title: KhES1_D6ng_sample8

description:
mRNA-seq (polyA+) data from blastoids derived from KhES1 cultured in iBlastoid medium without hydrogel, sample 4
KhES1_D6ng_2


title: KhES1_D4ng_sample3

status: Public on Jun 29 2024

type: SRA

city: Abu Dhabi

first: Ken-ichiro

last: Kamei

address: Saadiyat Campus, #C1-032

country: United Arab Emirates

institute: New York University Abu Dhabi

description:
mRNA-seq (polyA+) data from blastoids derived from KhES1 cultured in DMEM without hydrogel, sample 3
KhES1_D4ng_1

library_source: transcriptomic single cell

data_processing:
Chromium barcodes were used for demultiplexing by using CellRanger program (10x Genomics; v6.1.1, https://support.10xgenomics.com/single-cell-gene-expression/software/overview/welcome).
Alignment and UMI counting were performed using CellRanger to map 373,641,788 sequencing reads to a custom version of the Ensembl GRCh38 reference genome.
Assembly: GRCh38
Supplementary files format and content: Gene expression values were calculated with CellRanger program.

molecule: polyA RNA

organism: Homo sapiens

growth_protocol: hESCs were used following the guidelines provided by the ethical committee of Kyoto University (Approved #ES3-9 and ES3-29). Prior to culturing, 1.3% (v/v) hESC-certified Matrigel (Corning, NY, USA) in DMEM/F12 medium was coated on a culture dish. Matrigel was incubated in a dish for 24 h at 4˚C. Then, excess Matrigel was removed, and the coated dish was washed with a fresh DMEM/F12 medium. A mTeSR-1 medium was used for the daily culturing of hPSCs. For passaging, cells were dissociated with TrypLE Express (Life Technologies, Carlsbad, CA, USA) for 3 min at 37 ˚C, and then harvested. A cell strainer was used to remove undesired cell aggregates from the cell suspension. The cells were centrifuged at 200 × g for 3 min and resuspended in the mTeSR-1 medium. The cells were counted using a NucleoCounter NC-200 (Chemetec, Baton Rouge, LA, USA). A mTeSR-1 medium containing 10 µM of Y27632 was used to prevent the apoptosis of the dissociated hPSCs, on day 1. mTeSR-1 medium without Y27632 was used on the subsequent days, with daily medium change. The cells were maintained in an incubator at 37°C with 5% (v/v) CO2.

extract_protocol:
Dissociated cells were applied to Chromium controller (10x Genomics, Pleasanton, CA, USA) to encapsulate cells, following the manufacture’s instruction (Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 (Dual Index)).
StepOnePlus (Applied Biosystems)

treatment_protocol: hESCs cultured on Matrigel-coated dishes with a mTeSR-1 medium were harvested with TrypLE Express for 3 min at 37°C and transferred in a 15-mL tube. The dissociated hPSCs were resuspended in mTeSR-1 medium supplemented with 10 µM of Y27632, and then transferred to Aggrewell 400 (Stem Cell Technologies) at 1.5 × 10^5 cells per well. After culturing in an incubator for 24 h at 37°C with 5% (v/v) CO2, the hPSC aggregates were resuspended in the HG solution {DMEM with 10%[w/v] PNIPAAm-β-PEG hydrogel at 4°C. 260 µL of an hPSC aggregate suspension with HG was transferred into the well of a 24-well plate, and then DMEM supplemented with 10%(v/v) FBS was added at 37°C. After 3-day culture, iBlastoid medium was changed on a daily basis, and the cells were maintained at 37°C with 5% (v/v) CO2 in an incubator.

tag: condition

value: DMEM without hydrogel

tag: derived tissue

value: Embryonic stem cells


title: Kasu-Ve1

city: Yokohama

first: Hiroyoshi

last: Kunimoto

address: 3-9 Fukuura, Kanazawa

department: Department of Stem Cell and Immune Regulation

country: Japan

institute: Yokohama City University Graduate School of Medicine

library_source: genomic

data_processing:
Peak calling and annotation were performed through the csaw bioconductor package.
Assembly: hg38
Supplementary files format and content: bigwig

molecule: genomic DNA

source_name: hematopoietic tissue

extract_protocol:
DNA was eluted using CUT&Tag-IT Assay Kit (Active Motif) according to the manufacturer’s instructions.
Libraries were prepared using CUT&Tag-IT Assay Kit (Active Motif) according to the manufacturer’s instructions.

tag: tissue

value: hematopoietic tissue

tag: cell line

tag: cell type

value: leukemia cells


title: Kasu-Ve2


title: Kasu-DS3201


title: Kasu-DS1


title: Kasu-DS2


title: Kasu-Vehicle


title: FKH-DS1


title: FKH-DS3201


title: FKH-Ve2


title: FKH-DS2


title: FKH-Vehicle


title: OCI-DS1


title: YCU-Ve1


title: FKH-Ve1


title: YCU-Ve2


title: YCU-DS1


title: OCI-Vehicle


title: OCI-Ve2


title: YCU-DS2


title: YCU-DS3201


title: OCI-DS3201


title: OCI-Ve1


title: OCI-DS2


title: UOS_H9_S88_Aligned.quant

city: New York City

first: Katherine

last: Stewart

state: NY

address: 1230 York Avenue

department: Laboratory of Mammalian Cell Biology and Development

country: USA

institute: The Rockefeller University

data_processing:
raw sequencing reads were aligned to the mouse reference genome (UCSC release mm39) using STAR (v2.6)
The expression values of each gene were quantified as both raw counts and transcripts per million (TPM) using Salmon (v.1.4.0), and compiled in R (v.3.6.1) using RStudio (v.3.4.2) by Tximport (v.1.12.3)
Raw count and metadata matrices for HFSCs across the hair cycle were loaded in SCANPY as an AnnData object. Single cell data was preprocessed to remove lowly detected genes (expressed in <75 cells) and cells with low complexity libraries (<2,000 genes detected).
SCANPY was used to normalize counts per cell, and highly variable genes were detected. Prior to dimensionality reduction by principal component analysis (PCA), data was centered and scaled. PCA was performed on highly variable genes, with 100 components and the svd_solver using ‘arpack’ (SCANPY default setting). To construct a k-nearest neighbours graph on Euclidean distance, 41 principal components were used (which captured 25% of the variance in the data). Data was visualized using uniform manifiold projection (UMAP) in SCANPY, and clustering was done using the Leiden algorithm (with a resolution setting of 0.5). Cluster resolution was chosen after iterating through resolution parameters from 0.1 to 0.75, as best capturing both hair follicle cycle stages and anatomic location (upper bulge region/upper ORS versus hair germ/upper-middle ORS versus lower ORS).
Assembly: mm39
Supplementary files format and content: raw count matrix as txt
Supplementary files format and content: metadata for samples as txt

organism: Mus musculus

source_name: skin

extract_protocol:
Cells from 3-6 animals were pooled prior to FACS-isolation. In brief, cells were sorted into hypotonic lysis buffer, snap frozen in liquid nitrogen and stored at -80oC until all samples were collected. Cells were lysed by heating at 72oC for 3 min, followed by reverse transcription of mRNA using dT30 oligos, template switching oligos and Maxima H- reverse transcriptase. The whole transcriptome was amplified (15 cycles) by KAPA HiFi DNA polymerase (Roche), and then size-selected using 0.6X AmpPure XP beads (Beckman Coulter). To exclude cells with poor amplification, and wells containing multiple cells, qPCR for Gapdh was performed.
Illumina sequencing libraries were indexed with unique 5’ and 3’ barcode combinations (up to 384 cells) using the Nextera XT DNA library preparation kit (Illumina). Libraries were pooled and size-selected with 0.9X AmpPure XP beads. Prior to sequencing on Illumina NextSeq500 using a 75 bp paired-end read mid-output setting, library quality was assessed by TapeStation (Agilent).

value: skin

value: hair follicle epithelial cell

tag: genotype

value: wild type

tag: hair follicle_epithelia_region

value: upper-middle outer root sheath

tag: hair cycle_stage

value: AnaVI


title: UOS_H5_S84_Aligned.quant


title: UOS_H7_S86_Aligned.quant


title: UOS_H6_S85_Aligned.quant


title: UOS_H8_S87_Aligned.quant


title: UOS_H12_S90_Aligned.quant


title: UOS_G9_S78_Aligned.quant


title: UOS_H4_S83_Aligned.quant


title: UOS_G9_S77_Aligned.quant


title: UOS_G8_S76_Aligned.quant


title: UOS_H3_S82_Aligned.quant


title: UOS_H2_S81_Aligned.quant


title: UOS_G6_S75_Aligned.quant


title: UOS_G8_S77_Aligned.quant


title: UOS_G5_S74_Aligned.quant


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title: UOS_G7_S76_Aligned.quant


title: UOS_G2_S70_Aligned.quant


title: UOS_G3_S71_Aligned.quant


title: UOS_H1_S80_Aligned.quant


title: UOS_G4_S72_Aligned.quant


title: UOS_G6_S74_Aligned.quant


title: UOS_H10_S89_Aligned.quant


title: UOS_G1_S70_Aligned.quant


title: UOS_F6_S62_Aligned.quant


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title: UOS_D1_S34_Aligned.quant


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title: UOS_C7_S28_Aligned.quant


title: UOS_C5_S26_Aligned.quant


title: UOS_C6_S27_Aligned.quant


title: UOS_C6_S28_Aligned.quant


title: UOS_C3_S24_Aligned.quant


title: UOS_C4_S25_Aligned.quant


title: UOS_C2_S24_Aligned.quant


title: UOS_C3_S25_Aligned.quant


title: UOS_C5_S27_Aligned.quant


title: UOS_C4_S26_Aligned.quant


title: UOS_C12_S33_Aligned.quant


title: UOS_C11_S32_Aligned.quant


title: UOS_C2_S23_Aligned.quant


title: UOS_C10_S32_Aligned.quant


title: UOS_D8_S41_Aligned.quant


title: UOS_C10_S31_Aligned.quant


title: UOS_C1_S23_Aligned.quant


title: UOS_C1_S22_Aligned.quant


title: UOS_B9_S20_Aligned.quant


title: UOS_C9_S30_Aligned.quant


title: UOS_B9_S19_Aligned.quant


title: UOS_B5_S16_Aligned.quant


title: UOS_B7_S18_Aligned.quant


title: UOS_B8_S18_Aligned.quant


title: UOS_B8_S19_Aligned.quant


title: UOS_B4_S15_Aligned.quant


title: UOS_B7_S17_Aligned.quant


title: UOS_B6_S16_Aligned.quant


title: UOS_B6_S17_Aligned.quant


title: UOS_B2_S13_Aligned.quant


title: UOS_D11_S44_Aligned.quant


title: UOS_B12_S22_Aligned.quant


title: UOS_B1_S12_Aligned.quant


title: UOS_A8_S8_Aligned.quant


title: UOS_A7_S7_Aligned.quant


title: UOS_B10_S21_Aligned.quant


title: UOS_A9_S9_Aligned.quant


title: UOS_B12_S21_Aligned.quant


title: UOS_A5_S5_Aligned.quant


title: UOS_A6_S6_Aligned.quant


title: UOS_B11_S20_Aligned.quant


title: UOS_A4_S4_Aligned.quant


title: UOS_A2_S2_Aligned.quant


title: UOS_A11_S11_Aligned.quant


title: UOS_A1_S1_Aligned.quant


title: UOS_A3_S3_Aligned.quant


title: UOS_A10_S10_Aligned.quant


title: P17f_pl6_NonPhagoHFSC_apop_H6_S68_Aligned.quant

value: upper outer root sheath

value: CatVI


title: UOS_B3_S14_Aligned.quant


title: P17f_pl6_NonPhagoHFSC_apop_H8_S69_Aligned.quant


title: P17f_pl6_NonPhagoHFSC_apop_H4_S66_Aligned.quant


title: P17f_pl6_NonPhagoHFSC_apop_H12_S70_Aligned.quant


title: P17f_pl6_NonPhagoHFSC_apop_H5_S67_Aligned.quant


title: P17f_pl6_NonPhagoHFSC_apop_G8_S61_Aligned.quant


title: P17f_pl6_NonPhagoHFSC_apop_G7_S60_Aligned.quant


title: P17f_pl6_NonPhagoHFSC_apop_G5_S58_Aligned.quant


title: P17f_pl6_NonPhagoHFSC_apop_G12_S64_Aligned.quant


title: P17f_pl6_NonPhagoHFSC_apop_F7_S52_Aligned.quant


title: P17f_pl6_NonPhagoHFSC_apop_G4_S57_Aligned.quant


title: P17f_pl6_NonPhagoHFSC_apop_F8_S53_Aligned.quant


title: P17f_pl6_NonPhagoHFSC_apop_G6_S59_Aligned.quant


title: P17f_pl6_NonPhagoHFSC_apop_F3_S48_Aligned.quant


title: P17f_pl6_NonPhagoHFSC_apop_F12_S55_Aligned.quant


title: P17f_pl6_NonPhagoHFSC_apop_G9_S62_Aligned.quant


title: P17f_pl6_NonPhagoHFSC_apop_E9_S44_Aligned.quant


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title: P17f_pl6_NonPhagoHFSC_apop_G11_S63_Aligned.quant


title: P17f_pl6_NonPhagoHFSC_apop_F11_S54_Aligned.quant


title: P17f_pl6_NonPhagoHFSC_apop_E7_S42_Aligned.quant


title: P17f_pl6_NonPhagoHFSC_apop_H3_S65_Aligned.quant


title: P17f_pl6_NonPhagoHFSC_apop_E5_S40_Aligned.quant


title: P17f_pl6_NonPhagoHFSC_apop_E6_S41_Aligned.quant


title: P17f_pl6_NonPhagoHFSC_apop_E2_S38_Aligned.quant


title: P17f_pl6_NonPhagoHFSC_apop_E3_S39_Aligned.quant


title: P17f_pl6_NonPhagoHFSC_apop_E12_S47_Aligned.quant


title: P17f_pl6_NonPhagoHFSC_apop_E11_S46_Aligned.quant


title: P17f_pl6_NonPhagoHFSC_apop_D9_S34_Aligned.quant


title: P17f_pl6_NonPhagoHFSC_apop_G1_S56_Aligned.quant


title: P17f_pl6_NonPhagoHFSC_apop_E10_S45_Aligned.quant


title: P17f_pl6_NonPhagoHFSC_apop_F6_S51_Aligned.quant


title: P17f_pl6_NonPhagoHFSC_apop_D6_S32_Aligned.quant


title: P17f_pl6_NonPhagoHFSC_apop_F5_S50_Aligned.quant


title: P17f_pl6_NonPhagoHFSC_apop_E8_S43_Aligned.quant


title: P17f_pl6_NonPhagoHFSC_apop_D3_S30_Aligned.quant


title: P17f_pl6_NonPhagoHFSC_apop_D4_S31_Aligned.quant


title: P17f_pl6_NonPhagoHFSC_apop_D2_S29_Aligned.quant


title: P17f_pl6_NonPhagoHFSC_apop_D10_S35_Aligned.quant


title: P17f_pl6_NonPhagoHFSC_apop_D11_S36_Aligned.quant


title: P17f_pl6_NonPhagoHFSC_apop_D12_S37_Aligned.quant


title: P17f_pl6_NonPhagoHFSC_apop_D1_S28_Aligned.quant


title: P17f_pl6_NonPhagoHFSC_apop_C8_S23_Aligned.quant


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title: P17f_pl6_NonPhagoHFSC_apop_C6_S21_Aligned.quant


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title: P17f_pl5_PhagoHFSC_apop_F6_S132_Aligned.quant


title: P17f_pl5_PhagoHFSC_apop_E9_S123_Aligned.quant


title: P17f_pl5_PhagoHFSC_apop_E7_S121_Aligned.quant


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title: P17f_pl5_PhagoHFSC_apop_E4_S118_Aligned.quant


title: P17f_pl5_PhagoHFSC_apop_F11_S137_Aligned.quant


title: P17f_pl5_PhagoHFSC_apop_F1_S127_Aligned.quant


title: P17f_pl5_PhagoHFSC_apop_E3_S117_Aligned.quant


title: P17f_pl5_PhagoHFSC_apop_E12_S126_Aligned.quant


title: P17f_pl5_PhagoHFSC_apop_E5_S119_Aligned.quant


title: P17f_pl5_PhagoHFSC_apop_F2_S128_Aligned.quant


title: P17f_pl5_PhagoHFSC_apop_E8_S122_Aligned.quant


title: P17f_pl5_PhagoHFSC_apop_E10_S124_Aligned.quant


title: P17f_pl5_PhagoHFSC_apop_E11_S125_Aligned.quant


title: P17f_pl5_PhagoHFSC_apop_D8_S112_Aligned.quant


title: P17f_pl5_PhagoHFSC_apop_D9_S113_Aligned.quant


title: P17f_pl5_PhagoHFSC_apop_E1_S116_Aligned.quant


title: P17f_pl5_PhagoHFSC_apop_D7_S111_Aligned.quant


title: P17f_pl5_PhagoHFSC_apop_D4_S108_Aligned.quant


title: P17f_pl5_PhagoHFSC_apop_D6_S110_Aligned.quant


title: P17f_pl5_PhagoHFSC_apop_D3_S107_Aligned.quant


title: P17f_pl5_PhagoHFSC_apop_D5_S109_Aligned.quant


title: P17f_pl5_PhagoHFSC_apop_D12_S115_Aligned.quant


title: P17f_pl5_PhagoHFSC_apop_C9_S102_Aligned.quant


title: P17f_pl5_PhagoHFSC_apop_D1_S106_Aligned.quant


title: P17f_pl5_PhagoHFSC_apop_D10_S114_Aligned.quant


title: P17f_pl5_PhagoHFSC_apop_C7_S100_Aligned.quant


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title: P17f_pl1_PhagoHFSC_alive_C3_S231_Aligned.quant


title: P17f_pl1_PhagoHFSC_alive_C4_S232_Aligned.quant


title: P17f_pl1_PhagoHFSC_alive_C2_S230_Aligned.quant


title: P17f_pl1_PhagoHFSC_alive_F5_S268_Aligned.quant


title: P17f_pl1_PhagoHFSC_alive_F9_S271_Aligned.quant


title: P17f_pl1_PhagoHFSC_alive_C7_S235_Aligned.quant


title: P17f_pl1_PhagoHFSC_alive_B9_S225_Aligned.quant


title: P17f_pl1_PhagoHFSC_alive_B7_S223_Aligned.quant


title: P17f_pl1_PhagoHFSC_alive_B5_S222_Aligned.quant


title: P17f_pl1_PhagoHFSC_alive_B4_S221_Aligned.quant


title: P17f_pl1_PhagoHFSC_alive_F1_S264_Aligned.quant


title: P17f_pl1_PhagoHFSC_alive_B3_S220_Aligned.quant


title: P17f_pl1_PhagoHFSC_alive_B12_S228_Aligned.quant


title: P17f_pl1_PhagoHFSC_alive_B10_S226_Aligned.quant


title: P17f_pl1_PhagoHFSC_alive_A9_S216_Aligned.quant


title: P17f_pl1_PhagoHFSC_alive_E9_S260_Aligned.quant


title: P17f_pl1_PhagoHFSC_alive_A8_S215_Aligned.quant


title: P17f_pl1_PhagoHFSC_alive_F6_S269_Aligned.quant


title: P17f_pl1_PhagoHFSC_alive_A7_S214_Aligned.quant


title: P17f_pl1_PhagoHFSC_alive_A3_S210_Aligned.quant


title: P17f_pl1_PhagoHFSC_alive_A11_S218_Aligned.quant


title: P17f_pl1_PhagoHFSC_alive_A10_S217_Aligned.quant


title: P17f_pl1_PhagoHFSC_alive_A12_S219_Aligned.quant


title: OSapop_H8_S155_Aligned.quant

value: CatVII


title: P17f_pl1_PhagoHFSC_alive_E10_S261_Aligned.quant


title: P17f_pl1_PhagoHFSC_alive_D7_S247_Aligned.quant


title: P17f_pl1_PhagoHFSC_alive_D4_S244_Aligned.quant


title: P17f_pl1_PhagoHFSC_alive_D3_S243_Aligned.quant


title: OSapop_H6_S140_Aligned.quant


title: OSapop_H5_S152_Aligned.quant


title: P17f_pl1_PhagoHFSC_alive_E2_S253_Aligned.quant


title: P17f_pl1_PhagoHFSC_alive_D11_S251_Aligned.quant


title: P17f_pl1_PhagoHFSC_alive_D1_S241_Aligned.quant


title: P17f_pl1_PhagoHFSC_alive_D10_S250_Aligned.quant


title: OSapop_H4_S151_Aligned.quant


title: P17f_pl1_PhagoHFSC_alive_C5_S233_Aligned.quant


title: P17f_pl1_PhagoHFSC_alive_D8_S248_Aligned.quant


title: OSapop_H3_S150_Aligned.quant


title: P17f_pl1_PhagoHFSC_alive_C12_S240_Aligned.quant


title: P17f_pl1_PhagoHFSC_alive_C10_S238_Aligned.quant


title: P17f_pl1_PhagoHFSC_alive_C11_S239_Aligned.quant


title: OSapop_H2_S137_Aligned.quant


title: P17f_pl1_PhagoHFSC_alive_C9_S237_Aligned.quant


title: OSapop_H10_S157_Aligned.quant


title: P17f_pl1_PhagoHFSC_alive_C1_S229_Aligned.quant


title: OSapop_G8_S133_Aligned.quant


title: P17f_pl1_PhagoHFSC_alive_A6_S213_Aligned.quant


title: P17f_pl1_PhagoHFSC_alive_B8_S224_Aligned.quant


title: P17f_pl1_PhagoHFSC_alive_A2_S209_Aligned.quant


title: P17f_pl1_PhagoHFSC_alive_A5_S212_Aligned.quant


title: OSapop_H9_S156_Aligned.quant


title: OSapop_G3_S140_Aligned.quant


title: OSapop_H9_S143_Aligned.quant


title: OSapop_G2_S139_Aligned.quant


title: OSapop_G12_S147_Aligned.quant


title: OSapop_H7_S154_Aligned.quant


title: OSapop_H7_S141_Aligned.quant


title: OSapop_H8_S142_Aligned.quant


title: OSapop_G11_S135_Aligned.quant


title: P17f_pl1_PhagoHFSC_alive_A4_S211_Aligned.quant


title: OSapop_H5_S139_Aligned.quant


title: OSapop_H6_S153_Aligned.quant


title: OSapop_G1_S127_Aligned.quant


title: OSapop_F9_S136_Aligned.quant


title: OSapop_F8_S125_Aligned.quant


title: OSapop_G11_S146_Aligned.quant


title: OSapop_F7_S135_Aligned.quant


title: OSapop_F7_S124_Aligned.quant


title: OSapop_F6_S134_Aligned.quant


title: OSapop_H2_S149_Aligned.quant


title: OSapop_F6_S123_Aligned.quant


title: OSapop_F4_S133_Aligned.quant


title: OSapop_G10_S145_Aligned.quant


title: OSapop_F3_S121_Aligned.quant


title: OSapop_H4_S138_Aligned.quant


title: OSapop_H11_S158_Aligned.quant


title: OSapop_F11_S137_Aligned.quant


title: OSapop_H1_S148_Aligned.quant


title: OSapop_F1_S131_Aligned.quant


title: OSapop_H1_S136_Aligned.quant


title: OSapop_E7_S126_Aligned.quant


title: OSapop_G9_S144_Aligned.quant


title: OSapop_F2_S120_Aligned.quant


title: OSapop_E7_S115_Aligned.quant


title: OSapop_G7_S132_Aligned.quant


title: OSapop_G6_S142_Aligned.quant


title: OSapop_G5_S130_Aligned.quant


title: OSapop_G6_S131_Aligned.quant


title: OSapop_G4_S141_Aligned.quant


title: OSapop_G4_S129_Aligned.quant


title: OSapop_E5_S124_Aligned.quant


title: OSapop_G3_S128_Aligned.quant


title: OSapop_E5_S114_Aligned.quant


title: OSapop_E3_S122_Aligned.quant


title: OSapop_G7_S143_Aligned.quant


title: OSapop_E9_S128_Aligned.quant


title: OSapop_G10_S134_Aligned.quant


title: OSapop_G1_S138_Aligned.quant


title: OSapop_D8_S118_Aligned.quant


title: OSapop_F5_S122_Aligned.quant


title: OSapop_D9_S110_Aligned.quant


title: OSapop_F3_S132_Aligned.quant


title: OSapop_F1_S119_Aligned.quant


title: OSapop_F10_S126_Aligned.quant


title: OSapop_E9_S117_Aligned.quant


title: OSapop_D7_S108_Aligned.quant


title: OSapop_D4_S105_Aligned.quant


title: OSapop_E2_S113_Aligned.quant


title: OSapop_E8_S127_Aligned.quant


title: OSapop_E8_S116_Aligned.quant


title: OSapop_D4_S115_Aligned.quant


title: OSapop_D2_S113_Aligned.quant


title: OSapop_E6_S125_Aligned.quant


title: OSapop_E4_S123_Aligned.quant


title: OSapop_E2_S121_Aligned.quant


title: OSapop_C9_S100_Aligned.quant


title: OSapop_E11_S130_Aligned.quant


title: OSapop_E10_S129_Aligned.quant


title: OSapop_D9_S119_Aligned.quant


title: OSapop_C8_S99_Aligned.quant


title: OSapop_C7_S98_Aligned.quant


title: OSapop_D1_S103_Aligned.quant


title: OSapop_C6_S97_Aligned.quant


title: OSapop_C5_S107_Aligned.quant


title: OSapop_C6_S108_Aligned.quant


title: OSapop_C3_S94_Aligned.quant


title: OSapop_C4_S106_Aligned.quant


title: OSapop_D7_S117_Aligned.quant


title: OSapop_D8_S109_Aligned.quant


title: OSapop_D6_S116_Aligned.quant


title: OSapop_D6_S107_Aligned.quant


title: OSapop_D5_S106_Aligned.quant


title: OSapop_C2_S93_Aligned.quant


title: OSapop_C2_S104_Aligned.quant


title: OSapop_C10_S101_Aligned.quant


title: OSapop_C12_S102_Aligned.quant


title: OSapop_C1_S103_Aligned.quant


title: OSapop_B9_S90_Aligned.quant


title: OSapop_D3_S104_Aligned.quant


title: OSapop_E12_S118_Aligned.quant


title: OSapop_B8_S89_Aligned.quant


title: OSapop_D12_S112_Aligned.quant


title: OSapop_D3_S114_Aligned.quant


title: OSapop_B6_S97_Aligned.quant


title: OSapop_D10_S120_Aligned.quant


title: OSapop_B7_S88_Aligned.quant


title: OSapop_D1_S112_Aligned.quant


title: OSapop_B5_S96_Aligned.quant


title: OSapop_C8_S110_Aligned.quant


title: OSapop_C5_S96_Aligned.quant


title: OSapop_C4_S95_Aligned.quant


title: OSapop_D11_S111_Aligned.quant


title: OSapop_C3_S105_Aligned.quant


title: OSapop_C10_S111_Aligned.quant


title: OSapop_C7_S109_Aligned.quant


title: OSapop_B9_S100_Aligned.quant


title: OSapop_B1_S92_Aligned.quant


title: OSapop_B8_S99_Aligned.quant


title: OSapop_B1_S83_Aligned.quant


title: OSapop_B7_S98_Aligned.quant


title: OSapop_A8_S82_Aligned.quant


title: OSapop_A7_S90_Aligned.quant


title: OSapop_B6_S87_Aligned.quant


title: OSapop_B3_S94_Aligned.quant


title: OSapop_A5_S81_Aligned.quant


title: OSapop_A6_S89_Aligned.quant


title: OSapop_A3_S86_Aligned.quant


title: OSapop_A3_S79_Aligned.quant


title: OSapop_B4_S95_Aligned.quant


title: OSapop_A2_S85_Aligned.quant


title: OSapop_A2_S78_Aligned.quant


title: OSapop_B4_S86_Aligned.quant


title: OSapop_B3_S85_Aligned.quant


title: OSapop_A1_S77_Aligned.quant


title: OSalive_H6_S74_Aligned.quant


title: OSapop_B2_S93_Aligned.quant


title: OSapop_B2_S84_Aligned.quant


title: OSalive_H5_S73_Aligned.quant


title: OSalive_H4_S72_Aligned.quant


title: OSapop_B12_S92_Aligned.quant


title: OSapop_B11_S102_Aligned.quant


title: OSalive_H2_S70_Aligned.quant


title: OSalive_H10_S82_Aligned.quant


title: OSalive_H1_S69_Aligned.quant


title: OSapop_B10_S101_Aligned.quant


title: OSapop_A9_S91_Aligned.quant


title: OSalive_G9_S70_Aligned.quant


title: OSalive_H4_S76_Aligned.quant


title: OSapop_A5_S88_Aligned.quant


title: OSapop_A4_S87_Aligned.quant


title: OSalive_G8_S66_Aligned.quant


title: OSapop_B10_S91_Aligned.quant


title: OSalive_G7_S65_Aligned.quant


title: OSalive_G6_S67_Aligned.quant


title: OSapop_A1_S84_Aligned.quant


title: OSalive_H9_S81_Aligned.quant


title: OSapop_A4_S80_Aligned.quant


title: OSalive_G5_S66_Aligned.quant


title: OSalive_G5_S63_Aligned.quant


title: OSalive_G3_S64_Aligned.quant


title: OSalive_H8_S80_Aligned.quant


title: OSalive_H8_S76_Aligned.quant


title: OP-4

city: Nanning

first: Sanbao

last: Zhang

address: No.100,Daxue East Road

country: China

institute: Guangxi University

library_source: transcriptomic

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Fragments per Kilobase per Million Mapped Fragments (FPKM)were calculated using a protocol from Trapnell, C. et al, 2010.Spliced Reads per Billion Mapping (SRPBM)  calculated using a protocol from Li, et al. 2015 . In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: mm9
Supplementary files format and content: tab-delimited text files include FPKM/TPM/SRPBM values for each Sample …
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

molecule: total RNA

source_name: Granulosa cells

extract_protocol:
Cloning of SERPINE2 gene CDs, double enzyme digestion, TOS189-1 vector double enzyme digestion, ligation, transformation, bacterial solution PCR and sequencing comparison, the lentivirus vector was packaged and constructed by Starfish Biotechnology (Suzhou) Co., Ltd. Consistently, control virus—pLV[Exp]-EGFP:T2A:Puro-EF1A>mCherry also provided by the company. GCs were transfected with a negative control duplex or siRNAs against SERPINE2 using Lipofectamine 3000 Transfection Reagent (Thermo Fisher Scientific) following the manufacturer’s instructions. After screening the multiplicity infection, lentivirus was transfected into GCs following the manufacturer’s instructions and the positive cells were screened by puromycin dihydrochloride. 48 h after transfection, the cells were collected for RNA sequencing.Total RNA was extracted from 1Í106 cells using TRIzol Reagent (Thermo Fisher Scientific). 3 mg per sample were constructed into libraries through TruSeq Stranded mRNA LTSample Prep Kit for Illumina (RS-122-2101) following manufacturer’s manuals. Sequencing data were generated on Illumina HiSeqTM 2500 platform with 150-bp paired-end read length by OE Biotech Co., Ltd (Shanghai, China).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: ovarian

tag: strain

tag: transfection

value: siRNAs against SERPINE2


title: OP-2


title: OP-1


title: OSalive_H7_S75_Aligned.quant


title: OSalive_H6_S78_Aligned.quant


title: OSalive_H7_S79_Aligned.quant


title: OSalive_H5_S77_Aligned.quant


title: OSalive_H2_S74_Aligned.quant


title: OSalive_H3_S75_Aligned.quant


title: OSalive_H11_S83_Aligned.quant


title: OSalive_G10_S71_Aligned.quant


title: Con-3

value: negative control duplex


title: OSalive_H3_S71_Aligned.quant


title: OSalive_H1_S73_Aligned.quant


title: OSalive_G9_S67_Aligned.quant


title: OSalive_G8_S69_Aligned.quant


title: OSalive_G6_S64_Aligned.quant


title: OSalive_F9_S56_Aligned.quant


title: OSalive_F8_S59_Aligned.quant


title: WT, salt, 15 min, rep 2

city: Chapel Hill

first: Henrik

middle: Gunnar

last: Dohlman

address: 120 Mason Farm Rd

institute: UNC Chapel Hill

description:
GroupA-vs-GroupG
GroupH-vs-GroupG

data_processing:
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36
The trimmed reads were mapped to the Saccharomyces cerevisiae S288c reference genome available on ENSEMBL using the STAR aligner v.2.5.2b
The STAR aligner is a splice aligner that detects splice junctions and incorporates them to help align the entire read sequences.
BAM files were generated as a result of this step.
Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2
Assembly: S288c
Supplementary files format and content: txt format of raw counts and differential expression analysis tables, including volcano, PCA, MA, PTM plots.

organism: Saccharomyces cerevisiae

source_name: single cell

growth_protocol: Cells were grown from a single colony to saturation overnight. Next day, cells were diluted and grown to OD600nm of 0.7 (~107 cells/mL). Then, cells were treated with 350 mM KCl, 30 μM mating pheromone or the combination of both for 15 min. At the 13-min mark, cells were harvested by centrifugation at 16,000 x g for two min and flash frozen in liquid nitrogen and stored on dry ice

extract_protocol:
We submit sample to Azenta Life Science for RNA extraction, sequencing and data analysis. Used Rnaeasy kit for extraction (Qiagen)
The RNA sequencing libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina using manufacturer’s instructions (New England Biolabs, Ipswich, MA, USA). Briefly, mRNAs were initially enriched with Oligo d(T) beads.

treatment_protocol: 350 mM KCl for 15 min

value: single cell

value: WT

tag: treatment

value: 350 mM KCl for 15 min


title: WT, salt, 15 min, rep 1

description:
GroupA-vs-GroupG
GroupH-vs-GroupG


title: OSalive_G4_S62_Aligned.quant


title: OSalive_F7_S58_Aligned.quant


title: OSalive_G4_S65_Aligned.quant


title: OSalive_F7_S54_Aligned.quant


title: OSalive_G7_S68_Aligned.quant


title: OSalive_G3_S61_Aligned.quant


title: OP-3


title: sho1𝛥𝛥, salt, 15min, rep2

description:
GroupC-vs-GroupI
GroupG-vs-GroupI


title: OSalive_G2_S60_Aligned.quant


title: OSalive_G2_S63_Aligned.quant


title: OSalive_G11_S72_Aligned.quant


title: Con-4


title: OSalive_G10_S68_Aligned.quant


title: sho1𝛥𝛥, salt, 15min, rep1

description:
GroupC-vs-GroupI
GroupG-vs-GroupI


title: Con-2


title: OSalive_G1_S59_Aligned.quant


title: Con-1


title: OSalive_F9_S60_Aligned.quant


title: WT, salt, 15 min, rep 3

description:
GroupA-vs-GroupG
GroupH-vs-GroupG


title: OSalive_F6_S57_Aligned.quant


title: WT, 0, 15 min, rep 1

description: GroupA-vs-GroupG

value: no treatment


title: sho1𝛥𝛥, salt, 15min, rep3

description:
GroupC-vs-GroupI
GroupG-vs-GroupI


title: OSalive_F6_S53_Aligned.quant


title: OSalive_F4_S51_Aligned.quant


title: ssk1𝛥, salt, 15min, rep3

description:
GroupB-vs-GroupH
GroupG-vs-GroupH


title: OSalive_F2_S53_Aligned.quant


title: sho1𝛥𝛥, 0, 15min, rep3

description: GroupC-vs-GroupI


title: OSalive_F2_S49_Aligned.quant


title: OSalive_F5_S56_Aligned.quant


title: OSalive_F8_S55_Aligned.quant


title: OSalive_F3_S54_Aligned.quant


title: sho1𝛥𝛥, 0, 15min, rep2

description: GroupC-vs-GroupI


title: WT, 0, 15 min, rep 3

description: GroupA-vs-GroupG


title: OSalive_F4_S55_Aligned.quant


title: OSalive_F5_S52_Aligned.quant


title: OSalive_F10_S61_Aligned.quant


title: WT, 0, 15 min, rep 2

description: GroupA-vs-GroupG


title: OSalive_F10_S57_Aligned.quant


title: ssk1𝛥, salt, 15min, rep2

description:
GroupB-vs-GroupH
GroupG-vs-GroupH


title: OSalive_F3_S50_Aligned.quant


title: ssk1𝛥kss1𝛥, 0, 15min, rep2

description: GroupE-vs-GroupK


title: sho1𝛥𝛥, 0, 15min, rep1

description: GroupC-vs-GroupI


title: ssk1𝛥, 0, 15min, rep2

description: GroupB-vs-GroupH


title: OSalive_F11_S62_Aligned.quant


title: OSalive_F11_S58_Aligned.quant


title: ssk1𝛥, 0, 15min, rep1

description: GroupB-vs-GroupH


title: ssk1𝛥, 0, 15min, rep3

description: GroupB-vs-GroupH


title: ssk1𝛥kss1𝛥, 0, 15min, rep3

description: GroupE-vs-GroupK


title: ssk1𝛥, salt, 15min, rep1

description:
GroupB-vs-GroupH
GroupG-vs-GroupH


title: ssk1𝛥kss1𝛥, salt, 15min, rep2

description: GroupE-vs-GroupK


title: ssk1𝛥kss1𝛥, 0, 15min, rep1

description: GroupE-vs-GroupK


title: OSalive_F1_S52_Aligned.quant


title: OSalive_E9_S49_Aligned.quant


title: OSalive_F1_S48_Aligned.quant


title: ssk1𝛥kss1𝛥, salt, 15min, rep3

description: GroupE-vs-GroupK


title: OSalive_E8_S48_Aligned.quant


title: ssk1𝛥kss1𝛥, salt, 15min, rep1

description:
The processed data is in a folder
GroupE-vs-GroupK


title: 585A1_hiPSCs_D0_sample4

description: mRNA-seq (polyA+) data from 585A1 hiPSCs cultured in mTeSR-1 on Matrigel, sample 4

organism: Homo

source_name: 585A1 hiPSCs

growth_protocol: Prior to culturing, 1.3% (v/v) hESC-certified Matrigel (Corning, NY, USA) in DMEM/F12 medium was coated on a culture dish. Matrigel was incubated in a dish for 24 h at 4˚C. Then, excess Matrigel was removed, and the coated dish was washed with a fresh DMEM/F12 medium. A mTeSR-1 medium was used for the daily culturing of hPSCs. For passaging, cells were dissociated with TrypLE Express (Life Technologies, Carlsbad, CA, USA) for 3 min at 37 ˚C, and then harvested. A cell strainer was used to remove undesired cell aggregates from the cell suspension. The cells were centrifuged at 200 × g for 3 min and resuspended in the mTeSR-1 medium. The cells were counted using a NucleoCounter NC-200 (Chemetec, Baton Rouge, LA, USA). A mTeSR-1 medium containing 10 µM of Y27632 was used to prevent the apoptosis of the dissociated hPSCs, on day 1. mTeSR-1 medium without Y27632 was used on the subsequent days, with daily medium change. The cells were maintained in an incubator at 37°C with 5% (v/v) CO2.

treatment_protocol: hPSCs cultured on Matrigel-coated dishes with a mTeSR-1 medium were harvested with TrypLE Express for 3 min at 37°C and transferred in a 15-mL tube. The dissociated hPSCs were resuspended in mTeSR-1 medium supplemented with 10 µM of Y27632, and then transferred to Aggrewell 400 (Stem Cell Technologies) at 6 × 10^5 cells per well. After culturing in an incubator for 24 h at 37°C with 5% (v/v) CO2, the hPSC aggregates were resuspended in the HG solution {DMEM with 10%[w/v] PNIPAAm-β-PEG hydrogel at 4°C. 260 µL of an hPSC aggregate suspension with HG was transferred into the well of a 24-well plate, and then DMEM supplemented with 10%(v/v) FBS was added at 37°C. After 3-day culture, iBlastoid medium was changed on a daily basis, and the cells were maintained at 37°C with 5% (v/v) CO2 in an incubator.

value: mTeSR-1 on Matrigel

value: Induced pluripotent stem cells


title: 585A1_hiPSCs_D0_sample3

description: mRNA-seq (polyA+) data from 585A1 hiPSCs cultured in mTeSR-1 on Matrigel, sample 3


title: OSalive_E8_S46_Aligned.quant

value: skin


title: OSalive_E9_S47_Aligned.quant

value: hair follicle epithelial cell


title: OSalive_E7_S45_Aligned.quant

value: wild type


title: OSalive_E5_S45_Aligned.quant


title: OSalive_E6_S46_Aligned.quant


title: 585A1_hiPSCs_D9_sample2

description: mRNA-seq (polyA+) data from blastoids derived from 585A1 hiPSCs cultured in iBlastoid medium with hydrogel, sample 2

value: iBlastoid medium with hydrogel

value: Early blastoid


title: 585A1_hiPSCs_D9_sample1

description: mRNA-seq (polyA+) data from blastoids derived from 585A1 hiPSCs cultured in iBlastoid medium with hydrogel, sample 1


title: Patient13_control

city: LIMOGES

first: Stéphanie

last: DURAND

address: 2 rue du Dr Marcland

department: UMR 1308 INSERM

country: France

institute: University of Limoges / INSERM

data_processing:
Quality control of 150 bp paired-end reads were checked by FastQC software, low-quality end reads were trimmed (Phred quality score < 30), and adapter removal was performed using Cutadapt (version 3.7).
The clean reads of each sample were mapped to the human reference genome (GRCh38 assembly) using STAR splice-mapper (2.7.9a).
Read counts for each gene were obtained using the featureCounts counting tool (Subread version 2.0.3).
Differential gene expression was conducted pair-wise using DESeq2 to identify differentially expressed genes (DEGs) in EVs-treated versus untreated NLCs according to the following selection criteria: absolute fold change superior to 1,5 and p-adjusted (after Benjamini-Hochberg (BH) multiple testing correction)  inferior to 0.1.
Assembly: Homo sapiensGRCh38.105
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: B cells

growth_protocol: B cells were isolated from CLL patients PBMCs using the MACSxpress Whole Blood B-CLL Cell Isolation Kit (#130104445, Miltenyi). They were cultivated in in RPMI 1640 medium (ThermoFisher) supplemented with 10% decomplemented fetal bovine serum (FBS) and 1% antibiotics (penicillin/streptomycin).

extract_protocol:
Total RNAs were extracted from cells using the Quick-RNA™ Microprep Kit (Zymo Research). The 2100 Bioanalyzer system (Agilent) was used to quantify and perform quality control of the samples before sending them to Novogene for subsequent analysis.
According to Novogene's protocol, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification.The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries were pooled and sequenced on Illumina platforms, according to effective library concentration and data amount.

treatment_protocol: B-cells from CLL patients were either treated with extracellular vesicles produced by nurse-like cells or left untreated for 24h (1.10-3 ng of EV protein per cell)

tag: individual

tag: tissue origin

value: blood

value: B cells

tag: binet stage

value: B

tag: tp53 mutation

value: mutated

tag: igvh mutation

value: unmutated

value: untreated


title: Patient12_control

value: C


title: OSalive_E5_S44_Aligned.quant

value: upper outer root sheath

value: CatVII


title: Patient10_control

value: A


title: OSalive_E2_S43_Aligned.quant


title: OSalive_E4_S44_Aligned.quant


title: OSalive_E3_S42_Aligned.quant


title: OSalive_E7_S47_Aligned.quant


title: Patient12_treated

value: treated


title: OSalive_E2_S41_Aligned.quant


title: Patient13_treated


title: Patient10_treated


title: OSalive_E10_S50_Aligned.quant


title: hpOsCas12f1_Tag-seq_Rep1

city: Guangzhou

first: Kechen

last: Chen

state: Guangdong

address: Shatai South Road

institute: Southern Medical University

description: Evaluation of the editing specificity of hpOsCas12f1 in the MCF7 cells, repeat 1

data_processing:
The analysis pipeline can be accessed at https://github.com/zhoujj2013/Tag-seq
Assembly: hg38
Supplementary files format and content: Bed file for all cutting sites

growth_protocol: MCF7 cells were maintained inRPMI-1640 medium supplemented with 10% fetal bovine serum (FBS) and 1% penicillin/streptomycin.

extract_protocol:
The MCF7 transfected cells were washed with 1x PBS, and harvested. The gDNA purified using the TIANamp Genomic DNA Kit.
The gDNA was fragmented, end-repaired, and ligated by dA-tail.

treatment_protocol: In 24-well plates, MCF7 cells were transfected with 490ng gRNA plasmids and 10ng CasMINI or hpCasMINI or SpCas9 or LbCas12a plasmids.

value: epithelial cell


title: hpOsCas12f1_Tag-seq_Rep3

description: Evaluation of the editing specificity of hpOsCas12f1 in the MCF7 cells, repeat 3


title: OSalive_E1_S40_Aligned.quant

value: skin


title: OSalive_D9_S40_Aligned.quant

value: hair follicle epithelial cell


title: enOsCas12f1_Tag-seq_Rep1

description: Evaluation of the editing specificity of enOsCas12f1 in the MCF7 cells, repeat 1


title: OSalive_E11_S51_Aligned.quant

value: wild type


title: enOsCas12f1_Tag-seq_Rep3

description: Evaluation of the editing specificity of enOsCas12f1 in the MCF7 cells, repeat 3


title: OSalive_D8_S36_Aligned.quant


title: OSalive_D7_S38_Aligned.quant


title: OSalive_D9_S37_Aligned.quant


title: SpCas9_Tag-seq_Rep3

description: Evaluation of the editing specificity of SpCas9 in the MCF7 cells, repeat 3


title: OSalive_D8_S39_Aligned.quant


title: SpCas9_Tag-seq_Rep2

description: Evaluation of the editing specificity of SpCas9 in the MCF7 cells, repeat 2


title: enOsCas12f1_Tag-seq_Rep2

description: Evaluation of the editing specificity of enOsCas12f1 in the MCF7 cells, repeat 2


title: OSalive_E4_S43_Aligned.quant


title: SpCas9_Tag-seq_Rep1

description: Evaluation of the editing specificity of SpCas9 in the MCF7 cells, repeat 1


title: LbCas12a_Tag-seq_Rep2

description: Evaluation of the editing specificity of LbCas12a in the MCF7 cells, repeat 2


title: LbCas12a_Tag-seq_Rep1

description: Evaluation of the editing specificity of LbCas12a in the MCF7 cells, repeat 1


title: LbCas12a_Tag-seq_Rep3

description: Evaluation of the editing specificity of LbCas12a in the MCF7 cells, repeat 3


title: hpOsCas12f1_Tag-seq_Rep2

description: Evaluation of the editing specificity of hpOsCas12f1 in the MCF7 cells, repeat 2


title: OSalive_D6_S37_Aligned.quant


title: OSalive_D5_S33_Aligned.quant


title: OSalive_D6_S34_Aligned.quant


title: OSalive_D5_S36_Aligned.quant


title: hpCasMINI_Tag-seq_Rep1

description: Evaluation of the editing specificity of hpCasMINI in the MCF7 cells, repeat 1


title: OSalive_D3_S34_Aligned.quant


title: hpCasMINI_Tag-seq_Rep3

description: Evaluation of the editing specificity of hpCasMINI in the MCF7 cells, repeat 3


title: hpCasMINI_L10_Deep-seq_gRNA-truncated_Rep3

description: The DNA cleavage efficiency in the MCF7 cells transfected with the hpCasMINI system targeting two different genomic sites, 10 base truncated gRNA repeat 3

data_processing:
Raw paired-end reads were subjected to sublibrary barcode removal (first 6 bp) using cutadapt.
Reads were then aligned to their respective reference sequences using Bowtie 2.
Editing events were quantified using CRISPResso2.
Assembly: hg38
Supplementary files format and content: txt file for deletion rate around the gRNA target sites.
Supplementary files format and content: txt file for indel rate for gRNA taget sites.

extract_protocol:
The MCF7 transfected cells were washed with 1x PBS, and harvested. The gDNA purified using the TIANamp Genomic DNA Kit.
Two round PCR were performed, the forward and reverse primers were used to amplify the target site of the first round of PCR, and then an equal amount of the first PCR product was mixed with primers containing P5 and p7 for a second round of PCR to generate the library.


title: hpCasMINI_L10_Deep-seq_gRNA-truncated_Rep2

description: The DNA cleavage efficiency in the MCF7 cells transfected with the hpCasMINI system targeting two different genomic sites, 10 base truncated gRNA repeat 2


title: OSalive_D3_S31_Aligned.quant


title: hpCasMINI_L8_Deep-seq_gRNA-truncated_Rep3

description: The DNA cleavage efficiency in the MCF7 cells transfected with the hpCasMINI system targeting two different genomic sites, 8 base truncated gRNA repeat 3


title: hpCasMINI_L10_Deep-seq_gRNA-truncated_Rep1

description: The DNA cleavage efficiency in the MCF7 cells transfected with the hpCasMINI system targeting two different genomic sites, 10 base truncated gRNA repeat 1


title: OSalive_D2_S33_Aligned.quant


title: OSalive_D7_S35_Aligned.quant


title: OSalive_D2_S30_Aligned.quant


title: CasMINI_Tag-seq

description: Evaluation of the editing specificity of CasMINI in the MCF7 cells


title: hpCasMINI_L8_Deep-seq_gRNA-truncated_Rep2

description: The DNA cleavage efficiency in the MCF7 cells transfected with the hpCasMINI system targeting two different genomic sites, 8 base truncated gRNA repeat 2


title: OSalive_D11_S42_Aligned.quant


title: hpCasMINI_L8_Deep-seq_gRNA-truncated_Rep1

description: The DNA cleavage efficiency in the MCF7 cells transfected with the hpCasMINI system targeting two different genomic sites, 8 base truncated gRNA repeat 1


title: OSalive_D11_S39_Aligned.quant


title: hpCasMINI_L6_Deep-seq_gRNA-truncated_Rep3

description: The DNA cleavage efficiency in the MCF7 cells transfected with the hpCasMINI system targeting two different genomic sites, 6 base truncated gRNA repeat 3


title: OSalive_D1_S32_Aligned.quant


title: hpCasMINI_L6_Deep-seq_gRNA-truncated_Rep1

description: The DNA cleavage efficiency in the MCF7 cells transfected with the hpCasMINI system targeting two different genomic sites, 6 base truncated gRNA repeat 1


title: OSalive_D4_S35_Aligned.quant


title: OSalive_D10_S38_Aligned.quant


title: OSalive_D10_S41_Aligned.quant


title: hpCasMINI_L6_Deep-seq_gRNA-truncated_Rep2

description: The DNA cleavage efficiency in the MCF7 cells transfected with the hpCasMINI system targeting two different genomic sites, 6 base truncated gRNA repeat 2


title: OSalive_D1_S29_Aligned.quant


title: hpCasMINI_Tag-seq_Rep2

description: Evaluation of the editing specificity of hpCasMINI in the MCF7 cells, repeat 2


title: hpCasMINI_L4_Deep-seq_gRNA-truncated_Rep3

description: The DNA cleavage efficiency in the MCF7 cells transfected with the hpCasMINI system targeting two different genomic sites, 4 base truncated gRNA repeat 3


title: hpCasMINI_L4_Deep-seq_gRNA-truncated_Rep2

description: The DNA cleavage efficiency in the MCF7 cells transfected with the hpCasMINI system targeting two different genomic sites, 4 base truncated gRNA repeat 2


title: OSalive_D4_S32_Aligned.quant


title: OSalive_C9_S29_Aligned.quant


title: hpCasMINI_L4_Deep-seq_gRNA-truncated_Rep1

description: The DNA cleavage efficiency in the MCF7 cells transfected with the hpCasMINI system targeting two different genomic sites, 4 base truncated gRNA repeat 1


title: hpCasMINI_L2_Deep-seq_gRNA-truncated_Rep2

description: The DNA cleavage efficiency in the MCF7 cells transfected with the hpCasMINI system targeting two different genomic sites, 2 base truncated gRNA repeat 2


title: OSalive_C8_S28_Aligned.quant


title: OSalive_C9_S27_Aligned.quant


title: OSalive_C8_S26_Aligned.quant


title: OSalive_C7_S27_Aligned.quant


title: hpCasMINI_L2_Deep-seq_gRNA-truncated_Rep3

description: The DNA cleavage efficiency in the MCF7 cells transfected with the hpCasMINI system targeting two different genomic sites, 2 base truncated gRNA repeat 3


title: hpCasMINI_L2_Deep-seq_gRNA-truncated_Rep1

description: The DNA cleavage efficiency in the MCF7 cells transfected with the hpCasMINI system targeting two different genomic sites, 2 base truncated gRNA repeat 1


title: OSalive_C7_S25_Aligned.quant


title: OSalive_C6_S26_Aligned.quant


title: OSalive_C6_S24_Aligned.quant


title: hpCasMINI_L0_Deep-seq_gRNA-truncated_Rep3

description: The DNA cleavage efficiency in the MCF7 cells transfected with the hpCasMINI system targeting two different genomic sites, no truncated gRNA repeat 3


title: CasMINI_L10_Deep-seq_gRNA-truncated_Rep3

description: The DNA cleavage efficiency in the MCF7 cells transfected with the CasMINI system targeting two different genomic sites, 10 base truncated gRNA repeat 3


title: hpCasMINI_L0_Deep-seq_gRNA-truncated_Rep2

description: The DNA cleavage efficiency in the MCF7 cells transfected with the hpCasMINI system targeting two different genomic sites, no truncated gRNA repeat 2


title: hpCasMINI_L0_Deep-seq_gRNA-truncated_Rep1

description: The DNA cleavage efficiency in the MCF7 cells transfected with the hpCasMINI system targeting two different genomic sites, no truncated gRNA repeat 1


title: OSalive_C5_S25_Aligned.quant


title: CasMINI_L10_Deep-seq_gRNA-truncated_Rep2

description: The DNA cleavage efficiency in the MCF7 cells transfected with the CasMINI system targeting two different genomic sites, 10 base truncated gRNA repeat 2


title: OSalive_C5_S23_Aligned.quant


title: CasMINI_L8_Deep-seq_gRNA-truncated_Rep3

description: The DNA cleavage efficiency in the MCF7 cells transfected with the CasMINI system targeting two different genomic sites, 8 base truncated gRNA repeat 3


title: OSalive_C4_S22_Aligned.quant


title: OSalive_C3_S23_Aligned.quant


title: CasMINI_L8_Deep-seq_gRNA-truncated_Rep1

description: The DNA cleavage efficiency in the MCF7 cells transfected with the CasMINI system targeting two different genomic sites, 8 base truncated gRNA repeat 1


title: CasMINI_L8_Deep-seq_gRNA-truncated_Rep2

description: The DNA cleavage efficiency in the MCF7 cells transfected with the CasMINI system targeting two different genomic sites, 8 base truncated gRNA repeat 2


title: CasMINI_L10_Deep-seq_gRNA-truncated_Rep1

description: The DNA cleavage efficiency in the MCF7 cells transfected with the CasMINI system targeting two different genomic sites, 10 base truncated gRNA repeat 1


title: OSalive_C3_S21_Aligned.quant


title: CasMINI_L6_Deep-seq_gRNA-truncated_Rep2

description: The DNA cleavage efficiency in the MCF7 cells transfected with the CasMINI system targeting two different genomic sites, 6 base truncated gRNA repeat 2


title: CasMINI_L6_Deep-seq_gRNA-truncated_Rep3

description: The DNA cleavage efficiency in the MCF7 cells transfected with the CasMINI system targeting two different genomic sites, 6 base truncated gRNA repeat 3


title: OSalive_C2_S20_Aligned.quant


title: CasMINI_L6_Deep-seq_gRNA-truncated_Rep1

description: The DNA cleavage efficiency in the MCF7 cells transfected with the CasMINI system targeting two different genomic sites, 6 base truncated gRNA repeat 1


title: OSalive_C2_S22_Aligned.quant


title: CasMINI_L4_Deep-seq_gRNA-truncated_Rep1

description: The DNA cleavage efficiency in the MCF7 cells transfected with the CasMINI system targeting two different genomic sites, 4 base truncated gRNA repeat 1


title: CasMINI_L4_Deep-seq_gRNA-truncated_Rep3

description: The DNA cleavage efficiency in the MCF7 cells transfected with the CasMINI system targeting two different genomic sites, 4 base truncated gRNA repeat 3


title: CasMINI_L4_Deep-seq_gRNA-truncated_Rep2

description: The DNA cleavage efficiency in the MCF7 cells transfected with the CasMINI system targeting two different genomic sites, 4 base truncated gRNA repeat 2


title: OSalive_C10_S30_Aligned.quant


title: OSalive_C11_S31_Aligned.quant


title: OSalive_C4_S24_Aligned.quant


title: OSalive_B9_S18_Aligned.quant


title: OSalive_B8_S16_Aligned.quant


title: OSalive_C1_S21_Aligned.quant


title: OSalive_B8_S17_Aligned.quant


title: CasMINI_L2_Deep-seq_gRNA-truncated_Rep2

description: The DNA cleavage efficiency in the MCF7 cells transfected with the CasMINI system targeting two different genomic sites, 2 base truncated gRNA repeat 2


title: Ctrl_Deep-seq_gRNA-truncated_Rep3

description: The DNA cleavage efficiency in the MCF7 cells transfected without the CasMINI or hpCasMINI system targeting two different genomic sites, repeat 3


title: CasMINI_L0_Deep-seq_gRNA-truncated_Rep3

description: The DNA cleavage efficiency in the MCF7 cells transfected with the CasMINI system targeting two different genomic sites, no truncated gRNA repeat 3


title: OSalive_B7_S15_Aligned.quant


title: CasMINI_L0_Deep-seq_gRNA-truncated_Rep1

description: The DNA cleavage efficiency in the MCF7 cells transfected with the CasMINI system targeting two different genomic sites, no truncated gRNA repeat 1


title: Ctrl_Deep-seq_gRNA-truncated_Rep1

description: The DNA cleavage efficiency in the MCF7 cells transfected without the CasMINI or hpCasMINI system targeting two different genomic sites, repeat 1


title: OSalive_B6_S14_Aligned.quant


title: Ctrl_Deep-seq_gRNA-truncated_Rep2

description: The DNA cleavage efficiency in the MCF7 cells transfected without the CasMINI or hpCasMINI system targeting two different genomic sites, repeat 2


title: hpCasMINI_DM10_Deep-seq_gRNA-mismatch_Rep3

description: The DNA cleavage efficiency in the MCF7 cells transfected with the hpCasMINI system targeting two different genomic sites, double mismatch gRNA site 10 repeat 3


title: OSalive_B4_S14_Aligned.quant


title: hpCasMINI_DM10_Deep-seq_gRNA-mismatch_Rep2

description: The DNA cleavage efficiency in the MCF7 cells transfected with the hpCasMINI system targeting two different genomic sites, double mismatch gRNA site 10 repeat 2


title: OSalive_C11_S28_Aligned.quant


title: OSalive_B5_S13_Aligned.quant


title: OSalive_B4_S12_Aligned.quant


title: CasMINI_L2_Deep-seq_gRNA-truncated_Rep3

description: The DNA cleavage efficiency in the MCF7 cells transfected with the CasMINI system targeting two different genomic sites, 2 base truncated gRNA repeat 3


title: CasMINI_L2_Deep-seq_gRNA-truncated_Rep1

description: The DNA cleavage efficiency in the MCF7 cells transfected with the CasMINI system targeting two different genomic sites, 2 base truncated gRNA repeat 1


title: OSalive_B3_S13_Aligned.quant


title: OSalive_B9_S17_Aligned.quant


title: hpCasMINI_DM10_Deep-seq_gRNA-mismatch_Rep1

description: The DNA cleavage efficiency in the MCF7 cells transfected with the hpCasMINI system targeting two different genomic sites, double mismatch gRNA site 10 repeat 1


title: OSalive_B3_S11_Aligned.quant


title: hpCasMINI_DM9_Deep-seq_gRNA-mismatch_Rep2

description: The DNA cleavage efficiency in the MCF7 cells transfected with the hpCasMINI system targeting two different genomic sites, double mismatch gRNA site 9 repeat 2


title: OSalive_B6_S16_Aligned.quant


title: CasMINI_L0_Deep-seq_gRNA-truncated_Rep2

description: The DNA cleavage efficiency in the MCF7 cells transfected with the CasMINI system targeting two different genomic sites, no truncated gRNA repeat 2


title: hpCasMINI_DM9_Deep-seq_gRNA-mismatch_Rep3

description: The DNA cleavage efficiency in the MCF7 cells transfected with the hpCasMINI system targeting two different genomic sites, double mismatch gRNA site 9 repeat 3


title: OSalive_B2_S12_Aligned.quant


title: OSalive_B2_S10_Aligned.quant


title: hpCasMINI_DM9_Deep-seq_gRNA-mismatch_Rep1

description: The DNA cleavage efficiency in the MCF7 cells transfected with the hpCasMINI system targeting two different genomic sites, double mismatch gRNA site 9 repeat 1


title: OSalive_B5_S15_Aligned.quant


title: OSalive_B11_S20_Aligned.quant


title: hpCasMINI_DM8_Deep-seq_gRNA-mismatch_Rep3

description: The DNA cleavage efficiency in the MCF7 cells transfected with the hpCasMINI system targeting two different genomic sites, double mismatch gRNA site 8 repeat 3


title: hpCasMINI_DM8_Deep-seq_gRNA-mismatch_Rep2

description: The DNA cleavage efficiency in the MCF7 cells transfected with the hpCasMINI system targeting two different genomic sites, double mismatch gRNA site 8 repeat 2


title: hpCasMINI_DM8_Deep-seq_gRNA-mismatch_Rep1

description: The DNA cleavage efficiency in the MCF7 cells transfected with the hpCasMINI system targeting two different genomic sites, double mismatch gRNA site 8 repeat 1


title: OSalive_B11_S19_Aligned.quant


title: OSalive_B1_S9_Aligned.quant


title: OSalive_B10_S18_Aligned.quant


title: hpCasMINI_DM7_Deep-seq_gRNA-mismatch_Rep2

description: The DNA cleavage efficiency in the MCF7 cells transfected with the hpCasMINI system targeting two different genomic sites, double mismatch gRNA site 7 repeat 2


title: hpCasMINI_DM7_Deep-seq_gRNA-mismatch_Rep1

description: The DNA cleavage efficiency in the MCF7 cells transfected with the hpCasMINI system targeting two different genomic sites, double mismatch gRNA site 7 repeat 1


title: hpCasMINI_DM6_Deep-seq_gRNA-mismatch_Rep3

description: The DNA cleavage efficiency in the MCF7 cells transfected with the hpCasMINI system targeting two different genomic sites, double mismatch gRNA site 6 repeat 3


title: hpCasMINI_DM7_Deep-seq_gRNA-mismatch_Rep3

description: The DNA cleavage efficiency in the MCF7 cells transfected with the hpCasMINI system targeting two different genomic sites, double mismatch gRNA site 7 repeat 3


title: OSalive_B1_S11_Aligned.quant


title: hpCasMINI_DM6_Deep-seq_gRNA-mismatch_Rep2

description: The DNA cleavage efficiency in the MCF7 cells transfected with the hpCasMINI system targeting two different genomic sites, double mismatch gRNA site 6 repeat 2


title: OSalive_A9_S8_Aligned.quant


title: OSalive_A8_S7_Aligned.quant


title: OSalive_A6_S5_Aligned.quant


title: hpCasMINI_DM6_Deep-seq_gRNA-mismatch_Rep1

description: The DNA cleavage efficiency in the MCF7 cells transfected with the hpCasMINI system targeting two different genomic sites, double mismatch gRNA site 6 repeat 1


title: OSalive_A7_S6_Aligned.quant


title: hpCasMINI_DM5_Deep-seq_gRNA-mismatch_Rep1

description: The DNA cleavage efficiency in the MCF7 cells transfected with the hpCasMINI system targeting two different genomic sites, double mismatch gRNA site 5 repeat 1


title: hpCasMINI_DM4_Deep-seq_gRNA-mismatch_Rep3

description: The DNA cleavage efficiency in the MCF7 cells transfected with the hpCasMINI system targeting two different genomic sites, double mismatch gRNA site 4 repeat 3


title: OSalive_A5_S4_Aligned.quant


title: OSalive_B10_S19_Aligned.quant


title: hpCasMINI_DM4_Deep-seq_gRNA-mismatch_Rep2

description: The DNA cleavage efficiency in the MCF7 cells transfected with the hpCasMINI system targeting two different genomic sites, double mismatch gRNA site 4 repeat 2


title: OSalive_A4_S3_Aligned.quant


title: hpCasMINI_DM4_Deep-seq_gRNA-mismatch_Rep1

description: The DNA cleavage efficiency in the MCF7 cells transfected with the hpCasMINI system targeting two different genomic sites, double mismatch gRNA site 4 repeat 1


title: OSalive_A3_S3_Aligned.quant


title: hpCasMINI_DM3_Deep-seq_gRNA-mismatch_Rep3

description: The DNA cleavage efficiency in the MCF7 cells transfected with the hpCasMINI system targeting two different genomic sites, double mismatch gRNA site 3 repeat 3


title: OSalive_A2_S2_Aligned.quant


title: hpCasMINI_DM3_Deep-seq_gRNA-mismatch_Rep2

description: The DNA cleavage efficiency in the MCF7 cells transfected with the hpCasMINI system targeting two different genomic sites, double mismatch gRNA site 3 repeat 2


title: OSalive_A3_S2_Aligned.quant


title: hpCasMINI_DM2_Deep-seq_gRNA-mismatch_Rep1

description: The DNA cleavage efficiency in the MCF7 cells transfected with the hpCasMINI system targeting two different genomic sites, double mismatch gRNA site 2 repeat 1


title: hpCasMINI_DM2_Deep-seq_gRNA-mismatch_Rep2

description: The DNA cleavage efficiency in the MCF7 cells transfected with the hpCasMINI system targeting two different genomic sites, double mismatch gRNA site 2 repeat 2


title: OSalive_A2_S1_Aligned.quant


title: hpCasMINI_DM5_Deep-seq_gRNA-mismatch_Rep2

description: The DNA cleavage efficiency in the MCF7 cells transfected with the hpCasMINI system targeting two different genomic sites, double mismatch gRNA site 5 repeat 2


title: hpCasMINI_DM1_Deep-seq_gRNA-mismatch_Rep3

description: The DNA cleavage efficiency in the MCF7 cells transfected with the hpCasMINI system targeting two different genomic sites, double mismatch gRNA site 1 repeat 3


title: MOS_H9_S175_Aligned.quant

value: upper-middle outer root sheath

value: AnaVI


title: OSalive_A11_S10_Aligned.quant


title: hpCasMINI_DM2_Deep-seq_gRNA-mismatch_Rep3

description: The DNA cleavage efficiency in the MCF7 cells transfected with the hpCasMINI system targeting two different genomic sites, double mismatch gRNA site 2 repeat 3


title: hpCasMINI_DM3_Deep-seq_gRNA-mismatch_Rep1

description: The DNA cleavage efficiency in the MCF7 cells transfected with the hpCasMINI system targeting two different genomic sites, double mismatch gRNA site 3 repeat 1


title: OSalive_A10_S9_Aligned.quant


title: hpCasMINI_DM5_Deep-seq_gRNA-mismatch_Rep3

description: The DNA cleavage efficiency in the MCF7 cells transfected with the hpCasMINI system targeting two different genomic sites, double mismatch gRNA site 5 repeat 3


title: OSalive_A5_S5_Aligned.quant


title: MOS_H8_S174_Aligned.quant


title: hpCasMINI_DM1_Deep-seq_gRNA-mismatch_Rep2

description: The DNA cleavage efficiency in the MCF7 cells transfected with the hpCasMINI system targeting two different genomic sites, double mismatch gRNA site 1 repeat 2


title: MOS_H7_S173_Aligned.quant


title: hpCasMINI_DM1_Deep-seq_gRNA-mismatch_Rep1

description: The DNA cleavage efficiency in the MCF7 cells transfected with the hpCasMINI system targeting two different genomic sites, double mismatch gRNA site 1 repeat 1


title: OSalive_A4_S4_Aligned.quant


title: hpCasMINI_SM10_Deep-seq_gRNA-mismatch_Rep3

description: The DNA cleavage efficiency in the MCF7 cells transfected with the hpCasMINI system targeting two different genomic sites, single mismatch gRNA site 10 repeat 3


title: MOS_H6_S172_Aligned.quant


title: MOS_H5_S171_Aligned.quant


title: hpCasMINI_SM10_Deep-seq_gRNA-mismatch_Rep1

description: The DNA cleavage efficiency in the MCF7 cells transfected with the hpCasMINI system targeting two different genomic sites, single mismatch gRNA site 10 repeat 1


title: hpCasMINI_SM9_Deep-seq_gRNA-mismatch_Rep3

description: The DNA cleavage efficiency in the MCF7 cells transfected with the hpCasMINI system targeting two different genomic sites, single mismatch gRNA site 9 repeat 3


title: hpCasMINI_SM10_Deep-seq_gRNA-mismatch_Rep2

description: The DNA cleavage efficiency in the MCF7 cells transfected with the hpCasMINI system targeting two different genomic sites, single mismatch gRNA site 10 repeat 2


title: MOS_H4_S170_Aligned.quant


title: hpCasMINI_SM9_Deep-seq_gRNA-mismatch_Rep2

description: The DNA cleavage efficiency in the MCF7 cells transfected with the hpCasMINI system targeting two different genomic sites, single mismatch gRNA site 9 repeat 2


title: MOS_H3_S169_Aligned.quant


title: OSalive_A1_S1_Aligned.quant


title: MOS_H2_S168_Aligned.quant


title: hpCasMINI_SM9_Deep-seq_gRNA-mismatch_Rep1

description: The DNA cleavage efficiency in the MCF7 cells transfected with the hpCasMINI system targeting two different genomic sites, single mismatch gRNA site 9 repeat 1


title: hpCasMINI_SM8_Deep-seq_gRNA-mismatch_Rep3

description: The DNA cleavage efficiency in the MCF7 cells transfected with the hpCasMINI system targeting two different genomic sites, single mismatch gRNA site 8 repeat 3


title: hpCasMINI_SM8_Deep-seq_gRNA-mismatch_Rep1

description: The DNA cleavage efficiency in the MCF7 cells transfected with the hpCasMINI system targeting two different genomic sites, single mismatch gRNA site 8 repeat 1


title: MOS_G9_S163_Aligned.quant


title: MOS_G6_S160_Aligned.quant


title: MOS_G7_S161_Aligned.quant


title: hpCasMINI_SM8_Deep-seq_gRNA-mismatch_Rep2

description: The DNA cleavage efficiency in the MCF7 cells transfected with the hpCasMINI system targeting two different genomic sites, single mismatch gRNA site 8 repeat 2


title: MOS_G8_S162_Aligned.quant


title: MOS_G4_S158_Aligned.quant


title: MOS_G3_S157_Aligned.quant


title: hpCasMINI_SM7_Deep-seq_gRNA-mismatch_Rep1

description: The DNA cleavage efficiency in the MCF7 cells transfected with the hpCasMINI system targeting two different genomic sites, single mismatch gRNA site 7 repeat 1


title: hpCasMINI_SM7_Deep-seq_gRNA-mismatch_Rep2

description: The DNA cleavage efficiency in the MCF7 cells transfected with the hpCasMINI system targeting two different genomic sites, single mismatch gRNA site 7 repeat 2


title: MOS_G2_S156_Aligned.quant


title: MOS_G5_S159_Aligned.quant


title: MOS_G1_S155_Aligned.quant


title: hpCasMINI_SM6_Deep-seq_gRNA-mismatch_Rep1

description: The DNA cleavage efficiency in the MCF7 cells transfected with the hpCasMINI system targeting two different genomic sites, single mismatch gRNA site 6 repeat 1


title: hpCasMINI_SM6_Deep-seq_gRNA-mismatch_Rep2

description: The DNA cleavage efficiency in the MCF7 cells transfected with the hpCasMINI system targeting two different genomic sites, single mismatch gRNA site 6 repeat 2


title: hpCasMINI_SM6_Deep-seq_gRNA-mismatch_Rep3

description: The DNA cleavage efficiency in the MCF7 cells transfected with the hpCasMINI system targeting two different genomic sites, single mismatch gRNA site 6 repeat 3


title: MOS_F9_S152_Aligned.quant


title: hpCasMINI_SM5_Deep-seq_gRNA-mismatch_Rep1

description: The DNA cleavage efficiency in the MCF7 cells transfected with the hpCasMINI system targeting two different genomic sites, single mismatch gRNA site 5 repeat 1


title: MOS_F8_S151_Aligned.quant


title: MOS_F7_S150_Aligned.quant


title: MOS_H1_S167_Aligned.quant


title: hpCasMINI_SM5_Deep-seq_gRNA-mismatch_Rep2

description: The DNA cleavage efficiency in the MCF7 cells transfected with the hpCasMINI system targeting two different genomic sites, single mismatch gRNA site 5 repeat 2


title: hpCasMINI_SM4_Deep-seq_gRNA-mismatch_Rep3

description: The DNA cleavage efficiency in the MCF7 cells transfected with the hpCasMINI system targeting two different genomic sites, single mismatch gRNA site 4 repeat 3


title: hpCasMINI_SM4_Deep-seq_gRNA-mismatch_Rep2

description: The DNA cleavage efficiency in the MCF7 cells transfected with the hpCasMINI system targeting two different genomic sites, single mismatch gRNA site 4 repeat 2


title: MOS_F5_S148_Aligned.quant


title: hpCasMINI_SM7_Deep-seq_gRNA-mismatch_Rep3

description: The DNA cleavage efficiency in the MCF7 cells transfected with the hpCasMINI system targeting two different genomic sites, single mismatch gRNA site 7 repeat 3


title: MOS_F6_S149_Aligned.quant


title: hpCasMINI_SM4_Deep-seq_gRNA-mismatch_Rep1

description: The DNA cleavage efficiency in the MCF7 cells transfected with the hpCasMINI system targeting two different genomic sites, single mismatch gRNA site 4 repeat 1


title: hpCasMINI_SM3_Deep-seq_gRNA-mismatch_Rep3

description: The DNA cleavage efficiency in the MCF7 cells transfected with the hpCasMINI system targeting two different genomic sites, single mismatch gRNA site 3 repeat 3


title: MOS_F1_S145_Aligned.quant


title: MOS_F3_S146_Aligned.quant


title: MOS_F4_S147_Aligned.quant


title: hpCasMINI_SM3_Deep-seq_gRNA-mismatch_Rep2

description: The DNA cleavage efficiency in the MCF7 cells transfected with the hpCasMINI system targeting two different genomic sites, single mismatch gRNA site 3 repeat 2


title: hpCasMINI_SM3_Deep-seq_gRNA-mismatch_Rep1

description: The DNA cleavage efficiency in the MCF7 cells transfected with the hpCasMINI system targeting two different genomic sites, single mismatch gRNA site 3 repeat 1


title: MOS_E9_S141_Aligned.quant


title: hpCasMINI_SM5_Deep-seq_gRNA-mismatch_Rep3

description: The DNA cleavage efficiency in the MCF7 cells transfected with the hpCasMINI system targeting two different genomic sites, single mismatch gRNA site 5 repeat 3


title: MOS_E7_S139_Aligned.quant


title: hpCasMINI_SM2_Deep-seq_gRNA-mismatch_Rep3

description: The DNA cleavage efficiency in the MCF7 cells transfected with the hpCasMINI system targeting two different genomic sites, single mismatch gRNA site 2 repeat 3


title: hpCasMINI_SM2_Deep-seq_gRNA-mismatch_Rep1

description: The DNA cleavage efficiency in the MCF7 cells transfected with the hpCasMINI system targeting two different genomic sites, single mismatch gRNA site 2 repeat 1


title: MOS_E5_S137_Aligned.quant


title: MOS_E4_S136_Aligned.quant


title: hpCasMINI_SM1_Deep-seq_gRNA-mismatch_Rep1

description: The DNA cleavage efficiency in the MCF7 cells transfected with the hpCasMINI system targeting two different genomic sites, single mismatch gRNA site 1 repeat 1


title: hpCasMINI_SM1_Deep-seq_gRNA-mismatch_Rep3

description: The DNA cleavage efficiency in the MCF7 cells transfected with the hpCasMINI system targeting two different genomic sites, single mismatch gRNA site 1 repeat 3


title: hpCasMINI_SM1_Deep-seq_gRNA-mismatch_Rep2

description: The DNA cleavage efficiency in the MCF7 cells transfected with the hpCasMINI system targeting two different genomic sites, single mismatch gRNA site 1 repeat 2


title: MOS_E6_S138_Aligned.quant


title: hpCasMINI_SM2_Deep-seq_gRNA-mismatch_Rep2

description: The DNA cleavage efficiency in the MCF7 cells transfected with the hpCasMINI system targeting two different genomic sites, single mismatch gRNA site 2 repeat 2


title: hpCasMINI_Full_Deep-seq_gRNA-mismatch_Rep3

description: The DNA cleavage efficiency in the MCF7 cells transfected with the hpCasMINI system targeting two different genomic sites, complete gRNA repeat 3


title: MOS_E3_S135_Aligned.quant


title: MOS_D7_S127_Aligned.quant


title: MOS_E2_S134_Aligned.quant


title: MOS_E1_S133_Aligned.quant


title: hpCasMINI_Ctrl_Deep-seq_gRNA-mismatch_Rep3

description: The DNA cleavage efficiency in the MCF7 cells transfected without the hpCasMINI system targeting two different genomic sites, repeat 3


title: hpCasMINI_Full_Deep-seq_gRNA-mismatch_Rep1

description: The DNA cleavage efficiency in the MCF7 cells transfected with the hpCasMINI system targeting two different genomic sites, complete gRNA repeat 1


title: hpCasMINI_Full_Deep-seq_gRNA-mismatch_Rep2

description: The DNA cleavage efficiency in the MCF7 cells transfected with the hpCasMINI system targeting two different genomic sites, complete gRNA repeat 2


title: hpCasMINI_Ctrl_Deep-seq_gRNA-mismatch_Rep2

description: The DNA cleavage efficiency in the MCF7 cells transfected without the hpCasMINI system targeting two different genomic sites, repeat 2


title: MOS_D8_S128_Aligned.quant


title: MOS_D9_S129_Aligned.quant


title: MOS_D3_S124_Aligned.quant


title: MOS_D4_S125_Aligned.quant


title: MOS_E8_S140_Aligned.quant


title: hpCasMINI_Ctrl_Deep-seq_gRNA-mismatch_Rep1

description: The DNA cleavage efficiency in the MCF7 cells transfected without the hpCasMINI system targeting two different genomic sites, repeat 1


title: MOS_D6_S126_Aligned.quant


title: CasMINI_DM10_Deep-seq_gRNA-mismatch_Rep3

description: The DNA cleavage efficiency in the MCF7 cells transfected with the CasMINI system targeting two different genomic sites, double mismatch gRNA site 10 repeat 3


title: MOS_D2_S123_Aligned.quant


title: CasMINI_DM10_Deep-seq_gRNA-mismatch_Rep1

description: The DNA cleavage efficiency in the MCF7 cells transfected with the CasMINI system targeting two different genomic sites, double mismatch gRNA site 10 repeat 1


title: CasMINI_DM10_Deep-seq_gRNA-mismatch_Rep2

description: The DNA cleavage efficiency in the MCF7 cells transfected with the CasMINI system targeting two different genomic sites, double mismatch gRNA site 10 repeat 2


title: CasMINI_DM9_Deep-seq_gRNA-mismatch_Rep3

description: The DNA cleavage efficiency in the MCF7 cells transfected with the CasMINI system targeting two different genomic sites, double mismatch gRNA site 9 repeat 3


title: CasMINI_DM9_Deep-seq_gRNA-mismatch_Rep2

description: The DNA cleavage efficiency in the MCF7 cells transfected with the CasMINI system targeting two different genomic sites, double mismatch gRNA site 9 repeat 2


title: MOS_D1_S122_Aligned.quant


title: CasMINI_DM8_Deep-seq_gRNA-mismatch_Rep3

description: The DNA cleavage efficiency in the MCF7 cells transfected with the CasMINI system targeting two different genomic sites, double mismatch gRNA site 8 repeat 3


title: MOS_C9_S119_Aligned.quant


title: MOS_C7_S117_Aligned.quant


title: CasMINI_DM8_Deep-seq_gRNA-mismatch_Rep2

description: The DNA cleavage efficiency in the MCF7 cells transfected with the CasMINI system targeting two different genomic sites, double mismatch gRNA site 8 repeat 2


title: CasMINI_DM9_Deep-seq_gRNA-mismatch_Rep1

description: The DNA cleavage efficiency in the MCF7 cells transfected with the CasMINI system targeting two different genomic sites, double mismatch gRNA site 9 repeat 1


title: MOS_C8_S118_Aligned.quant


title: MOS_C6_S116_Aligned.quant


title: MOS_C5_S115_Aligned.quant


title: CasMINI_DM7_Deep-seq_gRNA-mismatch_Rep2

description: The DNA cleavage efficiency in the MCF7 cells transfected with the CasMINI system targeting two different genomic sites, double mismatch gRNA site 7 repeat 2


title: CasMINI_DM7_Deep-seq_gRNA-mismatch_Rep1

description: The DNA cleavage efficiency in the MCF7 cells transfected with the CasMINI system targeting two different genomic sites, double mismatch gRNA site 7 repeat 1


title: MOS_C2_S112_Aligned.quant


title: CasMINI_DM6_Deep-seq_gRNA-mismatch_Rep3

description: The DNA cleavage efficiency in the MCF7 cells transfected with the CasMINI system targeting two different genomic sites, double mismatch gRNA site 6 repeat 3


title: MOS_C3_S113_Aligned.quant


title: CasMINI_DM6_Deep-seq_gRNA-mismatch_Rep2

description: The DNA cleavage efficiency in the MCF7 cells transfected with the CasMINI system targeting two different genomic sites, double mismatch gRNA site 6 repeat 2


title: MOS_C1_S111_Aligned.quant


title: CasMINI_DM5_Deep-seq_gRNA-mismatch_Rep3

description: The DNA cleavage efficiency in the MCF7 cells transfected with the CasMINI system targeting two different genomic sites, double mismatch gRNA site 5 repeat 3


title: MOS_B6_S106_Aligned.quant


title: CasMINI_DM6_Deep-seq_gRNA-mismatch_Rep1

description: The DNA cleavage efficiency in the MCF7 cells transfected with the CasMINI system targeting two different genomic sites, double mismatch gRNA site 6 repeat 1


title: MOS_B2_S103_Aligned.quant


title: MOS_B4_S105_Aligned.quant


title: MOS_B3_S104_Aligned.quant


title: CasMINI_DM5_Deep-seq_gRNA-mismatch_Rep1

description: The DNA cleavage efficiency in the MCF7 cells transfected with the CasMINI system targeting two different genomic sites, double mismatch gRNA site 5 repeat 1


title: MOS_B12_S110_Aligned.quant


title: CasMINI_DM4_Deep-seq_gRNA-mismatch_Rep2

description: The DNA cleavage efficiency in the MCF7 cells transfected with the CasMINI system targeting two different genomic sites, double mismatch gRNA site 4 repeat 2


title: CasMINI_DM4_Deep-seq_gRNA-mismatch_Rep1

description: The DNA cleavage efficiency in the MCF7 cells transfected with the CasMINI system targeting two different genomic sites, double mismatch gRNA site 4 repeat 1


title: CasMINI_DM8_Deep-seq_gRNA-mismatch_Rep1

description: The DNA cleavage efficiency in the MCF7 cells transfected with the CasMINI system targeting two different genomic sites, double mismatch gRNA site 8 repeat 1


title: CasMINI_DM3_Deep-seq_gRNA-mismatch_Rep3

description: The DNA cleavage efficiency in the MCF7 cells transfected with the CasMINI system targeting two different genomic sites, double mismatch gRNA site 3 repeat 3


title: MOS_B9_S107_Aligned.quant


title: MOS_B1_S102_Aligned.quant


title: MOS_B10_S108_Aligned.quant


title: CasMINI_DM7_Deep-seq_gRNA-mismatch_Rep3

description: The DNA cleavage efficiency in the MCF7 cells transfected with the CasMINI system targeting two different genomic sites, double mismatch gRNA site 7 repeat 3


title: CasMINI_DM3_Deep-seq_gRNA-mismatch_Rep2

description: The DNA cleavage efficiency in the MCF7 cells transfected with the CasMINI system targeting two different genomic sites, double mismatch gRNA site 3 repeat 2


title: CasMINI_DM5_Deep-seq_gRNA-mismatch_Rep2

description: The DNA cleavage efficiency in the MCF7 cells transfected with the CasMINI system targeting two different genomic sites, double mismatch gRNA site 5 repeat 2


title: CasMINI_DM3_Deep-seq_gRNA-mismatch_Rep1

description: The DNA cleavage efficiency in the MCF7 cells transfected with the CasMINI system targeting two different genomic sites, double mismatch gRNA site 3 repeat 1


title: MOS_C4_S114_Aligned.quant


title: MOS_A8_S98_Aligned.quant


title: CasMINI_DM2_Deep-seq_gRNA-mismatch_Rep3

description: The DNA cleavage efficiency in the MCF7 cells transfected with the CasMINI system targeting two different genomic sites, double mismatch gRNA site 2 repeat 3


title: MOS_A7_S97_Aligned.quant


title: MOS_A9_S99_Aligned.quant


title: MOS_A5_S95_Aligned.quant


title: MOS_A6_S96_Aligned.quant


title: CasMINI_DM1_Deep-seq_gRNA-mismatch_Rep3

description: The DNA cleavage efficiency in the MCF7 cells transfected with the CasMINI system targeting two different genomic sites, double mismatch gRNA site 1 repeat 3


title: CasMINI_DM4_Deep-seq_gRNA-mismatch_Rep3

description: The DNA cleavage efficiency in the MCF7 cells transfected with the CasMINI system targeting two different genomic sites, double mismatch gRNA site 4 repeat 3


title: MOS_A4_S94_Aligned.quant


title: CasMINI_DM2_Deep-seq_gRNA-mismatch_Rep1

description: The DNA cleavage efficiency in the MCF7 cells transfected with the CasMINI system targeting two different genomic sites, double mismatch gRNA site 2 repeat 1


title: CasMINI_DM1_Deep-seq_gRNA-mismatch_Rep2

description: The DNA cleavage efficiency in the MCF7 cells transfected with the CasMINI system targeting two different genomic sites, double mismatch gRNA site 1 repeat 2


title: CasMINI_DM1_Deep-seq_gRNA-mismatch_Rep1

description: The DNA cleavage efficiency in the MCF7 cells transfected with the CasMINI system targeting two different genomic sites, double mismatch gRNA site 1 repeat 1


title: MOS_B11_S109_Aligned.quant


title: CasMINI_DM2_Deep-seq_gRNA-mismatch_Rep2

description: The DNA cleavage efficiency in the MCF7 cells transfected with the CasMINI system targeting two different genomic sites, double mismatch gRNA site 2 repeat 2


title: MOS_A11_S101_Aligned.quant


title: MOS_A3_S93_Aligned.quant


title: MOS_A10_S100_Aligned.quant


title: CasMINI_SM10_Deep-seq_gRNA-mismatch_Rep1

description: The DNA cleavage efficiency in the MCF7 cells transfected with the CasMINI system targeting two different genomic sites, single mismatch gRNA site 10 repeat 1


title: CasMINI_SM9_Deep-seq_gRNA-mismatch_Rep3

description: The DNA cleavage efficiency in the MCF7 cells transfected with the CasMINI system targeting two different genomic sites, single mismatch gRNA site 9 repeat 3


title: CasMINI_SM9_Deep-seq_gRNA-mismatch_Rep2

description: The DNA cleavage efficiency in the MCF7 cells transfected with the CasMINI system targeting two different genomic sites, single mismatch gRNA site 9 repeat 2


title: LOS_H9_S266_Aligned.quant

value: lower outer root sheath


title: CasMINI_SM10_Deep-seq_gRNA-mismatch_Rep2

description: The DNA cleavage efficiency in the MCF7 cells transfected with the CasMINI system targeting two different genomic sites, single mismatch gRNA site 10 repeat 2


title: CasMINI_SM9_Deep-seq_gRNA-mismatch_Rep1

description: The DNA cleavage efficiency in the MCF7 cells transfected with the CasMINI system targeting two different genomic sites, single mismatch gRNA site 9 repeat 1


title: LOS_H8_S265_Aligned.quant


title: MOS_A2_S92_Aligned.quant


title: LOS_H7_S264_Aligned.quant


title: CasMINI_SM8_Deep-seq_gRNA-mismatch_Rep3

description: The DNA cleavage efficiency in the MCF7 cells transfected with the CasMINI system targeting two different genomic sites, single mismatch gRNA site 8 repeat 3


title: LOS_H6_S263_Aligned.quant


title: CasMINI_SM8_Deep-seq_gRNA-mismatch_Rep2

description: The DNA cleavage efficiency in the MCF7 cells transfected with the CasMINI system targeting two different genomic sites, single mismatch gRNA site 8 repeat 2


title: CasMINI_SM10_Deep-seq_gRNA-mismatch_Rep3

description: The DNA cleavage efficiency in the MCF7 cells transfected with the CasMINI system targeting two different genomic sites, single mismatch gRNA site 10 repeat 3


title: LOS_H5_S262_Aligned.quant


title: LOS_H4_S261_Aligned.quant


title: CasMINI_SM8_Deep-seq_gRNA-mismatch_Rep1

description: The DNA cleavage efficiency in the MCF7 cells transfected with the CasMINI system targeting two different genomic sites, single mismatch gRNA site 8 repeat 1