title: Patient5_treated_15d_ETP-ALL_285


title: Patient5_treated_15d_ETP-ALL_268

status: Public on Jan 01 2021

type: SRA

city: Boston

first: Birgit

last: Knoechel

state: MA

address: 450 Brookline Ave

department: pediatric oncology

country: USA

institute: Dana Farber Cancer Institute

library_source: transcriptomic

data_processing:
Adapter trimming was performed using trimmomatic version 0.36
Sequence quality was assessed using fastqc version 0.11.5
Alignment agains human genome was performed using START version 2.5.2b using following parameters -  --twopassMode Basic          --alignIntronMax 100000 --alignMatesGapMax 100000   --alignSJDBoverhangMin 10   --alignSJstitchMismatchNmax 5   -1   5   5 --outSAMstrandField intronMotif --outSAMattributes NH HI NM MD AS XS
Raw counts were obtained from aligned bam files using htseq version 0.9.1
Genome_build: hg19
Supplementary_files_format_and_content: htseq count file with raw raw counts for all the human genes for individual cells

molecule: total RNA

organism: Homo sapiens

source_name: Blood

extract_protocol:
PBMCs were isolated using Ficoll-Paque, stained with anti-CD45 FITC, anti-CD3 PerCP-Cy5.5, anti-CD14 APC-Cy7, anti-CD19 PE and DAPI. Live single cells were sorted into 96 well plates containing TCL buffer.
Full-length single cell RNA-seq libraries were prepared using the SMART-seq2 protocol. cDNA was fragmented using Nextera XT (Illumina) and amplified with indexed Nextera PCR primers.

tag: who classification

value: ETP-ALL

tag: cell type

value: Peripherial blood mononuclear cells


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title: Patient4_treated_1d_ETP-ALL_196


title: Patient4_treated_1d_ETP-ALL_192


title: Patient4_treated_1d_ETP-ALL_189


title: Patient4_treated_1d_ETP-ALL_186


title: Patient4_treated_1d_ETP-ALL_188


title: Patient4_treated_1d_ETP-ALL_197


title: Patient4_treated_1d_ETP-ALL_194


title: Patient4_treated_1d_ETP-ALL_187


title: Patient4_treated_1d_ETP-ALL_193


title: Patient4_treated_1d_ETP-ALL_190


title: Patient4_treated_1d_ETP-ALL_184


title: Patient4_treated_1d_ETP-ALL_185


title: Patient4_treated_1d_ETP-ALL_182


title: Patient4_treated_1d_ETP-ALL_183


title: Patient4_treated_1d_ETP-ALL_195


title: Patient4_treated_1d_ETP-ALL_179


title: Patient4_treated_1d_ETP-ALL_181


title: Patient4_treated_1d_ETP-ALL_178


title: Patient4_treated_1d_ETP-ALL_177


title: Patient4_treated_1d_ETP-ALL_176


title: Patient4_treated_1d_ETP-ALL_175


title: Patient4_treated_1d_ETP-ALL_171