI 36 (HTA-MELATLAS-1)


title: Melanoma in situ mROI 28 (HTA-MELATLAS-1)


title: Melanoma in situ mROI 25 (HTA-MELATLAS-1)


title: Inflammatory regression mROI 17 (HTA-MELATLAS-1)


title: Melanoma in situ mROI 39 (HTA-MELATLAS-1)


title: Melanoma in situ mROI 26 (HTA-MELATLAS-1)


title: Melanoma in situ mROI 22 (HTA-MELATLAS-1)


title: Melanoma in situ mROI 30 (HTA-MELATLAS-1)


title: Melanoma in situ mROI 34 (HTA-MELATLAS-1)


title: Melanoma in situ mROI 23 (HTA-MELATLAS-1)


title: Melanoma in situ mROI 20 (HTA-MELATLAS-1)


title: Melanoma in situ mROI 19 (HTA-MELATLAS-1)


title: Melanoma in situ mROI 17 (HTA-MELATLAS-1)


title: Melanoma in situ mROI 27 (HTA-MELATLAS-1)


title: Melanoma in situ mROI 15 (HTA-MELATLAS-1)


title: Melanoma in situ mROI 18 (HTA-MELATLAS-1)


title: Exophytic melanoma mROI 3 (HTA-MELATLAS-1)


title: Melanoma in situ mROI 21 (HTA-MELATLAS-1)


title: Melanoma in situ mROI 13 (HTA-MELATLAS-1)


title: Exophytic melanoma mROI 2 (HTA-MELATLAS-1)


title: Melanoma in situ mROI 24 (HTA-MELATLAS-1)


title: Melanoma in situ mROI 16 (HTA-MELATLAS-1)


title: Melanoma in situ mROI 31 (HTA-MELATLAS-1)


title: Invasive melanoma mROI 16 (HTA-MELATLAS-1)

source_name: Invasive melanoma

value: Invasive melanoma


title: Exophytic melanoma mROI 1 (HTA-MELATLAS-1)


title: Invasive melanoma mROI 15 (HTA-MELATLAS-1)


title: Invasive melanoma mROI 13 (HTA-MELATLAS-1)


title: Invasive melanoma mROI 11 (HTA-MELATLAS-1)


title: Invasive melanoma mROI 14 (HTA-MELATLAS-1)


title: Invasive melanoma mROI 6 (HTA-MELATLAS-1)


title: Invasive melanoma mROI 12 (HTA-MELATLAS-1)


title: Invasive melanoma mROI 9 (HTA-MELATLAS-1)


title: Invasive melanoma mROI 10 (HTA-MELATLAS-1)


title: Invasive melanoma mROI 7 (HTA-MELATLAS-1)


title: Invasive melanoma mROI 4 (HTA-MELATLAS-1)


title: Invasive melanoma mROI 1 (HTA-MELATLAS-1)


title: Invasive melanoma mROI 5 (HTA-MELATLAS-1)


title: Invasive melanoma mROI 8 (HTA-MELATLAS-1)


title: Invasive melanoma boundary mROI 12 (HTA-MELATLAS-1)

source_name: Invasive melanoma boundary

value: Invasive melanoma boundary


title: Melanoma in situ mROI 14 (HTA-MELATLAS-1)


title: Invasive melanoma mROI 2 (HTA-MELATLAS-1)


title: Invasive melanoma boundary mROI 8 (HTA-MELATLAS-1)


title: Invasive melanoma boundary mROI 11 (HTA-MELATLAS-1)


title: Invasive melanoma boundary mROI 9 (HTA-MELATLAS-1)


title: Invasive melanoma boundary mROI 6 (HTA-MELATLAS-1)


title: Invasive melanoma mROI 3 (HTA-MELATLAS-1)


title: Invasive melanoma boundary mROI 5 (HTA-MELATLAS-1)


title: Invasive melanoma boundary mROI 2 (HTA-MELATLAS-1)


title: Invasive melanoma boundary mROI 3 (HTA-MELATLAS-1)


title: Invasive melanoma boundary mROI 10 (HTA-MELATLAS-1)


title: Brisk TIL mROI 15 (HTA-MELATLAS-1)

source_name: Brisk TIL

value: Brisk TIL


title: Invasive melanoma boundary mROI 1 (HTA-MELATLAS-1)


title: Brisk TIL mROI 16 (HTA-MELATLAS-1)


title: Brisk TIL mROI 13 (HTA-MELATLAS-1)


title: Brisk TIL mROI 5 (HTA-MELATLAS-1)


title: Brisk TIL mROI 6 (HTA-MELATLAS-1)


title: Brisk TIL mROI 11 (HTA-MELATLAS-1)


title: Brisk TIL mROI 12 (HTA-MELATLAS-1)


title: Brisk TIL mROI 10 (HTA-MELATLAS-1)


title: Brisk TIL mROI 2 (HTA-MELATLAS-1)


title: Brisk TIL mROI 8 (HTA-MELATLAS-1)


title: Inflammatory regression mROI 16 (HTA-MELATLAS-1)


title: Invasive melanoma boundary mROI 4 (HTA-MELATLAS-1)


title: Brisk TIL mROI 4 (HTA-MELATLAS-1)


title: Brisk TIL mROI 1 (HTA-MELATLAS-1)


title: Brisk TIL mROI 14 (HTA-MELATLAS-1)


title: Brisk TIL mROI 3 (HTA-MELATLAS-1)


title: Brisk TIL mROI 7 (HTA-MELATLAS-1)


title: Brisk TIL mROI 9 (HTA-MELATLAS-1)


title: Inflammatory regression mROI 12 (HTA-MELATLAS-1)


title: Inflammatory regression mROI 9 (HTA-MELATLAS-1)


title: Inflammatory regression mROI 11 (HTA-MELATLAS-1)


title: Inflammatory regression mROI 10 (HTA-MELATLAS-1)


title: Inflammatory regression mROI 15 (HTA-MELATLAS-1)


title: Inflammatory regression mROI 8 (HTA-MELATLAS-1)


title: Inflammatory regression mROI 14 (HTA-MELATLAS-1)


title: Inflammatory regression mROI 5 (HTA-MELATLAS-1)


title: Invasive melanoma boundary mROI 7 (HTA-MELATLAS-1)


title: Inflammatory regression mROI 13 (HTA-MELATLAS-1)


title: Inflammatory regression mROI 3 (HTA-MELATLAS-1)


title: Inflammatory regression mROI 6 (HTA-MELATLAS-1)


title: Inflammatory regression mROI 1 (HTA-MELATLAS-1)


title: Inflammatory regression mROI 7 (HTA-MELATLAS-1)


title: Melanoma in situ mROI 11 (HTA-MELATLAS-1)


title: Inflammatory regression mROI 4 (HTA-MELATLAS-1)


title: Melanoma in situ mROI 9 (HTA-MELATLAS-1)


title: Inflammatory regression mROI 2 (HTA-MELATLAS-1)


title: Jurkat Cs (E)

city: Bethesda

first: Sukhbir

last: Kaur

address: 10 Center Drive

department: NCI

institute: NIH

data_processing:
About 96% of pass filter reads had a score of Q30 or above. Reads for each sample were trimmed for adapters and low quality bases using Trimmomatic software. Reads were trimmed to a maximum of 27 bases to carry out miRNA analysis. CLC Genomics Workbench workflow was used for miRNA sequencing analysis .
The miRNA sequencing analysis was performed using default setting of CLC Genomics Workbench with Biomedical Genomics Analysis plugin and the Quantify miRNA expression with the QIAseq miRNA Quantification ready-to-use workflow. The mature and seed miRNAs were visualized using the Create Combined Report tool and the QIA seq miRNA Differential Expression workflow
Supplementary_files_format_and_content: CLC files ((UMI reads, grouped on mature, annotated) and (UMI reads, grouped on seed))

source_name: Jurkat cell line

growth_protocol:
The Jurkat T cell line (E6.1) was purchased from ATCC. The cells were maintained using RPMI 1640 containing 10% FBS, glutamine, penicillin, and streptomycin (Gibco). The Jurkat and JinB8 T cells used for experiments were maintained less than 6 weeks in culture.
The cultured Jurkat and JinB8 cells were washed with IXPBs followed by a second wash with HITES medium (DMEM/F12 supplemented with, bovine serum albumin, hydrocortisone, insulin, transferrin, and trace elements). EVs were isolated from Jurkat T cells were cultured overnight using HITES medium. The conditioned media from Jurkat T cells were collected, and cell debris were removed using centrifugation at 300 g for 5 minutes and 2500 g for 10 minutes respectively. Centrifuged media were concentrated using Ultra-4 centrifugal filters to about 1 ml volume and further centrifuged at 10,000 rpm for 10 minutes. EVs were isolated using an Exo-Quick kit (SBI) and CD63, CD47 and MHC1 positive EVs were captured using conjugating MNPs( 15nM) with respective antibodies. The uncaptured samples ( not bonded) used as Flow samples.

extract_protocol:
miRNeasy Mini Kit (Qiagen) kit was used to extract total RNA according to the manufacturer's instructions.
miRNA samples were prepared using the Qiagen miRNA kit and sequenced on one NextSeq run with 76 bases single end reads using QIAseq™ miRNA Library.
QC PCR -For quality control of RNA isolation for small RNA next-generation sequencing.

treatment_protocol: Untreated

value: Jurkat

tag: sample type

value: total cellular


title: Jurkat EVs (B)

value: EVs


title: Jurkat Evs (A)


title: Jurkat EVs (D)


title: JinB8EVs (1)

source_name: JinB8_Jurkat cell line


title: JinB8 EVs (3)


title: Lymphocytes T CD8+ sample_8 (d15_kidney)

city: Paris

first: Sebastien

last: Mella

state: IDF

address: 28 rue du Dr Roux

department: CBUTechs

country: France

institute: Pasteur Institut

data_processing:
Chromium Single Cell 5p RNA library v1
Illumina sequencing system
Cell Ranger 3.1.0, mkfastq (bcl2fastq v2.20.0) to generate fastq files from .bcl
Cell Ranger 3.1.0, count  to make the count matrix from fastq files
Seurat V3 for normalization (SCTransform)
Genome_build: GRCh38
Supplementary_files_format_and_content: Comma-delimited files includes Seurat SCTranformed normalized integrated data for all samples

source_name: Kidney Tumor

extract_protocol:
Fresh renal tumors were collected in Hank’s Balanced Salt Solution (HBSS). After being mechanically dissociated with a scalpel, they were digested with DNAse I (30IU/mL, Roche) and Collagenase D (1mg/mL, Roche) at 37°C for one hour. Primary cells were then isolated by successive filtration on a 70μm Falcon cell strainer (BD Falcon) and a 20μm Falcon cell strainer (BD Falcon) and counted on a Malassez chamber.Cells were then stained with a fixable viability stain FVS 520 (eBioscience), an anti-CD8a labeled with APC fluorophore (Biolegend) and an anti-NKP46 labeled with BV421 (Biolegend) in order to eliminate natural killer cells from the analysis during the cell sorting.
RNA libraries were prepared for sequencing using standard Illumina protocols
Single cell RNA-Seq

value: Kidney

tag: age

tag: gender

value: Female


title: Melanoma in situ mROI 10 (HTA-MELATLAS-1)


title: Melanoma in situ mROI 4 (HTA-MELATLAS-1)


title: Melanoma in situ mROI 8 (HTA-MELATLAS-1)


title: Lymphocytes T CD8+ sample_7 (d14_kidney)

value: Male


title: Melanoma in situ mROI 6 (HTA-MELATLAS-1)


title: Melanoma in situ mROI 3 (HTA-MELATLAS-1)


title: Lymphocytes T CD8+ sample_4 (d7_kidney)

description:
Lymphocytes T CD8+
sample_4 (d7_kidney)


title: JinB8 Cs (6)


title: Melanoma in situ mROI 2 (HTA-MELATLAS-1)


title: Melanoma in situ mROI 5 (HTA-MELATLAS-1)


title: Melanoma in situ mROI 7 (HTA-MELATLAS-1)


title: JinB8 EVs (2)


title: 12-mo day30

city: Beijing

first: Zheng

last: Wang

address: 7 Science Park Road ZGC Life Science Park, Beijing

country: China

institute: National Institute of Biological Sciences, Beijing

data_processing:
Droplet-based sequencing data was aligned and quantified using the Cell Ranger Single-Cell Software Suite (version 2.2.0, 10x Genomics Inc) using the Mus musculus genome (mm10).
The expressional datasets were further processed using R “Seurat” package (V3.2.2). The distribution of nGenes, nUMI, and mitochondrial reads ratio were plotted. The cells used in the study were extracted using cutoff for nGene<5000, nUMI<25000, percent.mito<0.1.to remove potential empty droplets and doublets.
The UMI count is normalized to 10,000 in each cell and log transformed.
Genome_build: mm10

organism: Mus musculus

source_name: lung

extract_protocol:
The lineage-labelled AT2 cells (CD45–CD31–GFP+) were sorted from PBS or bleomycin-treated 3-month old or 12-month old mice (3 mice were pooled for each experiment group). The AT2 cell suspension were co‐encapsulated in droplets with barcoded beads by using the Chromium Controller (10X Genomics).
Single cell cDNA synthesis, amplification and sequencing libraries were generated using the Single Cell 3' Reagent Kit as the 10x Genomics protocol. The libraries were sequenced by Illumina HiSeq 2500.

treatment_protocol: Mice were given four dose of 75mg/g body weight tamoxifen via intraperitoneal injection before bleomycin treatment.  After tamoxifen treatment day 14,a single dose of 0.8U/kg body weight of bleomycin, or PBS control, were intratracheally delivered into 3-month old and 12-month old mice.

value: alveolar epithelial type 2 cells

value: Bleomycin

tag: genotype


title: 3-mo day30


title: Lymphocytes T CD8+ sample_6 (d10_kidney)


title: Jurkat Cs (G)


title: Melanoma in situ mROI 12 (HTA-MELATLAS-1)


title: JinB8 Cs (5)


title: Melanoma in situ mROI 1 (HTA-MELATLAS-1)


title: Jurkat Cs (F)


title: Con HSC 4

city: SAN DIEGO

first: gaowei

last: wang

state: CALIFORNIA

address: 3393 Lebon DR, APT 202

institute: University of California San Diego

description:
Con-HSC-4
fpkm_2.xls

data_processing:
In order to remove technical sequences, including adapters, polymerase chain reaction (PCR) primers, or fragments thereof, and quality of bases lower than 20, pass filter data of fastq format were processed by Cutadapt (V1.9.1) to be high quality clean data.
Mapping: Firstly, reference genome sequences and gene model annotation files of relative species were downloaded from genome website, such as UCSC, NCBI, ENSEMBL. Secondly, Hisat2 (v2.0.1) was used to index reference genome sequence. Finally, clean data were aligned to reference genome via software Hisat2 (v2.0.1).
Genome_build: mm10
Supplementary_files_format_and_content: xls, gene expression matrix

source_name: Hepatic stellate cells

growth_protocol: hepatocytes were cultured in Williams Medium E containing 10% FBS on collagen-coated plates and antibiotics. Hepatic stellate cells were cultured in DMEM containing 10% FBS and antibiotics.

extract_protocol:
the Zymo Quick-RNA MicroPrep kit.
Sequencing libraries were prepared using the Illumina TruSeq Small RNA protocol with minor modifications following the manufacturer’s instructions, including 12 cycles of PCR amplification after ligation of the 3′ and 5′ adapters. Samples were then ligated to unique adaptors and subjected to PCR amplification. Libraries were validated using an Agilent 2100 Bioanalyzer, normalized and pooled for  sequencing. RNA-sequencing (RNA-seq) libraries prepared using four biological replicates for each group were sequenced on an Illumina HiSeq 2500 using barcoded multiplexing

treatment_protocol: DFO (100 uM), iron (100 uM)

value: Wild type

tag: strain

value: Placebo

tag: diet

value: chow diet


title: Iron HSC 1

description:
Fe-HSC-1
fpkm_2.xls

value: Iron


title: Con HSC 5

description:
Con-HSC-5
fpkm_2.xls


title: Iron HSC 3

description:
Fe-HSC-3
fpkm_2.xls


title: Con HSC 1

description:
Con-HSC-1
fpkm_2.xls


title: DFO Hepa 6

description:
DFO-Hepa-6
fpkm_1.xls

source_name: Hepatocytes

value: DFO


title: DFO Hepa 2

description:
DFO-Hepa-2
fpkm_1.xls


title: Con Hepa 4

description:
Con-Hepa-4
fpkm_1.xls


title: Con Hepa 5

description:
Con-Hepa-5
fpkm_1.xls


title: ChIP-seq_WT_H3K27me3_rep1

first: Yu

last: Juan

address: 15 Datun Road, Chaoyang District

institute: Chinese Academy of Sciences

data_processing:
ChIP-seq: the ChIP-seq data were mapped to the Mus musculus genome (mm9) and D. melanogaster genome assembly (dm6) using bowtie2 with the default parameters. Low quality reads and PCR duplicates were removed by samtools and retained the uniquely mapped tags. Enriched peaks were called using MACS . Reads were normalized with fly reference as previous study
ChOR-seq: all sequencing data were mapped to the Mus musculus genome assembly (mm9) and D. melanogaster genome assembly (dm6) using bowtie2, with the default parameters. Low quality reads and PCR duplicates were removed by samtools and only uniquely mapped reads which mapping to a unique genomic location and strand were kept. Reads were normalized with fly reference as previous study. The enriched regions (peaks) were detected using MACS.
RNA-seq: the pair-end RNA-seq reads were mapped to the Mus musculus mm9 gene annotation model using Subread (Liao et al., 2013) with the default parameters, and the only uniquely mapped reads were used for further analysis. The differential expression between samples was performed with featureCounts (Liao et al., 2014) and R package DESeq2
Genome_build: mm9, dm6
Supplementary_files_format_and_content: peak files
Supplementary_files_format_and_content: bedgraph
Supplementary_files_format_and_content: normalized counts

source_name: mouse embryonic stem cells

growth_protocol: mES cells were cultured in medium in the presence of 1,000 U/ml LIF, with 90% DMEM, 10%FBS,1% nonessential amino acids,1% 2-mercaptoethanol, 1% L-glutamine,1% nucleosides, 1% Pen/Strep  in standard incubator with 5% CO2 at 37°C.

extract_protocol:
Cells were first crosslinked by formaldehyde, then sonicated in SDS containing buffer to dissolve the chromatin. The clarified chromatin were immunoprecipitated with dyno beas conjucated with antibodies. For ChOR-seq, EdU pulse labeled DNA was biotinylated by Click Reaction, then  chromatin were  immunoprecipitated with streptavidin dyno beads( Invitrogent, M280).The ChIP-seq antibodies are as following: Anti-H3K27me3,GST, 9733S;Anti-V5,Gene-Protein Link,P01L075
H3K27me3,V5-H1e Libraries(sample 1-4, 5) were prepared according to NEBNext Ultra DNA Library Prep Kit for Illumina (E7370L) and were sequenced using HiSeq2000 or Nova seq.

value: mouse embryonic stem cells


title: Implant_Day14_Rep3

city: New York

first: David

last: Oliver

address: 535 E 70th St

department: Research

institute: Hospital for Special Surgery

data_processing:
fastp -q 15 -n 10 -l 20 Mouse-Implant-Cancellous-Bone.fastq (v0.19.10)
STAR –readFilesIn Sample_Mouse-Implant-Cancellous-Bone.fastq --outFilterMultimapNmax 20 --outSAMmultNmax 1 --outFilterMismatchNoverReadLmax 0.1 --outSAMstrandField intronMotif --quantMode GeneCounts –outReadsUnmapped Fastx (v2.7.3a)
Genome_build: mm10
Supplementary_files_format_and_content: Tab delimited gene level count matrix

source_name: Implant_Day14_Lymph nodes

extract_protocol:
Lymph nodes and joint soft tissues were removed, flash frozen on dry ice, and RNA was harvested using RLT and Trizol reagent, respectively. NEBNext® Ultra™ II RNA Library Prep Kit for Illumina® was used with 100ng of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using NEBNext® Ultra™ II RNA Library Prep Kit for Illumina®

value: wild type

tag: time point

value: Lymph nodes


title: ChIP-seq_H1KO_H3K27me3_rep1


title: Con HSC 3

description:
Con-HSC-3
fpkm_2.xls


title: Iron HSC 2

description:
Fe-HSC-2
fpkm_2.xls


title: Iron HSC 4

description:
Fe-HSC-4
fpkm_2.xls


title: Con HSC 2

description:
Con-HSC-2
fpkm_2.xls


title: Implant_Day14_Rep1


title: 3-mo day0

value: PBS


title: Jurkat EVs (C)

value: Jurkat


title: 12-mo day0


title: DFO Hepa 4

description:
DFO-Hepa-4
fpkm_1.xls


title: DFO Hepa 5

description:
DFO-Hepa-5
fpkm_1.xls


title: Iron HSC 5

description:
Fe-HSC-5
fpkm_2.xls


title: DFO Hepa 1

description:
DFO-Hepa-1
fpkm_1.xls


title: ContraImplant_Day7_Rep2

source_name: ContraImplant_Day7_Lymph nodes


title: ContraImplant_Day7_Rep1


title: DFO Hepa 3

description:
DFO-Hepa-3
fpkm_1.xls


title: NoImplant_Day14_Rep3

source_name: NoImplant_Day14_Lymph nodes


title: Con Hepa 2

description:
Con-Hepa-2
fpkm_1.xls


title: Implant_Day14_Rep2


title: NoImplant_Day7_Rep2

source_name: NoImplant_Day7_Lymph nodes


title: Con Hepa 6

description:
Con-Hepa-6
fpkm_1.xls


title: Con Hepa 1

description:
Con-Hepa-1
fpkm_1.xls


title: ContraImplant_Day14_Rep3

source_name: ContraImplant_Day14_Lymph nodes


title: Implant_Day7_Rep3

source_name: Implant_Day7_Lymph nodes


title: Implant_Day7_Rep1


title: LST_day35_rep3

source_name: LST_day35_Joint soft tissue

value: Joint soft tissue


title: Implant_Day7_Rep2


title: ContraImplant_Day14_Rep1


title: LST_day35_rep2


title: ContraImplant_Day7_Rep3


title: Con Hepa 3

description:
Con-Hepa-3
fpkm_1.xls


title: ContraImplant_Day14_Rep2


title: RST_day35_rep3

source_name: RST_day35_Joint soft tissue


title: RST_day21_rep3

source_name: RST_day21_Joint soft tissue


title: RST_day21_rep1


title: NoImplant_Day14_Rep1


title: NoImplant_Day7_Rep1


title: LST_day35_rep4


title: RST_day7_rep4

source_name: RST_day7_Joint soft tissue


title: NoImplant_Day14_Rep2


title: RST_day14_rep1

source_name: RST_day14_Joint soft tissue


title: NoImplant_Day7_Rep3


title: RST_day7_rep3


title: LST_day35_rep1


title: RST_day3_rep4

source_name: RST_day3_Joint soft tissue


title: RST_day3_rep2


title: RST_day35_rep4


title: RST_day21_rep2


title: RST_day3_rep3


title: RST_day35_rep1


title: RST_day3_rep1


title: RST_day21_rep4


title: RST_day14_rep4


title: R2i_BMPi_rep1

city: Daegu

first: Ji Hwan

last: Park

state: Gyeongbuk

address: 333, Techno jungang-daero, Hyeonpung-eup, Dalseong-gun

department: Newbiology

country: South Korea

institute: DGIST

description: Gene expression in R2i cultured with BMP inhibitor treatment mESCs, [rep1]

data_processing:
Illumina CASAVA v1.8.2 software was used for basecalling.
The adaptor sequences were trimmed by the cutadapt (v1.4.2) and then aligned to the reference mouse genome (GRCm38.p6) using the STAR aligner(ver 2.6.1).
The align data were quantified to the gene features (GRCm38.95.gtf) in gene count using HTSeq (ver 0.9.1). Gene count of each sample are attached (Sample_*.gene.counts).
The gene count value of each sample were normalied with varience stabilizing transformation method (VST) using DESeq2.
Genome_build: GRCm38.p6

source_name: Mouse embryonic stem cells (mESCs), R2i cultured with BMP inhibitor treatment, replicated 1

growth_protocol: we used a previously established mES cell line, Royan B20. The cells were cultured on 0.1% gelatin-coated plates (Sigma-Aldrich) and passaged seven times in R2i/LIF. R2i culture contained 1µM PD0329501 and 10 µM SB431542 which inhibited TGFβ signaling pathway.

extract_protocol:
Total RNA was isolated from the R2i cultured mESCs and BMP inhibitor treated R2i cultured mESCs (3 biological replicates per each group) using Qiagen RNeasy mini Kit. mRNA was then isolated from the total RNA and fragmented using Illumina Truseq™ Stranded mRNA LT Sample Prep Kit with poly-T oligo magnetic beads, and reverse transcription of the mRNA fragments was conducted using Superscript III reverse transcriptase (Life Technologies).
Adaptor ligated libraries were generated according to the manufacture’s standard protocol and sequenced using HiSeq 2500 system.

treatment_protocol: We added noggin (250nM) plus dorsomorphin (5μM), two potent BMP signaling inhibitors, to the R2i cultures.

value: Royan B20

value: R2i (1microM PD0329501 and 10 microM SB431542) + BMP inhibitor(250nM noggin  and 5μM dorsomorphin)


title: R2i_BMPi_rep3

description: Gene expression in R2i cultured with BMP inhibitor treatment mESCs, [rep3]

source_name: Mouse embryonic stem cells (mESCs), R2i cultured with BMP inhibitor treatment, replicated 3


title: RST_day35_rep2


title: R2i_control_rep1

description: Gene expression in R2i cultured mESCs, [rep1]

source_name: Mouse embryonic stem cells (mESCs), R2i cultured, replicated 1

value: R2i (1microM PD0329501 and 10 microM SB431542)


title: RST_day14_rep2


title: RST_day7_rep1


title: RST_day7_rep2


title: R2i_control_rep3

description: Gene expression in R2i cultured mESCs, [rep3]

source_name: Mouse embryonic stem cells (mESCs), R2i cultured, replicated 3


title: R2i_BMPi_rep2

description: Gene expression in R2i cultured with BMP inhibitor treatment mESCs, [rep2]

source_name: Mouse embryonic stem cells (mESCs), R2i cultured with BMP inhibitor treatment, replicated 2


title: ATAC-seq_mESC_IEOE19-Cy3_rep2

city: Kanazawa

first: Yusuke

last: Miyanari

address: Kakuma

department: NanoLSI

country: Japan

institute: Kanazawa University

data_processing:
Reads were trimmed for adaptor sequences by using trimgalore
Bowtie2 with the parameter “-- very-sensitive --maxins 2000” mapped ATAC-seq reads to mm10.
he mapped reads were filtered for low-quality reads (MAPQ < 30) and sorted by using sambamba.
PCR duplicates and reads mapped on the blacklisted regions were removed
Genome_build: mm10
Supplementary_files_format_and_content: bigWig file was generated by using deeptools bamCoverage with option --normalizeUsing RPKM --bin 30

source_name: mouse embryonic stem cells

growth_protocol: mESCs (E14) were cultured in DMEM containing 20% FBS, leukemia inhibitory factor, 3 mM CHIR99021 (a GSK3b inhibitor, Sigma), 1 mM PD0325901 (a MEK inhibitor, Sigma), 1 mM sodium pyruvate, penicillin/streptomycin, and 0.1 mM 2-mercaptoethanol. All the mammalian cells were grown at 37˚C with 5% CO2.

extract_protocol:
1x105 mES cells were transposed using Tn5 complex with 19 bp of IEOE adaptor DNAs at 37°C for 30min. Genomic DNA was extracted with Monarch PCR clean-up kit (NEB)
Since sequences of IE and OE display low melting temperature (Tm) as 56 and 54 °C respectively, custom primers with Locked Nucleic Acid (LNA, IDT) with Tm at 63 and 61 °C were used for the 1st PCR amplification. Transposed DNA was first amplified for 4 cycles with KOD FxNeo polymerase (TOYOBO) using the following PCR conditions; 72 °C for 5 min; 98 °C for 30 s; and thermo cycling at 98 °C for 10s, 63 °C for 30s and 72 °C for 1 min. After the removal of the LNA primers using Monarch PCR & DNA Cleanup Kit, 2nd PCR for indexing was performed using Q5 High-Fidelity 2X Master Mix for 5 cycles with primers designed to amplify 1st PCR products. The libraries were sequenced on HiSeq2500 for 50 bp paired-end reads using custom sequencing primers designed for IE and OE sequences. All the primer sequences are listed in supplementary table. ATAC-seq with MEAB34 adaptors was performed as described in previously[Buenrostro 2013 Nat Methods]. Three biological replicates were analyzed for each experimental condition.

value: wild-type


title: ATAC-seq_mESC_IEOE19-Cy3_rep1


title: ATAC-seq_mESC_IEOE19-Cy3_rep3


title: ATAC-seq_mESC_IEOE19_rep3


title: 5gy_day3

city: Shenyang

first: Lutian

last: Yao

address: 155 Nanjing st

department: Department of Orthopedic

institute: the First Affiliated Hospital of China Medical University

data_processing:
cell ranger 2.2.0
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: barcodes.tsv, genes.tsv, matrix.mtx

source_name: bone marrow

extract_protocol: 10X Single Cell 3' v2

value: bone marrow Col2/Td+ cells

value: radiation

value: day 3 post radiation


title: R2i_control_rep2

description: Gene expression in R2i cultured mESCs, [rep2]

source_name: Mouse embryonic stem cells (mESCs), R2i cultured, replicated 2


title: ATAC-seq_mESC_MEAB34_rep3


title: ATAC-seq_mESC_MEAB34_rep1


title: ATAC-seq_mESC_MEAB34_rep2


title: ATAC-seq_mESC_IEOE19_rep1


title: RST_day14_rep3


title: CBNY057_A_AzaVitC_WGS

city: Stanford

first: Ravindra

last: Majeti

state: CA

address: 875 Blake Wilbur Dr Clinic F

institute: Stanford University

description:
Whole Genome Sequencing Input Control
CBNY057 AAVS1 in HSC Expansion media (Not CD34+, Live HDR double positive cells) - A+V

data_processing:
Library strategy: WGS
Seventy-five base-pair, paired-end DNA sequencing was completed using a NextSeq550 instrument with NovaSeq Hi Output version 2.5 reagent kits (Illumina, San Diego, CA, USA).
Raw data processing and demultiplexing to sample-specific FASTQ output was performed using the Illumina BaseSpace Sequence Hub.
Sequencing reads were aligned to the hg19 reference genome using default parameters of BWA-MEM.
Duplicate reads were marked and removed using Picard MarkDuplicates.
Assembly: hg19
Supplementary files format and content: Raw reads in peaks or reads in gene bodies data across all samples, RNA kallisto output normalized counts matrix

source_name: Human Cord Blood HSPCs

growth_protocol:
Healthy hematopoietic cells were sorted and enriched
Cord blood cells were CD34 enriched, edited, and subjected to engraftment or other assays.

extract_protocol:
All the samples were collected into 1.5 mL microcentrifuge tubes and snap-freezed until further processing. Genomic DNA was extracted using the DNeasy Blood & Tissue Kit (QIAGEN, Germany) according to manufacturer’s instructions. Genomic DNA eluates were quantified using the Qubit dsDNA High Sensitivity assay (Thermo Fisher Scientific, Waltham, MA, USA) and stored at -20C until further processing. Prior to sequencing library construction, genomic DNA was fragmented to a modal 150 base pair size using an ME220 focused ultrasonicator (Covaris, Inc., Woburn, MA, USA). Modal fragmented DNA sizes were verified using the TapeStation 2200 dsDNA high sensitivity assay (Agilent Technologies, Santa Clara, CA, USA) and quantified as described above prior to commencing library construction.
Preparation of 5hmC enriched sequencing libraries was performed as described previously24. For each sample, two libraries were generated: a library derived from 5hmC enriched reads, and a library derived from input unenriched DNA. Fragmented DNA was normalized to 20 ng total input for each assay and ligated to sequencing adapters. Adapter ligated products were either prepared for whole genome sequencing using the KAPA Hyper Prep kit (Roche, Switzerland) according to manufacturer's instructions, or 5hmC bases were biotinylated via a two-step chemistry and subsequently enriched by binding to Dynabeads M270 Streptavidin (Thermo Fisher Scientific). All libraries were quantified using a Qubit dsDNA High Sensitivity Assay (Thermo Fisher Scientific) and normalized in preparation for sequencing. Fragment size profiles of sequencing libraries were verified with the Bioanalyzer dsDNA High Sensitivity assay (Agilent Technologies) prior to sequencing.

treatment_protocol: For TET2 edited and control samples, cells were grown in steady state or drug treated conditions before being assayed using the 5hmC sequencing protocol. See sample descriptioins for specific treatment conditions.

tag: source

value: Human Cord Blood HSPCs


title: CBNY056_T_Met_WGS

description:
Whole Genome Sequencing Input Control
CBNY056 TET2 in HSC Expansion media (Not CD34+, Live HDR double positive cells) - Metformin


title: CBNY057_A_Aza_WGS

description:
Whole Genome Sequencing Input Control
CBNY057 AAVS1 in HSC Expansion media (Not CD34+, Live HDR double positive cells) - Azacitidine


title: CBNY057_T_NoDrug_WGS

description:
Whole Genome Sequencing Input Control
CBNY057 TET2 in HSC Expansion media (Not CD34+, Live HDR double positive cells) - No drug


title: CBNY057_T_VitC_WGS

description:
Whole Genome Sequencing Input Control
CBNY057 TET2 in HSC Expansion media (Not CD34+, Live HDR double positive cells) - Vitamin C


title: CBNY057_A_VitC_WGS

description:
Whole Genome Sequencing Input Control
CBNY057 AAVS1 in HSC Expansion media (Not CD34+, Live HDR double positive cells) - Vitamin C


title: CBNY057_T_Met_WGS

description:
Whole Genome Sequencing Input Control
CBNY057 TET2 in HSC Expansion media (Not CD34+, Live HDR double positive cells) - Metformin


title: CBNY057_A_Met_WGS

description:
Whole Genome Sequencing Input Control
CBNY057 AAVS1 in HSC Expansion media (Not CD34+, Live HDR double positive cells) - Metformin


title: CBNY057_A_NoDrug_WGS

description:
Whole Genome Sequencing Input Control
CBNY057 AAVS1 in HSC Expansion media (Not CD34+, Live HDR double positive cells) - No drug


title: CBNY056_T_Aza_WGS

description:
Whole Genome Sequencing Input Control
CBNY056 TET2 in HSC Expansion media (Not CD34+, Live HDR double positive cells) - Azacitidine


title: ATAC-seq_mESC_IEOE19_rep2


title: CBNY056_T_AzaVitC_WGS

description:
Whole Genome Sequencing Input Control
CBNY056 TET2 in HSC Expansion media (Not CD34+, Live HDR double positive cells) - A+V


title: CBNY056_A_Met_WGS

description:
Whole Genome Sequencing Input Control
CBNY056 AAVS1 in HSC Expansion media (Not CD34+, Live HDR double positive cells) - Metformin


title: CBNY056_T_NoDrug_WGS

description:
Whole Genome Sequencing Input Control
CBNY056 TET2 in HSC Expansion media (Not CD34+, Live HDR double positive cells) - No drug


title: CBNY056_A_AzaVitC_WGS

description:
Whole Genome Sequencing Input Control
CBNY056 AAVS1 in HSC Expansion media (Not CD34+, Live HDR double positive cells) - A+V


title: CBNY056_A_VitC_WGS

description:
Whole Genome Sequencing Input Control
CBNY056 AAVS1 in HSC Expansion media (Not CD34+, Live HDR double positive cells) - Vitamin C


title: CBNY056_A_NoDrug_WGS

description:
Whole Genome Sequencing Input Control
CBNY056 AAVS1 in HSC Expansion media (Not CD34+, Live HDR double positive cells) - No drug


title: CBNY056_A_Aza_WGS

description:
Whole Genome Sequencing Input Control
CBNY056 AAVS1 in HSC Expansion media (Not CD34+, Live HDR double positive cells) - Azacitidine


title: CBNY055_T_VitC_WGS

description:
Whole Genome Sequencing Input Control
CBNY055 TET2 in HSC Expansion media (Not CD34+, Live HDR double positive cells) - Vitamin C


title: CBNY055_T_Aza_WGS

description:
Whole Genome Sequencing Input Control
CBNY055 TET2 in HSC Expansion media (Not CD34+, Live HDR double positive cells) - Azacitidine


title: CBNY057_T_AzaVitC_WGS

description:
Whole Genome Sequencing Input Control
CBNY057 TET2 in HSC Expansion media (Not CD34+, Live HDR double positive cells) - A+V


title: CBNY057_T_Aza_WGS

description:
Whole Genome Sequencing Input Control
CBNY057 TET2 in HSC Expansion media (Not CD34+, Live HDR double positive cells) - Azacitidine


title: CBNY055_A_Met_WGS

description:
Whole Genome Sequencing Input Control
CBNY055 AAVS1 in HSC Expansion media (Not CD34+, Live HDR double positive cells) - Metformin


title: CBNY055_T_NoDrug_WGS

description:
Whole Genome Sequencing Input Control
CBNY055 TET2 in HSC Expansion media (Not CD34+, Live HDR double positive cells) - No drug


title: CBNY055_A_AzaVitC_WGS

description:
Whole Genome Sequencing Input Control
CBNY055 AAVS1 in HSC Expansion media (Not CD34+, Live HDR double positive cells) - A+V


title: CBNY055_A_Aza_WGS

description:
Whole Genome Sequencing Input Control
CBNY055 AAVS1 in HSC Expansion media (Not CD34+, Live HDR double positive cells) - Azacitidine


title: CBNY056_T_VitC_WGS

description:
Whole Genome Sequencing Input Control
CBNY056 TET2 in HSC Expansion media (Not CD34+, Live HDR double positive cells) - Vitamin C


title: CBNY055_T_AzaVitC_WGS

description:
Whole Genome Sequencing Input Control
CBNY055 TET2 in HSC Expansion media (Not CD34+, Live HDR double positive cells) - A+V


title: CBNY054_T_Met_WGS

description:
Whole Genome Sequencing Input Control
CBNY054 TET2 in HSC Expansion media (Not CD34+, Live HDR double positive cells) - Metformin


title: CBNY055_A_NoDrug_WGS

description:
Whole Genome Sequencing Input Control
CBNY055 AAVS1 in HSC Expansion media (Not CD34+, Live HDR double positive cells) - No drug


title: CBNY054_T_Aza_WGS

description:
Whole Genome Sequencing Input Control
CBNY054 TET2 in HSC Expansion media (Not CD34+, Live HDR double positive cells) - Azacitidine


title: CBNY054_T_NoDrug_WGS

description:
Whole Genome Sequencing Input Control
CBNY054 TET2 in HSC Expansion media (Not CD34+, Live HDR double positive cells) - No drug


title: CBNY054_A_Met_WGS

description:
Whole Genome Sequencing Input Control
CBNY054 AAVS1 in HSC Expansion media (Not CD34+, Live HDR double positive cells) - Metformin


title: CBNY054_A_VitC_WGS

description:
Whole Genome Sequencing Input Control
CBNY054 AAVS1 in HSC Expansion media (Not CD34+, Live HDR double positive cells) - Vitamin C


title: CBNY054_T_AzaVitC_WGS

description:
Whole Genome Sequencing Input Control
CBNY054 TET2 in HSC Expansion media (Not CD34+, Live HDR double positive cells) - A+V


title: CB1221_AAVS1_Mouse4-1_before_vitc_WGS

description:
Whole Genome Sequencing Input Control
CB1221 Hit&Run AAVS1 Before treatment hCD34+ (CD33 %) (Mouse#4-1, Eng %)


title: CBNY054_A_AzaVitC_WGS

description:
Whole Genome Sequencing Input Control
CBNY054 AAVS1 in HSC Expansion media (Not CD34+, Live HDR double positive cells) - A+V


title: CBNY055_A_VitC_WGS

description:
Whole Genome Sequencing Input Control
CBNY055 AAVS1 in HSC Expansion media (Not CD34+, Live HDR double positive cells) - Vitamin C


title: CBNY055_T_Met_WGS

description:
Whole Genome Sequencing Input Control
CBNY055 TET2 in HSC Expansion media (Not CD34+, Live HDR double positive cells) - Metformin


title: CB1221_AAVS1_Mouse4-1_after_vitc_WGS

description:
Whole Genome Sequencing Input Control
CB1221 Hit&Run AAVS1 After VitC treatment hCD34+ (CD33 %) (Mouse#4-1, Eng %)


title: CBNY054_A_NoDrug_WGS

description:
Whole Genome Sequencing Input Control
CBNY054 AAVS1 in HSC Expansion media (Not CD34+, Live HDR double positive cells) - No drug


title: CB1221_TET2_Mouse2-1_before_vitc_WGS

description:
Whole Genome Sequencing Input Control
CB1221 Hit&Run TET2-B1B2 Before treatment hCD34+ (CD33 %) (Mouse#2-1, Eng %)


title: CBNY029_HitRun_AAVS1_before_vitc_WGS

description:
Whole Genome Sequencing Input Control
CBNY029 Hit&Run AAVS1 Before VitaminC treatment hCD34+ (CD33 5.9%) (Mouse#13-2, Eng 84%)


title: CBNY029_HitRun_AAVS1_after_aza_WGS

description:
Whole Genome Sequencing Input Control
CBNY029 Hit&Run AAVS1 After Azacitidine treatment hCD34+ (CD33 60.5%) (Mouse#13-1, Eng 95.5%)


title: CB1221_TET2_Mouse4-2_before_aza_WGS

description:
Whole Genome Sequencing Input Control
CB1221 Hit&Run TET2-B1B2 Before treatment hCD34+ (CD33 %) (Mouse#4-2, Eng %)


title: CBNY030_HitRun_TET2_before_aza_WGS

description:
Whole Genome Sequencing Input Control
CBNY030 Hit&Run TET2-B1B2 Before Azacitidine treatment hCD34+ (CD33 4.2%) (Mouse#11-4, Eng 77%)


title: CBNY030_HitRun_TET2_before_vitc_WGS

description:
Whole Genome Sequencing Input Control
CBNY030 Hit&Run TET2-B1B2 Before VitaminC treatment hCD34+ (CD33 20.2%) (Mouse#11-5, Eng 83%)


title: CB407_HitRun_TET2_2-3_WGS

description:
Whole Genome Sequencing Input Control
CB407 Hit&Run 1T2T Week44 TET2#2-3 sorted hCD34+ (CD33 90%)


title: CBNY029_HitRun_AAVS1_before_aza_WGS

description:
Whole Genome Sequencing Input Control
CBNY029 Hit&Run AAVS1 Before Azacitidine treatment hCD34+ (CD33 8.9%) (Mouse#13-1, Eng 86%)


title: CBNY030_HitRun_TET2_after_aza_WGS

description:
Whole Genome Sequencing Input Control
CBNY030 Hit&Run TET2-B1B2 After Azacitidine treatment hCD34+ (CD33 84.3%) (Mouse#11-4, Eng 36.8%)


title: CBNY030_HitRun_TET2_after_vitc_WGS

description:
Whole Genome Sequencing Input Control
CBNY030 Hit&Run TET2-B1B2 After VitaminC treatment hCD34+ (CD33 53.7%) (Mouse#11-5, Eng 62.7%)


title: CBNY054_A_Aza_WGS

description:
Whole Genome Sequencing Input Control
CBNY054 AAVS1 in HSC Expansion media (Not CD34+, Live HDR double positive cells) - Azacitidine


title: CB407_HitRun_AAVS1_2-3_WGS

description:
Whole Genome Sequencing Input Control
CB407 Hit&Run 1T2T Week44 AAVS1#2-3 sorted hCD34+ (CD33 %)


title: CB1221_TET2_Mouse2-1_after_vitc_WGS

description:
Whole Genome Sequencing Input Control
CB1221 Hit&Run TET2-B1B2 After VitC treatment hCD34+ (CD33 %) (Mouse#2-1, Eng %)


title: CB1210_TET2_control_WGS

description:
Whole Genome Sequencing Input Control
CB1210 TET2 in HSC Retention media (Not CD34+, Live HDR double positive cells) - No drug


title: CB1210_TET2_vitc+aza_WGS

description:
Whole Genome Sequencing Input Control
CB1210 TET2 in HSC Retention media (Not CD34+, Live HDR double positive cells) - V+A


title: CB407_HitRun_AAVS1_B-5_WGS

description:
Whole Genome Sequencing Input Control
CB407 Hit&Run 1T2T Week45 AAVS1#B-5 sorted hCD34+ (CD33 35%)


title: CBNY029_HitRun_AAVS1_after_vitc_WGS

description:
Whole Genome Sequencing Input Control
CBNY029 Hit&Run AAVS1 After VitaminC treatment hCD34+ (CD33 19.9%) (Mouse#13-2, Eng 83.1%)


title: CBNY054_T_VitC_WGS

description:
Whole Genome Sequencing Input Control
CBNY054 TET2 in HSC Expansion media (Not CD34+, Live HDR double positive cells) - Vitamin C


title: CB1210_TET2_metformin_WGS

description:
Whole Genome Sequencing Input Control
CB1210 TET2 in HSC Retention media (Not CD34+, Live HDR double positive cells) - Metformin


title: CB1221_TET2_Mouse4-2_after_aza_WGS

description:
Whole Genome Sequencing Input Control
CB1221 Hit&Run TET2-B1B2 After Azacitidine treatment hCD34+ (CD33 %) (Mouse#4-2, Eng %)


title: CB1210_Unmodified_vitc+aza_WGS

description:
Whole Genome Sequencing Input Control
CB1210 Unmodified in HSC Retention media (Not CD34+, Bulk cells) - V+A


title: CB407_HitRun_AAVS1_3-4_WGS

description:
Whole Genome Sequencing Input Control
CB407 Hit&Run 1T2T Week44 AAVS1#3-4 sorted hCD34+ (CD33 58%)


title: CB407_HitRun_TET2_2-1_WGS

description:
Whole Genome Sequencing Input Control
CB407 Hit&Run 1T2T Week44 TET2#2-1 sorted hCD34+ (CD33 12.1%)


title: CB407_HitRun_TET2_4-1_WGS

description:
Whole Genome Sequencing Input Control
CB407 Hit&Run 1T2T Week44 TET2#4-1 sorted hCD34+ (CD33 95.9%)


title: CBD002_TET2_metformin_WGS

description:
Whole Genome Sequencing Input Control
CBD002 TET2 in HSC Retention media (Not CD34+, Live HDR double positive cells) - Metformin


title: CB1210_TET2_vitc_WGS

description:
Whole Genome Sequencing Input Control
CB1210 TET2 in HSC Retention media (Not CD34+, Live HDR double positive cells) - VitC


title: CBD002_TET2_vitc+aza_WGS

description:
Whole Genome Sequencing Input Control
CBD002 TET2 in HSC Retention media (Not CD34+, Live HDR double positive cells) - V+A


title: CB1210_Unmodified_control_WGS

description:
Whole Genome Sequencing Input Control
CB1210 Unmodified in HSC Retention media (Not CD34+, Bulk cells) - No drug


title: CB1210_TET2_aza_WGS

description:
Whole Genome Sequencing Input Control
CB1210 TET2 in HSC Retention media (Not CD34+, Live HDR double positive cells) - Azacitidine


title: CB1210_Unmodified_metformin_WGS

description:
Whole Genome Sequencing Input Control
CB1210 Unmodified in HSC Retention media (Not CD34+, Bulk cells) - Metformin


title: CBD002_TET2_vitc_WGS

description:
Whole Genome Sequencing Input Control
CBD002 TET2 in HSC Retention media (Not CD34+, Live HDR double positive cells) - VitC


title: CBD002_TET2_control_WGS

description:
Whole Genome Sequencing Input Control
CBD002 TET2 in HSC Retention media (Not CD34+, Live HDR double positive cells) - No drug


title: CB1210_Unmodified_vitc_WGS

description:
Whole Genome Sequencing Input Control
CB1210 Unmodified in HSC Retention media (Not CD34+, Bulk cells) - VitC


title: CBD002_Unmodified_vitc+aza_WGS

description:
Whole Genome Sequencing Input Control
CBD002 Unmodified in HSC Retention media (Not CD34+, Live bulk cells) - V+A


title: CB407_HitRun_TET2_1-1_WGS

description:
Whole Genome Sequencing Input Control
CB407 Hit&Run 1T2T Week44 TET2#1-1 sorted hCD34+ (CD33 98.1%)


title: CBD002_Unmodified_aza_WGS

description:
Whole Genome Sequencing Input Control
CBD002 Unmodified in HSC Retention media (Not CD34+, Live bulk cells) - Azacitidine


title: CB916_colony_TET2_plate_2_WGS

description:
Whole Genome Sequencing Input Control
CB916 Colony Assay (after 2nd plating) TET2 GFP+mCherry+ (DP) not CD34 stained


title: CBD002_Unmodified_control_WGS

description:
Whole Genome Sequencing Input Control
CBD002 Unmodified in HSC Retention media (Not CD34+, Live bulk cells) - No drug


title: CB1210_Unmodified_aza_WGS

description:
Whole Genome Sequencing Input Control
CB1210 Unmodified in HSC Retention media (Not CD34+, Bulk cells) - Azacitidine


title: CBD002_TET2_aza_WGS

description:
Whole Genome Sequencing Input Control
CBD002 TET2 in HSC Retention media (Not CD34+, Live HDR double positive cells) - Azacitidine


title: CB916_colony_AAVS1_plate_2_WGS

description:
Whole Genome Sequencing Input Control
CB916 Colony Assay (after 2nd plating) AAVS1 GFP+mCherry+ (DP) not CD34 stained


title: CBD002_Unmodified_metformin_WGS

description:
Whole Genome Sequencing Input Control
CBD002 Unmodified in HSC Retention media (Not CD34+, Live bulk cells) - Metformin


title: CB916_colony_TET2_plate_1_WGS

description:
Whole Genome Sequencing Input Control
CB916 Colony Assay (after 1st plating) TET2 GFP+mCherry+ (DP) not CD34 stained


title: CBD002_Unmodified_vitc_WGS

description:
Whole Genome Sequencing Input Control
CBD002 Unmodified in HSC Retention media (Not CD34+, Live bulk cells) - VitC


title: CB916_colony_AAVS1_plate_0_WGS

description:
Whole Genome Sequencing Input Control
CB916 Colony Assay (before plating) AAVS1 GFP+mCherry+ (DP) not CD34 stained


title: CB1210_TET2_WGS

description:
Whole Genome Sequencing Input Control
CB1210 HDR TET2 GFP-mCherry Double positive in HSC Expansion media (CD34+)


title: CB1210_Unmodified_WGS

description:
Whole Genome Sequencing Input Control
CB1210 Unmodified in HSC Expansion media (CD34+)


title: CB916_colony_AAVS1_plate_1_WGS

description:
Whole Genome Sequencing Input Control
CB916 Colony Assay (after 1st plating) AAVS1 GFP+mCherry+ (DP) not CD34 stained


title: CB1115_AAVS1_WGS

description:
Whole Genome Sequencing Input Control
CB1115 HDR AAVS1 GFP-mCherry Double positive in HSC Expansion media (CD34+)


title: CB1115_TET2_WGS

description:
Whole Genome Sequencing Input Control
CB1115 HDR TET2 GFP-mCherry Double positive in HSC Expansion media (CD34+)


title: CBJ002_colony_TET2_plate_0_WGS

description:
Whole Genome Sequencing Input Control
CBJ002 Colony Assay (before plating) TET2 GFP+mCherry+ (DP) not CD34 stained


title: CB916_colony_TET2_plate_0_WGS

description:
Whole Genome Sequencing Input Control
CB916 Colony Assay (before plating) TET2 GFP+mCherry+ (DP) not CD34 stained


title: CBJ002_colony_AAVS1_bulk_plate_2_WGS

description:
Whole Genome Sequencing Input Control
CBJ002 Colony Assay (after 2nd plating) AAVS1 bulk cells not CD34 stained


title: CB1210_AAVS1_WGS

description:
Whole Genome Sequencing Input Control
CB1210 HDR AAVS1 GFP-mCherry Double positive in HSC Expansion media (CD34+)


title: CBJ002_colony_TET2_plate_2_WGS

description:
Whole Genome Sequencing Input Control
CBJ002 Colony Assay (after 2nd plating) TET2 GFP+mCherry+ (DP) not CD34 stained


title: CBJ002_colony_AAVS1_plate_1_WGS

description:
Whole Genome Sequencing Input Control
CBJ002 Colony Assay (after 1st plating) AAVS1 GFP+mCherry+ (DP) not CD34 stained


title: CBD002_AAVS1_WGS

description:
Whole Genome Sequencing Input Control
CBD002 HDR AAVS1 GFP-mCherry Double positive in HSC Expansion media (CD34+)


title: PBSU005_CD8T_WGS

description:
Whole Genome Sequencing Input Control
PBSU005_T(CD8)

source_name: Human Peripheral Blood

value: Human Peripheral Blood


title: CBJ002_colony_TET2_plate_1_WGS

description:
Whole Genome Sequencing Input Control
CBJ002 Colony Assay (after 1st plating) TET2 GFP+mCherry+ (DP) not CD34 stained


title: CBD002_TET2_WGS

description:
Whole Genome Sequencing Input Control
CBD002 HDR TET2 GFP-mCherry Double positive in HSC Expansion media (CD34+)


title: PBSU005_Monocyte_WGS

description:
Whole Genome Sequencing Input Control
PBSU005_Monocyte

value: Monocyte


title: CBJ002_colony_AAVS1_plate_0_WGS

description:
Whole Genome Sequencing Input Control
CBJ002 Colony Assay (before plating) AAVS1 GFP+mCherry+ (DP) not CD34 stained


title: CBD002_Unmodified_WGS

description:
Whole Genome Sequencing Input Control
CBD002 Unmodified in HSC Expansion media (CD34+)


title: PBSU005_CD4T_WGS

description:
Whole Genome Sequencing Input Control
PBSU005_T(CD4)


title: CB1115_Unmodified_WGS

description:
Whole Genome Sequencing Input Control
CB1115 Unmodified in HSC Expansion media (CD34+)


title: PBSU004_CD8T_WGS

description:
Whole Genome Sequencing Input Control
PBSU004_T(CD8)


title: PBSU005_B_WGS

description:
Whole Genome Sequencing Input Control
PBSU005_B

value: B


title: PBSU005_NK_WGS

description:
Whole Genome Sequencing Input Control
PBSU005_NK

value: NK


title: PBSU004_B_WGS

description:
Whole Genome Sequencing Input Control
PBSU004_B


title: PBSU004_NK_WGS

description:
Whole Genome Sequencing Input Control
PBSU004_NK


title: PBSU004_CD4T_WGS

description:
Whole Genome Sequencing Input Control
PBSU004_T(CD4)


title: PBSU004_Monocyte_WGS

description:
Whole Genome Sequencing Input Control
PBSU004_Monocyte


title: PBSU003_CD8T_WGS

description:
Whole Genome Sequencing Input Control
PBSU003_T(CD8)


title: PBSU003_NK_WGS

description:
Whole Genome Sequencing Input Control
PBSU003_NK


title: PBSU003_CD4T_WGS

description:
Whole Genome Sequencing Input Control
PBSU003_T(CD4)


title: PBSU002_CD8T_WGS

description:
Whole Genome Sequencing Input Control
PBSU002_T(CD8)


title: PBSU003_B_WGS

description:
Whole Genome Sequencing Input Control
PBSU003_B


title: PBSU002_NK_WGS

description:
Whole Genome Sequencing Input Control
PBSU002_NK


title: PBSU002_B_WGS

description:
Whole Genome Sequencing Input Control
PBSU002_B


title: ACBM005_pMPP_WGS

description:
Whole Genome Sequencing Input Control
ACBM005_pMPP

source_name: Human Bone Marrow HSPCs

value: Human Bone Marrow HSPCs

value: MPP


title: ACBM005_pLMPP_WGS

description:
Whole Genome Sequencing Input Control
ACBM005_pLMPP

value: LMPP


title: PBSU001_B_WGS

description:
Whole Genome Sequencing Input Control
PBSU001_B


title: PBSU001_Monocyte_WGS

description:
Whole Genome Sequencing Input Control
PBSU001_Monocyte


title: PBSU002_Monocyte_WGS

description:
Whole Genome Sequencing Input Control
PBSU002_Monocyte


title: ACBM005_pCLP_WGS

description:
Whole Genome Sequencing Input Control
ACBM005_pCLP

value: CLP


title: ACBM005_pGMP_WGS

description:
Whole Genome Sequencing Input Control
ACBM005_pGMP

value: GMP


title: ACBM004_pCMP_WGS

description:
Whole Genome Sequencing Input Control
ACBM004_pCMP

value: CMP


title: ACBM004_pLMPP_WGS

description:
Whole Genome Sequencing Input Control
ACBM004_pLMPP


title: ACBM004_pHSC_WGS

description:
Whole Genome Sequencing Input Control
ACBM004_pHSC

value: HSC


title: ACBM005_pHSC_WGS

description:
Whole Genome Sequencing Input Control
ACBM005_pHSC


title: ACBM004_pGMP_WGS

description:
Whole Genome Sequencing Input Control
ACBM004_pGMP


title: ACBM005_pCMP_WGS

description:
Whole Genome Sequencing Input Control
ACBM005_pCMP


title: ACBM004_pMEP_WGS

description:
Whole Genome Sequencing Input Control
ACBM004_pMEP

value: MEP


title: ACBM004_pCLP_WGS

description:
Whole Genome Sequencing Input Control
ACBM004_pCLP


title: PBSU003_Monocyte_WGS

description:
Whole Genome Sequencing Input Control
PBSU003_Monocyte


title: ACBM005_pMEP_WGS

description:
Whole Genome Sequencing Input Control
ACBM005_pMEP


title: PBSU002_CD4T_WGS

description:
Whole Genome Sequencing Input Control
PBSU002_T(CD4)


title: ACBM003_pLMPP_WGS

description:
Whole Genome Sequencing Input Control
ACBM003_pLMPP


title: ACBM002_pMEP_WGS

description:
Whole Genome Sequencing Input Control
ACBM002_pMEP


title: ACBM002_pMPP_WGS

description:
Whole Genome Sequencing Input Control
ACBM002_pMPP


title: PBSU001_NK_WGS

description:
Whole Genome Sequencing Input Control
PBSU001_NK


title: ACBM002_pLMPP_WGS

description:
Whole Genome Sequencing Input Control
ACBM002_pLMPP


title: ACBM003_pGMP_WGS

description:
Whole Genome Sequencing Input Control
ACBM003_pGMP


title: ACBM003_pHSC_WGS

description:
Whole Genome Sequencing Input Control
ACBM003_pHSC


title: ACBM004_pMPP_WGS

description:
Whole Genome Sequencing Input Control
ACBM004_pMPP


title: ACBM002_pCLP_WGS

description:
Whole Genome Sequencing Input Control
ACBM002_pCLP


title: ACBM002_pCMP_WGS

description:
Whole Genome Sequencing Input Control
ACBM002_pCMP


title: ACBM002_pGMP_WGS

description:
Whole Genome Sequencing Input Control
ACBM002_pGMP


title: ACBM003_pCMP_WGS

description:
Whole Genome Sequencing Input Control
ACBM003_pCMP


title: ACBM002_pHSC_WGS

description:
Whole Genome Sequencing Input Control
ACBM002_pHSC


title: ACBM001_pMEP_WGS

description:
Whole Genome Sequencing Input Control
ACBM001_pMEP


title: ACBM001_pMPP_WGS

description:
Whole Genome Sequencing Input Control
ACBM001_pMPP


title: ACBM001_pHSC_WGS

description:
Whole Genome Sequencing Input Control
ACBM001_pHSC


title: ACBM001_pLMPP_WGS

description:
Whole Genome Sequencing Input Control
ACBM001_pLMPP


title: CBNY057_T_VitC_5hmC

description:
5hmC pulldown sequencing data
CBNY057 TET2 in HSC Expansion media (Not CD34+, Live HDR double positive cells) - Vitamin C

data_processing:
Library strategy: 5hmC-seq
Seventy-five base-pair, paired-end DNA sequencing was completed using a NextSeq550 instrument with NovaSeq Hi Output version 2.5 reagent kits (Illumina, San Diego, CA, USA).
Raw data processing and demultiplexing to sample-specific FASTQ output was performed using the Illumina BaseSpace Sequence Hub.
Sequencing reads were aligned to the hg19 reference genome using default parameters of BWA-MEM.
Duplicate reads were marked and removed using Picard MarkDuplicates.
Assembly: hg19
Supplementary files format and content: Raw reads in peaks or reads in gene bodies data across all samples, RNA kallisto output normalized counts matrix


title: CBNY057_T_AzaVitC_5hmC

description:
5hmC pulldown sequencing data
CBNY057 TET2 in HSC Expansion media (Not CD34+, Live HDR double positive cells) - A+V


title: ACBM003_pCLP_WGS

description:
Whole Genome Sequencing Input Control
ACBM003_pCLP


title: CBNY057_T_NoDrug_5hmC

description:
5hmC pulldown sequencing data
CBNY057 TET2 in HSC Expansion media (Not CD34+, Live HDR double positive cells) - No drug


title: CBNY057_T_Met_5hmC

description:
5hmC pulldown sequencing data
CBNY057 TET2 in HSC Expansion media (Not CD34+, Live HDR double positive cells) - Metformin


title: ACBM001_pGMP_WGS

description:
Whole Genome Sequencing Input Control
ACBM001_pGMP


title: CBNY057_T_Aza_5hmC

description:
5hmC pulldown sequencing data
CBNY057 TET2 in HSC Expansion media (Not CD34+, Live HDR double positive cells) - Azacitidine


title: ACBM001_pCLP_WGS

description:
Whole Genome Sequencing Input Control
ACBM001_pCLP


title: CBNY057_A_VitC_5hmC

description:
5hmC pulldown sequencing data
CBNY057 AAVS1 in HSC Expansion media (Not CD34+, Live HDR double positive cells) - Vitamin C


title: CBNY057_A_Met_5hmC

description:
5hmC pulldown sequencing data
CBNY057 AAVS1 in HSC Expansion media (Not CD34+, Live HDR double positive cells) - Metformin


title: CBNY057_A_AzaVitC_5hmC

description:
5hmC pulldown sequencing data
CBNY057 AAVS1 in HSC Expansion media (Not CD34+, Live HDR double positive cells) - A+V


title: CBNY056_T_Met_5hmC

description:
5hmC pulldown sequencing data
CBNY056 TET2 in HSC Expansion media (Not CD34+, Live HDR double positive cells) - Metformin


title: CBNY057_A_Aza_5hmC

description:
5hmC pulldown sequencing data
CBNY057 AAVS1 in HSC Expansion media (Not CD34+, Live HDR double positive cells) - Azacitidine


title: CBNY056_T_AzaVitC_5hmC

description:
5hmC pulldown sequencing data
CBNY056 TET2 in HSC Expansion media (Not CD34+, Live HDR double positive cells) - A+V


title: CBNY056_A_Met_5hmC

description:
5hmC pulldown sequencing data
CBNY056 AAVS1 in HSC Expansion media (Not CD34+, Live HDR double positive cells) - Metformin


title: CBNY056_T_Aza_5hmC

description:
5hmC pulldown sequencing data
CBNY056 TET2 in HSC Expansion media (Not CD34+, Live HDR double positive cells) - Azacitidine


title: CBNY056_A_AzaVitC_5hmC

description:
5hmC pulldown sequencing data
CBNY056 AAVS1 in HSC Expansion media (Not CD34+, Live HDR double positive cells) - A+V


title: CBNY056_A_VitC_5hmC

description:
5hmC pulldown sequencing data
CBNY056 AAVS1 in HSC Expansion media (Not CD34+, Live HDR double positive cells) - Vitamin C


title: CBNY056_T_NoDrug_5hmC

description:
5hmC pulldown sequencing data
CBNY056 TET2 in HSC Expansion media (Not CD34+, Live HDR double positive cells) - No drug


title: CBNY056_A_NoDrug_5hmC

description:
5hmC pulldown sequencing data
CBNY056 AAVS1 in HSC Expansion media (Not CD34+, Live HDR double positive cells) - No drug


title: CBNY056_A_Aza_5hmC

description:
5hmC pulldown sequencing data
CBNY056 AAVS1 in HSC Expansion media (Not CD34+, Live HDR double positive cells) - Azacitidine


title: CBNY055_T_Met_5hmC

description:
5hmC pulldown sequencing data
CBNY055 TET2 in HSC Expansion media (Not CD34+, Live HDR double positive cells) - Metformin


title: CBNY055_T_AzaVitC_5hmC

description:
5hmC pulldown sequencing data
CBNY055 TET2 in HSC Expansion media (Not CD34+, Live HDR double positive cells) - A+V


title: ACBM001_pCMP_WGS

description:
Whole Genome Sequencing Input Control
ACBM001_pCMP


title: ACBM003_pMEP_WGS

description:
Whole Genome Sequencing Input Control
ACBM003_pMEP


title: CBNY055_T_VitC_5hmC

description:
5hmC pulldown sequencing data
CBNY055 TET2 in HSC Expansion media (Not CD34+, Live HDR double positive cells) - Vitamin C


title: CBNY055_A_AzaVitC_5hmC

description:
5hmC pulldown sequencing data
CBNY055 AAVS1 in HSC Expansion media (Not CD34+, Live HDR double positive cells) - A+V


title: CBNY055_A_NoDrug_5hmC

description:
5hmC pulldown sequencing data
CBNY055 AAVS1 in HSC Expansion media (Not CD34+, Live HDR double positive cells) - No drug


title: CBNY055_A_VitC_5hmC

description:
5hmC pulldown sequencing data
CBNY055 AAVS1 in HSC Expansion media (Not CD34+, Live HDR double positive cells) - Vitamin C


title: CBNY054_T_Met_5hmC

description:
5hmC pulldown sequencing data
CBNY054 TET2 in HSC Expansion media (Not CD34+, Live HDR double positive cells) - Metformin


title: CBNY054_T_AzaVitC_5hmC

description:
5hmC pulldown sequencing data
CBNY054 TET2 in HSC Expansion media (Not CD34+, Live HDR double positive cells) - A+V


title: CBNY055_A_Aza_5hmC

description:
5hmC pulldown sequencing data
CBNY055 AAVS1 in HSC Expansion media (Not CD34+, Live HDR double positive cells) - Azacitidine


title: CBNY055_A_Met_5hmC

description:
5hmC pulldown sequencing data
CBNY055 AAVS1 in HSC Expansion media (Not CD34+, Live HDR double positive cells) - Metformin


title: CBNY055_T_Aza_5hmC

description:
5hmC pulldown sequencing data
CBNY055 TET2 in HSC Expansion media (Not CD34+, Live HDR double positive cells) - Azacitidine


title: CBNY054_T_Aza_5hmC

description:
5hmC pulldown sequencing data
CBNY054 TET2 in HSC Expansion media (Not CD34+, Live HDR double positive cells) - Azacitidine


title: CBNY056_T_VitC_5hmC

description:
5hmC pulldown sequencing data
CBNY056 TET2 in HSC Expansion media (Not CD34+, Live HDR double positive cells) - Vitamin C


title: CBNY055_T_NoDrug_5hmC

description:
5hmC pulldown sequencing data
CBNY055 TET2 in HSC Expansion media (Not CD34+, Live HDR double positive cells) - No drug


title: CBNY054_T_VitC_5hmC

description:
5hmC pulldown sequencing data
CBNY054 TET2 in HSC Expansion media (Not CD34+, Live HDR double positive cells) - Vitamin C


title: CBNY057_A_NoDrug_5hmC

description:
5hmC pulldown sequencing data
CBNY057 AAVS1 in HSC Expansion media (Not CD34+, Live HDR double positive cells) - No drug


title: CBNY054_T_NoDrug_5hmC

description:
5hmC pulldown sequencing data
CBNY054 TET2 in HSC Expansion media (Not CD34+, Live HDR double positive cells) - No drug


title: CBNY054_A_Met_5hmC

description:
5hmC pulldown sequencing data
CBNY054 AAVS1 in HSC Expansion media (Not CD34+, Live HDR double positive cells) - Metformin


title: CBNY054_A_AzaVitC_5hmC

description:
5hmC pulldown sequencing data
CBNY054 AAVS1 in HSC Expansion media (Not CD34+, Live HDR double positive cells) - A+V


title: CB1221_TET2_Mouse4-2_after_aza_5hmC

description:
5hmC pulldown sequencing data
CB1221 Hit&Run TET2-B1B2 After Azacitidine treatment hCD34+ (CD33 %) (Mouse#4-2, Eng %)


title: CBNY054_A_Aza_5hmC

description:
5hmC pulldown sequencing data
CBNY054 AAVS1 in HSC Expansion media (Not CD34+, Live HDR double positive cells) - Azacitidine


title: CBNY054_A_NoDrug_5hmC

description:
5hmC pulldown sequencing data
CBNY054 AAVS1 in HSC Expansion media (Not CD34+, Live HDR double positive cells) - No drug


title: CB1221_AAVS1_Mouse4-1_before_vitc_5hmC

description:
5hmC pulldown sequencing data
CB1221 Hit&Run AAVS1 Before treatment hCD34+ (CD33 %) (Mouse#4-1, Eng %)


title: CB1221_AAVS1_Mouse4-1_after_vitc_5hmC

description:
5hmC pulldown sequencing data
CB1221 Hit&Run AAVS1 After VitC treatment hCD34+ (CD33 %) (Mouse#4-1, Eng %)


title: CB1221_TET2_Mouse2-1_after_vitc_5hmC

description:
5hmC pulldown sequencing data
CB1221 Hit&Run TET2-B1B2 After VitC treatment hCD34+ (CD33 %) (Mouse#2-1, Eng %)


title: CBNY029_HitRun_AAVS1_after_vitc_5hmC

description:
5hmC pulldown sequencing data
CBNY029 Hit&Run AAVS1 After VitaminC treatment hCD34+ (CD33 19.9%) (Mouse#13-2, Eng 83.1%)


title: CB1221_TET2_Mouse4-2_before_aza_5hmC

description:
5hmC pulldown sequencing data
CB1221 Hit&Run TET2-B1B2 Before treatment hCD34+ (CD33 %) (Mouse#4-2, Eng %)


title: CBNY029_HitRun_AAVS1_after_aza_5hmC

description:
5hmC pulldown sequencing data
CBNY029 Hit&Run AAVS1 After Azacitidine treatment hCD34+ (CD33 60.5%) (Mouse#13-1, Eng 95.5%)


title: CB1221_TET2_Mouse2-1_before_vitc_5hmC

description:
5hmC pulldown sequencing data
CB1221 Hit&Run TET2-B1B2 Before treatment hCD34+ (CD33 %) (Mouse#2-1, Eng %)


title: CBNY030_HitRun_TET2_after_vitc_5hmC

description:
5hmC pulldown sequencing data
CBNY030 Hit&Run TET2-B1B2 After VitaminC treatment hCD34+ (CD33 53.7%) (Mouse#11-5, Eng 62.7%)


title: CBNY029_HitRun_AAVS1_before_aza_5hmC

description:
5hmC pulldown sequencing data
CBNY029 Hit&Run AAVS1 Before Azacitidine treatment hCD34+ (CD33 8.9%) (Mouse#13-1, Eng 86%)


title: CBNY030_HitRun_TET2_before_vitc_5hmC

description:
5hmC pulldown sequencing data
CBNY030 Hit&Run TET2-B1B2 Before VitaminC treatment hCD34+ (CD33 20.2%) (Mouse#11-5, Eng 83%)


title: CBNY029_HitRun_AAVS1_before_vitc_5hmC

description:
5hmC pulldown sequencing data
CBNY029 Hit&Run AAVS1 Before VitaminC treatment hCD34+ (CD33 5.9%) (Mouse#13-2, Eng 84%)


title: CBNY030_HitRun_TET2_after_aza_5hmC

description:
5hmC pulldown sequencing data
CBNY030 Hit&Run TET2-B1B2 After Azacitidine treatment hCD34+ (CD33 84.3%) (Mouse#11-4, Eng 36.8%)


title: CBNY054_A_VitC_5hmC

description:
5hmC pulldown sequencing data
CBNY054 AAVS1 in HSC Expansion media (Not CD34+, Live HDR double positive cells) - Vitamin C


title: CB407_HitRun_TET2_2-3_5hmC

description:
5hmC pulldown sequencing data
CB407 Hit&Run 1T2T Week44 TET2#2-3 sorted hCD34+ (CD33 90%)


title: CB1210_TET2_aza_5hmC

description:
5hmC pulldown sequencing data
CB1210 TET2 in HSC Retention media (Not CD34+, Live HDR double positive cells) - Azacitidine


title: CB407_HitRun_AAVS1_3-4_5hmC

description:
5hmC pulldown sequencing data
CB407 Hit&Run 1T2T Week44 AAVS1#3-4 sorted hCD34+ (CD33 58%)


title: CB407_HitRun_TET2_1-1_5hmC

description:
5hmC pulldown sequencing data
CB407 Hit&Run 1T2T Week44 TET2#1-1 sorted hCD34+ (CD33 98.1%)


title: CBNY030_HitRun_TET2_before_aza_5hmC

description:
5hmC pulldown sequencing data
CBNY030 Hit&Run TET2-B1B2 Before Azacitidine treatment hCD34+ (CD33 4.2%) (Mouse#11-4, Eng 77%)


title: CB407_HitRun_TET2_2-1_5hmC

description:
5hmC pulldown sequencing data
CB407 Hit&Run 1T2T Week44 TET2#2-1 sorted hCD34+ (CD33 12.1%)


title: CB407_HitRun_AAVS1_B-5_5hmC

description:
5hmC pulldown sequencing data
CB407 Hit&Run 1T2T Week45 AAVS1#B-5 sorted hCD34+ (CD33 35%)


title: CB407_HitRun_TET2_4-1_5hmC

description:
5hmC pulldown sequencing data
CB407 Hit&Run 1T2T Week44 TET2#4-1 sorted hCD34+ (CD33 95.9%)


title: CB407_HitRun_AAVS1_2-3_5hmC

description:
5hmC pulldown sequencing data
CB407 Hit&Run 1T2T Week44 AAVS1#2-3 sorted hCD34+ (CD33 %)


title: CB1210_TET2_metformin_5hmC

description:
5hmC pulldown sequencing data
CB1210 TET2 in HSC Retention media (Not CD34+, Live HDR double positive cells) - Metformin


title: CB1210_Unmodified_vitc+aza_5hmC

description:
5hmC pulldown sequencing data
CB1210 Unmodified in HSC Retention media (Not CD34+, Bulk cells) - V+A


title: CB1210_Unmodified_vitc_5hmC

description:
5hmC pulldown sequencing data
CB1210 Unmodified in HSC Retention media (Not CD34+, Bulk cells) - VitC


title: CB1210_Unmodified_aza_5hmC

description:
5hmC pulldown sequencing data
CB1210 Unmodified in HSC Retention media (Not CD34+, Bulk cells) - Azacitidine


title: CB1210_TET2_control_5hmC

description:
5hmC pulldown sequencing data
CB1210 TET2 in HSC Retention media (Not CD34+, Live HDR double positive cells) - No drug


title: CB1210_TET2_vitc_5hmC

description:
5hmC pulldown sequencing data
CB1210 TET2 in HSC Retention media (Not CD34+, Live HDR double positive cells) - VitC


title: CB1210_TET2_vitc+aza_5hmC

description:
5hmC pulldown sequencing data
CB1210 TET2 in HSC Retention media (Not CD34+, Live HDR double positive cells) - V+A


title: CB1210_Unmodified_metformin_5hmC

description:
5hmC pulldown sequencing data
CB1210 Unmodified in HSC Retention media (Not CD34+, Bulk cells) - Metformin


title: CBD002_TET2_aza_5hmC

description:
5hmC pulldown sequencing data
CBD002 TET2 in HSC Retention media (Not CD34+, Live HDR double positive cells) - Azacitidine


title: CBD002_TET2_metformin_5hmC

description:
5hmC pulldown sequencing data
CBD002 TET2 in HSC Retention media (Not CD34+, Live HDR double positive cells) - Metformin


title: CB1210_Unmodified_control_5hmC

description:
5hmC pulldown sequencing data
CB1210 Unmodified in HSC Retention media (Not CD34+, Bulk cells) - No drug


title: CBD002_TET2_vitc+aza_5hmC

description:
5hmC pulldown sequencing data
CBD002 TET2 in HSC Retention media (Not CD34+, Live HDR double positive cells) - V+A


title: CBD002_Unmodified_vitc+aza_5hmC

description:
5hmC pulldown sequencing data
CBD002 Unmodified in HSC Retention media (Not CD34+, Live bulk cells) - V+A


title: CBD002_Unmodified_metformin_5hmC

description:
5hmC pulldown sequencing data
CBD002 Unmodified in HSC Retention media (Not CD34+, Live bulk cells) - Metformin


title: CBD002_TET2_control_5hmC

description:
5hmC pulldown sequencing data
CBD002 TET2 in HSC Retention media (Not CD34+, Live HDR double positive cells) - No drug


title: CBD002_TET2_vitc_5hmC

description:
5hmC pulldown sequencing data
CBD002 TET2 in HSC Retention media (Not CD34+, Live HDR double positive cells) - VitC


title: CBD002_Unmodified_control_5hmC

description:
5hmC pulldown sequencing data
CBD002 Unmodified in HSC Retention media (Not CD34+, Live bulk cells) - No drug


title: CBD002_Unmodified_vitc_5hmC

description:
5hmC pulldown sequencing data
CBD002 Unmodified in HSC Retention media (Not CD34+, Live bulk cells) - VitC


title: CB916_colony_AAVS1_plate_1_5hmC

description:
5hmC pulldown sequencing data
CB916 Colony Assay (after 1st plating) AAVS1 GFP+mCherry+ (DP) not CD34 stained


title: CB916_colony_AAVS1_plate_2_5hmC

description:
5hmC pulldown sequencing data
CB916 Colony Assay (after 2nd plating) AAVS1 GFP+mCherry+ (DP) not CD34 stained


title: CB916_colony_TET2_plate_2_5hmC

description:
5hmC pulldown sequencing data
CB916 Colony Assay (after 2nd plating) TET2 GFP+mCherry+ (DP) not CD34 stained


title: CB916_colony_TET2_plate_0_5hmC

description:
5hmC pulldown sequencing data
CB916 Colony Assay (before plating) TET2 GFP+mCherry+ (DP) not CD34 stained


title: CB916_colony_TET2_plate_1_5hmC

description:
5hmC pulldown sequencing data
CB916 Colony Assay (after 1st plating) TET2 GFP+mCherry+ (DP) not CD34 stained


title: CB916_colony_AAVS1_plate_0_5hmC

description:
5hmC pulldown sequencing data
CB916 Colony Assay (before plating) AAVS1 GFP+mCherry+ (DP) not CD34 stained


title: CBJ002_colony_AAVS1_bulk_plate_2_5hmC

description:
5hmC pulldown sequencing data
CBJ002 Colony Assay (after 2nd plating) AAVS1 bulk cells not CD34 stained


title: CBJ002_colony_TET2_plate_2_5hmC

description:
5hmC pulldown sequencing data
CBJ002 Colony Assay (after 2nd plating) TET2 GFP+mCherry+ (DP) not CD34 stained


title: CB1210_Unmodified_5hmC

description:
5hmC pulldown sequencing data
CB1210 Unmodified in HSC Expansion media (CD34+)


title: CB1115_AAVS1_5hmC

description:
5hmC pulldown sequencing data
CB1115 HDR AAVS1 GFP-mCherry Double positive in HSC Expansion media (CD34+)


title: CB1210_AAVS1_5hmC

description:
5hmC pulldown sequencing data
CB1210 HDR AAVS1 GFP-mCherry Double positive in HSC Expansion media (CD34+)


title: CB1115_TET2_5hmC

description:
5hmC pulldown sequencing data
CB1115 HDR TET2 GFP-mCherry Double positive in HSC Expansion media (CD34+)


title: PBSU005_CD4T_5hmC

description:
5hmC pulldown sequencing data
PBSU005_T(CD4)


title: CBD002_Unmodified_5hmC

description:
5hmC pulldown sequencing data
CBD002 Unmodified in HSC Expansion media (CD34+)


title: CBJ002_colony_AAVS1_plate_0_5hmC

description:
5hmC pulldown sequencing data
CBJ002 Colony Assay (before plating) AAVS1 GFP+mCherry+ (DP) not CD34 stained


title: CBJ002_colony_AAVS1_plate_1_5hmC

description:
5hmC pulldown sequencing data
CBJ002 Colony Assay (after 1st plating) AAVS1 GFP+mCherry+ (DP) not CD34 stained


title: PBSU005_CD8T_5hmC

description:
5hmC pulldown sequencing data
PBSU005_T(CD8)


title: CBD002_AAVS1_5hmC

description:
5hmC pulldown sequencing data
CBD002 HDR AAVS1 GFP-mCherry Double positive in HSC Expansion media (CD34+)


title: CBJ002_colony_TET2_plate_0_5hmC

description:
5hmC pulldown sequencing data
CBJ002 Colony Assay (before plating) TET2 GFP+mCherry+ (DP) not CD34 stained


title: CB1210_TET2_5hmC

description:
5hmC pulldown sequencing data
CB1210 HDR TET2 GFP-mCherry Double positive in HSC Expansion media (CD34+)


title: CBD002_Unmodified_aza_5hmC

description:
5hmC pulldown sequencing data
CBD002 Unmodified in HSC Retention media (Not CD34+, Live bulk cells) - Azacitidine


title: PBSU005_B_5hmC

description:
5hmC pulldown sequencing data
PBSU005_B


title: PBSU004_CD4T_5hmC

description:
5hmC pulldown sequencing data
PBSU004_T(CD4)


title: PBSU005_NK_5hmC

description:
5hmC pulldown sequencing data
PBSU005_NK


title: PBSU005_Monocyte_5hmC

description:
5hmC pulldown sequencing data
PBSU005_Monocyte


title: PBSU003_CD4T_5hmC

description:
5hmC pulldown sequencing data
PBSU003_T(CD4)


title: PBSU004_CD8T_5hmC

description:
5hmC pulldown sequencing data
PBSU004_T(CD8)


title: PBSU003_NK_5hmC

description:
5hmC pulldown sequencing data
PBSU003_NK


title: PBSU003_B_5hmC

description:
5hmC pulldown sequencing data
PBSU003_B


title: PBSU003_CD8T_5hmC

description:
5hmC pulldown sequencing data
PBSU003_T(CD8)


title: PBSU004_Monocyte_5hmC

description:
5hmC pulldown sequencing data
PBSU004_Monocyte


title: PBSU003_Monocyte_5hmC

description:
5hmC pulldown sequencing data
PBSU003_Monocyte


title: CBJ002_colony_TET2_plate_1_5hmC

description:
5hmC pulldown sequencing data
CBJ002 Colony Assay (after 1st plating) TET2 GFP+mCherry+ (DP) not CD34 stained


title: PBSU002_CD8T_5hmC

description:
5hmC pulldown sequencing data
PBSU002_T(CD8)


title: PBSU004_NK_5hmC

description:
5hmC pulldown sequencing data
PBSU004_NK


title: CBD002_TET2_5hmC

description:
5hmC pulldown sequencing data
CBD002 HDR TET2 GFP-mCherry Double positive in HSC Expansion media (CD34+)


title: PBSU004_B_5hmC

description:
5hmC pulldown sequencing data
PBSU004_B


title: CB1115_Unmodified_5hmC

description:
5hmC pulldown sequencing data
CB1115 Unmodified in HSC Expansion media (CD34+)


title: ACBM005_pMEP_5hmC

description:
5hmC pulldown sequencing data
ACBM005_pMEP


title: PBSU002_B_5hmC

description:
5hmC pulldown sequencing data
PBSU002_B


title: PBSU002_CD4T_5hmC

description:
5hmC pulldown sequencing data
PBSU002_T(CD4)


title: PBSU002_NK_5hmC

description:
5hmC pulldown sequencing data
PBSU002_NK


title: PBSU002_Monocyte_5hmC

description:
5hmC pulldown sequencing data
PBSU002_Monocyte


title: PBSU001_NK_5hmC

description:
5hmC pulldown sequencing data
PBSU001_NK


title: PBSU001_Monocyte_5hmC

description:
5hmC pulldown sequencing data
PBSU001_Monocyte


title: ACBM004_pMEP_5hmC

description:
5hmC pulldown sequencing data
ACBM004_pMEP


title: ACBM005_pMPP_5hmC

description:
5hmC pulldown sequencing data
ACBM005_pMPP


title: ACBM005_pCMP_5hmC

description:
5hmC pulldown sequencing data
ACBM005_pCMP


title: ACBM005_pHSC_5hmC

description:
5hmC pulldown sequencing data
ACBM005_pHSC


title: ACBM005_pLMPP_5hmC

description:
5hmC pulldown sequencing data
ACBM005_pLMPP


title: ACBM004_pMPP_5hmC

description:
5hmC pulldown sequencing data
ACBM004_pMPP


title: ACBM004_pGMP_5hmC

description:
5hmC pulldown sequencing data
ACBM004_pGMP


title: ACBM004_pLMPP_5hmC

description:
5hmC pulldown sequencing data
ACBM004_pLMPP


title: ACBM003_pGMP_5hmC

description:
5hmC pulldown sequencing data
ACBM003_pGMP


title: ACBM004_pCLP_5hmC

description:
5hmC pulldown sequencing data
ACBM004_pCLP


title: ACBM003_pLMPP_5hmC

description:
5hmC pulldown sequencing data
ACBM003_pLMPP


title: ACBM002_pMPP_5hmC

description:
5hmC pulldown sequencing data
ACBM002_pMPP


title: ACBM003_pCMP_5hmC

description:
5hmC pulldown sequencing data
ACBM003_pCMP


title: ACBM003_pCLP_5hmC

description:
5hmC pulldown sequencing data
ACBM003_pCLP


title: ACBM004_pCMP_5hmC

description:
5hmC pulldown sequencing data
ACBM004_pCMP


title: ACBM004_pHSC_5hmC

description:
5hmC pulldown sequencing data
ACBM004_pHSC


title: ACBM003_pMEP_5hmC

description:
5hmC pulldown sequencing data
ACBM003_pMEP


title: ACBM002_pLMPP_5hmC

description:
5hmC pulldown sequencing data
ACBM002_pLMPP


title: ACBM002_pMEP_5hmC

description:
5hmC pulldown sequencing data
ACBM002_pMEP


title: ACBM003_pHSC_5hmC

description:
5hmC pulldown sequencing data
ACBM003_pHSC


title: PBSU001_B_5hmC

description:
5hmC pulldown sequencing data
PBSU001_B


title: ACBM002_pHSC_5hmC

description:
5hmC pulldown sequencing data
ACBM002_pHSC


title: ACBM005_pGMP_5hmC

description:
5hmC pulldown sequencing data
ACBM005_pGMP


title: ACBM002_pCMP_5hmC

description:
5hmC pulldown sequencing data
ACBM002_pCMP


title: ACBM005_pCLP_5hmC

description:
5hmC pulldown sequencing data
ACBM005_pCLP


title: ACBM002_pGMP_5hmC

description:
5hmC pulldown sequencing data
ACBM002_pGMP


title: ACBM001_pLMPP_5hmC

description:
5hmC pulldown sequencing data
ACBM001_pLMPP


title: ACBM001_pMPP_5hmC

description:
5hmC pulldown sequencing data
ACBM001_pMPP


title: ACBM001_pHSC_5hmC

description:
5hmC pulldown sequencing data
ACBM001_pHSC