title: aRGC10

data_processing:
Sample demultiplexing with the mkfastq function from Cell Ranger software(version 2.1.0, 10X Genomics)
Sample alignment with the count function from Cell Ranger software(version 2.1.0, 10X Genomics)
Genome_build: mm10
Supplementary_files_format_and_content: Csv files including gene expression matrix from all samples

source_name: Mouse retina, P56

extract_protocol:
Retinas were dissected in oxygenated AMES, digested in papain, and dissociated to single cell suspensions using manual trituration in ovomucoid solution.  Single cell suspensions were incubated with 0.5ul of 1µg/µl anti-CD90 (conjugated to various fluorophores) (Thermo Fisher Scientific) for 10 million cells per 100µl.  Cells were sorted using a MoFlo Astrios. Cellular debris, doublets, and dead cells were excluded, and RGCs were collected based on high Cd90  and GFP co-expression.  Collected cells were loading into 10X Chromium Single Cell A Chips at ~1,000 cell/ul.
Single cell libraries were made with Chromium 3’ v2 platform (10X Genomics, Pleasanton, CA) following the manufacturer’s protocol. Briefly, single cells were partitioned into Gel bead in EMulsion (GEMs) in the GemCode instrument with cell lysis and barcoded reverse transcription of RNA, followed by amplification, shearing and 5’ adaptor and sample index attachment. On average, approximately 10,000 single cells were loaded on each channel and approximately 6,000 cells were recovered. Libraries were sequenced on Illumina HiSeq 2500.
Chromium 3’ v2 platform (10X Genomics, Pleasanton, CA)

treatment_protocol: Vglut2:cre;Stp15 mice mice were used.  Retinas were dissected in Ames solution (Sigma-Aldrich; equilibrated with 95% O2/5% CO2 for all use) immediately following enucleation.


title: aRGC9

status: Public on Nov 27 2019

type: SRA

city: Cambridge

first: Wenjun

last: Yan

state: MA

address: 52 Oxford Street

department: Department of Molecular  and Cellular Biology

country: USA

institute: Harvard University

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: tissue

value: retina


title: aRGC8


title: Subject34_mucosa_CD69-

status: Public on Dec 08 2019

city: Seattle,

first: Stephanie

last: Osmond

state: WA

address: 1201 9th Ave

institute: Benaroya Research Institute

description: BulkRNAseqCounts.csv

data_processing:
Base-calling was performed automatically in Illumina BaseSpace after sequencing; FASTQ reads were trimmed in Galaxy in two steps: 1) hard-trimming to remove 1 3'-end base (FASTQ Trimmer tool, v.1.0.0); 2) quality trimming from both ends until minimum base quality for each read >= 30 (FASTQ Quality Trimmer tool, v.1.0.0).
Reads were aligned in Galaxy using bowtie and TopHat (Tophat for Illumina tool, v.1.5.0).
Read counts per Ensembl gene ID were estimated in Galaxy using htseq-count (htseq-count tool, v.0.4.1).
Sequencing, alignment, and quantitation metrics were obtained for FASTQ, BAM/SAM, and count files in Galaxy using FastQC, Picard, TopHat, Samtools, and ht-seq-count.
Genome_build: GRCh38

organism: Homo sapiens

source_name: CD4 T cells from oral mucosa

extract_protocol:
Full-length cDNA was prepared from 250-1000 sorted CD4+CCR5+ cells using SMARTer Ultra Low Input RNA Kit for Sequencing - v4 according to manufacturer’s instructions (Clontech, Mountain View, CA).
Libraries were prepared from amplified cDNA using the NexteraXT kit according to manufacturer’s instructions (Illumina, San Diego, CA).

tag: subject id

tag: cell sort

tag: pathology score

tag: number of cells


title: aRGC7


title: aRGC6


title: lib3911

status: Public on Feb 03 2020

data_processing:
Base-calling was performed automatically by Illumina real time analysis software and demultiplexing was performed on Illumina BaseSpace.
Hard trimming was performed in Galaxy; 1 3'-end base was removed from all reads using the FASTQ Trimmer tool (v1.0.0)
Quality-based trimming was performed in Galaxy; reads were trimmed from both ends using the FASTQ Quality Trimmer tool (v1.0.0) until minimum base quality for each read was >= 30.
Reads were aligned in Galaxy using bowtie and TopHat (Tophat for Illumina tool, v.1.5.0)
Read counts per Ensembl gene ID were estimated in Galaxy using htseq-count (htseq-count tool, v.0.4.1).
Sequencing, alignment, and quantitation metrics were obtained for FASTQ, BAM/SAM, and count files in Galaxy using FastQC, Picard, TopHat, Samtools, and htseq-count.
Genome_build: GRCh38
Supplementary_files_format_and_content: CAV_Replicate_testing_RNAseq_cell_subset_counts.csv is a comma-delimited matrix. The first column ("ensgene") contains Ensembl gene IDs. The remaining columns include raw read counts assigned for each library. Data have not been filtered or normalized.

extract_protocol:
RNA was isolated from purified cell subsets (CD4+ T cells, CD8+ T cells, B cells and monocytes) using a Qiagen RNeasy micro kit with on-column DNase digestion
Libraries were constructed from RNA using the Illumina TruSeq RNA Sample Preparation kit v2. Libraries were clustered on flow cells using the TruSeq Single Read Cluster Kit v3.

tag: subject - disease status

value: Screened Healthy Control

tag: subject

tag: age at draw

tag: Sex

value: Female

tag: median cv coverage

tag: fastq total reads

tag: unpaired reads examined

tag: unpaired read duplicates

tag: primary race

value: Biracial


title: aRGC5


title: aRGC4


title: aRGC3


title: lib26229: VT PTID 5807 CD8+CD103-CD69+

status: Public on Sep 10 2019

data_processing:
Base-calling was performed using CASAVA v.1.8.2.
FASTQ reads were trimmed using fastq-mcf (ea-utils, v.1.1.2) to remove SMARTer adapter sequences.
Reads were aligned in Galaxy using bowtie and TopHat (Tophat for Illumina tool, v.1.5.0); duplicate alignments were marked and removed using Picard MarkDuplicates.
Read counts per Ensembl gene ID were estimated in Galaxy using htseq-count (htseq-count tool, v.0.4.1).
Sequencing, alignment, and quantitation metrics were obtained for FASTQ, BAM/SAM, and count files in Galaxy using FastQC, Picard, TopHat, Samtools, and htseq-count.
Genome_build: Homo sapiens GRCh38.77 (version 77)
Supplementary_files_format_and_content: raw_counts_P179.txt is a tab-delimited matrix. The first column contains Ensembl gene IDs The remaining columns include raw read counts assigned for each library.  The data have not been gene filtered or normalized, outlier samples remain in the raw set.

extract_protocol:
250 cells were sorted into lysis buffer from the SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Takara)
Reverse transcription was performed followed by PCR amplification to generate full length amplified cDNA. Sequencing libraries were constructed using the NexteraXT DNA sample preparation kit (Illumina) to generate Illumina-compatible barcoded libraries. Libraries were pooled and quantified using a Qubit® Fluorometer (Life Technologies).

value: Vaginal Tissue

tag: cell type

tag: cell counts

tag: hiv status

value: FALSE

tag: flow cell

value: CBWVTANXX


title: lib26230: VT PTID 5807 CD8+CD103+CD69+

tag: tissue


title: aRGC2


title: lib26232: VT PTID 5807 CD4+


title: lib26231: Bld PTID 5807 CD4+

value: Blood


title: lib26227: Bld PTID 5807 CD8+CD103-CD69+


title: lib26224: VT PTID 5806 CD8+CD103-CD69+

value: Vaginal tissue


title: lib26223: VT PTID 5806 CD8+CD103-CD69-


title: lib26222: Bld PTID 5806 CD8+CD103-CD69+


title: lib26226: Bld PTID 5807 CD8+CD103-CD69-


title: aRGC1


title: lib26228: VT PTID 5807 CD8+CD103-CD69-


title: lib26225: VT PTID 5806 CD8+CD103+CD69+


title: lib26221: Bld PTID 5806 CD8+CD103-CD69-


title: lib26219: VT PTID 5779 CD8+CD103-CD69+

value: TRUE


title: lib26217: Bld PTID 5779 CD8+CD103-CD69+


title: lib26218: VT PTID 5779 CD8+CD103-CD69-


title: lib26220: VT PTID 5779 CD8+CD103+CD69+


title: lib26216: Bld PTID 5779 CD8+CD103-CD69-


title: lib26215: VT PTID 5777 CD4+


title: lib26211: VT PTID 5777 CD103-CD69-


title: lib26210: Cx PTID 5777 CD103+CD69+

value: Cervical tissue


title: lib26212: VT PTID 5777 CD103-CD69+


title: lib26208: Cx PTID 5777 CD103-CD69-


title: lib26207: Bld PTID 5777 CD103-CD69+


title: lib26213: VT PTID 5777 CD103+CD69+


title: lib26214: Bld PTID 5777 CD4+


title: lib26203: VT PTID 5772 CD8+CD103+CD69+


title: lib26200: Bld PTID 5772 CD8+CD103-CD69-


title: lib26205: VT PTID 5772 CD4+


title: lib26202: VT PTID 5772 CD8+CD103-CD69+


title: lib26209: Cx PTID 5777 CD103-CD69+


title: lib26201: Bld PTID 5772 CD8+CD103-CD69+


title: lib26204: Bld PTID 5772 CD4+


title: lib26206: Bld PTID 5777 CD103-CD69-


title: lib26198: Bld PTID 5771 CD4+


title: lib26199: VT PTID 5771 CD4+


title: lib26195: VT PTID 5771 CD8+CD103-CD69-


title: lib26197: VT PTID 5771 CD8+CD103+CD69+


title: lib26191: VT PTID 5144 CD8+CD103-CD69+


title: lib26194: Bld PTID 5771 CD8+CD103-CD69+


title: lib26193: Bld PTID 5771 CD8+CD103-CD69-


title: lib26192: VT PTID 5144 CD8+CD103-CD69+


title: lib26196: VT PTID 5771 CD8+CD103-CD69+


title: lib26189: Bld PTID 5144 CD8+CD103-CD69-


title: lib26190: VT PTID 5144 CD8+CD103+CD69+


title: lib26187: VT PTID 5482 CD8+CD103+CD69+


title: lib26188: Bld PTID 5144 CD8+CD103-CD69+


title: lib21266: Ecto PTID 444 CD8+CD103-CD69-

value: Ecto Cervix


title: lib26186: VT PTID 5482 CD8+CD103-CD69+


title: lib26185: VT PTID 5482 CD8+CD103-CD69-


title: lib21264: Ecto PTID 444 CD8+CD103+CD69+


title: lib21265: Ecto PTID 444 CD8+CD103-CD69+


title: lib21261: Endo PTID 444 CD8+CD103+CD69+

value: Endo Cervix


title: lib21260: VT PTID 444 CD8+CD103-CD69-


title: lib21262: Endo PTID 444CD8+CD103-CD69+


title: lib21263: Endo PTID 444 CD8+CD103-CD69-


title: lib21259: VT PTID 444 CD8+CD103-CD69+


title: lib21255: Ecto PTID 443 CD8+CD103-CD69-


title: lib21256: Bld PTID 444 CD8+CCR7-


title: lib21254: Ecto PTID 443 CD8+CD103-CD69+


title: lib21258: VT PTID 444 CD8+CD103+CD69+


title: lib21252: Endo PTID 443 CD8+CD103-CD69-


title: lib21251: Endo PTID 443 CD8+CD103-CD69+


title: lib21249: VT PTID 443 CD8+CD103-CD69-


title: lib21247: VT PTID 443 CD8+CD103+CD69+


title: lib21248: VT PTID 443 CD8+CD103-CD69+


title: lib21250: Endo PTID 443 CD8+CD103+CD69+


title: lib21246: Bld PTID 443 CD8+CD103-CD69+


title: lib21244: Ecto PTID 421 CD8+CD103-CD69-


title: lib21245: Bld PTID 443 CD8+CCR7-


title: lib21241: Endo PTID 421 CD8+CD103-CD69-


title: lib21253: Ecto PTID 443 CD8+CD103+CD69+


title: lib21239: Endo PTID 421 CD8+CD103+CD69+


title: lib21242: Ecto PTID 421 CD8+CD103+CD69+


title: lib21240: Endo PTID 421 CD8+CD103-CD69+


title: lib21238: VT PTID 421 CD8+CD103-CD69-


title: lib21237: VT PTID 421 CD8+CD103-CD69+


title: lib21236: VT PTID 421 CD8+CD103+CD69+


title: lib21235: Bld PTID 421 CD8+CD103-CD69+


title: lib21234: Bld PTID 421 CD8+CCR7-


title: lib21233: Ecto PTID 417 CD8+CD103-CD69+


title: lib21232: Ecto PTID 417 CD8+CD103-CD69-


title: lib21257: Bld PTID 444 CD8+CD103-CD69+


title: lib21227: VT PTID 417 CD8+CD103-CD69+


title: lib21229: Endo PTID 417 CD8+CD103-CD69-


title: lib21225: VT PTID 417 CD8+CD103+CD69+


title: lib21226: VT PTID 417 CD8+CD103-CD69-


title: lib21243: Ecto PTID 421 CD8+CD103-CD69+


title: lib21228: Endo PTID 417 CD8+CD103+CD69+


title: lib21223: Bld PTID 417 CD8+CD103-CD69-


title: lib21224: Bld PTID 417 CD8+CD103-CD69+


title: 5810 BrafCA;Cdkn2af/f

status: Public on Jul 01 2019

city: Salt Lake City

first: Allie

last: Grossmann

state: Utah

address: 2000 Circle of Hope

department: Pathology

institute: University of Utah

data_processing:
The mouse GRCm38 FASTA and GTF files were downloaded from Ensembl release 90.
The reference database was created using STAR version 2.5.2b with splice junctions optimized for 125 base pair reads.
Reads were trimmed of adapters and aligned to the reference database using STAR in two pass mode to output a BAM file sorted by coordinates.
Mapped reads were assigned to annotated genes in the GTF file using featureCounts version 1.5.1.
Differentially expressed genes were identified using a 5% false discovery rate with DESeq2 version 1.18.0.
Genome_build: GRCm38
Supplementary_files_format_and_content: Raw counts (featureCounts output files combined into a single tab-delimited matrix).

molecule: polyA RNA

source_name: Mouse tumor

extract_protocol:
Qiagen RNAeasy Plus Universal Mini Kit
Illumina TruSeq Stranded mRNA Library Preparation Kit with polyA selection

tag: ID

value: melanoma tumor

tag: genotype


title: 5682 BrafCA;Cdkn2af/f; Arf6Q67L

value: BrafCA;Cdkn2af/f; Arf6Q67L


title: 7285 BrafCA;Cdkn2af/f


title: 5684 BrafCA;Cdkn2af/f; Arf6Q67L


title: 4894 BrafCA;Cdkn2af/f; Arf6Q67L


title: lib21231: Ecto PTID 417 CD8+CD103+CD69+


title: 5681 BrafCA;Cdkn2af/f; Arf6Q67L


title: lib21230: Endo PTID 417 CD8+CD103-CD69+


title: 5610 BrafCA;Cdkn2af/f


title: 5685 BrafCA;Cdkn2af/f; Arf6Q67L


title: 5809 BrafCA;Cdkn2af/f


title: 4893 BrafCA;Cdkn2af/f; Arf6Q67L


title: middle_temporal_gyrus_AD_182_95-31

status: Public on Jun 19 2019

type: RNA

city: Phoenix

first: Ignazio

middle: Stefano

last: Piras

state: Arizona

address: 445 N. Fifth Street, Phoenix

institute: Translational Genomic Research Institute

hyb_protocol: Samples were hybridized to HumanHT-12 v4 BeadChip array (Illumina) according to manufacturer’s protocol. Samples were randomized across batch runs, and no batch effects for age, sex, RIN and PMI were detected

scan_protocol: not provided

data_processing: The raw data probe file was produced and background corrected using GenomeStudio data analysis software (Illumina). Raw expression data were exported and then analyzed at the probe level using R-package Lumi [18]. After computing the detection rate, 3 samples were removed (detection rate < 0.1), obtaining a final dataset of 195 samples (AD = 97; ND = 98). The dataset consisting of 42,179 transcripts was variance-stabilized using the variance-stabilizing transformation (VST) [19]. Data were then normalized with the quantile method using the lumiExpresso function included in the R-package Lumi [18] with default parameters. The raw data file includes the Array Address ID as identifiers. The file GSE132903_Matrix_Normalized.xlsx includes both Illumina probe ID and Array Address ID.

label: biotin

label_protocol: The remaining 198 samples were prepared using TargetAMp – Nano labeling Kit (Ilumina, CA, USA).

extract_protocol: Total RNA extracted from frozen MTG tissue was isolated with RNEasy Mini Kit (Qiagen) starting with 30 mg of tissue. A total of 2 samples were removed due to low RNA quality (RIN < 7).

value: middle temporal gyrus

value: male

tag: expired_age (years)

tag: diagnosis

value: AD


title: middle_temporal_gyrus_ND_16_97-02

value: ND


title: middle_temporal_gyrus_ND_18_97-37


title: middle_temporal_gyrus_ND_23_98-22


title: middle_temporal_gyrus_AD_180_96-21

value: female


title: middle_temporal_gyrus_ND_14_97-09


title: middle_temporal_gyrus_AD_181_98-10


title: middle_temporal_gyrus_AD_178_97-48


title: middle_temporal_gyrus_ND_22_99-02


title: middle_temporal_gyrus_ND_17_97-14


title: middle_temporal_gyrus_ND_200_94-35


title: middle_temporal_gyrus_ND_20_99-29


title: middle_temporal_gyrus_AD_197_00-47


title: middle_temporal_gyrus_AD_179_98-07


title: middle_temporal_gyrus_AD_176_96-04


title: middle_temporal_gyrus_AD_198_01-13


title: middle_temporal_gyrus_ND_21_99-22


title: middle_temporal_gyrus_ND_24_98-32


title: middle_temporal_gyrus_AD_195_08-59


title: middle_temporal_gyrus_ND_15_97-10


title: middle_temporal_gyrus_AD_199_98-18


title: middle_temporal_gyrus_AD_194_05-57


title: middle_temporal_gyrus_ND_13_96-45


title: middle_temporal_gyrus_AD_196_99-06


title: middle_temporal_gyrus_AD_193_01-33


title: middle_temporal_gyrus_AD_191_07-02


title: middle_temporal_gyrus_ND_19_98-33


title: middle_temporal_gyrus_AD_190_99-24


title: middle_temporal_gyrus_AD_192_03-19


title: middle_temporal_gyrus_AD_177_97-39


title: middle_temporal_gyrus_ND_188_95-38


title: middle_temporal_gyrus_ND_186_95-30


title: middle_temporal_gyrus_ND_187_95-36


title: middle_temporal_gyrus_AD_173_03-54


title: middle_temporal_gyrus_AD_172_03-40


title: middle_temporal_gyrus_AD_171_05-01


title: middle_temporal_gyrus_AD_175_98-12


title: middle_temporal_gyrus_AD_185_05-19


title: middle_temporal_gyrus_ND_189_95-03


title: middle_temporal_gyrus_AD_174_05-25


title: middle_temporal_gyrus_AD_169_04-28


title: middle_temporal_gyrus_AD_165_04-49


title: middle_temporal_gyrus_AD_168_04-16


title: middle_temporal_gyrus_AD_162_06-52


title: middle_temporal_gyrus_AD_164_06-37


title: middle_temporal_gyrus_AD_160_99-13


title: middle_temporal_gyrus_AD_161_05-37


title: middle_temporal_gyrus_AD_167_06-67


title: middle_temporal_gyrus_AD_157_00-50


title: middle_temporal_gyrus_AD_159_99-48


title: middle_temporal_gyrus_AD_170_04-06


title: middle_temporal_gyrus_AD_154_00-04


title: middle_temporal_gyrus_AD_156_00-33


title: middle_temporal_gyrus_AD_151_99-21


title: middle_temporal_gyrus_AD_155_00-13


title: middle_temporal_gyrus_AD_158_99-15


title: middle_temporal_gyrus_AD_166_05-52


title: middle_temporal_gyrus_AD_152_01-11


title: middle_temporal_gyrus_AD_153_98-28


title: middle_temporal_gyrus_AD_163_05-39


title: middle_temporal_gyrus_AD_184_04-33


title: middle_temporal_gyrus_AD_150_00-08


title: middle_temporal_gyrus_AD_135_03-34


title: middle_temporal_gyrus_AD_140_02-19


title: middle_temporal_gyrus_AD_146_00-28


title: middle_temporal_gyrus_AD_143_01-07


title: middle_temporal_gyrus_AD_149_99-61


title: middle_temporal_gyrus_AD_138_02-07


title: middle_temporal_gyrus_AD_141_03-32


title: middle_temporal_gyrus_AD_144_00-35


title: middle_temporal_gyrus_AD_183_97-24


title: middle_temporal_gyrus_AD_145_00-54


title: middle_temporal_gyrus_AD_136_01-16


title: middle_temporal_gyrus_AD_123_07-27


title: middle_temporal_gyrus_AD_133_02-35


title: middle_temporal_gyrus_AD_124_07-29


title: middle_temporal_gyrus_AD_137_01-28


title: middle_temporal_gyrus_AD_139_02-09


title: middle_temporal_gyrus_AD_131_02-39


title: middle_temporal_gyrus_AD_128_08-29


title: middle_temporal_gyrus_AD_147_00-10


title: middle_temporal_gyrus_AD_134_03-14


title: middle_temporal_gyrus_AD_130_08-37


title: middle_temporal_gyrus_AD_127_08-01


title: middle_temporal_gyrus_AD_126_08-48


title: middle_temporal_gyrus_AD_129_08-30


title: middle_temporal_gyrus_AD_132_01-32


title: middle_temporal_gyrus_AD_142_03-36


title: middle_temporal_gyrus_AD_122_08-10


title: middle_temporal_gyrus_AD_121_07-15


title: middle_temporal_gyrus_AD_112_07-64


title: middle_temporal_gyrus_AD_110_08-89


title: middle_temporal_gyrus_AD_115_07-54


title: middle_temporal_gyrus_AD_119_07-49


title: middle_temporal_gyrus_AD_111_08-06


title: middle_temporal_gyrus_AD_114_08-05


title: middle_temporal_gyrus_AD_113_07-57


title: middle_temporal_gyrus_AD_104_01-53


title: middle_temporal_gyrus_AD_120_08-69


title: middle_temporal_gyrus_AD_108_07-69


title: middle_temporal_gyrus_AD_116_07-21


title: middle_temporal_gyrus_AD_118_08-82


title: middle_temporal_gyrus_AD_105_08-45


title: middle_temporal_gyrus_AD_107_07-50


title: middle_temporal_gyrus_AD_98_02-28


title: middle_temporal_gyrus_AD_100_03-21


title: middle_temporal_gyrus_AD_101_03-27


title: middle_temporal_gyrus_AD_103_01-48


title: middle_temporal_gyrus_AD_102_01-45


title: middle_temporal_gyrus_AD_106_08-20


title: middle_temporal_gyrus_ND_93_03-58


title: middle_temporal_gyrus_AD_99_03-18


title: middle_temporal_gyrus_AD_97_03-04


title: middle_temporal_gyrus_AD_109_07-34


title: middle_temporal_gyrus_ND_95_03-66


title: middle_temporal_gyrus_ND_92_02-08


title: middle_temporal_gyrus_ND_91_02-06


title: middle_temporal_gyrus_ND_94_99-58


title: middle_temporal_gyrus_AD_96_02-41


title: middle_temporal_gyrus_ND_87_03-11


title: middle_temporal_gyrus_ND_86_00-38


title: middle_temporal_gyrus_ND_90_99-31


title: middle_temporal_gyrus_ND_88_03-47


title: middle_temporal_gyrus_ND_79_03-15


title: middle_temporal_gyrus_ND_69_08-04


title: middle_temporal_gyrus_ND_72_07-30


title: middle_temporal_gyrus_ND_74_08-55


title: middle_temporal_gyrus_ND_80_03-41


title: middle_temporal_gyrus_ND_81_00-49


title: middle_temporal_gyrus_ND_83_02-12


title: middle_temporal_gyrus_ND_78_04-19


title: middle_temporal_gyrus_ND_73_08-40


title: middle_temporal_gyrus_ND_76_03-17


title: middle_temporal_gyrus_ND_75_02-24


title: middle_temporal_gyrus_ND_82_02-04


title: middle_temporal_gyrus_ND_66_07-18


title: middle_temporal_gyrus_ND_77_03-28


title: middle_temporal_gyrus_ND_71_07-11


title: middle_temporal_gyrus_ND_64_06-63


title: middle_temporal_gyrus_ND_85_01-36


title: middle_temporal_gyrus_ND_70_08-35


title: middle_temporal_gyrus_ND_84_00-53


title: middle_temporal_gyrus_ND_89_04-05


title: middle_temporal_gyrus_ND_65_07-70


title: middle_temporal_gyrus_ND_62_04-64


title: middle_temporal_gyrus_ND_67_08-44


title: middle_temporal_gyrus_ND_61_04-31


title: middle_temporal_gyrus_ND_68_07-46


title: middle_temporal_gyrus_ND_63_05-28


title: middle_temporal_gyrus_ND_59_06-21


title: middle_temporal_gyrus_ND_58_06-15


title: middle_temporal_gyrus_ND_55_06-49


title: middle_temporal_gyrus_ND_53_04-30


title: middle_temporal_gyrus_ND_57_05-36


title: middle_temporal_gyrus_ND_56_06-61


title: middle_temporal_gyrus_ND_49_04-62


title: middle_temporal_gyrus_ND_47_06-13


title: middle_temporal_gyrus_ND_50_05-18


title: middle_temporal_gyrus_ND_54_06-32


title: middle_temporal_gyrus_ND_48_06-53


title: middle_temporal_gyrus_ND_51_06-35


title: middle_temporal_gyrus_ND_42_06-68


title: middle_temporal_gyrus_ND_38_96-32


title: middle_temporal_gyrus_ND_44_04-38


title: middle_temporal_gyrus_ND_37_96-28


title: middle_temporal_gyrus_ND_39_96-35


title: middle_temporal_gyrus_ND_52_06-57


title: middle_temporal_gyrus_ND_45_06-02


title: middle_temporal_gyrus_ND_34_96-30


title: middle_temporal_gyrus_ND_43_04-52


title: middle_temporal_gyrus_ND_40_96-16


title: middle_temporal_gyrus_ND_60_05-20


title: middle_temporal_gyrus_ND_31_95-02


title: middle_temporal_gyrus_ND_32_96-44


title: middle_temporal_gyrus_ND_36_96-22


title: middle_temporal_gyrus_ND_41_05-14


title: middle_temporal_gyrus_ND_33_96-39


title: middle_temporal_gyrus_ND_30_93-07


title: middle_temporal_gyrus_ND_46_06-03


title: middle_temporal_gyrus_ND_29_92-32


title: REP 1 VP160

status: Public on Jun 11 2019

city: Ottawa

first: Ruth

last: McPherson

state: Ontario

address: 40 Ruskin

country: Canada

institute: UOHI

description: Expression console values

hyb_protocol: Samples were hybridized with Clariom D chips (Affymetrix) and scanned at the Centre for Applied Genomics (TCAG), Toronto

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix)

data_processing: RMA algorithm. Relative expression changes assessed by Expression Console

label: Biotin

label_protocol: Standard Affymetrix protocol

growth_protocol: High glucose DMEM

extract_protocol: High Pure RNA isolation

treatment_protocol: Plasmid transfection with lipofectamine 3000 in 24 well plates; 0.5 ug plasmid (0.35 ug of dCas9 VP16 and 0.15 ug of pCRU6cg-286 or Pcru6); ratio of 1.5 lipof3000:1 ul p3000: 0.5 ug DNA

value: Human embryonic Kidney cell line

tag: cell line

tag: experiment

value: cgRNA (SG -286) construct expressing either a targeting the promoter region of a lncRNA (RP11-326A19.4)


title: REP2 TrcrRNA

description: Expression console values

value: tracrRNA


title: REP1 TrcrRNA

description: Expression console values


title: REP 3 VP160

description: Expression console values


title: REP3 TrcrRNA

description: Expression console values


title: REP 2 VP160

description: Expression console values


title: middle_temporal_gyrus_ND_10_97-19

tag: Sex


title: middle_temporal_gyrus_ND_25_99-04


title: middle_temporal_gyrus_ND_9_97-17


title: middle_temporal_gyrus_ND_26_99-27


title: middle_temporal_gyrus_ND_6_97-53


title: Mϕ THP-1_RNA-seq [Mϕ_2]

status: Public on Apr 19 2019

city: Camperdown

first: RENHUA

last: SONG

state: NSW

address: Charles Perkins Centre - D17, Level 4 West. The University of Sydney Johns Hopkins Drive

country: Australia

institute: Centenary Institute

description:
THP1_M0_2
processed data file:
ND_M0_M1.rlog.txt
M0_ND.tab
M1_M0.tab

data_processing:
For RNA-seq data: The original raw data from Illumina CASAVA v1.8 software are transformed to Sequenced Reads by base calling.
Raw reads are filtered to remove reads containing adapters or reads of low quality reads, then were mapped to Ensembl human reference genome (GRCh38.v86) using STAR_2.5.2a.
Quantification of intron retention (IR) and Differential IR analysis were run by IRFinder (v1.2.3) and its built-in script via Audic and Claverie test respectively.
Gene-leve expression was measured using featureCounts (1.5.0-p3).Differential expression was assessed with Deseq2 (1.22.2)
For WGBS data: Bisulphite reads were processed and aligned to the human genome reference using Meth10X, https://github.com/luuloi/Meth10X (Nair et al., 2018).
Genome_build: GRCh38.v86 (Ensembl)
Supplementary_files_format_and_content: Tab delimited txt file including rlog normalized counts for ND_M0_M1 and differetial IR quantification. A count table and bigwig files of methylated and coverage at each CpG site in the genome.

source_name: THP-1 macrophage_Mϕ

growth_protocol: Human THP-1 monocytic cells were maintained in RPMI medium supplemented with 2 mM L-glutamine, 25 mM HEPES, 10% (v/v) FBS, 1 mM sodium pyruvate, 1% (v/v) non-essential amino acids, and 0.1 mg/mL penicillin/streptomycin at 37°C in the presence of 5% CO2.

extract_protocol:
Total RNA was extracted using Trizol. Genomic DNA was extracted using standard phenol-chloroform method.
Poly-A-enriched mRNA libraries were prepared from 2 μg of TURBOTM DNase-treated, total RNA using the TruSeq® Stranded Library Preparation Kit (Illumina), according to the manufacturers’ instructions. mRNA sequencing was performed on each cell population in triplicates by Novogene (China). A total of 100 million paired-end strand-specific reads were sequenced per sample on an Illumina HiSeq 2500 Platform.Whole-genome bisulphite sequencing (WGBS) was performed on a HiSeq X Ten platform (Illumina) following library preparation using the TruMethyl WG method v.1.9 (Cambridge Epigenetix).

treatment_protocol: 1.5 × 10^7 cells per 75 cm2 culture flask of THP-1 cells were differentiated using phorbol-12-myristate 13-acetate (PMA) into macrophages. Resting macrophages are further polarised into pro-inflammatory macrophages using lipopolysaccharide (LPS) and interferon gamma (IFN-γ). To inhibit nuclear degradation by the RNA exosome, THP-1 macrophages were transfected with 300 nM EXOSC10 siRNA (sense: 5′ – GAAGGCAGCUGAGCAAACAdTdT – 3′, antisense: 5′ – UGUUUGCUCAGCUGCCUUCdTdT). ON-TARGETplus non-targeting siRNA (GE Dharmacon) was used as a negative control.

value: THP-1-derived macrophage


title: middle_temporal_gyrus_ND_12_97-03


title: M1 THP-1_RNA-seq [MLPS+IFN-γ_2]

description:
THP1_M1_2
processed data file:
ND_M0_M1.rlog.txt
M1_M0.tab

source_name: THP-1 macrophage (polarised)_M1

value: THP-1-derived macrophage (polarised)


title: Mϕ THP-1_RNA-seq [Mϕ_3]

description:
THP1_M0_3
processed data file:
ND_M0_M1.rlog.txt
M0_ND.tab
M1_M0.tab


title: middle_temporal_gyrus_ND_8_97-46


title: Mϕ THP-1_RNA-seq [Mϕ_1]

description:
THP1_M0_1
processed data file:
ND_M0_M1.rlog.txt
M0_ND.tab
M1_M0.tab


title: M1 THP-1_RNA-seq [MLPS+IFN-γ_3]

description:
THP1_M1_3
processed data file:
ND_M0_M1.rlog.txt
M1_M0.tab


title: M1 THP-1_RNA-seq [MLPS+IFN-γ_1]

description:
THP1_M1_1
processed data file:
ND_M0_M1.rlog.txt
M1_M0.tab


title: Mo THP-1_RNA-seq [Mo_3]

description:
THP1_ND_3
processed data file:
ND_M0_M1.rlog.txt
M0_ND.tab

source_name: THP-1 monocytic cells_Mo

value: Monocytic cell line


title: Mo THP-1_RNA-seq [Mo_2]

description:
THP1_ND_2
processed data file:
ND_M0_M1.rlog.txt
M0_ND.tab


title: middle_temporal_gyrus_ND_7_98-19


title: middle_temporal_gyrus_ND_1_08-81


title: middle_temporal_gyrus_ND_4_08-72


title: middle_temporal_gyrus_ND_2_08-85


title: middle_temporal_gyrus_ND_5_08-83


title: Mo THP-1_RNA-seq [Mo_1]

description:
THP1_ND_1
processed data file:
ND_M0_M1.rlog.txt
M0_ND.tab


title: middle_temporal_gyrus_ND_28_92-14


title: ID132 HSC

status: Public on Apr 16 2019

city: Zurich

first: Slavica

last: Dimitrieva Janeva

state: Zurich

address: Winterthurerstrasse 190

department: Functional Genomics Center Zurich

country: Switzerland

institute: ETH Zürich / University of Zurich

data_processing:
Generation of fastq files was done using bcl2fastq software version 2.19.0
Reads were trimmed with Trimmomatic version 0.33 (4 and 3 bases were hard-trimmed from the start and end respectively; adapter trimming was done at the end).
Trimmed reads were aligned to the Ensembl GRCh38 human reference genome and transcriptome with STAR version 2.5.1b.
Read quantification was done using the R/Bioconductor package Rsubread version 1.26.0.
Genome_build: Ensembl Human reference GRCh38 release 86
Supplementary_files_format_and_content: tab-delimited text file showing raw read counts for each sample (columns) and each gene (rows)

source_name: Blood

growth_protocol: Fresh human hematopoietic stem/progenitor cells were obtained from 5 healthy donors aged between 28 and 57 years old (average: 39.8); 4 males, 1 female; with informed consent and approval of the local ethics committee (KEK-ZH-Nr: 2015-0564, Clinical Hematology, University Hospital Zurich, Zurich Switzerland).

extract_protocol:
After mobilization with granulocyte-colony stimulating factor (G-CSF), stem-cell enriched mononuclear leukocytes were obtained via plasmapheresis from peripheral blood of donors for clinical stem cell transplantation (Clinical Hematology, University Hospital Zurich, Zurich Switzerland). Left-over material after clinical transplantation was enrichted for CD34+ stem/progenitor cells using immunomagnetic beads according to manufacturer instructions (CD34 MicroBead Kit; Miltenyi Biotec). Fluorescence-activated cell sorting and antibodies specific for CD2, CD3, CD4, CD7, CD8, CD14, CD19, CD56, CD10, CD11b, CD20, CD235a, CD34, CD38, CD123, CD45RA were used to isolate the various cell types (HSC, CMP, GMP, MEP). 10'000 cells of each subpopulations were sorted into RNeasy lysis buffer containing beta-mercaptoethanol. Total RNA was purified according to manufacturer instructions using the RNeasy Plus Micro Kit (Qiagen). The samples were of high enough quality for a poly-A tail based approach for RNA sequencing. RNA sequencing was performed as described in Picelli S. et al. Nature Protocols 2014 using the Illumina HiSeq 4000 sequencing platform.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Stem-cell enriched mononuclear leukocytes were mobilized from the bone marrow using granulocyte-colony stimulating factor (G-CSF) (twice daily administrations over 4 days).

value: hematopoietic stem cells

tag: donor age

value: 28 years

tag: donor sex


title: middle_temporal_gyrus_ND_27_92-10


title: lib15177_CB5HFANXX

status: Public on Apr 10 2019

data_processing:
Base-calling was performed using CASAVA v.1.8.2.
FASTQ reads were trimmed using fastq-mcf (ea-utils, v.1.1.2) to remove SMARTer adapter sequences.
Reads were aligned in Galaxy using bowtie and TopHat (Tophat for Illumina tool, v.1.5.0); duplicate alignments were marked and removed using Picard MarkDuplicates.
Read counts per Ensembl gene ID were estimated in Galaxy using htseq-count (htseq-count tool, v.0.4.1).
Sequencing, alignment, and quantitation metrics were obtained for FASTQ, BAM/SAM, and count files in Galaxy using FastQC, Picard, TopHat, Samtools, and htseq-count.
Genome_build: GRCh37
Supplementary_files_format_and_content: raw_counts_nasal_muppits523.txt is a tab-delimited matrix. The first column contains Ensembl gene IDs The remaining columns include raw read counts assigned for each library. Outlier samples have been removed but data have not been gene filtered or normalized.

extract_protocol:
RNA was extracted from TRIzol following the manufacturer’s protocol (Invitrogen)
RNA quality was assessed using RNA electrophoresis (Agilent). All samples had RIN values ≥7. Sequencing libraries were constructed from total RNA using TruSeq RNA Sample Preparation Kits v2 (Illumina)

tag: source tissue

value: Nasal Lavage

tag: flowcell

value: M

value: Visit 0

tag: mediancvcoverage

tag: percentaligned


title: lib15174_CB5HFANXX

value: F


title: lib15173_CB5HFANXX

value: Visit 2b


title: lib15175_CB5HFANXX

value: Visit 1b


title: lib15176_CB5HFANXX

value: Visit 1a


title: lib15178_CB5HFANXX


title: lib15179_CB5HFANXX


title: lib15172_CB5HFANXX

value: Visit 2a


title: lib15167_CB5HFANXX


title: lib15170_CB5HFANXX


title: lib15165_CB5HFANXX


title: lib15166_CB5HFANXX


title: lib15163_CB5HFANXX


title: lib15164_CB5HFANXX


title: lib12489_C95GDANXX


title: lib15161_CB5HFANXX


title: lib15159_CB5HFANXX


title: lib15160_CB5HFANXX


title: lib12364_C95GDANXX


title: lib12380_C95GDANXX


title: lib12385_C95GDANXX


title: ID185 HSC

tag: cell type

value: 51 years

value: male


title: lib15171_CB5HFANXX


title: lib16688_CB5HFANXX

status: Public on Apr 08 2019

data_processing:
Base-calling was performed using CASAVA v.1.8.2.
FASTQ reads were trimmed using fastq-mcf (ea-utils, v.1.1.2) to remove SMARTer adapter sequences.
Reads were aligned in Galaxy using bowtie and TopHat (Tophat for Illumina tool, v.1.5.0); duplicate alignments were marked and removed using Picard MarkDuplicates.
Read counts per Ensembl gene ID were estimated in Galaxy using htseq-count (htseq-count tool, v.0.4.1).
Sequencing, alignment, and quantitation metrics were obtained for FASTQ, BAM/SAM, and count files in Galaxy using FastQC, Picard, TopHat, Samtools, and htseq-count.
Genome_build: GRCh37
Supplementary_files_format_and_content: raw_counts_blood_muppits511.txt is a tab-delimited matrix. The first column contains Ensembl gene IDs The remaining columns include raw read counts assigned for each library. Outlier samples have been removed but data have not been gene filtered or normalized.

value: Peripheral Blood


title: lib16692_CB5HFANXX


title: lib16668_CB5HFANXX


title: lib15162_CB5HFANXX


title: lib16651_CB5HFANXX


title: lib16650_CB5HFANXX


title: lib16632_CB5HFANXX


title: lib16633_CB5HFANXX


title: lib16648_CB5HFANXX


title: lib16587_CB5HFANXX


title: lib16649_CB5HFANXX


title: lib16586_CB5HFANXX


title: lib16647_CB5HFANXX


title: lib16558_CB5HFANXX


title: lib16570_CB5HFANXX


title: lib16560_CB5HFANXX


title: lib16588_CB5HFANXX


title: lib16555_CB5HFANXX


title: lib16571_CB5HFANXX


title: lib16561_CB5HFANXX


title: lib16559_CB5HFANXX


title: lib16557_CB5HFANXX


title: lib16552_CB5HFANXX


title: lib16554_CB5HFANXX


title: lib16562_CB5HFANXX


title: lib16556_CB5HFANXX


title: lib16542_CB4FNANXX


title: lib16525_CB4FNANXX


title: lib16543_CB4FNANXX


title: lib16515_CB4FNANXX


title: lib16514_CB4FNANXX


title: lib16506_CB4FNANXX


title: lib16511_CB4FNANXX


title: lib16504_CB4FNANXX


title: lib16535_CB4FNANXX


title: lib16503_CB4FNANXX


title: lib16505_CB4FNANXX


title: lib16455_CB4FNANXX


title: lib16482_CB4FNANXX


title: lib16484_CB4FNANXX


title: lib16452_CB4FNANXX


title: lib16447_CB4FNANXX


title: lib16502_CB4FNANXX


title: lib16454_CB4FNANXX


title: lib16449_CB4FNANXX


title: lib16483_CB4FNANXX


title: lib16453_CB4FNANXX


title: lib16441_CB4FNANXX


title: lib16450_CB4FNANXX


title: lib16442_CB4FNANXX


title: lib16443_CB4FNANXX


title: lib16440_CB4FNANXX


title: lib16448_CB4FNANXX


title: lib16446_CB4FNANXX


title: lib16451_CB4FNANXX


title: lib16439_CB4FNANXX


title: lib16444_CB4FNANXX


title: lib16438_CB4FNANXX


title: lib16436_CB4FNANXX


title: lib16435_CB4FNANXX


title: lib16433_CB4FNANXX


title: lib16434_CB4FNANXX


title: lib16431_CB4FNANXX


title: lib16409_CB4FNANXX


title: lib16410_CB4FNANXX


title: lib16386_CB4FNANXX


title: lib16387_CB4FNANXX


title: lib16408_CB4FNANXX


title: lib16430_CB4FNANXX


title: lib15151_CAJMRANXX

value: CAJMRANXX


title: lib15154_CAJMRANXX


title: lib15156_CAJMRANXX


title: lib15146_CAJMRANXX


title: lib15144_CAJMRANXX


title: lib15133_CAJMRANXX


title: lib15153_CAJMRANXX


title: lib15147_CAJMRANXX


title: lib15145_CAJMRANXX


title: lib15150_CAJMRANXX


title: lib15113_CAJMRANXX


title: lib15108_CAJMRANXX


title: lib15107_CAJMRANXX


title: lib15104_CAJMRANXX


title: lib16432_CB4FNANXX


title: lib15103_CAJMRANXX


title: lib15155_CAJMRANXX


title: lib15152_CAJMRANXX


title: lib15120_CAJMRANXX


title: lib15143_CAJMRANXX


title: lib15090_CAJMRANXX


title: lib15088_CAJMRANXX


title: lib15099_CAJMRANXX


title: lib15134_CAJMRANXX


title: lib12964_C97JMANXX


title: lib15149_CAJMRANXX


title: lib15128_CAJMRANXX


title: lib12916_C97JMANXX


title: lib12940_C97JMANXX


title: lib12889_C97JMANXX


title: lib12891_C97JMANXX


title: lib11365_C8B30ANXX


title: lib11363_C8B30ANXX


title: lib11354_C8B30ANXX


title: lib11348_C8B30ANXX


title: lib11370_C8B30ANXX


title: middle_temporal_gyrus_ND_11_97-45

value: middle temporal gyrus

value: ND


title: lib15101_CAJMRANXX


title: lib15100_CAJMRANXX


title: lib11341_C8B30ANXX


title: lib11345_C8B30ANXX


title: lib15098_CAJMRANXX


title: lib12958_C97JMANXX


title: lib11364_C8B30ANXX


title: lib11340_C8B30ANXX


title: lib11335_C8B30ANXX


title: lib11336_C8B30ANXX


title: lib11334_C8B30ANXX


title: lib11332_C8B30ANXX


title: lib15102_CAJMRANXX


title: lib11371_C8B30ANXX


title: lib11329_C8B30ANXX


title: lib11328_C8B30ANXX


title: lib11337_C8B30ANXX


title: lib11366_C8B30ANXX


title: lib18001_CB5HFANXX

data_processing:
Base-calling was performed using CASAVA v.1.8.2.
FASTQ reads were trimmed using fastq-mcf (ea-utils, v.1.1.2) to remove SMARTer adapter sequences.
Reads were aligned in Galaxy using bowtie and TopHat (Tophat for Illumina tool, v.1.5.0); duplicate alignments were marked and removed using Picard MarkDuplicates.
Read counts per Ensembl gene ID were estimated in Galaxy using htseq-count (htseq-count tool, v.0.4.1).
Sequencing, alignment, and quantitation metrics were obtained for FASTQ, BAM/SAM, and count files in Galaxy using FastQC, Picard, TopHat, Samtools, and htseq-count.
Genome_build: GRCh37
Supplementary_files_format_and_content: raw_counts_nasal_muppits500.txt is a tab-delimited matrix. The first column contains Ensembl gene IDs The remaining columns include raw read counts assigned for each library. Outlier samples have been removed but data have not been gene filtered or normalized.


title: lib18000_CB5HFANXX


title: lib18006_CB5HFANXX


title: lib17999_CB5HFANXX


title: lib18005_CB5HFANXX


title: lib17998_CB5HFANXX


title: lib17997_CB5HFANXX


title: lib18003_CB5HFANXX


title: lib17996_CB5HFANXX


title: lib18004_CB5HFANXX


title: lib17989_CB4FNANXX


title: lib11333_C8B30ANXX


title: lib17991_CB5HFANXX


title: lib17995_CB5HFANXX


title: lib17990_CB5HFANXX


title: lib17982_CB4FNANXX


title: lib17986_CB4FNANXX


title: lib17976_CB4FNANXX


title: lib17977_CB4FNANXX


title: lib11330_C8B30ANXX


title: lib17981_CB4FNANXX


title: lib17987_CB4FNANXX


title: lib17980_CB4FNANXX


title: lib17974_CB4FNANXX


title: lib17973_CB4FNANXX


title: lib17975_CB4FNANXX


title: lib17970_CB4FNANXX


title: lib17972_CB4FNANXX


title: lib15168_CB5HFANXX


title: lib15414_CAJMRANXX


title: lib15169_CB5HFANXX


title: lib15410_CAJMRANXX


title: lib15408_CAJMRANXX


title: lib15316_CAJMRANXX


title: lib15302_CAJMRANXX


title: lib15409_CAJMRANXX


title: lib15317_CAJMRANXX


title: lib15315_CAJMRANXX


title: lib15407_CAJMRANXX


title: lib15301_CAJMRANXX


title: lib15298_CAJMRANXX


title: lib17979_CB4FNANXX


title: lib15299_CAJMRANXX


title: lib15222_CAJMRANXX


title: lib15262_CAJMRANXX


title: lib15254_CAJMRANXX


title: lib15221_CAJMRANXX


title: lib15202_CAJMRANXX


title: lib15217_CAJMRANXX


title: lib15201_CAJMRANXX


title: lib15200_CAJMRANXX


title: lib15199_CAJMRANXX


title: lib15198_CAJMRANXX


title: lib15293_CAJMRANXX


title: lib15195_CAJMRANXX


title: lib15186_CAJMRANXX


title: lib15169_CAJMRANXX


title: lib15168_CAJMRANXX


title: lib12513_C95GDANXX


title: lib12508_C95GDANXX


title: lib12507_C95GDANXX


title: lib15260_CAJMRANXX


title: lib12445_C95GDANXX


title: lib12510_C95GDANXX


title: lib12444_C95GDANXX


title: lib12443_C95GDANXX


title: lib12465_C95GDANXX


title: lib12440_C95GDANXX


title: lib12425_C95GDANXX


title: lib12424_C95GDANXX


title: lib12441_C95GDANXX


title: lib12423_C95GDANXX


title: lib12422_C95GDANXX


title: lib12421_C95GDANXX


title: lib12376_C95GDANXX


title: lib12374_C95GDANXX


title: lib12375_C95GDANXX


title: lib16689_CB5HFANXX

tag: used in analysis

value: Yes

value: Control

value: Viral

value: No

tag: libcounts


title: lib16691_CB5HFANXX

value: Non-viral


title: lib12511_C95GDANXX

tag: tissue

value: Nasal Lavage


title: lib16686_CB5HFANXX

value: M

value: Case

value: After


title: lib12469_C95GDANXX

value: Visit 1a


title: lib12446_C95GDANXX

value: Visit 1b


title: lib16687_CB5HFANXX

value: Visit 0


title: lib16683_CB5HFANXX

tag: used in module construction

value: F


title: lib16690_CB5HFANXX

value: Peripheral Blood


title: lib16682_CB5HFANXX


title: lib16681_CB5HFANXX


title: lib16678_CB5HFANXX


title: lib16680_CB5HFANXX


title: lib16679_CB5HFANXX


title: lib16676_CB5HFANXX


title: lib16677_CB5HFANXX


title: lib16675_CB5HFANXX


title: lib16674_CB5HFANXX

value: Before


title: lib16671_CB5HFANXX


title: lib16672_CB5HFANXX


title: lib16673_CB5HFANXX


title: lib12420_C95GDANXX


title: lib16670_CB5HFANXX


title: lib16669_CB5HFANXX


title: lib16666_CB5HFANXX


title: lib16685_CB5HFANXX

value: Visit 2b


title: lib16684_CB5HFANXX

value: Visit 2a


title: lib16665_CB5HFANXX

value: Yes


title: lib16662_CB5HFANXX

value: Control


title: lib16664_CB5HFANXX


title: lib16661_CB5HFANXX


title: lib16667_CB5HFANXX


title: lib16659_CB5HFANXX

value: Viral


title: lib16660_CB5HFANXX

value: No


title: lib16654_CB5HFANXX


title: lib16652_CB5HFANXX


title: lib16655_CB5HFANXX


title: lib16656_CB5HFANXX

value: Non-viral


title: lib16646_CB5HFANXX


title: lib16645_CB5HFANXX


title: lib16643_CB5HFANXX


title: lib16663_CB5HFANXX


title: lib16641_CB5HFANXX


title: lib16642_CB5HFANXX


title: lib16638_CB5HFANXX


title: lib16640_CB5HFANXX


title: lib16637_CB5HFANXX


title: lib16639_CB5HFANXX


title: lib16653_CB5HFANXX


title: lib16636_CB5HFANXX


title: lib16635_CB5HFANXX


title: lib16629_CB5HFANXX


title: lib16634_CB5HFANXX


title: lib16631_CB5HFANXX


title: lib16658_CB5HFANXX


title: lib16626_CB5HFANXX


title: lib16630_CB5HFANXX


title: lib16627_CB5HFANXX


title: lib16624_CB5HFANXX


title: lib16644_CB5HFANXX


title: lib16628_CB5HFANXX


title: lib16622_CB5HFANXX


title: lib16623_CB5HFANXX


title: lib16625_CB5HFANXX


title: lib16610_CB5HFANXX


title: lib16614_CB5HFANXX


title: lib16615_CB5HFANXX


title: lib16609_CB5HFANXX


title: lib16605_CB5HFANXX


title: lib16616_CB5HFANXX


title: lib16617_CB5HFANXX


title: lib16607_CB5HFANXX


title: lib16613_CB5HFANXX


title: lib16618_CB5HFANXX


title: lib16602_CB5HFANXX


title: lib16603_CB5HFANXX


title: lib16620_CB5HFANXX


title: lib16619_CB5HFANXX


title: lib16621_CB5HFANXX


title: lib16611_CB5HFANXX


title: lib16608_CB5HFANXX


title: lib16604_CB5HFANXX


title: lib16606_CB5HFANXX


title: lib16593_CB5HFANXX


title: lib16600_CB5HFANXX


title: lib16598_CB5HFANXX


title: lib16597_CB5HFANXX


title: lib16612_CB5HFANXX


title: lib16594_CB5HFANXX


title: lib16595_CB5HFANXX


title: lib16592_CB5HFANXX


title: lib16599_CB5HFANXX


title: lib16601_CB5HFANXX


title: lib16589_CB5HFANXX


title: lib16585_CB5HFANXX


title: lib16590_CB5HFANXX


title: lib16591_CB5HFANXX


title: lib16584_CB5HFANXX


title: lib17994_CB5HFANXX

value: Nasal Lavage


title: lib16577_CB5HFANXX


title: lib16578_CB5HFANXX

value: M


title: lib16575_CB5HFANXX


title: lib16581_CB5HFANXX


title: lib16582_CB5HFANXX


title: lib16572_CB5HFANXX


title: lib16569_CB5HFANXX

value: Case


title: lib16580_CB5HFANXX


title: lib16573_CB5HFANXX


title: lib16576_CB5HFANXX


title: lib16567_CB5HFANXX


title: lib16574_CB5HFANXX


title: lib16568_CB5HFANXX

value: After


title: lib16565_CB5HFANXX


title: lib16566_CB5HFANXX


title: lib16564_CB5HFANXX


title: lib16583_CB5HFANXX


title: lib16563_CB5HFANXX


title: lib16548_CB4FNANXX


title: lib16547_CB4FNANXX

value: Visit 1a


title: lib16545_CB4FNANXX


title: lib16546_CB4FNANXX

value: Visit 1b


title: lib16579_CB5HFANXX

value: Visit 0


title: lib16544_CB4FNANXX


title: lib16540_CB4FNANXX

value: F


title: lib16538_CB4FNANXX

value: Peripheral Blood


title: lib16537_CB4FNANXX

value: Before


title: lib16539_CB4FNANXX


title: lib16536_CB4FNANXX


title: lib16532_CB4FNANXX

value: Visit 2b


title: lib16541_CB4FNANXX


title: lib16528_CB4FNANXX


title: lib16534_CB4FNANXX


title: lib16529_CB4FNANXX


title: lib16530_CB4FNANXX


title: lib16527_CB4FNANXX


title: lib16533_CB4FNANXX


title: lib16531_CB4FNANXX

value: Visit 2a


title: lib16523_CB4FNANXX

value: Yes


title: lib16519_CB4FNANXX

value: Control


title: lib16521_CB4FNANXX


title: lib16518_CB4FNANXX


title: lib16522_CB4FNANXX

value: Viral


title: lib16520_CB4FNANXX

value: No


title: lib16526_CB4FNANXX

value: Non-viral


title: lib16516_CB4FNANXX


title: lib16517_CB4FNANXX


title: lib16510_CB4FNANXX


title: lib16512_CB4FNANXX


title: lib16513_CB4FNANXX


title: lib16509_CB4FNANXX


title: lib16501_CB4FNANXX


title: lib16507_CB4FNANXX


title: lib16498_CB4FNANXX


title: lib16499_CB4FNANXX


title: lib16500_CB4FNANXX


title: lib16524_CB4FNANXX


title: lib16495_CB4FNANXX


title: lib16497_CB4FNANXX


title: lib16496_CB4FNANXX


title: lib16508_CB4FNANXX


title: lib16494_CB4FNANXX


title: lib16491_CB4FNANXX


title: lib16492_CB4FNANXX


title: lib16493_CB4FNANXX


title: lib16490_CB4FNANXX


title: lib16488_CB4FNANXX


title: lib16485_CB4FNANXX


title: lib16489_CB4FNANXX


title: lib16480_CB4FNANXX


title: lib16487_CB4FNANXX


title: lib16481_CB4FNANXX


title: lib16475_CB4FNANXX


title: lib16486_CB4FNANXX


title: lib16477_CB4FNANXX


title: lib16479_CB4FNANXX


title: lib16478_CB4FNANXX


title: lib16472_CB4FNANXX


title: lib16473_CB4FNANXX


title: lib16474_CB4FNANXX


title: lib16476_CB4FNANXX


title: lib16470_CB4FNANXX


title: lib16471_CB4FNANXX


title: lib16467_CB4FNANXX


title: lib16466_CB4FNANXX


title: lib16465_CB4FNANXX


title: lib16464_CB4FNANXX


title: lib16463_CB4FNANXX


title: lib16462_CB4FNANXX


title: lib16459_CB4FNANXX


title: lib16456_CB4FNANXX


title: lib16445_CB4FNANXX


title: lib16458_CB4FNANXX


title: lib16425_CB4FNANXX


title: lib16418_CB4FNANXX


title: lib16468_CB4FNANXX


title: lib16417_CB4FNANXX


title: lib16416_CB4FNANXX


title: lib16428_CB4FNANXX


title: lib16427_CB4FNANXX


title: lib16426_CB4FNANXX


title: lib16437_CB4FNANXX


title: lib16461_CB4FNANXX


title: lib16424_CB4FNANXX


title: lib16457_CB4FNANXX


title: lib16422_CB4FNANXX


title: lib16411_CB4FNANXX


title: lib16460_CB4FNANXX


title: lib16423_CB4FNANXX


title: lib16405_CB4FNANXX


title: lib16421_CB4FNANXX


title: lib16469_CB4FNANXX


title: lib16420_CB4FNANXX


title: lib16402_CB4FNANXX


title: lib16415_CB4FNANXX


title: lib16406_CB4FNANXX


title: lib16413_CB4FNANXX


title: lib16404_CB4FNANXX


title: lib16414_CB4FNANXX


title: lib16400_CB4FNANXX


title: lib16397_CB4FNANXX


title: lib16419_CB4FNANXX


title: lib16407_CB4FNANXX


title: lib16412_CB4FNANXX


title: lib16391_CB4FNANXX


title: lib16399_CB4FNANXX


title: lib16396_CB4FNANXX


title: lib16389_CB4FNANXX


title: lib16395_CB4FNANXX


title: lib16394_CB4FNANXX


title: lib16393_CB4FNANXX


title: lib16403_CB4FNANXX


title: lib16390_CB4FNANXX


title: lib16383_CB4FNANXX


title: lib16381_CB4FNANXX


title: lib16401_CB4FNANXX


title: lib16385_CB4FNANXX


title: lib16398_CB4FNANXX


title: lib16392_CB4FNANXX


title: lib15141_CAJMRANXX

value: CAJMRANXX


title: lib15142_CAJMRANXX

value: M


title: lib16384_CB4FNANXX


title: lib16388_CB4FNANXX

value: Case


title: lib15148_CAJMRANXX


title: lib15136_CAJMRANXX


title: lib15135_CAJMRANXX


title: lib15131_CAJMRANXX


title: lib15140_CAJMRANXX

value: After


title: lib15139_CAJMRANXX


title: lib15132_CAJMRANXX


title: lib15137_CAJMRANXX


title: lib15129_CAJMRANXX

value: Visit 1a


title: lib16382_CB4FNANXX


title: lib15124_CAJMRANXX


title: lib15123_CAJMRANXX

value: Visit 1b


title: lib15125_CAJMRANXX


title: lib15122_CAJMRANXX


title: lib15127_CAJMRANXX

value: Visit 0


title: lib15121_CAJMRANXX


title: lib15119_CAJMRANXX


title: lib15118_CAJMRANXX

value: F


title: lib15116_CAJMRANXX

value: Peripheral Blood


title: lib15138_CAJMRANXX


title: lib15114_CAJMRANXX


title: lib15115_CAJMRANXX


title: lib15117_CAJMRANXX


title: lib15097_CAJMRANXX


title: lib15110_CAJMRANXX


title: lib15112_CAJMRANXX


title: lib15096_CAJMRANXX


title: lib15130_CAJMRANXX


title: lib15094_CAJMRANXX

value: Before


title: lib15095_CAJMRANXX


title: lib15091_CAJMRANXX


title: lib15087_CAJMRANXX

value: Visit 2b


title: lib15086_CAJMRANXX

value: Visit 2a


title: lib15093_CAJMRANXX

value: Yes


title: lib12982_C97JMANXX


title: lib15126_CAJMRANXX

value: Control


title: lib15092_CAJMRANXX


title: lib15085_CAJMRANXX

value: Viral


title: lib12981_C97JMANXX

value: No


title: lib12980_C97JMANXX

value: Non-viral


title: lib12979_C97JMANXX


title: lib12978_C97JMANXX


title: lib12976_C97JMANXX


title: lib12974_C97JMANXX


title: lib12975_C97JMANXX


title: lib12977_C97JMANXX


title: lib15111_CAJMRANXX

value: CAJMRANXX


title: lib12972_C97JMANXX

value: M


title: lib12971_C97JMANXX


title: lib12969_C97JMANXX


title: lib12970_C97JMANXX


title: lib12968_C97JMANXX


title: lib12965_C97JMANXX


title: lib12967_C97JMANXX


title: lib12962_C97JMANXX


title: lib12963_C97JMANXX


title: lib12953_C97JMANXX


title: lib12950_C97JMANXX

value: Case


title: lib12959_C97JMANXX


title: lib12960_C97JMANXX


title: lib12956_C97JMANXX


title: lib12951_C97JMANXX

value: After


title: lib12954_C97JMANXX


title: lib12949_C97JMANXX


title: lib12973_C97JMANXX


title: lib12955_C97JMANXX

value: Visit 1a


title: lib12947_C97JMANXX

value: Visit 1b


title: lib12957_C97JMANXX


title: lib12966_C97JMANXX


title: lib12945_C97JMANXX

value: Visit 0


title: lib12942_C97JMANXX


title: lib12943_C97JMANXX


title: lib12941_C97JMANXX

value: F


title: lib12944_C97JMANXX

value: Peripheral Blood


title: lib12939_C97JMANXX

value: Before


title: lib12935_C97JMANXX

value: Visit 2b


title: lib12938_C97JMANXX


title: lib12936_C97JMANXX


title: lib12937_C97JMANXX


title: lib12961_C97JMANXX


title: lib12931_C97JMANXX


title: lib12933_C97JMANXX


title: lib12930_C97JMANXX


title: lib12934_C97JMANXX

value: Visit 2a


title: lib12948_C97JMANXX

value: Yes


title: lib12932_C97JMANXX

value: Control


title: lib12925_C97JMANXX


title: lib12927_C97JMANXX


title: lib12926_C97JMANXX

value: Viral


title: lib12946_C97JMANXX

value: No


title: lib12928_C97JMANXX

value: Non-viral


title: lib12920_C97JMANXX

value: RV-C6, RV-C17


title: lib12923_C97JMANXX

value: M


title: lib12922_C97JMANXX


title: lib12917_C97JMANXX


title: lib12921_C97JMANXX


title: lib12914_C97JMANXX


title: lib12919_C97JMANXX

value: Case


title: lib12915_C97JMANXX


title: lib12911_C97JMANXX


title: lib12912_C97JMANXX


title: lib12913_C97JMANXX


title: lib12910_C97JMANXX


title: lib12907_C97JMANXX


title: lib12906_C97JMANXX


title: lib12909_C97JMANXX


title: lib12908_C97JMANXX


title: lib12929_C97JMANXX


title: lib12905_C97JMANXX


title: lib12904_C97JMANXX


title: lib12903_C97JMANXX


title: lib12924_C97JMANXX


title: lib12902_C97JMANXX


title: lib12901_C97JMANXX


title: lib12899_C97JMANXX


title: lib12897_C97JMANXX


title: lib12900_C97JMANXX


title: lib12896_C97JMANXX


title: lib12898_C97JMANXX


title: lib12895_C97JMANXX


title: lib12918_C97JMANXX


title: lib12892_C97JMANXX


title: lib12893_C97JMANXX


title: lib11372_C8B30ANXX


title: lib11373_C8B30ANXX


title: lib11369_C8B30ANXX

value: After


title: lib11367_C8B30ANXX


title: lib12890_C97JMANXX

value: Visit 1a


title: lib11362_C8B30ANXX


title: lib11361_C8B30ANXX

value: Visit 1b


title: lib11359_C8B30ANXX


title: lib11358_C8B30ANXX


title: lib11360_C8B30ANXX


title: lib11356_C8B30ANXX


title: lib11357_C8B30ANXX


title: lib11355_C8B30ANXX

value: Visit 0


title: lib12894_C97JMANXX

value: F


title: lib11346_C8B30ANXX

value: Peripheral Blood


title: lib11343_C8B30ANXX


title: lib11350_C8B30ANXX


title: lib11352_C8B30ANXX


title: lib11351_C8B30ANXX


title: lib11331_C8B30ANXX


title: lib11347_C8B30ANXX


title: lib11349_C8B30ANXX


title: lib11338_C8B30ANXX


title: lib11342_C8B30ANXX


title: lib11368_C8B30ANXX

value: Before


title: lib11344_C8B30ANXX


title: lib18008_CB5HFANXX

value: Nasal Lavage

tag: used in analaysis


title: lib18009_CB5HFANXX


title: lib18011_CB5HFANXX


title: lib18007_CB5HFANXX


title: lib17988_CB4FNANXX


title: lib17985_CB4FNANXX


title: lib17992_CB5HFANXX


title: lib17984_CB4FNANXX


title: lib17993_CB5HFANXX


title: lib17971_CB4FNANXX


title: lib17983_CB4FNANXX


title: lib11353_C8B30ANXX


title: lib15452_CAJMRANXX

value: CAJMRANXX


title: lib17978_CB4FNANXX

value: Yes


title: lib17969_CB4FNANXX


title: lib15451_CAJMRANXX

value: Control


title: lib15450_CAJMRANXX


title: lib15449_CAJMRANXX

value: Viral


title: lib15447_CAJMRANXX

value: Visit 2b

value: No


title: lib15448_CAJMRANXX


title: lib15446_CAJMRANXX

value: Non-viral


title: lib15444_CAJMRANXX


title: lib15445_CAJMRANXX

value: Visit 2a


title: lib18002_CB5HFANXX

value: M

value: Case


title: lib15443_CAJMRANXX

value: Visit 1a


title: lib15442_CAJMRANXX

value: Visit 1b


title: lib15440_CAJMRANXX

value: Visit 0


title: lib15437_CAJMRANXX

value: F


title: lib15436_CAJMRANXX


title: lib15441_CAJMRANXX


title: lib15439_CAJMRANXX


title: lib15438_CAJMRANXX


title: lib15432_CAJMRANXX

value: After


title: lib15435_CAJMRANXX


title: lib15433_CAJMRANXX


title: lib15434_CAJMRANXX


title: lib15429_CAJMRANXX


title: lib15430_CAJMRANXX


title: lib15428_CAJMRANXX


title: lib15426_CAJMRANXX


title: lib15424_CAJMRANXX


title: lib15431_CAJMRANXX


title: lib15423_CAJMRANXX


title: lib15427_CAJMRANXX


title: lib15422_CAJMRANXX


title: lib15420_CAJMRANXX


title: lib15418_CAJMRANXX


title: lib15421_CAJMRANXX


title: lib15419_CAJMRANXX


title: lib15413_CAJMRANXX


title: lib15405_CAJMRANXX

value: Before


title: lib15412_CAJMRANXX

value: Nasal Lavage


title: lib15417_CAJMRANXX

value: CAJMRANXX


title: lib15404_CAJMRANXX

value: Yes


title: lib15403_CAJMRANXX


title: lib15402_CAJMRANXX


title: lib15406_CAJMRANXX


title: lib15398_CAJMRANXX

value: Control


title: lib15400_CAJMRANXX

value: Viral


title: lib15399_CAJMRANXX


title: lib15397_CAJMRANXX


title: lib15401_CAJMRANXX


title: lib15392_CAJMRANXX


title: lib15395_CAJMRANXX


title: lib15388_CAJMRANXX

value: Visit 2b


title: lib15396_CAJMRANXX

value: No


title: lib15425_CAJMRANXX


title: lib15393_CAJMRANXX

value: Non-viral


title: lib15391_CAJMRANXX


title: lib15389_CAJMRANXX


title: lib15390_CAJMRANXX


title: lib15415_CAJMRANXX


title: lib15387_CAJMRANXX


title: lib15383_CAJMRANXX

value: Visit 2a


title: lib15385_CAJMRANXX

value: M


title: lib15384_CAJMRANXX


title: lib15386_CAJMRANXX


title: lib15382_CAJMRANXX


title: lib15380_CAJMRANXX

value: Case


title: lib15378_CAJMRANXX


title: lib15375_CAJMRANXX

value: Visit 1a


title: lib15376_CAJMRANXX


title: lib15374_CAJMRANXX

value: Visit 1b


title: lib15367_CAJMRANXX


title: lib15381_CAJMRANXX


title: lib15371_CAJMRANXX

value: Visit 0


title: lib15369_CAJMRANXX


title: lib15368_CAJMRANXX


title: lib15365_CAJMRANXX


title: lib15363_CAJMRANXX

value: F


title: lib15373_CAJMRANXX


title: lib15362_CAJMRANXX

value: After


title: lib15364_CAJMRANXX


title: lib15370_CAJMRANXX


title: lib15372_CAJMRANXX


title: lib15366_CAJMRANXX


title: lib15360_CAJMRANXX

value: Before


title: lib15361_CAJMRANXX

value: Nasal Lavage


title: lib15358_CAJMRANXX

value: CAJMRANXX


title: lib15357_CAJMRANXX

value: Yes


title: lib15352_CAJMRANXX

value: Control


title: lib15356_CAJMRANXX


title: lib15394_CAJMRANXX


title: lib15359_CAJMRANXX

value: Viral


title: lib15348_CAJMRANXX


title: lib15353_CAJMRANXX


title: lib15355_CAJMRANXX


title: lib15347_CAJMRANXX


title: lib15354_CAJMRANXX

value: Visit 2b


title: lib15350_CAJMRANXX

value: No


title: lib15344_CAJMRANXX


title: lib15351_CAJMRANXX


title: lib15349_CAJMRANXX


title: lib15341_CAJMRANXX


title: lib15342_CAJMRANXX


title: lib15340_CAJMRANXX

value: Non-viral


title: lib15336_CAJMRANXX


title: lib15346_CAJMRANXX


title: lib15338_CAJMRANXX


title: lib15334_CAJMRANXX


title: lib15345_CAJMRANXX


title: lib15335_CAJMRANXX


title: lib15331_CAJMRANXX


title: lib15328_CAJMRANXX


title: lib15330_CAJMRANXX


title: lib15333_CAJMRANXX


title: lib15329_CAJMRANXX


title: lib15327_CAJMRANXX


title: lib15343_CAJMRANXX


title: lib15320_CAJMRANXX


title: lib15318_CAJMRANXX

value: RV-C6, RV-C17


title: lib15322_CAJMRANXX


title: lib15339_CAJMRANXX

value: M


title: lib15321_CAJMRANXX


title: lib15311_CAJMRANXX

value: Case


title: lib15309_CAJMRANXX


title: lib15308_CAJMRANXX

value: Visit 1a


title: lib15332_CAJMRANXX

value: Visit 2a


title: lib15305_CAJMRANXX


title: lib15303_CAJMRANXX

value: Visit 1b


title: lib15304_CAJMRANXX

value: F


title: lib15300_CAJMRANXX

value: Visit 0


title: lib15292_CAJMRANXX


title: lib15291_CAJMRANXX

value: Before


title: lib15290_CAJMRANXX

value: Nasal Lavage

value: After


title: lib15326_CAJMRANXX

value: CAJMRANXX

value: Yes


title: lib15323_CAJMRANXX

value: Control

value: Viral


title: lib15289_CAJMRANXX

value: No


title: lib15288_CAJMRANXX

value: Visit 2b


title: lib15312_CAJMRANXX


title: lib15314_CAJMRANXX


title: lib15306_CAJMRANXX

value: Non-viral


title: lib15282_CAJMRANXX


title: lib15287_CAJMRANXX


title: lib15313_CAJMRANXX

value: M


title: lib15285_CAJMRANXX


title: lib15307_CAJMRANXX

value: Case


title: lib15286_CAJMRANXX


title: lib15276_CAJMRANXX


title: lib15281_CAJMRANXX


title: lib15279_CAJMRANXX


title: lib15277_CAJMRANXX


title: lib15280_CAJMRANXX

value: Visit 1a


title: lib15297_CAJMRANXX


title: lib15272_CAJMRANXX


title: lib15271_CAJMRANXX


title: lib15284_CAJMRANXX


title: lib15278_CAJMRANXX


title: lib15270_CAJMRANXX


title: lib15269_CAJMRANXX

value: Visit 2a


title: lib15275_CAJMRANXX

value: Visit 1b


title: lib15268_CAJMRANXX


title: lib15310_CAJMRANXX


title: lib15273_CAJMRANXX


title: lib15266_CAJMRANXX


title: lib15261_CAJMRANXX

value: F


title: lib15283_CAJMRANXX


title: lib15263_CAJMRANXX

value: Visit 0


title: lib15264_CAJMRANXX


title: lib15257_CAJMRANXX


title: lib15258_CAJMRANXX


title: lib15274_CAJMRANXX


title: lib15255_CAJMRANXX


title: lib15259_CAJMRANXX


title: lib15253_CAJMRANXX


title: lib15251_CAJMRANXX


title: lib15249_CAJMRANXX


title: lib15250_CAJMRANXX


title: lib15267_CAJMRANXX


title: lib15296_CAJMRANXX


title: lib15245_CAJMRANXX


title: lib15246_CAJMRANXX


title: lib15247_CAJMRANXX


title: lib15244_CAJMRANXX


title: lib15243_CAJMRANXX


title: lib15241_CAJMRANXX


title: lib15240_CAJMRANXX

value: Before


title: lib15238_CAJMRANXX

value: Nasal Lavage


title: lib15239_CAJMRANXX


title: lib15224_CAJMRANXX


title: lib15223_CAJMRANXX


title: lib15237_CAJMRANXX


title: lib15226_CAJMRANXX


title: lib15225_CAJMRANXX


title: lib15248_CAJMRANXX

value: After


title: lib15214_CAJMRANXX

value: CAJMRANXX


title: lib15227_CAJMRANXX

value: Yes


title: lib15211_CAJMRANXX

value: Control


title: lib15252_CAJMRANXX


title: lib15220_CAJMRANXX

value: Viral


title: lib15219_CAJMRANXX

value: No


title: lib15216_CAJMRANXX


title: lib15215_CAJMRANXX


title: lib15209_CAJMRANXX


title: lib15194_CAJMRANXX


title: lib15213_CAJMRANXX


title: lib15242_CAJMRANXX


title: lib15212_CAJMRANXX


title: lib15210_CAJMRANXX

value: Visit 2b


title: lib15203_CAJMRANXX

value: Non-viral


title: lib15256_CAJMRANXX


title: lib15207_CAJMRANXX

value: M


title: lib15208_CAJMRANXX


title: lib15187_CAJMRANXX

value: Case


title: lib15206_CAJMRANXX

value: Visit 1a


title: lib15180_CAJMRANXX


title: lib15205_CAJMRANXX


title: lib15189_CAJMRANXX


title: lib15182_CAJMRANXX


title: lib15196_CAJMRANXX


title: lib15190_CAJMRANXX


title: lib15184_CAJMRANXX


title: lib15179_CAJMRANXX


title: lib15181_CAJMRANXX


title: lib15175_CAJMRANXX


title: lib15191_CAJMRANXX


title: lib15174_CAJMRANXX


title: lib15176_CAJMRANXX


title: lib15173_CAJMRANXX


title: lib15171_CAJMRANXX


title: lib15172_CAJMRANXX

value: Visit 2a


title: lib15177_CAJMRANXX


title: lib15192_CAJMRANXX

value: Visit 1b


title: lib15166_CAJMRANXX

value: F


title: lib15170_CAJMRANXX


title: lib15163_CAJMRANXX


title: lib15167_CAJMRANXX


title: lib15162_CAJMRANXX


title: lib15164_CAJMRANXX


title: lib15159_CAJMRANXX

value: Visit 0


title: lib12534_C95GDANXX


title: lib15160_CAJMRANXX


title: lib12536_C95GDANXX


title: lib12535_C95GDANXX


title: lib12531_C95GDANXX


title: lib12530_C95GDANXX


title: lib15161_CAJMRANXX


title: lib15178_CAJMRANXX


title: lib12528_C95GDANXX

tag: used in analaysis:


title: lib12527_C95GDANXX


title: lib12525_C95GDANXX


title: lib12529_C95GDANXX


title: lib12526_C95GDANXX


title: lib12521_C95GDANXX

value: Before


title: lib12524_C95GDANXX

value: Nasal Lavage


title: lib15165_CAJMRANXX


title: lib12519_C95GDANXX

value: After


title: lib12518_C95GDANXX


title: lib12502_C95GDANXX


title: lib12500_C95GDANXX


title: lib12501_C95GDANXX


title: lib12503_C95GDANXX


title: lib12499_C95GDANXX


title: lib12493_C95GDANXX


title: lib12496_C95GDANXX


title: lib12492_C95GDANXX


title: lib12495_C95GDANXX


title: lib12487_C95GDANXX


title: lib12494_C95GDANXX


title: lib12485_C95GDANXX


title: lib12488_C95GDANXX


title: lib12481_C95GDANXX


title: lib12479_C95GDANXX


title: lib12478_C95GDANXX


title: lib12475_C95GDANXX


title: lib12480_C95GDANXX


title: lib12477_C95GDANXX


title: lib12470_C95GDANXX


title: lib12473_C95GDANXX


title: lib12520_C95GDANXX


title: lib12467_C95GDANXX


title: lib12512_C95GDANXX


title: lib12466_C95GDANXX


title: lib12464_C95GDANXX


title: lib12468_C95GDANXX


title: lib12463_C95GDANXX


title: lib12461_C95GDANXX


title: lib12460_C95GDANXX


title: lib12458_C95GDANXX


title: lib12462_C95GDANXX


title: lib12456_C95GDANXX


title: lib12453_C95GDANXX


title: lib12452_C95GDANXX


title: lib12448_C95GDANXX


title: lib12471_C95GDANXX


title: lib12442_C95GDANXX


title: lib12451_C95GDANXX


title: lib12447_C95GDANXX


title: lib12450_C95GDANXX


title: lib12438_C95GDANXX


title: lib12439_C95GDANXX


title: lib12474_C95GDANXX


title: lib12437_C95GDANXX


title: lib12455_C95GDANXX


title: lib12436_C95GDANXX


title: lib12435_C95GDANXX


title: lib12430_C95GDANXX


title: lib12434_C95GDANXX


title: lib12428_C95GDANXX


title: lib12429_C95GDANXX


title: lib12433_C95GDANXX


title: lib12419_C95GDANXX


title: lib12454_C95GDANXX


title: lib12432_C95GDANXX


title: lib12412_C95GDANXX


title: lib12418_C95GDANXX


title: lib12416_C95GDANXX


title: lib12449_C95GDANXX


title: lib12415_C95GDANXX


title: lib12405_C95GDANXX


title: lib12413_C95GDANXX


title: lib12414_C95GDANXX


title: lib12427_C95GDANXX


title: lib12411_C95GDANXX


title: lib12409_C95GDANXX


title: lib12397_C95GDANXX


title: lib12396_C95GDANXX


title: lib12395_C95GDANXX


title: lib12410_C95GDANXX


title: lib12406_C95GDANXX


title: lib12404_C95GDANXX


title: lib12402_C95GDANXX


title: lib12392_C95GDANXX


title: lib12390_C95GDANXX


title: lib12407_C95GDANXX


title: lib12403_C95GDANXX


title: lib12399_C95GDANXX


title: lib12400_C95GDANXX


title: lib12408_C95GDANXX


title: lib12378_C95GDANXX


title: lib12393_C95GDANXX


title: lib12394_C95GDANXX


title: lib12391_C95GDANXX


title: lib12379_C95GDANXX


title: lib12389_C95GDANXX


title: lib12373_C95GDANXX


title: lib12370_C95GDANXX


title: lib12372_C95GDANXX


title: lib12388_C95GDANXX


title: lib12371_C95GDANXX


title: lib12387_C95GDANXX


title: lib12367_C95GDANXX


title: lib12386_C95GDANXX

value: RV-C6, RV-C17


title: lib12383_C95GDANXX

value: Yes


title: lib12384_C95GDANXX

value: Control


title: lib12382_C95GDANXX

value: Viral


title: lib12401_C95GDANXX

value: No


title: lib12359_C95GDANXX


title: lib12361_C95GDANXX


title: lib12377_C95GDANXX


title: lib12358_C95GDANXX

value: Visit 2b


title: lib12398_C95GDANXX


title: lib12357_C95GDANXX

value: Non-viral


title: lib11126_C893JANXX

value: M


title: lib12360_C95GDANXX


title: lib11125_C893JANXX


title: lib11124_C893JANXX


title: lib12369_C95GDANXX


title: lib12366_C95GDANXX


title: lib12426_C95GDANXX

value: Case


title: lib11120_C893JANXX

value: Visit 1a


title: lib12368_C95GDANXX

value: Visit 2a


title: lib12365_C95GDANXX


title: lib11122_C893JANXX

value: Visit 1b


title: lib12362_C95GDANXX

value: F


title: lib11115_C893JANXX


title: lib11121_C893JANXX


title: lib11119_C893JANXX


title: lib11118_C893JANXX


title: lib11117_C893JANXX

value: Visit 0


title: lib11107_C893JANXX


title: lib11105_C893JANXX


title: lib11116_C893JANXX


title: lib11114_C893JANXX


title: lib11113_C893JANXX


title: lib11111_C893JANXX


title: lib11101_C893JANXX


title: lib11110_C893JANXX


title: lib11099_C893JANXX


title: lib11106_C893JANXX


title: lib11097_C893JANXX


title: lib11108_C893JANXX


title: lib11109_C893JANXX


title: lib11093_C893JANXX


title: lib11103_C893JANXX


title: lib11091_C893JANXX


title: lib11087_C893JANXX


title: lib11088_C893JANXX


title: lib11086_C893JANXX


title: lib11100_C893JANXX


title: lib11102_C893JANXX


title: lib11085_C893JANXX


title: lib11090_C893JANXX


title: lib11081_C893JANXX


title: lib11092_C893JANXX


title: lib11094_C893JANXX


title: lib11089_C893JANXX


title: TLR7_1_iHPC_24304

status: Public on Jan 15 2019

data_processing:
Base-calling was performed using CASAVA v.1.8.2.
FASTQ reads were trimmed using fastq-mcf (ea-utils, v.1.1.2) to remove SMARTer adapter sequences.
Reads were aligned in Galaxy using bowtie and TopHat (Tophat for Illumina tool, v.1.5.0); duplicate alignments were marked and removed using Picard MarkDuplicates.
Read counts per Ensembl gene ID were estimated in Galaxy using htseq-count (htseq-count tool, v.0.4.1).
Sequencing, alignment, and quantitation metrics were obtained for FASTQ, BAM/SAM, and count files in Galaxy using FastQC, Picard, TopHat, Samtools, and htseq-count.
Genome_build: Mus musculus NCBIM37.67
Supplementary_files_format_and_content: raw_counts_P203.txt is a tab-delimited matrix. The first column contains Ensembl gene IDs The remaining columns include raw read counts assigned for each library. Outlier samples have been removed but data have not been gene filtered or normalized.

extract_protocol:
500 cells were sorted into lysis buffer from the SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Takara)
Reverse transcription was performed followed by PCR amplification to generate full length amplified cDNA. Sequencing libraries were constructed using the NexteraXT DNA sample preparation kit (Illumina) to generate Illumina-compatible barcoded libraries. Libraries were pooled and quantified using a Qubit® Fluorometer (Life Technologies).

tag: genotype

value: iHPC

tag: age

value: Female

tag: collection date


title: TLR7_1_Mono_24304

value: Mono

tag: Sex


title: TLR7_1_RPM_24380

value: RPM


title: WT_Mono_24416

value: WT


title: TLR7_1_iHPC_24380


title: TLR7_1_Mono_24380


title: lib11082_C893JANXX

value: Nasal Lavage

value: Yes


title: WT_RPM_24415


title: TLR7_1_RPM_24304


title: lib11083_C893JANXX

value: Viral

value: No


title: TLR7_1_RPM_24261


title: lib11104_C893JANXX

value: Control


title: TLR7_1_iHPC_24261


title: TLR7_1_Mono_24261


title: WT_Mono_24214


title: WT_Mono_24415


title: TLR7_1_iHPC_24308


title: TLR7_1_RPM_24308


title: TLR7_1_Mono_24308


title: WT_Mono_24117


title: WT_Mono_24323


title: WT_RPM_24117


title: TLR7_1_iHPC_24107


title: TLR7_1_Mono_24107


title: lib11098_C893JANXX


title: E14_WT2

status: Public on Jan 14 2019

city: Chapel Hill

first: Mark

last: Zylka

state: NC

address: 5109D Neuroscience Research Building

institute: University of North Carolina - Chapel Hill

description: Single-cell isolation using Drop-seq

data_processing:
FASTQ files were converted to BAM format, tagged with cell and molecular barcodes, quality-filtered, trimmed, polyA-trimmed, and converted back to FASTQ as previously described (Macosko et al, Cell, 2015; Shekhar et al, Cell, 2016)
Reads were aligned to a mouse-human hybrid genome (mm10-hg19) using STAR, then sorted, merged, and exon-tagged as described (Macosko et al, Cell, 2015; Shekhar et al, Cell, 2016)
Bead synthesis errors were corrected as described (Shekhar et al, Cell, 2016), and BAM files were separated into those containing mouse or human reads. UMIs were determined to be species-specific if >90% of the transcripts came from that species, or considered a doublet if neither species achieved 90% specificity. UMIs were not considered if the transcript count sum (mouse+human) was less than 500
Gene expression matrices were then created using only the mouse-specific UMIs, as described (Macosko et al, Cell, 2015; Shekhar et al, Cell, 2016). Gene expression matrices were combined from multiple biological replicates; data values for one or more replicates that did not detect a given gene were assigned to zero.
Subsequent analytical processes were performed as described at: https://github.com/jeremymsimon/MouseCortex
Genome_build: mm10
Supplementary_files_format_and_content: Gene expression matrices for all cells and all genes for a given developmental age. Data values are not filtered or normalized.

source_name: E14.5 cortex, male and female littermates

growth_protocol: Mice were maintained on a 12 h:12 h light:dark cycle and given food and water ad libitum. Timed matings were set up in the evening, using one male and two female C57Bl/6J mice (Jackson Labs) per breeding cage. The male mouse was separated from female mice the next morning. 14 days after separation, pregnant female mice were euthanized and embryonic day 14.5 (E14.5) embryos were collected for dissections. For P0 pups, cages were monitored daily from E18.5 to postnatal day 0 (P0) for newborn pups.

extract_protocol:
Drop-seq was performed largely as described (Macosko et al, Cell, 2015). Briefly, cortical cells were diluted to an estimated concentration of 400 cells/µL in Ca2+ and Mg2+ free HBSS with ion channel inhibitors and HEK293T cells were spiked in at a concentration of 3% of total cells (12 cells/µL) while barcoded beads (ChemGenes Corporation, catalogue number Macosko201110) were resuspended in lysis buffer to an estimated concentration of 400 beads/µL. Cells and beads were co-encapsulated with oil (QX200™ Droplet Generation Oil for EvaGreen, Biorad) using a microfluidics chip (Part number 3200455, Dolomite). Droplets of around 3 mL of aqueous volume (1.5 mL of cells and beads) were broken with perfluorooctanol in 30 mL of 6x SSC. The harvested beads were then washed twice with 6x SSC and hybridized RNA was reverse transcribed using Maxima H minus Reverse Transcriptase (ThermoFisher). Populations of 2,500 reverse-transcribed beads (~100 cells) were separately amplified with 13 cycles of PCR (primers, chemistry, and cycle conditions identical to those previously described) and PCR products were purified with 0.6x AMPure XP beads (Agencourt).
cDNA from an estimated 12,000 E14.5 cells and 8,000 P0 cells were pooled, purified and tagmented with Nextera XT DNA Library Preparation kit (Illumina). Input cDNA (1 ng) from each replicate was amplified with custom primer P5_TSO_Hybrid and Nextera index primers (N701, N702, N703, N704, N711, N712, N715, N716 and N718). Tagmented samples were purified twice with 0.6x and 1x AMPure XP beads. All replicates were pooled and sequenced on one Illumina HiSeq 4000 flowcell (eight lanes) to avoid sequencing bias. Read 1 was 20 bp; bases 1-12 represent the cell barcode, bases 13-20 represent UMI. Read 2 was 50 bp and Read 3 (sample index) was 8 bp. The 8bp indexes are found within the Read 2 headers. Samples were de-multiplexed using bcl2fastq version 2.18.0.12.

treatment_protocol: Cerebral cortices (both halves) from E14.5 and P0 mice were dissected in neurobasal medium and rinsed with Hank's Balanced Salt Solution (HBSS; 14175095 Gibco). All procedures were done at room temperature, unless otherwise stated. Cortices were then incubated for 30 min at 37°C in papain (1 vial diluted with 2.5 mL of HBSS; Pierce 88285) with DNase I (20 mg/mL; D4513 Sigma) in Ca2+ and Mg2+ free HBSS. Next, 1 mL of neurobasal medium containing 5% FBS was added to the cortical mixture and triturated to deactivate the papain. The cells were centrifuged for 2 min at 4,000 rpm, washed twice, and resuspended in Ca2+ and Mg2+ free HBSS with ion channel inhibitors (5 µM TTX ab120054 Abcam, 25 µM DL-AP5 ab120004 Abcam, 5 µM DNQX 2312 Tocris). Cells were kept on ice until the microfluidics run. A total of nine replicates were prepared from two developmental time points (6 replicates for E14.5 embryos and 3 replicates for P0 pups). Each replicate contained cortical cells from male and female littermates.

tag: strain

tag: secondary title

value: cerebral cortex

tag: gender

value: pooled male and female


title: E14_WT1

description: Single-cell isolation using Drop-seq


title: WT_RPM_24323


title: P0_WT3

description: Single-cell isolation using Drop-seq

source_name: P0 cortex, male and female littermates


title: E14_WT5

description: Single-cell isolation using Drop-seq


title: WT_RPM_24416


title: P0_WT2

description: Single-cell isolation using Drop-seq


title: E14_WT6

description: Single-cell isolation using Drop-seq


title: P0_WT1

description: Single-cell isolation using Drop-seq


title: WT_RPM_24214


title: TLR7_1_RPM_24107


title: lib3418

status: Public on Dec 05 2018

description:
924471XG-30
924471XG-30_S101_L008

data_processing:
Base-calling was performed automatically by Illumina real time analysis software and demultiplexing was performed on Illumina BaseSpace.
Hard trimming was performed in Galaxy; 1 3'-end base was removed from all reads using the FASTQ Trimmer tool (v1.0.0)
Quality-based trimming was performed in Galaxy; reads were trimmed from both ends using the FASTQ Quality Trimmer tool (v1.0.0) until minimum base quality for each read was >= 30.
Reads were aligned in Galaxy using bowtie and TopHat (Tophat for Illumina tool, v.1.5.0)
Read counts per Ensembl gene ID were estimated in Galaxy using htseq-count (htseq-count tool, v.0.4.1).
Sequencing, alignment, and quantitation metrics were obtained for FASTQ, BAM/SAM, and count files in Galaxy using FastQC, Picard, TopHat, Samtools, and htseq-count.
Genome_build: GRCh38
Supplementary_files_format_and_content: raw_counts_TN-05.txt is a tab-delimited matrix. The first column ("geneName") contains Ensembl gene IDs The remaining columns include raw read counts assigned for each library. Outlier samples have been removed but data have not been gene filtered or normalized.

source_name: Active_Wk 104

extract_protocol:
RNA was isolated from whole blood samples using the Total RNA Isolation chemistry on an ABI Prism 6100 (Applied Biosystems, CA).
Samples were globin- reduced with the GLOBINclear kit (Ambion, CA), and libraries were constructed from globin- reduced RNA using the Illumina TruSeq RNA Sample Preparation kit v2.

tag: subject id

tag: subject status

value: newly diagnosed T1D patient

tag: race

value: White

tag: ethnicity

value: Not Hispanic or Latino

tag: visit

tag: treatment

value: Active

tag: responder

value: Y

value: whole blood


title: lib3417

description:
921778B-32
921778B-32_S100_L008

source_name: Placebo_Wk 52

value: Male

value: Wk 52

value: Placebo

value: N

tag: tissue


title: lib3416

description:
924488XH-32
924488XH-32_S99_L008

source_name: Active_Wk 52


title: TLR7_1_Mono_24068

tag: cell type

value: Mono

value: Female


title: lib3421

description:
923096B-30
923096B-30_S104_L008

source_name: Placebo_Wk 104


title: TLR7_1_RPM_24068

value: RPM


title: WT_RPM_24028

value: WT


title: lib3414

description:
918651B-30
918651B-30_S97_L008


title: E14_WT3

description: Single-cell isolation using Drop-seq


title: lib3410

description:
923094B-32
923094B-32_S93_L008


title: lib3411

description:
930339B-32
930339B-32_S94_L008


title: lib3408

description:
918765B-32
918765B-32_S91_L007


title: lib3409

description:
921336B-32
921336B-32_S92_L008

source_name: Active_Wk 78

value: Wk 78


title: lib3406

description:
915588B-30
915588B-30_S89_L007

value: Baseline


title: lib3404

description:
923107B-32
923107B-32_S87_L007


title: lib3407

description:
921338B-32
921338B-32_S90_L007

value: Hispanic or Latino


title: lib3415

description:
923070B-32
923070B-32_S98_L008

value: newly diagnosed T1D patient


title: lib3413

description:
923098B-30
923098B-30_S96_L008

value: White


title: lib3405

description:
921339B-32
921339B-32_S88_L007

source_name: Placebo_Wk 78

value: Not Hispanic or Latino


title: lib3402

description:
930523B-32
930523B-32_S85_L007

value: Active


title: lib3401

description:
923086B-32
923086B-32_S84_L007


title: lib3397

description:
923111B-30
923111B-30_S80_L007

value: Y


title: lib3412

description:
930347B-32
930347B-32_S95_L008

value: whole blood


title: lib3398

description:
923110B-32
923110B-32_S81_L007

value: Male


title: lib3392

description:
930501B-32
930501B-32_S75_L006


title: lib3391

description:
925966XG-32
925966XG-32_S74_L006


title: lib3385

description:
923059B-32
923059B-32_S68_L006


title: lib3394

description:
923153B-32
923153B-32_S77_L006


title: lib3386

description:
924957B-32
924957B-32_S69_L006

value: Wk 52


title: lib3390

description:
936434B-32
936434B-32_S73_L006


title: lib3388

description:
921779B-32
921779B-32_S71_L006


title: lib3389

description:
923063B-32
923063B-32_S72_L006

value: Placebo


title: lib3400

description:
923087B-32
923087B-32_S83_L007


title: lib3387

description:
919786B-30
919786B-30_S70_L006


title: lib3395

description:
930507B-32
930507B-32_S78_L006


title: lib3384

description:
923045B-32
923045B-32_S67_L006


title: lib3396

description:
940220B-32
940220B-32_S79_L007

value: N


title: lib3381

description:
914693B-30
914693B-30_S64_L005

source_name: Active_Wk 26

value: Black or African American

value: Wk 26


title: lib3380

description:
920174B-32
920174B-32_S63_L005


title: lib3382

description:
914624B-32
914624B-32_S65_L005


title: lib3403

description:
918669B-30
918669B-30_S86_L007


title: lib3379

description:
918709B-30
918709B-30_S62_L005


title: lib3378

description:
914106B-32
914106B-32_S61_L005


title: lib3374

description:
921335B-30
921335B-30_S57_L005


title: lib3375

description:
918858B-30
918858B-30_S58_L005


title: lib3373

description:
914648B-32
914648B-32_S56_L005

source_name: Placebo_Wk 26


title: lib3370

description:
914056B-30
914056B-30_S53_L005

value: Female


title: lib3376

description:
920172B-30
920172B-30_S59_L005


title: lib3383

description:
924472XD-30
924472XD-30_S66_L006


title: lib3369

description:
914074B-30
914074B-30_S52_L004


title: lib3366

description:
914177B-32
914177B-32_S49_L004


title: lib3364

description:
914641B-32
914641B-32_S47_L004


title: lib3365

description:
914158B-31
914158B-31_S48_L004


title: lib3363

description:
915609B-32
915609B-32_S46_L004


title: lib3360

description:
923082B-32
923082B-32_S43_L004


title: lib3362

description:
914179B-32
914179B-32_S45_L004


title: lib3358

description:
914127B-32
914127B-32_S41_L004


title: lib3361

description:
918715B-30
918715B-30_S44_L004


title: TLR7_1_iHPC_24068

value: iHPC


title: lib3371

description:
914574B-30
914574B-30_S54_L005


title: lib3368

description:
914646B-32
914646B-32_S51_L004


title: lib3355

description:
918030B-32
918030B-32_S38_L003


title: lib3356

description:
918737B-30
918737B-30_S39_L003


title: lib3354

description:
924505XG-30
924505XG-30_S37_L003

value: Wk 78


title: lib3357

description:
918732B-30
918732B-30_S40_L004


title: lib3377

description:
914107B-32
914107B-32_S60_L005

value: Baseline


title: lib3353

description:
921117B-32
921117B-32_S36_L003


title: lib3352

description:
923090A-32
923090A-32_S35_L003


title: lib3367

description:
915586B-30
915586B-30_S50_L004


title: lib3350

description:
923097A-30
923097A-30_S33_L003


title: lib3349

description:
924480A-32
924480A-32_S32_L003


title: lib3347

description:
923062A-32
923062A-32_S30_L003


title: lib3346

description:
914698B-30
914698B-30_S29_L003


title: lib3344

description:
921314B-32
921314B-32_S27_L003


title: lib3345

description:
921292B-30
921292B-30_S28_L003


title: E14_WT4

description: Single-cell isolation using Drop-seq

value: WT

value: cerebral cortex

value: pooled male and female


title: lib3359

description:
920191B-30
920191B-30_S42_L004

value: newly diagnosed T1D patient

value: White

value: Not Hispanic or Latino


title: lib3339

description:
930106A-32
930106A-32_S22_L002

value: Y

value: whole blood


title: lib3341

description:
914082B-32
914082B-32_S24_L002

value: Male


title: lib3340

description:
923203A-30
923203A-30_S23_L002

value: Placebo


title: lib3338

description:
924481XB-32
924481XB-32_S21_L002

value: N


title: lib3342

description:
914081B-32
914081B-32_S25_L002

value: Active


title: lib3343

description:
920193B-32
920193B-32_S26_L002

value: Wk 26


title: lib3332

description:
923142A-32
923142A-32_S15_L002

value: Wk 52


title: lib3334

description:
930105A-32
930105A-32_S17_L002


title: lib3329

description:
923099A-30
923099A-30_S12_L001

value: Female


title: lib3328

description:
925973A-32
925973A-32_S11_L001


title: lib3320

description:
923198A-32
923198A-32_S3_L001

value: Wk 78


title: lib3336

description:
930503A-32
930503A-32_S19_L002


title: lib3331

description:
921780A-30
921780A-30_S14_L002


title: lib3333

description:
930338A-32
930338A-32_S16_L002


title: lib3326

description:
923071A-32
923071A-32_S9_L001


title: lib3330

description:
923069A-32
923069A-32_S13_L001


title: lib3319

description:
923196A-32
923196A-32_S2_L001


title: lib3323

description:
925965A-33
925965A-33_S6_L001


title: lib3321

description:
923105A-32
923105A-32_S4_L001

value: Hispanic or Latino


title: lib3316

description:
921349A-32
921349A-32_S100_L008


title: lib3324

description:
930115A-32
930115A-32_S7_L001


title: lib3315

description:
918887A-32
918887A-32_S99_L008


title: lib3317

description:
923091A-32
923091A-32_S101_L008


title: lib3314

description:
918783A-32
918783A-32_S98_L008


title: lib3313

description:
918784A-32
918784A-32_S97_L008


title: lib3335

description:
923156A-32
923156A-32_S18_L002


title: lib3311

description:
918010A-30
918010A-30_S95_L008

value: Baseline


title: lib3318

description:
923237A-32
923237A-32_S1_L001


title: lib3312

description:
921351A-33
921351A-33_S96_L008


title: lib3325

description:
924489A-32
924489A-32_S8_L001


title: lib3327

description:
921165A-30
921165A-30_S10_L001


title: lib3322

description:
905143A-32
905143A-32_S5_L001


title: lib3310

description:
918780A-32
918780A-32_S94_L008


title: lib3300

description:
921802A-32
921802A-32_S84_L007


title: lib3303

description:
924513A-32
924513A-32_S87_L007


title: lib3301

description:
923154A-32
923154A-32_S85_L007


title: lib3304

description:
924511A-32
924511A-32_S88_L007


title: lib3420

description:
914160B-30
914160B-30_S103_L008


title: lib3298

description:
921797A-32
921797A-32_S82_L007


title: lib3306

description:
930517A-32
930517A-32_S90_L008


title: lib3294

description:
930520A-32
930520A-32_S78_L007


title: lib3305

description:
930518A-32
930518A-32_S89_L008


title: lib3293

description:
921188A-32
921188A-32_S77_L007


title: lib3308

description:
923230A-30
923230A-30_S92_L008


title: lib3307

description:
923238A-30
923238A-30_S91_L008


title: lib3290

description:
923047A-32
923047A-32_S74_L006


title: lib3299

description:
921801A-32
921801A-32_S83_L007


title: lib3297

description:
921800A-32
921800A-32_S81_L007


title: lib3285

description:
921815A-32
921815A-32_S69_L006


title: lib3289

description:
931064A-32
931064A-32_S73_L006


title: lib3288

description:
921168A-33
921168A-33_S72_L006


title: lib3286

description:
921337A-32
921337A-32_S70_L006


title: lib3291

description:
923072A-33
923072A-33_S75_L006


title: lib3309

description:
930108A-32
930108A-32_S93_L008


title: lib3302

description:
923106A-32
923106A-32_S86_L007


title: lib3296

description:
921350A-32
921350A-32_S80_L007

source_name: Active_Wk 104 (or M30)


title: lib3287

description:
921346A-32
921346A-32_S71_L006


title: lib3284

description:
921803A-32
921803A-32_S68_L006


title: WT_Mono_24028

value: WT

value: Mono


title: lib3292

description:
930340A-32
930340A-32_S76_L007

value: newly diagnosed T1D patient


title: lib3295

description:
924474A-32
924474A-32_S79_L007

value: White


title: lib3283

description:
923151A-32
923151A-32_S67_L006

value: Not Hispanic or Latino


title: lib3281

description:
915595A-32
915595A-32_S65_L006

value: Y


title: lib3282

description:
923088A-32
923088A-32_S66_L006

value: whole blood


title: lib3276

description:
914108A-32
914108A-32_S60_L005


title: lib3277

description:
920173A-32
920173A-32_S61_L005


title: lib3279

description:
914626A-30
914626A-30_S63_L006


title: lib3274

description:
918008A-32
918008A-32_S58_L005

value: Male


title: lib3280

description:
922788A-32
922788A-32_S64_L006

value: Placebo


title: lib3275

description:
921786A-30
921786A-30_S59_L005


title: lib3273

description:
918036XC-32
918036XC-32_S57_L005

value: N


title: lib3271

description:
918819A-30
918819A-30_S55_L005

value: Active


title: lib3264

description:
918766A-32
918766A-32_S48_L004


title: lib3269

description:
921785A-32
921785A-32_S53_L005


title: lib3266

description:
918761A-32
918761A-32_S50_L005


title: lib3265

description:
921804XG-32
921804XG-32_S49_L004


title: lib3260

description:
914669A-30
914669A-30_S44_L004


title: lib3267

description:
921816A-32
921816A-32_S51_L005


title: lib3270

description:
914576A-30
914576A-30_S54_L005


title: lib3261

description:
914054A-30
914054A-30_S45_L004


title: lib3257

description:
914621A-32
914621A-32_S41_L004


title: lib3259

description:
918799XA-32
918799XA-32_S43_L004


title: lib3272

description:
915607A-30
915607A-30_S56_L005

value: Wk 26


title: lib3256

description:
914619A-32
914619A-32_S40_L004


title: lib3254

description:
915587A-30
915587A-30_S38_L004


title: lib3252

description:
914622A-32
914622A-32_S36_L003


title: lib3255

description:
914674A-30
914674A-30_S39_L004


title: lib3251

description:
914572A-30
914572A-30_S35_L003


title: lib3253

description:
914105A-30
914105A-30_S37_L004


title: lib3248

description:
918712A-32
918712A-32_S32_L003


title: lib3249

description:
921115A-32
921115A-32_S33_L003


title: lib3247

description:
914570A-30
914570A-30_S31_L003


title: lib3244

description:
914625A-30
914625A-30_S28_L003


title: lib3243

description:
918733A-30
918733A-30_S27_L003


title: lib3263

description:
918768A-32
918768A-32_S47_L004

value: Wk 52


title: lib3268

description:
921777A-30
921777A-30_S52_L005

value: Female


title: lib3246

description:
918713A-32
918713A-32_S30_L003


title: lib3250

description:
919785A-30
919785A-30_S34_L003


title: lib3245

description:
914057A-30
914057A-30_S29_L003


title: lib3258

description:
914696A-32
914696A-32_S42_L004


title: lib3241

description:
918735A-30
918735A-30_S25_L003


title: lib3238

description:
918730A-32
918730A-32_S22_L002


title: lib3237

description:
922542A-30
922542A-30_S21_L002


title: lib3239

description:
925969XD-30
925969XD-30_S23_L002


title: lib3242

description:
918717A-30
918717A-30_S26_L003


title: lib3233

description:
924961XC-32
924961XC-32_S17_L002

value: Wk 78


title: lib3231

description:
921144A-32
921144A-32_S15_L002


title: lib3235

description:
925968XF-32
925968XF-32_S19_L002


title: lib3236

description:
924960A-32
924960A-32_S20_L002


title: lib3229

description:
914128A-32
914128A-32_S13_L002


title: lib3228

description:
921320A-32
921320A-32_S12_L001

value: Hispanic or Latino


title: lib3225

description:
914162A-30
914162A-30_S9_L001

value: Baseline


title: lib3226

description:
914671A-32
914671A-32_S10_L001

value: Black or African American


title: lib3227

description:
921319A-30
921319A-30_S11_L001


title: lib3234

description:
921116A-32
921116A-32_S18_L002


title: lib3224

description:
914125A-32
914125A-32_S8_L001


title: lib3223

description:
914689A-30
914689A-30_S7_L001


title: lib3219

description:
914126A-30
914126A-30_S3_L001


title: lib3221

description:
914639A-32
914639A-32_S5_L001


title: lib3222

description:
914690A-30
914690A-30_S6_L001


title: lib3220

description:
914642A-32
914642A-32_S4_L001


title: lib3217

description:
924504XF-30
924504XF-30_S1_L001


title: lib3232

description:
921135A-32
921135A-32_S16_L002


title: Frontal Cortex [P60FCRep2P2]

status: Public on Aug 22 2018

city: Boston

first: Arpiar

last: Saunders

address: 77 Avenue Louis Pasteur

department: Genetics

institute: Harvard Medical School

description:
P60FCRep2P2
Single-cell gene expression data based on 3' transcript counts.
mRNA (cDNA)
processed data file: F_GRCm38.81.P60Cortex_noRep5_FRONTALonly.raw.dge.txt

data_processing:
Sequencing was performed on an Illumina NextSeq500 using a 75 cycle kit (Read1: 20bp; Read2: 50 bp).
Sequencing Reads were aligned against the GRCm38.81 mouse genome draft using STAR.
Aligned Reads within a gene were collapsed to UMI(XM)-Gene Pairs and associated with single-cells through a cell barcode (XC) shared on Read 1.
A count matrix - called the digital gene expression (DGE) matrix - was output. Columns belong to STAMPs (cells) and transcript counts (rows).
Genome_build: GRCm38.81
Supplementary_files_format_and_content: *.raw.dge.txt: Digital gene expression matrix; comma-delimited file with columns = cells, and rows = transcript counts.
Supplementary_files_format_and_content: metacells.BrainCellAtlas_Saunders_version_2018.04.01.csv: Comma-delimited digital gene expression matrix (ncol = 565, nrow =32307).

source_name: P60-70 Male Mice

extract_protocol: Drop-seq (Macosko et al. 2014 Cell).

treatment_protocol: Acute brain slices digested for 3 hrs with a protease cocktail before titration, centrifugation to isolate debris-depleted single cells.

tag: strain/background

value: Frontal Cortex


title: Frontal Cortex [P60FCAldh1l1Rep1P4]

description:
P60FCAldh1l1Rep1P4
Single-cell gene expression data based on 3' transcript counts.
mRNA (cDNA)
processed data file: F_GRCm38.81.P60Cortex_noRep5_FRONTALonly.raw.dge.txt

value: Ald1l1-EGFP (Jackson Labs, 026033); C57Blk6/N background


title: Frontal Cortex [P60FCRep1P2]

description:
P60FCRep1P2
Single-cell gene expression data based on 3' transcript counts.
mRNA (cDNA)
processed data file: F_GRCm38.81.P60Cortex_noRep5_FRONTALonly.raw.dge.txt


title: Frontal Cortex [P60FCCx3cr1Rep1P3]

description:
P60FCCx3cr1Rep1P3
Single-cell gene expression data based on 3' transcript counts.
mRNA (cDNA)
processed data file: F_GRCm38.81.P60Cortex_noRep5_FRONTALonly.raw.dge.txt

value: Cx3cr1-GFP (Jackson Labs, 005582); C57Blk6/N background


title: Frontal Cortex [P60FCRep6P3]

description:
P60FCRep6P3
Single-cell gene expression data based on 3' transcript counts.
mRNA (cDNA)
processed data file: F_GRCm38.81.P60Cortex_noRep5_FRONTALonly.raw.dge.txt


title: Frontal Cortex [P60FCAldh1l1Rep1P2]

description:
P60FCAldh1l1Rep1P2
Single-cell gene expression data based on 3' transcript counts.
mRNA (cDNA)
processed data file: F_GRCm38.81.P60Cortex_noRep5_FRONTALonly.raw.dge.txt


title: Frontal Cortex [P60FCRep6P1]

description:
P60FCRep6P1
Single-cell gene expression data based on 3' transcript counts.
mRNA (cDNA)
processed data file: F_GRCm38.81.P60Cortex_noRep5_FRONTALonly.raw.dge.txt


title: Frontal Cortex [P60FCCx3cr1Rep1P1]

description:
P60FCCx3cr1Rep1P1
Single-cell gene expression data based on 3' transcript counts.
mRNA (cDNA)
processed data file: F_GRCm38.81.P60Cortex_noRep5_FRONTALonly.raw.dge.txt


title: Frontal Cortex [P60FCCx3cr1Rep1P2]

description:
P60FCCx3cr1Rep1P2
Single-cell gene expression data based on 3' transcript counts.
mRNA (cDNA)
processed data file: F_GRCm38.81.P60Cortex_noRep5_FRONTALonly.raw.dge.txt


title: Frontal Cortex [P60FCRep6P2]

description:
P60FCRep6P2
Single-cell gene expression data based on 3' transcript counts.
mRNA (cDNA)
processed data file: F_GRCm38.81.P60Cortex_noRep5_FRONTALonly.raw.dge.txt


title: Frontal Cortex [P60FCAldh1l1Rep1P1]

description:
P60FCAldh1l1Rep1P1
Single-cell gene expression data based on 3' transcript counts.
mRNA (cDNA)
processed data file: F_GRCm38.81.P60Cortex_noRep5_FRONTALonly.raw.dge.txt


title: Frontal Cortex [P60FCRep4P1]

description:
P60FCRep4P1
Single-cell gene expression data based on 3' transcript counts.
mRNA (cDNA)
processed data file: F_GRCm38.81.P60Cortex_noRep5_FRONTALonly.raw.dge.txt


title: Frontal Cortex [P60FCRep4P2]

description:
P60FCRep4P2
Single-cell gene expression data based on 3' transcript counts.
mRNA (cDNA)
processed data file: F_GRCm38.81.P60Cortex_noRep5_FRONTALonly.raw.dge.txt


title: Frontal Cortex [P60FCRep3P4]

description:
P60FCRep3P4
Single-cell gene expression data based on 3' transcript counts.
mRNA (cDNA)
processed data file: F_GRCm38.81.P60Cortex_noRep5_FRONTALonly.raw.dge.txt


title: Frontal Cortex [P60FCRep4P3]

description:
P60FCRep4P3
Single-cell gene expression data based on 3' transcript counts.
mRNA (cDNA)
processed data file: F_GRCm38.81.P60Cortex_noRep5_FRONTALonly.raw.dge.txt


title: Frontal Cortex [P60FCRep3P2]

description:
P60FCRep3P2
Single-cell gene expression data based on 3' transcript counts.
mRNA (cDNA)
processed data file: F_GRCm38.81.P60Cortex_noRep5_FRONTALonly.raw.dge.txt


title: Frontal Cortex [P60FCRep3P1]

description:
P60FCRep3P1
Single-cell gene expression data based on 3' transcript counts.
mRNA (cDNA)
processed data file: F_GRCm38.81.P60Cortex_noRep5_FRONTALonly.raw.dge.txt


title: Frontal Cortex [P60FCRep1P1]

description:
P60FCRep1P1
Single-cell gene expression data based on 3' transcript counts.
mRNA (cDNA)
processed data file: F_GRCm38.81.P60Cortex_noRep5_FRONTALonly.raw.dge.txt


title: Frontal Cortex [P60FCRep3P3]

description:
P60FCRep3P3
Single-cell gene expression data based on 3' transcript counts.
mRNA (cDNA)
processed data file: F_GRCm38.81.P60Cortex_noRep5_FRONTALonly.raw.dge.txt


title: lib8440

status: Public on Mar 27 2018

description:
07-01-130-1-NS
Processed data file: raw_counts_ureca23.txt

data_processing:
Base-calling was performed using CASAVA v.1.8.2.
FASTQ reads were trimmed using fastq-mcf (ea-utils, v.1.1.2) to remove SMARTer adapter sequences.
Reads were aligned in Galaxy using bowtie and TopHat (Tophat for Illumina tool, v.1.5.0); duplicate alignments were marked and removed using Picard MarkDuplicates.
Read counts per Ensembl gene ID were estimated in Galaxy using htseq-count (htseq-count tool, v.0.4.1).
Sequencing, alignment, and quantitation metrics were obtained for FASTQ, BAM/SAM, and count files in Galaxy using FastQC, Picard, TopHat, Samtools, and htseq-count.
Genome_build: GRCh37
Supplementary_files_format_and_content: raw_counts_ureca23.txt is a tab-delimited matrix. The first column contains Ensembl gene IDs. The remaining columns include raw read counts assigned for each library. Outlier samples have been removed but data have not been gene filtered or normalized.

extract_protocol:
RNA was extracted using TRIzol following the manufacturer's protocol (Invitrogen).
RNA quality was assessed using RNA electrophoresis (Agilent). All samples had RIN values ≥7. Sequencing libraries were constructed from total RNA using TruSeq RNA Sample Preparation Kits v2 (Illumina).

value: Peripheral blood mononuclear cell (PBMC)

tag: stim

value: NS

tag: group

value: Case

tag: cohort 2 classification

value: CR-Late

tag: full cohort classification

tag: bla g 1 bedroom level

tag: bla g 1 living room level

tag: der f 1 bedroom level

tag: der p 1 bedroom level

tag: der f 1 living room level

tag: der p 1 living room level

tag: phase


title: Frontal Cortex [P60FCAldh1l1Rep1P3]

description:
P60FCAldh1l1Rep1P3
Single-cell gene expression data based on 3' transcript counts.
mRNA (cDNA)
processed data file: F_GRCm38.81.P60Cortex_noRep5_FRONTALonly.raw.dge.txt

tag: gender

value: Male

tag: age


title: lib8439

description:
07-01-130-1-CR
Processed data file: raw_counts_ureca23.txt

value: CR


title: lib8438

description:
07-02-088-3-NS
Processed data file: raw_counts_ureca23.txt

value: Control


title: lib8433

description:
07-01-030-2-NS
Processed data file: raw_counts_ureca23.txt


title: lib8437

description:
07-02-088-3-CR
Processed data file: raw_counts_ureca23.txt


title: lib8435

description:
07-01-154-6-NS
Processed data file: raw_counts_ureca23.txt

value: Neither


title: lib8432

description:
07-01-030-2-CR
Processed data file: raw_counts_ureca23.txt


title: lib8428

description:
07-08-110-3-CR
Processed data file: raw_counts_ureca23.txt


title: lib8429

description:
07-08-110-3-NS
Processed data file: raw_counts_ureca23.txt


title: lib8419

description:
07-07-018-6-NS
Processed data file: raw_counts_ureca23.txt

value: Asthma


title: lib8427

description:
07-08-047-4-NS
Processed data file: raw_counts_ureca23.txt


title: lib8426

description:
07-08-047-4-CR
Processed data file: raw_counts_ureca23.txt


title: lib8418

description:
07-07-018-6-CR
Processed data file: raw_counts_ureca23.txt


title: lib8417

description:
07-02-005-6-NS
Processed data file: raw_counts_ureca23.txt


title: lib8420

description:
07-02-141-7-CR
Processed data file: raw_counts_ureca23.txt


title: lib8409

description:
07-01-026-3-NS
Processed data file: raw_counts_ureca23.txt

value: CR sensitized


title: Frontal Cortex [P60FCRep2P1]

description:
P60FCRep2P1
Single-cell gene expression data based on 3' transcript counts.
mRNA (cDNA)
processed data file: F_GRCm38.81.P60Cortex_noRep5_FRONTALonly.raw.dge.txt


title: lib8408

description:
07-01-026-3-CR
Processed data file: raw_counts_ureca23.txt


title: lib8421

description:
07-02-141-7-NS
Processed data file: raw_counts_ureca23.txt


title: lib8407

description:
07-01-123-6-NS
Processed data file: raw_counts_ureca23.txt


title: lib8416

description:
07-02-005-6-CR
Processed data file: raw_counts_ureca23.txt


title: lib8406

description:
07-01-123-6-CR
Processed data file: raw_counts_ureca23.txt


title: lib8405

description:
07-02-010-4-NS
Processed data file: raw_counts_ureca23.txt