title: 1248_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR214_1_MDA_MECOM_AMP_B11_S407/CRISPResso_on_MR214_1_MDA_MECOM_AMP_B11_S407_L001_R1_001_MR214_1_MDA_MECOM_AMP_B11_S407_L001_R2_001/Alleles_frequency_table.zip


title: 1249_Mecom amplicon seq

status: Public on Nov 23 2022

type: SRA

city: Cambridge

first: Liming

last: Tao

address: 415 Main Street

country: USA

institute: Broad Institute of Harvard and MIT

description:
single cell genotyping:
processed data file:
./MR912_3_MDA_MECOM_AMP_A1_S577/CRISPResso_on_MR912_3_MDA_MECOM_AMP_A1_S577_L001_R1_001_MR912_3_MDA_MECOM_AMP_A1_S577_L001_R2_001/Alleles_frequency_table.zip

library_source: genomic

data_processing:
Library strategy: amplicon-seq
Basecalls performed using CASAVA version 1.4 and bcl2fastq2 v2.20.0
CRISPResso2
Genome_build:  Human reference genome GRCh38 and gene annotation reference Homo_sapiens.GRCh38.93.gtf
Supplementary_files_format_and_content: txt

molecule: genomic DNA

organism: Homo sapiens

source_name: HSC

growth_protocol: cells were cultured at 37oC and 5%O2 in serum-free HSC media comprised of StemSpan  II medium (Stem Cell Technologies) supplemented with CC100 cytokine cocktail (Stem Cell Technologies), 100ng/ml TPO (Peprotech) and 35nM UM171 (Stem Cell Technologies). Confluency was maintained between 2e5-1e6 cells/ml.

extract_protocol: genomic DNA or cDNA  isolated by  beads

treatment_protocol: MECOM KO

tag: cell type

value: HSC

tag: chip antibody

tag: treatment

value: Mecom KO


title: 1247_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912_3_MDA_MECOM_AMP_H11_S575/CRISPResso_on_MR912_3_MDA_MECOM_AMP_H11_S575_L001_R1_001_MR912_3_MDA_MECOM_AMP_H11_S575_L001_R2_001/Alleles_frequency_table.zip


title: 1253_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912_3_MDA_MECOM_AMP_A5_S581/CRISPResso_on_MR912_3_MDA_MECOM_AMP_A5_S581_L001_R1_001_MR912_3_MDA_MECOM_AMP_A5_S581_L001_R2_001/Alleles_frequency_table.zip


title: 1265_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912_3_MDA_MECOM_AMP_B5_S593/CRISPResso_on_MR912_3_MDA_MECOM_AMP_B5_S593_L001_R1_001_MR912_3_MDA_MECOM_AMP_B5_S593_L001_R2_001/Alleles_frequency_table.zip


title: 1245_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR214_1_MDA_MECOM_AMP_C2_S410/CRISPResso_on_MR214_1_MDA_MECOM_AMP_C2_S410_L001_R1_001_MR214_1_MDA_MECOM_AMP_C2_S410_L001_R2_001/Alleles_frequency_table.zip


title: 1267_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-2-WTA-MECOM-AMP_A5_S101/CRISPResso_on_MR912-2-WTA-MECOM-AMP_A5_S101_L001_R1_001_MR912-2-WTA-MECOM-AMP_A5_S101_L001_R2_001/Alleles_frequency_table.zip


title: 1246_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-2-WTA-MECOM-AMP_A6_S102/CRISPResso_on_MR912-2-WTA-MECOM-AMP_A6_S102_L001_R1_001_MR912-2-WTA-MECOM-AMP_A6_S102_L001_R2_001/Alleles_frequency_table.zip


title: 1257_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912_3_MDA_MECOM_AMP_A9_S585/CRISPResso_on_MR912_3_MDA_MECOM_AMP_A9_S585_L001_R1_001_MR912_3_MDA_MECOM_AMP_A9_S585_L001_R2_001/Alleles_frequency_table.zip


title: 1238_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-2-WTA-MECOM-AMP_B8_S116/CRISPResso_on_MR912-2-WTA-MECOM-AMP_B8_S116_L001_R1_001_MR912-2-WTA-MECOM-AMP_B8_S116_L001_R2_001/Alleles_frequency_table.zip


title: 1235_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-2-WTA-MECOM-AMP_H10_S190/CRISPResso_on_MR912-2-WTA-MECOM-AMP_H10_S190_L001_R1_001_MR912-2-WTA-MECOM-AMP_H10_S190_L001_R2_001/Alleles_frequency_table.zip


title: 1236_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-2-WTA-MECOM-AMP_E7_S151/CRISPResso_on_MR912-2-WTA-MECOM-AMP_E7_S151_L001_R1_001_MR912-2-WTA-MECOM-AMP_E7_S151_L001_R2_001/Alleles_frequency_table.zip


title: 1237_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR214_1_Cat_H9_S93/CRISPResso_on_MR214_1_Cat_H9_S93_L001_R1_001_MR214_1_Cat_H9_S93_L001_R2_001/Alleles_frequency_table.zip


title: 1259_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-5-WTA-MECOM-AMP_F2_S350/CRISPResso_on_MR912-5-WTA-MECOM-AMP_F2_S350_L001_R1_001_MR912-5-WTA-MECOM-AMP_F2_S350_L001_R2_001/Alleles_frequency_table.zip


title: 1234_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912_3_MDA_MECOM_AMP_G10_S562/CRISPResso_on_MR912_3_MDA_MECOM_AMP_G10_S562_L001_R1_001_MR912_3_MDA_MECOM_AMP_G10_S562_L001_R2_001/Alleles_frequency_table.zip


title: 1231_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-5-WTA-MECOM-AMP_B7_S307/CRISPResso_on_MR912-5-WTA-MECOM-AMP_B7_S307_L001_R1_001_MR912-5-WTA-MECOM-AMP_B7_S307_L001_R2_001/Alleles_frequency_table.zip


title: 1229_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-5-MDA-MECOM-AMP_B2_S206/CRISPResso_on_MR912-5-MDA-MECOM-AMP_B2_S206_L001_R1_001_MR912-5-MDA-MECOM-AMP_B2_S206_L001_R2_001/Alleles_frequency_table.zip


title: 1230_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-2-MDA-MECOM-AMP_B11_S23/CRISPResso_on_MR912-2-MDA-MECOM-AMP_B11_S23_L001_R1_001_MR912-2-MDA-MECOM-AMP_B11_S23_L001_R2_001/Alleles_frequency_table.zip


title: 1228_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912_3_MDA_MECOM_AMP_A5_S485/CRISPResso_on_MR912_3_MDA_MECOM_AMP_A5_S485_L001_R1_001_MR912_3_MDA_MECOM_AMP_A5_S485_L001_R2_001/Alleles_frequency_table.zip


title: 1232_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912_3_MDA_MECOM_AMP_G8_S560/CRISPResso_on_MR912_3_MDA_MECOM_AMP_G8_S560_L001_R1_001_MR912_3_MDA_MECOM_AMP_G8_S560_L001_R2_001/Alleles_frequency_table.zip


title: 1244_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-2-WTA-MECOM-AMP_H7_S187/CRISPResso_on_MR912-2-WTA-MECOM-AMP_H7_S187_L001_R1_001_MR912-2-WTA-MECOM-AMP_H7_S187_L001_R2_001/Alleles_frequency_table.zip


title: 1226_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912_3_MDA_MECOM_AMP_G2_S554/CRISPResso_on_MR912_3_MDA_MECOM_AMP_G2_S554_L001_R1_001_MR912_3_MDA_MECOM_AMP_G2_S554_L001_R2_001/Alleles_frequency_table.zip


title: 1227_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR214_1_MDA_MECOM_AMP_F5_S449/CRISPResso_on_MR214_1_MDA_MECOM_AMP_F5_S449_L001_R1_001_MR214_1_MDA_MECOM_AMP_F5_S449_L001_R2_001/Alleles_frequency_table.zip


title: 1242_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-2-WTA-MECOM-AMP_A5_S101/CRISPResso_on_MR912-2-WTA-MECOM-AMP_A5_S101_L001_R1_001_MR912-2-WTA-MECOM-AMP_A5_S101_L001_R2_001/Alleles_frequency_table.zip


title: 1243_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912_3_Dog_E12_S252/CRISPResso_on_MR912_3_Dog_E12_S252_L001_R1_001_MR912_3_Dog_E12_S252_L001_R2_001/Alleles_frequency_table.zip


title: 1241_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-5-MDA-MECOM-AMP_G12_S276/CRISPResso_on_MR912-5-MDA-MECOM-AMP_G12_S276_L001_R1_001_MR912-5-MDA-MECOM-AMP_G12_S276_L001_R2_001/Alleles_frequency_table.zip


title: 1233_Mecom amplicon seq


title: 1224_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-5-WTA-MECOM-AMP_B2_S302/CRISPResso_on_MR912-5-WTA-MECOM-AMP_B2_S302_L001_R1_001_MR912-5-WTA-MECOM-AMP_B2_S302_L001_R2_001/Alleles_frequency_table.zip


title: 1225_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR214_1_MDA_MECOM_AMP_A8_S392/CRISPResso_on_MR214_1_MDA_MECOM_AMP_A8_S392_L001_R1_001_MR214_1_MDA_MECOM_AMP_A8_S392_L001_R2_001/Alleles_frequency_table.zip


title: 1240_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR214_1_MDA_MECOM_AMP_D11_S431/CRISPResso_on_MR214_1_MDA_MECOM_AMP_D11_S431_L001_R1_001_MR214_1_MDA_MECOM_AMP_D11_S431_L001_R2_001/Alleles_frequency_table.zip


title: 1222_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912_3_MDA_MECOM_AMP_F10_S550/CRISPResso_on_MR912_3_MDA_MECOM_AMP_F10_S550_L001_R1_001_MR912_3_MDA_MECOM_AMP_F10_S550_L001_R2_001/Alleles_frequency_table.zip


title: 1220_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912_3_MDA_MECOM_AMP_H8_S668/CRISPResso_on_MR912_3_MDA_MECOM_AMP_H8_S668_L001_R1_001_MR912_3_MDA_MECOM_AMP_H8_S668_L001_R2_001/Alleles_frequency_table.zip


title: 1218_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-2-WTA-MECOM-AMP_E1_S145/CRISPResso_on_MR912-2-WTA-MECOM-AMP_E1_S145_L001_R1_001_MR912-2-WTA-MECOM-AMP_E1_S145_L001_R2_001/Alleles_frequency_table.zip


title: 1217_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-2-WTA-MECOM-AMP_F12_S168/CRISPResso_on_MR912-2-WTA-MECOM-AMP_F12_S168_L001_R1_001_MR912-2-WTA-MECOM-AMP_F12_S168_L001_R2_001/Alleles_frequency_table.zip


title: 1214_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-2-WTA-MECOM-AMP_D1_S133/CRISPResso_on_MR912-2-WTA-MECOM-AMP_D1_S133_L001_R1_001_MR912-2-WTA-MECOM-AMP_D1_S133_L001_R2_001/Alleles_frequency_table.zip


title: 1212_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-2-WTA-MECOM-AMP_F7_S163/CRISPResso_on_MR912-2-WTA-MECOM-AMP_F7_S163_L001_R1_001_MR912-2-WTA-MECOM-AMP_F7_S163_L001_R2_001/Alleles_frequency_table.zip


title: 1219_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912_3_MDA_MECOM_AMP_F7_S547/CRISPResso_on_MR912_3_MDA_MECOM_AMP_F7_S547_L001_R1_001_MR912_3_MDA_MECOM_AMP_F7_S547_L001_R2_001/Alleles_frequency_table.zip


title: 1216_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-5-WTA-MECOM-AMP_B3_S303/CRISPResso_on_MR912-5-WTA-MECOM-AMP_B3_S303_L001_R1_001_MR912-5-WTA-MECOM-AMP_B3_S303_L001_R2_001/Alleles_frequency_table.zip


title: 1215_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR214_1_MDA_MECOM_AMP_H7_S475/CRISPResso_on_MR214_1_MDA_MECOM_AMP_H7_S475_L001_R1_001_MR214_1_MDA_MECOM_AMP_H7_S475_L001_R2_001/Alleles_frequency_table.zip


title: 1208_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR214_1_MDA_MECOM_AMP_G11_S467/CRISPResso_on_MR214_1_MDA_MECOM_AMP_G11_S467_L001_R1_001_MR214_1_MDA_MECOM_AMP_G11_S467_L001_R2_001/Alleles_frequency_table.zip


title: 1209_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912_3_MDA_MECOM_AMP_G7_S655/CRISPResso_on_MR912_3_MDA_MECOM_AMP_G7_S655_L001_R1_001_MR912_3_MDA_MECOM_AMP_G7_S655_L001_R2_001/Alleles_frequency_table.zip


title: 1207_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-2-WTA-MECOM-AMP_E7_S151/CRISPResso_on_MR912-2-WTA-MECOM-AMP_E7_S151_L001_R1_001_MR912-2-WTA-MECOM-AMP_E7_S151_L001_R2_001/Alleles_frequency_table.zip


title: 1206_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-2-WTA-MECOM-AMP_C5_S125/CRISPResso_on_MR912-2-WTA-MECOM-AMP_C5_S125_L001_R1_001_MR912-2-WTA-MECOM-AMP_C5_S125_L001_R2_001/Alleles_frequency_table.zip


title: 1211_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-2-MDA-MECOM-AMP_C7_S31/CRISPResso_on_MR912-2-MDA-MECOM-AMP_C7_S31_L001_R1_001_MR912-2-MDA-MECOM-AMP_C7_S31_L001_R2_001/Alleles_frequency_table.zip


title: 1205_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-5-WTA-MECOM-AMP_C1_S313/CRISPResso_on_MR912-5-WTA-MECOM-AMP_C1_S313_L001_R1_001_MR912-5-WTA-MECOM-AMP_C1_S313_L001_R2_001/Alleles_frequency_table.zip


title: 1202_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912_3_MDA_MECOM_AMP_E2_S530/CRISPResso_on_MR912_3_MDA_MECOM_AMP_E2_S530_L001_R1_001_MR912_3_MDA_MECOM_AMP_E2_S530_L001_R2_001/Alleles_frequency_table.zip


title: 1200_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912_3_MDA_MECOM_AMP_D12_S528/CRISPResso_on_MR912_3_MDA_MECOM_AMP_D12_S528_L001_R1_001_MR912_3_MDA_MECOM_AMP_D12_S528_L001_R2_001/Alleles_frequency_table.zip


title: 1198_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-5-MDA-MECOM-AMP_B10_S214/CRISPResso_on_MR912-5-MDA-MECOM-AMP_B10_S214_L001_R1_001_MR912-5-MDA-MECOM-AMP_B10_S214_L001_R2_001/Alleles_frequency_table.zip


title: 1210_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-5-WTA-MECOM-AMP_H2_S374/CRISPResso_on_MR912-5-WTA-MECOM-AMP_H2_S374_L001_R1_001_MR912-5-WTA-MECOM-AMP_H2_S374_L001_R2_001/Alleles_frequency_table.zip


title: 1201_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-2-MDA-MECOM-AMP_B6_S18/CRISPResso_on_MR912-2-MDA-MECOM-AMP_B6_S18_L001_R1_001_MR912-2-MDA-MECOM-AMP_B6_S18_L001_R2_001/Alleles_frequency_table.zip


title: 1196_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-5-WTA-MECOM-AMP_G3_S363/CRISPResso_on_MR912-5-WTA-MECOM-AMP_G3_S363_L001_R1_001_MR912-5-WTA-MECOM-AMP_G3_S363_L001_R2_001/Alleles_frequency_table.zip


title: 1223_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-2-MDA-MECOM-AMP_G11_S83/CRISPResso_on_MR912-2-MDA-MECOM-AMP_G11_S83_L001_R1_001_MR912-2-MDA-MECOM-AMP_G11_S83_L001_R2_001/Alleles_frequency_table.zip


title: 1195_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912_3_MDA_MECOM_AMP_D7_S523/CRISPResso_on_MR912_3_MDA_MECOM_AMP_D7_S523_L001_R1_001_MR912_3_MDA_MECOM_AMP_D7_S523_L001_R2_001/Alleles_frequency_table.zip


title: 1221_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-5-WTA-MECOM-AMP_F2_S350/CRISPResso_on_MR912-5-WTA-MECOM-AMP_F2_S350_L001_R1_001_MR912-5-WTA-MECOM-AMP_F2_S350_L001_R2_001/Alleles_frequency_table.zip


title: 1199_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-5-WTA-MECOM-AMP_C2_S314/CRISPResso_on_MR912-5-WTA-MECOM-AMP_C2_S314_L001_R1_001_MR912-5-WTA-MECOM-AMP_C2_S314_L001_R2_001/Alleles_frequency_table.zip


title: 1197_Mecom amplicon seq


title: 1203_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912_3_MDA_MECOM_AMP_E3_S531/CRISPResso_on_MR912_3_MDA_MECOM_AMP_E3_S531_L001_R1_001_MR912_3_MDA_MECOM_AMP_E3_S531_L001_R2_001/Alleles_frequency_table.zip


title: 1239_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR214_1_MDA_MECOM_AMP_G6_S462/CRISPResso_on_MR214_1_MDA_MECOM_AMP_G6_S462_L001_R1_001_MR214_1_MDA_MECOM_AMP_G6_S462_L001_R2_001/Alleles_frequency_table.zip


title: 1213_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-5-WTA-MECOM-AMP_E12_S348/CRISPResso_on_MR912-5-WTA-MECOM-AMP_E12_S348_L001_R1_001_MR912-5-WTA-MECOM-AMP_E12_S348_L001_R2_001/Alleles_frequency_table.zip


title: 1193_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912_3_MDA_MECOM_AMP_D5_S521/CRISPResso_on_MR912_3_MDA_MECOM_AMP_D5_S521_L001_R1_001_MR912_3_MDA_MECOM_AMP_D5_S521_L001_R2_001/Alleles_frequency_table.zip


title: 1194_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR214_1_MDA_MECOM_AMP_B2_S398/CRISPResso_on_MR214_1_MDA_MECOM_AMP_B2_S398_L001_R1_001_MR214_1_MDA_MECOM_AMP_B2_S398_L001_R2_001/Alleles_frequency_table.zip


title: 1192_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912_3_MDA_MECOM_AMP_D4_S520/CRISPResso_on_MR912_3_MDA_MECOM_AMP_D4_S520_L001_R1_001_MR912_3_MDA_MECOM_AMP_D4_S520_L001_R2_001/Alleles_frequency_table.zip


title: 1191_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-5-MDA-MECOM-AMP_E5_S245/CRISPResso_on_MR912-5-MDA-MECOM-AMP_E5_S245_L001_R1_001_MR912-5-MDA-MECOM-AMP_E5_S245_L001_R2_001/Alleles_frequency_table.zip


title: 1190_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912_3_MDA_MECOM_AMP_D2_S518/CRISPResso_on_MR912_3_MDA_MECOM_AMP_D2_S518_L001_R1_001_MR912_3_MDA_MECOM_AMP_D2_S518_L001_R2_001/Alleles_frequency_table.zip


title: BF-C1

city: Nanjing

first: Jiawei

last: Li

state: Jiangsu

address: Zhongshan road No.321

department: State Key Laboratory of Pharmaceutical Biotechnology, Division of Sports Medicine and Adult Reconstructive Surgery, Department of Orthopedic Surgery

country: China

institute: Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School Nanjing

library_source: transcriptomic

data_processing:
illumina Casava1.7 software used for basecalling
Sequence reads were trimmed for adaptor sequence, and masked for low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2
Reads Per Kilobase of exon per Megabases of library size (RPKM) using a protocal from Chepelev et.al., Nucleic Acids Research, 2009.
Assembly: Rn6
Supplementary files format and content: RPKM values for each Sample

molecule: total RNA

organism: Rattus norvegicus

source_name: bone marrow

growth_protocol: BMSCs were maintained in DMEM-LG; 1 g/L with chondrogenic induced medium and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) .

treatment_protocol:
Then the cells of BMSC_CT groups were treated with CTGF for 1 weeks followed by TGF-β1.
The cells of BF-D groups were treated with docetaxels

tag: tissue

value: bone marrow

tag: cell line

value: BMSCs

value: fibrotic Bone marrow-mesenchymal stem cells (BMSCs)

tag: genotype

value: WT

value: Control


title: 1186_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-5-WTA-MECOM-AMP_A7_S295/CRISPResso_on_MR912-5-WTA-MECOM-AMP_A7_S295_L001_R1_001_MR912-5-WTA-MECOM-AMP_A7_S295_L001_R2_001/Alleles_frequency_table.zip


title: 1184_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-2-MDA-MECOM-AMP_B12_S24/CRISPResso_on_MR912-2-MDA-MECOM-AMP_B12_S24_L001_R1_001_MR912-2-MDA-MECOM-AMP_B12_S24_L001_R2_001/Alleles_frequency_table.zip


title: 1183_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912_3_MDA_MECOM_AMP_C7_S511/CRISPResso_on_MR912_3_MDA_MECOM_AMP_C7_S511_L001_R1_001_MR912_3_MDA_MECOM_AMP_C7_S511_L001_R2_001/Alleles_frequency_table.zip


title: 1182_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912_3_MDA_MECOM_AMP_A5_S581/CRISPResso_on_MR912_3_MDA_MECOM_AMP_A5_S581_L001_R1_001_MR912_3_MDA_MECOM_AMP_A5_S581_L001_R2_001/Alleles_frequency_table.zip


title: 1187_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR214_1_Cat_C8_S32/CRISPResso_on_MR214_1_Cat_C8_S32_L001_R1_001_MR214_1_Cat_C8_S32_L001_R2_001/Alleles_frequency_table.zip


title: 1185_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912_3_MDA_MECOM_AMP_C9_S513/CRISPResso_on_MR912_3_MDA_MECOM_AMP_C9_S513_L001_R1_001_MR912_3_MDA_MECOM_AMP_C9_S513_L001_R2_001/Alleles_frequency_table.zip


title: BMSC-CT1

value: Bone marrow-mesenchymal stem cells (BMSCs)

value: CTGF+TGFβ1 treatment


title: 1179_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912_3_MDA_MECOM_AMP_C3_S507/CRISPResso_on_MR912_3_MDA_MECOM_AMP_C3_S507_L001_R1_001_MR912_3_MDA_MECOM_AMP_C3_S507_L001_R2_001/Alleles_frequency_table.zip


title: 1181_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912_3_MDA_MECOM_AMP_C5_S509/CRISPResso_on_MR912_3_MDA_MECOM_AMP_C5_S509_L001_R1_001_MR912_3_MDA_MECOM_AMP_C5_S509_L001_R2_001/Alleles_frequency_table.zip


title: 1176_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912_3_MDA_MECOM_AMP_B12_S504/CRISPResso_on_MR912_3_MDA_MECOM_AMP_B12_S504_L001_R1_001_MR912_3_MDA_MECOM_AMP_B12_S504_L001_R2_001/Alleles_frequency_table.zip


title: 1175_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-2-WTA-MECOM-AMP_C9_S129/CRISPResso_on_MR912-2-WTA-MECOM-AMP_C9_S129_L001_R1_001_MR912-2-WTA-MECOM-AMP_C9_S129_L001_R2_001/Alleles_frequency_table.zip


title: 1174_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-2-WTA-MECOM-AMP_C5_S125/CRISPResso_on_MR912-2-WTA-MECOM-AMP_C5_S125_L001_R1_001_MR912-2-WTA-MECOM-AMP_C5_S125_L001_R2_001/Alleles_frequency_table.zip


title: 1204_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-2-MDA-MECOM-AMP_F4_S64/CRISPResso_on_MR912-2-MDA-MECOM-AMP_F4_S64_L001_R1_001_MR912-2-MDA-MECOM-AMP_F4_S64_L001_R2_001/Alleles_frequency_table.zip


title: 1177_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912_3_MDA_MECOM_AMP_C1_S505/CRISPResso_on_MR912_3_MDA_MECOM_AMP_C1_S505_L001_R1_001_MR912_3_MDA_MECOM_AMP_C1_S505_L001_R2_001/Alleles_frequency_table.zip


title: 1178_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-5-WTA-MECOM-AMP_C8_S320/CRISPResso_on_MR912-5-WTA-MECOM-AMP_C8_S320_L001_R1_001_MR912-5-WTA-MECOM-AMP_C8_S320_L001_R2_001/Alleles_frequency_table.zip


title: 1180_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-5-MDA-MECOM-AMP_H11_S287/CRISPResso_on_MR912-5-MDA-MECOM-AMP_H11_S287_L001_R1_001_MR912-5-MDA-MECOM-AMP_H11_S287_L001_R2_001/Alleles_frequency_table.zip


title: 1173_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-2-MDA-MECOM-AMP_A1_S1/CRISPResso_on_MR912-2-MDA-MECOM-AMP_A1_S1_L001_R1_001_MR912-2-MDA-MECOM-AMP_A1_S1_L001_R2_001/Alleles_frequency_table.zip


title: 1170_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912_3_MDA_MECOM_AMP_G4_S652/CRISPResso_on_MR912_3_MDA_MECOM_AMP_G4_S652_L001_R1_001_MR912_3_MDA_MECOM_AMP_G4_S652_L001_R2_001/Alleles_frequency_table.zip


title: 1171_Mecom amplicon seq


title: 1169_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912_3_MDA_MECOM_AMP_B5_S497/CRISPResso_on_MR912_3_MDA_MECOM_AMP_B5_S497_L001_R1_001_MR912_3_MDA_MECOM_AMP_B5_S497_L001_R2_001/Alleles_frequency_table.zip


title: 1188_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-2-WTA-MECOM-AMP_G6_S174/CRISPResso_on_MR912-2-WTA-MECOM-AMP_G6_S174_L001_R1_001_MR912-2-WTA-MECOM-AMP_G6_S174_L001_R2_001/Alleles_frequency_table.zip


title: 1189_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912_3_MDA_MECOM_AMP_D1_S517/CRISPResso_on_MR912_3_MDA_MECOM_AMP_D1_S517_L001_R1_001_MR912_3_MDA_MECOM_AMP_D1_S517_L001_R2_001/Alleles_frequency_table.zip


title: 1167_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR214_1_Cat_H9_S93/CRISPResso_on_MR214_1_Cat_H9_S93_L001_R1_001_MR214_1_Cat_H9_S93_L001_R2_001/Alleles_frequency_table.zip


title: 1164_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912_3_MDA_MECOM_AMP_A12_S492/CRISPResso_on_MR912_3_MDA_MECOM_AMP_A12_S492_L001_R1_001_MR912_3_MDA_MECOM_AMP_A12_S492_L001_R2_001/Alleles_frequency_table.zip


title: 1168_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-2-WTA-MECOM-AMP_B6_S114/CRISPResso_on_MR912-2-WTA-MECOM-AMP_B6_S114_L001_R1_001_MR912-2-WTA-MECOM-AMP_B6_S114_L001_R2_001/Alleles_frequency_table.zip


title: 1166_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912_3_Dog_E11_S251/CRISPResso_on_MR912_3_Dog_E11_S251_L001_R1_001_MR912_3_Dog_E11_S251_L001_R2_001/Alleles_frequency_table.zip


title: 1165_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912_3_Dog_C12_S228/CRISPResso_on_MR912_3_Dog_C12_S228_L001_R1_001_MR912_3_Dog_C12_S228_L001_R2_001/Alleles_frequency_table.zip


title: 1163_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912_3_MDA_MECOM_AMP_A11_S491/CRISPResso_on_MR912_3_MDA_MECOM_AMP_A11_S491_L001_R1_001_MR912_3_MDA_MECOM_AMP_A11_S491_L001_R2_001/Alleles_frequency_table.zip


title: 1162_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912_3_MDA_MECOM_AMP_A10_S490/CRISPResso_on_MR912_3_MDA_MECOM_AMP_A10_S490_L001_R1_001_MR912_3_MDA_MECOM_AMP_A10_S490_L001_R2_001/Alleles_frequency_table.zip


title: 1161_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912_3_MDA_MECOM_AMP_A9_S489/CRISPResso_on_MR912_3_MDA_MECOM_AMP_A9_S489_L001_R1_001_MR912_3_MDA_MECOM_AMP_A9_S489_L001_R2_001/Alleles_frequency_table.zip


title: 1156_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912_3_MDA_MECOM_AMP_A4_S484/CRISPResso_on_MR912_3_MDA_MECOM_AMP_A4_S484_L001_R1_001_MR912_3_MDA_MECOM_AMP_A4_S484_L001_R2_001/Alleles_frequency_table.zip


title: 1157_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912_3_MDA_MECOM_AMP_A5_S485/CRISPResso_on_MR912_3_MDA_MECOM_AMP_A5_S485_L001_R1_001_MR912_3_MDA_MECOM_AMP_A5_S485_L001_R2_001/Alleles_frequency_table.zip


title: 1158_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR214_1_Cat_G12_S84/CRISPResso_on_MR214_1_Cat_G12_S84_L001_R1_001_MR214_1_Cat_G12_S84_L001_R2_001/Alleles_frequency_table.zip


title: 1152_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR214_1_MDA_MECOM_AMP_H12_S480/CRISPResso_on_MR214_1_MDA_MECOM_AMP_H12_S480_L001_R1_001_MR214_1_MDA_MECOM_AMP_H12_S480_L001_R2_001/Alleles_frequency_table.zip


title: 1153_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912_3_MDA_MECOM_AMP_A1_S481/CRISPResso_on_MR912_3_MDA_MECOM_AMP_A1_S481_L001_R1_001_MR912_3_MDA_MECOM_AMP_A1_S481_L001_R2_001/Alleles_frequency_table.zip


title: 1160_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912_3_MDA_MECOM_AMP_A8_S488/CRISPResso_on_MR912_3_MDA_MECOM_AMP_A8_S488_L001_R1_001_MR912_3_MDA_MECOM_AMP_A8_S488_L001_R2_001/Alleles_frequency_table.zip


title: 1150_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR214_1_MDA_MECOM_AMP_H10_S478/CRISPResso_on_MR214_1_MDA_MECOM_AMP_H10_S478_L001_R1_001_MR214_1_MDA_MECOM_AMP_H10_S478_L001_R2_001/Alleles_frequency_table.zip


title: 1151_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR214_1_MDA_MECOM_AMP_H11_S479/CRISPResso_on_MR214_1_MDA_MECOM_AMP_H11_S479_L001_R1_001_MR214_1_MDA_MECOM_AMP_H11_S479_L001_R2_001/Alleles_frequency_table.zip


title: 1172_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912_3_MDA_MECOM_AMP_H5_S665/CRISPResso_on_MR912_3_MDA_MECOM_AMP_H5_S665_L001_R1_001_MR912_3_MDA_MECOM_AMP_H5_S665_L001_R2_001/Alleles_frequency_table.zip


title: 1148_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR214_1_MDA_MECOM_AMP_H8_S476/CRISPResso_on_MR214_1_MDA_MECOM_AMP_H8_S476_L001_R1_001_MR214_1_MDA_MECOM_AMP_H8_S476_L001_R2_001/Alleles_frequency_table.zip


title: 1146_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR214_1_MDA_MECOM_AMP_H6_S474/CRISPResso_on_MR214_1_MDA_MECOM_AMP_H6_S474_L001_R1_001_MR214_1_MDA_MECOM_AMP_H6_S474_L001_R2_001/Alleles_frequency_table.zip


title: 1144_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR214_1_MDA_MECOM_AMP_H4_S472/CRISPResso_on_MR214_1_MDA_MECOM_AMP_H4_S472_L001_R1_001_MR214_1_MDA_MECOM_AMP_H4_S472_L001_R2_001/Alleles_frequency_table.zip


title: 1159_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-5-MDA-MECOM-AMP_A1_S193/CRISPResso_on_MR912-5-MDA-MECOM-AMP_A1_S193_L001_R1_001_MR912-5-MDA-MECOM-AMP_A1_S193_L001_R2_001/Alleles_frequency_table.zip


title: 1147_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR214_1_MDA_MECOM_AMP_H7_S475/CRISPResso_on_MR214_1_MDA_MECOM_AMP_H7_S475_L001_R1_001_MR214_1_MDA_MECOM_AMP_H7_S475_L001_R2_001/Alleles_frequency_table.zip


title: 1143_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR214_1_MDA_MECOM_AMP_H3_S471/CRISPResso_on_MR214_1_MDA_MECOM_AMP_H3_S471_L001_R1_001_MR214_1_MDA_MECOM_AMP_H3_S471_L001_R2_001/Alleles_frequency_table.zip


title: 1142_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-5-WTA-MECOM-AMP_B11_S311/CRISPResso_on_MR912-5-WTA-MECOM-AMP_B11_S311_L001_R1_001_MR912-5-WTA-MECOM-AMP_B11_S311_L001_R2_001/Alleles_frequency_table.zip


title: 1140_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912_3_MDA_MECOM_AMP_B12_S504/CRISPResso_on_MR912_3_MDA_MECOM_AMP_B12_S504_L001_R1_001_MR912_3_MDA_MECOM_AMP_B12_S504_L001_R2_001/Alleles_frequency_table.zip


title: 1154_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912_3_MDA_MECOM_AMP_A2_S482/CRISPResso_on_MR912_3_MDA_MECOM_AMP_A2_S482_L001_R1_001_MR912_3_MDA_MECOM_AMP_A2_S482_L001_R2_001/Alleles_frequency_table.zip


title: 1145_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR214_1_MDA_MECOM_AMP_H5_S473/CRISPResso_on_MR214_1_MDA_MECOM_AMP_H5_S473_L001_R1_001_MR214_1_MDA_MECOM_AMP_H5_S473_L001_R2_001/Alleles_frequency_table.zip


title: 1139_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR214_1_MDA_MECOM_AMP_G11_S467/CRISPResso_on_MR214_1_MDA_MECOM_AMP_G11_S467_L001_R1_001_MR214_1_MDA_MECOM_AMP_G11_S467_L001_R2_001/Alleles_frequency_table.zip


title: 1155_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912_3_MDA_MECOM_AMP_A3_S483/CRISPResso_on_MR912_3_MDA_MECOM_AMP_A3_S483_L001_R1_001_MR912_3_MDA_MECOM_AMP_A3_S483_L001_R2_001/Alleles_frequency_table.zip


title: 1136_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR214_1_MDA_MECOM_AMP_G8_S464/CRISPResso_on_MR214_1_MDA_MECOM_AMP_G8_S464_L001_R1_001_MR214_1_MDA_MECOM_AMP_G8_S464_L001_R2_001/Alleles_frequency_table.zip


title: 1135_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR214_1_MDA_MECOM_AMP_G7_S463/CRISPResso_on_MR214_1_MDA_MECOM_AMP_G7_S463_L001_R1_001_MR214_1_MDA_MECOM_AMP_G7_S463_L001_R2_001/Alleles_frequency_table.zip


title: 1137_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR214_1_MDA_MECOM_AMP_G9_S465/CRISPResso_on_MR214_1_MDA_MECOM_AMP_G9_S465_L001_R1_001_MR214_1_MDA_MECOM_AMP_G9_S465_L001_R2_001/Alleles_frequency_table.zip


title: 1138_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR214_1_MDA_MECOM_AMP_G10_S466/CRISPResso_on_MR214_1_MDA_MECOM_AMP_G10_S466_L001_R1_001_MR214_1_MDA_MECOM_AMP_G10_S466_L001_R2_001/Alleles_frequency_table.zip


title: 1132_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR214_1_MDA_MECOM_AMP_G4_S460/CRISPResso_on_MR214_1_MDA_MECOM_AMP_G4_S460_L001_R1_001_MR214_1_MDA_MECOM_AMP_G4_S460_L001_R2_001/Alleles_frequency_table.zip


title: 1133_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR214_1_MDA_MECOM_AMP_G5_S461/CRISPResso_on_MR214_1_MDA_MECOM_AMP_G5_S461_L001_R1_001_MR214_1_MDA_MECOM_AMP_G5_S461_L001_R2_001/Alleles_frequency_table.zip


title: 1134_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR214_1_MDA_MECOM_AMP_G6_S462/CRISPResso_on_MR214_1_MDA_MECOM_AMP_G6_S462_L001_R1_001_MR214_1_MDA_MECOM_AMP_G6_S462_L001_R2_001/Alleles_frequency_table.zip


title: 1131_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR214_1_MDA_MECOM_AMP_G3_S459/CRISPResso_on_MR214_1_MDA_MECOM_AMP_G3_S459_L001_R1_001_MR214_1_MDA_MECOM_AMP_G3_S459_L001_R2_001/Alleles_frequency_table.zip


title: 1127_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR214_1_MDA_MECOM_AMP_F11_S455/CRISPResso_on_MR214_1_MDA_MECOM_AMP_F11_S455_L001_R1_001_MR214_1_MDA_MECOM_AMP_F11_S455_L001_R2_001/Alleles_frequency_table.zip


title: 1126_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR214_1_MDA_MECOM_AMP_F10_S454/CRISPResso_on_MR214_1_MDA_MECOM_AMP_F10_S454_L001_R1_001_MR214_1_MDA_MECOM_AMP_F10_S454_L001_R2_001/Alleles_frequency_table.zip


title: 1124_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR214_1_MDA_MECOM_AMP_F8_S452/CRISPResso_on_MR214_1_MDA_MECOM_AMP_F8_S452_L001_R1_001_MR214_1_MDA_MECOM_AMP_F8_S452_L001_R2_001/Alleles_frequency_table.zip


title: 1130_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR214_1_MDA_MECOM_AMP_G2_S458/CRISPResso_on_MR214_1_MDA_MECOM_AMP_G2_S458_L001_R1_001_MR214_1_MDA_MECOM_AMP_G2_S458_L001_R2_001/Alleles_frequency_table.zip


title: 1123_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR214_1_MDA_MECOM_AMP_F7_S451/CRISPResso_on_MR214_1_MDA_MECOM_AMP_F7_S451_L001_R1_001_MR214_1_MDA_MECOM_AMP_F7_S451_L001_R2_001/Alleles_frequency_table.zip


title: 1121_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR214_1_MDA_MECOM_AMP_F5_S449/CRISPResso_on_MR214_1_MDA_MECOM_AMP_F5_S449_L001_R1_001_MR214_1_MDA_MECOM_AMP_F5_S449_L001_R2_001/Alleles_frequency_table.zip


title: 1128_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR214_1_MDA_MECOM_AMP_F12_S456/CRISPResso_on_MR214_1_MDA_MECOM_AMP_F12_S456_L001_R1_001_MR214_1_MDA_MECOM_AMP_F12_S456_L001_R2_001/Alleles_frequency_table.zip


title: 1125_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR214_1_MDA_MECOM_AMP_F9_S453/CRISPResso_on_MR214_1_MDA_MECOM_AMP_F9_S453_L001_R1_001_MR214_1_MDA_MECOM_AMP_F9_S453_L001_R2_001/Alleles_frequency_table.zip


title: 1122_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912_3_MDA_MECOM_AMP_H8_S668/CRISPResso_on_MR912_3_MDA_MECOM_AMP_H8_S668_L001_R1_001_MR912_3_MDA_MECOM_AMP_H8_S668_L001_R2_001/Alleles_frequency_table.zip


title: 1119_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR214_1_MDA_MECOM_AMP_F3_S447/CRISPResso_on_MR214_1_MDA_MECOM_AMP_F3_S447_L001_R1_001_MR214_1_MDA_MECOM_AMP_F3_S447_L001_R2_001/Alleles_frequency_table.zip


title: 1118_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR214_1_MDA_MECOM_AMP_F2_S446/CRISPResso_on_MR214_1_MDA_MECOM_AMP_F2_S446_L001_R1_001_MR214_1_MDA_MECOM_AMP_F2_S446_L001_R2_001/Alleles_frequency_table.zip


title: 1120_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR214_1_MDA_MECOM_AMP_F4_S448/CRISPResso_on_MR214_1_MDA_MECOM_AMP_F4_S448_L001_R1_001_MR214_1_MDA_MECOM_AMP_F4_S448_L001_R2_001/Alleles_frequency_table.zip


title: 1116_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR214_1_MDA_MECOM_AMP_E12_S444/CRISPResso_on_MR214_1_MDA_MECOM_AMP_E12_S444_L001_R1_001_MR214_1_MDA_MECOM_AMP_E12_S444_L001_R2_001/Alleles_frequency_table.zip


title: 1117_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR214_1_MDA_MECOM_AMP_F1_S445/CRISPResso_on_MR214_1_MDA_MECOM_AMP_F1_S445_L001_R1_001_MR214_1_MDA_MECOM_AMP_F1_S445_L001_R2_001/Alleles_frequency_table.zip


title: 1114_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR214_1_MDA_MECOM_AMP_E10_S442/CRISPResso_on_MR214_1_MDA_MECOM_AMP_E10_S442_L001_R1_001_MR214_1_MDA_MECOM_AMP_E10_S442_L001_R2_001/Alleles_frequency_table.zip


title: 1115_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR214_1_MDA_MECOM_AMP_E11_S443/CRISPResso_on_MR214_1_MDA_MECOM_AMP_E11_S443_L001_R1_001_MR214_1_MDA_MECOM_AMP_E11_S443_L001_R2_001/Alleles_frequency_table.zip


title: 1111_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR214_1_MDA_MECOM_AMP_E7_S439/CRISPResso_on_MR214_1_MDA_MECOM_AMP_E7_S439_L001_R1_001_MR214_1_MDA_MECOM_AMP_E7_S439_L001_R2_001/Alleles_frequency_table.zip


title: 1113_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR214_1_MDA_MECOM_AMP_E9_S441/CRISPResso_on_MR214_1_MDA_MECOM_AMP_E9_S441_L001_R1_001_MR214_1_MDA_MECOM_AMP_E9_S441_L001_R2_001/Alleles_frequency_table.zip


title: 1110_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR214_1_MDA_MECOM_AMP_E6_S438/CRISPResso_on_MR214_1_MDA_MECOM_AMP_E6_S438_L001_R1_001_MR214_1_MDA_MECOM_AMP_E6_S438_L001_R2_001/Alleles_frequency_table.zip


title: 1109_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR214_1_MDA_MECOM_AMP_E5_S437/CRISPResso_on_MR214_1_MDA_MECOM_AMP_E5_S437_L001_R1_001_MR214_1_MDA_MECOM_AMP_E5_S437_L001_R2_001/Alleles_frequency_table.zip


title: 1108_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR214_1_MDA_MECOM_AMP_E4_S436/CRISPResso_on_MR214_1_MDA_MECOM_AMP_E4_S436_L001_R1_001_MR214_1_MDA_MECOM_AMP_E4_S436_L001_R2_001/Alleles_frequency_table.zip


title: 1129_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR214_1_MDA_MECOM_AMP_G1_S457/CRISPResso_on_MR214_1_MDA_MECOM_AMP_G1_S457_L001_R1_001_MR214_1_MDA_MECOM_AMP_G1_S457_L001_R2_001/Alleles_frequency_table.zip


title: 1107_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR214_1_MDA_MECOM_AMP_E3_S435/CRISPResso_on_MR214_1_MDA_MECOM_AMP_E3_S435_L001_R1_001_MR214_1_MDA_MECOM_AMP_E3_S435_L001_R2_001/Alleles_frequency_table.zip


title: 1106_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR214_1_MDA_MECOM_AMP_E2_S434/CRISPResso_on_MR214_1_MDA_MECOM_AMP_E2_S434_L001_R1_001_MR214_1_MDA_MECOM_AMP_E2_S434_L001_R2_001/Alleles_frequency_table.zip


title: 1105_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR214_1_MDA_MECOM_AMP_E1_S433/CRISPResso_on_MR214_1_MDA_MECOM_AMP_E1_S433_L001_R1_001_MR214_1_MDA_MECOM_AMP_E1_S433_L001_R2_001/Alleles_frequency_table.zip


title: 1102_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR214_1_MDA_MECOM_AMP_D10_S430/CRISPResso_on_MR214_1_MDA_MECOM_AMP_D10_S430_L001_R1_001_MR214_1_MDA_MECOM_AMP_D10_S430_L001_R2_001/Alleles_frequency_table.zip


title: 1101_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR214_1_MDA_MECOM_AMP_D9_S429/CRISPResso_on_MR214_1_MDA_MECOM_AMP_D9_S429_L001_R1_001_MR214_1_MDA_MECOM_AMP_D9_S429_L001_R2_001/Alleles_frequency_table.zip


title: 1098_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR214_1_MDA_MECOM_AMP_D6_S426/CRISPResso_on_MR214_1_MDA_MECOM_AMP_D6_S426_L001_R1_001_MR214_1_MDA_MECOM_AMP_D6_S426_L001_R2_001/Alleles_frequency_table.zip


title: 1100_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR214_1_MDA_MECOM_AMP_D8_S428/CRISPResso_on_MR214_1_MDA_MECOM_AMP_D8_S428_L001_R1_001_MR214_1_MDA_MECOM_AMP_D8_S428_L001_R2_001/Alleles_frequency_table.zip


title: 1093_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR214_1_MDA_MECOM_AMP_D1_S421/CRISPResso_on_MR214_1_MDA_MECOM_AMP_D1_S421_L001_R1_001_MR214_1_MDA_MECOM_AMP_D1_S421_L001_R2_001/Alleles_frequency_table.zip


title: 1097_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR214_1_MDA_MECOM_AMP_D5_S425/CRISPResso_on_MR214_1_MDA_MECOM_AMP_D5_S425_L001_R1_001_MR214_1_MDA_MECOM_AMP_D5_S425_L001_R2_001/Alleles_frequency_table.zip


title: 1095_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR214_1_MDA_MECOM_AMP_D3_S423/CRISPResso_on_MR214_1_MDA_MECOM_AMP_D3_S423_L001_R1_001_MR214_1_MDA_MECOM_AMP_D3_S423_L001_R2_001/Alleles_frequency_table.zip


title: 1096_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912_3_Bird_C5_S125/CRISPResso_on_MR912_3_Bird_C5_S125_L001_R1_001_MR912_3_Bird_C5_S125_L001_R2_001/Alleles_frequency_table.zip


title: 1094_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR214_1_MDA_MECOM_AMP_D2_S422/CRISPResso_on_MR214_1_MDA_MECOM_AMP_D2_S422_L001_R1_001_MR214_1_MDA_MECOM_AMP_D2_S422_L001_R2_001/Alleles_frequency_table.zip


title: 1091_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR214_1_MDA_MECOM_AMP_C11_S419/CRISPResso_on_MR214_1_MDA_MECOM_AMP_C11_S419_L001_R1_001_MR214_1_MDA_MECOM_AMP_C11_S419_L001_R2_001/Alleles_frequency_table.zip


title: 1092_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR214_1_MDA_MECOM_AMP_C12_S420/CRISPResso_on_MR214_1_MDA_MECOM_AMP_C12_S420_L001_R1_001_MR214_1_MDA_MECOM_AMP_C12_S420_L001_R2_001/Alleles_frequency_table.zip


title: 1089_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR214_1_MDA_MECOM_AMP_C9_S417/CRISPResso_on_MR214_1_MDA_MECOM_AMP_C9_S417_L001_R1_001_MR214_1_MDA_MECOM_AMP_C9_S417_L001_R2_001/Alleles_frequency_table.zip


title: 1090_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-2-WTA-MECOM-AMP_H11_S191/CRISPResso_on_MR912-2-WTA-MECOM-AMP_H11_S191_L001_R1_001_MR912-2-WTA-MECOM-AMP_H11_S191_L001_R2_001/Alleles_frequency_table.zip


title: 1112_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR214_1_MDA_MECOM_AMP_E8_S440/CRISPResso_on_MR214_1_MDA_MECOM_AMP_E8_S440_L001_R1_001_MR214_1_MDA_MECOM_AMP_E8_S440_L001_R2_001/Alleles_frequency_table.zip


title: 1086_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR214_1_MDA_MECOM_AMP_C6_S414/CRISPResso_on_MR214_1_MDA_MECOM_AMP_C6_S414_L001_R1_001_MR214_1_MDA_MECOM_AMP_C6_S414_L001_R2_001/Alleles_frequency_table.zip


title: 1085_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR214_1_MDA_MECOM_AMP_C5_S413/CRISPResso_on_MR214_1_MDA_MECOM_AMP_C5_S413_L001_R1_001_MR214_1_MDA_MECOM_AMP_C5_S413_L001_R2_001/Alleles_frequency_table.zip


title: 1087_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR214_1_MDA_MECOM_AMP_C7_S415/CRISPResso_on_MR214_1_MDA_MECOM_AMP_C7_S415_L001_R1_001_MR214_1_MDA_MECOM_AMP_C7_S415_L001_R2_001/Alleles_frequency_table.zip


title: 1084_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR214_1_MDA_MECOM_AMP_C4_S412/CRISPResso_on_MR214_1_MDA_MECOM_AMP_C4_S412_L001_R1_001_MR214_1_MDA_MECOM_AMP_C4_S412_L001_R2_001/Alleles_frequency_table.zip


title: 1104_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR214_1_MDA_MECOM_AMP_D12_S432/CRISPResso_on_MR214_1_MDA_MECOM_AMP_D12_S432_L001_R1_001_MR214_1_MDA_MECOM_AMP_D12_S432_L001_R2_001/Alleles_frequency_table.zip


title: 1082_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR214_1_MDA_MECOM_AMP_C2_S410/CRISPResso_on_MR214_1_MDA_MECOM_AMP_C2_S410_L001_R1_001_MR214_1_MDA_MECOM_AMP_C2_S410_L001_R2_001/Alleles_frequency_table.zip


title: 1083_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR214_1_MDA_MECOM_AMP_C3_S411/CRISPResso_on_MR214_1_MDA_MECOM_AMP_C3_S411_L001_R1_001_MR214_1_MDA_MECOM_AMP_C3_S411_L001_R2_001/Alleles_frequency_table.zip


title: 1081_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR214_1_MDA_MECOM_AMP_C1_S409/CRISPResso_on_MR214_1_MDA_MECOM_AMP_C1_S409_L001_R1_001_MR214_1_MDA_MECOM_AMP_C1_S409_L001_R2_001/Alleles_frequency_table.zip


title: 1079_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR214_1_MDA_MECOM_AMP_B11_S407/CRISPResso_on_MR214_1_MDA_MECOM_AMP_B11_S407_L001_R1_001_MR214_1_MDA_MECOM_AMP_B11_S407_L001_R2_001/Alleles_frequency_table.zip


title: 1103_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR214_1_MDA_MECOM_AMP_D11_S431/CRISPResso_on_MR214_1_MDA_MECOM_AMP_D11_S431_L001_R1_001_MR214_1_MDA_MECOM_AMP_D11_S431_L001_R2_001/Alleles_frequency_table.zip


title: 1080_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR214_1_MDA_MECOM_AMP_B12_S408/CRISPResso_on_MR214_1_MDA_MECOM_AMP_B12_S408_L001_R1_001_MR214_1_MDA_MECOM_AMP_B12_S408_L001_R2_001/Alleles_frequency_table.zip


title: 1099_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR214_1_Cat_D12_S48/CRISPResso_on_MR214_1_Cat_D12_S48_L001_R1_001_MR214_1_Cat_D12_S48_L001_R2_001/Alleles_frequency_table.zip


title: 1078_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR214_1_MDA_MECOM_AMP_B10_S406/CRISPResso_on_MR214_1_MDA_MECOM_AMP_B10_S406_L001_R1_001_MR214_1_MDA_MECOM_AMP_B10_S406_L001_R2_001/Alleles_frequency_table.zip


title: 1077_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR214_1_MDA_MECOM_AMP_B9_S405/CRISPResso_on_MR214_1_MDA_MECOM_AMP_B9_S405_L001_R1_001_MR214_1_MDA_MECOM_AMP_B9_S405_L001_R2_001/Alleles_frequency_table.zip


title: 1076_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR214_1_MDA_MECOM_AMP_B8_S404/CRISPResso_on_MR214_1_MDA_MECOM_AMP_B8_S404_L001_R1_001_MR214_1_MDA_MECOM_AMP_B8_S404_L001_R2_001/Alleles_frequency_table.zip


title: 1074_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR214_1_MDA_MECOM_AMP_B6_S402/CRISPResso_on_MR214_1_MDA_MECOM_AMP_B6_S402_L001_R1_001_MR214_1_MDA_MECOM_AMP_B6_S402_L001_R2_001/Alleles_frequency_table.zip


title: 1075_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR214_1_MDA_MECOM_AMP_B7_S403/CRISPResso_on_MR214_1_MDA_MECOM_AMP_B7_S403_L001_R1_001_MR214_1_MDA_MECOM_AMP_B7_S403_L001_R2_001/Alleles_frequency_table.zip


title: 1073_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR214_1_MDA_MECOM_AMP_B5_S401/CRISPResso_on_MR214_1_MDA_MECOM_AMP_B5_S401_L001_R1_001_MR214_1_MDA_MECOM_AMP_B5_S401_L001_R2_001/Alleles_frequency_table.zip


title: 1088_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR214_1_MDA_MECOM_AMP_C8_S416/CRISPResso_on_MR214_1_MDA_MECOM_AMP_C8_S416_L001_R1_001_MR214_1_MDA_MECOM_AMP_C8_S416_L001_R2_001/Alleles_frequency_table.zip


title: 800 ppm_biol_rep_3

city: Wonju-si

first: Sun-Goo

last: Hwang

address: 83 Sangjidae-gil, Wonju-si, Gangwon-do, Korea

country: South Korea

institute: Sangji University

data_processing:
The raw RNA sequencing data were used for de novo transcriptome assembly using Trinity assembler
The assembled contigs were used to find transcripts, including open reading frames (ORF) over 100 amino acids, using Trans Decoder.
The annotation of long ORFs was performed by BLAST using UniProtKB/Swiss-Prot data.
The differentially expressed genes between plants under 400 ppm and 800 ppm CO2 conditions were identified using the edgeR method with a threshold FDR of 0.05.
Supplementary files format and content: tab-delimited text files include FRKM values for each Sample

organism: Anethum foeniculum

source_name: leaves

extract_protocol:
RNA was extracted from leaf tissues subjected to 400 and 800 ppm CO2 concentrations using the Accuprep® Universal RNA Extraction Kit with three replicates. RNA quality was estimated using a spectrophotometer (NanoDrop-nabi, MicroDigital, Korea).
The RNA extracted from the six samples were subjected to library preparation according to the manufacturer’s instructions.

value: leaves

value: 800 ppm CO2 concentration

tag: time

value: Five weeks


title: 400 ppm_biol_rep_3

value: 400 ppm CO2 concentration


title: 400 ppm_biol_rep_2


title: 400 ppm_biol_rep_1


title: 800 ppm_biol_rep_1


title: 800 ppm_biol_rep_2


title: 477_pustule

city: Indianapolis

first: Julie

last: Brothwell

state: IN

address: 635 Barnhill Dr., MS420

department: Department of Microbiology & Immunology

institute: Indiana University

data_processing:
Basecalling was performed with Illumina RTA v3.4.4 and bcl2fastq v2.20.
Sequenced reads were aligned to the Haemophilus ducreyi 35000HP genome (AE017143.1) using Bowtie2 or human genome (hg38) using STAR.
Human reads in pustule samples were subsampled to 125 million reads. H. ducreyi reads in cultures were subsampled to 1 million reads.
Count matricies were made for human and H. ducreyi reads using featureCounts.
Library normalization and statistical analysis was performed in R v4.1.0 with the DESeq2 package.
Assembly: hg38; AE017143.1
Supplementary files format and content: txt file for the count matrix of the 12 H. ducreyi samples from this study and the reanalyzed samples from 8 H. ducreyi samples from GSE130901
Supplementary files format and content: txt file for the count matrix of the 16 human samples from this study and the reanalyzed samples from 8 human samples from GSE130901

organism:
[Haemophilus] ducreyi
Homo sapiens

source_name: skin

growth_protocol: The inocula consisted of H. ducreyi cultured in GC broth supplemented with 1% IsoVitaleX, 50 𝜇g/mL hemin, and 5% heat-inactivated fetal bovine serum and shaken at 33°C in ambient air to mid-log phase (OD660 0.200-0.250). 10 mL of mid-log (OD660 0.200-0.250) culture was pelleted and stored in 2 mL of RNALater at -80°C. The culture was processed and diluted in PBS so that ~70 CFU of H. ducreyi would be delivered to the upper arm skin of volunteers using a allergy testing device. Volunteers were both infected with the inoculum and sham inoculated with PBS. The infection progressed for 6-8 days, at which point painful pustules had developed at the infected sites. A 6 mm punch biopsy was taken of both the pustule and wound. Biopsies were placed in 2 mL of RNALater at the bedside and then stored at -80°C.

extract_protocol:
RNA was extracted from samples the day after collection using the Qiagen RNeasy Fibrous Tissue Mini Kit with on-column DNase digestion. RNA was eluted from the column with nuclease free water and then treated with Turbo DNase (Invitrogen) for an in-solution DNase digestion.
Purified RNA was treated with Qiagen FastSelect for bacteria and human rRNA depletion. Libraries were prepared with a Roche KAPA kit.

value: skin

value: pustule


title: 476_pustule


title: 1070_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR214_1_MDA_MECOM_AMP_B2_S398/CRISPResso_on_MR214_1_MDA_MECOM_AMP_B2_S398_L001_R1_001_MR214_1_MDA_MECOM_AMP_B2_S398_L001_R2_001/Alleles_frequency_table.zip


title: 475_pustule


title: 1071_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR214_1_MDA_MECOM_AMP_B3_S399/CRISPResso_on_MR214_1_MDA_MECOM_AMP_B3_S399_L001_R1_001_MR214_1_MDA_MECOM_AMP_B3_S399_L001_R2_001/Alleles_frequency_table.zip


title: 1069_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR214_1_MDA_MECOM_AMP_B1_S397/CRISPResso_on_MR214_1_MDA_MECOM_AMP_B1_S397_L001_R1_001_MR214_1_MDA_MECOM_AMP_B1_S397_L001_R2_001/Alleles_frequency_table.zip


title: 474_pustule


title: 1068_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR214_1_MDA_MECOM_AMP_A12_S396/CRISPResso_on_MR214_1_MDA_MECOM_AMP_A12_S396_L001_R1_001_MR214_1_MDA_MECOM_AMP_A12_S396_L001_R2_001/Alleles_frequency_table.zip


title: 1149_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR214_1_MDA_MECOM_AMP_H9_S477/CRISPResso_on_MR214_1_MDA_MECOM_AMP_H9_S477_L001_R1_001_MR214_1_MDA_MECOM_AMP_H9_S477_L001_R2_001/Alleles_frequency_table.zip


title: 471_pustule


title: 473_pustule


title: 470_pustule


title: 1066_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR214_1_MDA_MECOM_AMP_A10_S394/CRISPResso_on_MR214_1_MDA_MECOM_AMP_A10_S394_L001_R1_001_MR214_1_MDA_MECOM_AMP_A10_S394_L001_R2_001/Alleles_frequency_table.zip


title: 1065_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR214_1_MDA_MECOM_AMP_A9_S393/CRISPResso_on_MR214_1_MDA_MECOM_AMP_A9_S393_L001_R1_001_MR214_1_MDA_MECOM_AMP_A9_S393_L001_R2_001/Alleles_frequency_table.zip


title: 469_pustule


title: 1072_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR214_1_MDA_MECOM_AMP_B4_S400/CRISPResso_on_MR214_1_MDA_MECOM_AMP_B4_S400_L001_R1_001_MR214_1_MDA_MECOM_AMP_B4_S400_L001_R2_001/Alleles_frequency_table.zip


title: T-10d-3

city: Fuzhou

first: Chi

last: Yang

address: No.15 Shangxiadian Road, Cangshan District

institute: Fujian Agriculture and Forestry University

data_processing:
Basecalling: Illumina Casava1.7 software used for basecalling.
Data filtering: Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to SP-C whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Alignment: HISAT2 builds index for genome sequence with method burrows-Wheeler Transformation and Ferragina-Manzini(FM) index.  Use StringTie to assembly the transcripts with mapped reads, StringTie uses a novel network flow algorithm to quantitate full-length transcripts representing multiple splice variants for each gene locus.
Generation of normalized abundance measurements: We used StringTie to estimates its expression level using a maximum flow algorithm, and used FPKM(Fragments Per Kilobase of transcript per Million fragments mapped) to measure the transcript or gene expression levels.
Genome_build: The genome version used in this study is version JAENRS010000000.
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Sparassis latifolia

source_name: mycelium

extract_protocol:
The purity, concentration and integrity of RNA samples are detected using advanced molecular biology equipment to ensure the use of qualified samples for transcriptome sequencing.
After RNA sample quality control, high-quality RNA was obtained and used for library construction. The pipeline was consisted of five main steps:  (1) Isolated mRNA from total RNA using the oligo(dT) magnetic beads;  (2) Mixed with the fragmentation buffer and fragment the mRNA randomly;  (3) Using mRNA as the template, six-base random primers (random hexamers) were used to synthesize the first strand cDNA. Then PCR buffer, dNTPs, RNase H and DNA polymerase I were added to do second strand cDNA synthesis. AMPure XP beads are used to purify cDNAs;  (4) Purified double-stranded cDNAs were resolved with EB buffer for end reparation and single nucleotide A addition. Then AMPure XP beads were used in size selection;  (5) Finally, cDNA sequencing library was obtained by PCR amplification.

tag: strain

value: SP-C

value: pinewood treatment 10d


title: T-10d-2


title: 1063_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR214_1_MDA_MECOM_AMP_A7_S391/CRISPResso_on_MR214_1_MDA_MECOM_AMP_A7_S391_L001_R1_001_MR214_1_MDA_MECOM_AMP_A7_S391_L001_R2_001/Alleles_frequency_table.zip

value: HSC


title: T-5d-3

value: pinewood treatment 5d


title: 1062_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR214_1_MDA_MECOM_AMP_A6_S390/CRISPResso_on_MR214_1_MDA_MECOM_AMP_A6_S390_L001_R1_001_MR214_1_MDA_MECOM_AMP_A6_S390_L001_R2_001/Alleles_frequency_table.zip

value: Mecom KO


title: T-5d-2


title: 1060_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR214_1_MDA_MECOM_AMP_A4_S388/CRISPResso_on_MR214_1_MDA_MECOM_AMP_A4_S388_L001_R1_001_MR214_1_MDA_MECOM_AMP_A4_S388_L001_R2_001/Alleles_frequency_table.zip


title: 1058_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR214_1_MDA_MECOM_AMP_A2_S386/CRISPResso_on_MR214_1_MDA_MECOM_AMP_A2_S386_L001_R1_001_MR214_1_MDA_MECOM_AMP_A2_S386_L001_R2_001/Alleles_frequency_table.zip


title: T-1d-3

value: pinewood treatment 1d


title: 1055_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-5-MDA-MECOM-AMP_C5_S221/CRISPResso_on_MR912-5-MDA-MECOM-AMP_C5_S221_L001_R1_001_MR912-5-MDA-MECOM-AMP_C5_S221_L001_R2_001/Alleles_frequency_table.zip


title: T-6h-3

value: pinewood treatment 6h


title: 1059_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR214_1_MDA_MECOM_AMP_A3_S387/CRISPResso_on_MR214_1_MDA_MECOM_AMP_A3_S387_L001_R1_001_MR214_1_MDA_MECOM_AMP_A3_S387_L001_R2_001/Alleles_frequency_table.zip


title: 1067_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR214_1_MDA_MECOM_AMP_A11_S395/CRISPResso_on_MR214_1_MDA_MECOM_AMP_A11_S395_L001_R1_001_MR214_1_MDA_MECOM_AMP_A11_S395_L001_R2_001/Alleles_frequency_table.zip


title: T-1d-1


title: T-1d-2


title: T-5d-1


title: 1057_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR214_1_MDA_MECOM_AMP_A1_S385/CRISPResso_on_MR214_1_MDA_MECOM_AMP_A1_S385_L001_R1_001_MR214_1_MDA_MECOM_AMP_A1_S385_L001_R2_001/Alleles_frequency_table.zip


title: 1053_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912_3_MDA_MECOM_AMP_H5_S665/CRISPResso_on_MR912_3_MDA_MECOM_AMP_H5_S665_L001_R1_001_MR912_3_MDA_MECOM_AMP_H5_S665_L001_R2_001/Alleles_frequency_table.zip


title: T-6h-2


title: 1052_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912_3_MDA_MECOM_AMP_C1_S505/CRISPResso_on_MR912_3_MDA_MECOM_AMP_C1_S505_L001_R1_001_MR912_3_MDA_MECOM_AMP_C1_S505_L001_R2_001/Alleles_frequency_table.zip


title: T-6h-1


title: T-1h-2

value: pinewood treatment 1h


title: 1064_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR214_1_MDA_MECOM_AMP_A8_S392/CRISPResso_on_MR214_1_MDA_MECOM_AMP_A8_S392_L001_R1_001_MR214_1_MDA_MECOM_AMP_A8_S392_L001_R2_001/Alleles_frequency_table.zip


title: 1051_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR214_1_MDA_MECOM_AMP_B5_S401/CRISPResso_on_MR214_1_MDA_MECOM_AMP_B5_S401_L001_R1_001_MR214_1_MDA_MECOM_AMP_B5_S401_L001_R2_001/Alleles_frequency_table.zip


title: T-10d-1


title: T-1h-3


title: 1061_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR214_1_MDA_MECOM_AMP_A5_S389/CRISPResso_on_MR214_1_MDA_MECOM_AMP_A5_S389_L001_R1_001_MR214_1_MDA_MECOM_AMP_A5_S389_L001_R2_001/Alleles_frequency_table.zip


title: 1050_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912_3_Dog_H6_S282/CRISPResso_on_MR912_3_Dog_H6_S282_L001_R1_001_MR912_3_Dog_H6_S282_L001_R2_001/Alleles_frequency_table.zip


title: T-1h-1


title: CK-3

value: CK


title: 1048_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912_3_MDA_MECOM_AMP_C11_S611/CRISPResso_on_MR912_3_MDA_MECOM_AMP_C11_S611_L001_R1_001_MR912_3_MDA_MECOM_AMP_C11_S611_L001_R2_001/Alleles_frequency_table.zip


title: 1047_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912_3_Bird_D5_S137/CRISPResso_on_MR912_3_Bird_D5_S137_L001_R1_001_MR912_3_Bird_D5_S137_L001_R2_001/Alleles_frequency_table.zip


title: CK-2


title: CK-1


title: 1054_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR214_1_Cat_E10_S58/CRISPResso_on_MR214_1_Cat_E10_S58_L001_R1_001_MR214_1_Cat_E10_S58_L001_R2_001/Alleles_frequency_table.zip


title: 1046_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-2-MDA-MECOM-AMP_G11_S83/CRISPResso_on_MR912-2-MDA-MECOM-AMP_G11_S83_L001_R1_001_MR912-2-MDA-MECOM-AMP_G11_S83_L001_R2_001/Alleles_frequency_table.zip


title: 1043_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912_3_Bird_F11_S167/CRISPResso_on_MR912_3_Bird_F11_S167_L001_R1_001_MR912_3_Bird_F11_S167_L001_R2_001/Alleles_frequency_table.zip


title: 1045_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR214_1_MDA_MECOM_AMP_C9_S417/CRISPResso_on_MR214_1_MDA_MECOM_AMP_C9_S417_L001_R1_001_MR214_1_MDA_MECOM_AMP_C9_S417_L001_R2_001/Alleles_frequency_table.zip


title: 1041_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR214_1_Cat_E7_S55/CRISPResso_on_MR214_1_Cat_E7_S55_L001_R1_001_MR214_1_Cat_E7_S55_L001_R2_001/Alleles_frequency_table.zip


title: 1042_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912_3_Dog_G10_S274/CRISPResso_on_MR912_3_Dog_G10_S274_L001_R1_001_MR912_3_Dog_G10_S274_L001_R2_001/Alleles_frequency_table.zip


title: 1040_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912_3_Dog_G8_S272/CRISPResso_on_MR912_3_Dog_G8_S272_L001_R1_001_MR912_3_Dog_G8_S272_L001_R2_001/Alleles_frequency_table.zip


title: 1039_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-2-MDA-MECOM-AMP_B11_S23/CRISPResso_on_MR912-2-MDA-MECOM-AMP_B11_S23_L001_R1_001_MR912-2-MDA-MECOM-AMP_B11_S23_L001_R2_001/Alleles_frequency_table.zip


title: 1037_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR214_1_MDA_MECOM_AMP_A6_S390/CRISPResso_on_MR214_1_MDA_MECOM_AMP_A6_S390_L001_R1_001_MR214_1_MDA_MECOM_AMP_A6_S390_L001_R2_001/Alleles_frequency_table.zip


title: 1049_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912_3_Dog_H5_S281/CRISPResso_on_MR912_3_Dog_H5_S281_L001_R1_001_MR912_3_Dog_H5_S281_L001_R2_001/Alleles_frequency_table.zip


title: 1035_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912_3_Dog_G3_S267/CRISPResso_on_MR912_3_Dog_G3_S267_L001_R1_001_MR912_3_Dog_G3_S267_L001_R2_001/Alleles_frequency_table.zip


title: 1034_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912_3_Bird_C10_S130/CRISPResso_on_MR912_3_Bird_C10_S130_L001_R1_001_MR912_3_Bird_C10_S130_L001_R2_001/Alleles_frequency_table.zip


title: 1033_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912_3_Dog_G1_S265/CRISPResso_on_MR912_3_Dog_G1_S265_L001_R1_001_MR912_3_Dog_G1_S265_L001_R2_001/Alleles_frequency_table.zip


title: 1044_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912_3_Dog_G12_S276/CRISPResso_on_MR912_3_Dog_G12_S276_L001_R1_001_MR912_3_Dog_G12_S276_L001_R2_001/Alleles_frequency_table.zip


title: single cell rna seq by 10x Genomics V3 R159_M1

description:
single cell rna seq by 10x Genomics V3
single cell RNA 10x: for two conditions: AAVS1 or MCOM KO

library_source: transcriptomic single cell

data_processing:
Basecalls performed using CASAVA version 1.4 and bcl2fastq2 v2.20.0
single cell RNA 10x: Cumulus pipeline for 10x
bulkrna: Cumulus pipeline for bulkRNA
Assembly:  Human reference genome GRCh38 and gene annotation reference Homo_sapiens.GRCh38.93.gtf
Supplementary files format and content: bulkrna: single cell RNA 10x: h5
Supplementary files format and content: txt

source_name: primary human CD34+ hematopoietic stem and progenitor cells

growth_protocol: HSPC cells were cultured at 37oC and 5%O2 in serum-free HSC media comprised of StemSpan  II medium (Stem Cell Technologies) supplemented with CC100 cytokine cocktail (Stem Cell Technologies), 100ng/ml TPO (Peprotech) and 35nM UM171 (Stem Cell Technologies). Confluency was maintained between 2e5-1e6 cells/ml.   F36P cells (DSMZ) were cultured at 37oC in alpha-MEM (Life Technologies) supplemented with 20% FBS, 20% conditioned media from 5637 cells (ATCC)75 and 1% penicillin/streptomycin. Confluency was maintained between 7e5-1.5e6/ml.    HNT34 cells (Creative Bioarrray) were cultured at 37oC in alpha-MEM (Life Technologies) supplemented with 20% FBS, 20% conditioned media from 5637 cells (ATCC)75 and 1% penicillin/streptomycin. Confluency was maintained between 5e5-1.5e6/ml.

extract_protocol:
SPRI beads
bulkRNA or 10X RNA V3
bulk RNA seq or single cell rna seq by 10x Genomics V3

treatment_protocol: AAVS1  KO or MECOM KO

value: MECOM KO


title: single cell rna seq by 10x Genomics V3 R159_M2

value: primary human CD34+ hematopoietic stem and progenitor cells


title: single cell rna seq by 10x Genomics V3 R159_A1

value: AAVS1 KO


title: 1031_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-2-WTA-MECOM-AMP_B2_S110/CRISPResso_on_MR912-2-WTA-MECOM-AMP_B2_S110_L001_R1_001_MR912-2-WTA-MECOM-AMP_B2_S110_L001_R2_001/Alleles_frequency_table.zip


title: 1029_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-2-WTA-MECOM-AMP_F9_S165/CRISPResso_on_MR912-2-WTA-MECOM-AMP_F9_S165_L001_R1_001_MR912-2-WTA-MECOM-AMP_F9_S165_L001_R2_001/Alleles_frequency_table.zip


title: single cell rna seq by 10x Genomics V3 R159_A2


title: 3wk CLO-2

type: RNA

city: Toyama

first: Tetsushi

last: Hirano

state: Toyama

address: 2630 sugitani

department: Life Science Research Center

country: Japan

institute: University of Toyama

hyb_protocol: The biotinylated cRNA was hybridized to arrays at 45°C for 16 hours.

scan_protocol: The arrays were washed and stained using wash and stain kit on the Affymetrix Fluidics Station 450 (Affymetrix).

data_processing: The data were normalized with the SST-RMA algorism using a Transcriptome analyses console (Affymetrix) software.

label: biotin

organism: Mus musculus

source_name: exposure group

label_protocol: The total RNA (250 ng) was used to synthesize cRNA with a GeneChip WT Amplification Kit. The cDNA was fragmentated and labeled with a GeneChip WT Terminal Labeling Kit (Affymetrix).

growth_protocol: At the age of 3 or 10 weeks, brains were dissected under the anesthesia.

extract_protocol: Total RNA was extracted from brain tissue using a NucleoSpin®  RNA plus isolation kit (MACHEREY-NAGEL, GmbH).  The quality of total RNA was analyzed using a Bioanalyzer 2100 (Agilent Technologies, Inc.). The RNA samples with RIN (RNA integrity number) values > 7.0 were considered acceptable.

treatment_protocol: Dams were orally administrated no-observed adverse effect level (NOAEL; 65 mg/kg/day) of CLO or vehicle during postnatal day 1 to 4.

tag: Sex

value: male

tag: age

value: 3 weeks

value: hippocampus

tag: agent

value: CLO


title: bulk rna sequence HNT34-2

description:
bulk rna sequence
bulkrna_seq of two conditions for each cell line


title: 1036_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-5-WTA-MECOM-AMP_C1_S313/CRISPResso_on_MR912-5-WTA-MECOM-AMP_C1_S313_L001_R1_001_MR912-5-WTA-MECOM-AMP_C1_S313_L001_R2_001/Alleles_frequency_table.zip


title: 1028_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-2-MDA-MECOM-AMP_H3_S87/CRISPResso_on_MR912-2-MDA-MECOM-AMP_H3_S87_L001_R1_001_MR912-2-MDA-MECOM-AMP_H3_S87_L001_R2_001/Alleles_frequency_table.zip


title: 1027_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR214_1_MDA_MECOM_AMP_B2_S398/CRISPResso_on_MR214_1_MDA_MECOM_AMP_B2_S398_L001_R1_001_MR214_1_MDA_MECOM_AMP_B2_S398_L001_R2_001/Alleles_frequency_table.zip


title: bulk rna sequence F36P-2


title: 3wk Ctrl-1

source_name: control group

value: vehicle


title: 10wk CLO-1

value: 10 weeks


title: 3wk Ctrl-2


title: bulk rna sequence F36P_CD34-2


title: 1026_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-5-MDA-MECOM-AMP_B12_S216/CRISPResso_on_MR912-5-MDA-MECOM-AMP_B12_S216_L001_R1_001_MR912-5-MDA-MECOM-AMP_B12_S216_L001_R2_001/Alleles_frequency_table.zip


title: 1141_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR214_1_MDA_MECOM_AMP_H1_S469/CRISPResso_on_MR214_1_MDA_MECOM_AMP_H1_S469_L001_R1_001_MR214_1_MDA_MECOM_AMP_H1_S469_L001_R2_001/Alleles_frequency_table.zip


title: 10wk Ctrl-2


title: 3wk CLO-1


title: 10wk Ctrl-1


title: 1032_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912_3_Dog_F12_S264/CRISPResso_on_MR912_3_Dog_F12_S264_L001_R1_001_MR912_3_Dog_F12_S264_L001_R2_001/Alleles_frequency_table.zip


title: 10wk CLO-2


title: Day 14 Primary Murine Neocortical Culture BioRep3

city: Portland

first: stephen

last: smith

state: Oregon

address: 3710 SW U.S. Veterans Hospital Rd., Building 101 Room 525

institute: VAPORHCS

description: Gene expression data from cultured neocortical cells

hyb_protocol: Image processing was performed using Affymetrix Command Console (AGCC) v.3.1.1 software and expression analysis was performed using Affymetrix Expression Console software

scan_protocol: Image processing of array DAT files to generate sample CEL files was completed in Affymetrix Command Console software. Next, each array was analyzed using Affymetrix Expression Console software to summarize probe set data to the “gene” level and to calculate quality assessment metrics.

data_processing: A multi-chip analysis incorporating all samples of this project set was performed using the MAS5 normalization and summarization algorithm. The resultant .chp files from this analysis are included in the data set

source_name: p14 primary murine neocortical cultures

growth_protocol:
Mouse cortices were isolated, dissociated, and grown in FBS supplemented MEM. 3 days after plating ARA-C was added to limit glial cells then  removed  after 2 days.
Samples were collected in ~350ul of RLT lysis buffer with 1% 2-mercaptoethanol in 2ml RB

extract_protocol: Labeled target cDNA was prepared using the Applied Biosystems WT Plus protocol.  Amplified and labeled cDNA target samples were each hybridized to a  GeneChipTM Clariom S Mouse Array (Affymetrix/Applied Biosystems).

treatment_protocol: All sample lysates were mechanically disrupted by vortexing for 1 minute. Lysates were further homogenized by passing through a QIAshredder spin column.  RNA was isolated by using the Qiagen RNeasy Mini kit protocol following the manufacturer’s recommended protocol that utilized the GPSR’s QIAcube isolation robot.

value: p14 primary murine neocortical cultures


title: Day 14 Primary Murine Neocortical Culture

label_protocol: Amplified and labeled cDNA target samples were each hybridized to a GeneChipTM Clariom S Mouse Array (Affymetrix/Applied Biosystems).


title: bulk rna sequence HSPC_d12-2

description:
bulk rna sequence
bulkrna_seq of two conditions for each cell line, day 12


title: 1024_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-5-WTA-MECOM-AMP_E12_S348/CRISPResso_on_MR912-5-WTA-MECOM-AMP_E12_S348_L001_R1_001_MR912-5-WTA-MECOM-AMP_E12_S348_L001_R2_001/Alleles_frequency_table.zip

value: HSC


title: bulk rna sequence HSPC_d7-2

description:
bulk rna sequence
bulkrna_seq of two conditions for each cell line, day 7


title: Day 14 Primary Murine Neocortical Culture BioRep2


title: bulk rna sequence HSPC_d5-2

description:
bulk rna sequence
bulkrna_seq of two conditions for each cell line, day 5


title: bulk rna sequence HNT34-1


title: 1022_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-2-MDA-MECOM-AMP_A4_S4/CRISPResso_on_MR912-2-MDA-MECOM-AMP_A4_S4_L001_R1_001_MR912-2-MDA-MECOM-AMP_A4_S4_L001_R2_001/Alleles_frequency_table.zip


title: 1021_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912_3_Dog_F1_S253/CRISPResso_on_MR912_3_Dog_F1_S253_L001_R1_001_MR912_3_Dog_F1_S253_L001_R2_001/Alleles_frequency_table.zip


title: bulk rna sequence F36P_CD34-1


title: 1020_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912_3_Dog_E12_S252/CRISPResso_on_MR912_3_Dog_E12_S252_L001_R1_001_MR912_3_Dog_E12_S252_L001_R2_001/Alleles_frequency_table.zip


title: 1019_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912_3_Dog_E11_S251/CRISPResso_on_MR912_3_Dog_E11_S251_L001_R1_001_MR912_3_Dog_E11_S251_L001_R2_001/Alleles_frequency_table.zip


title: bulk rna sequence F36P-1


title: 1017_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-5-WTA-MECOM-AMP_F9_S357/CRISPResso_on_MR912-5-WTA-MECOM-AMP_F9_S357_L001_R1_001_MR912-5-WTA-MECOM-AMP_F9_S357_L001_R2_001/Alleles_frequency_table.zip


title: 1016_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912_3_Dog_E8_S248/CRISPResso_on_MR912_3_Dog_E8_S248_L001_R1_001_MR912_3_Dog_E8_S248_L001_R2_001/Alleles_frequency_table.zip


title: bulk rna sequence HSPC_d7-1


title: bulk rna sequence HSPC_d9-2

description:
bulk rna sequence
bulkrna_seq of two conditions for each cell line, day 9


title: bulk rna sequence HSPC_d12-1


title: 1025_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912_3_MDA_MECOM_AMP_C7_S607/CRISPResso_on_MR912_3_MDA_MECOM_AMP_C7_S607_L001_R1_001_MR912_3_MDA_MECOM_AMP_C7_S607_L001_R2_001/Alleles_frequency_table.zip


title: 1015_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-2-WTA-MECOM-AMP_A2_S98/CRISPResso_on_MR912-2-WTA-MECOM-AMP_A2_S98_L001_R1_001_MR912-2-WTA-MECOM-AMP_A2_S98_L001_R2_001/Alleles_frequency_table.zip


title: 1012_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-5-WTA-MECOM-AMP_H5_S377/CRISPResso_on_MR912-5-WTA-MECOM-AMP_H5_S377_L001_R1_001_MR912-5-WTA-MECOM-AMP_H5_S377_L001_R2_001/Alleles_frequency_table.zip


title: 1013_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-2-MDA-MECOM-AMP_G12_S84/CRISPResso_on_MR912-2-MDA-MECOM-AMP_G12_S84_L001_R1_001_MR912-2-MDA-MECOM-AMP_G12_S84_L001_R2_001/Alleles_frequency_table.zip


title: bulk rna sequence HSPC_d9-1


title: 1011_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912_3_Dog_E3_S243/CRISPResso_on_MR912_3_Dog_E3_S243_L001_R1_001_MR912_3_Dog_E3_S243_L001_R2_001/Alleles_frequency_table.zip


title: MUTZ-3 AAVS edited  AAVS_3

data_processing:
Basecalls were performed using bcl2fastq.
ChIP-seq reads were trimmed from 3' end until the final base had a quality score > 30, using Trimmomatic v0.33, discarding reads left with < 20 bp
ChIP-seq reads were aligned to the UCSC hg19 genome using Bowtie 2. Only uniquely mapping reads with at most two mismatches were retained.
To create ChIP-seq coverage plots, the locations of the mapped ChIP-seq reads were extended to 150 bp to represent sequenced fragments, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
Peaks were called uing MACS v2.1.0 with the significance cut-off q-value <=0.01
bigWig files were generated using the genomicRanges R package. Score represents the normalized coverage of DNA fragments at a given genomic coordinate. narrowPeak files were generated using MACS v2 with default settings.
Assembly: hg19
Supplementary files format and content: bigWig, narrowPeak (except for Input sample)

extract_protocol:
Chromatin immunoprecipitation followed by sequencing (ChIP-seq) was performed on chromatin from 2e6 MUTZ-3 MECOM and AAVS1 edited cells after magnetic sorting for CD34+ cells (Stemcell 17856). Sorted cells were cross-linked with 1% methanol-free formaldehyde (Pierce Life Technologies, 28906), quenched with 0.125 M glycine and frozen at -80 °C and stored until further processing.
ChIP reaction was performed with iDeal ChIP-seq kit for Transcription Factors (Diagenode, C01010055) with modifications of the manual detailed below. Lysed samples were sonicated using the E220 sonicator (Covaris, 500239) in microTUBE AFA Fiber Pre-Slit Snap-Cap tubes (Covaris, 520045) with settings for 200bp DNA shearing. Sheared chromatin was immunoprecipitated with 2.5μg CTCF antibody (abcam, ab128873, RRID:AB_11144295) or 2.5μg IgG antibody (Diagenode, C15410206, RRID: AB_2722554). Eluted and decross-linked DNA was purified with MicroChIP DiaPure columns (Diagenode, C03040001) and eluted in 30μL of NucleaseFree water. ChIP and input libraries for sequencing were prepared with ThruPLEX® DNA-Seq Kit (Takara, R400674) and DNA Single Index Kit - 12S Set A (Takara, R400695). Size selection steps were performed with Magbio Genomics Inc HighPrep PCR beads (Fisher Scientific, 50-165-6582). Subsequently, ChIP-seq library was quantified with Agilent Bioanalyzer. The libraries were sequenced at Broad Institute Genomic Services by using the Illumina NextSeq 500 platform and the 150-bp paired-end configuration to obtain at least 30 million reads per sample.

value: Acute myelomonocytic leukemia

value: CTCF antibody (abcam, ab128873)


title: MUTZ-3 AAVS edited  AAVS_1


title: bulk rna sequence HSPC_d5-1


title: MUTZ-3 AAVS edited  AAVS_2


title: 1010_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-5-MDA-MECOM-AMP_C5_S221/CRISPResso_on_MR912-5-MDA-MECOM-AMP_C5_S221_L001_R1_001_MR912-5-MDA-MECOM-AMP_C5_S221_L001_R2_001/Alleles_frequency_table.zip

value: Mecom KO


title: MUTZ-3 MECOM edited  MECOM_3


title: MUTZ-3 MECOM edited  MECOM_2


title: 1009_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-5-MDA-MECOM-AMP_D7_S235/CRISPResso_on_MR912-5-MDA-MECOM-AMP_D7_S235_L001_R1_001_MR912-5-MDA-MECOM-AMP_D7_S235_L001_R2_001/Alleles_frequency_table.zip


title: 1008_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912_3_Bird_B6_S114/CRISPResso_on_MR912_3_Bird_B6_S114_L001_R1_001_MR912_3_Bird_B6_S114_L001_R2_001/Alleles_frequency_table.zip


title: MUTZ-3 MECOM edited  MECOM_1


title: 1005_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-5-WTA-MECOM-AMP_F1_S349/CRISPResso_on_MR912-5-WTA-MECOM-AMP_F1_S349_L001_R1_001_MR912-5-WTA-MECOM-AMP_F1_S349_L001_R2_001/Alleles_frequency_table.zip


title: THESC scRNA-seq

city: RTP

first: Franco

last: Demayo

state: NC

address: 111 TW Alexander Drive

institute: NIEHS

data_processing:
Raw reads were processed by Cell Ranger with default setting.
Genome_build: hg38
Supplementary_files_format_and_content: Cell Ranger output files (barcodes.tsv, features.tsv, matrix.mtx)

source_name: endometrium

growth_protocol: The primary HESCs and THESC were cultured at the culture medium. The primary HESCs were collected at 4-5 passages.

extract_protocol:
The cells were dissociated from the cell plate by 0.25% trypsin-EDTA, then filtered through 40µm cell strainer for scRNA-Seq analysis.
RNA libraries were prepared by Chromium Single Cell 3’ Library & Gel Bead Kit v3.1
scRNA-seq

treatment_protocol: No treatment

value: endometrium

tag: tissue collection

value: single cell isolation

value: Telomerase-immortalized endometrial stromal cells (THESC)

tag: culture condition

value: culture medium


title: 1023_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912_3_Dog_F3_S255/CRISPResso_on_MR912_3_Dog_F3_S255_L001_R1_001_MR912_3_Dog_F3_S255_L001_R2_001/Alleles_frequency_table.zip


title: P3 scRNA-seq

tag: individual

value: patient P3

value: Primary human endometrial stromal cells (HESCs)


title: 1003_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-5-WTA-MECOM-AMP_D6_S330/CRISPResso_on_MR912-5-WTA-MECOM-AMP_D6_S330_L001_R1_001_MR912-5-WTA-MECOM-AMP_D6_S330_L001_R2_001/Alleles_frequency_table.zip


title: 1018_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912_3_Bird_G11_S179/CRISPResso_on_MR912_3_Bird_G11_S179_L001_R1_001_MR912_3_Bird_G11_S179_L001_R2_001/Alleles_frequency_table.zip


title: P2 scRNA-seq

value: patient P2


title: P1 scRNA-seq

value: patient P1


title: 1004_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-5-WTA-MECOM-AMP_H9_S381/CRISPResso_on_MR912-5-WTA-MECOM-AMP_H9_S381_L001_R1_001_MR912-5-WTA-MECOM-AMP_H9_S381_L001_R2_001/Alleles_frequency_table.zip


title: Control knockdown replicate 2

city: Heidelberg

first: Christian

last: Rohde

address: Im Neuenheimer Feld 410

country: Germany

institute: Heidelberg University

description: ribosome protected mRNA

data_processing:
Library strategy: Ribo-seq
Raw FASTQ reads were trimmed for adapter contamination and quality issues using cutadapt 2.10 using the parameters quality-cutoff=20, minimum-length=20 and the adapter AGATCGGAAGAGC.
Next, to filter reads an initial mapped using bowtie2 to the human rRNA region which was obtained from https://www.ncbi.nlm.nih.gov/nuccore/555853 was conducted. The unmapped reads were written to file with the paramtere –un and used in the next step.
Next, to filter reads another mapping using bowtie2 to human tRNA regions which were obtained from GtRNAdb (http://gtrnadb.ucsc.edu/genomes/eukaryota/Hsapi19/hg19-tRNAs.fa) was conducted. The unmapped reads were written to file with the paramtere –un and used in the next step.
Finally the clean reads were mapped using bowtie2 to the human coding transcriptome which was obtained from ftp://ftp.ensembl.org/pub/release-102/fasta/homo_sapiens/cdna/ and saved as BAM with samtools view.
Mapped reads in BAM format with the respective GTF annotation file (ftp://ftp.ensembl.org/pub/release-102/gtf/homo_sapiens/) were uploaded to riboWaltz. Reads mapped on the same transcript and shared both the 5' estremity and the 3' extremity were regarded as duplicates and removed. Then reads with length between 25 and 38 bp were selected for all downstream analysis.
Genome_build: GRCh38
Supplementary_files_format_and_content: The number of in-frame P-sites mapping on its annotated coding region for all samples

growth_protocol: The cells were cultured in RPMI1640 with 20% FBS and 1% Penicillin-Streptomycin. For FBL knockdown, the cells were induced with 100 ng/ml doxycycline.

extract_protocol:
Ribosome protected mRNA fragments (RPF) were generated by treating cell lysate with RNase I, then the mRNA fragments were purified with RNA Clean & Concentrator-25 kit (Zymo Research).
End repair of RPF was performed with 10 U T4 PNK treatment (Cat. M0201S, NEB) at 37 °C for 1 hour. The libraries were prepared with NEBNext® Small RNA Library Prep Set for Illumina®.

value: 100 ng/ml doxycycline

tag: knockdown or knockout

value: Ctrl knockdown


title: Control knockdown replicate 1

description: ribosome protected mRNA


title: FBL knockdown replicate 2

description: ribosome protected mRNA

value: FBL knockdown


title: 999_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-2-MDA-MECOM-AMP_B7_S19/CRISPResso_on_MR912-2-MDA-MECOM-AMP_B7_S19_L001_R1_001_MR912-2-MDA-MECOM-AMP_B7_S19_L001_R2_001/Alleles_frequency_table.zip


title: 997_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912_3_Dog_D1_S229/CRISPResso_on_MR912_3_Dog_D1_S229_L001_R1_001_MR912_3_Dog_D1_S229_L001_R2_001/Alleles_frequency_table.zip


title: 996_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912_3_Dog_C12_S228/CRISPResso_on_MR912_3_Dog_C12_S228_L001_R1_001_MR912_3_Dog_C12_S228_L001_R2_001/Alleles_frequency_table.zip


title: 994_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912_3_Dog_C10_S226/CRISPResso_on_MR912_3_Dog_C10_S226_L001_R1_001_MR912_3_Dog_C10_S226_L001_R2_001/Alleles_frequency_table.zip


title: Monocyte, Monocyte5

data_processing:
Library strategy: Ribometh-Seq
Basecalls were performed using on-instrument real time analysis (RTA) on an Illumina NextSeq500
Adapter sequences were removed using Cutadapt with a minimum length of 15 nt,
Reads were mapped using Bowtie2 to a reference sequence file containing rDNA sequences of U18, U28 and U5.8S
For each position the number of 5’-read ends was counted.
2’O-methyation was calculated as scoreC based on 5’-end frequencies as described before by Birkedal et al., 2015
Genome_build: Annotation of modification sites as well as rRNA sequence was downloaded from https://www-snorna.biotoul.fr. Furthermore we considered novel sites reported by Krogh 2016, Jorjani 2016 and Sharma 2017.
Supplementary_files_format_and_content: RiboMethSeq_scoreC.txt contains calculated scoreC for annotated modification sites: subunit TAB pos TAB annotation TAB sample_scoreC

source_name: Monocyte

extract_protocol:
Total RNA was extracte with mirRNeay mini kit (NEB).
100 ng total RNA was fragmented by alkaline hydrolysis at 95°C for 12 min. to achieve a fragment length of about 30 nucleotides. Libraries were prepared using the NEBNext® Small RNA library prep kit.

tag: disease state

value: healthy control

tag: aml status

tag: fab

value: Monocyte

tag: sample type

value: sample from healthy human individual


title: 995_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-5-WTA-MECOM-AMP_B9_S309/CRISPResso_on_MR912-5-WTA-MECOM-AMP_B9_S309_L001_R1_001_MR912-5-WTA-MECOM-AMP_B9_S309_L001_R2_001/Alleles_frequency_table.zip

tag: cell type

value: HSC

tag: chip antibody

tag: treatment


title: 998_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-2-MDA-MECOM-AMP_D1_S37/CRISPResso_on_MR912-2-MDA-MECOM-AMP_D1_S37_L001_R1_001_MR912-2-MDA-MECOM-AMP_D1_S37_L001_R2_001/Alleles_frequency_table.zip


title: Monocyte, Monocyte4


title: 993_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912_3_Dog_C9_S225/CRISPResso_on_MR912_3_Dog_C9_S225_L001_R1_001_MR912_3_Dog_C9_S225_L001_R2_001/Alleles_frequency_table.zip


title: Monocyte, Monocyte2


title: Monocyte, Monocyte3


title: 990_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR214_1_MDA_MECOM_AMP_H7_S475/CRISPResso_on_MR214_1_MDA_MECOM_AMP_H7_S475_L001_R1_001_MR214_1_MDA_MECOM_AMP_H7_S475_L001_R2_001/Alleles_frequency_table.zip


title: AML_subpopulation, HD77CD34posCD38pos

value: AML

value: leukemia blast cells

value: AML diagnosis sample


title: 992_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912_3_MDA_MECOM_AMP_C1_S505/CRISPResso_on_MR912_3_MDA_MECOM_AMP_C1_S505_L001_R1_001_MR912_3_MDA_MECOM_AMP_C1_S505_L001_R2_001/Alleles_frequency_table.zip

value: Mecom KO


title: AML_subpopulation, HD77CD34posCD38neg


title: AML_subpopulation, HD77CD34negCD38pos


title: Monocyte, Monocyte1


title: 991_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-2-WTA-MECOM-AMP_A2_S98/CRISPResso_on_MR912-2-WTA-MECOM-AMP_A2_S98_L001_R1_001_MR912-2-WTA-MECOM-AMP_A2_S98_L001_R2_001/Alleles_frequency_table.zip


title: 988_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912_3_Dog_G3_S267/CRISPResso_on_MR912_3_Dog_G3_S267_L001_R1_001_MR912_3_Dog_G3_S267_L001_R2_001/Alleles_frequency_table.zip


title: 987_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912_3_MDA_MECOM_AMP_G8_S656/CRISPResso_on_MR912_3_MDA_MECOM_AMP_G8_S656_L001_R1_001_MR912_3_MDA_MECOM_AMP_G8_S656_L001_R2_001/Alleles_frequency_table.zip


title: 1002_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-2-MDA-MECOM-AMP_C1_S25/CRISPResso_on_MR912-2-MDA-MECOM-AMP_C1_S25_L001_R1_001_MR912-2-MDA-MECOM-AMP_C1_S25_L001_R2_001/Alleles_frequency_table.zip


title: 989_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912_3_MDA_MECOM_AMP_E8_S632/CRISPResso_on_MR912_3_MDA_MECOM_AMP_E8_S632_L001_R1_001_MR912_3_MDA_MECOM_AMP_E8_S632_L001_R2_001/Alleles_frequency_table.zip


title: AML_subpopulation, HD72CD34posCD38neg


title: AML_subpopulation, HD72CD34negCD38pos


title: FBL knockdown replicate 1

description: ribosome protected mRNA


title: 986_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-5-MDA-MECOM-AMP_B1_S205/CRISPResso_on_MR912-5-MDA-MECOM-AMP_B1_S205_L001_R1_001_MR912-5-MDA-MECOM-AMP_B1_S205_L001_R2_001/Alleles_frequency_table.zip


title: AML_subpopulation, HD57CD34posCD38pos


title: 985_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-5-MDA-MECOM-AMP_B5_S209/CRISPResso_on_MR912-5-MDA-MECOM-AMP_B5_S209_L001_R1_001_MR912-5-MDA-MECOM-AMP_B5_S209_L001_R2_001/Alleles_frequency_table.zip


title: 984_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR214_1_MDA_MECOM_AMP_A3_S387/CRISPResso_on_MR214_1_MDA_MECOM_AMP_A3_S387_L001_R1_001_MR214_1_MDA_MECOM_AMP_A3_S387_L001_R2_001/Alleles_frequency_table.zip


title: AML_subpopulation, HD57CD34posCD38neg


title: AML_subpopulation, HD57CD34negCD38pos


title: 983_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-2-WTA-MECOM-AMP_G10_S178/CRISPResso_on_MR912-2-WTA-MECOM-AMP_G10_S178_L001_R1_001_MR912-2-WTA-MECOM-AMP_G10_S178_L001_R2_001/Alleles_frequency_table.zip


title: Granulocyte, Granulocyte5

source_name: Granulocyte

value: Granulocyte


title: Granulocyte, Granulocyte4


title: 981_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-2-WTA-MECOM-AMP_E1_S145/CRISPResso_on_MR912-2-WTA-MECOM-AMP_E1_S145_L001_R1_001_MR912-2-WTA-MECOM-AMP_E1_S145_L001_R2_001/Alleles_frequency_table.zip


title: 980_Mecom amplicon seq


title: Granulocyte, Granulocyte3


title: 976_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912_3_Dog_B4_S208/CRISPResso_on_MR912_3_Dog_B4_S208_L001_R1_001_MR912_3_Dog_B4_S208_L001_R2_001/Alleles_frequency_table.zip


title: Granulocyte, Granulocyte2


title: 978_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-2-WTA-MECOM-AMP_B8_S116/CRISPResso_on_MR912-2-WTA-MECOM-AMP_B8_S116_L001_R1_001_MR912-2-WTA-MECOM-AMP_B8_S116_L001_R2_001/Alleles_frequency_table.zip


title: 979_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR214_1_MDA_MECOM_AMP_E6_S438/CRISPResso_on_MR214_1_MDA_MECOM_AMP_E6_S438_L001_R1_001_MR214_1_MDA_MECOM_AMP_E6_S438_L001_R2_001/Alleles_frequency_table.zip


title: AML, DR99

source_name: AML

value: de novo

value: f


title: AML_subpopulation, HD72CD34posCD38pos


title: AML, DR98

value: m


title: AML, DR95


title: AML, DR96


title: 975_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912_3_MDA_MECOM_AMP_H12_S672/CRISPResso_on_MR912_3_MDA_MECOM_AMP_H12_S672_L001_R1_001_MR912_3_MDA_MECOM_AMP_H12_S672_L001_R2_001/Alleles_frequency_table.zip


title: 974_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-5-WTA-MECOM-AMP_E11_S347/CRISPResso_on_MR912-5-WTA-MECOM-AMP_E11_S347_L001_R1_001_MR912-5-WTA-MECOM-AMP_E11_S347_L001_R2_001/Alleles_frequency_table.zip


title: 973_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR214_1_MDA_MECOM_AMP_G2_S458/CRISPResso_on_MR214_1_MDA_MECOM_AMP_G2_S458_L001_R1_001_MR214_1_MDA_MECOM_AMP_G2_S458_L001_R2_001/Alleles_frequency_table.zip


title: AML, DR97


title: 972_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-5-WTA-MECOM-AMP_F4_S352/CRISPResso_on_MR912-5-WTA-MECOM-AMP_F4_S352_L001_R1_001_MR912-5-WTA-MECOM-AMP_F4_S352_L001_R2_001/Alleles_frequency_table.zip


title: AML, DR93


title: AML, DR94


title: 970_Mecom amplicon seq


title: 982_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-5-MDA-MECOM-AMP_D2_S230/CRISPResso_on_MR912-5-MDA-MECOM-AMP_D2_S230_L001_R1_001_MR912-5-MDA-MECOM-AMP_D2_S230_L001_R2_001/Alleles_frequency_table.zip


title: AML, DR92


title: AML, DR91


title: 969_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR214_1_MDA_MECOM_AMP_D12_S432/CRISPResso_on_MR214_1_MDA_MECOM_AMP_D12_S432_L001_R1_001_MR214_1_MDA_MECOM_AMP_D12_S432_L001_R2_001/Alleles_frequency_table.zip


title: AML, DR90


title: 965_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912_3_Bird_C10_S130/CRISPResso_on_MR912_3_Bird_C10_S130_L001_R1_001_MR912_3_Bird_C10_S130_L001_R2_001/Alleles_frequency_table.zip


title: AML, DR88


title: AML, DR89


title: 963_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-2-WTA-MECOM-AMP_C5_S125/CRISPResso_on_MR912-2-WTA-MECOM-AMP_C5_S125_L001_R1_001_MR912-2-WTA-MECOM-AMP_C5_S125_L001_R2_001/Alleles_frequency_table.zip


title: 962_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912_3_MDA_MECOM_AMP_B5_S497/CRISPResso_on_MR912_3_MDA_MECOM_AMP_B5_S497_L001_R1_001_MR912_3_MDA_MECOM_AMP_B5_S497_L001_R2_001/Alleles_frequency_table.zip


title: AML, DR87


title: AML, DR86


title: AML, DR84


title: 971_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912_3_Dog_A11_S203/CRISPResso_on_MR912_3_Dog_A11_S203_L001_R1_001_MR912_3_Dog_A11_S203_L001_R2_001/Alleles_frequency_table.zip


title: AML, DR85

value: sAML


title: 961_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-5-MDA-MECOM-AMP_E3_S243/CRISPResso_on_MR912-5-MDA-MECOM-AMP_E3_S243_L001_R1_001_MR912-5-MDA-MECOM-AMP_E3_S243_L001_R2_001/Alleles_frequency_table.zip


title: AML, DR82


title: AML, DR83


title: AML, DR80


title: AML, DR79

value: tAML


title: AML, DR81


title: 955_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912_3_Bird_H7_S187/CRISPResso_on_MR912_3_Bird_H7_S187_L001_R1_001_MR912_3_Bird_H7_S187_L001_R2_001/Alleles_frequency_table.zip


title: 957_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912_3_Bird_H9_S189/CRISPResso_on_MR912_3_Bird_H9_S189_L001_R1_001_MR912_3_Bird_H9_S189_L001_R2_001/Alleles_frequency_table.zip


title: 958_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-2-WTA-MECOM-AMP_A5_S101/CRISPResso_on_MR912-2-WTA-MECOM-AMP_A5_S101_L001_R1_001_MR912-2-WTA-MECOM-AMP_A5_S101_L001_R2_001/Alleles_frequency_table.zip


title: 953_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR214_1_Cat_E10_S58/CRISPResso_on_MR214_1_Cat_E10_S58_L001_R1_001_MR214_1_Cat_E10_S58_L001_R2_001/Alleles_frequency_table.zip


title: 954_Mecom amplicon seq


title: 968_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912_3_Bird_C5_S125/CRISPResso_on_MR912_3_Bird_C5_S125_L001_R1_001_MR912_3_Bird_C5_S125_L001_R2_001/Alleles_frequency_table.zip


title: AML, DR78


title: 950_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR214_1_Cat_F7_S67/CRISPResso_on_MR214_1_Cat_F7_S67_L001_R1_001_MR214_1_Cat_F7_S67_L001_R2_001/Alleles_frequency_table.zip


title: 952_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-5-WTA-MECOM-AMP_B4_S304/CRISPResso_on_MR912-5-WTA-MECOM-AMP_B4_S304_L001_R1_001_MR912-5-WTA-MECOM-AMP_B4_S304_L001_R2_001/Alleles_frequency_table.zip


title: AML, DR76


title: AML, DR77


title: 951_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912_3_Bird_H3_S183/CRISPResso_on_MR912_3_Bird_H3_S183_L001_R1_001_MR912_3_Bird_H3_S183_L001_R2_001/Alleles_frequency_table.zip


title: 949_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912_3_Bird_H1_S181/CRISPResso_on_MR912_3_Bird_H1_S181_L001_R1_001_MR912_3_Bird_H1_S181_L001_R2_001/Alleles_frequency_table.zip


title: 948_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-2-WTA-MECOM-AMP_E1_S145/CRISPResso_on_MR912-2-WTA-MECOM-AMP_E1_S145_L001_R1_001_MR912-2-WTA-MECOM-AMP_E1_S145_L001_R2_001/Alleles_frequency_table.zip


title: 959_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912_3_Bird_H11_S191/CRISPResso_on_MR912_3_Bird_H11_S191_L001_R1_001_MR912_3_Bird_H11_S191_L001_R2_001/Alleles_frequency_table.zip


title: 967_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-2-WTA-MECOM-AMP_G11_S179/CRISPResso_on_MR912-2-WTA-MECOM-AMP_G11_S179_L001_R1_001_MR912-2-WTA-MECOM-AMP_G11_S179_L001_R2_001/Alleles_frequency_table.zip


title: AML, DR74


title: AML, DR75


title: 946_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-5-WTA-MECOM-AMP_B11_S311/CRISPResso_on_MR912-5-WTA-MECOM-AMP_B11_S311_L001_R1_001_MR912-5-WTA-MECOM-AMP_B11_S311_L001_R2_001/Alleles_frequency_table.zip


title: AML, DR72


title: 945_Mecom amplicon seq


title: AML, DR71


title: AML, DR70


title: 943_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912_3_Bird_G7_S175/CRISPResso_on_MR912_3_Bird_G7_S175_L001_R1_001_MR912_3_Bird_G7_S175_L001_R2_001/Alleles_frequency_table.zip


title: 944_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-5-WTA-MECOM-AMP_C6_S318/CRISPResso_on_MR912-5-WTA-MECOM-AMP_C6_S318_L001_R1_001_MR912-5-WTA-MECOM-AMP_C6_S318_L001_R2_001/Alleles_frequency_table.zip


title: AML, DR69


title: AML, DR68


title: AML, DR67


title: 939_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912_3_Bird_G3_S171/CRISPResso_on_MR912_3_Bird_G3_S171_L001_R1_001_MR912_3_Bird_G3_S171_L001_R2_001/Alleles_frequency_table.zip


title: 940_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912_3_Bird_G4_S172/CRISPResso_on_MR912_3_Bird_G4_S172_L001_R1_001_MR912_3_Bird_G4_S172_L001_R2_001/Alleles_frequency_table.zip


title: AML, DR62


title: 934_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-2-WTA-MECOM-AMP_F7_S163/CRISPResso_on_MR912-2-WTA-MECOM-AMP_F7_S163_L001_R1_001_MR912-2-WTA-MECOM-AMP_F7_S163_L001_R2_001/Alleles_frequency_table.zip


title: AML, DR65


title: 936_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-5-MDA-MECOM-AMP_B3_S207/CRISPResso_on_MR912-5-MDA-MECOM-AMP_B3_S207_L001_R1_001_MR912-5-MDA-MECOM-AMP_B3_S207_L001_R2_001/Alleles_frequency_table.zip


title: AML, DR64


title: AML, DR66


title: AML, DR61


title: AML, DR73


title: 932_Mecom amplicon seq


title: 941_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-2-MDA-MECOM-AMP_B1_S13/CRISPResso_on_MR912-2-MDA-MECOM-AMP_B1_S13_L001_R1_001_MR912-2-MDA-MECOM-AMP_B1_S13_L001_R2_001/Alleles_frequency_table.zip


title: AML, DR59

value: AL


title: 947_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912_3_Bird_G11_S179/CRISPResso_on_MR912_3_Bird_G11_S179_L001_R1_001_MR912_3_Bird_G11_S179_L001_R2_001/Alleles_frequency_table.zip


title: AML, DR60


title: 931_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-2-MDA-MECOM-AMP_G11_S83/CRISPResso_on_MR912-2-MDA-MECOM-AMP_G11_S83_L001_R1_001_MR912-2-MDA-MECOM-AMP_G11_S83_L001_R2_001/Alleles_frequency_table.zip


title: 935_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912_3_Bird_F11_S167/CRISPResso_on_MR912_3_Bird_F11_S167_L001_R1_001_MR912_3_Bird_F11_S167_L001_R2_001/Alleles_frequency_table.zip


title: 933_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912_3_Bird_F9_S165/CRISPResso_on_MR912_3_Bird_F9_S165_L001_R1_001_MR912_3_Bird_F9_S165_L001_R2_001/Alleles_frequency_table.zip


title: AML, DR58