title: 929_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: 930_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_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

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: 942_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-2-MDA-MECOM-AMP_E10_S58/CRISPResso_on_MR912-2-MDA-MECOM-AMP_E10_S58_L001_R1_001_MR912-2-MDA-MECOM-AMP_E10_S58_L001_R2_001/Alleles_frequency_table.zip


title: 928_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-5-MDA-MECOM-AMP_D9_S237/CRISPResso_on_MR912-5-MDA-MECOM-AMP_D9_S237_L001_R1_001_MR912-5-MDA-MECOM-AMP_D9_S237_L001_R2_001/Alleles_frequency_table.zip


title: 927_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: AML, DR56

city: Heidelberg

first: Christian

last: Rohde

address: Im Neuenheimer Feld 410

country: Germany

institute: Heidelberg University

library_source: transcriptomic

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

molecule: total RNA

source_name: AML

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: AML

tag: aml status

value: de novo

tag: fab

value: leukemia blast cells

tag: sample type

value: AML diagnosis sample

tag: age

tag: Sex

value: m


title: AML, DR57

value: sAML


title: AML, DR55

value: f


title: 926_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: 925_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: 924_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912_3_Bird_E12_S156/CRISPResso_on_MR912_3_Bird_E12_S156_L001_R1_001_MR912_3_Bird_E12_S156_L001_R2_001/Alleles_frequency_table.zip


title: AML, DR53


title: 923_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912_3_Bird_E11_S155/CRISPResso_on_MR912_3_Bird_E11_S155_L001_R1_001_MR912_3_Bird_E11_S155_L001_R2_001/Alleles_frequency_table.zip


title: AML, DR50


title: AML, DR49


title: AML, DR51


title: 921_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912_3_Bird_E9_S153/CRISPResso_on_MR912_3_Bird_E9_S153_L001_R1_001_MR912_3_Bird_E9_S153_L001_R2_001/Alleles_frequency_table.zip


title: 919_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: AML, DR48


title: 920_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-5-MDA-MECOM-AMP_A10_S202/CRISPResso_on_MR912-5-MDA-MECOM-AMP_A10_S202_L001_R1_001_MR912-5-MDA-MECOM-AMP_A10_S202_L001_R2_001/Alleles_frequency_table.zip


title: AML, DR46


title: 918_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912_3_Bird_E6_S150/CRISPResso_on_MR912_3_Bird_E6_S150_L001_R1_001_MR912_3_Bird_E6_S150_L001_R2_001/Alleles_frequency_table.zip


title: AML, DR44


title: 917_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: AML, DR47

value: BAL


title: AML, DR42


title: 915_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912_3_MDA_MECOM_AMP_G5_S653/CRISPResso_on_MR912_3_MDA_MECOM_AMP_G5_S653_L001_R1_001_MR912_3_MDA_MECOM_AMP_G5_S653_L001_R2_001/Alleles_frequency_table.zip


title: 916_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-2-WTA-MECOM-AMP_C10_S130/CRISPResso_on_MR912-2-WTA-MECOM-AMP_C10_S130_L001_R1_001_MR912-2-WTA-MECOM-AMP_C10_S130_L001_R2_001/Alleles_frequency_table.zip


title: AML, DR54


title: 913_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: AML, DR41


title: AML, DR40


title: 914_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-5-WTA-MECOM-AMP_A6_S294/CRISPResso_on_MR912-5-WTA-MECOM-AMP_A6_S294_L001_R1_001_MR912-5-WTA-MECOM-AMP_A6_S294_L001_R2_001/Alleles_frequency_table.zip


title: 912_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912_3_Bird_D12_S144/CRISPResso_on_MR912_3_Bird_D12_S144_L001_R1_001_MR912_3_Bird_D12_S144_L001_R2_001/Alleles_frequency_table.zip


title: AML, DR39


title: AML, DR52


title: AML, DR38


title: 922_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: 911_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912_3_Bird_D11_S143/CRISPResso_on_MR912_3_Bird_D11_S143_L001_R1_001_MR912_3_Bird_D11_S143_L001_R2_001/Alleles_frequency_table.zip


title: 910_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: 909_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-2-MDA-MECOM-AMP_A11_S11/CRISPResso_on_MR912-2-MDA-MECOM-AMP_A11_S11_L001_R1_001_MR912-2-MDA-MECOM-AMP_A11_S11_L001_R2_001/Alleles_frequency_table.zip


title: AML, DR33


title: AML, DR32


title: AML, DR43


title: AML, DR34


title: 907_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: AML, DR31


title: 908_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: 904_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-5-WTA-MECOM-AMP_F10_S358/CRISPResso_on_MR912-5-WTA-MECOM-AMP_F10_S358_L001_R1_001_MR912-5-WTA-MECOM-AMP_F10_S358_L001_R2_001/Alleles_frequency_table.zip


title: AML, DR29


title: AML, DR30


title: 905_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: AML, DR27

value: tAML


title: 903_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912_3_Bird_D3_S135/CRISPResso_on_MR912_3_Bird_D3_S135_L001_R1_001_MR912_3_Bird_D3_S135_L001_R2_001/Alleles_frequency_table.zip


title: AML, DR26


title: 901_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912_3_Bird_D1_S133/CRISPResso_on_MR912_3_Bird_D1_S133_L001_R1_001_MR912_3_Bird_D1_S133_L001_R2_001/Alleles_frequency_table.zip


title: 899_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: AML, DR23


title: AML, DR25


title: 898_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, DR22


title: AML, DR36


title: AML, DR21


title: 897_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-5-MDA-MECOM-AMP_B9_S213/CRISPResso_on_MR912-5-MDA-MECOM-AMP_B9_S213_L001_R1_001_MR912-5-MDA-MECOM-AMP_B9_S213_L001_R2_001/Alleles_frequency_table.zip


title: AML, DR20


title: 896_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: 895_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912_3_Bird_C7_S127/CRISPResso_on_MR912_3_Bird_C7_S127_L001_R1_001_MR912_3_Bird_C7_S127_L001_R2_001/Alleles_frequency_table.zip


title: 894_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912_3_Bird_C6_S126/CRISPResso_on_MR912_3_Bird_C6_S126_L001_R1_001_MR912_3_Bird_C6_S126_L001_R2_001/Alleles_frequency_table.zip


title: AML, DR19


title: 892_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912_3_Bird_C4_S124/CRISPResso_on_MR912_3_Bird_C4_S124_L001_R1_001_MR912_3_Bird_C4_S124_L001_R2_001/Alleles_frequency_table.zip


title: AML, DR18


title: AML, DR28


title: 891_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: AML, DR16


title: 889_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-5-MDA-MECOM-AMP_C12_S228/CRISPResso_on_MR912-5-MDA-MECOM-AMP_C12_S228_L001_R1_001_MR912-5-MDA-MECOM-AMP_C12_S228_L001_R2_001/Alleles_frequency_table.zip


title: AML, DR14


title: AML, DR15


title: AML, DR17


title: 890_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912_3_Bird_C2_S122/CRISPResso_on_MR912_3_Bird_C2_S122_L001_R1_001_MR912_3_Bird_C2_S122_L001_R2_001/Alleles_frequency_table.zip


title: 900_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: 893_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: 888_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912_3_Bird_B12_S120/CRISPResso_on_MR912_3_Bird_B12_S120_L001_R1_001_MR912_3_Bird_B12_S120_L001_R2_001/Alleles_frequency_table.zip


title: AML, DR13


title: 902_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-2-WTA-MECOM-AMP_D12_S144/CRISPResso_on_MR912-2-WTA-MECOM-AMP_D12_S144_L001_R1_001_MR912-2-WTA-MECOM-AMP_D12_S144_L001_R2_001/Alleles_frequency_table.zip


title: 887_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-5-MDA-MECOM-AMP_G10_S274/CRISPResso_on_MR912-5-MDA-MECOM-AMP_G10_S274_L001_R1_001_MR912-5-MDA-MECOM-AMP_G10_S274_L001_R2_001/Alleles_frequency_table.zip


title: AML, DR12


title: 886_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912_3_Bird_B10_S118/CRISPResso_on_MR912_3_Bird_B10_S118_L001_R1_001_MR912_3_Bird_B10_S118_L001_R2_001/Alleles_frequency_table.zip


title: AML, DR11


title: AML, DR09


title: AML, DR10


title: 885_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912_3_Bird_B9_S117/CRISPResso_on_MR912_3_Bird_B9_S117_L001_R1_001_MR912_3_Bird_B9_S117_L001_R2_001/Alleles_frequency_table.zip


title: 884_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912_3_Bird_B8_S116/CRISPResso_on_MR912_3_Bird_B8_S116_L001_R1_001_MR912_3_Bird_B8_S116_L001_R2_001/Alleles_frequency_table.zip


title: 881_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912_3_Bird_B5_S113/CRISPResso_on_MR912_3_Bird_B5_S113_L001_R1_001_MR912_3_Bird_B5_S113_L001_R2_001/Alleles_frequency_table.zip


title: AML, DR08


title: 882_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: AML, DR07


title: 880_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, DR05


title: 879_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912_3_Bird_B3_S111/CRISPResso_on_MR912_3_Bird_B3_S111_L001_R1_001_MR912_3_Bird_B3_S111_L001_R2_001/Alleles_frequency_table.zip


title: 878_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912_3_Bird_B2_S110/CRISPResso_on_MR912_3_Bird_B2_S110_L001_R1_001_MR912_3_Bird_B2_S110_L001_R2_001/Alleles_frequency_table.zip


title: AML, DR04


title: 877_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-2-MDA-MECOM-AMP_D2_S38/CRISPResso_on_MR912-2-MDA-MECOM-AMP_D2_S38_L001_R1_001_MR912-2-MDA-MECOM-AMP_D2_S38_L001_R2_001/Alleles_frequency_table.zip


title: 876_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912_3_Bird_A12_S108/CRISPResso_on_MR912_3_Bird_A12_S108_L001_R1_001_MR912_3_Bird_A12_S108_L001_R2_001/Alleles_frequency_table.zip


title: 875_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: AML, DR02


title: AML, DR03


title: 874_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: 873_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912_3_Bird_A9_S105/CRISPResso_on_MR912_3_Bird_A9_S105_L001_R1_001_MR912_3_Bird_A9_S105_L001_R2_001/Alleles_frequency_table.zip


title: 872_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912_3_Bird_A8_S104/CRISPResso_on_MR912_3_Bird_A8_S104_L001_R1_001_MR912_3_Bird_A8_S104_L001_R2_001/Alleles_frequency_table.zip


title: HSPC, CD34s2

source_name: HSPC

value: healthy control

value: HSPC

value: sample from healthy human individual


title: 871_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912_3_Bird_A7_S103/CRISPResso_on_MR912_3_Bird_A7_S103_L001_R1_001_MR912_3_Bird_A7_S103_L001_R2_001/Alleles_frequency_table.zip


title: 869_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912_3_Bird_A5_S101/CRISPResso_on_MR912_3_Bird_A5_S101_L001_R1_001_MR912_3_Bird_A5_S101_L001_R2_001/Alleles_frequency_table.zip


title: HSPC, CD34s10


title: HSPC, CD34s1


title: AML, DR06


title: 867_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912_3_Bird_A3_S99/CRISPResso_on_MR912_3_Bird_A3_S99_L001_R1_001_MR912_3_Bird_A3_S99_L001_R2_001/Alleles_frequency_table.zip


title: T cell, CD32

source_name: T cell

value: T cell


title: T cell, CD31


title: 868_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912_3_Bird_A4_S100/CRISPResso_on_MR912_3_Bird_A4_S100_L001_R1_001_MR912_3_Bird_A4_S100_L001_R2_001/Alleles_frequency_table.zip


title: B Cell, CD195

source_name: B Cell

value: B Cell


title: 864_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR214_1_Cat_H12_S96/CRISPResso_on_MR214_1_Cat_H12_S96_L001_R1_001_MR214_1_Cat_H12_S96_L001_R2_001/Alleles_frequency_table.zip


title: T cell, CD33


title: B Cell, CD191


title: T cell, CD35


title: AML_subpopulation, 145CD34negativeCD38positive


title: 863_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR214_1_Cat_D9_S45/CRISPResso_on_MR214_1_Cat_D9_S45_L001_R1_001_MR214_1_Cat_D9_S45_L001_R2_001/Alleles_frequency_table.zip


title: HSPC, CD34s12


title: HSPC, CD34s11


title: 862_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR214_1_Cat_H10_S94/CRISPResso_on_MR214_1_Cat_H10_S94_L001_R1_001_MR214_1_Cat_H10_S94_L001_R2_001/Alleles_frequency_table.zip


title: AML_subpopulation, 145CD34positiveCD38positive


title: 870_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR214_1_Cat_F11_S71/CRISPResso_on_MR214_1_Cat_F11_S71_L001_R1_001_MR214_1_Cat_F11_S71_L001_R2_001/Alleles_frequency_table.zip


title: AML_subpopulation, 119CD34positiveCD38positive


title: 859_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR214_1_Cat_H7_S91/CRISPResso_on_MR214_1_Cat_H7_S91_L001_R1_001_MR214_1_Cat_H7_S91_L001_R2_001/Alleles_frequency_table.zip


title: 858_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR214_1_Cat_H6_S90/CRISPResso_on_MR214_1_Cat_H6_S90_L001_R1_001_MR214_1_Cat_H6_S90_L001_R2_001/Alleles_frequency_table.zip


title: AML_subpopulation, 145CD34positiveCD38negative


title: AML_subpopulation, 119CD34negativeCD38positive


title: AML, 11H142

description:
11H142
Further sample information can be obtained from the following publication: Pabst, C. et al. GPR56 identifies primary human acute myeloid leukemia cells with high repopulating potential in vivo. Blood (2016). doi:10.1182/blood-2015-11-683649


title: 866_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912_3_Bird_A2_S98/CRISPResso_on_MR912_3_Bird_A2_S98_L001_R1_001_MR912_3_Bird_A2_S98_L001_R2_001/Alleles_frequency_table.zip


title: 861_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: 855_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR214_1_Cat_H3_S87/CRISPResso_on_MR214_1_Cat_H3_S87_L001_R1_001_MR214_1_Cat_H3_S87_L001_R2_001/Alleles_frequency_table.zip


title: 856_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR214_1_Cat_H4_S88/CRISPResso_on_MR214_1_Cat_H4_S88_L001_R1_001_MR214_1_Cat_H4_S88_L001_R2_001/Alleles_frequency_table.zip


title: AML_subpopulation, 119CD34positiveCD38negative


title: B Cell, CD193


title: 857_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR214_1_Cat_H5_S89/CRISPResso_on_MR214_1_Cat_H5_S89_L001_R1_001_MR214_1_Cat_H5_S89_L001_R2_001/Alleles_frequency_table.zip


title: AML, 11H095

description:
11H095
Further sample information can be obtained from the following publication: Pabst, C. et al. GPR56 identifies primary human acute myeloid leukemia cells with high repopulating potential in vivo. Blood (2016). doi:10.1182/blood-2015-11-683649


title: AML, 11H129

description:
11H129
Further sample information can be obtained from the following publication: Pabst, C. et al. GPR56 identifies primary human acute myeloid leukemia cells with high repopulating potential in vivo. Blood (2016). doi:10.1182/blood-2015-11-683649


title: 853_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-2-WTA-MECOM-AMP_F5_S161/CRISPResso_on_MR912-2-WTA-MECOM-AMP_F5_S161_L001_R1_001_MR912-2-WTA-MECOM-AMP_F5_S161_L001_R2_001/Alleles_frequency_table.zip


title: AML, 11H009

description:
11H009
Further sample information can be obtained from the following publication: Pabst, C. et al. GPR56 identifies primary human acute myeloid leukemia cells with high repopulating potential in vivo. Blood (2016). doi:10.1182/blood-2015-11-683649


title: 854_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: AML, 10H101

description:
10H101
Further sample information can be obtained from the following publication: Pabst, C. et al. GPR56 identifies primary human acute myeloid leukemia cells with high repopulating potential in vivo. Blood (2016). doi:10.1182/blood-2015-11-683649


title: 860_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR214_1_Cat_H8_S92/CRISPResso_on_MR214_1_Cat_H8_S92_L001_R1_001_MR214_1_Cat_H8_S92_L001_R2_001/Alleles_frequency_table.zip


title: 851_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: 850_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-2-MDA-MECOM-AMP_H1_S85/CRISPResso_on_MR912-2-MDA-MECOM-AMP_H1_S85_L001_R1_001_MR912-2-MDA-MECOM-AMP_H1_S85_L001_R2_001/Alleles_frequency_table.zip


title: AML, 10H056

description:
10H056
Further sample information can be obtained from the following publication: Pabst, C. et al. GPR56 identifies primary human acute myeloid leukemia cells with high repopulating potential in vivo. Blood (2016). doi:10.1182/blood-2015-11-683649


title: 852_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: AML, 09H043

description:
09H043
Further sample information can be obtained from the following publication: Pabst, C. et al. GPR56 identifies primary human acute myeloid leukemia cells with high repopulating potential in vivo. Blood (2016). doi:10.1182/blood-2015-11-683649


title: AML, 09H115

description:
09H115
Further sample information can be obtained from the following publication: Pabst, C. et al. GPR56 identifies primary human acute myeloid leukemia cells with high repopulating potential in vivo. Blood (2016). doi:10.1182/blood-2015-11-683649


title: 849_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: 848_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: 847_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-2-MDA-MECOM-AMP_A7_S7/CRISPResso_on_MR912-2-MDA-MECOM-AMP_A7_S7_L001_R1_001_MR912-2-MDA-MECOM-AMP_A7_S7_L001_R2_001/Alleles_frequency_table.zip


title: AML, 06H028

description:
06H028
Further sample information can be obtained from the following publication: Pabst, C. et al. GPR56 identifies primary human acute myeloid leukemia cells with high repopulating potential in vivo. Blood (2016). doi:10.1182/blood-2015-11-683649


title: 845_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: 844_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR214_1_Cat_F11_S71/CRISPResso_on_MR214_1_Cat_F11_S71_L001_R1_001_MR214_1_Cat_F11_S71_L001_R2_001/Alleles_frequency_table.zip


title: AML, 06H135

description:
06H135
Further sample information can be obtained from the following publication: Pabst, C. et al. GPR56 identifies primary human acute myeloid leukemia cells with high repopulating potential in vivo. Blood (2016). doi:10.1182/blood-2015-11-683649


title: 843_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: 842_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: AML, 04H112

description:
04H112
Further sample information can be obtained from the following publication: Pabst, C. et al. GPR56 identifies primary human acute myeloid leukemia cells with high repopulating potential in vivo. Blood (2016). doi:10.1182/blood-2015-11-683649


title: AML, 11H006

description:
11H006
Further sample information can be obtained from the following publication: Pabst, C. et al. GPR56 identifies primary human acute myeloid leukemia cells with high repopulating potential in vivo. Blood (2016). doi:10.1182/blood-2015-11-683649


title: AML, 03H116

description:
03H116
Further sample information can be obtained from the following publication: Pabst, C. et al. GPR56 identifies primary human acute myeloid leukemia cells with high repopulating potential in vivo. Blood (2016). doi:10.1182/blood-2015-11-683649


title: AML, 05H181

description:
05H181
Further sample information can be obtained from the following publication: Pabst, C. et al. GPR56 identifies primary human acute myeloid leukemia cells with high repopulating potential in vivo. Blood (2016). doi:10.1182/blood-2015-11-683649


title: AML, 03H041

description:
03H041
Further sample information can be obtained from the following publication: Pabst, C. et al. GPR56 identifies primary human acute myeloid leukemia cells with high repopulating potential in vivo. Blood (2016). doi:10.1182/blood-2015-11-683649


title: 841_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR214_1_Cat_G1_S73/CRISPResso_on_MR214_1_Cat_G1_S73_L001_R1_001_MR214_1_Cat_G1_S73_L001_R2_001/Alleles_frequency_table.zip


title: 840_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR214_1_Cat_F12_S72/CRISPResso_on_MR214_1_Cat_F12_S72_L001_R1_001_MR214_1_Cat_F12_S72_L001_R2_001/Alleles_frequency_table.zip


title: AML, 02H053

description:
02H053
Further sample information can be obtained from the following publication: Pabst, C. et al. GPR56 identifies primary human acute myeloid leukemia cells with high repopulating potential in vivo. Blood (2016). doi:10.1182/blood-2015-11-683649


title: 839_Mecom amplicon seq


title: Kasumi-1 cells, SNORD127  knockout clone C34

data_processing:
Library strategy: Ribometh-Seq
Basecalls were performed using on-instrument real time analysis (RTA) on an Illumina NextSeq 500 or HiScanSQ respectively
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 and splicosomal RNA U1, U12, U2, U4, U5 and U6
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 & snRNA sequence were 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

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:
Total RNA was extracted with mirRNeasy 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: cell line

value: AML cell

value: no

tag: expression

value: SNORD127 knockout

tag: re-expression

value: no re-expression


title: 838_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR214_1_Cat_F10_S70/CRISPResso_on_MR214_1_Cat_F10_S70_L001_R1_001_MR214_1_Cat_F10_S70_L001_R2_001/Alleles_frequency_table.zip

value: HSC

value: Mecom KO


title: Kasumi-1 cells, SNORD127  knockout clone C1 plus SNORD127

value: SNORD127 reexpression


title: 836_Mecom amplicon seq


title: Kasumi-1 cells, SNORD127  knockout clone C1 plus empty

value: empty reexpression


title: 835_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: 846_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-2-MDA-MECOM-AMP_H1_S85/CRISPResso_on_MR912-2-MDA-MECOM-AMP_H1_S85_L001_R1_001_MR912-2-MDA-MECOM-AMP_H1_S85_L001_R2_001/Alleles_frequency_table.zip


title: 832_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: Kasumi-1 cells, SNORD127  knockout clone C1


title: AML, 05H094

description:
05H094
Further sample information can be obtained from the following publication: Pabst, C. et al. GPR56 identifies primary human acute myeloid leukemia cells with high repopulating potential in vivo. Blood (2016). doi:10.1182/blood-2015-11-683649

value: AML

value: leukemia blast cells

value: AML diagnosis sample


title: 833_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: Kasumi-1 cells, Control knockdown plus empty replicate 2

value: 100 ng/ml doxycycline

value: Ctrl knockdown


title: 837_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: Kasumi-1 cells, Control knockdown plus empty replicate 1


title: 831_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR214_1_Cat_F3_S63/CRISPResso_on_MR214_1_Cat_F3_S63_L001_R1_001_MR214_1_Cat_F3_S63_L001_R2_001/Alleles_frequency_table.zip


title: Kasumi-1 cells, FBL knockdown plus wildtype FBL replicate 2

value: FBL knockdown

value: FBL wildtype reexpression


title: Kasumi-1 cells, SNORD127 control knockout clone

value: Ctrl knockout


title: 829_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: 830_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-2-WTA-MECOM-AMP_F2_S158/CRISPResso_on_MR912-2-WTA-MECOM-AMP_F2_S158_L001_R1_001_MR912-2-WTA-MECOM-AMP_F2_S158_L001_R2_001/Alleles_frequency_table.zip


title: 828_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-2-WTA-MECOM-AMP_D12_S144/CRISPResso_on_MR912-2-WTA-MECOM-AMP_D12_S144_L001_R1_001_MR912-2-WTA-MECOM-AMP_D12_S144_L001_R2_001/Alleles_frequency_table.zip


title: Kasumi-1 cells, FBL knockdown plus FBLQua mutant replicate 2

value: FBLQua mutant reexpression


title: Kasumi-1 cells, FBL knockdown plus wildtype FBL replicate 1

value: AML cell


title: Kasumi-1 cells, FBL knockdown plus empty replicate 2


title: 827_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR214_1_Cat_E11_S59/CRISPResso_on_MR214_1_Cat_E11_S59_L001_R1_001_MR214_1_Cat_E11_S59_L001_R2_001/Alleles_frequency_table.zip


title: Kasumi-1 cells, FBL knockdown plus empty replicate 1


title: Kasumi-1 cells, FBL knockdown plus FBLTri mutant replicate 1

value: FBLTri mutant mutant re-expression


title: 824_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-2-MDA-MECOM-AMP_H12_S96/CRISPResso_on_MR912-2-MDA-MECOM-AMP_H12_S96_L001_R1_001_MR912-2-MDA-MECOM-AMP_H12_S96_L001_R2_001/Alleles_frequency_table.zip


title: Kasumi-1 cells, FBL knockdown plus FBLTri mutant replicate 2


title: 825_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: 823_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: 822_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: Kasumi-1 cells, FBL knockdown replicate 3

data_processing:
Raw data FASTQ PE reads were trimmed with cutadapt 1.18 using parameters --nextseq-trim=20 -m 20.
Reference genome and gene model annotation files for GRCh38 were downloaded from genome browser Ensembl website. Paired-end clean reads were mapped to the reference genome using HISAT2 software.
Featurecounts was used to count the read numbers mapped of each gene.
Differential expression analysis between two conditions/groups  (three biological replicates per condition) was performed using edgeR R package. RPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Genome_build: GRCh38
Supplementary_files_format_and_content: counts, RPKMs

extract_protocol:
Total RNA was extracted with miRNeasy Kits (NEB).
A total amount of 1µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for lliumina® (NEB, USA) following manufacturer 's recommendations.
Transcriptomic RNA-sequencing

value: shFBL

tag: genotype


title: Kasumi-1 cells, FBL knockdown replicate 1


title: Kasumi-1 cells, FBL knockdown replicate 2


title: 821_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR214_1_Cat_E5_S53/CRISPResso_on_MR214_1_Cat_E5_S53_L001_R1_001_MR214_1_Cat_E5_S53_L001_R2_001/Alleles_frequency_table.zip


title: Kasumi-1 cells, Control replicate 3

value: shLUC

value: Control


title: 820_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

value: HSC

value: Mecom KO


title: Kasumi-1 cells, Control replicate 2


title: 819_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: 818_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912_3_MDA_MECOM_AMP_D8_S620/CRISPResso_on_MR912_3_MDA_MECOM_AMP_D8_S620_L001_R1_001_MR912_3_MDA_MECOM_AMP_D8_S620_L001_R2_001/Alleles_frequency_table.zip


title: CS024097_T2_S03

city: Cincinnati

first: Nancy

last: Ratner

state: OH

address: 3333 Burnet Avenue

institute: Cincinnati Children's Hospital Medical Center

data_processing:
The 10X scRNA-Seq libraries from human samples were aligned to the hg19 human genome using the Cell Ranger pipeline (version 3.0.2) with default parameters.
Genome_build: hg19
Supplementary_files_format_and_content: filtered_feature_bc_matrix.h5 for each sample from Cell Ranger output

extract_protocol:
Human tumors were collected from the operation room and placed in DMEM. Tissue was cut into 1 mm3 pieces and placed into dissociation medium in 50 mL tubes containing 20 mL DMEM, 10 mg Collagenase type I (Worthington Biochemical, LS004196), and 50 mg Dispase II (Sigma-Aldrich, 04942078001) and DNaseI and processed on a GentleMACS dissociator followed by incubation at 37°C incubator for 45 min., with 170 rpm shaking. The dissociation process was stopped by adding 30mL DMEM (Fisher Scientific, 11-965-1188) containing 10% FBS. Samples were centrifuged at 300 x g for 5 minutes at 4°C. Supernatants were removed and cell pellets were re-suspended into 50 mL of 1X PBS containing 0.1% BSA. Suspensions were sequentially filtered with 70 µm, 40 µm, and 20 µm cell strainers and centrifuged at 600 x g for 5 minutes at 4°C. Pellets were resuspended into 100 ul of 1X PBS/0.1% BSA. Trypan blue negative viable cells were counted to determine the cell concentration for droplet based single-cell RNA sequencing (scRNA-seq).
Library synthesis was performed according to manufacturer’s instructions to generate barcoded cDNA libraries for scRNA-seq. Ten thousand viable cells per lane from each sample were loaded using the 10X Chromium platform version 2 or 3 chemistries (3’) (10X Genomics).
single cell RNA-seq

tag: tissue

value: plexiform neurofibroma

tag: tumor sample

value: Tumor 4

tag: gender

value: female


title: 817_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR214_1_Cat_E1_S49/CRISPResso_on_MR214_1_Cat_E1_S49_L001_R1_001_MR214_1_Cat_E1_S49_L001_R2_001/Alleles_frequency_table.zip


title: 826_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: 815_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: Kasumi-1 cells, FBL knockdown plus FBLQuamutant replicate 1


title: Kasumi-1 cells, Control replicate 1


title: 814_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: CS024097_T2_S02


title: CS024097_T1_S04

value: Tumor 3


title: CS024097_T2_S01


title: 865_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912_3_Bird_A1_S97/CRISPResso_on_MR912_3_Bird_A1_S97_L001_R1_001_MR912_3_Bird_A1_S97_L001_R2_001/Alleles_frequency_table.zip


title: 813_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR214_1_Cat_D9_S45/CRISPResso_on_MR214_1_Cat_D9_S45_L001_R1_001_MR214_1_Cat_D9_S45_L001_R2_001/Alleles_frequency_table.zip


title: CS024097_T1_S02


title: CS024097_T1_S03


title: 812_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-2-MDA-MECOM-AMP_C9_S33/CRISPResso_on_MR912-2-MDA-MECOM-AMP_C9_S33_L001_R1_001_MR912-2-MDA-MECOM-AMP_C9_S33_L001_R2_001/Alleles_frequency_table.zip


title: 811_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR214_1_Cat_D7_S43/CRISPResso_on_MR214_1_Cat_D7_S43_L001_R1_001_MR214_1_Cat_D7_S43_L001_R2_001/Alleles_frequency_table.zip


title: 810_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-5-WTA-MECOM-AMP_F10_S358/CRISPResso_on_MR912-5-WTA-MECOM-AMP_F10_S358_L001_R1_001_MR912-5-WTA-MECOM-AMP_F10_S358_L001_R2_001/Alleles_frequency_table.zip


title: CS023066_S07

value: Tumor 2


title: CS024097_T1_S01


title: CS023066_S08


title: CS023066_S06


title: CS023066_S05


title: 809_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR214_1_Cat_D5_S41/CRISPResso_on_MR214_1_Cat_D5_S41_L001_R1_001_MR214_1_Cat_D5_S41_L001_R2_001/Alleles_frequency_table.zip


title: 806_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: 808_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR214_1_Cat_D4_S40/CRISPResso_on_MR214_1_Cat_D4_S40_L001_R1_001_MR214_1_Cat_D4_S40_L001_R2_001/Alleles_frequency_table.zip


title: 807_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: 816_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: CS023066_S04


title: 805_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR214_1_Cat_D1_S37/CRISPResso_on_MR214_1_Cat_D1_S37_L001_R1_001_MR214_1_Cat_D1_S37_L001_R2_001/Alleles_frequency_table.zip


title: 803_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR214_1_Cat_C11_S35/CRISPResso_on_MR214_1_Cat_C11_S35_L001_R1_001_MR214_1_Cat_C11_S35_L001_R2_001/Alleles_frequency_table.zip


title: CS023066_S03


title: 804_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR214_1_Cat_C12_S36/CRISPResso_on_MR214_1_Cat_C12_S36_L001_R1_001_MR214_1_Cat_C12_S36_L001_R2_001/Alleles_frequency_table.zip


title: CS023066_S02


title: CS023066_S01


title: 802_Mecom amplicon seq


title: 800_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: CS022514_S07

value: Tumor 1

value: male


title: 801_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR214_1_Cat_C9_S33/CRISPResso_on_MR214_1_Cat_C9_S33_L001_R1_001_MR214_1_Cat_C9_S33_L001_R2_001/Alleles_frequency_table.zip


title: CS022514_S08


title: CS022514_S06


title: 799_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


title: CS022514_S04


title: CS022514_S05


title: 798_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912_3_Bird_A5_S101/CRISPResso_on_MR912_3_Bird_A5_S101_L001_R1_001_MR912_3_Bird_A5_S101_L001_R2_001/Alleles_frequency_table.zip


title: 797_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR214_1_Cat_C5_S29/CRISPResso_on_MR214_1_Cat_C5_S29_L001_R1_001_MR214_1_Cat_C5_S29_L001_R2_001/Alleles_frequency_table.zip


title: CS022514_S03


title: CS022514_S02


title: CS022514_S01


title: 792_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR214_1_Cat_B12_S24/CRISPResso_on_MR214_1_Cat_B12_S24_L001_R1_001_MR214_1_Cat_B12_S24_L001_R2_001/Alleles_frequency_table.zip


title: 794_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-5-MDA-MECOM-AMP_A8_S200/CRISPResso_on_MR912-5-MDA-MECOM-AMP_A8_S200_L001_R1_001_MR912-5-MDA-MECOM-AMP_A8_S200_L001_R2_001/Alleles_frequency_table.zip


title: 791_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR214_1_Cat_B11_S23/CRISPResso_on_MR214_1_Cat_B11_S23_L001_R1_001_MR214_1_Cat_B11_S23_L001_R2_001/Alleles_frequency_table.zip


title: 790_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: 789_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: 787_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: 786_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-5-MDA-MECOM-AMP_E4_S244/CRISPResso_on_MR912-5-MDA-MECOM-AMP_E4_S244_L001_R1_001_MR912-5-MDA-MECOM-AMP_E4_S244_L001_R2_001/Alleles_frequency_table.zip


title: 788_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: 796_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-5-MDA-MECOM-AMP_E6_S246/CRISPResso_on_MR912-5-MDA-MECOM-AMP_E6_S246_L001_R1_001_MR912-5-MDA-MECOM-AMP_E6_S246_L001_R2_001/Alleles_frequency_table.zip


title: 784_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR214_1_Cat_G1_S73/CRISPResso_on_MR214_1_Cat_G1_S73_L001_R1_001_MR214_1_Cat_G1_S73_L001_R2_001/Alleles_frequency_table.zip


title: 793_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: in_vitro_TuMon1_2

city: TARRYTOWN

first: Jing

last: He

state: NEW YORK

address: 777 OLD SAW MILL RIVER ROAD

institute: Regeneron Pharmaceuticals

data_processing:
Raw sequence data (BCL files) were converted to Fastq format via Illumina Casava 1.8.2.
Reads were mapped to the mouse transcriptome (GRCm38 with NCBI annotation release 104), and reads mapping to sense strand exons were summed at the gene level using the RNA-Seq workflow of CLC Genomics Server version 6.0 (Qiagen)
Assembly: mm10
Supplementary files format and content: counts

organism: Mus musculus

source_name: Bone Marrow

extract_protocol:
Samples were homogenized in TRIzol reagent for RNA isolation by phase separation using chloroform.
Strand-specific RNA-seq libraries were prepared from 100 ng RNA using KAPA stranded mRNA-Seq Kit (KAPA Biosystems). Fourteen-cycle PCR was performed to amplify libraries.

value: Bone Marrow

tag: strain

value: Ly6C+ CD88+ Sca1+ Monocyte

tag: culture

value: in vitro


title: in_vitro_TuMon1_3

tag: cell type


title: 783_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR214_1_Cat_B3_S15/CRISPResso_on_MR214_1_Cat_B3_S15_L001_R1_001_MR214_1_Cat_B3_S15_L001_R2_001/Alleles_frequency_table.zip

tag: chip antibody

tag: treatment


title: in_vitro_TuMon1_1


title: 795_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912_3_Bird_E11_S155/CRISPResso_on_MR912_3_Bird_E11_S155_L001_R1_001_MR912_3_Bird_E11_S155_L001_R2_001/Alleles_frequency_table.zip


title: 781_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR214_1_Cat_B1_S13/CRISPResso_on_MR214_1_Cat_B1_S13_L001_R1_001_MR214_1_Cat_B1_S13_L001_R2_001/Alleles_frequency_table.zip


title: in_vitro_TuMon2_3

value: Ly6C+ CD88+ Sca1- Monocyte

value: LLC-supernatant


title: 780_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR214_1_Cat_A12_S12/CRISPResso_on_MR214_1_Cat_A12_S12_L001_R1_001_MR214_1_Cat_A12_S12_L001_R2_001/Alleles_frequency_table.zip


title: in_vitro_TuMon2_2


title: 779_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR214_1_Cat_A11_S11/CRISPResso_on_MR214_1_Cat_A11_S11_L001_R1_001_MR214_1_Cat_A11_S11_L001_R2_001/Alleles_frequency_table.zip


title: Sall1-overexpressing mutant ovaries rep 2

city: Berlin

first: Francisca

last: Martinez Real

address: Ihnestrasse 73

institute: Max Planck Institute for Molecular Genetics

data_processing:
Read mapping was performed with the STAR v2.6.1d software. Read counts were created using the R function “summarizeOverlaps” and normalized to RPKM based on the number of uniquely mapped reads.
For the analysis of differential expression between samples, the DESeq2 tool was used with default settings
Assembly: mm9
Supplementary files format and content: Text file include counts values for each sample

source_name: Developing ovaries

extract_protocol:
For gene expression analysis, embryos at E13.5 were dissected and RNA was extracted from these samples using the RNeasy Mini Kit (QIAGEN) according to the manufacturer’s instructions
The samples were sequenced using Illumina HiSeq technology according to standard procedures

value: Developing ovaries

value: Mutant

value: Sall1 overexpression

tag: time

value: Embryonic day E13.5


title: Wildtype ovaries rep 1

value: Wt


title: in_vitro_TuMon2_1


title: Wildtype ovaries rep 2


title: TOF-2

type: RNA

city: Suzhou

first: Xinxin

last: Yan

state: Jiangsu

address: 242 Guangji Road

department: Department of Pharmacy

country: China

institute: Affiliated Suzhou Hospital of Nanjing Medical University

description: lncRNA expression data of heart tissue from TOF

hyb_protocol: Following labeling, 5.5 ug of cDNA were hybridized for 16 hr at 45℃ on GeneChip Human Transcriptome Array 2.0 in Hybridization Oven 645. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scaned by using Affymetrix® GeneChip Command Console (AGCC) which installed in GeneChip® Scanner 3000 7G.

data_processing: The data were analyzed with Robust Multichip Analysis (RMA) algorithm using Affymetrix default analysis settings and global scaling as normalization method.

label: biotin

source_name: TOF

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 250 ng total RNA by using Ambion® WT Expression Kit. WT Expression Kit

extract_protocol: Total RNA was isolated from cells at indicated time point with Trizol.

tag: disease state

value: Tetralogy of Fallot

value: heart


title: 785_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

value: HSC

value: Mecom KO


title: control 3

description: lncRNA expression data of heart tissue from controls

source_name: control

value: Control


title: 778_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR214_1_Cat_A10_S10/CRISPResso_on_MR214_1_Cat_A10_S10_L001_R1_001_MR214_1_Cat_A10_S10_L001_R2_001/Alleles_frequency_table.zip


title: in_vitro_Ctl_4

value: Ly6C+ Monocyte

value: Control (untreated)


title: 782_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: 776_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-2-WTA-MECOM-AMP_A1_S97/CRISPResso_on_MR912-2-WTA-MECOM-AMP_A1_S97_L001_R1_001_MR912-2-WTA-MECOM-AMP_A1_S97_L001_R2_001/Alleles_frequency_table.zip


title: control 2


title: 777_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR214_1_Cat_A9_S9/CRISPResso_on_MR214_1_Cat_A9_S9_L001_R1_001_MR214_1_Cat_A9_S9_L001_R2_001/Alleles_frequency_table.zip


title: in_vitro_Ctl_3

value: Bone Marrow


title: Sall1-overexpressing mutant ovaries rep 1


title: TOF-3


title: in_vivo_MC38_spMon_4

source_name: Spleen

value: Spleen

value: in vivo

tag: tumor


title: in_vitro_Ctl_2

value: in vitro


title: TOF-1


title: in_vivo_MC38_spMon_3


title: 775_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR214_1_Cat_A7_S7/CRISPResso_on_MR214_1_Cat_A7_S7_L001_R1_001_MR214_1_Cat_A7_S7_L001_R2_001/Alleles_frequency_table.zip


title: in_vitro_Ctl_1


title: 773_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: 772_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR214_1_Cat_A4_S4/CRISPResso_on_MR214_1_Cat_A4_S4_L001_R1_001_MR214_1_Cat_A4_S4_L001_R2_001/Alleles_frequency_table.zip


title: in_vivo_MC38_spMon_2


title: 770_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: in_vivo_MC38_TuMac_4

source_name: Tumor

value: Tumor

value: Macrophage


title: in_vivo_MC38_spMon_1


title: in_vivo_MC38_TuMac_3


title: 769_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR214_1_Cat_A1_S1/CRISPResso_on_MR214_1_Cat_A1_S1_L001_R1_001_MR214_1_Cat_A1_S1_L001_R2_001/Alleles_frequency_table.zip


title: 771_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: 671_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-5-WTA-MECOM-AMP_H11_S383/CRISPResso_on_MR912-5-WTA-MECOM-AMP_H11_S383_L001_R1_001_MR912-5-WTA-MECOM-AMP_H11_S383_L001_R2_001/Alleles_frequency_table.zip


title: control 1


title: 672_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-5-WTA-MECOM-AMP_H12_S384/CRISPResso_on_MR912-5-WTA-MECOM-AMP_H12_S384_L001_R1_001_MR912-5-WTA-MECOM-AMP_H12_S384_L001_R2_001/Alleles_frequency_table.zip


title: 774_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR214_1_Cat_A6_S6/CRISPResso_on_MR214_1_Cat_A6_S6_L001_R1_001_MR214_1_Cat_A6_S6_L001_R2_001/Alleles_frequency_table.zip


title: 670_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-5-WTA-MECOM-AMP_H10_S382/CRISPResso_on_MR912-5-WTA-MECOM-AMP_H10_S382_L001_R1_001_MR912-5-WTA-MECOM-AMP_H10_S382_L001_R2_001/Alleles_frequency_table.zip


title: 668_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-5-WTA-MECOM-AMP_H8_S380/CRISPResso_on_MR912-5-WTA-MECOM-AMP_H8_S380_L001_R1_001_MR912-5-WTA-MECOM-AMP_H8_S380_L001_R2_001/Alleles_frequency_table.zip


title: in_vivo_MC38_TuMac_2


title: in_vivo_MC38_TuMon1_3

value: Ly6C+ CD88+ Sca1+ Monocyte


title: 669_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: in_vivo_MC38_TuMon1_2


title: 667_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-5-WTA-MECOM-AMP_H7_S379/CRISPResso_on_MR912-5-WTA-MECOM-AMP_H7_S379_L001_R1_001_MR912-5-WTA-MECOM-AMP_H7_S379_L001_R2_001/Alleles_frequency_table.zip


title: in_vivo_LLC_spMon_4

value: LLC


title: 665_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: in_vivo_MC38_TuMac_1


title: in_vivo_MC38_TuMon1_1


title: 664_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: 666_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-5-WTA-MECOM-AMP_H6_S378/CRISPResso_on_MR912-5-WTA-MECOM-AMP_H6_S378_L001_R1_001_MR912-5-WTA-MECOM-AMP_H6_S378_L001_R2_001/Alleles_frequency_table.zip


title: 663_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-5-WTA-MECOM-AMP_H3_S375/CRISPResso_on_MR912-5-WTA-MECOM-AMP_H3_S375_L001_R1_001_MR912-5-WTA-MECOM-AMP_H3_S375_L001_R2_001/Alleles_frequency_table.zip


title: in_vivo_LLC_spMon_1


title: in_vivo_LLC_TuMac_4


title: in_vivo_MC38_TuMon1_4


title: 661_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-5-WTA-MECOM-AMP_H1_S373/CRISPResso_on_MR912-5-WTA-MECOM-AMP_H1_S373_L001_R1_001_MR912-5-WTA-MECOM-AMP_H1_S373_L001_R2_001/Alleles_frequency_table.zip


title: in_vivo_LLC_TuMon2_4

value: Ly6C+ CD88+ Sca1- Monocyte


title: in_vivo_LLC_spMon_2


title: in_vivo_LLC_spMon_3


title: in_vivo_LLC_TuMon2_3


title: 657_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-5-WTA-MECOM-AMP_G9_S369/CRISPResso_on_MR912-5-WTA-MECOM-AMP_G9_S369_L001_R1_001_MR912-5-WTA-MECOM-AMP_G9_S369_L001_R2_001/Alleles_frequency_table.zip


title: 658_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-5-WTA-MECOM-AMP_G10_S370/CRISPResso_on_MR912-5-WTA-MECOM-AMP_G10_S370_L001_R1_001_MR912-5-WTA-MECOM-AMP_G10_S370_L001_R2_001/Alleles_frequency_table.zip


title: 659_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR214_1_Cat_F3_S63/CRISPResso_on_MR214_1_Cat_F3_S63_L001_R1_001_MR214_1_Cat_F3_S63_L001_R2_001/Alleles_frequency_table.zip


title: in_vivo_LLC_TuMac_2


title: 655_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-5-WTA-MECOM-AMP_G7_S367/CRISPResso_on_MR912-5-WTA-MECOM-AMP_G7_S367_L001_R1_001_MR912-5-WTA-MECOM-AMP_G7_S367_L001_R2_001/Alleles_frequency_table.zip


title: 656_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-5-WTA-MECOM-AMP_G8_S368/CRISPResso_on_MR912-5-WTA-MECOM-AMP_G8_S368_L001_R1_001_MR912-5-WTA-MECOM-AMP_G8_S368_L001_R2_001/Alleles_frequency_table.zip


title: in_vivo_LLC_TuMon2_1


title: AML, 05H050

description:
05H050
Further sample information can be obtained from the following publication: Pabst, C. et al. GPR56 identifies primary human acute myeloid leukemia cells with high repopulating potential in vivo. Blood (2016). doi:10.1182/blood-2015-11-683649

value: AML

value: leukemia blast cells

tag: sample type

value: AML diagnosis sample


title: 653_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-5-WTA-MECOM-AMP_G5_S365/CRISPResso_on_MR912-5-WTA-MECOM-AMP_G5_S365_L001_R1_001_MR912-5-WTA-MECOM-AMP_G5_S365_L001_R2_001/Alleles_frequency_table.zip

value: HSC


title: 652_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-5-WTA-MECOM-AMP_G4_S364/CRISPResso_on_MR912-5-WTA-MECOM-AMP_G4_S364_L001_R1_001_MR912-5-WTA-MECOM-AMP_G4_S364_L001_R2_001/Alleles_frequency_table.zip

value: Mecom KO


title: 654_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-5-WTA-MECOM-AMP_G6_S366/CRISPResso_on_MR912-5-WTA-MECOM-AMP_G6_S366_L001_R1_001_MR912-5-WTA-MECOM-AMP_G6_S366_L001_R2_001/Alleles_frequency_table.zip


title: in_vivo_LLC_TuMon2_2


title: AML, DR01

tag: aml status

value: sAML

tag: fab

tag: age

tag: Sex

value: f


title: 662_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: 660_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-5-WTA-MECOM-AMP_G12_S372/CRISPResso_on_MR912-5-WTA-MECOM-AMP_G12_S372_L001_R1_001_MR912-5-WTA-MECOM-AMP_G12_S372_L001_R2_001/Alleles_frequency_table.zip


title: in_vivo_LLC_TuMac_3


title: Nat, 1216

first: Kwangmin

last: Choi

state: Ohio

address: 333 Burnet Avenue

department: Experimental Hematology & Cancer Biology

data_processing:
Basecalls performed using CASAVA version 1.4
The quality of paired reads were checked using FASTQC (v0.11.0)
Reads were aligned with tophat/2.0.9 against mm10 genome
Raw gene counts were calculated using featureCounts/1.5.2
Gene counts were normalized using edgeR (v3.16.5)’s TMM method
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text file including raw/normalized gene counts

source_name: Neurofibroma

growth_protocol: Mice were housed in temperature- and humidity-controlled facilities on 12-hour dark-light cycles with free access to food and water.

extract_protocol:
Total RNAs were isolated by phenol/chloriform method and purified with QIAGEN mini RNA isolation kit.
RNA libraries were  amplified using the Ovation RNA-Seq System v2 (NuGEN) according to the manufacturer’s protocol and sequenced using standard Illumina protocols

tag: background strain

value: C57BL/6, I-129 and FVBN miixed

tag: genotype

value: No drug treatment

value: Neurofibroma

value: Nat Hist Fast growth


title: Nat, 1214

tag: tissue


title: Nat, 1191


title: 645_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: 648_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-5-WTA-MECOM-AMP_F12_S360/CRISPResso_on_MR912-5-WTA-MECOM-AMP_F12_S360_L001_R1_001_MR912-5-WTA-MECOM-AMP_F12_S360_L001_R2_001/Alleles_frequency_table.zip


title: 643_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-5-WTA-MECOM-AMP_F7_S355/CRISPResso_on_MR912-5-WTA-MECOM-AMP_F7_S355_L001_R1_001_MR912-5-WTA-MECOM-AMP_F7_S355_L001_R2_001/Alleles_frequency_table.zip


title: 651_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: 650_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-5-WTA-MECOM-AMP_G2_S362/CRISPResso_on_MR912-5-WTA-MECOM-AMP_G2_S362_L001_R1_001_MR912-5-WTA-MECOM-AMP_G2_S362_L001_R2_001/Alleles_frequency_table.zip


title: 646_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-5-WTA-MECOM-AMP_F10_S358/CRISPResso_on_MR912-5-WTA-MECOM-AMP_F10_S358_L001_R1_001_MR912-5-WTA-MECOM-AMP_F10_S358_L001_R2_001/Alleles_frequency_table.zip


title: 649_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-5-WTA-MECOM-AMP_G1_S361/CRISPResso_on_MR912-5-WTA-MECOM-AMP_G1_S361_L001_R1_001_MR912-5-WTA-MECOM-AMP_G1_S361_L001_R2_001/Alleles_frequency_table.zip


title: 647_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-5-WTA-MECOM-AMP_F11_S359/CRISPResso_on_MR912-5-WTA-MECOM-AMP_F11_S359_L001_R1_001_MR912-5-WTA-MECOM-AMP_F11_S359_L001_R2_001/Alleles_frequency_table.zip


title: in_vivo_LLC_TuMac_1

value: in vivo


title: Nat, 1071


title: 640_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: 641_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-5-WTA-MECOM-AMP_F5_S353/CRISPResso_on_MR912-5-WTA-MECOM-AMP_F5_S353_L001_R1_001_MR912-5-WTA-MECOM-AMP_F5_S353_L001_R2_001/Alleles_frequency_table.zip


title: Nat, 1179


title: Nat, 1053


title: Nat, 1206

value: Nat Hist Slow growth


title: 639_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-5-WTA-MECOM-AMP_F3_S351/CRISPResso_on_MR912-5-WTA-MECOM-AMP_F3_S351_L001_R1_001_MR912-5-WTA-MECOM-AMP_F3_S351_L001_R2_001/Alleles_frequency_table.zip


title: 638_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: 637_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: 636_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: Nat, 1202


title: Nat, 1198A


title: 635_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: 644_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-5-WTA-MECOM-AMP_F8_S356/CRISPResso_on_MR912-5-WTA-MECOM-AMP_F8_S356_L001_R1_001_MR912-5-WTA-MECOM-AMP_F8_S356_L001_R2_001/Alleles_frequency_table.zip


title: 634_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-5-WTA-MECOM-AMP_E10_S346/CRISPResso_on_MR912-5-WTA-MECOM-AMP_E10_S346_L001_R1_001_MR912-5-WTA-MECOM-AMP_E10_S346_L001_R2_001/Alleles_frequency_table.zip


title: Nat, 1079


title: 642_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-5-WTA-MECOM-AMP_F6_S354/CRISPResso_on_MR912-5-WTA-MECOM-AMP_F6_S354_L001_R1_001_MR912-5-WTA-MECOM-AMP_F6_S354_L001_R2_001/Alleles_frequency_table.zip


title: DRG, DRG5

source_name: DRG

value: DRG


title: 633_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-5-WTA-MECOM-AMP_E9_S345/CRISPResso_on_MR912-5-WTA-MECOM-AMP_E9_S345_L001_R1_001_MR912-5-WTA-MECOM-AMP_E9_S345_L001_R2_001/Alleles_frequency_table.zip


title: DRG, DRG4


title: 631_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-5-WTA-MECOM-AMP_E7_S343/CRISPResso_on_MR912-5-WTA-MECOM-AMP_E7_S343_L001_R1_001_MR912-5-WTA-MECOM-AMP_E7_S343_L001_R2_001/Alleles_frequency_table.zip


title: 632_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-5-WTA-MECOM-AMP_E8_S344/CRISPResso_on_MR912-5-WTA-MECOM-AMP_E8_S344_L001_R1_001_MR912-5-WTA-MECOM-AMP_E8_S344_L001_R2_001/Alleles_frequency_table.zip


title: 630_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-5-WTA-MECOM-AMP_E6_S342/CRISPResso_on_MR912-5-WTA-MECOM-AMP_E6_S342_L001_R1_001_MR912-5-WTA-MECOM-AMP_E6_S342_L001_R2_001/Alleles_frequency_table.zip


title: 629_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-5-WTA-MECOM-AMP_E5_S341/CRISPResso_on_MR912-5-WTA-MECOM-AMP_E5_S341_L001_R1_001_MR912-5-WTA-MECOM-AMP_E5_S341_L001_R2_001/Alleles_frequency_table.zip


title: DRG, DRG3


title: 627_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-5-WTA-MECOM-AMP_E3_S339/CRISPResso_on_MR912-5-WTA-MECOM-AMP_E3_S339_L001_R1_001_MR912-5-WTA-MECOM-AMP_E3_S339_L001_R2_001/Alleles_frequency_table.zip


title: Nf2832

data_processing:
The 10X scRNA-Seq libraries from mouse samples were aligned to the mm10 mouse genome using the Cell Ranger pipeline (version 3.0.2) with default parameters.
Genome_build: mm10
Supplementary_files_format_and_content: filtered_feature_bc_matrix.h5 for each sample from Cell Ranger output

extract_protocol:
Immediately following euthanasia, paraspinal tumors (2 or 7 mo. Dhh-Cre;Nf1fl/fl) (n=6), and age-matched wild type dorsal root ganglia (DRG) with nerve roots (n=2) were excised within 5 min. and placed into ice-cold L-15 medium (Fisher Scientific, MT-10-045-CV). Tissue was cut into 1 mm3 pieces and placed into dissociation medium in 50 mL tubes containing 20 mL L-15 medium, 10 mg Collagenase type I (Worthington Biochemical, LS004196), and 50 mg Dispase II (Sigma-Aldrich, 04942078001) at 37°C incubator for 2 hours, with 170 rpm shaking. The dissociation process was stopped by adding 30mL DMEM (Fisher Scientific, 11-965-1188) containing 10% FBS. Samples were centrifuged at 800 x g for 5 minutes at 4°C. Supernatants were removed and cell pellets were re-suspended into 50 mL of 1X PBS containing 0.1% BSA. Suspensions were sequentially filtered with 70 µm, 40 µm, and 20 µm cell strainers and centrifuged at 600 x g for 5 minutes at 4°C. Pellets were resuspended into 100 ul of 1X PBS/0.1% BSA. Trypan blue negative viable cells were counted to determine the cell concentration for droplet based single-cell RNA sequencing (scRNA-seq).
Library synthesis was performed according to manufacturer’s instructions to generate barcoded cDNA libraries for scRNA-seq. Ten thousand viable cells per lane from each sample (mouse or human) were loaded using the 10X Chromium platform version 2 or 3 chemistries (3’) (10X Genomics). We performed 1 full-lane sequence on 2 paired-end 75-bp flow cells using an Illumina HiSeq2500.
single cell RNA-seq

value: 2 months

value: Nf1 fl/fl; DhhCre-


title: Nf2615

source_name: paraspinal tumor

value: 7 months

value: Nf1 fl/fl; DhhCre+

value: paraspinal tumor


title: 624_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-5-WTA-MECOM-AMP_D12_S336/CRISPResso_on_MR912-5-WTA-MECOM-AMP_D12_S336_L001_R1_001_MR912-5-WTA-MECOM-AMP_D12_S336_L001_R2_001/Alleles_frequency_table.zip


title: Nf2830


title: 625_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-5-WTA-MECOM-AMP_E1_S337/CRISPResso_on_MR912-5-WTA-MECOM-AMP_E1_S337_L001_R1_001_MR912-5-WTA-MECOM-AMP_E1_S337_L001_R2_001/Alleles_frequency_table.zip


title: Nf1344


title: Nf2617


title: Nf2613


title: 626_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-5-WTA-MECOM-AMP_E2_S338/CRISPResso_on_MR912-5-WTA-MECOM-AMP_E2_S338_L001_R1_001_MR912-5-WTA-MECOM-AMP_E2_S338_L001_R2_001/Alleles_frequency_table.zip


title: Nat, 1203


title: Nf1381


title: 622_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-5-WTA-MECOM-AMP_D10_S334/CRISPResso_on_MR912-5-WTA-MECOM-AMP_D10_S334_L001_R1_001_MR912-5-WTA-MECOM-AMP_D10_S334_L001_R2_001/Alleles_frequency_table.zip


title: 621_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-5-WTA-MECOM-AMP_D9_S333/CRISPResso_on_MR912-5-WTA-MECOM-AMP_D9_S333_L001_R1_001_MR912-5-WTA-MECOM-AMP_D9_S333_L001_R2_001/Alleles_frequency_table.zip


title: 620_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-5-WTA-MECOM-AMP_D8_S332/CRISPResso_on_MR912-5-WTA-MECOM-AMP_D8_S332_L001_R1_001_MR912-5-WTA-MECOM-AMP_D8_S332_L001_R2_001/Alleles_frequency_table.zip


title: sh-MNX1-AS1-2

city: Hefei

first: Qidong

last: Li

state: Anhui

address: 443 Huangshan Road, Shushan district

institute: Lianxin Liu Lab

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: hg18
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: Liver

growth_protocol: HepG2 mesenchymal cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) 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.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: HepG2 cells were infected with sh-ctrl and sh-MNX1-AS1 lentivirus

value: Liver

tag: cell line

value: epithelial

value: WT

value: MNX1-AS1 KD


title: sh-MNX1-AS1-1


title: sh-MNX1-AS1-3


title: sh-ctrl-3 (MNX1-AS1 Knockdown control)

value: ctrl


title: 619_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-5-WTA-MECOM-AMP_D7_S331/CRISPResso_on_MR912-5-WTA-MECOM-AMP_D7_S331_L001_R1_001_MR912-5-WTA-MECOM-AMP_D7_S331_L001_R2_001/Alleles_frequency_table.zip

value: HSC

value: Mecom KO


title: Nf2833

tag: strain


title: 616_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-5-WTA-MECOM-AMP_D4_S328/CRISPResso_on_MR912-5-WTA-MECOM-AMP_D4_S328_L001_R1_001_MR912-5-WTA-MECOM-AMP_D4_S328_L001_R2_001/Alleles_frequency_table.zip


title: sh-ctrl-1 (MNX1-AS1 Knockdown control)


title: sh-ctrl-2 (MNX1-AS1 Knockdown control)


title: 628_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-5-WTA-MECOM-AMP_E4_S340/CRISPResso_on_MR912-5-WTA-MECOM-AMP_E4_S340_L001_R1_001_MR912-5-WTA-MECOM-AMP_E4_S340_L001_R2_001/Alleles_frequency_table.zip


title: HMDM, SIMALR ASO 3

city: New York

first: Chenyi

last: Xue

state: NY

institute: Columbia University

data_processing:
Reads were aligned to human genome build hg19 using STAR_2.5.1b
Read alignment was filtered using the following criteria: 1) reads were uniquely mapped; 2) read pairs were mapped to the same chromosome with expected orientation; 3) mapping distance within each read pair <500,000bp
Differential expression was tested by Cuffdiff 2.1.1 with options "-u --max-bundle-frags 50000000 --library-type fr-firststrand". Annotation included RefSeq coding genes, stringent set of lincRNAs from Cabili et al. 2011, GENCODE v19 lincRNAs, and newly annotated lincRNAs from Zhang et al. 2017.
Assembly: hg19
Supplementary files format and content: Tab-delimited text file from Cuffdiff output: ctrl_ASO_8h_gene_exp.diff contains differential expression from control and SIMALR ASO. "sample_1" = control, "sample_2" = SIMALR ASO

molecule: polyA RNA

source_name: PBMC derived macrophage (HMDM)

growth_protocol: Human peripheral blood mononuclear cells (PBMCs) were differentiated to human monocyte-derived macrophages (HMDMs) using 100 ng/mL macrophage colony-stimulating factor.

extract_protocol:
RNA from SIMALR KD and control samples were extracted using Quick-RNA kit (Zymo Research; R1054).
Poly-A libraries were constructed following manufacturer's protocols.

treatment_protocol: HMDMs were treated with 100 ng/mL lipopolysaccharide (LPS) and 20 ng/mL IFNγ.

value: PBMC derived macrophage (HMDM)

value: SIMALR knockdown

value: M-CSF differentiation

value: LPS and IFNγ

value: 8 hours


title: 614_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-5-WTA-MECOM-AMP_D2_S326/CRISPResso_on_MR912-5-WTA-MECOM-AMP_D2_S326_L001_R1_001_MR912-5-WTA-MECOM-AMP_D2_S326_L001_R2_001/Alleles_frequency_table.zip


title: HMDM, control 3


title: 623_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-5-WTA-MECOM-AMP_D11_S335/CRISPResso_on_MR912-5-WTA-MECOM-AMP_D11_S335_L001_R1_001_MR912-5-WTA-MECOM-AMP_D11_S335_L001_R2_001/Alleles_frequency_table.zip


title: 615_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-5-WTA-MECOM-AMP_D3_S327/CRISPResso_on_MR912-5-WTA-MECOM-AMP_D3_S327_L001_R1_001_MR912-5-WTA-MECOM-AMP_D3_S327_L001_R2_001/Alleles_frequency_table.zip


title: 612_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-5-WTA-MECOM-AMP_C12_S324/CRISPResso_on_MR912-5-WTA-MECOM-AMP_C12_S324_L001_R1_001_MR912-5-WTA-MECOM-AMP_C12_S324_L001_R2_001/Alleles_frequency_table.zip


title: HMDM, control 2


title: HMDM, control 1


title: 611_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-5-WTA-MECOM-AMP_C11_S323/CRISPResso_on_MR912-5-WTA-MECOM-AMP_C11_S323_L001_R1_001_MR912-5-WTA-MECOM-AMP_C11_S323_L001_R2_001/Alleles_frequency_table.zip


title: 610_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-5-WTA-MECOM-AMP_C10_S322/CRISPResso_on_MR912-5-WTA-MECOM-AMP_C10_S322_L001_R1_001_MR912-5-WTA-MECOM-AMP_C10_S322_L001_R2_001/Alleles_frequency_table.zip


title: 613_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-5-WTA-MECOM-AMP_D1_S325/CRISPResso_on_MR912-5-WTA-MECOM-AMP_D1_S325_L001_R1_001_MR912-5-WTA-MECOM-AMP_D1_S325_L001_R2_001/Alleles_frequency_table.zip


title: panc1_bruUVseq_KDM6AKOC22_1

city: Ann Arbor

first: Karan

last: Bedi

state: MI

address: 1600 Huron Pkwy

department: Biostatistics

institute: University of Michigan

description: panc1 bruUVseq KDM6A KO C22 replicate 1

data_processing:
Illumina Casava v1.8.2 software used for basecalling.
Reads were pre-mapped to the ribosomal RNA (rRNA) repeating unit (GenBank U13369.1) and the mitochondrial and EBV genomes (from the hg38 analysis set) using Bowtie2 (2.3.3)
Reads that did not align with rRNA, mitochondrial and EBV genomes were subsequently mapped to human genome build hg38/GRCh38 using STAR (v 2.5.3a) and a STAR index created from GENCODE annotation version 27
A coverage determination was then made for every base in the genome using Bedtools v.2.16.2 such that a base covered by one read was recorded as having a coverage of 1/read_length
Assembly: hg38
Supplementary files format and content: The columns of the genes.bed indicate: (1) chromosome; (2) start; (3) end; (4) name; (5) strand; (6) gene length (7) read count (8) RPKM
Library strategy: BruSeq

growth_protocol: PANC-1 cells were cultured in DMEM (GIBCO) supplemented with 10% FBS (GIBCO) and 1% penicillin/streptomycin (GIBCO).

extract_protocol:
For bruseq and bruUVseq, total RNA was isolated by using TRIzol reagent (Invitrogen), and Bru-labeled RNA was isolated from the total RNA by incubation with anti-BrdU antibodies (BD Biosciences) conjugated to magnetic beads (Dynabeads, Goat anti-Mouse IgG; Invitrogen) under gentle agitation at room temperature for 1 h. For more detail, see Paulsen et. al 2013
Bru-labeled RNA was mixed with first strand buffer and random primers and fragmented by heating at 85 ̊C for 10 minutes. The first strand cDNA was then  synthesized, in the presence of Actinomycin D to result in strand specific reads (only applicable to certain samples as indicated in sample table above). After purifying the first strand cDNA using AMPure RNAclean beads (Beckman Coulter), the second strand cDNA was synthesized. The resulting cDNA was purified with AMPure XP beads, after which the Illumina TruSeq RNA Sample Prep Kit was used to repair the cDNA ends, adenylate and ligate adaptors to the cDNA. The samples were then run on a 3% agarose gel and size-selected by excising gel slices in the 300bp region. These gel slices were purified using the QIAEX II Gel Extraction Kit (Qiagen) and then the Illumina TruSeq Kit PCR reagents were used to enrich the DNA fragments. After a final purification using AMPure XP beads, the quality and concentration of the DNA libraries were determined using an Agilent Bioanalyzer.

treatment_protocol: KDM6A/UTX was knocked out in PANC-1 cells using CRISPR/cas9. Bru-seq and BruUV-seq analyses were performed in two KDM6A/UTX-knockout PANC-1 clones (KO1 and KO2) comparing to a control PANC-1 cell line. For BruUV-seq, cells were irradiated with 100 J/m2 in addition to 2 mM BrU treatment for 30 min before collection.

value: KDM6A KO C22

tag: bru labeling time

value: 0.5 hours

tag: assay

value: bruUVseq

tag: time between end of bru labeling and rna extraction

value: 0 hours

tag: labeling agent

value: Bromouridine (Bru)

tag: molecule subtype

value: bru-labeled RNA


title: panc1_bruUVseq_KDM6AKOC28_1

description: panc1 bruUVseq KDM6A KO C28 replicate 1

value: KDM6A KO C28


title: 609_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-5-WTA-MECOM-AMP_C9_S321/CRISPResso_on_MR912-5-WTA-MECOM-AMP_C9_S321_L001_R1_001_MR912-5-WTA-MECOM-AMP_C9_S321_L001_R2_001/Alleles_frequency_table.zip

tag: cell type

tag: chip antibody

tag: treatment


title: panc1_bruUVseq_wt_1

description: panc1 bruUVseq WT replicate 1

value: WT


title: 608_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: 618_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: panc1_bruseq0h_KDM6AKOC22_2

description: panc1 bruseq KDM6A KO C22 replicate 2

value: bruseq


title: panc1_bruseq0h_KDM6AKOC28_1

description: panc1 bruseq KDM6A KO C28 replicate 1


title: panc1_bruseq0h_KDM6AKOC28_2

description: panc1 bruseq KDM6A KO C28 replicate 2


title: 606_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: HMDM, SIMALR ASO 2

tag: time


title: 617_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-5-WTA-MECOM-AMP_D5_S329/CRISPResso_on_MR912-5-WTA-MECOM-AMP_D5_S329_L001_R1_001_MR912-5-WTA-MECOM-AMP_D5_S329_L001_R2_001/Alleles_frequency_table.zip


title: 607_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-5-WTA-MECOM-AMP_C7_S319/CRISPResso_on_MR912-5-WTA-MECOM-AMP_C7_S319_L001_R1_001_MR912-5-WTA-MECOM-AMP_C7_S319_L001_R2_001/Alleles_frequency_table.zip


title: HMDM, SIMALR ASO 1


title: 604_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-5-WTA-MECOM-AMP_C4_S316/CRISPResso_on_MR912-5-WTA-MECOM-AMP_C4_S316_L001_R1_001_MR912-5-WTA-MECOM-AMP_C4_S316_L001_R2_001/Alleles_frequency_table.zip


title: panc1_bruseq0h_KDM6AKOC22_1

description: panc1 bruseq KDM6A KO C22 replicate 1


title: panc1_bruseq0h_wt_2

description: panc1 bruseq WT replicate 2


title: 605_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-5-WTA-MECOM-AMP_C5_S317/CRISPResso_on_MR912-5-WTA-MECOM-AMP_C5_S317_L001_R1_001_MR912-5-WTA-MECOM-AMP_C5_S317_L001_R2_001/Alleles_frequency_table.zip


title: 602_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: Bisulfite converted DNA from nasopharyngeal carcinoma tissue 17

city: Hong Kong

first: Ka Yue Larry

last: Chow

address: 21 Sassoon Road

department: Clinical Oncology

country: Hong Kong

institute: The University of Hong Kong

data_processing:
Trimmomatic was used for removing adapter sequences and poor quality bases.
BSMAP was used for aligning the reads onto hg19
BSMAP was used to quantify the methylation ratio of each CpG sites
Genome_build: hg19
Supplementary_files_format_and_content: The Bigwig files were generated using UCSC utility. The score represents the methylation ratio. Only CpG sites covered by at least 10 reads were included.

source_name: Nasopharyngeal carcinoma tissue

extract_protocol:
DNA was extracted by AllPrep DNA/RNA Mini Kit (Qiagen).
Accel-NGS Methyl-Seq Kit (Swift Biosciences) was used for library preparation according to the protocl instruction

treatment_protocol: EpiTect Bisulfite Kit was used for bisulfite conversion of DNA. Experimental procedure follows the protocol instruction.

value: Nasopharyngeal carcinoma tissue


title: 599_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

source_name: HSC

value: HSC


title: 600_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-5-WTA-MECOM-AMP_B12_S312/CRISPResso_on_MR912-5-WTA-MECOM-AMP_B12_S312_L001_R1_001_MR912-5-WTA-MECOM-AMP_B12_S312_L001_R2_001/Alleles_frequency_table.zip

value: Mecom KO


title: NT

first: Arthur

middle: W.

last: Lambert

state: MA

address: 455 Main street

institute: Whitehead Institute

data_processing:
Fastq files were generated and demultiplexed with the bcl2fastq Conversion Software (Illumina). Counts matrix were generated using cellrangerv4 (10X genomics) using mixed species reference genome (refdata-gex-GRCh38_and_mm10-2020-A) and human only reference genome (refdata-gex-GRCh38-2020-A). Reference genomes were downloaded from 10x genomics website (https://support.10xgenomics.com/single-cell-gene-expression/software/downloads/latest). From dual species analysis, the cell barcodes classified as human were identified from the gem_classification.csv file. We used the list of human cell barcodes to select for cells in the count matrix that was generated using human only reference genome, using cellranger reanalyze option.
Genome_build: hg38
Supplementary_files_format_and_content: filtered_gene_bc_matrices text output files from Cell Ranger count.

source_name: ITGB4-hi with non-targeting guide

growth_protocol: cancer cells (tdTom+) were isolated from dissociated lungs 3 days after tail-vein injection.

extract_protocol: Cells were processed using the 10X Genomics Chromium Controller with the Single Cell 3ʹ v3 Reagent Kit, according to manufacturer’s directions. Briefly, a target number of 1250 cells per library was roughly achieved by loading 1.6 times the target number of cells in suspension. The Chromium Controller process each individual cells so that each cell is marked with its own unique barcode during reverse transcription. The end result is a single library representing one cell suspension, containing data for each individual cell.

tag: parental line

tag: subline

value: mammary carcinoma cells isolated from the lungs the NSG mice


title: 598_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-5-WTA-MECOM-AMP_B10_S310/CRISPResso_on_MR912-5-WTA-MECOM-AMP_B10_S310_L001_R1_001_MR912-5-WTA-MECOM-AMP_B10_S310_L001_R2_001/Alleles_frequency_table.zip


title: 601_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: Bisulfite converted DNA from nasopharyngeal carcinoma tissue 14


title: panc1_bruseq0h_wt_1

description: panc1 bruseq WT replicate 1


title: Bisulfite converted DNA from nasopharyngeal carcinoma tissue 16


title: 596_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-5-WTA-MECOM-AMP_B8_S308/CRISPResso_on_MR912-5-WTA-MECOM-AMP_B8_S308_L001_R1_001_MR912-5-WTA-MECOM-AMP_B8_S308_L001_R2_001/Alleles_frequency_table.zip


title: Bisulfite converted DNA from nasopharyngeal carcinoma tissue 12


title: 595_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: Bisulfite converted DNA from nasopharyngeal carcinoma tissue 13


title: Bisulfite converted DNA from nasopharyngeal carcinoma tissue 10


title: 603_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-5-WTA-MECOM-AMP_C3_S315/CRISPResso_on_MR912-5-WTA-MECOM-AMP_C3_S315_L001_R1_001_MR912-5-WTA-MECOM-AMP_C3_S315_L001_R2_001/Alleles_frequency_table.zip


title: 593_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-5-WTA-MECOM-AMP_B5_S305/CRISPResso_on_MR912-5-WTA-MECOM-AMP_B5_S305_L001_R1_001_MR912-5-WTA-MECOM-AMP_B5_S305_L001_R2_001/Alleles_frequency_table.zip


title: 592_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: Bisulfite converted DNA from nasopharyngeal carcinoma tissue 09


title: dKO

source_name: ITGB4-hi with KO of p63/p73


title: 591_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: Bisulfite converted DNA from nasopharyngeal carcinoma tissue 08


title: 589_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-5-WTA-MECOM-AMP_B1_S301/CRISPResso_on_MR912-5-WTA-MECOM-AMP_B1_S301_L001_R1_001_MR912-5-WTA-MECOM-AMP_B1_S301_L001_R2_001/Alleles_frequency_table.zip


title: Bisulfite converted DNA from nasopharyngeal carcinoma tissue 06


title: 594_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-5-WTA-MECOM-AMP_B6_S306/CRISPResso_on_MR912-5-WTA-MECOM-AMP_B6_S306_L001_R1_001_MR912-5-WTA-MECOM-AMP_B6_S306_L001_R2_001/Alleles_frequency_table.zip


title: 590_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: Bisulfite converted DNA from nasopharyngeal carcinoma tissue 04


title: 586_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-5-WTA-MECOM-AMP_A10_S298/CRISPResso_on_MR912-5-WTA-MECOM-AMP_A10_S298_L001_R1_001_MR912-5-WTA-MECOM-AMP_A10_S298_L001_R2_001/Alleles_frequency_table.zip


title: Bisulfite converted DNA from nasopharyngeal carcinoma tissue 03


title: 588_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: Bisulfite converted DNA from nasopharyngeal carcinoma tissue 05


title: 597_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


title: 584_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-5-WTA-MECOM-AMP_A8_S296/CRISPResso_on_MR912-5-WTA-MECOM-AMP_A8_S296_L001_R1_001_MR912-5-WTA-MECOM-AMP_A8_S296_L001_R2_001/Alleles_frequency_table.zip


title: Bisulfite converted DNA from nasopharyngeal carcinoma tissue 01


title: Bisulfite converted DNA from nasopharyngeal carcinoma tissue 02


title: 585_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-5-WTA-MECOM-AMP_A9_S297/CRISPResso_on_MR912-5-WTA-MECOM-AMP_A9_S297_L001_R1_001_MR912-5-WTA-MECOM-AMP_A9_S297_L001_R2_001/Alleles_frequency_table.zip


title: 583_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: Bisulfite converted DNA from normal nasopharyngeal epithelial tissue 02

source_name: Normal nasopharyngeal epithelial tissue

value: Normal nasopharyngeal epithelial tissue


title: Bisulfite converted DNA from normal nasopharyngeal epithelial tissue 03


title: 582_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-5-WTA-MECOM-AMP_A6_S294/CRISPResso_on_MR912-5-WTA-MECOM-AMP_A6_S294_L001_R1_001_MR912-5-WTA-MECOM-AMP_A6_S294_L001_R2_001/Alleles_frequency_table.zip


title: Bisulfite converted DNA from nasopharyngeal carcinoma tissue 11


title: Bisulfite converted DNA from normal nasopharyngeal epithelial tissue 01


title: 581_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-5-WTA-MECOM-AMP_A5_S293/CRISPResso_on_MR912-5-WTA-MECOM-AMP_A5_S293_L001_R1_001_MR912-5-WTA-MECOM-AMP_A5_S293_L001_R2_001/Alleles_frequency_table.zip


title: 580_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-5-WTA-MECOM-AMP_A4_S292/CRISPResso_on_MR912-5-WTA-MECOM-AMP_A4_S292_L001_R1_001_MR912-5-WTA-MECOM-AMP_A4_S292_L001_R2_001/Alleles_frequency_table.zip


title: 579_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-5-WTA-MECOM-AMP_A3_S291/CRISPResso_on_MR912-5-WTA-MECOM-AMP_A3_S291_L001_R1_001_MR912-5-WTA-MECOM-AMP_A3_S291_L001_R2_001/Alleles_frequency_table.zip


title: 578_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-5-WTA-MECOM-AMP_A2_S290/CRISPResso_on_MR912-5-WTA-MECOM-AMP_A2_S290_L001_R1_001_MR912-5-WTA-MECOM-AMP_A2_S290_L001_R2_001/Alleles_frequency_table.zip


title: Bisulfite converted DNA from nasopharyngeal carcinoma tissue 07


title: Tumor_Spleen

description: GEX + ADT Tumor_Spleen

library_source: transcriptomic single cell

data_processing:
Cell Ranger Single-Cell Software Suite (10X Genomics) was used to perform sample de-multiplexing, alignment, filtering, and UMI counting.
Assembly: Mouse mm10

source_name: spleen

extract_protocol:
Single cells suspended in PBS with 0.04% BSA were loaded on a Chromium Single Cell Instrument (10X Genomics).
RNAseq and antibody-derived-tag libraries were prepared using Chromium Single Cell 3’ Library, Gel Beads & Multiplex Kit (10X Genomics) with antibody-derived-tag primer addition.

value: spleen

tag: disease state

value: LLC tumor

value: CD11b+ enriched

tag: tumor stage

value: day 14


title: 577_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-5-WTA-MECOM-AMP_A1_S289/CRISPResso_on_MR912-5-WTA-MECOM-AMP_A1_S289_L001_R1_001_MR912-5-WTA-MECOM-AMP_A1_S289_L001_R2_001/Alleles_frequency_table.zip


title: Tumor_BM

description: GEX + ADT Tumor_BM

source_name: bone marrow

value: bone marrow


title: Tumor_Tumor

description: GEX + ADT Tumor_Tumor

value: Tumor


title: Naive_Spleen

description: GEX + ADT Naive_Spleen

value: Naïve


title: Naive_BM

description: GEX + ADT Naive_BM


title: 480_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-2-WTA-MECOM-AMP_F2_S158/CRISPResso_on_MR912-2-WTA-MECOM-AMP_F2_S158_L001_R1_001_MR912-2-WTA-MECOM-AMP_F2_S158_L001_R2_001/Alleles_frequency_table.zip


title: 587_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-5-WTA-MECOM-AMP_A11_S299/CRISPResso_on_MR912-5-WTA-MECOM-AMP_A11_S299_L001_R1_001_MR912-5-WTA-MECOM-AMP_A11_S299_L001_R2_001/Alleles_frequency_table.zip


title: 479_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: Naive_Blood

description: GEX + ADT Naive_Blood

source_name: blood

value: blood


title: 478_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-5-MDA-MECOM-AMP_H10_S286/CRISPResso_on_MR912-5-MDA-MECOM-AMP_H10_S286_L001_R1_001_MR912-5-MDA-MECOM-AMP_H10_S286_L001_R2_001/Alleles_frequency_table.zip


title: Tumor_Blood

description: GEX + ADT Tumor_Blood


title: 476_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: 477_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