title: Sample S27: Psoriasis CD4 T cells treated with NR


title: Sample S21: Healthy CD4 T cells treated with NR

status: Public on Jul 18 2023

type: SRA

city: Bethesda

first: Komudi

last: Singh

address: Building 10

country: USA

institute: NIH

library_source: transcriptomic

data_processing:
QC performed usinf fastQC
Trmming applied using trimmomatic
Alignment performed using STAR
Gene expression quantification with featureCounts
Assembly: GrCh38
Supplementary files format and content: Gene Expression Counts matrix
Supplementary files format and content: Sample ID and treatment

molecule: total RNA

organism: Homo sapiens

source_name: Primary CD4 T cells

growth_protocol: Primary peripheral blood mononuclear cells (PBMCs) were isolated from human blood by density centrifugation using Lymphocyte Separation Medium (MP Biomedicals). CD4+ T cells were negatively selected from PBMCs using the CD4+ T Cell Isolation Kit (Miltenyi Biotec) and cultured in RPMI 1640 media supplemented with 25 mM HEPES, 10% heat-inactivated FBS, and Penicillin/Streptomycin.

extract_protocol:
Total RNA from CD4+ T cells was extracted with the miRNeasy Micro Kit (Qiagen) and RNA quality and integrity was assessed by Qubit 3.0 fluorometer (Thermo Fisher Scientific) and Agilent Bioanalyzer (Agilent Technologies).
Libraries were prepared using TruSeq stranded Total RNA HT kit (Illumina) and sequenced in a HISeq 3000 (Illumina) by the DNA Sequencing and Genomics Core at NHLBI.

treatment_protocol: CD4+ Cells were treated with NR (0.5 mM from ChromaDex) during TCR activation.

tag: tissue

value: Primary CD4 T cells

tag: cell type

value: CD4 T cells

tag: treatment

value: NR

tag: disease state

value: Healthy


title: Sample S23: Healthy CD4 T cells treated with vehicle

value: Vehicle


title: Sample S15: Healthy CD4 T cells treated with NR


title: 9A_M_2490

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

library_source: genomic

data_processing:
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted mm10 reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Assembly: mm10
Supplementary files format and content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column
Library strategy: snmC-seq2

molecule: genomic DNA

organism: Mus musculus

source_name: C57BL/6J Male P56 Mouse Brain

growth_protocol: All mice are C57BL/6J Male, brain dissected in P56

extract_protocol:
the brain of P56 male C57BL/6J mouse will be removed and cut into 600 microns thick coronal sections using a tissue matrix. Then each region will be microdissected from the coronal tissue sections based on identified landmarks and brain atlas coordinates, as defined in Allen brain atlas CCF3 (Avaliable at: http://atlas.brain-map.org). For each dissection region, the tissue from several littermate mice will be combined together into to separate replicate groups. The number of animals in a replicate depends on the size of the tissue. Nuclei preparation will be stained with the fluorescently labeled anti-NeuN body and nucleic acid stain Hoechst 33342.
Library prepared following protocol discribed in Luo, Chongyuan, Angeline Rivkin, Jingtian Zhou, Justin P. Sandoval, Laurie Kurihara, Jacinta Lucero, Rosa Castanon, et al. 2018. “Robust Single-Cell DNA Methylome Profiling with snmC-seq2.” Nature Communications 9 (1): 3824.

tag: brain region

tag: age

tag: strain


title: Sample S17: Healthy CD4 T cells treated with vehicle


title: Sample S18: Healthy CD4 T cells treated with NR


title: Sample S14: Healthy CD4 T cells treated with vehicle


title: Sample S12: Healthy CD4 T cells treated with NR


title: Sample S11: Healthy CD4 T treated with vehicle


title: Sample S2: Healthy CD4 T cells treated with vehicle


title: 9A_M_2488


title: 9A_M_2486


title: 9A_M_2485


title: 9A_M_2484


title: 9A_M_2483


title: 9A_M_2482


title: 9A_M_2480


title: 9A_M_2481


title: Sample S29: Psoriasis CD4 T cells treated with vehicle

value: Psoriasis


title: Sample S20: Healthy CD4 T cells treated with vehicle


title: 9A_M_2479


title: 9A_M_2487


title: 9A_M_2478


title: 9A_M_2477


title: Sample S24: Healthy CD4 T cells treated with NR


title: 9A_M_2491


title: 9A_M_2476


title: 9A_M_2459


title: 9A_M_2463


title: 9A_M_2472


title: 9A_M_2464


title: 9A_M_2473


title: 9A_M_2475


title: 9A_M_2469


title: 9A_M_2460


title: 9A_M_2467


title: 9A_M_2465


title: 9A_M_2456


title: 9A_M_2462


title: 9A_M_2468


title: 9A_M_2461


title: 9A_M_2466


title: 9A_M_2470


title: 9A_M_2458


title: 9A_M_2471


title: 9A_M_2489


title: 9A_M_2457


title: 9A_M_2455


title: 9A_M_2453


title: 9A_M_2451


title: 9A_M_2450


title: 9A_M_2474


title: 9A_M_2452


title: 9A_M_2454


title: 9A_M_2447


title: 9A_M_2449


title: 9A_M_2448


title: 9A_M_2444


title: 9A_M_2445


title: 9A_M_2436


title: 9A_M_2443


title: 9A_M_2440


title: 9A_M_2446


title: 9A_M_2432


title: 9A_M_2430


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title: 9A_M_2435


title: 9A_M_2427


title: 9A_M_2422


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title: 9A_M_2428


title: 9A_M_2418


title: 9A_M_2420


title: 9A_M_2415


title: 9A_M_2414


title: 9A_M_2419


title: 9A_M_2442


title: 9A_M_2441


title: 9A_M_2437


title: 9A_M_2413


title: 9A_M_2411


title: 9A_M_2421


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title: Memory CD4 T cell TCR panel

city: Glasgow

first: John

middle: Joseph

last: Cole

address: University Avenue

country: United Kingdom

institute: University of Glasgow

description: BD Rhapsody TCR CD3

library_source: transcriptomic single cell

data_processing:
Data were initially processed on SevenBridges using the BDAbSeq_allReferences and with supplemental probes added for custom genes
Supplementary files format and content: TRACE-TCR-full_SampleTag01_mm_Spleen1_DBEC_MolsPerCell.csv: reads per cell for cells from spleen 1
Supplementary files format and content: TRACE-TCR-full_SampleTag02_mm_Spleen2_DBEC_MolsPerCell.csv:  reads per cell for cells from spleen 2
Supplementary files format and content: TRACE-TCR-full_SampleTag03_mm_Spleen3_DBEC_MolsPerCell.csv:  reads per cell for cells from spleen 3
Supplementary files format and content: TRACE-TCR-full_SampleTag04_mm_Spleen4_DBEC_MolsPerCell.csv:  reads per cell for cells from spleen 4
Supplementary files format and content: TRACE-TCR-full_SampleTag05_mm_Lung1_DBEC_MolsPerCell.csv:  reads per cell for cells from lung 1
Supplementary files format and content: TRACE-TCR-full_SampleTag06_mm_Lung2_DBEC_MolsPerCell.csv: :  reads per cell for cells from lung 2
Supplementary files format and content: TRACE-TCR-full_SampleTag07_mm_Lung3_DBEC_MolsPerCell.csv: :  reads per cell for cells from lung 3
Supplementary files format and content: TRACE-TCR-full_SampleTag08_mm_Lung4_DBEC_MolsPerCell.csv: :  reads per cell for cells from lung 4
Supplementary files format and content: TRACE-TCR-full_Sample_Tag_Calls.csv: lists cell index number with sample tag and sample name
Supplementary files format and content: TRACE-TCR-full_VDJ_perCell.csv: lists TCR alpha and beta CDR3 sequences present in indexed cells
Supplementary files format and content: Supplemental information_MacLeod_Westerhof.xlsx: contains sample Tag sequences; information on custom genes added to BD mouse immune respoonse panel, and TCR primers used in library genration

source_name: spleen and lung

extract_protocol:
Spleens were processed into a single cell suspicion using a 40mm filter, resuspended in PBS-2%FCS, 2mM EDTA (MACS buffer) and the StemCell EasySep CD4 isolation kit (19852) used to isolate CD4+ cells by negative selection. Lungs were snipped and digested with Dispase II (3.2mg/ml), Collagenase P (0.4mg/ml) and DNase I (0.2mg/ml) for 25minutes in a shaking 37°C incubator. Digested tissue was processed into a single cell suspension by passing through a 40mm filter. Cells were resuspended in MACS buffer and CD4+ cells isolated with StemCell EasySep CD4 isolation kit. Isolated CD4 cells were stimulated for 4 hours with bone marrow dendritic cells incubated the night before with sonicated influenza A virus antigen. Cells were then stained with cell surface antibodies: anti-CD4 APC-Alexa647, anti-CD44-PerCP-Cy5.5, anti-MHCII-e450, anti-B220-e450, CD8-e450, F4/80-e450 and CD45 Sample Tags (BD Bioscience 1-8) to enable multiplexing and AbSeq antibodies to ICOS (AMM2072) and PD1 (AMM2138). Cells were FACS sorted on an ARIA IIU isolating IAV specific EYFP+ CD4+ CD44hi cells from the spleen (5000 cells/mouse) and lung (1000 cells/mouse) and naïve CD4+EYFPnegative CD44lo cells from the spleen (5000 cells/mouse). Cells were combined to generate one sample.
Sorted cells were combined and resuspended in BD Rhapsody sample buffer and loaded onto a scRNAseq BD Rhapsody cartridge using the BD Rhapsody reagent kit (633731) according to the manufacturer’s protocol. Libraries were prepared as per the Mouse VDJ, Sample Tag, and BD AbSeq library preparation protocol (23-22688-00). In brief, single cell cDNA was prepared using BD Rhapsody kit (633773) and template switching performed using the template switch oligo: 5' T TTT TTT TTT TTT TTT TTT TTT TTT rG rG rG 3 (IDT) followed by Klenow extension (NEB: M0212L), exonuclease treatment and then library generation with the BD Rhapsody Immune Response Targeted Panel (mouse) supplemented with an extra 10 genes. At the same time, libraries were prepared for the sample Tags, Abseq antibodies. PCR products were purified by double-sided size selection and index PCR performed for each library.

value: spleen and lung

tag: Sex

value: male

tag: genotype

value: TRACE transgenic

value: Influenza A virus infection


title: 9A_M_270


title: 9A_M_268


title: 9A_M_253


title: 9A_M_252


title: Memory CD4 T cells gene panel

description: BD Rhapsody targeted mouse panel


title: 9A_M_251


title: 9A_M_265


title: 9A_M_250


title: 9A_M_264


title: 9A_M_248


title: 9A_M_25


title: 9A_M_249


title: 9A_M_254


title: 9A_M_245


title: 9A_M_247


title: 9A_M_244


title: MSC_CM_ KIJ265T, biological rep 2

type: RNA

city: Warsaw

first: Agnieszka

last: Piekiełko-Witkowska

address: Marymoncka 99/103

department: Department of Biochemistry and Molecular Biology

country: Poland

institute: Centre of Postgraduate Medical Education

hyb_protocol: Samples were hybridized with Affymetrix™ HuGene 2.1 ST Array Strips (Affymetrix, Santa Clara, CA, USA)

scan_protocol: Arrays were scanned in Gene Atlas Imaging Station (Affymetrix)

data_processing: The data were analyzed with Transcriptome Analysis Console (TAC) v4.0.3 with default settings

label: biotin

source_name: MSC cells treated with conditioned media from RCC cell line KIJ265T

label_protocol: Total RNA was treated according to manufacturers protocol for GeneChip™ WT PLUS Reagent Kit (ThermoFisher Scientific, Waltham, MA, USA)

growth_protocol: MSCs were cultured in Dulbecco’s modified Eagle’s medium with low glucose (Biowest, Riverside, MO, USA) supplemented with 10% FBS (Biowest, Riverside, MO, USA), Glutamine-Penicillin-Streptomycin (Biowest, Riverside, MO, USA), and amphotericin B (Biowest, Riverside, MO, USA). Caki-1 cells were cultured in accordance with manufacturer’s protocol (ATCC). KIJ265T were cultured as previously described (Boguslawska J, Piekielko-Witkowska A, Wojcicka A, Kedzierska H, Poplawski P, Nauman A. Regulatory feedback loop between T3 and microRNAs in renal cancer. Mol Cell Endocrinol. 2014;384(1–2):61–70). For the collection of conditioned media (CM), 10^6 cells were seeded at 75cm2 flasks, cultured for 24h, rinsed once with PBS and four times with DMEM (low glucose, no glutamine, no phenol red) (Gibco/Thermo Fisher Scientific, Paisley, UK) with GLUTAMAX (Gibco/Thermo Fisher Scientific, Paisley, UK). Following the addition of 15ml of DMEM (no phenol red) supplemented with GLUTAMAX, the cells were cultured for another 24h. CM were collected, centrifuged, aliquoted, and stored at -80oC.

extract_protocol: RNA from cell lines was isolated using GeneMATRIX Universal RNA/miRNA Purification Kit (EURX, Gdansk, Poland) following manufacturer’s protocol.

treatment_protocol: For the CM treaments, 50,000 MSC cells were seeded on a well of 12-well plate, cultured for 24h, rinsed twice with DMEM (low glucose, no glutamine, no phenol red) (Gibco/Thermo Fisher Scientific, Paisley, UK) supplemented with GLUTAMAX (Gibco/Thermo Fisher Scientific, Paisley, UK), and cultured for 24h in medium without FBS. Next, the cells were rinsed once with PBS and four times with DMEM supplemented with GLUTAMAX and cultured for 24h in CM from RPTEC/TERT1, Caki-1 or KIJ265T cells.   MSCs were treated with CM collected from Caki-1 (n=3), KIJ265T (n=3), and RPTEC/TERT1 (n=3).

value: MSCs

value: CM from KIJ265T

tag: the origin of cell line used from cm collection and mscs treatment

value: clear cell renal cell cancer, stage IV tumor


title: MSC_CM_ RPTEC/TERT1, biological rep 2

source_name: MSC cells treated with conditioned media from RCC cell line RPTEC/TERT1

value: CM from RPTEC/TERT1

value: proximal tubules


title: MSC_CM_ KIJ265T, biological rep 3


title: MSC_CM_ RPTEC/TERT1, biological rep 3


title: 9A_M_243


title: MSC_CM_ Caki-1, biological rep 3

source_name: MSC cells treated with conditioned media from RCC cell line Caki-1

value: CM from Caki-1

value: clear cell renal cell cancer, skin metastasis


title: MSC_CM_ RPTEC/TERT1, biological rep 1


title: MSC_CM_ Caki-1, biological rep 1


title: 9A_M_241


title: MSC_CM_ Caki-1, biological rep 2


title: 9A_M_242


title: MSC_CM_ KIJ265T, biological rep 1


title: PrimeEd CD34 Mouse3

city: Milan

first: Stefano

last: Beretta

address: Via Olgettina, 60

country: Italy

institute: San Raffaele Telethon Institute for Gene Therapy

data_processing:
Data analyzed with the CRISPResso2 pipeline:
Reads were trimmed using the Trimmomatic
Trimmed sequences were mapped to the input amplicon reference (by providing the sequences for the pegRNA spacer, extension and scaffold, as well as for the additional nicking sgRNA and the reference amplicon) and the quantification window was set to 3
Computed alleles were quantified by measuring the number of reads and their relative abundance based on total read counts
Assembly: Custom reference vector AAV sequence and guides
Supplementary files format and content: CRISPResso_quantification_of_editing_frequency
Library strategy: amplicon sequencing

extract_protocol:
gDNA was isolated with QIAamp DNA Micro Kit (QIAGEN) according to the manufacturer’s instructions.
Custom library construction protocol. PCR amplicons for each individual sample were generated by nested PCR starting from >50-100 ng of purified gDNA.The first PCR step was performed using the following amplification protocol: 95°C x 10’, (95°C x 30’’, 59°C x 30’’, 72°C x 20’’) x 20 cycles, 72°C x 10’. The second PCR step was performed using the same reagents of the first step, 5 μl of the PCR product and the following amplification protocol: 95°C x 10’, (95°C x 30’’, 59°C x 30’’, 72°C x 20’’) x 20 cycles, 72°C x 10’. Primers used for the second PCR step contained P5/P7 sequences, i5/i7 Illumina tags to allow multiplexed sequencing and R1/R2 primer binding sites. The PCR amplicon from each sample was separately purified by QIAquick PCR Purification Kit (QIAGEN). Concentration and quality of amplicons were assessed by QuantiFluor ONE dsDNA system and 4200 Tapestation System (Agilent). Amplicons from up to 25 differently tagged samples were multiplexed at equimolar ratios.

value: Prime Editing

tag: time

value: 7 days


title: PrimeEd CD34 Mouse5


title: PrimeEd CD34 Mouse1


title: MockElectro CD34 Mouse0

value: Mock electro


title: PrimeEd CD34 Mouse2


title: PrimeEd CD34 Mouse4


title: PrimeEd BM HSC Mouse5

source_name: Bone Marrow

value: Bone Marrow

value: Hematopoietic Cells

value: 15 Weeks


title: PrimeEd CD34 Mouse0


title: PrimeEd BM HSC Mouse4


title: 9A_M_240


title: 9A_M_24


title: 9A_M_239


title: 9A_M_246


title: PrimeEd BM HSC Mouse3


title: 9A_M_238


title: 9A_M_237


title: PrimeEd BM HSC Mouse2


title: 9A_M_235


title: PrimeEd BM HSC Mouse1


title: 9A_M_236


title: PrimeEd PB 15Weeks Mouse5

source_name: Blood

value: Blood

value: PB Mononuclear Cells


title: PrimeEd PB 15Weeks Mouse4


title: PrimeEd PB 15Weeks Mouse2


title: PrimeEd PB 15Weeks Mouse3


title: 9A_M_232


title: 9A_M_233


title: 9A_M_231


title: PrimeEd PB 9Weeks Mouse5

value: 9 Weeks


title: PrimeEd PB 15Weeks Mouse0


title: 9A_M_327


title: PrimeEd PB 9Weeks Mouse2


title: 9A_M_228


title: PrimeEd PB 9Weeks Mouse3


title: 9A_M_229


title: 9A_M_230


title: PrimeEd PB 15Weeks Mouse1


title: PrimeEd PB 9Weeks Mouse4


title: 9A_M_225


title: 9A_M_23


title: 9A_M_227


title: 9A_M_224


title: PrimeEd BM HSC Mouse0


title: 9A_M_234


title: 9A_M_222


title: PrimeEd PB 9Weeks Mouse0


title: PrimeEd PB 9Weeks Mouse1


title: UT on CB CD34 edited at day 1 collected at day 7 - rep. 1

data_processing:
Data analyzed with the CRISPResso2 pipeline:
Reads were trimmed using the Trimmomatic
Trimmed sequences were mapped to the input amplicon reference, by providing also the targeted and the edited nucleotide
Computed alleles were quantified by measuring the number of reads and their relative abundance based on total read counts
Output alleles were post-processed by correcting all the mismatch positions outside the quantification window and re-quantifying the total read counts and, consequently, the corresponding relative abundances
Assembly: Custom reference vector AAV sequence and guides
Supplementary files format and content: Tab-separated results of the different allele found with corresponding quantifications
Library strategy: amplicon sequencing

source_name: Cord Blood

extract_protocol:
gDNA was isolated with QIAamp DNA Micro Kit (QIAGEN) according to the manufacturer’s instructions.
Custom library construction protocol. PCR amplicons for each individual sample were generated by nested PCR starting from >50-100 ng of purified gDNA. The first PCR step was performed with GoTaq G2 DNA Polymerase (Promega) according to manufacturer instruction using the following amplification protocol: 95°C x 10’, (95°C x 30’’, 63°C x 30’’, 72°C x 30’’) x 20 cycles, 72°C x 10’. The second PCR step was performed using the same reagents of the first step, 5 μl of the PCR product and the following amplification protocol: 95°C x 10’, (95°C x 30’’, 63°C x 30’’, 72°C x 30’’) x 20 cycles, 72°C x 10’. Primers used for the second PCR step contained P5/P7 sequences, i5/i7 Illumina tags to allow multiplexed sequencing and R1/R2 primer binding sites. The PCR amplicon from each sample was separately purified by QIAquick PCR Purification Kit (QIAGEN). Concentration and quality of amplicons were assessed by QuantiFluor ONE dsDNA system and 4200 Tapestation System (Agilent). Amplicons from up to 49 differently tagged samples were multiplexed at equimolar ratios.

value: Cord Blood

value: CB CD34

value: UT

tag: editing time

value: day 1

tag: time of collection

value: day 7


title: ABE8.20-m on CB CD34 edited at day 1 collected at day 7 - rep. 7

value: day 3


title: ABE8.20-m on CB CD34 edited at day 1 collected at day 7 - rep. 1


title: Cas9 on CB CD34 edited at day 1 collected at day 7 - rep. 1


title: 9A_M_220


title: 9A_M_22


title: BE4max on CB CD34 edited at day 1 collected at day 7 - rep. 1


title: 9A_M_226


title: ABE8.20-m on CB CD34 edited at day 1 collected at day 7 - rep. 6


title: 9A_M_216


title: BE4max on mPB CD34 edited at day 1 collected at day 7 - rep. 4

source_name: Mobilized Peripheral Blood

value: Mobilized Peripheral Blood

value: mPB CD34


title: 9A_M_218


title: 9A_M_217


title: 9A_M_219


title: Cas9 on mPB CD34 edited at day 1 collected at day 7 - rep. 4


title: ABE8.20-m on mPB CD34 edited at day 1 collected at day 7 - rep. 4


title: 9A_M_215


title: 9A_M_223


title: Mock electro on mPB CD34 edited at day 1 collected at day 7 - rep. 1


title: ABE8.20-m on mPB CD34 edited at day 1 collected at day 7 - rep. 2


title: 9A_M_214


title: UT on CB CD34 edited at day 3 collected at day 7 - rep. 1


title: 9A_M_213


title: Cas9 on mPB CD34 edited at day 1 collected at day 7 - rep. 2


title: 9A_M_221


title: 9A_M_210


title: 9A_M_212


title: Cas9 on CB CD34 edited at day 1 collected at day 7 - rep. 10


title: 9A_M_21


title: Cas9 on CB CD34 edited at day 1 collected at day 7 - rep. 8


title: ABE8.20-m on CB CD34 edited at day 1 collected at day 7 - rep. 12


title: 9A_M_207


title: ABE8.20-m on CB CD34 edited at day 1 collected at day 7 - rep. 10


title: ABE8.20-m on CB CD34 edited at day 1 collected at day 7 - rep. 11


title: BE4max on CB CD34 edited at day 1 collected at day 7 - rep. 12


title: 9A_M_206


title: 9A_M_202


title: 9A_M_203


title: 9A_M_211


title: 9A_M_208


title: Mock electro on mPB CD34 edited at day 1 collected at day 7 - rep. 3


title: 9A_M_201


title: Cas9 on CB CD34 edited at day 1 collected at day 7 - rep. 3


title: 9A_M_20


title: 9A_M_199


title: Cas9 on CB CD34 edited at day 1 collected at day 7 - rep. 5


title: 9A_M_200


title: ABE8.20-m on CB CD34 edited at day 1 collected at day 7 - rep. 4


title: ABE8.20-m on CB CD34 edited at day 1 collected at day 7 - rep. 5


title: 9A_M_198


title: Cas9 on CB CD34 edited at day 1 collected at day 7 - rep. 9


title: 9A_M_204


title: 9A_M_209


title: 9A_M_197


title: BE4max on CB CD34 edited at day 1 collected at day 7 - rep. 5


title: ABE8.20-m on CB CD34 edited at day 1 collected at day 7 - rep. 3


title: BE4max on CB CD34 edited at day 1 collected at day 7 - rep. 10


title: 9A_M_196


title: 9A_M_195


title: UT on CB CD34 edited at day 1 collected at day 7 - rep. 2


title: 9A_M_194


title: BE4max on CB CD34 edited at day 1 collected at day 7 - rep. 3


title: BE4max on CB CD34 edited at day 1 collected at day 7 - rep. 11


title: 9A_M_193


title: Mock electro on CB CD34 edited at day 1 collected at day 7 - rep. 3


title: Cas9 on CB CD34 edited at day 1 collected at day 7 - rep. 11


title: 9A_M_192


title: 9A_M_2


title: 9A_M_190


title: 9A_M_191


title: ABE8.20-m on CB CD34 edited at day 1 collected at day 7 - rep. 13


title: BE4max on CB CD34 edited at day 1 collected at day 7 - rep. 13


title: Mock electro on mPB CD34 edited at day 1 collected at day 7 - rep. 2


title: 9A_M_189


title: 9A_M_19


title: BE4max on CB CD34 edited at day 1 collected at day 7 - rep. 4


title: BE4max on mPB CD34 edited at day 1 collected at day 7 - rep. 3


title: 9A_M_188


title: 9A_M_186


title: BE4max on mPB CD34 edited at day 3 collected at day 7 - rep. 1


title: ABE8.20-m on mPB CD34 edited at day 3 collected at day 7 - rep. 1


title: Cas9 on mPB CD34 edited at day 3 collected at day 7 - rep. 1


title: Cas9 on mPB CD34 edited at day 1 collected at day 7 - rep. 1


title: 9A_M_184


title: BE4max on mPB CD34 edited at day 1 collected at day 7 - rep. 1


title: 9A_M_185


title: Mock electro on Hematopoietic Cells edited at day 3 collected at 15 weeks - rep. 5

value: 15 weeks


title: Mock electro on Hematopoietic Cells edited at day 3 collected at 15 weeks - rep. 4


title: 9A_M_181


title: ABE8.20-m on mPB CD34 edited at day 1 collected at day 7 - rep. 1


title: 9A_M_182


title: Mock electro on Hematopoietic Cells edited at day 3 collected at 15 weeks - rep. 3


title: 9A_M_180


title: Mock electro on Hematopoietic Cells edited at day 3 collected at 15 weeks - rep. 2


title: 9A_M_18


title: Mock electro on Hematopoietic Cells edited at day 3 collected at 15 weeks - rep. 1


title: 9A_M_179


title: 9A_M_178


title: Cas9 on Hematopoietic Cells edited at day 1 collected at 15 weeks - rep. 10


title: 9A_M_177


title: 9A_M_174


title: Cas9 on Hematopoietic Cells edited at day 1 collected at 15 weeks - rep. 8


title: Cas9 on Hematopoietic Cells edited at day 1 collected at 15 weeks - rep. 7


title: Cas9 on Hematopoietic Cells edited at day 1 collected at 15 weeks - rep. 6


title: ABE8.20-m on Hematopoietic Cells edited at day 1 collected at 15 weeks - rep. 9


title: 9A_M_176


title: 9A_M_173


title: 9A_M_172


title: 9A_M_171


title: BE4max on Hematopoietic Cells edited at day 1 collected at 15 weeks - rep. 9


title: ABE8.20-m on Hematopoietic Cells edited at day 1 collected at 15 weeks - rep. 6


title: 9A_M_170


title: 9A_M_169


title: ABE8.20-m on Hematopoietic Cells edited at day 1 collected at 15 weeks - rep. 5


title: 9A_M_17


title: Cas9 on Hematopoietic Cells edited at day 1 collected at 15 weeks - rep. 9


title: BE4max on Hematopoietic Cells edited at day 1 collected at 15 weeks - rep. 7


title: BE4max on Hematopoietic Cells edited at day 1 collected at 15 weeks - rep. 8


title: BE4max on Hematopoietic Cells edited at day 1 collected at 15 weeks - rep. 6


title: 9A_M_168


title: Mock electro on Hematopoietic Cells edited at day 1 collected at 15 weeks - rep. 4


title: 9A_M_166


title: 9A_M_167


title: 9A_M_175


title: 9A_M_165


title: ABE8.20-m on Hematopoietic Cells edited at day 1 collected at 15 weeks - rep. 8


title: ABE8.20-m on Hematopoietic Cells edited at day 1 collected at 15 weeks - rep. 7


title: Mock electro on Hematopoietic Cells edited at day 1 collected at 15 weeks - rep. 1


title: 9A_M_164


title: 9A_M_163


title: Mock electro on Hematopoietic Cells edited at day 1 collected at 15 weeks - rep. 2


title: 9A_M_162


title: Cas9 on Hematopoietic Cells edited at day 1 collected at 15 weeks - rep. 5


title: 9A_M_161


title: Mock electro on Hematopoietic Cells edited at day 1 collected at 15 weeks - rep. 3


title: 9A_M_160


title: 9A_M_159


title: Cas9 on Hematopoietic Cells edited at day 1 collected at 15 weeks - rep. 1


title: Cas9 on Hematopoietic Cells edited at day 1 collected at 15 weeks - rep. 3


title: 9A_M_16


title: Cas9 on Hematopoietic Cells edited at day 1 collected at 15 weeks - rep. 2


title: 9A_M_155


title: 9A_M_157


title: ABE8.20-m on Hematopoietic Cells edited at day 1 collected at 15 weeks - rep. 4


title: 9A_M_154


title: ABE8.20-m on Hematopoietic Cells edited at day 1 collected at 15 weeks - rep. 3


title: ABE8.20-m on Hematopoietic Cells edited at day 1 collected at 15 weeks - rep. 2


title: ABE8.20-m on Hematopoietic Cells edited at day 1 collected at 15 weeks - rep. 1


title: BE4max on Hematopoietic Cells edited at day 1 collected at 15 weeks - rep. 5


title: 9A_M_158


title: 9A_M_153


title: BE4max on Hematopoietic Cells edited at day 1 collected at 15 weeks - rep. 4


title: 9A_M_152


title: Cas9 on Hematopoietic Cells edited at day 1 collected at 15 weeks - rep. 4


title: 9A_M_1506


title: BE4max on Hematopoietic Cells edited at day 1 collected at 15 weeks - rep. 1


title: BE4max on Hematopoietic Cells edited at day 1 collected at 15 weeks - rep. 3


title: 9A_M_1505


title: BE4max on Hematopoietic Cells edited at day 1 collected at 15 weeks - rep. 2


title: 9A_M_151


title: Mock electro on CB CD34 edited at day 1 collected at day 7 - rep. 2


title: 9A_M_1504


title: 9A_M_1503


title: 9A_M_1502


title: BE4max on CB CD34 edited at day 1 collected at day 7 - rep. 9


title: 9A_M_156


title: Cas9 on CB CD34 edited at day 1 collected at day 7 - rep. 7


title: 9A_M_1500


title: 9A_M_150


title: 9A_M_15


title: ABE8.20-m on CB CD34 edited at day 1 collected at day 7 - rep. 2


title: BE4max on CB CD34 edited at day 1 collected at day 7 - rep. 2


title: Cas9 on CB CD34 edited at day 1 collected at day 7 - rep. 2


title: Mock electro on PB Mononuclear Cells edited at day 3 collected at 6 weeks - rep. 5

value: 6 weeks


title: Mock electro on CB CD34 edited at day 1 collected at day 7 - rep. 1

value: Mock electro


title: 9A_M_1499


title: Mock electro on PB Mononuclear Cells edited at day 3 collected at 6 weeks - rep. 4


title: 9A_M_1497


title: ABE8.20-m on CB CD34 edited at day 1 collected at day 7 - rep. 9


title: Mock electro on PB Mononuclear Cells edited at day 3 collected at 6 weeks - rep. 3


title: Mock electro on PB Mononuclear Cells edited at day 3 collected at 6 weeks - rep. 2


title: 9A_M_1498


title: Cas9 on PB Mononuclear Cells edited at day 3 collected at 6 weeks - rep. 5


title: 9A_M_1496


title: Cas9 on PB Mononuclear Cells edited at day 3 collected at 6 weeks - rep. 4


title: 9A_M_1501


title: 9A_M_187


title: Mock electro on PB Mononuclear Cells edited at day 3 collected at 6 weeks - rep. 1


title: 9A_M_1495


title: 9A_M_1494


title: 9A_M_1492


title: 9A_M_1491


title: Cas9 on CB CD34 edited at day 1 collected at day 7 - rep. 4


title: 9A_M_1490


title: Cas9 on PB Mononuclear Cells edited at day 3 collected at 6 weeks - rep. 2


title: 9A_M_149


title: 9A_M_1488


title: 9A_M_1489


title: ABE8.20-m on PB Mononuclear Cells edited at day 3 collected at 6 weeks - rep. 6


title: Cas9 on PB Mononuclear Cells edited at day 3 collected at 6 weeks - rep. 1


title: ABE8.20-m on PB Mononuclear Cells edited at day 3 collected at 6 weeks - rep. 4


title: ABE8.20-m on PB Mononuclear Cells edited at day 3 collected at 6 weeks - rep. 5


title: 9A_M_1487


title: 9A_M_1485


title: 9A_M_1486


title: BE4max on PB Mononuclear Cells edited at day 3 collected at 6 weeks - rep. 4


title: BE4max on PB Mononuclear Cells edited at day 3 collected at 6 weeks - rep. 3


title: ABE8.20-m on PB Mononuclear Cells edited at day 3 collected at 6 weeks - rep. 1


title: 9A_M_1493


title: BE4max on PB Mononuclear Cells edited at day 3 collected at 6 weeks - rep. 2


title: ABE8.20-m on PB Mononuclear Cells edited at day 3 collected at 6 weeks - rep. 3


title: 9A_M_1483


title: BE4max on PB Mononuclear Cells edited at day 3 collected at 6 weeks - rep. 1


title: Cas9 on PB Mononuclear Cells edited at day 3 collected at 6 weeks - rep. 3


title: Mock electro on PB Mononuclear Cells edited at day 1 collected at 6 weeks - rep. 5


title: 9A_M_1482


title: 9A_M_1481


title: 9A_M_148


title: Mock electro on PB Mononuclear Cells edited at day 1 collected at 6 weeks - rep. 3


title: 9A_M_1484


title: Mock electro on PB Mononuclear Cells edited at day 1 collected at 6 weeks - rep. 4


title: 9A_M_1479


title: 9A_M_1478


title: 9A_M_1477


title: Mock electro on PB Mononuclear Cells edited at day 1 collected at 6 weeks - rep. 1


title: 9A_M_1476


title: Cas9 on PB Mononuclear Cells edited at day 1 collected at 6 weeks - rep. 4


title: Cas9 on PB Mononuclear Cells edited at day 1 collected at 6 weeks - rep. 5


title: Cas9 on PB Mononuclear Cells edited at day 1 collected at 6 weeks - rep. 3


title: 9A_M_1475


title: 9A_M_1480


title: 9A_M_1474


title: Cas9 on PB Mononuclear Cells edited at day 1 collected at 6 weeks - rep. 2


title: 9A_M_1470


title: 9A_M_1471


title: ABE8.20-m on PB Mononuclear Cells edited at day 1 collected at 6 weeks - rep. 4


title: ABE8.20-m on PB Mononuclear Cells edited at day 1 collected at 6 weeks - rep. 5


title: Cas9 on PB Mononuclear Cells edited at day 1 collected at 6 weeks - rep. 1


title: Mock electro on PB Mononuclear Cells edited at day 1 collected at 6 weeks - rep. 2


title: 9A_M_1472


title: ABE8.20-m on PB Mononuclear Cells edited at day 1 collected at 6 weeks - rep. 1


title: 9A_M_1469


title: 9A_M_1467


title: 9A_M_147


title: ABE8.20-m on PB Mononuclear Cells edited at day 1 collected at 6 weeks - rep. 2


title: 9A_M_1468


title: 9A_M_1466


title: ABE8.20-m on PB Mononuclear Cells edited at day 1 collected at 6 weeks - rep. 3


title: BE4max on PB Mononuclear Cells edited at day 1 collected at 6 weeks - rep. 3


title: BE4max on PB Mononuclear Cells edited at day 1 collected at 6 weeks - rep. 2


title: 9A_M_1465


title: BE4max on PB Mononuclear Cells edited at day 1 collected at 6 weeks - rep. 5


title: 9A_M_183


title: 9A_M_1473


title: 9A_M_1464


title: 9A_M_1463


title: 9A_M_1462


title: BE4max on PB Mononuclear Cells edited at day 1 collected at 6 weeks - rep. 1


title: BE4max on CB CD34 edited at day 1 collected at day 7 - rep. 6


title: BE4max on CB CD34 edited at day 1 collected at day 7 - rep. 7


title: 9A_M_1460


title: BE4max on PB Mononuclear Cells edited at day 1 collected at 6 weeks - rep. 4


title: 9A_M_1461


title: 9A_M_146


title: 9A_M_1459


title: BE4max on mPB CD34 edited at day 1 collected at day 7 - rep. 2


title: ABE8.20-m on mPB CD34 edited at day 1 collected at day 7 - rep. 3


title: Cas9 on mPB CD34 edited at day 1 collected at day 7 - rep. 3


title: Mock electro on PB Mononuclear Cells edited at day 3 collected at 15 weeks - rep. 5


title: 9A_M_1457


title: 9A_M_1456


title: 9A_M_1454


title: 9A_M_1455


title: 9A_M_1453


title: 9A_M_1452


title: 9A_M_1451


title: Mock electro on PB Mononuclear Cells edited at day 3 collected at 15 weeks - rep. 3


title: Mock electro on PB Mononuclear Cells edited at day 3 collected at 15 weeks - rep. 1


title: Mock electro on PB Mononuclear Cells edited at day 3 collected at 15 weeks - rep. 2


title: Cas9 on PB Mononuclear Cells edited at day 3 collected at 15 weeks - rep. 3


title: 9A_M_1450


title: 9A_M_145


title: 9A_M_1449


title: Cas9 on PB Mononuclear Cells edited at day 3 collected at 15 weeks - rep. 1


title: Cas9 on PB Mononuclear Cells edited at day 3 collected at 15 weeks - rep. 2


title: Mock electro on PB Mononuclear Cells edited at day 3 collected at 15 weeks - rep. 4


title: 9A_M_1447


title: 9A_M_1448


title: ABE8.20-m on PB Mononuclear Cells edited at day 3 collected at 15 weeks - rep. 5


title: 9A_M_1446


title: 9A_M_1444


title: Cas9 on PB Mononuclear Cells edited at day 3 collected at 15 weeks - rep. 5


title: ABE8.20-m on PB Mononuclear Cells edited at day 3 collected at 15 weeks - rep. 4


title: ABE8.20-m on PB Mononuclear Cells edited at day 3 collected at 15 weeks - rep. 3


title: 9A_M_1443


title: Cas9 on PB Mononuclear Cells edited at day 3 collected at 15 weeks - rep. 4


title: 9A_M_1445


title: BE4max on PB Mononuclear Cells edited at day 3 collected at 15 weeks - rep. 4


title: BE4max on PB Mononuclear Cells edited at day 3 collected at 15 weeks - rep. 2


title: ABE8.20-m on PB Mononuclear Cells edited at day 3 collected at 15 weeks - rep. 2


title: 9A_M_144


title: 9A_M_1442


title: BE4max on PB Mononuclear Cells edited at day 3 collected at 15 weeks - rep. 1


title: BE4max on PB Mononuclear Cells edited at day 3 collected at 15 weeks - rep. 3


title: ABE8.20-m on PB Mononuclear Cells edited at day 3 collected at 15 weeks - rep. 1


title: 9A_M_1440


title: 9A_M_1438


title: 9A_M_1437


title: Mock electro on PB Mononuclear Cells edited at day 1 collected at 15 weeks - rep. 2


title: Mock electro on PB Mononuclear Cells edited at day 1 collected at 15 weeks - rep. 4


title: Mock electro on PB Mononuclear Cells edited at day 1 collected at 15 weeks - rep. 1


title: 9A_M_1435


title: 9A_M_1436


title: 9A_M_1434


title: Cas9 on PB Mononuclear Cells edited at day 1 collected at 15 weeks - rep. 4


title: 9A_M_1433


title: Cas9 on PB Mononuclear Cells edited at day 1 collected at 15 weeks - rep. 3


title: 9A_M_1432


title: Cas9 on PB Mononuclear Cells edited at day 1 collected at 15 weeks - rep. 2


title: ABE8.20-m on PB Mononuclear Cells edited at day 1 collected at 15 weeks - rep. 4


title: 9A_M_1430


title: Cas9 on PB Mononuclear Cells edited at day 1 collected at 15 weeks - rep. 1


title: 9A_M_1431


title: ABE8.20-m on PB Mononuclear Cells edited at day 1 collected at 15 weeks - rep. 3


title: Mock electro on PB Mononuclear Cells edited at day 1 collected at 15 weeks - rep. 3


title: ABE8.20-m on PB Mononuclear Cells edited at day 1 collected at 15 weeks - rep. 1


title: ABE8.20-m on PB Mononuclear Cells edited at day 1 collected at 15 weeks - rep. 2


title: BE4max on PB Mononuclear Cells edited at day 1 collected at 15 weeks - rep. 5


title: 9A_M_143


title: 9A_M_1439


title: BE4max on PB Mononuclear Cells edited at day 1 collected at 15 weeks - rep. 4


title: 9A_M_1427


title: 9A_M_1426


title: 9A_M_1428


title: BE4max on PB Mononuclear Cells edited at day 1 collected at 15 weeks - rep. 3


title: Cas9 on PB Mononuclear Cells edited at day 1 collected at 15 weeks - rep. 5


title: 9A_M_1424


title: BE4max on PB Mononuclear Cells edited at day 1 collected at 15 weeks - rep. 2


title: 9A_M_1429


title: 9A_M_1422


title: 9A_M_1423


title: ABE8.20-m on CB CD34 edited at day 1 collected at day 7 - rep. 8


title: Cas9 on CB CD34 edited at day 1 collected at day 7 - rep. 6


title: BE4max on CB CD34 edited at day 1 collected at day 7 - rep. 8


title: 9A_M_1420


title: 9A_M_1418


title: Cas9 on Hematopoietic Cells edited at day 1 collected at 15 weeks - rep. 16

value: Bone Marrow


title: Mock electro on Hematopoietic Cells edited at day 3 collected at 15 weeks - rep. 9

value: Hematopoietic Cells


title: Mock electro on Hematopoietic Cells edited at day 3 collected at 15 weeks - rep. 11


title: Mock electro on Hematopoietic Cells edited at day 3 collected at 15 weeks - rep. 10


title: 9A_M_142


title: ABE8.20-m on Hematopoietic Cells edited at day 1 collected at 15 weeks - rep. 15


title: Mock electro on Hematopoietic Cells edited at day 3 collected at 15 weeks - rep. 7


title: 9A_M_1417


title: 9A_M_1412


title: 9A_M_1414


title: 9A_M_1415


title: 9A_M_1416


title: Mock electro on Hematopoietic Cells edited at day 3 collected at 15 weeks - rep. 6


title: 9A_M_1425


title: 9A_M_1411


title: Cas9 on Hematopoietic Cells edited at day 1 collected at 15 weeks - rep. 15


title: BE4max on Hematopoietic Cells edited at day 1 collected at 15 weeks - rep. 15


title: BE4max on PB Mononuclear Cells edited at day 1 collected at 15 weeks - rep. 1


title: 9A_M_1413


title: 9A_M_1421


title: 9A_M_1419


title: Cas9 on Hematopoietic Cells edited at day 1 collected at 15 weeks - rep. 14


title: Cas9 on Hematopoietic Cells edited at day 1 collected at 15 weeks - rep. 13


title: Cas9 on Hematopoietic Cells edited at day 1 collected at 15 weeks - rep. 12


title: Cas9 on Hematopoietic Cells edited at day 1 collected at 15 weeks - rep. 11


title: Mock electro on Hematopoietic Cells edited at day 3 collected at 15 weeks - rep. 8


title: 9A_M_1410


title: 9A_M_1409


title: 9A_M_141


title: 9A_M_1408


title: 9A_M_1407


title: ABE8.20-m on Hematopoietic Cells edited at day 1 collected at 15 weeks - rep. 14


title: ABE8.20-m on Hematopoietic Cells edited at day 1 collected at 15 weeks - rep. 13


title: 9A_M_1406


title: ABE8.20-m on Hematopoietic Cells edited at day 1 collected at 15 weeks - rep. 12


title: ABE8.20-m on Hematopoietic Cells edited at day 1 collected at 15 weeks - rep. 10


title: ABE8.20-m on Hematopoietic Cells edited at day 1 collected at 15 weeks - rep. 11


title: 9A_M_1401


title: 9A_M_1400


title: 9A_M_1403


title: 9A_M_1402


title: BE4max on Hematopoietic Cells edited at day 1 collected at 15 weeks - rep. 13


title: BE4max on Hematopoietic Cells edited at day 1 collected at 15 weeks - rep. 11


title: BE4max on Hematopoietic Cells edited at day 1 collected at 15 weeks - rep. 12


title: 9A_M_140


title: 9A_M_14


title: BE4max on Hematopoietic Cells edited at day 1 collected at 15 weeks - rep. 10


title: Mock electro on PB Mononuclear Cells edited at day 3 collected at 15 weeks - rep. 8


title: Cas9 on PB Mononuclear Cells edited at day 3 collected at 15 weeks - rep. 13


title: 9A_M_1398


title: 9A_M_1399


title: ABE8.20-m on PB Mononuclear Cells edited at day 3 collected at 15 weeks - rep. 11


title: 9A_M_1397


title: 9A_M_1405


title: 9A_M_1404


title: 9A_M_1396


title: 9A_M_1395


title: 9A_M_1394


title: BE4max on Hematopoietic Cells edited at day 1 collected at 15 weeks - rep. 14


title: 9A_M_1393


title: BE4max on PB Mononuclear Cells edited at day 3 collected at 15 weeks - rep. 10


title: Cas9 on PB Mononuclear Cells edited at day 3 collected at 15 weeks - rep. 11


title: Cas9 on PB Mononuclear Cells edited at day 3 collected at 15 weeks - rep. 12


title: ABE8.20-m on PB Mononuclear Cells edited at day 3 collected at 6 weeks - rep. 2


title: Mock electro on PB Mononuclear Cells edited at day 3 collected at 6 weeks - rep. 11


title: 9A_M_1391


title: 9A_M_1389


title: ABE8.20-m on PB Mononuclear Cells edited at day 3 collected at 6 weeks - rep. 12


title: 9A_M_1390


title: 9A_M_1392


title: 9A_M_1388


title: 9A_M_139


title: 9A_M_1387


title: Mock electro on PB Mononuclear Cells edited at day 3 collected at 6 weeks - rep. 10


title: Mock electro on PB Mononuclear Cells edited at day 3 collected at 6 weeks - rep. 9


title: Mock electro on PB Mononuclear Cells edited at day 3 collected at 6 weeks - rep. 8


title: Mock electro on PB Mononuclear Cells edited at day 3 collected at 6 weeks - rep. 7


title: 9A_M_1385


title: 9A_M_1383


title: 9A_M_1384


title: Cas9 on PB Mononuclear Cells edited at day 3 collected at 6 weeks - rep. 11


title: 9A_M_1382


title: 9A_M_1380


title: 9A_M_138


title: BE4max on PB Mononuclear Cells edited at day 3 collected at 6 weeks - rep. 10


title: Cas9 on PB Mononuclear Cells edited at day 3 collected at 6 weeks - rep. 9


title: Cas9 on PB Mononuclear Cells edited at day 3 collected at 6 weeks - rep. 10


title: Cas9 on PB Mononuclear Cells edited at day 3 collected at 15 weeks - rep. 10


title: Cas9 on PB Mononuclear Cells edited at day 3 collected at 6 weeks - rep. 8


title: Mock electro on PB Mononuclear Cells edited at day 3 collected at 15 weeks - rep. 7


title: Cas9 on PB Mononuclear Cells edited at day 3 collected at 6 weeks - rep. 7


title: Mock electro on PB Mononuclear Cells edited at day 3 collected at 15 weeks - rep. 6


title: 9A_M_1375


title: Cas9 on PB Mononuclear Cells edited at day 3 collected at 15 weeks - rep. 8


title: 9A_M_1376


title: 9A_M_1378


title: Cas9 on PB Mononuclear Cells edited at day 3 collected at 15 weeks - rep. 9


title: 9A_M_1379


title: 9A_M_1386


title: 9A_M_1373


title: 9A_M_1374


title: Cas9 on PB Mononuclear Cells edited at day 3 collected at 15 weeks - rep. 7


title: Cas9 on PB Mononuclear Cells edited at day 3 collected at 15 weeks - rep. 6


title: Mock electro on PB Mononuclear Cells edited at day 3 collected at 6 weeks - rep. 6


title: 9A_M_1371


title: 9A_M_1372


title: ABE8.20-m on PB Mononuclear Cells edited at day 3 collected at 15 weeks - rep. 10


title: ABE8.20-m on PB Mononuclear Cells edited at day 3 collected at 15 weeks - rep. 9


title: Cas9 on PB Mononuclear Cells edited at day 3 collected at 6 weeks - rep. 6


title: ABE8.20-m on PB Mononuclear Cells edited at day 3 collected at 15 weeks - rep. 8


title: 9A_M_1377


title: 9A_M_1370


title: 9A_M_137


title: ABE8.20-m on PB Mononuclear Cells edited at day 3 collected at 15 weeks - rep. 7


title: ABE8.20-m on PB Mononuclear Cells edited at day 3 collected at 15 weeks - rep. 6


title: 9A_M_1369


title: 9A_M_1367


title: 9A_M_1366


title: BE4max on PB Mononuclear Cells edited at day 3 collected at 15 weeks - rep. 7


title: 9A_M_1368


title: BE4max on PB Mononuclear Cells edited at day 3 collected at 15 weeks - rep. 5


title: 9A_M_1365


title: BE4max on PB Mononuclear Cells edited at day 3 collected at 15 weeks - rep. 6


title: 9A_M_1364


title: BE4max on PB Mononuclear Cells edited at day 3 collected at 15 weeks - rep. 8


title: Cas9 on mPB CD34 edited at day 3 collected at day 7 - rep. 19


title: BE4max on PB Mononuclear Cells edited at day 3 collected at 15 weeks - rep. 9


title: Cas9 on mPB CD34 edited at day 3 collected at day 7 - rep. 21


title: Cas9 on mPB CD34 edited at day 3 collected at day 7 - rep. 20


title: 9A_M_1361


title: Cas9 on mPB CD34 edited at day 3 collected at day 7 - rep. 18


title: 9A_M_1360


title: ABE8.20-m on mPB CD34 edited at day 3 collected at day 7 - rep. 21


title: ABE8.20-m on mPB CD34 edited at day 3 collected at day 7 - rep. 20


title: 9A_M_1359


title: 9A_M_136


title: 9A_M_1358


title: ABE8.20-m on mPB CD34 edited at day 3 collected at day 7 - rep. 19


title: 9A_M_1357


title: BE4max on mPB CD34 edited at day 3 collected at day 7 - rep. 20


title: BE4max on mPB CD34 edited at day 3 collected at day 7 - rep. 21


title: ABE8.20-m on mPB CD34 edited at day 3 collected at day 7 - rep. 18


title: 9A_M_1356


title: 9A_M_1362


title: 9A_M_1355


title: 9A_M_1363


title: BE4max on mPB CD34 edited at day 3 collected at day 7 - rep. 19


title: 9A_M_1353


title: Cas9 on mPB CD34 edited at day 1 collected at day 7 - rep. 19


title: 9A_M_1352


title: 9A_M_1351


title: 9A_M_1350


title: Mock electro on mPB CD34 edited at day 1 collected at day 7 - rep. 8


title: BE4max on mPB CD34 edited at day 3 collected at day 7 - rep. 18


title: Cas9 on mPB CD34 edited at day 1 collected at day 7 - rep. 18


title: Cas9 on mPB CD34 edited at day 3 collected at day 7 - rep. 5


title: ABE8.20-m on mPB CD34 edited at day 3 collected at day 7 - rep. 5


title: 9A_M_1349


title: 9A_M_1348


title: ABE8.20-m on PB Mononuclear Cells edited at day 3 collected at 6 weeks - rep. 10


title: ABE8.20-m on PB Mononuclear Cells edited at day 3 collected at 6 weeks - rep. 9


title: 9A_M_1344


title: 9A_M_1346


title: ABE8.20-m on PB Mononuclear Cells edited at day 3 collected at 6 weeks - rep. 8


title: 9A_M_1343


title: ABE8.20-m on PB Mononuclear Cells edited at day 3 collected at 6 weeks - rep. 7


title: 9A_M_1354


title: 9A_M_1342


title: ABE8.20-m on PB Mononuclear Cells edited at day 3 collected at 6 weeks - rep. 11


title: 9A_M_1340


title: 9A_M_1341


title: 9A_M_135


title: BE4max on PB Mononuclear Cells edited at day 3 collected at 6 weeks - rep. 8


title: BE4max on PB Mononuclear Cells edited at day 3 collected at 6 weeks - rep. 7


title: 9A_M_1339


title: BE4max on PB Mononuclear Cells edited at day 3 collected at 6 weeks - rep. 6


title: 9A_M_1337


title: BE4max on PB Mononuclear Cells edited at day 3 collected at 6 weeks - rep. 5


title: 9A_M_134


title: 9A_M_1345


title: 9A_M_1335


title: ABE8.20-m on mPB CD34 edited at day 1 collected at day 7 - rep. 19


title: 9A_M_1338


title: BE4max on mPB CD34 edited at day 3 collected at day 7 - rep. 5


title: 9A_M_1336


title: ABE8.20-m on mPB CD34 edited at day 1 collected at day 7 - rep. 17


title: ABE8.20-m on mPB CD34 edited at day 1 collected at day 7 - rep. 18


title: BE4max on mPB CD34 edited at day 1 collected at day 7 - rep. 19


title: BE4max on PB Mononuclear Cells edited at day 3 collected at 6 weeks - rep. 9


title: 9A_M_1332


title: 9A_M_1333


title: BE4max on mPB CD34 edited at day 1 collected at day 7 - rep. 20


title: BE4max on mPB CD34 edited at day 1 collected at day 7 - rep. 18


title: Cas9 on mPB CD34 edited at day 1 collected at day 7 - rep. 17


title: 9A_M_1330


title: 9A_M_1329


title: 9A_M_1328


title: Cas9 on mPB CD34 edited at day 1 collected at day 7 - rep. 20


title: 9A_M_133


title: ABE8.20-m on mPB CD34 edited at day 1 collected at day 7 - rep. 20


title: 9A_M_1326


title: 9A_M_1327


title: BE4max on mPB CD34 edited at day 1 collected at day 7 - rep. 17


title: Cas9 on mPB CD34 edited at day 3 collected at day 7 - rep. 16


title: Cas9 on mPB CD34 edited at day 3 collected at day 7 - rep. 15


title: 9A_M_1334


title: 9A_M_1324


title: 9A_M_1325


title: Cas9 on mPB CD34 edited at day 3 collected at day 7 - rep. 17


title: ABE8.20-m on mPB CD34 edited at day 3 collected at day 7 - rep. 15


title: 9A_M_1331


title: ABE8.20-m on mPB CD34 edited at day 3 collected at day 7 - rep. 17


title: 9A_M_1323


title: 9A_M_1322


title: 9A_M_1321


title: ABE8.20-m on mPB CD34 edited at day 3 collected at day 7 - rep. 16


title: BE4max on mPB CD34 edited at day 3 collected at day 7 - rep. 17


title: 9A_M_1320


title: 9A_M_132


title: BE4max on mPB CD34 edited at day 3 collected at day 7 - rep. 15


title: BE4max on mPB CD34 edited at day 3 collected at day 7 - rep. 16


title: 9A_M_1319


title: ABE8.20-m on mPB CD34 edited at day 3 collected at day 7 - rep. 14


title: 9A_M_1318


title: 9A_M_1317


title: 9A_M_1316


title: Cas9 on mPB CD34 edited at day 3 collected at day 7 - rep. 14


title: BE4max on mPB CD34 edited at day 3 collected at day 7 - rep. 14


title: ABE8.20-m on mPB CD34 edited at day 1 collected at day 7 - rep. 16


title: 9A_M_1315


title: 9A_M_1313


title: 9A_M_1312


title: 9A_M_1314


title: BE4max on mPB CD34 edited at day 1 collected at day 7 - rep. 16


title: ABE8.20-m on mPB CD34 edited at day 1 collected at day 7 - rep. 15


title: ABE8.20-m on mPB CD34 edited at day 1 collected at day 7 - rep. 13


title: BE4max on mPB CD34 edited at day 1 collected at day 7 - rep. 15


title: ABE8.20-m on mPB CD34 edited at day 1 collected at day 7 - rep. 14


title: 9A_M_1311


title: 9A_M_131


title: 9A_M_1310


title: 9A_M_1309


title: Cas9 on mPB CD34 edited at day 1 collected at day 7 - rep. 15


title: Cas9 on mPB CD34 edited at day 1 collected at day 7 - rep. 13


title: Cas9 on mPB CD34 edited at day 1 collected at day 7 - rep. 14


title: BE4max on mPB CD34 edited at day 1 collected at day 7 - rep. 14


title: Cas9 on mPB CD34 edited at day 3 collected at day 7 - rep. 12


title: 9A_M_1306


title: Cas9 on mPB CD34 edited at day 1 collected at day 7 - rep. 16


title: 9A_M_1307


title: 9A_M_1305


title: Cas9 on mPB CD34 edited at day 3 collected at day 7 - rep. 11


title: Cas9 on mPB CD34 edited at day 3 collected at day 7 - rep. 13


title: 9A_M_1303


title: 9A_M_1304


title: Cas9 on mPB CD34 edited at day 3 collected at day 7 - rep. 10


title: 9A_M_1302


title: ABE8.20-m on mPB CD34 edited at day 3 collected at day 7 - rep. 13


title: ABE8.20-m on mPB CD34 edited at day 3 collected at day 7 - rep. 12


title: ABE8.20-m on mPB CD34 edited at day 3 collected at day 7 - rep. 11


title: ABE8.20-m on mPB CD34 edited at day 3 collected at day 7 - rep. 10


title: 9A_M_1308


title: 9A_M_13


title: 9A_M_130


title: 9A_M_1300


title: BE4max on mPB CD34 edited at day 3 collected at day 7 - rep. 13


title: BE4max on mPB CD34 edited at day 1 collected at day 7 - rep. 13


title: 9A_M_1299


title: BE4max on mPB CD34 edited at day 3 collected at day 7 - rep. 12


title: BE4max on mPB CD34 edited at day 3 collected at day 7 - rep. 10


title: BE4max on mPB CD34 edited at day 3 collected at day 7 - rep. 11


title: 9A_M_1297


title: 9A_M_1298


title: Cas9 on mPB CD34 edited at day 1 collected at day 7 - rep. 11


title: Cas9 on mPB CD34 edited at day 1 collected at day 7 - rep. 10


title: 9A_M_1294


title: 9A_M_1296


title: Cas9 on mPB CD34 edited at day 1 collected at day 7 - rep. 12


title: Cas9 on mPB CD34 edited at day 1 collected at day 7 - rep. 9


title: ABE8.20-m on mPB CD34 edited at day 1 collected at day 7 - rep. 12


title: 9A_M_1292


title: 9A_M_1293


title: 9A_M_1291


title: ABE8.20-m on mPB CD34 edited at day 1 collected at day 7 - rep. 11


title: 9A_M_1290


title: 9A_M_129


title: 9A_M_1301


title: ABE8.20-m on mPB CD34 edited at day 1 collected at day 7 - rep. 9


title: BE4max on mPB CD34 edited at day 1 collected at day 7 - rep. 11


title: BE4max on mPB CD34 edited at day 1 collected at day 7 - rep. 12


title: 9A_M_1287


title: 9A_M_1288


title: 9A_M_1289


title: BE4max on mPB CD34 edited at day 1 collected at day 7 - rep. 10


title: 9A_M_1286


title: 9A_M_1285


title: UT on mPB CD34 edited at day 3 collected at day 7 - rep. 1


title: BE4max on mPB CD34 edited at day 1 collected at day 7 - rep. 9


title: 9A_M_1284


title: 9A_M_1283


title: Mock electro on mPB CD34 edited at day 1 collected at day 7 - rep. 9


title: Cas9 on mPB CD34 edited at day 3 collected at day 7 - rep. 6


title: Cas9 on mPB CD34 edited at day 3 collected at day 7 - rep. 7


title: Cas9 on mPB CD34 edited at day 3 collected at day 7 - rep. 8


title: ABE8.20-m on mPB CD34 edited at day 1 collected at day 7 - rep. 10


title: 9A_M_1281


title: ABE8.20-m on mPB CD34 edited at day 3 collected at day 7 - rep. 8


title: 9A_M_1280


title: ABE8.20-m on mPB CD34 edited at day 3 collected at day 7 - rep. 9


title: 9A_M_1278


title: 9A_M_1279


title: 9A_M_128


title: 9A_M_1282


title: 9A_M_1277


title: ABE8.20-m on mPB CD34 edited at day 3 collected at day 7 - rep. 6


title: 9A_M_1276


title: ABE8.20-m on mPB CD34 edited at day 3 collected at day 7 - rep. 7


title: BE4max on mPB CD34 edited at day 3 collected at day 7 - rep. 9


title: BE4max on mPB CD34 edited at day 3 collected at day 7 - rep. 8


title: BE4max on mPB CD34 edited at day 3 collected at day 7 - rep. 6


title: 9A_M_1273


title: 9A_M_1271


title: 9A_M_1270


title: 9A_M_1272


title: Cas9 on mPB CD34 edited at day 3 collected at day 7 - rep. 9


title: Cas9 on mPB CD34 edited at day 1 collected at day 7 - rep. 8


title: ABE8.20-m on mPB CD34 edited at day 1 collected at day 7 - rep. 8


title: 9A_M_127


title: ABE8.20-m on mPB CD34 edited at day 1 collected at day 7 - rep. 6


title: BE4max on mPB CD34 edited at day 1 collected at day 7 - rep. 8


title: 9A_M_1266


title: 9A_M_1265


title: 9A_M_1267


title: UT on mPB CD34 edited at day 1 collected at day 7 - rep. 1


title: ABE8.20-m on mPB CD34 edited at day 1 collected at day 7 - rep. 5


title: 9A_M_1263


title: 9A_M_1264


title: 9A_M_1274


title: BE4max on mPB CD34 edited at day 1 collected at day 7 - rep. 6


title: BE4max on mPB CD34 edited at day 1 collected at day 7 - rep. 7


title: 9A_M_1269


title: Mock electro on mPB CD34 edited at day 1 collected at day 7 - rep. 4


title: BE4max on mPB CD34 edited at day 3 collected at day 7 - rep. 7


title: Cas9 on mPB CD34 edited at day 1 collected at day 7 - rep. 6


title: 9A_M_1262


title: 9A_M_1260


title: 9A_M_1261


title: ABE8.20-m on mPB CD34 edited at day 1 collected at day 7 - rep. 7


title: Cas9 on mPB CD34 edited at day 1 collected at day 7 - rep. 7


title: Cas9 on mPB CD34 edited at day 1 collected at day 7 - rep. 5


title: 9A_M_126


title: BE4max on mPB CD34 edited at day 1 collected at day 7 - rep. 5


title: Mock electro on mPB CD34 edited at day 1 collected at day 7 - rep. 7


title: 9A_M_1259


title: 9A_M_1268


title: 9A_M_1257


title: 9A_M_1255


title: 9A_M_1256


title: 9A_M_1254


title: ABE8.20-m on mPB CD34 edited at day 3 collected at day 7 - rep. 4


title: BE4max on mPB CD34 edited at day 3 collected at day 7 - rep. 4


title: 9A_M_1253


title: BE4max on mPB CD34 edited at day 3 collected at day 7 - rep. 3


title: 9A_M_1252


title: ABE8.20-m on mPB CD34 edited at day 3 collected at day 7 - rep. 3


title: Cas9 on mPB CD34 edited at day 3 collected at day 7 - rep. 3


title: Mock electro on mPB CD34 edited at day 1 collected at day 7 - rep. 5


title: 9A_M_1258


title: 9A_M_1251


title: Cas9 on mPB CD34 edited at day 3 collected at day 7 - rep. 2


title: 9A_M_1250


title: Mock electro on mPB CD34 edited at day 1 collected at day 7 - rep. 6


title: ABE8.20-m on mPB CD34 edited at day 3 collected at day 7 - rep. 2


title: 9A_M_1244


title: 9A_M_1245


title: BE4max on mPB CD34 edited at day 3 collected at day 7 - rep. 2


title: 9A_M_1248


title: Cas9 on mPB CD34 edited at day 3 collected at day 7 - rep. 4


title: Bone Marrow HSPC mock electro Mouse4

data_processing:
Barcodes computed with BAR-seq2 pipeline: barcode sequences were extracted with the TagDust software (v2.33) and processed to merge similar (erroneous) barcodes
Assembly: none
Supplementary files format and content: Tab-separated matrix with barcode counts
Library strategy: BAR-Seq

extract_protocol:
QIAamp DNA Micro Kit (QIAGEN)
Custom library construction protocol. PCR amplicons for each individual sample were generated by nested PCR starting from >50-100 ng of purified gDNA. The first PCR step was performed with GoTaq G2 DNA Polymerase (Promega) according to the manufacturer’s instructions using the following amplification protocol: 95°C x 10’, (95°C x 30’’, 63°C x 30’’, 72°C x 30’’) x 20 cycles, 72 °C for 10’. The second PCR step was performed using the same reagents of the first step, 5 μl of the PCR product and the following amplification protocol: 95°C x 10’, (95°C x 30’’, 63°C x 30’’, 72°C x 30’’) x 20 cycles, 72°C x 10’. Primers used for the second PCR step contained P5/P7 sequences, i5/i7 Illumina tags to allow multiplexed sequencing and R1/R2 primer binding sites. The PCR amplicon from each sample was separately purified by QIAquick PCR Purification Kit (QIAGEN). Concentration and quality of amplicons were assessed by QuantiFluor ONE dsDNA system and 4200 Tapestation System (Agilent). Amplicons from up to 85 differently tagged samples were multiplexed at equimolar ratios.

value: HSPC

value: Mock Electro

value: 15 Weeks


title: 9A_M_1242


title: 9A_M_1247


title: Bone Marrow HSPC mock electro Mouse0


title: Bone Marrow HSPC mock electro Mouse2


title: Bone Marrow HSPC mock electro Mouse1


title: Bone Marrow HSPC Cas9 Mouse0


title: 9A_M_1240


title: 9A_M_1243


title: 9A_M_1239


title: 9A_M_124


title: Bone Marrow HSPC Cas9 Mouse1


title: 9A_M_1246


title: 9A_M_1241


title: 9A_M_125


title: Bone Marrow HSPC ABE8.20-m Mouse2


title: Bone Marrow HSPC ABE8.20-m Mouse4


title: Bone Marrow HSPC ABE8.20-m Mouse1


title: Bone Marrow HSPC ABE8.20-m Mouse3


title: 9A_M_1249


title: 9A_M_1238


title: Bone Marrow HSPC Cas9 Mouse4


title: Bone Marrow HSPC mock electro Mouse3


title: 9A_M_1235


title: 9A_M_1233


title: 9A_M_1232


title: 9A_M_1237


title: Spleen T Cells mock electro Mouse4

source_name: Spleen

value: Spleen

value: T Cells


title: Bone Marrow HSPC BE4max Mouse1


title: Bone Marrow HSPC BE4max Mouse2


title: 9A_M_1234


title: Bone Marrow HSPC BE4max Mouse0


title: 9A_M_1230


title: Bone Marrow HSPC ABE8.20-m Mouse0


title: Spleen T Cells mock electro Mouse3


title: 9A_M_1231


title: 9A_M_1236


title: 9A_M_1229


title: Spleen T Cells mock electro Mouse1


title: Spleen T Cells mock electro Mouse0


title: Bone Marrow HSPC BE4max Mouse3


title: Spleen T Cells Cas9 Mouse0


title: Spleen T Cells ABE8.20-m Mouse4


title: 9A_M_123


title: Spleen T Cells mock electro Mouse2


title: Spleen T Cells Cas9 Mouse4


title: 9A_M_1223


title: 9A_M_1228


title: 9A_M_1222


title: Spleen T Cells ABE8.20-m Mouse1


title: Spleen T Cells ABE8.20-m Mouse3


title: 9A_M_1227


title: 9A_M_1226


title: 9A_M_1225


title: Spleen T Cells BE4max Mouse3


title: 9A_M_1224


title: Spleen T Cells ABE8.20-m Mouse2


title: Spleen T Cells BE4max Mouse2


title: 9A_M_1219


title: Spleen T Cells ABE8.20-m Mouse0


title: 9A_M_1221


title: 9A_M_1220


title: 9A_M_122


title: Spleen T Cells Cas9 Mouse1


title: Spleen Myeloid Cells mock electro Mouse4

value: Myeloid Cells


title: Spleen T Cells BE4max Mouse1


title: Spleen T Cells BE4max Mouse0


title: 9A_M_1218


title: 9A_M_1216


title: 9A_M_1217


title: Spleen Myeloid Cells mock electro Mouse3


title: 9A_M_1214


title: Spleen Myeloid Cells mock electro Mouse2


title: 9A_M_1215


title: Spleen Myeloid Cells mock electro Mouse1


title: 9A_M_1213


title: Spleen Myeloid Cells Cas9 Mouse4


title: 9A_M_1211


title: Spleen Myeloid Cells Cas9 Mouse0


title: 9A_M_1210


title: 9A_M_1206


title: Spleen Myeloid Cells Cas9 Mouse1


title: Spleen Myeloid Cells ABE8.20-m Mouse4


title: Spleen Myeloid Cells ABE8.20-m Mouse2


title: Spleen Myeloid Cells ABE8.20-m Mouse1


title: 9A_M_1209


title: 9A_M_1208


title: Spleen Myeloid Cells ABE8.20-m Mouse0


title: 9A_M_121


title: 9A_M_1205


title: 9A_M_1207


title: Spleen Myeloid Cells BE4max Mouse3


title: Spleen Myeloid Cells BE4max Mouse2


title: Spleen Myeloid Cells BE4max Mouse1


title: 9A_M_1203


title: Spleen Myeloid Cells ABE8.20-m Mouse3


title: 9A_M_1201


title: 9A_M_1200


title: PB 9 Weeks mock electro Mouse4

value: Blood

value: PB Mononuclear Cells

value: 9 Weeks


title: Spleen Myeloid Cells mock electro Mouse0


title: Spleen Myeloid Cells BE4max Mouse0


title: PB 9 Weeks mock electro Mouse3


title: 9A_M_1212


title: PB 9 Weeks mock electro Mouse0


title: 9A_M_1199


title: 9A_M_12


title: PB 9 Weeks mock electro Mouse1


title: PB 9 Weeks Cas9 Mouse0


title: 9A_M_1196


title: PB 9 Weeks Cas9 Mouse1


title: 9A_M_1195


title: PB 9 Weeks ABE8.20-m Mouse4


title: PB 9 Weeks Cas9 Mouse4


title: 9A_M_1198


title: 9A_M_1194


title: 9A_M_1204


title: PB 9 Weeks ABE8.20-m Mouse1


title: 9A_M_1192


title: 9A_M_1187


title: PB 9 Weeks BE4max Mouse3


title: 9A_M_1202


title: PB 9 Weeks BE4max Mouse2


title: 9A_M_1191


title: PB 9 Weeks ABE8.20-m Mouse3


title: PB 9 Weeks mock electro Mouse2


title: 9A_M_119


title: 9A_M_1189


title: 9A_M_1188


title: 9A_M_1184


title: PB 9 Weeks ABE8.20-m Mouse0


title: Spleen B Cells mock electro Mouse4

value: B cells


title: Spleen B Cells mock electro Mouse2


title: PB 9 Weeks BE4max Mouse1


title: 9A_M_1185


title: 9A_M_1183


title: 9A_M_1177


title: 9A_M_1182


title: 9A_M_1176


title: 9A_M_1186


title: 9A_M_1181


title: PB 9 Weeks BE4max Mouse0


title: Spleen B Cells mock electro Mouse3


title: PB 9 Weeks ABE8.20-m Mouse2


title: 9A_M_1174


title: 9A_M_1180


title: 9A_M_1173


title: 9A_M_1175


title: Spleen B Cells ABE8.20-m Mouse3


title: Spleen B Cells BE4max Mouse3


title: Spleen B Cells ABE8.20-m Mouse0


title: Spleen B Cells mock electro Mouse1


title: Spleen B Cells mock electro Mouse0


title: 9A_M_118


title: Spleen B Cells Cas9 Mouse4


title: 9A_M_1179


title: Spleen B Cells Cas9 Mouse1


title: 9A_M_1178


title: Spleen B Cells Cas9 Mouse0


title: Spleen B Cells BE4max Mouse0


title: 9A_M_1169


title: 9A_M_120


title: Spleen B Cells ABE8.20-m Mouse4


title: Spleen B Cells ABE8.20-m Mouse1


title: PB 15 Weeks mock electro Mouse3


title: PB 15 Weeks mock electro Mouse2


title: 9A_M_1166


title: 9A_M_1172


title: 9A_M_1164


title: PB 15 Weeks Cas9 Mouse4


title: 9A_M_1171


title: Spleen B Cells BE4max Mouse2


title: PB 15 Weeks Cas9 Mouse1


title: 9A_M_1170


title: Spleen B Cells BE4max Mouse1


title: 9A_M_117


title: Spleen B Cells ABE8.20-m Mouse2


title: PB 15 Weeks ABE8.20-m Mouse4


title: 9A_M_116


title: PB 15 Weeks ABE8.20-m Mouse3


title: PB 15 Weeks mock electro Mouse4


title: PB 15 Weeks ABE8.20-m Mouse1


title: 9A_M_1168


title: PB 15 Weeks ABE8.20-m Mouse0


title: PB 15 Weeks mock electro Mouse1


title: 9A_M_1158


title: 9A_M_1165


title: PB 15 Weeks BE4max Mouse2


title: PB 15 Weeks BE4max Mouse1


title: PB 15 Weeks mock electro Mouse0


title: 9A_M_1154


title: 9A_M_1163


title: PB 15 Weeks BE4max Mouse0


title: 9A_M_1153


title: Spleen mock electro Mouse4


title: 9A_M_1162


title: PB 15 Weeks Cas9 Mouse0


title: 9A_M_1161


title: Spleen mock electro Mouse3


title: 9A_M_1160


title: 9A_M_1151


title: Spleen mock electro Mouse2


title: Spleen mock electro Mouse1


title: 9A_M_1167


title: PB 15 Weeks ABE8.20-m Mouse2


title: 9A_M_1159


title: Spleen Cas9 Mouse4


title: 9A_M_1157


title: 9A_M_1146


title: 9A_M_1155


title: PB 15 Weeks BE4max Mouse3


title: 9A_M_1152


title: 9A_M_115


title: 9A_M_1156


title: 9A_M_1150


title: Spleen mock electro Mouse0


title: Spleen ABE8.20-m Mouse3


title: 9A_M_1144


title: 9A_M_1141


title: 9A_M_1148


title: 9A_M_1147


title: Spleen Cas9 Mouse0


title: Spleen ABE8.20-m Mouse1


title: 9A_M_1149


title: Spleen Cas9 Mouse1


title: 9A_M_114


title: 9A_M_1142


title: Spleen ABE8.20-m Mouse2


title: 9A_M_1145


title: Spleen BE4max Mouse2


title: Spleen ABE8.20-m Mouse0


title: Spleen BE4max Mouse3


title: Spleen BE4max Mouse0


title: 9A_M_1140


title: Spleen BE4max Mouse1


title: 9A_M_1137


title: 9A_M_1139


title: Spleen ABE8.20-m Mouse4


title: 9A_M_1138


title: 9A_M_1133


title: Bone Marrow mock electro Mouse3


title: Bone Marrow mock electro Mouse4


title: 9A_M_1135


title: Bone Marrow mock electro Mouse0


title: Bone Marrow Cas9 Mouse4


title: 9A_M_1136


title: Bone Marrow Cas9 Mouse0


title: Bone Marrow mock electro Mouse1


title: Bone Marrow mock electro Mouse2


title: Bone Marrow ABE8.20-m Mouse4


title: Bone Marrow Cas9 Mouse1


title: 9A_M_1127


title: 9A_M_113


title: Bone Marrow ABE8.20-m Mouse3


title: Bone Marrow ABE8.20-m Mouse2


title: 9A_M_1129


title: 9A_M_1126


title: 9A_M_1125


title: Bone Marrow ABE8.20-m Mouse0


title: 9A_M_1132


title: 9A_M_1128


title: 9A_M_1131


title: primary rat microvessels, soft ECM, without A83-01

city: Qingdao

first: Dong

last: Wang

email: dongwang@qdu.edu.cn, dwang2100@163.com

address: 38 Dengzhou Road

country: China

institute: Qingdao University

description: soft (mem-CY)

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data(clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30, GC-content and sequence duplication level of the clean data were calculated. All the downstream analyses were based on clean data with high quality.
The adaptor sequences and low-quality sequence reads were removed from the data sets. Raw sequences were transformed into clean reads after data processing. These clean reads were then mapped to the reference genome sequence. Only reads with a perfect match or one mismatch were further analyzed and annotated based on the reference genome. Hisat2 tools soft were used to map with reference genome.
Prior to differential gene expression analysis, for each sequenced library, the read counts were adjusted by edgeR program package through one scaling normalized factor. Differential expression analysis of two samples was performed using the EBSeq R package. The resulting FDR (false discovery rate) were adjusted using the PPDE(posterior probability of being DE) .The FDR < 0.05 & |log2（foldchange）| ≥1 was set as the threshold for significantly differential expression.
Assembly: Rattus_norvegicus.Rnor_6.0.89.chr
Supplementary files format and content: All_gene_counts.list
Supplementary files format and content: heatmap.xlsx
Supplementary files format and content: bubble plot.xlsx

organism: Rattus norvegicus

source_name: subcutaneous soft connective tissue

extract_protocol:
Total RNA was extracted from the microvascular cells using Trizol (Invitrogen, Cat#15596026) according to the manufacture instruction. The cells of a 60mm dish were homogenized in 1ml Trizol, centrifuged at 12,000×g for 5min at 4°C, and then the supernatant was transferred into a tube with 0.3ml chloroform/isoamyl alcohol (24:1). The mixture was centrifuged at 12,000×g for 10min at 4°C, the upper aqueous RNA layer was transferred into a new tube with equal volume of isopropyl alcohol, and then cen trifuged at 12,000×g for 20min at 4°C. The RNA pellet was washed with 1ml 75% ethanol, and then centrifuged at 12,000×g for 3min at 4°C. The pellet was dried in air for 5–10min. Finally, 50µl DEPC water was added to dis solve the RNA, which was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer (ThermoFisher).
The mRNA was purified by Oligo(dT)-attached magnetic beads and fragmented into small pieces. First-strand cDNA was generated by random hexamer-primed reverse tran scription and a second-strand cDNA synthesis. A-Tailing Mix and RNA Index Adapters were added. The cDNA fragments were amplified by PCR, and then purified by Ampure XP Beads and dissolved in EB solution. The product was validated on an Agilent Tech 2100 bioanalyzer. The double stranded PCR products were denatured and circularized by the splint oligo sequence to make the final library, which was amplified with phi29 to make DNA nanoball with more than 300 copies of one molecular, which were loaded into the patterned nanoarray and pair end 150 bases reads were generated on DNBSEQ-T7 platform.

value: subcutaneous soft connective tissue

tag: cell line

value: primary cell

value: vascular cell

value: wild type


title: primary rat microvessels, stiff ECM, with A83-01

description: stiff+A83-01 (CAY-1)


title: Bone Marrow BE4max Mouse2


title: primary rat microvessels, stiff ECM, without A83-01

description: stiff (CY-1)


title: Bone Marrow BE4max Mouse1


title: primary rat microvessels, soft ECM, with A83-01

description: soft+A83-01 (mem-CAY)


title: Bone Marrow BE4max Mouse3


title: 9A_M_1124


title: 9A_M_1123


title: 9A_M_1130


title: 9A_M_1122


title: danRer11_WT_7dpi

city: Madison

first: jianhong

last: ou

state: WI

address: 330 N Orchard Street

institute: Morgridge institute for research

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.0.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: danRer11
Supplementary files format and content: h5 files for count table

organism: Danio rerio

source_name: spinal cord

extract_protocol: Samples were processed following the 10X Chromium platform following the manufacturer’s guidelines, using 10X Single Cell 3’ v3 chemistry (10X Genomics, Pleasanton, USA).

value: WT

value: spinal cord

value: Ekkwill (EK)

value: 6 months


title: 9A_M_1121


title: Bone Marrow ABE8.20-m Mouse1

value: Bone Marrow

value: Hematopoietic Cells


title: 9A_M_1119


title: Bone Marrow BE4max Mouse0

value: 15 Weeks


title: CM_αKG_3

city: Bad Nauheim

first: Carsten

last: Kuenne

address: Ludwigstrasse 43

department: Bioinformatics

country: Germany

institute: Max Planck Institute for Heart and Lung Research

data_processing:
Raw reads were assessed for quality, adapter content and duplication rates with FastQC 0.11.8 (Andrews S. 2010, FastQC: a quality control tool for high throughput sequence data. Available online at: http://www.bioinformatics.babraham.ac.uk/projects/fastqc).
Trimmomatic version 0.39 was employed to trim reads after a quality drop below a mean of Q15 in a window of 5 nucleotides (Bolger et al., Trimmomatic: a flexible trimmer for Illumina sequence data). Only reads longer than 15 nucleotides were cleared for further analyses.
Reads were aligned versus Ensembl mouse genome version mm10 (Ensembl release 101) with STAR 2.7.10a (Dobin et al., STAR: ultrafast universal RNA-seq aligner).
Aligned reads were filtered to remove: duplicates with Picard 2.27.1 (Picard: A set of tools (in Java) for working with next generation sequencing data in the BAM format), multi-mapping, ribosomal, or mitochondrial reads.
Gene counts were established with featureCounts 2.0.3 by aggregating reads overlapping exons on the correct strand excluding those overlapping multiple genes (Liao et al., featureCounts: an efficient general purpose program for assigning sequence reads to genomic features).
The raw count matrix was normalized with DESeq2 version 1.30.1 (Love et al., Moderated estimation of fold change and dispersion for RNA-Seq data with DESeq2). Contrasts were created with DESeq2 based on the raw count matrix.
The Ensemble annotation was enriched with UniProt data based on Ensembl gene identifiers (Activities at the Universal Protein Resource (UniProt)).
Assembly: mm10 / GRCm38.p5
Supplementary files format and content: Tab-delimited matrix with DESeq normalized gene counts.

source_name: cardiomyocyte

extract_protocol:
RNA was extracted from DMSO or αKG treated neonatal cardiomyocytes using the Direct-zol Total Kit (Zymo Research) combined with on-column DNase digestion (DNase-Free DNase Set, Qiagen) to avoid contamination by genomic DNA.
RNA and library preparation integrity were verified LabChip Gx Touch 24 (Perkin Elmer). 200ng of total RNA was used as input for SMARTer Stranded Total RNA Sample Prep Kit - HI Mammalian (Clontech) following the manufactures instructions.

treatment_protocol: Cells were treated with DMSO or cell-permeable aKG (100uM) for 96 hours

value: cardiomyocyte

value: aKG


title: 9A_M_112


title: danRer11_hbegfaKO_7dpi

value: hbegfaKO


title: 9A_M_1120


title: 9A_M_1118


title: CM_αKG_2


title: danRer11_hbegfaKO_sham

value: sham


title: CM_DMSO_2

value: DMSO


title: CM_αKG_1


title: CM_DMSO_1


title: 9A_M_1117


title: 9A_M_1116


title: danRer11_WT_sham


title: 9A_M_1114


title: mouse_oviduct 3

city: Vancouver

first: Yemin

state: BC

address: 2660 Oak Street

country: Canada

institute: University of British Columbia

description: oviduct 3

data_processing:
Analysis ofthe miRNAseq data was performed using BaseSpacemiRNA Analysisappversion 1.0.0 (Illumina, San Diego, CA, USA)
The adapterswere trimmed using cutadapt and thetrimmed reads werealigned to the miRBase v.21using SHRiMPS alignerversion 2.0.1(http://compbio.cs.toronto.edu/shrimp/)
Assembly: miRBase v.21
Supplementary files format and content: tab-delimited text files include raw counts for each Sample

source_name: oviduct

growth_protocol: primary normal and tumor tissues from mice

extract_protocol:
Total RNA was extracted using miRNeasy kit (Qiagen).
Library preparation was conducted using Illumina TruSeq small RNA library preparation kit  following the manufacutrer' instruction.

treatment_protocol: no treatment.

value: oviduct


title: mouse_primary tumor 3

description: ADT tumor-3


title: mouse_oviduct 1

description: oviduct 1


title: mouse_oviduct 2

description: oviduct 2


title: mouse_primary tumor 1

description: ADT tumor-1


title: 9A_M_1115


title: HCT116 cells, VCP 3

city: Guangzhou

first: Youwei

last: Huang

state: Guangdong

address: West Huangpu Avenue no.601

department: Department of pharmacology

institute: Jinan University

data_processing:
Illumina Casava1.4 software used for basecalling.
Data were filtered the low-quality sequences, including adapter sequence and low-quality bases (mass value ≤20) using the software FASTP.
Reads were referenced to the genome using HISAT2 (Hierarchical Indexing for Spliced Alignment of Transcripts) software.
Reads were calculated using fragments per kilobaseof exon per million fragments mapped (FPKM) software.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: Large intestine, Colon

growth_protocol: HCT116 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and 1× penicillin-streptomycin in humidified atmosphere with 5% CO2 at 37℃.

extract_protocol:
Cells were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: Large intestine, Colon

value: Colorectal cancer cell

value: VCP overexpression


title: CM_DMSO_3


title: E12-2

city: New York

first: Nandan

middle: L

last: Nerurkar

state: NEW YORK

department: Biomedical Engineering

institute: Columbia University

data_processing:
Quality control of sequenced data was performed using FastQC v0.11.9
Residual adapter sequences were cleaned using (cutadapt v3.1 (trim_galore extension))
Genome alignment was performed using hisat2 v2.2.1
read count matrix was obtained with htseq v0.13.5
differential expression was obtained with DESeq2
Assembly: GRCg6a, Ensembl 105
Supplementary files format and content: tab-delimited text file with raw counts for every sample

molecule: polyA RNA

organism: Gallus gallus

growth_protocol: Fertilized White Leghorn chicken (Gallus gallus domesticus) eggs were incubated at 37°C and 60% humidity. At E8, 12, and 16, eggs were opened, and embryos sacrificed by decapitation, followed by microdissection in PBS to isolate the small intestine. the intestinal tube and superior mesenteric artery were removed from the mesentery. Mesenteries were collected and flash frozen on dry ice. All dissections were done in DEPC-PBS with sterile tools. Tissues from 3 embryos were pooled for each replicate (3 for each condition) in order to reach the minimum tissue mass required. Samples were shipped as whole frozen tissue to Genewiz for RNA isolation, library preparation, and sequencing.

extract_protocol:
Total RNA was extracted from fresh frozen cell pellet samples using Qiagen RNeasy Plus Universal mini kit following manufacturer’s instructions (Qiagen, Hilden, Germany). RNA samples were quantified using Qubit 2.0 Fluorometer (Life Technologies, Carlsbad, CA,USA) and RNA integrity was checked using Agilent TapeStation 4200 (Agilent Technologies,Palo Alto, CA, USA).
RNA sequencing libraries were prepared using the NEBNext Ultra RNA Library Prep Kit for Illumina using manufacturer’s instructions (NEB, Ipswich, MA, USA). Briefly, mRNAs were initially enriched with Oligod(T) beads. Enriched mRNAs were fragmented for 15 minutes at 94 °C. First strand and second strand cDNA were subsequently synthesized. cDNA fragments were end repaired and adenylated at 3’ends, and universal adapters were ligated to cDNA fragments, followed by index addition and library enrichment by PCR with limited cycles. The sequencing library was validated on the Agilent TapeStation (Agilent Technologies, Palo Alto, CA, USA), and quantified by using Qubit 2.0 Fluorometer (Invitrogen, Carlsbad, CA) as well as by quantitative PCR (KAPA Biosystems, Wilmington, MA, USA). The sequencing libraries were clustered on 1 lane of a flowcell. After clustering, the flowcell was loaded on the Illumina instrument (4000 or equivalent) according to manufacturer’s instructions. The samples were sequenced using a 2x150bp Paired End (PE) configuration. Image analysis and base calling were conducted by the Control software. Raw sequence data (.bcl files) generated the sequencer were converted into fastq files and de-multiplexed using Illumina's bcl2fastq 2.17 software. One mismatch was allowed for index sequence identification.

value: dorsal mesentery

value: wild type

tag: embryonic day


title: HCT116 cells, VCP 2


title: E16-1


title: HCT116 cells, VCP 1


title: E16-2


title: E16-3


title: E12-3


title: E12-1


title: 9A_M_1113


title: 9A_M_1112


title: HCT116 cells, Vector 1

value: Vector


title: mouse_primary tumor 2

description: ADT tumor-2


title: 9A_M_1110


title: E8-3


title: 9A_M_1111


title: E8-2


title: E8-1