title: post-mortem tissue [CGND-HRA-02076]


title: post-mortem tissue [CGND-HRA-02066]

status: Public on Oct 20 2020

type: SRA

city: New York

first: Hemali

last: Phatnani

state: NY

address: 101 Avenue of the Americas

country: USA

institute: New York Genome Center

library_source: transcriptomic

data_processing:
Paired-end reads in raw fastq files were subject to adapter trimming with trimmomatic (v0.36) (Bolger, Lohse, and Usadel 2014; https://pubmed.ncbi.nlm.nih.gov/24695404/)
Reads were aligned to the hg38 build (GRCh38.primary_assembly) of the human reference genome using STAR (2.7.2a)  (Dobin et al. 2013; https://pubmed.ncbi.nlm.nih.gov/23104886/) with indexes created from GENCODE (v30) (“GENCODE - Human Release 30” n.d.).
Gene expression was quantified using RSEM (1.3.1) (B.   Li and Dewey 2011; https://pubmed.ncbi.nlm.nih.gov/21816040/) using gene models from GENCODE (v30).
A matrix of read counts per gene in each sample was generated using tximport (v1.12.0) (Soneson et al, 2015; https://pubmed.ncbi.nlm.nih.gov/26925227/).
Genome_build: hg38 (GRCh38.primary_assembly)
Supplementary_files_format_and_content: tximport (v1.12.0) generated matrix of RSEM read counts per gene in txt file format for all samples retained for analysis in Prudencio et al., 2020; Differential STMN2 gene expression (processed count data in Gene_counts_matrix_RSEM_Prudencio_et_al_2020.txt) and splicing analyses of Amyotrophic Lateral Sclerosis (ALS), ALS-FTD and Control postmortem samples in Prudencio et al. 2020 were performed on samples from this release and prior NYGC ALS Consortium releases.

molecule: total RNA

organism: Homo sapiens

source_name: Cortex Frontal

extract_protocol:
Total RNA is extracted from flash frozen post-mortem tissue using Trizol/Chloroform, followed by Qiagen RNeasy minikit column purification. RNA is quantified on a Nanodrop 2000 and Qubit™ 2.0 Fluorometer; the quality and integrity of the RNA are verified on an Agilent Bioanalyzer.
Starting from 500 ng of total RNA, rRNA is depleted and cDNA libraries prepared using the KAPA Stranded RNA-Seq Kit with RiboErase (KAPA, Roche) and either i) Illumina platform-compatible PCR primers (NEXTflex RNA-seq indexes, BioScientific) for the manual  library preparation protocol and sequencing on Illumina HiSeq 2500 or ii) Illumina sequencing adapters with dual indexes (IDT for Illumina – TruSeq DNA UD Indexes Cat# 20022370) and amplified with 9 cycles of PCR for sequencing on the NovaSeq 6000 (automated library preparation protocol). Libraries are ~ 500bp in length and sequenced PE 125 (HiSeq 2500) or PE 100 (NovaSeq 6000).

treatment_protocol: Flash frozen autopsy tissue

tag: project

value: NYGC ALS Consortium

tag: tissue

value: Cortex Frontal

tag: subject id

tag: group

value: Other Neurological Disorders

tag: sample id alt

tag: library preparation method

value: Automated KAPA Total


title: post-mortem tissue [CGND-HRA-02060]

source_name: Cortex Occipital

value: Cortex Occipital


title: post-mortem tissue [CGND-HRA-01858]

value: ALS Spectrum MND


title: post-mortem tissue [CGND-HRA-02048]

source_name: Cerebellum

value: Cerebellum


title: post-mortem tissue [CGND-HRA-02059]


title: post-mortem tissue [CGND-HRA-02068]

source_name: Cortex Motor Medial

value: Cortex Motor Medial


title: post-mortem tissue [CGND-HRA-02039]

value: Non-Neurological Control


title: post-mortem tissue [CGND-HRA-02037]

source_name: Cortex Motor Lateral

value: Cortex Motor Lateral


title: post-mortem tissue [CGND-HRA-02032]

source_name: Spinal Cord Cervical

value: Spinal Cord Cervical

value: Other Neurological DIsorders


title: post-mortem tissue [CGND-HRA-02036]


title: post-mortem tissue [CGND-HRA-02038]


title: post-mortem tissue [CGND-HRA-02033]

source_name: Spinal Cord Lumbar

value: Spinal Cord Lumbar


title: post-mortem tissue [CGND-HRA-02031]


title: post-mortem tissue [CGND-HRA-02030]


title: post-mortem tissue [CGND-HRA-02019]


title: post-mortem tissue [CGND-HRA-02020]


title: post-mortem tissue [CGND-HRA-02021]


title: post-mortem tissue [CGND-HRA-02044]


title: post-mortem tissue [CGND-HRA-01936]

source_name: Cortex Motor Unspecified

value: Cortex Motor Unspecified


title: post-mortem tissue [CGND-HRA-01940]

source_name: Hippocampus

value: Hippocampus


title: post-mortem tissue [CGND-HRA-01951]


title: post-mortem tissue [CGND-HRA-01948]


title: post-mortem tissue [CGND-HRA-01945]


title: post-mortem tissue [CGND-HRA-01949]


title: post-mortem tissue [CGND-HRA-01950]


title: post-mortem tissue [CGND-HRA-01937]


title: post-mortem tissue [CGND-HRA-01935]


title: post-mortem tissue [CGND-HRA-02029]


title: post-mortem tissue [CGND-HRA-01839]


title: post-mortem tissue [CGND-HRA-01837]


title: post-mortem tissue [CGND-HRA-01939]


title: post-mortem tissue [CGND-HRA-01938]


title: post-mortem tissue [CGND-HRA-01848]


title: post-mortem tissue [CGND-HRA-01836]


title: post-mortem tissue [CGND-HRA-02028]


title: post-mortem tissue [CGND-HRA-02027]


title: post-mortem tissue [CGND-HRA-01835]


title: post-mortem tissue [CGND-HRA-01838]


title: post-mortem tissue [CGND-HRA-01870]


title: post-mortem tissue [CGND-HRA-01834]


title: post-mortem tissue [CGND-HRA-01833]


title: post-mortem tissue [CGND-HRA-01832]


title: post-mortem tissue [CGND-HRA-01831]

value: ALS Spectrum MND, Other Neurological Disorders


title: post-mortem tissue [CGND-HRA-01942]


title: post-mortem tissue [CGND-HRA-01934]


title: post-mortem tissue [CGND-HRA-01850]


title: post-mortem tissue [CGND-HRA-01830]


title: post-mortem tissue [CGND-HRA-01827]


title: post-mortem tissue [CGND-HRA-01825]


title: post-mortem tissue [CGND-HRA-01829]


title: post-mortem tissue [CGND-HRA-01824]


title: post-mortem tissue [CGND-HRA-01826]


title: post-mortem tissue [CGND-HRA-01823]


title: post-mortem tissue [CGND-HRA-01849]


title: post-mortem tissue [CGND-HRA-01818]


title: post-mortem tissue [CGND-HRA-01822]


title: post-mortem tissue [CGND-HRA-01817]


title: post-mortem tissue [CGND-HRA-01820]


title: post-mortem tissue [CGND-HRA-01819]


title: post-mortem tissue [CGND-HRA-01821]


title: post-mortem tissue [CGND-HRA-01815]


title: post-mortem tissue [CGND-HRA-01813]


title: post-mortem tissue [CGND-HRA-01812]


title: post-mortem tissue [CGND-HRA-01799]


title: post-mortem tissue [CGND-HRA-01811]


title: post-mortem tissue [CGND-HRA-01798]


title: post-mortem tissue [CGND-HRA-01810]


title: post-mortem tissue [CGND-HRA-01797]


title: post-mortem tissue [CGND-HRA-01795]


title: post-mortem tissue [CGND-HRA-01796]


title: post-mortem tissue [CGND-HRA-01794]


title: post-mortem tissue [CGND-HRA-01793]


title: post-mortem tissue [CGND-HRA-01828]


title: post-mortem tissue [CGND-HRA-01792]


title: post-mortem tissue [CGND-HRA-01791]


title: post-mortem tissue [CGND-HRA-02058]


title: post-mortem tissue [CGND-HRA-02040]


title: post-mortem tissue [CGND-HRA-02042]


title: post-mortem tissue [CGND-HRA-02026]


title: post-mortem tissue [CGND-HRA-02041]


title: post-mortem tissue [CGND-HRA-01816]


title: post-mortem tissue [CGND-HRA-01814]


title: post-mortem tissue [CGND-HRA-02025]


title: post-mortem tissue [CGND-HRA-02075]


title: post-mortem tissue [CGND-HRA-02017]


title: post-mortem tissue [CGND-HRA-02009]


title: post-mortem tissue [CGND-HRA-02012]


title: post-mortem tissue [CGND-HRA-02023]


title: post-mortem tissue [CGND-HRA-02007]


title: post-mortem tissue [CGND-HRA-02024]


title: post-mortem tissue [CGND-HRA-02022]


title: post-mortem tissue [CGND-HRA-02010]


title: post-mortem tissue [CGND-HRA-02005]


title: post-mortem tissue [CGND-HRA-02016]


title: post-mortem tissue [CGND-HRA-02018]


title: post-mortem tissue [CGND-HRA-02006]


title: post-mortem tissue [CGND-HRA-02001]


title: post-mortem tissue [CGND-HRA-02008]


title: post-mortem tissue [CGND-HRA-02000]


title: post-mortem tissue [CGND-HRA-02003]


title: post-mortem tissue [CGND-HRA-01999]


title: post-mortem tissue [CGND-HRA-01996]


title: post-mortem tissue [CGND-HRA-01998]


title: post-mortem tissue [CGND-HRA-01997]


title: post-mortem tissue [CGND-HRA-01993]


title: post-mortem tissue [CGND-HRA-01991]


title: post-mortem tissue [CGND-HRA-01990]


title: post-mortem tissue [CGND-HRA-01988]


title: post-mortem tissue [CGND-HRA-01987]


title: post-mortem tissue [CGND-HRA-01929]


title: post-mortem tissue [CGND-HRA-01933]


title: post-mortem tissue [CGND-HRA-01931]


title: post-mortem tissue [CGND-HRA-01932]


title: post-mortem tissue [CGND-HRA-01924]


title: post-mortem tissue [CGND-HRA-01925]


title: post-mortem tissue [CGND-HRA-01923]


title: post-mortem tissue [CGND-HRA-01805]


title: post-mortem tissue [CGND-HRA-01928]


title: post-mortem tissue [CGND-HRA-01807]


title: post-mortem tissue [CGND-HRA-01800]


title: post-mortem tissue [CGND-HRA-01801]


title: post-mortem tissue [CGND-HRA-01808]


title: post-mortem tissue [CGND-HRA-01809]


title: post-mortem tissue [CGND-HRA-01802]


title: post-mortem tissue [CGND-HRA-01790]


title: post-mortem tissue [CGND-HRA-01806]


title: post-mortem tissue [CGND-HRA-01926]


title: post-mortem tissue [CGND-HRA-01803]


title: post-mortem tissue [CGND-HRA-01788]


title: post-mortem tissue [CGND-HRA-01787]


title: post-mortem tissue [CGND-HRA-01785]


title: post-mortem tissue [CGND-HRA-01789]


title: post-mortem tissue [CGND-HRA-01989]


title: post-mortem tissue [CGND-HRA-01992]


title: post-mortem tissue [CGND-HRA-01783]


title: post-mortem tissue [CGND-HRA-01784]


title: post-mortem tissue [CGND-HRA-01782]


title: post-mortem tissue [CGND-HRA-01779]


title: post-mortem tissue [CGND-HRA-01804]


title: post-mortem tissue [CGND-HRA-01780]


title: post-mortem tissue [CGND-HRA-01786]


title: post-mortem tissue [CGND-HRA-01777]


title: post-mortem tissue [CGND-HRA-01778]


title: post-mortem tissue [CGND-HRA-01771]


title: post-mortem tissue [CGND-HRA-01775]


title: post-mortem tissue [CGND-HRA-01776]


title: post-mortem tissue [CGND-HRA-01772]


title: post-mortem tissue [CGND-HRA-01773]


title: post-mortem tissue [CGND-HRA-01769]


title: post-mortem tissue [CGND-HRA-01774]


title: post-mortem tissue [CGND-HRA-01765]


title: post-mortem tissue [CGND-HRA-01762]


title: post-mortem tissue [CGND-HRA-01770]


title: post-mortem tissue [CGND-HRA-01764]


title: post-mortem tissue [CGND-HRA-01758]


title: post-mortem tissue [CGND-HRA-01756]


title: post-mortem tissue [CGND-HRA-01755]


title: post-mortem tissue [CGND-HRA-01760]


title: post-mortem tissue [CGND-HRA-01763]


title: post-mortem tissue [CGND-HRA-01754]


title: post-mortem tissue [CGND-HRA-01781]


title: post-mortem tissue [CGND-HRA-01757]


title: post-mortem tissue [CGND-HRA-01759]


title: post-mortem tissue [CGND-HRA-01752]


title: post-mortem tissue [CGND-HRA-01753]


title: post-mortem tissue [CGND-HRA-01751]


title: post-mortem tissue [CGND-HRA-01750]


title: post-mortem tissue [CGND-HRA-01747]


title: post-mortem tissue [CGND-HRA-01766]


title: post-mortem tissue [CGND-HRA-01749]


title: post-mortem tissue [CGND-HRA-01748]


title: post-mortem tissue [CGND-HRA-01746]


title: post-mortem tissue [CGND-HRA-01744]


title: post-mortem tissue [CGND-HRA-01743]


title: post-mortem tissue [CGND-HRA-01738]


title: post-mortem tissue [CGND-HRA-01740]


title: post-mortem tissue [CGND-HRA-01761]


title: post-mortem tissue [CGND-HRA-01737]


title: post-mortem tissue [CGND-HRA-01742]


title: post-mortem tissue [CGND-HRA-01739]


title: post-mortem tissue [CGND-HRA-01736]


title: post-mortem tissue [CGND-HRA-01734]


title: post-mortem tissue [CGND-HRA-01733]


title: post-mortem tissue [CGND-HRA-01735]


title: post-mortem tissue [CGND-HRA-01732]


title: post-mortem tissue [CGND-HRA-01729]


title: post-mortem tissue [CGND-HRA-01731]


title: post-mortem tissue [CGND-HRA-01727]


title: post-mortem tissue [CGND-HRA-01726]


title: post-mortem tissue [CGND-HRA-01728]


title: post-mortem tissue [CGND-HRA-01730]


title: post-mortem tissue [CGND-HRA-01725]


title: post-mortem tissue [CGND-HRA-01721]


title: post-mortem tissue [CGND-HRA-01741]


title: post-mortem tissue [CGND-HRA-01722]


title: post-mortem tissue [CGND-HRA-01723]


title: post-mortem tissue [CGND-HRA-01717]


title: post-mortem tissue [CGND-HRA-01724]


title: post-mortem tissue [CGND-HRA-01719]


title: post-mortem tissue [CGND-HRA-01718]


title: post-mortem tissue [CGND-HRA-01716]


title: post-mortem tissue [CGND-HRA-01714]


title: post-mortem tissue [CGND-HRA-01713]


title: post-mortem tissue [CGND-HRA-01712]


title: post-mortem tissue [CGND-HRA-01711]


title: post-mortem tissue [CGND-HRA-01708]


title: post-mortem tissue [CGND-HRA-01705]


title: post-mortem tissue [CGND-HRA-01706]


title: post-mortem tissue [CGND-HRA-01710]


title: post-mortem tissue [CGND-HRA-01704]


title: post-mortem tissue [CGND-HRA-01703]


title: post-mortem tissue [CGND-HRA-01701]


title: post-mortem tissue [CGND-HRA-01700]


title: post-mortem tissue [CGND-HRA-01720]


title: post-mortem tissue [CGND-HRA-01699]


title: post-mortem tissue [CGND-HRA-01697]


title: post-mortem tissue [CGND-HRA-01715]


title: post-mortem tissue [CGND-HRA-01696]


title: post-mortem tissue [CGND-HRA-01695]


title: post-mortem tissue [CGND-HRA-01694]


title: post-mortem tissue [CGND-HRA-01687]


title: post-mortem tissue [CGND-HRA-01691]


title: post-mortem tissue [CGND-HRA-01709]


title: post-mortem tissue [CGND-HRA-01692]


title: post-mortem tissue [CGND-HRA-01690]


title: post-mortem tissue [CGND-HRA-01689]


title: post-mortem tissue [CGND-HRA-01686]


title: post-mortem tissue [CGND-HRA-01685]


title: post-mortem tissue [CGND-HRA-01707]


title: post-mortem tissue [CGND-HRA-01684]


title: post-mortem tissue [CGND-HRA-01683]


title: post-mortem tissue [CGND-HRA-01682]


title: post-mortem tissue [CGND-HRA-01688]


title: post-mortem tissue [CGND-HRA-01680]


title: post-mortem tissue [CGND-HRA-01679]


title: post-mortem tissue [CGND-HRA-01702]


title: post-mortem tissue [CGND-HRA-01698]


title: post-mortem tissue [CGND-HRA-01676]


title: post-mortem tissue [CGND-HRA-01674]


title: post-mortem tissue [CGND-HRA-01673]


title: post-mortem tissue [CGND-HRA-01675]


title: post-mortem tissue [CGND-HRA-01693]


title: post-mortem tissue [CGND-HRA-01671]


title: post-mortem tissue [CGND-HRA-01670]


title: post-mortem tissue [CGND-HRA-01667]


title: post-mortem tissue [CGND-HRA-01669]


title: post-mortem tissue [CGND-HRA-01668]


title: post-mortem tissue [CGND-HRA-01672]


title: post-mortem tissue [CGND-HRA-01664]


title: post-mortem tissue [CGND-HRA-01665]


title: post-mortem tissue [CGND-HRA-01681]


title: post-mortem tissue [CGND-HRA-01368-2]

value: Target ALS PM core


title: post-mortem tissue [CGND-HRA-01666]

value: NYGC ALS Consortium


title: post-mortem tissue [CGND-HRA-00749]


title: post-mortem tissue [CGND-HRA-01678]

value: Cortex Frontal


title: post-mortem tissue [CGND-HRA-01663]


title: post-mortem tissue [CGND-HRA-01347]


title: post-mortem tissue [CGND-HRA-01346]

source_name: Spinal Cord Thoracic

value: Spinal Cord Thoracic


title: post-mortem tissue [CGND-HRA-01351-2]

value: Automated KAPA Total


title: post-mortem tissue [CGND-HRA-01301]

value: Cortex Occipital


title: post-mortem tissue [CGND-HRA-00747]

value: ALS Spectrum MND


title: post-mortem tissue [CGND-HRA-01288-2-N]


title: post-mortem tissue [CGND-HRA-00683]


title: post-mortem tissue [CGND-HRA-00748]


title: post-mortem tissue [CGND-HRA-00679]


title: post-mortem tissue [CGND-HRA-00677]


title: post-mortem tissue [CGND-HRA-00630]


title: post-mortem tissue [CGND-HRA-00646]


title: post-mortem tissue [CGND-HRA-00678]


title: post-mortem tissue [CGND-HRA-00629]


title: post-mortem tissue [CGND-HRA-00682]


title: post-mortem tissue [CGND-HRA-00628]


title: post-mortem tissue [CGND-HRA-00627]


title: post-mortem tissue [CGND-HRA-00647]


title: post-mortem tissue [CGND-HRA-00591-2]


title: post-mortem tissue [CGND-HRA-00490]


title: post-mortem tissue [CGND-HRA-00489]


title: post-mortem tissue [CGND-HRA-00488]


title: post-mortem tissue [CGND-HRA-00485]


title: post-mortem tissue [CGND-HRA-00484]


title: post-mortem tissue [CGND-HRA-00483]


title: post-mortem tissue [CGND-HRA-00482]


title: post-mortem tissue [CGND-HRA-00468]


title: post-mortem tissue [CGND-HRA-00475]

value: Cerebellum


title: post-mortem tissue [CGND-HRA-00464]


title: post-mortem tissue [CGND-HRA-00477]

value: Cortex Motor Medial


title: post-mortem tissue [CGND-HRA-00462]


title: post-mortem tissue [CGND-HRA-00474]


title: post-mortem tissue [CGND-HRA-00467]

value: Non-Neurological Control


title: post-mortem tissue [CGND-HRA-00478]

value: Cortex Motor Lateral


title: post-mortem tissue [CGND-HRA-00461]


title: post-mortem tissue [CGND-HRA-00463]

value: Spinal Cord Cervical


title: post-mortem tissue [CGND-HRA-00278-2]


title: post-mortem tissue [CGND-HRA-00147]


title: post-mortem tissue [CGND-HRA-00290]


title: post-mortem tissue [CGND-HRA-00257-2]


title: post-mortem tissue [CGND-HRA-00174]


title: post-mortem tissue [CGND-HRA-00146]


title: post-mortem tissue [CGND-HRA-00141]


title: post-mortem tissue [CGND-HRA-00130]


title: post-mortem tissue [CGND-HRA-00131]


title: post-mortem tissue [CGND-HRA-00132]


title: post-mortem tissue [CGND-HRA-00140]

value: Other MND


title: post-mortem tissue [CGND-HRA-00142]


title: post-mortem tissue [CGND-HRA-00125]


title: post-mortem tissue [CGND-HRA-00115]


title: post-mortem tissue [CGND-HRA-00097]

source_name: Cortex Sensory

value: Cortex Sensory


title: post-mortem tissue [CGND-HRA-01172]


title: post-mortem tissue [CGND-HRA-00473]


title: post-mortem tissue [CGND-HRA-01171]

source_name: Cortex Temporal

value: Cortex Temporal


title: post-mortem tissue [CGND-HRA-01165]


title: post-mortem tissue [CGND-HRA-01170]


title: post-mortem tissue [CGND-HRA-01162]


title: post-mortem tissue [CGND-HRA-01159]


title: post-mortem tissue [CGND-HRA-01164]


title: post-mortem tissue [CGND-HRA-01160]


title: post-mortem tissue [CGND-HRA-01157]


title: post-mortem tissue [CGND-HRA-01163]


title: post-mortem tissue [CGND-HRA-01167]


title: post-mortem tissue [CGND-HRA-01158]


title: post-mortem tissue [CGND-HRA-01156]


title: post-mortem tissue [CGND-HRA-01155]


title: post-mortem tissue [CGND-HRA-01149]


title: post-mortem tissue [CGND-HRA-01151]


title: post-mortem tissue [CGND-HRA-01154]


title: post-mortem tissue [CGND-HRA-01150]


title: post-mortem tissue [CGND-HRA-01153]


title: post-mortem tissue [CGND-HRA-01146]


title: post-mortem tissue [CGND-HRA-01143]

value: Other Neurological Disorders


title: post-mortem tissue [CGND-HRA-01147]


title: post-mortem tissue [CGND-HRA-01142]


title: post-mortem tissue [CGND-HRA-01139]


title: post-mortem tissue [CGND-HRA-01140]


title: post-mortem tissue [CGND-HRA-01141]


title: post-mortem tissue [CGND-HRA-01145]


title: post-mortem tissue [CGND-HRA-01138]


title: post-mortem tissue [CGND-HRA-01137]


title: post-mortem tissue [CGND-HRA-01161]


title: post-mortem tissue [CGND-HRA-01134]


title: post-mortem tissue [CGND-HRA-01133]


title: post-mortem tissue [CGND-HRA-01128]


title: post-mortem tissue [CGND-HRA-01129]


title: post-mortem tissue [CGND-HRA-01127]


title: post-mortem tissue [CGND-HRA-01131]


title: post-mortem tissue [CGND-HRA-01124]


title: post-mortem tissue [CGND-HRA-01130]


title: post-mortem tissue [CGND-HRA-01123]


title: post-mortem tissue [CGND-HRA-01121]


title: post-mortem tissue [CGND-HRA-01119]


title: post-mortem tissue [CGND-HRA-01117]


title: post-mortem tissue [CGND-HRA-01118]


title: post-mortem tissue [CGND-HRA-01112]


title: post-mortem tissue [CGND-HRA-01111]


title: post-mortem tissue [CGND-HRA-01106]

value: Pre-fALS


title: post-mortem tissue [CGND-HRA-01168]


title: post-mortem tissue [CGND-HRA-01105]


title: post-mortem tissue [CGND-HRA-01108]


title: post-mortem tissue [CGND-HRA-01136]


title: post-mortem tissue [CGND-HRA-01107]


title: post-mortem tissue [CGND-HRA-01132]


title: post-mortem tissue [CGND-HRA-01102]


title: post-mortem tissue [CGND-HRA-01103]


title: post-mortem tissue [CGND-HRA-01101]


title: post-mortem tissue [CGND-HRA-01126]


title: post-mortem tissue [CGND-HRA-01100]


title: post-mortem tissue [CGND-HRA-01097]


title: post-mortem tissue [CGND-HRA-01099]


title: post-mortem tissue [CGND-HRA-01125]


title: post-mortem tissue [CGND-HRA-01122]


title: post-mortem tissue [CGND-HRA-01098]


title: post-mortem tissue [CGND-HRA-01120]


title: post-mortem tissue [CGND-HRA-01113]


title: post-mortem tissue [CGND-HRA-01095]


title: post-mortem tissue [CGND-HRA-01092]


title: post-mortem tissue [CGND-HRA-01093]


title: post-mortem tissue [CGND-HRA-01110]


title: post-mortem tissue [CGND-HRA-01094]


title: post-mortem tissue [CGND-HRA-01090]


title: post-mortem tissue [CGND-HRA-01086]


title: post-mortem tissue [CGND-HRA-01085]


title: post-mortem tissue [CGND-HRA-01091]


title: post-mortem tissue [CGND-HRA-01089]


title: post-mortem tissue [CGND-HRA-01079]


title: post-mortem tissue [CGND-HRA-01078]


title: post-mortem tissue [CGND-HRA-01074]


title: post-mortem tissue [CGND-HRA-01084]


title: post-mortem tissue [CGND-HRA-01073]


title: post-mortem tissue [CGND-HRA-01075]


title: post-mortem tissue [CGND-HRA-01080]


title: post-mortem tissue [CGND-HRA-01069]


title: post-mortem tissue [CGND-HRA-01072]


title: post-mortem tissue [CGND-HRA-01070]


title: post-mortem tissue [CGND-HRA-01067]


title: post-mortem tissue [CGND-HRA-01071]


title: post-mortem tissue [CGND-HRA-01096]


title: post-mortem tissue [CGND-HRA-01065]


title: post-mortem tissue [CGND-HRA-01077]


title: post-mortem tissue [CGND-HRA-01066]


title: post-mortem tissue [CGND-HRA-01063]


title: post-mortem tissue [CGND-HRA-01062]


title: post-mortem tissue [CGND-HRA-01061]


title: post-mortem tissue [CGND-HRA-01059]


title: post-mortem tissue [CGND-HRA-01056]


title: post-mortem tissue [CGND-HRA-01076]


title: post-mortem tissue [CGND-HRA-01064]


title: post-mortem tissue [CGND-HRA-01060]


title: post-mortem tissue [CGND-HRA-01053]


title: post-mortem tissue [CGND-HRA-01052]


title: post-mortem tissue [CGND-HRA-01068]


title: post-mortem tissue [CGND-HRA-01051]


title: post-mortem tissue [CGND-HRA-01047]


title: post-mortem tissue [CGND-HRA-01049]


title: post-mortem tissue [CGND-HRA-01048]


title: post-mortem tissue [CGND-HRA-01058]


title: post-mortem tissue [CGND-HRA-01046]


title: post-mortem tissue [CGND-HRA-01054]


title: post-mortem tissue [CGND-HRA-01037]


title: post-mortem tissue [CGND-HRA-01039]


title: post-mortem tissue [CGND-HRA-01038]


title: post-mortem tissue [CGND-HRA-01040]


title: post-mortem tissue [CGND-HRA-01050]


title: post-mortem tissue [CGND-HRA-01057]


title: post-mortem tissue [CGND-HRA-01036]


title: post-mortem tissue [CGND-HRA-01055]


title: post-mortem tissue [CGND-HRA-01033]


title: post-mortem tissue [CGND-HRA-01032]


title: post-mortem tissue [CGND-HRA-01035]


title: post-mortem tissue [CGND-HRA-01030]


title: post-mortem tissue [CGND-HRA-01031]


title: post-mortem tissue [CGND-HRA-01029]


title: post-mortem tissue [CGND-HRA-01024]


title: post-mortem tissue [CGND-HRA-01026]


title: post-mortem tissue [CGND-HRA-01023]


title: post-mortem tissue [CGND-HRA-01022]


title: post-mortem tissue [CGND-HRA-01027]


title: post-mortem tissue [CGND-HRA-01017]


title: post-mortem tissue [CGND-HRA-01021]


title: post-mortem tissue [CGND-HRA-01014]


title: post-mortem tissue [CGND-HRA-01018]


title: post-mortem tissue [CGND-HRA-01016]


title: post-mortem tissue [CGND-HRA-01019]


title: post-mortem tissue [CGND-HRA-01015]


title: post-mortem tissue [CGND-HRA-01013]


title: post-mortem tissue [CGND-HRA-01045]


title: post-mortem tissue [CGND-HRA-01043]


title: post-mortem tissue [CGND-HRA-01028]


title: post-mortem tissue [CGND-HRA-01034]


title: post-mortem tissue [CGND-HRA-01042]


title: post-mortem tissue [CGND-HRA-01041]


title: post-mortem tissue [CGND-HRA-01025]


title: post-mortem tissue [CGND-HRA-01020]


title: post-mortem tissue [CGND-HRA-01011]


title: post-mortem tissue [CGND-HRA-01010]


title: post-mortem tissue [CGND-HRA-01009]


title: post-mortem tissue [CGND-HRA-01007]


title: post-mortem tissue [CGND-HRA-01005]


title: post-mortem tissue [CGND-HRA-01001]


title: post-mortem tissue [CGND-HRA-01008]


title: post-mortem tissue [CGND-HRA-00999]


title: post-mortem tissue [CGND-HRA-01000]


title: post-mortem tissue [CGND-HRA-01003]


title: post-mortem tissue [CGND-HRA-00993]


title: post-mortem tissue [CGND-HRA-00994]


title: post-mortem tissue [CGND-HRA-00996]


title: post-mortem tissue [CGND-HRA-01004]


title: post-mortem tissue [CGND-HRA-00992]

value: Spinal Cord Lumbar


title: post-mortem tissue [CGND-HRA-00990]

value: NYGC ALS Consortium


title: post-mortem tissue [CGND-HRA-00988]


title: post-mortem tissue [CGND-HRA-00998]

value: Cortex Frontal


title: post-mortem tissue [CGND-HRA-00986]


title: post-mortem tissue [CGND-HRA-00985]


title: post-mortem tissue [CGND-HRA-00980]


title: post-mortem tissue [CGND-HRA-00982]


title: post-mortem tissue [CGND-HRA-00983]


title: post-mortem tissue [CGND-HRA-00981]


title: post-mortem tissue [CGND-HRA-00979]


title: post-mortem tissue [CGND-HRA-00978]


title: post-mortem tissue [CGND-HRA-00976]


title: post-mortem tissue [CGND-HRA-00973]


title: post-mortem tissue [CGND-HRA-00975]


title: post-mortem tissue [CGND-HRA-00971]


title: post-mortem tissue [CGND-HRA-00997]


title: post-mortem tissue [CGND-HRA-00972]


title: post-mortem tissue [CGND-HRA-00969]


title: post-mortem tissue [CGND-HRA-00970]


title: post-mortem tissue [CGND-HRA-00968]


title: post-mortem tissue [CGND-HRA-00967]


title: post-mortem tissue [CGND-HRA-00965]


title: post-mortem tissue [CGND-HRA-00964]


title: post-mortem tissue [CGND-HRA-00962]


title: post-mortem tissue [CGND-HRA-00963]


title: post-mortem tissue [CGND-HRA-00966]


title: post-mortem tissue [CGND-HRA-00961]


title: post-mortem tissue [CGND-HRA-00960]


title: post-mortem tissue [CGND-HRA-01044]


title: post-mortem tissue [CGND-HRA-00987]


title: post-mortem tissue [CGND-HRA-00959]


title: post-mortem tissue [CGND-HRA-00957]


title: post-mortem tissue [CGND-HRA-00953]


title: post-mortem tissue [CGND-HRA-00955]


title: post-mortem tissue [CGND-HRA-00954]


title: post-mortem tissue [CGND-HRA-00951]


title: post-mortem tissue [CGND-HRA-00956]


title: post-mortem tissue [CGND-HRA-00949]


title: post-mortem tissue [CGND-HRA-00950]


title: post-mortem tissue [CGND-HRA-00974]


title: post-mortem tissue [CGND-HRA-00948]


title: post-mortem tissue [CGND-HRA-00943]


title: post-mortem tissue [CGND-HRA-00946]


title: post-mortem tissue [CGND-HRA-00947]


title: post-mortem tissue [CGND-HRA-00944]


title: post-mortem tissue [CGND-HRA-00942]


title: post-mortem tissue [CGND-HRA-00945]


title: post-mortem tissue [CGND-HRA-00937]


title: post-mortem tissue [CGND-HRA-00939]


title: post-mortem tissue [CGND-HRA-00934]


title: post-mortem tissue [CGND-HRA-00940]


title: post-mortem tissue [CGND-HRA-00932]


title: post-mortem tissue [CGND-HRA-00938]


title: post-mortem tissue [CGND-HRA-00933]


title: post-mortem tissue [CGND-HRA-00931]


title: post-mortem tissue [CGND-HRA-00958]


title: post-mortem tissue [CGND-HRA-00930]


title: post-mortem tissue [CGND-HRA-00923]


title: post-mortem tissue [CGND-HRA-00920]


title: post-mortem tissue [CGND-HRA-00918]


title: post-mortem tissue [CGND-HRA-00919]


title: post-mortem tissue [CGND-HRA-00921]


title: post-mortem tissue [CGND-HRA-00917]


title: post-mortem tissue [CGND-HRA-00915]


title: post-mortem tissue [CGND-HRA-00916]


title: post-mortem tissue [CGND-HRA-01012]


title: post-mortem tissue [CGND-HRA-00911]


title: post-mortem tissue [CGND-HRA-00941]


title: post-mortem tissue [CGND-HRA-00913]


title: post-mortem tissue [CGND-HRA-00910]


title: post-mortem tissue [CGND-HRA-00912]


title: post-mortem tissue [CGND-HRA-00936]


title: post-mortem tissue [CGND-HRA-00914]


title: post-mortem tissue [CGND-HRA-00905]


title: post-mortem tissue [CGND-HRA-00924]


title: post-mortem tissue [CGND-HRA-00909]


title: post-mortem tissue [CGND-HRA-00907]


title: post-mortem tissue [CGND-HRA-00901]


title: post-mortem tissue [CGND-HRA-00906]


title: post-mortem tissue [CGND-HRA-00904]


title: post-mortem tissue [CGND-HRA-00903]


title: post-mortem tissue [CGND-HRA-00898]


title: post-mortem tissue [CGND-HRA-00897]


title: post-mortem tissue [CGND-HRA-00896]


title: post-mortem tissue [CGND-HRA-00895]

value: ALS Spectrum MND, Other Neurological Disorders


title: post-mortem tissue [CGND-HRA-00893]

value: Automated KAPA Total


title: post-mortem tissue [CGND-HRA-00891]


title: post-mortem tissue [CGND-HRA-00894]


title: post-mortem tissue [CGND-HRA-00892]


title: post-mortem tissue [CGND-HRA-01605]


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title: post-mortem tissue [CGND-HRA-00885]


title: post-mortem tissue [CGND-HRA-00900]


title: post-mortem tissue [CGND-HRA-00882]


title: post-mortem tissue [CGND-HRA-00881]


title: post-mortem tissue [CGND-HRA-00870]


title: post-mortem tissue [CGND-HRA-00877]


title: post-mortem tissue [CGND-HRA-00869]


title: post-mortem tissue [CGND-HRA-00879]


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title: post-mortem tissue [CGND-HRA-00884]


title: post-mortem tissue [CGND-HRA-00878]


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title: post-mortem tissue [CGND-HRA-00876]


title: post-mortem tissue [CGND-HRA-01604]


title: post-mortem tissue [CGND-HRA-00865]


title: post-mortem tissue [CGND-HRA-00864]


title: post-mortem tissue [CGND-HRA-00855]


title: post-mortem tissue [CGND-HRA-00863]


title: post-mortem tissue [CGND-HRA-00857]


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title: post-mortem tissue [CGND-HRA-00838]


title: post-mortem tissue [CGND-HRA-00839]


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title: post-mortem tissue [CGND-HRA-00835]


title: post-mortem tissue [CGND-HRA-00845]


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title: post-mortem tissue [CGND-HRA-00836]


title: post-mortem tissue [CGND-HRA-00866]


title: post-mortem tissue [CGND-HRA-00832]


title: post-mortem tissue [CGND-HRA-00842]


title: post-mortem tissue [CGND-HRA-00853]


title: post-mortem tissue [CGND-HRA-00851]


title: post-mortem tissue [CGND-HRA-00830]


title: post-mortem tissue [CGND-HRA-00829]


title: post-mortem tissue [CGND-HRA-00828]


title: post-mortem tissue [CGND-HRA-00825]


title: post-mortem tissue [CGND-HRA-00827]


title: post-mortem tissue [CGND-HRA-00819]


title: post-mortem tissue [CGND-HRA-00823]


title: post-mortem tissue [CGND-HRA-00822]


title: post-mortem tissue [CGND-HRA-00821]


title: post-mortem tissue [CGND-HRA-00818]


title: post-mortem tissue [CGND-HRA-00813]


title: post-mortem tissue [CGND-HRA-00815]


title: post-mortem tissue [CGND-HRA-00824]


title: post-mortem tissue [CGND-HRA-00812]


title: post-mortem tissue [CGND-HRA-00820]


title: post-mortem tissue [CGND-HRA-00814]


title: post-mortem tissue [CGND-HRA-00810]


title: post-mortem tissue [CGND-HRA-00809]


title: post-mortem tissue [CGND-HRA-00811]


title: post-mortem tissue [CGND-HRA-00817]


title: post-mortem tissue [CGND-HRA-00805]


title: post-mortem tissue [CGND-HRA-00806]


title: post-mortem tissue [CGND-HRA-00816]


title: post-mortem tissue [CGND-HRA-00804]


title: post-mortem tissue [CGND-HRA-00807]


title: post-mortem tissue [CGND-HRA-00803]


title: post-mortem tissue [CGND-HRA-00802]


title: post-mortem tissue [CGND-HRA-00826]


title: post-mortem tissue [CGND-HRA-00782]


title: post-mortem tissue [CGND-HRA-00779]


title: post-mortem tissue [CGND-HRA-00781]


title: post-mortem tissue [CGND-HRA-00808]


title: post-mortem tissue [CGND-HRA-00772]


title: post-mortem tissue [CGND-HRA-00771]


title: post-mortem tissue [CGND-HRA-00770]


title: post-mortem tissue [CGND-HRA-00769]


title: post-mortem tissue [CGND-HRA-00767]


title: S9B_SWOLL

status: Public on Aug 11 2020

type: RNA

city: Stirling

first: James

last: Timmons

address: Bridge of Allan

country: United Kingdom

institute: Augur Precision Medicine LTD

description: In vivo human muscle

hyb_protocol: 5 μg of fragmented, end–labelled sense strand target cDNA was hybridized to each array and scanned using a Gene Chip Scanner 30007G

scan_protocol: standard protocol

data_processing: Custom CDF process as described in Timmons et al Nucleic Acid Research 2018. https://academic.oup.com/nar/article/46/15/7772/5050628

label: biotin

source_name: vastus lateralis

label_protocol: The RNA was processed to single-stranded sense fragmented DNA using the GeneChip® WT PLUS Reagent Kit which relies on a reverse transcription priming strategy that primes both poly-A and non-poly-A RNA

growth_protocol: Human in vivo studies

extract_protocol: Snap_frozen muscle tissue, RNA was isolated using a tissuelyser and TRizol® (Life Technologies) and dissolved in 20 μl RNAse-free water.

treatment_protocol: Various - See https://doi.org/10.1016/j.celrep.2020.107980

value: vastus lateralis

tag: training status

value: POST

tag: age group

value: young adult


title: S9A_SWOLL

description: In vivo human muscle

value: PRE


title: S8B_SWOLL

description: In vivo human muscle


title: Control: uninfected 1

status: Public on Oct 07 2020

city: Edmonton

first: Maya

last: Shmulevitz

state: AB

country: Canada

institute: University of Alberta

description: Gene expression of uninfected cells

hyb_protocol: Hybridization of quantified and amplified RNA were purified and hybridized to Agilent Whole Mouse Genome Microarrays, 8x60K according to manufacturer's protocol. Agilent's SurePrint G3 Mouse GE 8x60K Microarray, (Agilent Microarray Design ID 028005).

scan_protocol: Agilent Scanner, according to the standard protocol of the manufacturer

data_processing: Raw microarray image files were extracted with Agilent’s Gene Expression Microarray Software, GeneSpring GX. Data processing and analysis was done using R.

organism: Mus musculus

source_name: Control: uninfected 1

growth_protocol: DMEM supplemented with 1mM sodium oyruvate and 10% NCS

extract_protocol: RNA was extracted from reovirus infected and mock infected samples and sent for microarray processing at MOgene LC (1005 North Warson Road, Suite 403, St. Louis, MO 63132 USA) using the Agilent Mouse SurePrint G3 GE, 8x60k – 028005 array type.

treatment_protocol: Virus infection at the dose empirically determined to cause 70% reovirus-antigen-positive cells on NIH/3T3 shEMPTY cells by immunofluorescence

tag: cell type

value: Fibroblasts

tag: genotype/variation

value: WT

tag: agent

value: uninfected

tag: cell line

value: NIH 3T3

value: Embryo


title: Control: uninfected 2

description: Gene expression of uninfected cells

source_name: Control: uninfected 2


title: shRIG-I: reo infected

description: Gene expression after 12 hr shRIG-I infection

source_name: shRIG-I: reo infected

value: RIG-I KD

value: reovirus


title: Control: reo infected 1

description: Gene expression after 12 hr reo infection

source_name: Control: reo infected 1


title: S4B_SWOLL

description: In vivo human muscle


title: S47B_SWOLL

description: In vivo human muscle


title: S58B_2_SWOLL

description: In vivo human muscle


title: S49B_SWOLL

description: In vivo human muscle


title: S50B_SWOLL

description: In vivo human muscle


title: Control: reo infected 2

source_name: Control: reo infected 2


title: S57A_2_SWOLL

description: In vivo human muscle


title: S58A_2_SWOLL

description: In vivo human muscle


title: S48A_SWOLL

description: In vivo human muscle


title: S7A_SWOLL

description: In vivo human muscle


title: S52B_2_SWOLL

description: In vivo human muscle


title: S50A_SWOLL

description: In vivo human muscle


title: S59A_2_SWOLL

description: In vivo human muscle


title: S49A_SWOLL

description: In vivo human muscle


title: S4A_SWOLL

description: In vivo human muscle


title: S59B_2_SWOLL

description: In vivo human muscle


title: S7B_SWOLL

description: In vivo human muscle


title: S52A_2_SWOLL

description: In vivo human muscle


title: S51A_2_SWOLL

description: In vivo human muscle


title: S48B_SWOLL

description: In vivo human muscle


title: S8A_SWOLL

description: In vivo human muscle


title: S57B_2_SWOLL

description: In vivo human muscle


title: S47A_SWOLL

description: In vivo human muscle


title: S45A_SWOLL

description: In vivo human muscle


title: S43A_SWOLL

description: In vivo human muscle


title: S51B_2_SWOLL

description: In vivo human muscle


title: S41A_SWOLL

description: In vivo human muscle


title: S43B_SWOLL

description: In vivo human muscle


title: S41B_SWOLL

description: In vivo human muscle


title: S40B_SWOLL

description: In vivo human muscle


title: S39B_SWOLL

description: In vivo human muscle


title: S39A_SWOLL

description: In vivo human muscle


title: S40A_SWOLL

description: In vivo human muscle


title: S35A_SWOLL

description: In vivo human muscle


title: S33A_SWOLL

description: In vivo human muscle


title: S38A_SWOLL

description: In vivo human muscle


title: S32A_SWOLL

description: In vivo human muscle


title: S33B_SWOLL

description: In vivo human muscle


title: S32B_SWOLL

description: In vivo human muscle


title: S38B_SWOLL

description: In vivo human muscle


title: S35B_SWOLL

description: In vivo human muscle


title: S45B_SWOLL

description: In vivo human muscle


title: S31A_SWOLL

description: In vivo human muscle


title: S28B_SWOLL

description: In vivo human muscle


title: S31B_SWOLL

description: In vivo human muscle


title: S28A_SWOLL

description: In vivo human muscle


title: S2A_SWOLL

description: In vivo human muscle


title: S19B_SWOLL

description: In vivo human muscle


title: S23A_2_SWOLL

description: In vivo human muscle


title: S23B_SWOLL

description: In vivo human muscle


title: S17b_SWOLL

description: In vivo human muscle


title: S2B_SWOLL

description: In vivo human muscle


title: S19A_SWOLL

description: In vivo human muscle


title: S18B_SWOLL

description: In vivo human muscle


title: S22B_SWOLL

description: In vivo human muscle


title: S17A_SWOLL

description: In vivo human muscle


title: S16B_SWOLL

description: In vivo human muscle


title: S16A_SWOLL

description: In vivo human muscle


title: S13B_2_SWOLL

description: In vivo human muscle


title: S13A_2_SWOLL

description: In vivo human muscle


title: S18A_SWOLL

description: In vivo human muscle


title: HYPAT2B

description: In vivo human muscle


title: S22A_SWOLL

description: In vivo human muscle


title: HYPAT4B

description: In vivo human muscle


title: HYPAT6B

description: In vivo human muscle


title: S10A_SWOLL

description: In vivo human muscle


title: HYPAT14A

description: In vivo human muscle


title: HYPAT8B

description: In vivo human muscle


title: HYPAT8A

description: In vivo human muscle


title: HYPAT1B

description: In vivo human muscle


title: HYPAT7B

description: In vivo human muscle


title: S10B_SWOLL

description: In vivo human muscle


title: HYPAT11B

description: In vivo human muscle


title: HYPAT9A

description: In vivo human muscle


title: HYPAT4A

description: In vivo human muscle


title: HYPAT7A

description: In vivo human muscle


title: HYPAT9B

description: In vivo human muscle


title: HYPAT2A

description: In vivo human muscle


title: HYPAT13A

description: In vivo human muscle


title: HYPAT14B

description: In vivo human muscle


title: HYPAT6A

description: In vivo human muscle


title: A584_post

description: In vivo human muscle


title: young LT-HSCs rep 3

status: Public on Jul 01 2020

city: Bar Harbor

first: Jennifer

last: Trowbridge

state: ME

address: 600 Main Street

institute: The Jackson Laboratory

data_processing:
Trimmed alignment files (with trimmed base quality value < 30, and 70% of read bases surpassing that threshold) were processed using the RSEM (v1.2.12; RNA-Seq by Expectation-Maximization) software and the Mus musculus reference GRCm38. This software estimates gene (and isoform) expression levels from RNA-Seq data with a statistical model that considers reads that map to multiple positions. Alignment was completed using Bowtie 2 (v2.2.0) and processed using SAMtools (v0.1.18). Fragment length mean was set to 280 and standard deviation to 50.
Expected read counts per gene produced by RSEM were rounded to integer values, filtered to include only genes that have at least one sample within a sample group having a cpm > 1.0, and were passed to edgeR (v3.5.3) for differential expression analysis.
Negative binomial conditional common likelihood was maximized to estimate a common dispersion value across all genes. Exact tests were used to elucidate statistical differences between the two sample groups of negative binomially distributed counts producing p-values per test.
The Benjamini and Hochberg’s algorithm (p-value adjustment) was used to control the false discovery rate (FDR). Features with an FDR-adjusted p-value < 0.05 were declared significantly differentially expressed.
Genome_build: mm10
Supplementary_files_format_and_content: Gene counts produced by RSEM (v1.2.12) for each sample stored in tab-delimited, text format

molecule: polyA RNA

source_name: bone marrow

extract_protocol:
Total RNA was isolated from cells using the RNeasy Micro kit (Qiagen)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: young (2mo), middle age (12mo) and old (22mo) LT-HSCs were isolated from 3 independent replicates of pooled mice for young, and single mice for middle age and old mice.  LT-HSC were sorted directly into RLT buffer

tag: strain

value: bone marrow

value: LT-HSC

tag: age

value: young


title: middle-aged LT-HSC rep 1

value: middle-aged


title: old LT-HSCs rep 2

value: old


title: middle-aged LT-HSC rep 2


title: HYPAT12A

description: In vivo human muscle


title: HYPAT11A

description: In vivo human muscle


title: HYPAT1A

description: In vivo human muscle


title: 19B_Post

status: Public on Feb 19 2020

first: Hanseul

last: Yang

address: 1230 York Avenue

institute: Rockefeller University

data_processing:
Alignment: Sequence reads were obtained and mapped to the mouse genome (mm10) using the Bowtie2 program (version 2.2.9).
The expression values of each gene were quantified as transcript per million (TPM) using RSEM (v1.2.30)
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include TPM and FPKM values for each Sample

source_name: Mouse back skin

extract_protocol:
Mouse hair follicle stem cells were purified from Krt14-H2BGFP mice along the hair cycle.
FACS-isolated cells were directly lysed into TRIzol LS (Invitrogen). Total RNA was purified using the Direct-zol RNA MiniPrep kit (Zymo Research) per manufacturer’s instructions. Quality of the RNA for sequencing was determined using an Agilent 2100 Bioanalyzer; all samples used had RNA integrity numbers >8. Library preparation using the Illumina TrueSeq mRNA sample preparation kit was performed at the Weill Cornell Medical College Genomic Core facility (New York), and RNAs were paired-end sequenced on Illumina HiSeq 4000 machines.

tag: Sex

value: pooled male and female

tag: genotype

value: transgenic for Krt14-H2B-GFP

value: back skin

tag: tissue location

value: posterior

value: hair follicle stem cells

tag: sorting markers

value: EGFP (high), CD45 (neg) CD31 (neg) CD140a (neg), DAPI (ned), Sca-1 (neg), Alfa 6 integrin  (pos) CD34 (pos)


title: middle-aged LT-HSC rep 3

tag: tissue


title: HYPAT10A

description: In vivo human muscle

value: vastus lateralis

value: PRE

value: young adult


title: old LT-HSCs rep 1


title: 19A_Ant

value: anterior


title: HYPAT10B

description: In vivo human muscle

value: POST


title: HYPAT13B

description: In vivo human muscle


title: HYPAT12B

description: In vivo human muscle


title: 23A_Post


title: 23B_post


title: young LT-HSCs rep 1


title: young LT-HSCs rep 2


title: old LT-HSCs rep 3


title: S101_P

status: Public on Nov 18 2019

city: Houston

first: Shervin

last: Assassi

state: TX

address: 6431 FanninSuite 5270

institute: University of Texas Health Science Center at Houston

description:
RNA sequencing
Sample 56

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using tophat v2.1.1 with default parameters
Fragments Per Kilobase of exon per million fragments mapped (FPKM) were calculated using cuffnorm v2.2.1.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: skin biopsy, SSc patient

extract_protocol:
3- or 4-mm diameter punch biopsies were obtained from the forearm skin and immersed in RNAlater solution (Qiagen). RNA was extracted using miRNeasy Mini kits (Qiagen).
cDNA libraries were prepared using the Illumina TruSeq stranded Total RNA Library Prep Gold kit, loaded on cBot (Illumina) at a final concentration of 10 pM to perform cluster generation. 2 x 76 bp paired-end sequencing on HiSeq 2500 (Illumina), generating on average around 50 million reads per sample

value: skin biopsy

tag: diagnosis

value: SSc patient

tag: biopsy number for this subject

tag: sex (0 = female, 1 = male)

tag: race (white = 0, black = 1, asian/asian american = 2, native american = 3, unknown = 4

tag: hispanic latino (no = 0, yes = 1)

tag: local skin score

tag: mrss

tag: fvc %predicted

tag: disease duration (years)


title: S098_N

description:
RNA sequencing
Sample 89

source_name: skin biopsy, healthy control

value: healthy control


title: S104_P

description:
RNA sequencing
Sample 58

tag: autoantibody (neither = 0, topoisomerase i = 1, rna polymerase iii = 2)


title: S102_N

description:
RNA sequencing
Sample 90


title: S099_P

description:
RNA sequencing
Sample 54


title: S103_P

description:
RNA sequencing
Sample 57


title: C459_post

description: In vivo human muscle

tag: training status

tag: age group


title: S096_P

description:
RNA sequencing
Sample 52

tag: age


title: S100_P

description:
RNA sequencing
Sample 55

tag: original biopsy for this patient


title: S097_P

description:
RNA sequencing
Sample 53


title: S105_N

description:
RNA sequencing
Sample 91


title: S091_N

description:
RNA sequencing
Sample 87


title: S093_P

description:
RNA sequencing
Sample 50


title: S094_N

description:
RNA sequencing
Sample 88


title: S092_P

description:
RNA sequencing
Sample 49


title: S095_P

description:
RNA sequencing
Sample 51


title: S087_P

description:
RNA sequencing
Sample 47


title: S085_N

description:
RNA sequencing
Sample 85


title: S084_P

description:
RNA sequencing
Sample 45


title: S086_P

description:
RNA sequencing
Sample 46


title: S089_P

description:
RNA sequencing
Sample 48


title: S083_P

description:
RNA sequencing
Sample 44


title: S080_P

description:
RNA sequencing
Sample 42


title: S079_P

description:
RNA sequencing
Sample 41


title: S082_N

description:
RNA sequencing
Sample 84


title: S076_P

description:
RNA sequencing
Sample 39


title: S078_N

description:
RNA sequencing
Sample 83


title: S075_N

description:
RNA sequencing
Sample 82


title: S073_P

description:
RNA sequencing
Sample 37


title: S072_N

description:
RNA sequencing
Sample 81


title: wild type mouse liver, biological rep1

status: Public on Jan 24 2020

city: Shanghai

first: Jianhui

last: Shi

state: Shanghai

address: Xiangyin road 800

country: China

institute: Navy Medical University

description: 12-week-old mice fed with high sucrose for further 1 week

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mus musculus Genome Array. GeneChips were washed and stained in the Affymetrix Gene Scanner 7G. Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mus musculus Genome Array. GeneChips were washed and stained in the Affymetrix Gene Scanner 7G.

scan_protocol: GeneChips were scanned using the Affymetrix Gcos/Genechip operating software.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: liver

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 8 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Liver-specific Chrebp knockout (ChLO) mice were generated by crossing Chrebpflox mice with albumin-Cre transgenic mice. They were raised at SPF grade animal housing as wild type mice.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: 12 weeks old wild type mice and ChLO mice were fed with 60% sucrose diet for 1 week. Then the mice were sacrificed and livers were harvested and quick frozen in nitrogen. 100mg frozen liver tissues (3 for each group) were  ground and homogenated in the Trizol solution.

tag: gender

value: male

tag: genotype

value: WT

value: liver


title: ChLO mouse liver, biological rep3

value: liver-specific ChREBP knockout

tag: tissue


title: S074_P

description:
RNA sequencing
Sample 38

tag: diagnosis


title: S071_P

description:
RNA sequencing
Sample 36

tag: biopsy number for this subject


title: S069_N

description:
RNA sequencing
Sample 80

tag: sex (0 = female, 1 = male)


title: S070_P

description:
RNA sequencing
Sample 35

tag: race (white = 0, black = 1, asian/asian american = 2, native american = 3, unknown = 4


title: ChLO mouse liver, biological rep1


title: ChLO mouse liver, biological rep2


title: S088_N

description:
RNA sequencing
Sample 86

tag: hispanic latino (no = 0, yes = 1)


title: S067_P

description:
RNA sequencing
Sample 34

tag: local skin score


title: wild type mouse liver, biological rep3


title: S066_N

description:
RNA sequencing
Sample 79


title: wild type mouse liver, biological rep2


title: S065_P

description:
RNA sequencing
Sample 33

tag: mrss


title: S081_P

description:
RNA sequencing
Sample 43

tag: fvc %predicted


title: S061_P

description:
RNA sequencing
Sample 30

tag: disease duration (years)


title: S060_P

description:
RNA sequencing
Sample 29

tag: autoantibody (neither = 0, topoisomerase i = 1, rna polymerase iii = 2)


title: S064_P

description:
RNA sequencing
Sample 32


title: S077_P

description:
RNA sequencing
Sample 40


title: S062_P

description:
RNA sequencing
Sample 31


title: S063_N

description:
RNA sequencing
Sample 78


title: S059_N

description:
RNA sequencing
Sample 77


title: S057_P

description:
RNA sequencing
Sample 27


title: S055_P

description:
RNA sequencing
Sample 26


title: S054_P

description:
RNA sequencing
Sample 25


title: S058_P

description:
RNA sequencing
Sample 28

value: #REF!


title: S056_N

description:
RNA sequencing
Sample 76


title: S050_N

description:
RNA sequencing
Sample 74


title: S040_N

description:
RNA sequencing
Sample 71


title: S053_N

description:
RNA sequencing
Sample 75


title: S044_N

description:
RNA sequencing
Sample 72


title: S041_P

description:
RNA sequencing
Sample 23


title: S047_N

description:
RNA sequencing
Sample 73


title: S039_P

description:
RNA sequencing
Sample 22


title: S036_P

description:
RNA sequencing
Sample 20


title: S037_N

description:
RNA sequencing
Sample 70


title: S035_P

description:
RNA sequencing
Sample 19


title: S034_N

description:
RNA sequencing
Sample 69


title: S031_N

description:
RNA sequencing
Sample 68


title: S038_P

description:
RNA sequencing
Sample 21


title: S033_P

description:
RNA sequencing
Sample 18


title: S032_P

description:
RNA sequencing
Sample 17


title: S026_P

description:
RNA sequencing
Sample 14


title: S025_N

description:
RNA sequencing
Sample 66


title: S023_P

description:
RNA sequencing
Sample 13


title: S027_P

description:
RNA sequencing
Sample 15


title: S029_P

description:
RNA sequencing
Sample 16


title: S022_N

description:
RNA sequencing
Sample 65


title: S019_N

description:
RNA sequencing
Sample 64


title: S049_P

description:
RNA sequencing
Sample 24


title: S016_N

description:
RNA sequencing
Sample 63


title: S021_P

description:
RNA sequencing
Sample 12


title: S015_P

description:
RNA sequencing
Sample 10


title: S020_P

description:
RNA sequencing
Sample 11


title: S013_N

description:
RNA sequencing
Sample 62


title: S012_P

description:
RNA sequencing
Sample 8


title: S009_P

description:
RNA sequencing
Sample 6


title: S010_N

description:
RNA sequencing
Sample 61


title: S011_P

description:
RNA sequencing
Sample 7


title: S006_P

description:
RNA sequencing
Sample 5


title: S007_N

description:
RNA sequencing
Sample 60


title: S005_P

description:
RNA sequencing
Sample 4


title: S001_P

description:
RNA sequencing
Sample 1


title: S028_N

description:
RNA sequencing
Sample 67


title: S003_P

description:
RNA sequencing
Sample 3


title: S002_P

description:
RNA sequencing
Sample 2


title: S014_P

description:
RNA sequencing
Sample 9


title: cellline 48h HOXBAS3-KD rep2

status: Public on Oct 15 2019

city: Columbus

first: Ayse

middle: Selen

last: Yilmaz

state: OH

address: 1800 Cannon Drive

department: Biomedical Informatics

institute: OSU

description:
AltAnalyze_AltResults.xlsx
150720_TRG2K48_V1T_TCTACC_L005_ctab

data_processing:
Alignment with STAR_2.5.2a to Homo_sapiens.GRCh37.75
Alternative Splicing calculated with AltAnalyze version 2.1.2
Genome_build: Homo sapiens GRCh37 and Homo_sapiens.GRCh37.75

extract_protocol:
On average, 20 million leukemic blasts isolated from cryopreserved samples were thawed and subjected to total RNA extraction using the Trizol reagent and previously published protocols.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: For the knock-down (KD) of genes in OCI-AML3 cells and samples from NPM1mut AML patients we used custom-designed locked nuclei acid-modified RNaseH recruiting oligonucleotides (gapmers, Exicon A/S). For the in vitro delivery of the gapmers, the Nucleofector device (Lonza) and the corresponding reagents (Solution T for OCI-AML3 cells and human Monocyte Solution for AML blasts, Lonza) were used according to the instructions of the manufacturer (program X-001 for OCI-AML3 cells and program Y-001 for patient blasts). Anti-HOXB-AS3, anti-NPM1mut or non-targeting control gapmers were delivered at a final concentration of 500 nM.

tag: npm1 status

value: unknown

tag: forced expression

tag: cell line

value: OCI-AML3 cells

tag: timepoint


title: cellline 12h HOXBAS3-KD rep2

description:
AltAnalyze_AltResults.xlsx
150720_TRG2K12_V1T_TCATTC_L005_ctab


title: cellline 48h HOXBAS3-KD rep1

description:
AltAnalyze_AltResults.xlsx
150720_TRG1K48_V1T_TACAGC_L005_ctab


title: cellline 48h HOXBAS3-KD rep3

description:
AltAnalyze_AltResults.xlsx
150720_TRG3K48_V1T_AACTTG_L006_ctab


title: cellline 24h HOXBAS3-KD rep2

description:
AltAnalyze_AltResults.xlsx
150720_TRG2K24_V1T_TCGGCA_L005_ctab


title: cellline 12h control rep2

description:
AltAnalyze_AltResults.xlsx
150720_TRG2C12_V1T_CACTCA_L006_ctab

value: control transfection


title: cellline 24h control rep3

description:
AltAnalyze_AltResults.xlsx
150720_TRG3C24_V1T_GGCCTG_L006_ctab


title: cellline 12h control rep3

description:
AltAnalyze_AltResults.xlsx
150720_TRG3C12_V1T_TGCCAT_L006_ctab


title: cellline 48h control rep3

description:
AltAnalyze_AltResults.xlsx
150720_TRG3C48_V1T_CACGAT_L005_ctab


title: cellline 48h control rep2

description:
AltAnalyze_AltResults.xlsx
150720_TRG2C48_V1T_TTCTCC_L006_ctab


title: cellline 24h HOXBAS3-KD rep3

description:
AltAnalyze_AltResults.xlsx
150720_TRG3K24_V1T_AATAGG_L006_ctab


title: cellline 24h HOXBAS3-KD rep1

description:
AltAnalyze_AltResults.xlsx
150720_TRG1K24_V1T_TAATCG_L005_ctab


title: cellline 12h HOXBAS3-KD rep1

description:
AltAnalyze_AltResults.xlsx
150720_TRG1K12_V1T_GGCCTG_L005_ctab


title: cellline 24h control rep2

description:
AltAnalyze_AltResults.xlsx
150720_TRG2C24_V1T_CATGGC_L006_ctab


title: S004_N

description:
RNA sequencing
Sample 59

tag: age


title: cellline 12h control rep1

description:
AltAnalyze_AltResults.xlsx
150720_TRG1C12_V1T_ACCGGC_L006_ctab


title: cellline 12h HOXBAS3-KD rep3

description:
AltAnalyze_AltResults.xlsx
150720_TRG3K12_V1T_TGAATG_L005_ctab


title: Moi-20

status: Public on Oct 31 2019

city: Cheongju-si

first: Kim

last: Jung-Hyun

address: 202, Osongsaengmyeong 2-ro, Osong-eup, Heungdeok-gu

department: Division of Intractable Diseases

country: South Korea

institute: Korea National Institute of Health

description:
sample name in processed data file:
hMDM_TB
GroupB_vsd.txt

data_processing:
RNA-seq reads were aligned to the hg38 reference genome assembly using STAR v2.6.0
The raw counts were normalized using variance stabilizing transformation (VST) method after excluded a minimum count of 1.0 in all of the samples.
Differentiall expressed genes were calculated using DESeq package in R
Genome_build: hg38 (GRCh 38)
Supplementary_files_format_and_content: tab-delimited text files include normalized read counts

source_name: monocyte

growth_protocol: The H9 hESC line was obtained from WiCell (Madison, WI, USA) and cultured in feeder-free TeSR-E8 or mTeSR-1 medium (STEMCELL Technologies, Vancouver, Canada) on tissue culture plates coated with Vitronectin (Gibco, Grand Island, NY, USA) or Matrigel hESC-qualified Matrix (Corning Inc., Corning, NY, USA), and were mechanically passaged. For differentiation into macrophage-like cells, hESCs were transitioned into Growth Factor-Reduced Matrigel (Corning Inc.) in mTeSR-1 medium at a density of 5–8 colonies/35-mm dish. Mesodermal differentiation was induced with APEL2 medium supplemented with 1× insulin-transferrin-selenium-X (Gibco) and BMP4. HSPC production was induced by treatment with APEL2 medium containing VEGF4 and SCF for 2 days, followed by SCF, IL-3 and IL-6 and TPO and Flt-3L. After 12-20 days, floating HSPCs were further differentiated into iMAC using macrophage M-CSF and RPMI1640 medium supplemented with 10% fetal bovine serum.     THP-1 pro-monocyte cells were maintained in RPMI1640 containing 10% FBS and 5% penicillin/streptomycin. For differentiation into macrophages, THP-1 cells were treated with phorbol 12-myristate 13-acetate (PMA, 100 ng/ml for 48 h). To generate hMDMs, we sorted CD14+ blood monocytes from hPBMCs using magnetic CD14 microbeads (Miltenyi Biotec, Bergisch Gladbach, Germany) and cultured the cells in the presence of M-CSF (100 ng/ml).

extract_protocol:
RNA was extracted using the RNeasy Plus Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer’s protocol. Briefly, cells were homogenized and transferred directly into a spin column. Tubes were centrifuged 2 min at maximum speed. Homogenized lysate were then transfered into spin column and centrifuged for 30min at 8000g, and save the flow-through and add 1 volume of 70% EtOH. Transfer 700 ul of sample into RNeasy spin column and centrifuged for 15s at 8000g. After 15s, 700 ul RPE buffer was added to spin column and centrifuged 15s at 8000g. Next, 500 ul RPE buffer was added to spin column and centrifuged 2min at 8000g. After 2min, transfer spin column in a new 1.5 ml collection tube and added 50ul RNase free water directly to the membrane and centrifuged for 1min at 8000g.
The library was prepared using Truseq stranded mRNA prep kit (Illumina, San Diego, CA, USA) and run on a HiSeq2500 sequencer (Illumina) with a 101-bp paired-end read length. Raw data were processed using STAR v.2.6 to align genome reads against human Reference genome (hg38) and differentially expressed genes were identified using DESeq21 after raw count data were normalized using variance stabilizing transformation (VST) method. Multidimensional scaling (MDS) and clustering analysis were calculated based on Poisson model. Spearman correlation coefficients between pairs of samples were computed.

treatment_protocol: Macrophages were infected with H37Rv-GFP Mtb at the desired multiplicity of infection (MOI) for 2h with mild shacking (120 rpm) at 37°C. For the high-throughput screening, a MOI of 5 was used. Infected cells were washed twice with fresh medium.

tag: cell type

value: monocyte

tag: infection status

value: infected with H37Rv-GFP Mtb


title: Ni

description:
sample name in processed data file:
hMDM4
GroupB_vsd.txt

value: not infected


title: cellline 48h control rep1

description:
AltAnalyze_AltResults.xlsx
150720_TRG1C48_V1T_CACGAT_L006_ctab


title: AML patient 07621 HOXBAS3-KD

description:
AltAnalyze_AltResults.xlsx
XDP07621HB153KO-V1T-1_S4_L001_ctab

source_name: leukapheresis

value: AML patient blasts


title: cellline 24h control rep1

description:
AltAnalyze_AltResults.xlsx
150720_TRG1C24_V1T_ATACGG_L006_ctab


title: AML patient 090096 HOXBAS3-KD

description:
AltAnalyze_AltResults.xlsx
XDP090096KD-V1T-1_S8_L001_ctab


title: AML patient 07621 control

description:
AltAnalyze_AltResults.xlsx
XDP07621cont-V1T-1_S3_L001_ctab


title: AML patient 071177 control

description:
AltAnalyze_AltResults.xlsx
XDP071177cont-V1T-1_S1_L001_ctab


title: AML patient 04370 HOXBAS3-KD

description:
AltAnalyze_AltResults.xlsx
XDP04370HB153KO-V1T-1_S6_L001_ctab


title: AML patient 071177 HOXBAS3-KD

description:
AltAnalyze_AltResults.xlsx
XDP071177KD-V1T-1_S2_L001_ctab


title: AML patient 04370 control

description:
AltAnalyze_AltResults.xlsx
XDP04370cont-V1T-1_S5_L001_ctab


title: CN-AML patient TDIMI758

description:
abdc_pt_gene_20171228.tsv
TDIMI758

source_name: blood or bone marrow

value: mutant

value: no

tag: Sex

value: female

tag: race

value: White

value: Intermediate


title: CN-AML patient TDIMI978

description:
abdc_pt_gene_20171228.tsv
TDIMI978

value: male

value: Favorable


title: CN-AML patient TDIMI117

description:
abdc_pt_gene_20171228.tsv
TDIMI117

value: Hispanic


title: CN-AML patient TDIMI819

description:
abdc_pt_gene_20171228.tsv
TDIMI819


title: CN-AML patient TDIMI972

description:
abdc_pt_gene_20171228.tsv
TDIMI972


title: CN-AML patient TDIMI555

description:
abdc_pt_gene_20171228.tsv
TDIMI555


title: CN-AML patient TDIMI893

description:
abdc_pt_gene_20171228.tsv
TDIMI893


title: CN-AML patient TDIMI860

description:
abdc_pt_gene_20171228.tsv
TDIMI860


title: CN-AML patient TDIMI1015

description:
abdc_pt_gene_20171228.tsv
TDIMI1015


title: CN-AML patient TDIMI1012

description:
abdc_pt_gene_20171228.tsv
TDIMI1012


title: CN-AML patient TDIMI719

description:
abdc_pt_gene_20171228.tsv
TDIMI719


title: AML patient 090096 control

description:
AltAnalyze_AltResults.xlsx
XDP090096cont-V1T-1_S7_L001_ctab


title: CN-AML patient TDIMI842

description:
abdc_pt_gene_20171228.tsv
TDIMI842


title: CN-AML patient TDIMI887

description:
abdc_pt_gene_20171228.tsv
TDIMI887


title: CN-AML patient TDIMI787

description:
abdc_pt_gene_20171228.tsv
TDIMI787


title: CN-AML patient TDIMI161

description:
abdc_pt_gene_20171228.tsv
TDIMI161


title: CN-AML patient TDIMI1030

description:
abdc_pt_gene_20171228.tsv
TDIMI1030


title: CN-AML patient TDIMI560

description:
abdc_pt_gene_20171228.tsv
TDIMI560


title: CN-AML patient TDIMI954

description:
abdc_pt_gene_20171228.tsv
TDIMI954


title: CN-AML patient TDIMI848

description:
abdc_pt_gene_20171228.tsv
TDIMI848


title: CN-AML patient TDIMI155

description:
abdc_pt_gene_20171228.tsv
TDIMI155


title: CN-AML patient TDIMI122

description:
abdc_pt_gene_20171228.tsv
TDIMI122


title: CN-AML patient TDIMI031

description:
abdc_pt_gene_20171228.tsv
TDIMI031


title: CN-AML patient TDIMI830

description:
abdc_pt_gene_20171228.tsv
TDIMI830


title: CN-AML patient TDIMI1024

description:
abdc_pt_gene_20171228.tsv
TDIMI1024


title: CN-AML patient TDIMI971

description:
abdc_pt_gene_20171228.tsv
TDIMI971

value: Black


title: CN-AML patient TDIMI751

description:
abdc_pt_gene_20171228.tsv
TDIMI751


title: CN-AML patient TDIMI116

description:
abdc_pt_gene_20171228.tsv
TDIMI116


title: CN-AML patient TDIMI780

description:
abdc_pt_gene_20171228.tsv
TDIMI780

value: Adverse


title: CN-AML patient TDIMI763

description:
abdc_pt_gene_20171228.tsv
TDIMI763


title: CN-AML patient TDIMI824

description:
abdc_pt_gene_20171228.tsv
TDIMI824


title: CN-AML patient TDIMI712

description:
abdc_pt_gene_20171228.tsv
TDIMI712


title: CN-AML patient TDIMI025

description:
abdc_pt_gene_20171228.tsv
TDIMI025


title: CN-AML patient TDIMI160

description:
abdc_pt_gene_20171228.tsv
TDIMI160


title: CN-AML patient TDIMI1009

description:
abdc_pt_gene_20171228.tsv
TDIMI1009


title: CN-AML patient TDIMI683

description:
abdc_pt_gene_20171228.tsv
TDIMI683


title: CN-AML patient TDIMI953

description:
abdc_pt_gene_20171228.tsv
TDIMI953


title: CN-AML patient TDIMI806

description:
abdc_pt_gene_20171228.tsv
TDIMI806


title: CN-AML patient TDIMI874

description:
abdc_pt_gene_20171228.tsv
TDIMI874


title: CN-AML patient TDIMI154

description:
abdc_pt_gene_20171228.tsv
TDIMI154


title: CN-AML patient TDIMI868

description:
abdc_pt_gene_20171228.tsv
TDIMI868


title: CN-AML patient TDIMI1027

description:
abdc_pt_gene_20171228.tsv
TDIMI1027


title: CN-AML patient TDIMI030

description:
abdc_pt_gene_20171228.tsv
TDIMI030


title: CN-AML patient TDIMI115

description:
abdc_pt_gene_20171228.tsv
TDIMI115


title: CN-AML patient TDIMI553

description:
abdc_pt_gene_20171228.tsv
TDIMI553


title: CN-AML patient TDIMI1000

description:
abdc_pt_gene_20171228.tsv
TDIMI1000


title: CN-AML patient TDIMI897

description:
abdc_pt_gene_20171228.tsv
TDIMI897


title: CN-AML patient TDIMI098

description:
abdc_pt_gene_20171228.tsv
TDIMI098


title: CN-AML patient TDIMI1005

description:
abdc_pt_gene_20171228.tsv
TDIMI1005

value: Asian


title: CN-AML patient TDIMI811

description:
abdc_pt_gene_20171228.tsv
TDIMI811

value: Native Hawaiian


title: CN-AML patient TDIMI1038

description:
abdc_pt_gene_20171228.tsv
TDIMI1038


title: CN-AML patient TDIMI1029

description:
abdc_pt_gene_20171228.tsv
TDIMI1029


title: CN-AML patient TDIMI909

description:
abdc_pt_gene_20171228.tsv
TDIMI909


title: CN-AML patient TDIMI829

description:
abdc_pt_gene_20171228.tsv
TDIMI829


title: CN-AML patient TDIMI774

description:
abdc_pt_gene_20171228.tsv
TDIMI774


title: CN-AML patient TDIMI1039

description:
abdc_pt_gene_20171228.tsv
TDIMI1039


title: CN-AML patient TDIMI964

description:
abdc_pt_gene_20171228.tsv
TDIMI964

value: Other


title: CN-AML patient TDIMI109

description:
abdc_pt_gene_20171228.tsv
TDIMI109


title: CN-AML patient TDIMI086

description:
abdc_pt_gene_20171228.tsv
TDIMI086


title: CN-AML patient TDIMI840

description:
abdc_pt_gene_20171228.tsv
TDIMI840


title: CN-AML patient TDIMI891

description:
abdc_pt_gene_20171228.tsv
TDIMI891


title: CN-AML patient TDIMI902

description:
abdc_pt_gene_20171228.tsv
TDIMI902


title: CN-AML patient TDIMI761

description:
abdc_pt_gene_20171228.tsv
TDIMI761


title: CN-AML patient TDIMI817

description:
abdc_pt_gene_20171228.tsv
TDIMI817


title: CN-AML patient TDIMI952

description:
abdc_pt_gene_20171228.tsv
TDIMI952


title: CN-AML patient TDIMI1043

description:
abdc_pt_gene_20171228.tsv
TDIMI1043


title: CN-AML patient TDIMI018

description:
abdc_pt_gene_20171228.tsv
TDIMI018


title: CN-AML patient TDIMI805

description:
abdc_pt_gene_20171228.tsv
TDIMI805


title: CN-AML patient TDIMI103

description:
abdc_pt_gene_20171228.tsv
TDIMI103


title: CN-AML patient TDIMI873

description:
abdc_pt_gene_20171228.tsv
TDIMI873


title: CN-AML patient TDIMI153

description:
abdc_pt_gene_20171228.tsv
TDIMI153


title: CN-AML patient TDIMI1002

description:
abdc_pt_gene_20171228.tsv
TDIMI1002


title: CN-AML patient TDIMI958

description:
abdc_pt_gene_20171228.tsv
TDIMI958


title: CN-AML patient TDIMI767

description:
abdc_pt_gene_20171228.tsv
TDIMI767


title: CN-AML patient TDIMI755

description:
abdc_pt_gene_20171228.tsv
TDIMI755


title: CN-AML patient TDIMI867

description:
abdc_pt_gene_20171228.tsv
TDIMI867


title: CN-AML patient TDIMI147

description:
abdc_pt_gene_20171228.tsv
TDIMI147


title: CN-AML patient TDIMI1010

description:
abdc_pt_gene_20171228.tsv
TDIMI1010


title: CN-AML patient TDIMI091

description:
abdc_pt_gene_20171228.tsv
TDIMI091


title: CN-AML patient TDIMI023

description:
abdc_pt_gene_20171228.tsv
TDIMI023


title: CN-AML patient TDIMI1016

description:
abdc_pt_gene_20171228.tsv
TDIMI1016


title: CN-AML patient TDIMI828

description:
abdc_pt_gene_20171228.tsv
TDIMI828


title: CN-AML patient TDIMI108

description:
abdc_pt_gene_20171228.tsv
TDIMI108


title: CN-AML patient TDIMI879

description:
abdc_pt_gene_20171228.tsv
TDIMI879


title: CN-AML patient TDIMI816

description:
abdc_pt_gene_20171228.tsv
TDIMI816


title: CN-AML patient TDIMI1004

description:
abdc_pt_gene_20171228.tsv
TDIMI1004


title: CN-AML patient TDIMI760

description:
abdc_pt_gene_20171228.tsv
TDIMI760


title: CN-AML patient TDIMI159

description:
abdc_pt_gene_20171228.tsv
TDIMI159


title: CN-AML patient TDIMI276

description:
abdc_pt_gene_20171228.tsv
TDIMI276


title: CN-AML patient TDIMI158

description:
abdc_pt_gene_20171228.tsv
TDIMI158


title: CN-AML patient TDIMI140

description:
abdc_pt_gene_20171228.tsv
TDIMI140


title: CN-AML patient TDIMI017

description:
abdc_pt_gene_20171228.tsv
TDIMI017


title: CN-AML patient TDIMI011

description:
abdc_pt_gene_20171228.tsv
TDIMI011


title: CN-AML patient TDIMI090

description:
abdc_pt_gene_20171228.tsv
TDIMI090


title: CN-AML patient TDIMI022

description:
abdc_pt_gene_20171228.tsv
TDIMI022


title: CN-AML patient TDIMI1003

description:
abdc_pt_gene_20171228.tsv
TDIMI1003


title: CN-AML patient TDIMI1033

description:
abdc_pt_gene_20171228.tsv
TDIMI1033


title: CN-AML patient TDIMI1040

description:
abdc_pt_gene_20171228.tsv
TDIMI1040


title: CN-AML patient TDIMI134

description:
abdc_pt_gene_20171228.tsv
TDIMI134


title: CN-AML patient TDIMI1037

description:
abdc_pt_gene_20171228.tsv
TDIMI1037


title: CN-AML patient TDIMI822

description:
abdc_pt_gene_20171228.tsv
TDIMI822


title: CN-AML patient TDIMI163

description:
abdc_pt_gene_20171228.tsv
TDIMI163


title: CN-AML patient TDIMI275

description:
abdc_pt_gene_20171228.tsv
TDIMI275


title: CN-AML patient TDIMI815

description:
abdc_pt_gene_20171228.tsv
TDIMI815


title: CN-AML patient TDIMI889

description:
abdc_pt_gene_20171228.tsv
TDIMI889


title: CN-AML patient TDIMI152

description:
abdc_pt_gene_20171228.tsv
TDIMI152


title: CN-AML patient TDIMI950

description:
abdc_pt_gene_20171228.tsv
TDIMI950


title: CN-AML patient TDIMI871

description:
abdc_pt_gene_20171228.tsv
TDIMI871


title: CN-AML patient TDIMI128

description:
abdc_pt_gene_20171228.tsv
TDIMI128


title: CN-AML patient TDIMI151

description:
abdc_pt_gene_20171228.tsv
TDIMI151


title: CN-AML patient TDIMI915

description:
abdc_pt_gene_20171228.tsv
TDIMI915


title: CN-AML patient TDIMI1028

description:
abdc_pt_gene_20171228.tsv
TDIMI1028


title: CN-AML patient TDIMI877

description:
abdc_pt_gene_20171228.tsv
TDIMI877


title: CN-AML patient TDIMI989

description:
abdc_pt_gene_20171228.tsv
TDIMI989


title: CN-AML patient TDIMI096

description:
abdc_pt_gene_20171228.tsv
TDIMI096


title: CN-AML patient TDIMI157

description:
abdc_pt_gene_20171228.tsv
TDIMI157


title: CN-AML patient TDIMI133

description:
abdc_pt_gene_20171228.tsv
TDIMI133


title: CN-AML patient TDIMI956

description:
abdc_pt_gene_20171228.tsv
TDIMI956


title: CN-AML patient TDIMI798

description:
abdc_pt_gene_20171228.tsv
TDIMI798


title: CN-AML patient TDIMI269

description:
abdc_pt_gene_20171228.tsv
TDIMI269


title: CN-AML patient TDIMI556

description:
abdc_pt_gene_20171228.tsv
TDIMI556


title: CN-AML patient TDIMI1007

description:
abdc_pt_gene_20171228.tsv
TDIMI1007


title: CN-AML patient TDIMI1023

description:
abdc_pt_gene_20171228.tsv
TDIMI1023


title: CN-AML patient TDIMI274

description:
abdc_pt_gene_20171228.tsv
TDIMI274


title: CN-AML patient TDIMI859

description:
abdc_pt_gene_20171228.tsv
TDIMI859


title: CN-AML patient TDIMI027

description:
abdc_pt_gene_20171228.tsv
TDIMI027


title: CN-AML patient TDIMI994

description:
abdc_pt_gene_20171228.tsv
TDIMI994


title: CN-AML patient TDIMI735

description:
abdc_pt_gene_20171228.tsv
TDIMI735


title: CN-AML patient TDIMI028

description:
abdc_pt_gene_20171228.tsv
TDIMI028


title: CN-AML patient TDIMI847

description:
abdc_pt_gene_20171228.tsv
TDIMI847


title: CN-AML patient TDIMI878

description:
abdc_pt_gene_20171228.tsv
TDIMI878


title: CN-AML patient TDIMI870

description:
abdc_pt_gene_20171228.tsv
TDIMI870


title: CN-AML patient TDIMI015

description:
abdc_pt_gene_20171228.tsv
TDIMI015


title: CN-AML patient TDIMI982

description:
abdc_pt_gene_20171228.tsv
TDIMI982


title: CN-AML patient TDIMI150

description:
abdc_pt_gene_20171228.tsv
TDIMI150


title: CN-AML patient TDIMI723

description:
abdc_pt_gene_20171228.tsv
TDIMI723


title: CN-AML patient TDIMI876

description:
abdc_pt_gene_20171228.tsv
TDIMI876


title: CN-AML patient TDIMI003

description:
abdc_pt_gene_20171228.tsv
TDIMI003


title: CN-AML patient TDIMI100

description:
abdc_pt_gene_20171228.tsv
TDIMI100


title: CN-AML patient TDIMI797

description:
abdc_pt_gene_20171228.tsv
TDIMI797


title: CN-AML patient TDIMI095

description:
abdc_pt_gene_20171228.tsv
TDIMI095


title: CN-AML patient TDIMI268

description:
abdc_pt_gene_20171228.tsv
TDIMI268


title: CN-AML patient TDIMI156

description:
abdc_pt_gene_20171228.tsv
TDIMI156


title: CN-AML patient TDIMI752

description:
abdc_pt_gene_20171228.tsv
TDIMI752


title: CN-AML patient TDIMI808

description:
abdc_pt_gene_20171228.tsv
TDIMI808


title: CN-AML patient TDIMI138

description:
abdc_pt_gene_20171228.tsv
TDIMI138


title: CN-AML patient TDIMI864

description:
abdc_pt_gene_20171228.tsv
TDIMI864


title: CN-AML patient TDIMI729

description:
abdc_pt_gene_20171228.tsv
TDIMI729


title: CN-AML patient TDIMI908

description:
abdc_pt_gene_20171228.tsv
TDIMI908


title: CN-AML patient TDIMI009

description:
abdc_pt_gene_20171228.tsv
TDIMI009


title: CN-AML patient TDIMI734

description:
abdc_pt_gene_20171228.tsv
TDIMI734


title: CN-AML patient TDIMI1026

description:
abdc_pt_gene_20171228.tsv
TDIMI1026


title: CN-AML patient TDIMI273

description:
abdc_pt_gene_20171228.tsv
TDIMI273


title: CN-AML patient TDIMI790

description:
abdc_pt_gene_20171228.tsv
TDIMI790


title: CN-AML patient TDIMI1018

description:
abdc_pt_gene_20171228.tsv
TDIMI1018


title: CN-AML patient TDIMI126

description:
abdc_pt_gene_20171228.tsv
TDIMI126


title: CN-AML patient TDIMI120

description:
abdc_pt_gene_20171228.tsv
TDIMI120


title: CN-AML patient TDIMI801

description:
abdc_pt_gene_20171228.tsv
TDIMI801


title: CN-AML patient TDIMI267

description:
abdc_pt_gene_20171228.tsv
TDIMI267


title: CN-AML patient TDIMI807

description:
abdc_pt_gene_20171228.tsv
TDIMI807


title: CN-AML patient TDIMI796

description:
abdc_pt_gene_20171228.tsv
TDIMI796


title: CN-AML patient TDIMI002

description:
abdc_pt_gene_20171228.tsv
TDIMI002


title: CN-AML patient TDIMI728

description:
abdc_pt_gene_20171228.tsv
TDIMI728


title: CN-AML patient TDIMI710

description:
abdc_pt_gene_20171228.tsv
TDIMI710


title: CN-AML patient TDIMI1022

description:
abdc_pt_gene_20171228.tsv
TDIMI1022


title: CN-AML patient TDIMI722

description:
abdc_pt_gene_20171228.tsv
TDIMI722


title: CN-AML patient TDIMI863

description:
abdc_pt_gene_20171228.tsv
TDIMI863


title: CN-AML patient TDIMI094

description:
abdc_pt_gene_20171228.tsv
TDIMI094


title: CN-AML patient TDIMI008

description:
abdc_pt_gene_20171228.tsv
TDIMI008


title: CN-AML patient TDIMI846

description:
abdc_pt_gene_20171228.tsv
TDIMI846


title: CN-AML patient TDIMI845

description:
abdc_pt_gene_20171228.tsv
TDIMI845


title: CN-AML patient TDIMI851

description:
abdc_pt_gene_20171228.tsv
TDIMI851


title: CN-AML patient TDIMI980

description:
abdc_pt_gene_20171228.tsv
TDIMI980


title: CN-AML patient TDIMI992

description:
abdc_pt_gene_20171228.tsv
TDIMI992


title: CN-AML patient TDIMI969

description:
abdc_pt_gene_20171228.tsv
TDIMI969


title: CN-AML patient TDIMI131

description:
abdc_pt_gene_20171228.tsv
TDIMI131


title: CN-AML patient TDIMI013

description:
abdc_pt_gene_20171228.tsv
TDIMI013


title: CN-AML patient TDIMI772

description:
abdc_pt_gene_20171228.tsv
TDIMI772


title: CN-AML patient TDIMI704

description:
abdc_pt_gene_20171228.tsv
TDIMI704


title: CN-AML patient TDIMI912

description:
abdc_pt_gene_20171228.tsv
TDIMI912


title: CN-AML patient TDIMI721

description:
abdc_pt_gene_20171228.tsv
TDIMI721


title: CN-AML patient TDIMI137

description:
abdc_pt_gene_20171228.tsv
TDIMI137


title: CN-AML patient TDIMI975

description:
abdc_pt_gene_20171228.tsv
TDIMI975


title: CN-AML patient TDIMI001

description:
abdc_pt_gene_20171228.tsv
TDIMI001


title: CN-AML patient TDIMI986

description:
abdc_pt_gene_20171228.tsv
TDIMI986


title: CN-AML patient TDIMI795

description:
abdc_pt_gene_20171228.tsv
TDIMI795


title: CN-AML patient TDIMI918

description:
abdc_pt_gene_20171228.tsv
TDIMI918


title: CN-AML patient TDIMI839

description:
abdc_pt_gene_20171228.tsv
TDIMI839


title: CN-AML patient TDIMI783

description:
abdc_pt_gene_20171228.tsv
TDIMI783


title: CN-AML patient TDIMI266

description:
abdc_pt_gene_20171228.tsv
TDIMI266


title: CN-AML patient TDIMI142

description:
abdc_pt_gene_20171228.tsv
TDIMI142


title: CN-AML patient TDIMI906

description:
abdc_pt_gene_20171228.tsv
TDIMI906


title: CN-AML patient TDIMI778

description:
abdc_pt_gene_20171228.tsv
TDIMI778


title: CN-AML patient TDIMI856

description:
abdc_pt_gene_20171228.tsv
TDIMI856


title: CN-AML patient TDIMI136

description:
abdc_pt_gene_20171228.tsv
TDIMI136


title: CN-AML patient TDIMI777

description:
abdc_pt_gene_20171228.tsv
TDIMI777


title: CN-AML patient TDIMI968

description:
abdc_pt_gene_20171228.tsv
TDIMI968


title: CN-AML patient TDIMI991

description:
abdc_pt_gene_20171228.tsv
TDIMI991


title: CN-AML patient TDIMI833

description:
abdc_pt_gene_20171228.tsv
TDIMI833


title: CN-AML patient TDIMI997

description:
abdc_pt_gene_20171228.tsv
TDIMI997


title: CN-AML patient TDIMI861

description:
abdc_pt_gene_20171228.tsv
TDIMI861


title: CN-AML patient TDIMI265

description:
abdc_pt_gene_20171228.tsv
TDIMI265


title: CN-AML patient TDIMI012

description:
abdc_pt_gene_20171228.tsv
TDIMI012


title: CN-AML patient TDIMI923

description:
abdc_pt_gene_20171228.tsv
TDIMI923


title: CN-AML patient TDIMI1046

description:
abdc_pt_gene_20171228.tsv
TDIMI1046


title: CN-AML patient TDIMI869

description:
abdc_pt_gene_20171228.tsv
TDIMI869


title: CN-AML patient TDIMI967

description:
abdc_pt_gene_20171228.tsv
TDIMI967


title: CN-AML patient TDIMI911

description:
abdc_pt_gene_20171228.tsv
TDIMI911


title: CN-AML patient TDIMI838

description:
abdc_pt_gene_20171228.tsv
TDIMI838


title: CN-AML patient TDIMI124

description:
abdc_pt_gene_20171228.tsv
TDIMI124


title: CN-AML patient TDIMI123

description:
abdc_pt_gene_20171228.tsv
TDIMI123


title: CN-AML patient TDIMI955

description:
abdc_pt_gene_20171228.tsv
TDIMI955


title: CN-AML patient TDIMI720

description:
abdc_pt_gene_20171228.tsv
TDIMI720


title: CN-AML patient TDIMI270

description:
abdc_pt_gene_20171228.tsv
TDIMI270


title: CN-AML patient TDIMI561

description:
abdc_pt_gene_20171228.tsv
TDIMI561


title: CN-AML patient TDIMI135

description:
abdc_pt_gene_20171228.tsv
TDIMI135


title: CN-AML patient TDIMI910

description:
abdc_pt_gene_20171228.tsv
TDIMI910


title: CN-AML patient TDIMI032

description:
abdc_pt_gene_20171228.tsv
TDIMI032


title: CN-AML patient TDIMI949

description:
abdc_pt_gene_20171228.tsv
TDIMI949

value: wild-type


title: CN-AML patient TDIMI026

description:
abdc_pt_gene_20171228.tsv
TDIMI026


title: CN-AML patient TDIMI837

description:
abdc_pt_gene_20171228.tsv
TDIMI837


title: CN-AML patient TDIMI690

description:
abdc_pt_gene_20171228.tsv
TDIMI690


title: CN-AML patient TDIMI825

description:
abdc_pt_gene_20171228.tsv
TDIMI825


title: CN-AML patient TDIMI782

description:
abdc_pt_gene_20171228.tsv
TDIMI782


title: CN-AML patient TDIMI271

description:
abdc_pt_gene_20171228.tsv
TDIMI271


title: CN-AML patient TDIMI854

description:
abdc_pt_gene_20171228.tsv
TDIMI854


title: CN-AML patient TDIMI960

description:
abdc_pt_gene_20171228.tsv
TDIMI960


title: CN-AML patient TDIMI990

description:
abdc_pt_gene_20171228.tsv
TDIMI990


title: CN-AML patient TDIMI1020

description:
abdc_pt_gene_20171228.tsv
TDIMI1020


title: CN-AML patient TDIMI684

description:
abdc_pt_gene_20171228.tsv
TDIMI684


title: CN-AML patient TDIMI769

description:
abdc_pt_gene_20171228.tsv
TDIMI769


title: CN-AML patient TDIMI836

description:
abdc_pt_gene_20171228.tsv
TDIMI836


title: CN-AML patient TDIMI892

description:
abdc_pt_gene_20171228.tsv
TDIMI892


title: CN-AML patient TDIMI110

description:
abdc_pt_gene_20171228.tsv
TDIMI110


title: CN-AML patient TDIMI849

description:
abdc_pt_gene_20171228.tsv
TDIMI849


title: CN-AML patient TDIMI099

description:
abdc_pt_gene_20171228.tsv
TDIMI099


title: CN-AML patient TDIMI948

description:
abdc_pt_gene_20171228.tsv
TDIMI948


title: CN-AML patient TDIMI812

description:
abdc_pt_gene_20171228.tsv
TDIMI812


title: CN-AML patient TDIMI898

description:
abdc_pt_gene_20171228.tsv
TDIMI898


title: CN-AML patient TDIMI093

description:
abdc_pt_gene_20171228.tsv
TDIMI093


title: CN-AML patient TDIMI019

description:
abdc_pt_gene_20171228.tsv
TDIMI019


title: CN-AML patient TDIMI121

description:
abdc_pt_gene_20171228.tsv
TDIMI121


title: CN-AML patient TDIMI768

description:
abdc_pt_gene_20171228.tsv
TDIMI768


title: CN-AML patient TDIMI104

description:
abdc_pt_gene_20171228.tsv
TDIMI104


title: CN-AML patient TDIMI1008

description:
abdc_pt_gene_20171228.tsv
TDIMI1008


title: CN-AML patient TDIMI959

description:
abdc_pt_gene_20171228.tsv
TDIMI959


title: CN-AML patient TDIMI036

description:
abdc_pt_gene_20171228.tsv
TDIMI036


title: CN-AML patient TDIMI970

description:
abdc_pt_gene_20171228.tsv
TDIMI970


title: CN-AML patient TDIMI148

description:
abdc_pt_gene_20171228.tsv
TDIMI148


title: CN-AML patient TDIMI835

description:
abdc_pt_gene_20171228.tsv
TDIMI835


title: CN-AML patient TDIMI092

description:
abdc_pt_gene_20171228.tsv
TDIMI092


title: CN-AML patient TDIMI823

description:
abdc_pt_gene_20171228.tsv
TDIMI823


title: CN-AML patient TDIMI973

description:
abdc_pt_gene_20171228.tsv
TDIMI973


title: CN-AML patient TDIMI024

description:
abdc_pt_gene_20171228.tsv
TDIMI024


title: CN-AML patient TDIMI773

description:
abdc_pt_gene_20171228.tsv
TDIMI773


title: CN-AML patient TDIMI1011

description:
abdc_pt_gene_20171228.tsv
TDIMI1011


title: CN-AML patient TDIMI682

description:
abdc_pt_gene_20171228.tsv
TDIMI682


title: CN-AML patient TDIMI834

description:
abdc_pt_gene_20171228.tsv
TDIMI834


title: CN-AML patient TDIMI977

description:
abdc_pt_gene_20171228.tsv
TDIMI977


title: CN-AML patient TDIMI035

description:
abdc_pt_gene_20171228.tsv
TDIMI035


title: CN-AML patient TDIMI890

description:
abdc_pt_gene_20171228.tsv
TDIMI890


title: CN-AML patient TDIMI743

description:
abdc_pt_gene_20171228.tsv
TDIMI743


title: CN-AML patient TDIMI946

description:
abdc_pt_gene_20171228.tsv
TDIMI946


title: CN-AML patient TDIMI029

description:
abdc_pt_gene_20171228.tsv
TDIMI029


title: CN-AML patient TDIMI558

description:
abdc_pt_gene_20171228.tsv
TDIMI558


title: CN-AML patient TDIMI934

description:
abdc_pt_gene_20171228.tsv
TDIMI934


title: CN-AML patient TDIMI693

description:
abdc_pt_gene_20171228.tsv
TDIMI693


title: CN-AML patient TDIMI884

description:
abdc_pt_gene_20171228.tsv
TDIMI884


title: CN-AML patient TDIMI749

description:
abdc_pt_gene_20171228.tsv
TDIMI749


title: CN-AML patient TDIMI102

description:
abdc_pt_gene_20171228.tsv
TDIMI102


title: CN-AML patient TDIMI963

description:
abdc_pt_gene_20171228.tsv
TDIMI963


title: CN-AML patient TDIMI810

description:
abdc_pt_gene_20171228.tsv
TDIMI810


title: CN-AML patient TDIMI1014

description:
abdc_pt_gene_20171228.tsv
TDIMI1014


title: CN-AML patient TDIMI996

description:
abdc_pt_gene_20171228.tsv
TDIMI996


title: CN-AML patient TDIMI951

description:
abdc_pt_gene_20171228.tsv
TDIMI951


title: CN-AML patient TDIMI804

description:
abdc_pt_gene_20171228.tsv
TDIMI804


title: CN-AML patient TDIMI766

description:
abdc_pt_gene_20171228.tsv
TDIMI766


title: CN-AML patient TDIMI034

description:
abdc_pt_gene_20171228.tsv
TDIMI034


title: CN-AML patient TDIMI866

description:
abdc_pt_gene_20171228.tsv
TDIMI866


title: CN-AML patient TDIMI146

description:
abdc_pt_gene_20171228.tsv
TDIMI146


title: CN-AML patient TDIMI281

description:
abdc_pt_gene_20171228.tsv
TDIMI281


title: CN-AML patient TDIMI551

description:
abdc_pt_gene_20171228.tsv
TDIMI551


title: CN-AML patient TDIMI821

description:
abdc_pt_gene_20171228.tsv
TDIMI821


title: CN-AML patient TDIMI097

description:
abdc_pt_gene_20171228.tsv
TDIMI097


title: CN-AML patient TDIMI101

description:
abdc_pt_gene_20171228.tsv
TDIMI101


title: CN-AML patient TDIMI730

description:
abdc_pt_gene_20171228.tsv
TDIMI730


title: CN-AML patient TDIMI748

description:
abdc_pt_gene_20171228.tsv
TDIMI748


title: CN-AML patient TDIMI010

description:
abdc_pt_gene_20171228.tsv
TDIMI010


title: CN-AML patient TDIMI1019

description:
abdc_pt_gene_20171228.tsv
TDIMI1019


title: CN-AML patient TDIMI557

description:
abdc_pt_gene_20171228.tsv
TDIMI557


title: CN-AML patient TDIMI921

description:
abdc_pt_gene_20171228.tsv
TDIMI921


title: CN-AML patient TDIMI809

description:
abdc_pt_gene_20171228.tsv
TDIMI809


title: CN-AML patient TDIMI016

description:
abdc_pt_gene_20171228.tsv
TDIMI016


title: CN-AML patient TDIMI1017

description:
abdc_pt_gene_20171228.tsv
TDIMI1017


title: CN-AML patient TDIMI753

description:
abdc_pt_gene_20171228.tsv
TDIMI753


title: CN-AML patient TDIMI786

description:
abdc_pt_gene_20171228.tsv
TDIMI786


title: CN-AML patient TDIMI853

description:
abdc_pt_gene_20171228.tsv
TDIMI853


title: CN-AML patient TDIMI021

description:
abdc_pt_gene_20171228.tsv
TDIMI021


title: CN-AML patient TDIMI747

description:
abdc_pt_gene_20171228.tsv
TDIMI747


title: CN-AML patient TDIMI865

description:
abdc_pt_gene_20171228.tsv
TDIMI865


title: CN-AML patient TDIMI162

description:
abdc_pt_gene_20171228.tsv
TDIMI162


title: CN-AML patient TDIMI139

description:
abdc_pt_gene_20171228.tsv
TDIMI139


title: CN-AML patient TDIMI882

description:
abdc_pt_gene_20171228.tsv
TDIMI882


title: CN-AML patient TDIMI802

description:
abdc_pt_gene_20171228.tsv
TDIMI802


title: CN-AML patient TDIMI685

description:
abdc_pt_gene_20171228.tsv
TDIMI685


title: CN-AML patient TDIMI089

description:
abdc_pt_gene_20171228.tsv
TDIMI089


title: CN-AML patient TDIMI914

description:
abdc_pt_gene_20171228.tsv
TDIMI914


title: CN-AML patient TDIMI976

description:
abdc_pt_gene_20171228.tsv
TDIMI976


title: CN-AML patient TDIMI144

description:
abdc_pt_gene_20171228.tsv
TDIMI144


title: CN-AML patient TDIMI679

description:
abdc_pt_gene_20171228.tsv
TDIMI679


title: CN-AML patient TDIMI132

description:
abdc_pt_gene_20171228.tsv
TDIMI132


title: CN-AML patient TDIMI746

description:
abdc_pt_gene_20171228.tsv
TDIMI746


title: CN-AML patient TDIMI004

description:
abdc_pt_gene_20171228.tsv
TDIMI004


title: CN-AML patient TDIMI852

description:
abdc_pt_gene_20171228.tsv
TDIMI852


title: CN-AML patient TDIMI779

description:
abdc_pt_gene_20171228.tsv
TDIMI779


title: CN-AML patient TDIMI020

description:
abdc_pt_gene_20171228.tsv
TDIMI020


title: CN-AML patient TDIMI724

description:
abdc_pt_gene_20171228.tsv
TDIMI724


title: CN-AML patient TDIMI280

description:
abdc_pt_gene_20171228.tsv
TDIMI280


title: CN-AML patient TDIMI1025

description:
abdc_pt_gene_20171228.tsv
TDIMI1025


title: CN-AML patient TDIMI993

description:
abdc_pt_gene_20171228.tsv
TDIMI993


title: CN-AML patient TDIMI881

description:
abdc_pt_gene_20171228.tsv
TDIMI881


title: CN-AML patient TDIMI858

description:
abdc_pt_gene_20171228.tsv
TDIMI858


title: CN-AML patient TDIMI999

description:
abdc_pt_gene_20171228.tsv
TDIMI999


title: CN-AML patient TDIMI981

description:
abdc_pt_gene_20171228.tsv
TDIMI981


title: CN-AML patient TDIMI813

description:
abdc_pt_gene_20171228.tsv
TDIMI813


title: CN-AML patient TDIMI926

description:
abdc_pt_gene_20171228.tsv
TDIMI926


title: CN-AML patient TDIMI088

description:
abdc_pt_gene_20171228.tsv
TDIMI088


title: CN-AML patient TDIMI919

description:
abdc_pt_gene_20171228.tsv
TDIMI919


title: CN-AML patient TDIMI716

description:
abdc_pt_gene_20171228.tsv
TDIMI716


title: CN-AML patient TDIMI998

description:
abdc_pt_gene_20171228.tsv
TDIMI998


title: CN-AML patient TDIMI272

description:
abdc_pt_gene_20171228.tsv
TDIMI272


title: CN-AML patient TDIMI1001

description:
abdc_pt_gene_20171228.tsv
TDIMI1001


title: CN-AML patient TDIMI727

description:
abdc_pt_gene_20171228.tsv
TDIMI727


title: CN-AML patient TDIMI875

description:
abdc_pt_gene_20171228.tsv
TDIMI875


title: CN-AML patient TDIMI862

description:
abdc_pt_gene_20171228.tsv
TDIMI862


title: CN-AML patient TDIMI007

description:
abdc_pt_gene_20171228.tsv
TDIMI007


title: CN-AML patient TDIMI119

description:
abdc_pt_gene_20171228.tsv
TDIMI119


title: CN-AML patient TDIMI974

description:
abdc_pt_gene_20171228.tsv
TDIMI974


title: CN-AML patient TDIMI107

description:
abdc_pt_gene_20171228.tsv
TDIMI107


title: CN-AML patient TDIMI130

description:
abdc_pt_gene_20171228.tsv
TDIMI130


title: CN-AML patient TDIMI794

description:
abdc_pt_gene_20171228.tsv
TDIMI794


title: CN-AML patient TDIMI850

description:
abdc_pt_gene_20171228.tsv
TDIMI850


title: CN-AML patient TDIMI844

description:
abdc_pt_gene_20171228.tsv
TDIMI844


title: CN-AML patient TDIMI709

description:
abdc_pt_gene_20171228.tsv
TDIMI709


title: CN-AML patient TDIMI112

description:
abdc_pt_gene_20171228.tsv
TDIMI112


title: CN-AML patient TDIMI014

description:
abdc_pt_gene_20171228.tsv
TDIMI014


title: CN-AML patient TDIMI141

description:
abdc_pt_gene_20171228.tsv
TDIMI141


title: CN-AML patient TDIMI006

description:
abdc_pt_gene_20171228.tsv
TDIMI006


title: CN-AML patient TDIMI905

description:
abdc_pt_gene_20171228.tsv
TDIMI905


title: CN-AML patient TDIMI826

description:
abdc_pt_gene_20171228.tsv
TDIMI826


title: CN-AML patient TDIMI985

description:
abdc_pt_gene_20171228.tsv
TDIMI985


title: CN-AML patient TDIMI857

description:
abdc_pt_gene_20171228.tsv
TDIMI857


title: CN-AML patient TDIMI843

description:
abdc_pt_gene_20171228.tsv
TDIMI843


title: CN-AML patient TDIMI922

description:
abdc_pt_gene_20171228.tsv
TDIMI922


title: CN-AML patient TDIMI129

description:
abdc_pt_gene_20171228.tsv
TDIMI129


title: CN-AML patient TDIMI764

description:
abdc_pt_gene_20171228.tsv
TDIMI764


title: CN-AML patient TDIMI111

description:
abdc_pt_gene_20171228.tsv
TDIMI111


title: CN-AML patient TDIMI984

description:
abdc_pt_gene_20171228.tsv
TDIMI984


title: CN-AML patient TDIMI264

description:
abdc_pt_gene_20171228.tsv
TDIMI264


title: CN-AML patient TDIMI1006

description:
abdc_pt_gene_20171228.tsv
TDIMI1006


title: CN-AML patient TDIMI1013

description:
abdc_pt_gene_20171228.tsv
TDIMI1013


title: CN-AML patient TDIMI961

description:
abdc_pt_gene_20171228.tsv
TDIMI961


title: CGND-HRA-01239

status: Public on Oct 04 2019

description: total RNA rRNA depleted

data_processing:
fastq Illumina RNASeq paired-end reads were aligned to the hg19 reference genome using STAR v2.5.2b with the following configurations: --outFilterMultimapNmax 100; --outFilterMismatchNoverReadLmax 0.04
Genes and transposable elements (TE) were quantified using TEcount (from TEtranscripts v2.0.3) with the following configurations: hg19 genic GTF from refGene (Jan 2018), custom hg19 TE GTF generated from repeatMasker; --stranded reverse
Genome_build: hg19
Supplementary_files_format_and_content: Individual count tables (SampleName_counts.txt) were generated as output from TEcount

source_name: Frontal Cortex

extract_protocol:
Total RNA is extracted from flash frozen post-mortem tissue using Trizol/Chloroform, followed by Qiagen RNeasy minikit column purification. RNA is quantified on a Nanodrop 2000 and Qubit™ 2.0 Fluorometer; the quality and integrity of the RNA are verified on an Agilent Bioanalyzer.
Starting from 500 ng of total RNA, rRNA are depleted and cDNA libraries prepared using the KAPA Stranded RNA-Seq Kit with RiboErase (KAPA, Roche) and Illumina platform-compatible PCR primers (NEXTflex RNA-seq indexes, BioScientific). Libraries are 500-550bp in length and sequenced PE 125.

tag: tissue type

value: post-mortem tissue

tag: cns subregion

value: Frontal Cortex

tag: subject id

tag: sample group

value: ALS Spectrum MND


title: CGND-HRA-00655

description: total RNA rRNA depleted

value: Other Neurological Disorders


title: CGND-HRA-01236

description: total RNA rRNA depleted

value: Non-Neurological Control


title: CGND-HRA-00756

description: total RNA rRNA depleted


title: CGND-HRA-01234

description: total RNA rRNA depleted


title: CGND-HRA-01179

description: total RNA rRNA depleted


title: CGND-HRA-00783

description: total RNA rRNA depleted


title: CGND-HRA-00871

description: total RNA rRNA depleted


title: CGND-HRA-01222

description: total RNA rRNA depleted

source_name: Motor Cortex

value: Motor Cortex (Lateral)


title: CGND-HRA-00925

description: total RNA rRNA depleted


title: CGND-HRA-00773

description: total RNA rRNA depleted


title: CGND-HRA-01251

description: total RNA rRNA depleted


title: CGND-HRA-00788

description: total RNA rRNA depleted


title: CGND-HRA-01353

description: total RNA rRNA depleted


title: CGND-HRA-00654

description: total RNA rRNA depleted


title: CGND-HRA-00792

description: total RNA rRNA depleted


title: CGND-HRA-01349

description: total RNA rRNA depleted


title: CGND-HRA-01266

description: total RNA rRNA depleted


title: CGND-HRA-01269

description: total RNA rRNA depleted


title: CGND-HRA-01361

description: total RNA rRNA depleted


title: CGND-HRA-01357

description: total RNA rRNA depleted


title: CGND-HRA-01365

description: total RNA rRNA depleted


title: CGND-HRA-01369

description: total RNA rRNA depleted


title: CGND-HRA-01219

description: total RNA rRNA depleted

value: Motor Cortex (Medial)


title: CGND-HRA-01218

description: total RNA rRNA depleted


title: CGND-HRA-00633

description: total RNA rRNA depleted

value: JHU 77


title: CGND-HRA-00631

description: total RNA rRNA depleted

value: JHU 75


title: CGND-HRA-00621

description: total RNA rRNA depleted


title: CGND-HRA-00751

description: total RNA rRNA depleted


title: CGND-HRA-00616

description: total RNA rRNA depleted


title: CGND-HRA-00590

description: total RNA rRNA depleted


title: CGND-HRA-00611

description: total RNA rRNA depleted


title: CGND-HRA-00603

description: total RNA rRNA depleted

value: Motor Cortex


title: CGND-HRA-00595

description: total RNA rRNA depleted


title: CGND-HRA-00612

description: total RNA rRNA depleted


title: CGND-HRA-00615

description: total RNA rRNA depleted


title: CGND-HRA-00581

description: total RNA rRNA depleted

value: JHU 83


title: CGND-HRA-00600

description: total RNA rRNA depleted


title: CGND-HRA-00582

description: total RNA rRNA depleted


title: CGND-HRA-00569

description: total RNA rRNA depleted

value: JHU 80


title: CGND-HRA-00553

description: total RNA rRNA depleted

value: JHU 73


title: CGND-HRA-00561

description: total RNA rRNA depleted

value: JHU 74


title: CGND-HRA-00596

description: total RNA rRNA depleted


title: CGND-HRA-00604

description: total RNA rRNA depleted


title: CGND-HRA-00550

description: total RNA rRNA depleted


title: CGND-HRA-00557

description: total RNA rRNA depleted


title: CGND-HRA-00562

description: total RNA rRNA depleted


title: CGND-HRA-00556

description: total RNA rRNA depleted


title: CGND-HRA-00575

description: total RNA rRNA depleted

value: JHU 82


title: CGND-HRA-00543

description: total RNA rRNA depleted


title: CGND-HRA-00546

description: total RNA rRNA depleted


title: CGND-HRA-00559

description: total RNA rRNA depleted


title: CGND-HRA-00529

description: total RNA rRNA depleted


title: CGND-HRA-00535

description: total RNA rRNA depleted


title: CGND-HRA-00481

description: total RNA rRNA depleted


title: CGND-HRA-00487

description: total RNA rRNA depleted


title: CGND-HRA-00578

description: total RNA rRNA depleted


title: CGND-HRA-00571

description: total RNA rRNA depleted


title: CGND-HRA-00466

description: total RNA rRNA depleted


title: CGND-HRA-00430

description: total RNA rRNA depleted


title: CGND-HRA-00460

description: total RNA rRNA depleted


title: CGND-HRA-00427

description: total RNA rRNA depleted


title: CGND-HRA-00436

description: total RNA rRNA depleted


title: CGND-HRA-00421

description: total RNA rRNA depleted


title: CGND-HRA-00424

description: total RNA rRNA depleted


title: CGND-HRA-00423

description: total RNA rRNA depleted


title: CGND-HRA-00412

description: total RNA rRNA depleted


title: CGND-HRA-00409

description: total RNA rRNA depleted


title: CGND-HRA-00406

description: total RNA rRNA depleted


title: CGND-HRA-00415

description: total RNA rRNA depleted


title: CGND-HRA-00433

description: total RNA rRNA depleted


title: CGND-HRA-00405

description: total RNA rRNA depleted


title: CGND-HRA-00393

description: total RNA rRNA depleted


title: CGND-HRA-00394

description: total RNA rRNA depleted


title: CGND-HRA-00397

description: total RNA rRNA depleted


title: CGND-HRA-00400

description: total RNA rRNA depleted


title: CGND-HRA-00399

description: total RNA rRNA depleted


title: CGND-HRA-00385

description: total RNA rRNA depleted


title: CGND-HRA-00387

description: total RNA rRNA depleted


title: CGND-HRA-00382

description: total RNA rRNA depleted