title: IHEC_35_scRNA-seq

description: Re-analysis of GSM2839617


title: IHEC_34_scRNA-seq

status: Public on Dec 14 2021

type: SRA

city: Toulouse

first: Juliette

last: Coudert

address: 205 route de Narbonne

country: France

institute: CNRS

description: Re-analysis of GSM2839616

library_source: transcriptomic

data_processing:
FASTQ file generated by Illumina CASAVA 1.8
Sequenced reads were trimmed for adaptors and low quality reads then mapped to the mm10 mouse genome using RSEM v1.2.18
FPKM measurements were compiled from RSEM output
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file includes FPKM values for all samples

molecule: total RNA

organism: Mus musculus

source_name: Lymph Node

extract_protocol:
Tumors were removed from mice, dissociated into single cell suspension and Tumor Associated High Endothelial Cells or Tumor Associated Blood Endothelial Cells were FACS sorted. Purified cells were sorted, RNA was extracted and cDNA constructed using the Fluidigm C1 System.
Libraries were constructed using the Nextera XT kit as per the manufacturer’s instructions

tag: strain

tag: tissue

value: Lymph Node

tag: cell type

value: High Endothelial Cell

tag: state

value: Inflamed

tag: treatment

value: Treated with 4% Oxazolone on Skin, Harvest Day 3


title: sample 121, RRMS - cladribine 6

type: RNA

city: Rostock

first: Michael

last: Hecker

address: Gehlsheimer Str. 20

department: Department of Neurology

country: Germany

institute: University of Rostock

description: Gene expression data for a patient with RRMS treated with cladribine

hyb_protocol: Labeled single-stranded DNA in the sense orientation was hybridized for 16 hours at 45 °C on Clariom D Arrays (Applied Biosystems). The microarrays were washed and stained with a streptavidin-phycoerythrin conjugate in a GeneChip Fluidics Station 450. Signal amplification with antibodies was applied following the instructions provided by Thermo Fisher Scientific.

scan_protocol: The microarrays were scanned with a GeneChip Scanner 3000 7G (Affymetrix).

data_processing:
Data preprocessing of the raw microarray scans was performed using the Affymetrix GeneChip Command Console software version 4.0. The signal intensities of the >6 million oligonucleotide probes were further processed using the Transcriptome Analysis Console (TAC) version 4.0.2 (Applied Biosystems) in the default configuration. The signal space transformation robust multi-array average (SST-RMA) algorithm was applied for background adjustment, quantile normalization, probe set summarization and log2 transformation. The TAC software was also utilized for differential gene expression analysis.
Exon-level processed data are available on the series record.

label: Biotin

organism: Homo sapiens

source_name: B cells from the peripheral blood

label_protocol: According to the GeneChip Whole Transcript (WT) manual, cRNA was prepared from 100 ng total RNA. The cRNA was then used to generate single-stranded DNA, which was fragmented and biotinylated.

growth_protocol: Twenty ml of peripheral blood were taken from MS patients during regular clinical visits as well as from healthy donors at the Rostock University Medical Center.

extract_protocol: Peripheral blood mononuclear cells (PBMC) were isolated using Ficoll density gradient separation (Histopaque-1077, Sigma-Aldrich). Untouched B cells were then enriched from the PBMC by negative selection using the Pan B Cell Isolation Kit (Miltenyi Biotec). Total RNA was isolated using the miRNeasy Mini Kit (Qiagen) in combination with the RNase-free DNase set (Qiagen).

treatment_protocol: The patients were treated with different therapies according to the approved labels and the guidelines and recommendations of the German Society of Neurology.

tag: subject identifier

tag: group

value: RRMS patient

tag: therapy

value: cladribine

tag: Sex

value: female

tag: age (years)

tag: disease duration (years)

tag: edss score

tag: relapses in previous year


title: sample 120, RRMS - cladribine 5


title: sample 119, RRMS - cladribine 4


title: IHEC_33_scRNA-seq

description: Re-analysis of GSM2839615


title: IHEC_32_scRNA-seq

description: Re-analysis of GSM2839614


title: sample 115, RRMS - alemtuzumab 38

description: Gene expression data for a patient with RRMS treated with alemtuzumab

value: alemtuzumab

value: male


title: sample 116, RRMS - cladribine 1


title: sample 118, RRMS - cladribine 3


title: IHEC_31_scRNA-seq

description: Re-analysis of GSM2839613


title: sample 113, RRMS - alemtuzumab 36


title: sample 114, RRMS - alemtuzumab 37


title: IHEC_30_scRNA-seq

description: Re-analysis of GSM2839612


title: sample 117, RRMS - cladribine 2


title: sample 108, RRMS - alemtuzumab 31


title: sample 109, RRMS - alemtuzumab 32


title: sample 110, RRMS - alemtuzumab 33


title: sample 106, RRMS - alemtuzumab 29


title: sample 107, RRMS - alemtuzumab 30


title: IHEC_28_scRNA-seq

description: Re-analysis of GSM2839610


title: sample 111, RRMS - alemtuzumab 34


title: IHEC_29_scRNA-seq

description: Re-analysis of GSM2839611


title: sample 105, RRMS - alemtuzumab 28


title: IHEC_27_scRNA-seq

description: Re-analysis of GSM2839609


title: sample 104, RRMS - alemtuzumab 27


title: IHEC_26_scRNA-seq

description: Re-analysis of GSM2839608


title: sample 103, RRMS - alemtuzumab 26


title: sample 102, RRMS - alemtuzumab 25


title: sample 101, RRMS - alemtuzumab 24


title: IHEC_24_scRNA-seq

description: Re-analysis of GSM2839606


title: sample 112, RRMS - alemtuzumab 35


title: IHEC_22_scRNA-seq

description: Re-analysis of GSM2839604


title: IHEC_25_scRNA-seq

description: Re-analysis of GSM2839607


title: IHEC_23_scRNA-seq

description: Re-analysis of GSM2839605


title: IHEC_21_scRNA-seq

description: Re-analysis of GSM2839603


title: IHEC_18_scRNA-seq

description: Re-analysis of GSM2839600


title: IHEC_17_scRNA-seq

description: Re-analysis of GSM2839599


title: IHEC_16_scRNA-seq

description: Re-analysis of GSM2839598


title: sample 99, RRMS - alemtuzumab 22


title: sample 100, RRMS - alemtuzumab 23


title: IHEC_19_scRNA-seq

description: Re-analysis of GSM2839601


title: IHEC_14_scRNA-seq

description: Re-analysis of GSM2839596


title: IHEC_20_scRNA-seq

description: Re-analysis of GSM2839602


title: sample 96, RRMS - alemtuzumab 19


title: sample 98, RRMS - alemtuzumab 21


title: IHEC_13_scRNA-seq

description: Re-analysis of GSM2839595


title: sample 94, RRMS - alemtuzumab 17


title: sample 88, RRMS - alemtuzumab 11


title: IHEC_11_scRNA-seq

description: Re-analysis of GSM2839593


title: sample 95, RRMS - alemtuzumab 18


title: sample 90, RRMS - alemtuzumab 13


title: sample 97, RRMS - alemtuzumab 20


title: sample 87, RRMS - alemtuzumab 10


title: sample 93, RRMS - alemtuzumab 16


title: IHEC_9_scRNA-seq

description: Re-analysis of GSM2839591


title: IHEC_12_scRNA-seq

description: Re-analysis of GSM2839594


title: IHEC_8_scRNA-seq

description: Re-analysis of GSM2839590


title: IHEC_10_scRNA-seq

description: Re-analysis of GSM2839592


title: IHEC_7_scRNA-seq

description: Re-analysis of GSM2839589


title: sample 91, RRMS - alemtuzumab 14


title: IHEC_6_scRNA-seq

description: Re-analysis of GSM2839588


title: IHEC_4_scRNA-seq

description: Re-analysis of GSM2839586


title: IHEC_3_scRNA-seq

description: Re-analysis of GSM2839585


title: IHEC_2_scRNA-seq

description: Re-analysis of GSM2839584


title: HHEC_78_scRNA-seq

description: Re-analysis of GSM2839581

value: Homeostatic

value: Untreated


title: IHEC_1_scRNA-seq

description: Re-analysis of GSM2839583


title: sample 86, RRMS - alemtuzumab 9


title: HHEC_77_scRNA-seq

description: Re-analysis of GSM2839580


title: sample 81, RRMS - alemtuzumab 4


title: sample 84, RRMS - alemtuzumab 7


title: sample 85, RRMS - alemtuzumab 8


title: sample 82, RRMS - alemtuzumab 5


title: IHEC_5_scRNA-seq

description: Re-analysis of GSM2839587


title: IHEC_15_scRNA-seq

description: Re-analysis of GSM2839597


title: sample 80, RRMS - alemtuzumab 3


title: sample 83, RRMS - alemtuzumab 6


title: HHEC_76_scRNA-seq

description: Re-analysis of GSM2839579


title: HHEC_79_scRNA-seq

description: Re-analysis of GSM2839582


title: sample 75, RRMS - before IRT 5

description: Gene expression data for a patient with RRMS before IRT

value: fingolimod


title: HHEC_75_scRNA-seq

description: Re-analysis of GSM2839578


title: sample 73, RRMS - before IRT 3

value: glatiramer acetate


title: sample 74, RRMS - before IRT 4


title: sample 76, RRMS - before IRT 6


title: sample 70, RRMS - natalizumab 29

description: Gene expression data for a patient with RRMS treated with natalizumab

value: natalizumab


title: sample 72, RRMS - before IRT 2


title: sample 69, RRMS - natalizumab 28


title: sample 71, RRMS - before IRT 1


title: sample 77, RRMS - before IRT 7


title: sample 67, RRMS - natalizumab 26


title: HHEC_69_scRNA-seq

description: Re-analysis of GSM2839572


title: HHEC_71_scRNA-seq

description: Re-analysis of GSM2839574


title: HHEC_72_scRNA-seq

description: Re-analysis of GSM2839575


title: sample 79, RRMS - alemtuzumab 2


title: HHEC_73_scRNA-seq

description: Re-analysis of GSM2839576


title: HHEC_68_scRNA-seq

description: Re-analysis of GSM2839571


title: HHEC_67_scRNA-seq

description: Re-analysis of GSM2839570


title: HHEC_65_scRNA-seq

description: Re-analysis of GSM2839568


title: sample 66, RRMS - natalizumab 25


title: HHEC_64_scRNA-seq

description: Re-analysis of GSM2839567


title: HHEC_66_scRNA-seq

description: Re-analysis of GSM2839569


title: HHEC_63_scRNA-seq

description: Re-analysis of GSM2839566


title: sample 63, RRMS - natalizumab 22


title: HHEC_62_scRNA-seq

description: Re-analysis of GSM2839565


title: sample 65, RRMS - natalizumab 24


title: HHEC_61_scRNA-seq

description: Re-analysis of GSM2839564


title: HHEC_60_scRNA-seq

description: Re-analysis of GSM2839563


title: sample 58, RRMS - natalizumab 17


title: sample 64, RRMS - natalizumab 23


title: sample 55, RRMS - natalizumab 14


title: HHEC_59_scRNA-seq

description: Re-analysis of GSM2839562


title: sample 92, RRMS - alemtuzumab 15


title: sample 59, RRMS - natalizumab 18


title: sample 56, RRMS - natalizumab 15


title: sample 78, RRMS - alemtuzumab 1


title: sample 62, RRMS - natalizumab 21


title: HHEC_57_scRNA-seq

description: Re-analysis of GSM2839560


title: sample 57, RRMS - natalizumab 16


title: sample 60, RRMS - natalizumab 19


title: HHEC_58_scRNA-seq

description: Re-analysis of GSM2839561


title: sample 53, RRMS - natalizumab 12


title: sample 61, RRMS - natalizumab 20


title: HHEC_56_scRNA-seq

description: Re-analysis of GSM2839559


title: HHEC_54_scRNA-seq

description: Re-analysis of GSM2839557


title: HHEC_53_scRNA-seq

description: Re-analysis of GSM2839556


title: HHEC_50_scRNA-seq

description: Re-analysis of GSM2839553


title: HHEC_51_scRNA-seq

description: Re-analysis of GSM2839554


title: HHEC_55_scRNA-seq

description: Re-analysis of GSM2839558


title: sample 52, RRMS - natalizumab 11


title: HHEC_52_scRNA-seq

description: Re-analysis of GSM2839555


title: HHEC_48_scRNA-seq

description: Re-analysis of GSM2839551


title: sample 54, RRMS - natalizumab 13


title: sample 49, RRMS - natalizumab 8


title: sample 47, RRMS - natalizumab 6


title: sample 51, RRMS - natalizumab 10


title: sample 48, RRMS - natalizumab 7


title: HHEC_47_scRNA-seq

description: Re-analysis of GSM2839550


title: HHEC_46_scRNA-seq

description: Re-analysis of GSM2839549


title: sample 42, RRMS - natalizumab 1


title: sample 44, RRMS - natalizumab 3


title: HHEC_44_scRNA-seq

description: Re-analysis of GSM2839547


title: HHEC_45_scRNA-seq

description: Re-analysis of GSM2839548


title: sample 50, RRMS - natalizumab 9


title: HHEC_42_scRNA-seq

description: Re-analysis of GSM2839545


title: sample 43, RRMS - natalizumab 2


title: HHEC_41_scRNA-seq

description: Re-analysis of GSM2839544


title: HHEC_40_scRNA-seq

description: Re-analysis of GSM2839543


title: HHEC_43_scRNA-seq

description: Re-analysis of GSM2839546


title: sample 46, RRMS - natalizumab 5


title: HHEC_49_scRNA-seq

description: Re-analysis of GSM2839552


title: HHEC_39_scRNA-seq

description: Re-analysis of GSM2839542


title: sample 41, PPMS 13

description: Gene expression data for a patient with PPMS

value: PPMS patient

value: glucocorticosteroids


title: HHEC_36_scRNA-seq

description: Re-analysis of GSM2839539


title: sample 40, PPMS 12


title: HHEC_33_scRNA-seq

description: Re-analysis of GSM2839536


title: HHEC_37_scRNA-seq

description: Re-analysis of GSM2839540


title: HHEC_38_scRNA-seq

description: Re-analysis of GSM2839541


title: HHEC_30_scRNA-seq

description: Re-analysis of GSM2839533


title: HHEC_32_scRNA-seq

description: Re-analysis of GSM2839535


title: HHEC_34_scRNA-seq

description: Re-analysis of GSM2839537


title: HHEC_31_scRNA-seq

description: Re-analysis of GSM2839534


title: HHEC_35_scRNA-seq

description: Re-analysis of GSM2839538


title: sample 45, RRMS - natalizumab 4


title: HHEC_29_scRNA-seq

description: Re-analysis of GSM2839532


title: HHEC_28_scRNA-seq

description: Re-analysis of GSM2839531


title: HHEC_24_scRNA-seq

description: Re-analysis of GSM2839527


title: HHEC_27_scRNA-seq

description: Re-analysis of GSM2839530


title: HHEC_25_scRNA-seq

description: Re-analysis of GSM2839528


title: HHEC_21_scRNA-seq

description: Re-analysis of GSM2839524


title: HHEC_26_scRNA-seq

description: Re-analysis of GSM2839529


title: HHEC_20_scRNA-seq

description: Re-analysis of GSM2839523


title: HHEC_22_scRNA-seq

description: Re-analysis of GSM2839525


title: HHEC_19_scRNA-seq

description: Re-analysis of GSM2839522


title: HHEC_14_scRNA-seq

description: Re-analysis of GSM2839517


title: HHEC_16_scRNA-seq

description: Re-analysis of GSM2839519


title: HHEC_15_scRNA-seq

description: Re-analysis of GSM2839518


title: HHEC_13_scRNA-seq

description: Re-analysis of GSM2839516


title: HHEC_18_scRNA-seq

description: Re-analysis of GSM2839521


title: HHEC_17_scRNA-seq

description: Re-analysis of GSM2839520


title: HHEC_12_scRNA-seq

description: Re-analysis of GSM2839515


title: Healthy Control-Ileum

city: Rotterdam

first: Henk

middle: P.

last: Roest

state: Choose State

address: Doctor Molewaterplein 40

department: Surgery

country: Netherlands

institute: Erasmus MC

data_processing:
.fastq files were uploaded to the Galaxy public server (usegalaxy.org) and quality checked using FASTQC
Remaining adapters were trimmed using Cutadapt (v1.16.5)
Quality filtered and trimmed sequences were mapped against the human genome using HISAT2 (v2.1.0)
Mapped reads were converted to counts using FeatureCounts (v2.0.1)
Genome_build: GRCh38 (hg38)
Supplementary_files_format_and_content: Matrix table (tab-delimited .txt format) with raw gene counts for every gene and every sample, PubMed and GeneID annotations, and transcript lengths

source_name: 2D-Organoids cultured on transwell membranes

growth_protocol:
Solidified Matrigel droplets in complete culture medium consisting of advanced DMEM/F12 supplemented with penicillin and streptomycin, 10 mM HEPES, Glutamax, N2, B27 (all from Invitrogen), 1 μM N-acetylcysteine (Sigma) and the following growth factors: 50 ng ml−1 mouse epidermal growth factor (mEGF), 50% Wnt3a-conditioned medium (WCM) and 10% noggin-conditioned medium (NCM), 20% Rspo1-conditioned medium, 10 μM nicotinamide (Sigma), 10 nM gastrin (Sigma), 500 nM A83-01 (Tocris) and 10 μM SB202190 (Sigma)
For culture of epithelial monolayers, organoid-derived cells were seeded on a Matrigel-coated (diluted 1:20 in phosphate buffered saline) permeable substrate (Transwell #3470; Corning). Culture medium was as for 3D cultures, except that CHIR99021 (10 μmol/L; Sigma-Aldrich) and Y-27632 (10 μmol/L; R&D Systems) were added during the first two days after seeding of ileum cultures, and that forskolin was absent from the BD-derived organoid culture medium. (10-14 days).

extract_protocol:
Total RNA was isolated using the miRNEAsy kit (Qiagen) according to the manufacturer's protocol and eluted in RNAse-free water. Samples were mRNA enriched using oligodT
Library construction was performed at the GBI RNA(transcriptome) sequencing facilities, Copenhagen, Denmark.  In short, purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First-strand cDNA was generated using random hexamer-primed reverse transcription, followed by a second-strand cDNA synthesis. afterwards, A-Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR, and products were purified by Ampure XP Beads, then dissolved in EB solution.The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA (ssCir DNA) was formatted as the final library.

treatment_protocol: Cells were cultured under 5% CO2 at 37°C until a confluent monolayer was obtained

value: Ileum

tag: age

tag: gender

value: Male

tag: origin

value: Resected tissue (surgery)

tag: disease state

value: healthy control


title: HHEC_8_scRNA-seq

description: Re-analysis of GSM2839511

tag: strain

value: Lymph Node

value: High Endothelial Cell


title: Healthy Control-BD

growth_protocol:
Solidified BME droplets in Advanced DMEM/F12 medium (Invitrogen) supplemented with 1% N2, 1% B27 (both Gibco), 1.25 mM N-Acetylcystein (Sigma), 10 nM gastrin (Sigma), 50 ng/ml EGF (Peprotech), 100 ng/ml FGF10 (Peprotech), 25 ng/ml HGF (Peprotech), 10% R-spondin (conditioned medium), 10 nM nicotinamide (Sigma), 5 µM A83.01 (Tocris), 10 µM forskolin (Tocris), 100 ng/ml DKK-1
For culture of epithelial monolayers, organoid-derived cells were seeded on a Matrigel-coated (diluted 1:20 in phosphate buffered saline) permeable substrate (Transwell #3470; Corning). Culture medium was as for 3D cultures, except that CHIR99021 (10 μmol/L; Sigma-Aldrich) and Y-27632 (10 μmol/L; R&D Systems) were added during the first two days after seeding of ileum cultures, and that forskolin was absent from the BD-derived organoid culture medium. (10-14 days).

tag: tissue

value: Liver

value: Female

value: Liver donor (deceased)


title: Cystic Fibrosis-BD

value: CF patient

value: cystic fibrosis


title: Cystic Fibrosis-Ileum


title: HHEC_10_scRNA-seq

description: Re-analysis of GSM2839513

tag: cell type

value: Homeostatic

value: Untreated


title: HHEC_5_scRNA-seq

description: Re-analysis of GSM2839508

tag: state


title: HHEC_11_scRNA-seq

description: Re-analysis of GSM2839514

tag: treatment


title: HHEC_23_scRNA-seq

description: Re-analysis of GSM2839526


title: HHEC_7_scRNA-seq

description: Re-analysis of GSM2839510


title: HHEC_6_scRNA-seq

description: Re-analysis of GSM2839509


title: HHEC_70_scRNA-seq

description: Re-analysis of GSM2839573


title: HHEC_4_scRNA-seq

description: Re-analysis of GSM2839507


title: HHEC_3_scRNA-seq

description: Re-analysis of GSM2839506


title: HHEC_9_scRNA-seq

description: Re-analysis of GSM2839512


title: HHEC_74_scRNA-seq

description: Re-analysis of GSM2839577


title: HHEC_2_scRNA-seq

description: Re-analysis of GSM2839505


title: Animal 16401, PBMC, index  CCGTCC, 1st run [A4_PBMC]

city: San Antonio

first: Melanie

middle: Anita

last: Carless

state: Texas

address: One UTSA Circle

country: USA

institute: The University of Texas at San Antonio

data_processing:
Raw sequence reads were obtained using Illumina's Pipeline v1.5 software following sequencing image analysis by Pipeline Firecrest Module and base calling by Pipeline Bustard Module.
Extracted sequence reads were aligned (Bowtie), normalized, annotated and abundance determined using mirDeep2.
Genome_build: miRbase v21
Supplementary_files_format_and_content: Excel spreadsheet with normalized read counts for 362 miRNAs.

organism: Papio hamadryas

source_name: Animal 16401, PBMC, index  CCGTCC

extract_protocol:
Baboons were sedated with ketamine (10mg/kg) prior to collection of blood in Cell Preparation Tubes (Becton-Dickinson, Franklin Lakes, NJ, USA), anesthetized (1-2% isoflurane), and euthanized via either intravenous injection of pentobarbital (>100mg/kg) or exsanguination while under general anesthesia. Necropsy was performed to obtain brain tissue. PBMCs were isolated according to the manufacturers’ protocol. Brain regions were dissected from fresh tissue, placed in a cryovial, and flash frozen in liquid nitrogen. All samples were stored at -80°C. Total RNA was isolated from PBMCs and brain regions using the miRNeasy Mini Kit (Qiagen, Germantown, MD).
Small RNA sequencing libraries were prepared using the Illumina Truseq Small RNA Sample Prep Kit.

value: PBMC

tag: animal id

value: Animal 16401

tag: molecule

value: miRNA


title: Animal 16401, PBMC, index  CCGTCC, 2nd run [A4_PBMC]


title: Animal 16401, medial orbitofrontal cortex, index  GTAGAG, 2nd run [A4_mOFC]

value: medial orbitofrontal cortex


title: Animal 16401, lateral orbitofrontal cortex, index  CGTACG, 2nd run [A4_lOFC]

value: lateral orbitofrontal cortex


title: Animal 16401, medial orbitofrontal cortex, index  GTAGAG, 1st run [A4_mOFC]


title: Animal 16401, posterior cingulate cortex, index  GTCCGC, 2nd run [A4_PCC]

value: posterior cingulate cortex


title: Animal 16401, lateral orbitofrontal cortex, index  CGTACG, 1st run [A4_lOFC]


title: Animal 16401, hypothalamus, index  GTTTCG, 2nd run [A4_Hyp]

value: hypothalamus


title: BEC_32_scRNA-seq

description: Re-analysis of GSM2839503

value: Blood Endothelial Cell


title: BEC_29_scRNA-seq

description: Re-analysis of GSM2839500

value: Lymph Node


title: Animal 16401, hypothalamus, index  GTTTCG, 1st run [A4_Hyp]


title: BEC_30_scRNA-seq

description: Re-analysis of GSM2839501


title: Animal 16401, dorsal anterior cingulate cortex, index  GTGAAA, 2nd run [A4_dACC]

value: dorsal anterior cingulate cortex


title: BEC_28_scRNA-seq

description: Re-analysis of GSM2839499


title: Animal 16401, posterior cingulate cortex, index  GTCCGC, 1st run [A4_PCC]


title: BEC_26_scRNA-seq

description: Re-analysis of GSM2839497


title: Animal 16401, dorsal anterior cingulate cortex, index  GTGAAA, 1st run [A4_dACC]


title: Animal 16401, prefrontal cortex (BA9), index  GTGGCC, 2nd run [A4_PFC]

value: prefrontal cortex (BA9)


title: BEC_25_scRNA-seq

description: Re-analysis of GSM2839496


title: Animal 16401, prefrontal cortex (BA9), index  GTGGCC, 1st run [A4_PFC]


title: BEC_24_scRNA-seq

description: Re-analysis of GSM2839495


title: Animal 16172, prefrontal cortex, index  GAGTGG, 2nd run [B6_dlPFC]

value: prefrontal cortex

value: Animal 16172


title: HHEC_1_scRNA-seq

description: Re-analysis of GSM2839504

value: High Endothelial Cell


title: BEC_23_scRNA-seq

description: Re-analysis of GSM2839494


title: BEC_22_scRNA-seq

description: Re-analysis of GSM2839493


title: BEC_21_scRNA-seq

description: Re-analysis of GSM2839492


title: Animal 16172, posterior parietal cortex, index  CGTACG, 2nd run [B6_PPC]

value: posterior parietal cortex


title: Animal 16172, prefrontal cortex, index  GAGTGG, 1st run [B6_dlPFC]


title: BEC_31_scRNA-seq

description: Re-analysis of GSM2839502

value: Homeostatic


title: Animal 16172, motor cortex, index  GTTTCG, 2nd run [B6_MC]

value: motor cortex


title: Animal 16172, motor cortex, index  GTTTCG, 1st run [B6_MC]


title: BEC_18_scRNA-seq

description: Re-analysis of GSM2839489

value: Untreated


title: BEC_17_scRNA-seq

description: Re-analysis of GSM2839488


title: BEC_27_scRNA-seq

description: Re-analysis of GSM2839498


title: BEC_16_scRNA-seq

description: Re-analysis of GSM2839487


title: Animal 16172, entorhinal cortex, index  GTGAAA, 2nd run [B6_EC]

value: entorhinal cortex


title: Animal 16172, entorhinal cortex, index  GTGAAA, 1st run [B6_EC]

value: miRNA


title: sample 68, RRMS - natalizumab 27

tag: subject identifier

tag: group

value: RRMS patient

tag: therapy

value: natalizumab

value: female


title: BEC_20_scRNA-seq

description: Re-analysis of GSM2839491


title: Animal 16172, hippocampus, index  GTGGCC, 2nd run [B6_HDG]

source_name: Animal 16172, hippocampus, index  GTGGCC

value: hippocampus


title: Animal 16172, occipital cortex, index  GGTAGC, 2nd run [B6_OC]

value: occipital cortex


title: BEC_14_scRNA-seq

description: Re-analysis of GSM2839485

value: Lymph Node

value: Blood Endothelial Cell


title: BEC_15_scRNA-seq

description: Re-analysis of GSM2839486


title: BEC_13_scRNA-seq

description: Re-analysis of GSM2839484


title: Animal 16172, cerebellum, index  GTCCGC, 2nd run [B6_Cb]

source_name: Animal 16172, cerebellum, index  GTCCGC

value: cerebellum


title: Animal 16172, occipital cortex, index  GGTAGC, 1st run [B6_OC]


title: Animal 16172, cerebellum, index  GTCCGC, 1st run [B6_Cb]


title: BEC_10_scRNA-seq

description: Re-analysis of GSM2839481


title: BEC_12_scRNA-seq

description: Re-analysis of GSM2839483


title: BEC_11_scRNA-seq

description: Re-analysis of GSM2839482


title: BEC_9_scRNA-seq

description: Re-analysis of GSM2839480


title: Animal 16172, posterior parietal cortex, index  CGTACG, 1st run [B6_PPC]


title: BEC_19_scRNA-seq

description: Re-analysis of GSM2839490


title: Animal 16172, PBMC, index  GTAGAG, 1st run [B6_PBMC]

source_name: Animal 16172, PBMC, index  GTAGAG

value: PBMC


title: Animal 16172, PBMC, index  GTAGAG, 2nd run [B6_PBMC]

value: Animal 16172


title: BEC_8_scRNA-seq

description: Re-analysis of GSM2839479


title: Animal 15987, posterior cingulate cortex, index  GTCCGC, 2nd run [A3_PCC]

value: posterior cingulate cortex

value: Animal 15987


title: BEC_7_scRNA-seq

description: Re-analysis of GSM2839478

value: Homeostatic


title: BEC_6_scRNA-seq

description: Re-analysis of GSM2839477


title: Animal 15987, posterior cingulate cortex, index  GTCCGC, 1st run [A3_PCC]


title: Animal 16172, hippocampus, index  GTGGCC, 1st run [B6_HDG]


title: Animal 15987, PBMC, index  GTAGAG, 2nd run [A3_PBMC]

source_name: Animal 15987, PBMC, index  GTAGAG


title: BEC_5_scRNA-seq

description: Re-analysis of GSM2839476


title: Animal 15987, medial orbitofrontal cortex, index  GTGAAA, 2nd run [A3_mOFC]

value: medial orbitofrontal cortex


title: BEC_3_scRNA-seq

description: Re-analysis of GSM2839474

value: Untreated


title: BEC_4_scRNA-seq

description: Re-analysis of GSM2839475


title: Animal 15987, medial orbitofrontal cortex, index  GTGAAA, 1st run [A3_mOFC]


title: Animal 15987, PBMC, index  GTAGAG, 1st run [A3_PBMC]


title: BEC_1_scRNA-seq

description: Re-analysis of GSM2839472


title: TA_HEC_36_scRNA-seq

description: Single s.c njection of 100*106 MCA Reg (fibrosarcoma), harvest Day 7

source_name: Fibrosarcoma

value: Fibrosarcoma

value: Tumor Associated High Endothelial Cell


title: TA_HEC_35_scRNA-seq


title: Animal 15987, hypothalamus, index  CGTACG, 1st run [A3_Hyp]

value: hypothalamus

value: miRNA


title: Animal 15987, lateral orbitofrontal cortex, index  GTTTCG, 2nd run [A3_lOFC]

value: lateral orbitofrontal cortex


title: TA_HEC_34_scRNA-seq


title: Animal 15987, hypothalamus, index  CGTACG, 2nd run [A3_Hyp]


title: Animal 15987, prefrontal cortex (BA9), index  GTGGCC, 2nd run [A3_PFC]

value: prefrontal cortex (BA9)


title: Animal 15987, dorsal anterior cingulate cortex, index  GAGTGG, 2nd run [A3_dACC]

value: dorsal anterior cingulate cortex


title: TA_HEC_31_scRNA-seq


title: TA_HEC_32_scRNA-seq


title: TA_HEC_33_scRNA-seq


title: Animal 15987, dorsal anterior cingulate cortex, index  GAGTGG, 1st run [A3_dACC]


title: Animal 15987, prefrontal cortex (BA9), index  GTGGCC, 1st run [A3_PFC]


title: Animal 15987, amygdala, index  GGTAGC, 4th run [A3_Amg]

value: amygdala


title: TA_HEC_30_scRNA-seq


title: Animal 15987, amygdala, index  GGTAGC, 2nd run [A3_Amg]

source_name: Animal 15987, amygdala, index  GGTAGC


title: TA_HEC_28_scRNA-seq


title: Animal 15987, amygdala, index  GGTAGC, 1st run [A3_Amg]


title: TA_HEC_27_scRNA-seq


title: Animal 15987, amygdala, index  GGTAGC, 3rd run [A3_Amg]


title: TA_HEC_26_scRNA-seq


title: BEC_2_scRNA-seq

description: Re-analysis of GSM2839473

value: Lymph Node

value: Blood Endothelial Cell


title: TA_HEC_25_scRNA-seq


title: Animal 15987, lateral orbitofrontal cortex, index  GTTTCG, 1st run [A3_lOFC]


title: TA_HEC_24_scRNA-seq


title: Animal 15942, PBMC, index  ATCACG, 2nd run [A2_PBMC]

source_name: Animal 15942, PBMC, index  ATCACG

value: PBMC

value: Animal 15942


title: Animal 15942, posterior cingulate cortex, index  TGACCA, 1st run [A2_PCC]

value: posterior cingulate cortex


title: Animal 15942, posterior cingulate cortex, index  TGACCA, 2nd run [A2_PCC]


title: TA_HEC_23_scRNA-seq


title: TA_HEC_20_scRNA-seq


title: Animal 15942, PBMC, index  ATCACG, 1st run [A2_PBMC]


title: TA_HEC_22_scRNA-seq


title: TA_HEC_29_scRNA-seq


title: TA_HEC_21_scRNA-seq


title: Animal 15942, medial orbitofrontal cortex, index  ACAGTG, 1st run [A2_mOFC]


title: Animal 15942, lateral orbitofrontal cortex, index  CGATGT, 2nd run [A2_lOFC]


title: Animal 15942, medial orbitofrontal cortex, index  ACAGTG, 2nd run [A2_mOFC]


title: Animal 15942, hypothalamus, index  GCCAAT, 2nd run [A2_Hyp]


title: Animal 15942, lateral orbitofrontal cortex, index  CGATGT, 1st run [A2_lOFC]


title: Animal 15942, hypothalamus, index  GCCAAT, 1st run [A2_Hyp]


title: TA_HEC_16_scRNA-seq


title: TA_HEC_19_scRNA-seq


title: TA_HEC_18_scRNA-seq


title: Animal 15942, dorsal anterior cingulate cortex, index  TTAGGC, 1st run [A2_dACC]


title: TA_HEC_15_scRNA-seq


title: TA_HEC_13_scRNA-seq


title: Animal 15942, dorsal anterior cingulate cortex, index  TTAGGC, 2nd run [A2_dACC]


title: TA_HEC_14_scRNA-seq


title: Animal 15942, prefrontal cortex (BA9), index  CAGATC, 2nd run [A2_PFC]


title: Animal 15942, prefrontal cortex (BA9), index  CAGATC, 1st run [A2_PFC]


title: TA_HEC_11_scRNA-seq


title: Animal 15942, amygdala, index  ACTTGA, 2nd run [A2_Amg]

source_name: Animal 15942, amygdala, index  ACTTGA


title: TA_HEC_10_scRNA-seq


title: Animal 15942, amygdala, index  ACTTGA, 1st run [A2_Amg]


title: Animal 14838, posterior cingulate cortex, index  AGTTCC, 2nd run [A1_PCC]

value: Animal 14838


title: TA_HEC_09_scRNA-seq


title: TA_HEC_08_scRNA-seq


title: TA_HEC_17_scRNA-seq


title: Animal 14838, PBMC, index  GATCAG, 2nd run [A1_PBMC]

source_name: Animal 14838, PBMC, index  GATCAG


title: TA_HEC_07_scRNA-seq


title: Animal 14838, PBMC, index  GATCAG, 1st run [A1_PBMC]


title: TA_HEC_06_scRNA-seq


title: Animal 14838, posterior cingulate cortex, index  AGTTCC, 1st run [A1_PCC]


title: Animal 14838, medial orbitofrontal cortex, index  ATGTCA, 1st run [A1_mOFC]


title: TA_HEC_03_scRNA-seq


title: Animal 14838, medial orbitofrontal cortex, index  ATGTCA, 2nd run [A1_mOFC]


title: TA_HEC_12_scRNA-seq


title: TA_HEC_01_scRNA-seq


title: Animal 14838, lateral orbitofrontal cortex, index  AGTCAA, 2nd run [A1_lOFC]


title: TA_HEC_02_scRNA-seq


title: TA_HEC_05_scRNA-seq


title: Animal 14838, dorsal anterior cingulate cortex, index  CTTGTA, 2nd run [A1_dACC]


title: Animal 14838, hypothalamus, index  TAGCTT, 2nd run [A1_Hyp]


title: Animal 14838, dorsal anterior cingulate cortex, index  CTTGTA, 1st run [A1_dACC]


title: Animal 14838, hypothalamus, index  TAGCTT, 1st run [A1_Hyp]


title: TA_bEC_43_scRNA-seq

value: Tumor Associated blood Endothelial Cell


title: Animal 14838, prefrontal cortex (BA9), index  GGCTAC, 2nd run [A1_PFC]


title: TA_bEC_41_scRNA-seq


title: TA_bEC_42_scRNA-seq


title: TA_bEC_40_scRNA-seq


title: Animal 14838, lateral orbitofrontal cortex, index  AGTCAA, 1st run [A1_lOFC]


title: Animal 14838, prefrontal cortex (BA9), index  GGCTAC, 1st run [A1_PFC]


title: TA_HEC_04_scRNA-seq


title: Animal 14838, amygdala, index  CCGTCC, 1st run [A1_Amg]

source_name: Animal 14838, amygdala, index  CCGTCC


title: TA_bEC_39_scRNA-seq


title: TA_bEC_45_scRNA-seq


title: TA_bEC_38_scRNA-seq


title: TA_bEC_37_scRNA-seq


title: Animal 13737, prefrontal cortex, index  ATGTCA, 1st run [B5_dlPFC]

value: prefrontal cortex

value: Animal 13737


title: TA_bEC_44_scRNA-seq

value: Fibrosarcoma


title: TA_bEC_36_scRNA-seq


title: Animal 13737, posterior parietal cortex, index  AGTTCC, 1st run [B5_PPC]

value: posterior parietal cortex


title: TA_bEC_35_scRNA-seq


title: TA_bEC_34_scRNA-seq


title: Animal 13737, posterior parietal cortex, index  AGTTCC, 2nd run [B5_PPC]


title: TA_bEC_33_scRNA-seq


title: Animal 14838, amygdala, index  CCGTCC, 2nd run [A1_Amg]


title: Animal 13737, motor cortex, index  AGTCAA, 2nd run [B5_MC]

value: motor cortex


title: Animal 13737, motor cortex, index  AGTCAA, 1st run [B5_MC]

value: miRNA


title: TA_bEC_32_scRNA-seq


title: Animal 13737, hippocampus, index  CTTGTA, 1st run [B5_HDG]

source_name: Animal 13737, hippocampus, index  CTTGTA

value: hippocampus


title: Animal 13737, occipital cortex, index  CCGTCC, 2nd run [B5_OC]

value: occipital cortex


title: Animal 13737, entorhinal cortex, index  GGCTAC, 1st run [B5_EC]

value: entorhinal cortex


title: TA_bEC_28_scRNA-seq


title: Animal 13737, occipital cortex, index  CCGTCC, 1st run [B5_OC]


title: Animal 13737, prefrontal cortex, index  ATGTCA, 2nd run [B5_dlPFC]


title: TA_bEC_27_scRNA-seq


title: Animal 13737, entorhinal cortex, index  GGCTAC, 2nd run [B5_EC]


title: TA_bEC_29_scRNA-seq


title: Animal 13737, cerebellum, index  TAGCTT, 2nd run [B5_Cb]

source_name: Animal 13737, cerebellum, index  TAGCTT

value: cerebellum


title: Animal 13737, cerebellum, index  TAGCTT, 1st run [B5_Cb]


title: TA_bEC_26_scRNA-seq


title: TA_bEC_25_scRNA-seq


title: TA_bEC_31_scRNA-seq


title: Animal 13737, PBMC, index  GATCAG, 2nd run [B5_PBMC]

source_name: Animal 13737, PBMC, index  GATCAG


title: Animal 13737, hippocampus, index  CTTGTA, 2nd run [B5_HDG]


title: Animal 13737, PBMC, index  GATCAG, 1st run [B5_PBMC]


title: TA_bEC_21_scRNA-seq


title: TA_bEC_23_scRNA-seq


title: TA_bEC_24_scRNA-seq


title: Animal 13669, prefrontal cortex, index  CAGATC, 2nd run [B4_dlPFC]

value: Animal 13669


title: Animal 13669, prefrontal cortex, index  CAGATC, 1st run [B4_dlPFC]


title: Animal 13669, posterior parietal cortex, index  GCCAAT, 1st run [B4_PPC]


title: Animal 13669, motor cortex, index  ACAGTG, 2nd run [B4_MC]


title: Animal 13669, posterior parietal cortex, index  GCCAAT, 2nd run [B4_PPC]


title: TA_bEC_18_scRNA-seq


title: TA_bEC_17_scRNA-seq


title: TA_bEC_22_scRNA-seq


title: TA_bEC_30_scRNA-seq


title: TA_bEC_19_scRNA-seq


title: Animal 13669, hippocampus, index  TGACCA, 2nd run [B4_HDG]

source_name: Animal 13669, hippocampus, index  TGACCA


title: TA_bEC_15_scRNA-seq


title: Animal 13669, motor cortex, index  ACAGTG, 1st run [B4_MC]


title: TA_bEC_16_scRNA-seq


title: TA_bEC_13_scRNA-seq


title: Animal 13669, hippocampus, index  TGACCA, 1st run [B4_HDG]


title: Animal 13669, entorhinal cortex, index  TTAGGC, 2nd run [B4_EC]


title: Animal 13669, cerebellum, index  CGATGT, 2nd run [B4_Cb]

source_name: Animal 13669, cerebellum, index  CGATGT


title: TA_bEC_10_scRNA-seq


title: TA_bEC_20_scRNA-seq


title: TA_bEC_12_scRNA-seq


title: Animal 13669, entorhinal cortex, index  TTAGGC, 1st run [B4_EC]


title: TA_bEC_14_scRNA-seq


title: Animal 13669, occipital cortex, index  ACTTGA, 2nd run [B4_OC]


title: Animal 13669, PBMC, index  ATCACG, 1st run [B4_PBMC]

source_name: Animal 13669, PBMC, index  ATCACG


title: Animal 13669, occipital cortex, index  ACTTGA, 1st run [B4_OC]


title: TA_bEC_09_scRNA-seq


title: TA_bEC_08_scRNA-seq


title: TA_bEC_04_scRNA-seq


title: TA_bEC_05_scRNA-seq


title: TA_bEC_02_scRNA-seq


title: TA_bEC_03_scRNA-seq


title: TA_bEC_11_scRNA-seq


title: Animal 13029, prefrontal cortex, index  CGTACG, 2nd run [B3_dlPFC]

value: Animal 13029


title: Animal 13029, motor cortex, index  GTGGCC, 1st run [B3_MC]


title: 120hr rps-11 RNAi rep 3

city: Los Angeles

first: Sean

last: Curran

state: CA

address: 3715 McClintock Ave

department: Davis School of Gerontology

institute: University of Southern California

description:
fpkm.txt
R120rps3
rps120vsL4424.Differential_analysis_results.xls

data_processing:
Raw reads were first cleaned by removing reads containing adapter, reads contraining poly-N , and low quality reads. Base quality and phred score relationship with CASAVA v1.8 software from Illumina was used for QC.
Index of reference genome was built using Bowtie v2.2.3 on files available publicly and paired-end clean reads were aligned to reference genome using TopHat v2.0.12.
HTSeq v0.6.1 was used to count reads numbers mapped to each gene. FPKM of each gene was calculated based on length of gene and reads count mapped. FPKM is most commonly used currently (Trapnell, Cole, et al., 2010).
Differential expression analysis of two conditions/groups was performed using DESeq R package (1.18.0). Resulting p-values were adjusted using Benjamini and Hochberg's approach.
Genome_build: ce11
Supplementary_files_format_and_content: xlsx file contains fpkm for all samples. .txt Differental analysis files contain DESeq results with normalized read counts comparing 24hr L2 C. elegans ("L4424") to arrested L2 animals after 48hr or 120hr on egl-45 or rps-11 RNAi (all wild type)

organism: Caenorhabditis elegans

source_name: whole worms

growth_protocol: Worms were egg prepped and eggs were allowed to hatch overnight. Synchronized L1 animals were dropped immediately onto food for the start of the experiment.

extract_protocol:
Animals are homogenized in Trizol and RNA extraction is performed following protocol in Zymo Direct-zol RNA Isolation Kit. 1ug of RNA was used per sample for library construction using NEBNext® UltraTM RNA Library Prep Kit  for Illumina® (NEB, USA).
Sequencing libraries were generated following manufacturer's recommendations and index codes were added to attribute sequences to each sample.

treatment_protocol: Worms were fed food containing either RNAi against a gene of interest (egl-45 or rps-11) or empty L4440 vector (Control RNAi). After 24hr for Control RNAi, and 48 or 120hr for egl-45 and rps-11-fed animals, worms were washed 3x with M9 and frozen at -80oC in TRI Reagent.

value: N2 Bristol

tag: developmental stage

value: arrested L2

tag: genotype

value: wildtype

tag: RNAi

value: rps-11 RNAi

tag: time

value: whole worm


title: Animal 13669, PBMC, index  ATCACG, 2nd run [B4_PBMC]

value: PBMC


title: TA_bEC_06_scRNA-seq

value: Tumor Associated blood Endothelial Cell


title: Animal 13029, hippocampus, index  GTGAAA, 2nd run [B3_HDG]

source_name: Animal 13029, hippocampus, index  GTGAAA


title: Animal 13029, prefrontal cortex, index  CGTACG, 1st run [B3_dlPFC]

value: prefrontal cortex


title: Animal 13029, posterior parietal cortex, index  GTTTCG, 2nd run [B3_PPC]

value: posterior parietal cortex


title: Animal 13029, posterior parietal cortex, index  GTTTCG, 1st run [B3_PPC]


title: Animal 13029, motor cortex, index  GTGGCC, 2nd run [B3_MC]

value: motor cortex


title: TA_bEC_01_scRNA-seq

value: Fibrosarcoma


title: 120hr rps-11 RNAi rep 1

description:
fpkm.txt
R120rps1
rps120vsL4424.Differential_analysis_results.xls


title: 120hr rps-11 RNAi rep 2

description:
fpkm.txt
R120rps2
rps120vsL4424.Differential_analysis_results.xls


title: 48hr rps-11 RNAi rep 3

description:
fpkm.txt
R48rps_3
rps48vsL4424.Differential_analysis_results.xls


title: Animal 13029, entorhinal cortex, index  GTCCGC, 1st run [B3_EC]

value: miRNA


title: 48hr rps-11 RNAi rep 1

description:
fpkm.txt
R48rps_1
rps48vsL4424.Differential_analysis_results.xls


title: 120hr egl-45 RNAi rep 3

description:
fpkm.txt
R120egl3
egl120vsL4424.Differential_analysis_results.xls

value: egl-45 RNAi


title: TA_bEC_07_scRNA-seq


title: Animal 13029, occipital cortex, index  GAGTGG, 2nd run [B3_OC]

value: occipital cortex


title: Animal 13029, entorhinal cortex, index  GTCCGC, 2nd run [B3_EC]

value: entorhinal cortex


title: 120hr egl-45 RNAi rep 2

description:
fpkm.txt
R120egl2
egl120vsL4424.Differential_analysis_results.xls


title: 48hr egl-45 RNAi rep 3

description:
fpkm.txt
R48egl_3
egl48vsL4424.Differential_analysis_results.xls


title: 48hr rps-11 RNAi rep 2

description:
fpkm.txt
R48rps_2
rps48vsL4424.Differential_analysis_results.xls


title: 48hr egl-45 RNAi rep 2

description:
fpkm.txt
R48egl_2
egl48vsL4424.Differential_analysis_results.xls


title: Animal 13029, hippocampus, index  GTGAAA, 1st run [B3_HDG]

value: hippocampus


title: 24hr Control RNAi rep 2

description:
fpkm.txt
R24L44_2

value: Control RNAi


title: Animal 13669, cerebellum, index  CGATGT, 1st run [B4_Cb]

value: cerebellum

value: Animal 13669


title: Animal 13029, cerebellum, index  GTAGAG, 2nd run [B3_Cb]

source_name: Animal 13029, cerebellum, index  GTAGAG

value: Animal 13029


title: Animal 13029, cerebellum, index  GTAGAG, 1st run [B3_Cb]


title: Animal 12656, posterior parietal cortex, index  GATCAG, 2nd run [B2_PPC]

value: Animal 12656


title: Animal 13029, occipital cortex, index  GAGTGG, 1st run [B3_OC]


title: Animal 12656, prefrontal cortex, index  TAGCTT, 2nd run [B2_dlPFC]


title: Animal 12656, prefrontal cortex, index  TAGCTT, 1st run [B2_dlPFC]


title: Animal 12656, motor cortex, index  CCGTCC, 2nd run [B2_MC]


title: Animal 13029, PBMC, index  GGTAGC, 1st run [B3_PBMC]

source_name: Animal 13029, PBMC, index  GGTAGC


title: Animal 12656, posterior parietal cortex, index  GATCAG, 1st run [B2_PPC]


title: Animal 13029, PBMC, index  GGTAGC, 2nd run [B3_PBMC]


title: 120hr egl-45 RNAi rep 1

description:
fpkm.txt
R120egl1
egl120vsL4424.Differential_analysis_results.xls

value: N2 Bristol

value: arrested L2

value: wildtype

value: whole worm


title: NTKO-2_S22

city: Kansas City

first: Hong-Min

last: Ni

state: KS

address: 3901 Rainbow Blvd, MS-1018

department: Pharmacology, Toxicology and Therapeutics

institute: University of Kansas Medical Center

description: Atg5/TSC1/Nrf2 TKO rep2

data_processing:
Adaptors and low-quality reads were trimmed by Trimmomatic v0.36
The trimmed high-quality reads were mapped to the mouse genome NCBI GRCm38 using HISAT2 v2.1.0
HTSeq-counts v0.6.0 was used to quantify the gene counts under the union model with NCBI GRCm38 genome annotations.
Genome_build: NCBI GRCm38
Supplementary_files_format_and_content: raw mapped gene counts

source_name: Liver

extract_protocol:
Livers were removed and snap frozen in liquid nitrogen. Total RNA was extracted using Trizol reagent and the quality was checked with Qubit quantification and TapeStation gel analysis
RNA libraries were prepared for sequencing using the NEBNext Stranded mRNA library kit with polyA selection of the mRNA
NextSeq 550 High Output Single Read 75 bp Sequencing

value: Liver

tag: age

value: hepatic Atg5/TSC1/Nrf2 TKO


title: Animal 12656, motor cortex, index  CCGTCC, 1st run [B2_MC]

value: motor cortex


title: NTKO-3_S23

description: Atg5/TSC1/Nrf2 TKO rep3


title: NTKO-1_S21

description: Atg5/TSC1/Nrf2 TKO rep1


title: 48hr egl-45 RNAi rep 1

description:
fpkm.txt
R48egl_1
egl48vsL4424.Differential_analysis_results.xls


title: PTKO-2_S18

description: Atg5/TSC1/p62 TKO rep2

value: hepatic Atg5/TSC1/p62 TKO


title: PTKO-3_S19

description: Atg5/TSC1/p62 TKO rep3


title: Animal 12656, hippocampus, index  ATGTCA, 2nd run [B2_HDG]

source_name: Animal 12656, hippocampus, index  ATGTCA

value: miRNA


title: PTKO-1_S17

description: Atg5/TSC1/p62 TKO rep1


title: 24hr Control RNAi rep 1

description:
fpkm.txt
R24L44_1


title: Animal 12656, entorhinal cortex, index  GGCTAC, 2nd run [B2_EC]


title: Animal 12656, hippocampus, index  ATGTCA, 1st run [B2_HDG]


title: NTKO-4_S24

description: Atg5/TSC1/Nrf2 TKO rep4


title: 24hr Control RNAi rep 3

description:
fpkm.txt
R24L44_3


title: DKO-1_S13

description: Atg5/TSC1 DKO rep1

value: hepatic Atg5/TSC1 DKO


title: DKO-3_S15

description: Atg5/TSC1 DKO rep3


title: DKO-2_S14

description: Atg5/TSC1 DKO rep2


title: Animal 12656, entorhinal cortex, index  GGCTAC, 1st run [B2_EC]

value: entorhinal cortex


title: TSCKO-3_S11

description: TSC1 KO rep3

value: hepatic TSC1 KO


title: DKO-4_S16

description: Atg5/TSC1 DKO rep4


title: FP_M_24_083V1

city: Baltimore

first: Josephine

middle: M.

last: Egan

state: MD

address: BRC Suite 100, 251 Bayview Boulevard

department: Laboratory of Clinical Investigation

institute: National Institute on Aging - NIH

hyb_protocol: A total of 600 ng Cy3-labeled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 microL containing 0.5x Agilent fragmentation buffer and 2x Agilent gene expression blocking agent following the manufacturer's instructions. On completion of the fragmentation reaction, 25 microL of 2× Hi-RPM Hybridization Buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint GE3 Human 8x60k v2 gene expression microarrays for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), and dried by slowly removing from Wash buffer 2.

scan_protocol: Following posthybridization rinses, arrays were scanned using an Agilent SureScan microarray Scanner at 5 micron, and hybridization intensity data extracted from the scanned images using Agilent’s Feature Extraction Software 9.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.

data_processing: Raw microarray hybridization intensity data from four separate experiments were log-transformed. Raw microarray data were log transformed to yield z-scores. The z-ratio was calculated as the difference between the observed gene z-scores for the experimental and the control comparisons, and dividing by the standard deviation associated with the distribution of these differences. Z-ratio values of ± 1.5 were used as cut-off values and calculated using a 5% false discovery rate (FDR) threshold. The complete set was tested for gene set enrichment using parametric analysis of gene set enrichment. For each pathway z-score, a p-value was computed using JMP 6.0 software to test for the statistical significance.

source_name: Tongue

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 200 ng total RNA using the Low-Input Quick Amp Labeling Kit (Agilent, Santa Clara, CA) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were evaluated with the NanoDrop ND-1000 Spectrophotometer (Wilmington, DE).

growth_protocol: Human fungiform taste papillae biopsies were done with prior IRB approval (IRB/NIH approval # 2018-AG-N010) and participants gave informed written consent. All biopsies were carried out at the NIA Clinical Unit, Baltimore, MD. The study involved two visits: a screening visit coupled to information sharing, verbal and written, related to the study, followed by a study visit. Participants were excluded if they had less than 40 fungiform papillae on the anterior third portion of the tongue, if they were taking steroids, if they had diabetes based on a fasting plasma glucose of less than 126mg/dl, if there was any evidence of gum or mouth disease and if they were known to be allergic to lidocaine. Participants were asked to refrain from taking non-steroidal anti-inflammatory medications for 4 days prior to the biopsy. Biopsies were performed in the fasting state between 07:30-09:30hrs, blood was drawn for serum and plasma collection and the anterior portion of the tongue was photographed and anesthetized using topical 1% lidocaine. Fungiform papillae were obtained using sterile curved spring micro-scissors (McPherson-Vannas) Type # SR5603 (Roboz Surgical Instrument Co, Gaithersburg, MD). Individual papilla for RNA isolation were immediately placed in sterile 1.6 mL tubes and flash frozen in liquid nitrogen.

extract_protocol: Individual frozen taste papillae were homogenized in RLT-DTT buffer (Qiagen) using a single 30 second, 6000 rpm cycle on a Precellys24 homogenizer (Bertin Corp., Rockville, MD). RNA extraction followed the recommended RNeasy Mini fibrous kit protocol (Qiagen, Germantown, MD). RNA quality and quantity were determined using the Agilent Bioanalyzer RNA6000 Chip (Agilent, Santa Clara, CA).

tag: sample

value: Fungiform papillae

tag: gender

value: Male


title: Animal 12656, occipital cortex, index  GGCTAC, 2nd run [B2_OC]

value: occipital cortex


title: FP_M_27_104V1


title: FP_M_32_070V2


title: PTKO-4_S20

description: Atg5/TSC1/p62 TKO rep4

tag: strain


title: TSCKO-2_S10

description: TSC1 KO rep2

tag: tissue


title: FP_F29_022V3

value: Female


title: Animal 12656, occipital cortex, index  GGCTAC, 1st run [B2_OC]

value: Animal 12656


title: TSCKO-1_S9

description: TSC1 KO rep1


title: Animal 12656, cerebellum, index  AGTCAA, 2nd run [B2_Cb]

source_name: Animal 12656, cerebellum, index  AGTCAA

value: cerebellum


title: AKO-2_S6

description: Atg5 KO rep2

value: hepatic Atg5 KO


title: AKO-4_S8

description: Atg5 KO rep4


title: AKO-3_S7

description: Atg5 KO rep3


title: AKO-1_S5

description: Atg5 KO rep1


title: TSCKO-4_S12

description: TSC1 KO rep4


title: FP_M_22_085V1


title: WT-3_S3

description: WT rep3

value: wild type


title: WT-4_S4

description: WT rep4


title: WT-2_S2

description: WT rep2


title: Animal 12656, cerebellum, index  AGTCAA, 1st run [B2_Cb]


title: Animal 12656, PBMC, index  CTTGTA, 1st run [B2_PBMC]

source_name: Animal 12656, PBMC, index  CTTGTA

value: PBMC


title: S6_3

city: Groningen

first: Rieza

last: Aprianto

state: Groningen

address: Nijenborg 7

department: Molecular Genetics Department

institute: University of Groningen

data_processing:
Read trimming (Trimmomatic 0.38)
Alignment into chrimeric genome (STAR 2.6.0a)
Summation (featureCounts, subread 1.6.3)
Genome_build: Streptococcus pneumoniae D39V (CP027540)
Supplementary_files_format_and_content: tab-delimited text files include raw counts for all 18 libraries

organism: Streptococcus pneumoniae

source_name: Exponentially growing pneumococcal cells in late competence (CSP, 20 min)

growth_protocol: Streptococcus pneumoniae strain D39V were pre-cultured in corresponding mediums before used to innoculate in the treatment protocol

extract_protocol:
Total RNA isolation based on phenol-chloroform, gDNA treatment using RNase-free DNase
RNA libraries were prepared for sequencing using standard Illumina protocols without rRNA depletion
non rRNA-depleted RNA-sequencing

treatment_protocol: Streptococcus pneumoniae strain D39V were grown in six different conditions, mimicking the host niches

value: strain D39V

value: wildtype

tag: condition

value: Late competence (CSP, 20 min)


title: S6_2


title: Animal 11641, prefrontal cortex, index  TGACCA, 2nd run [B1_dlPFC]

value: prefrontal cortex

value: Animal 11641


title: Animal 11641, posterior parietal cortex, index  TTAGGC, 2nd run [B1_PPC]

value: posterior parietal cortex

value: miRNA


title: Animal 11641, prefrontal cortex, index  TGACCA, 1st run [B1_dlPFC]


title: Animal 12656, PBMC, index  CTTGTA, 2nd run [B2_PBMC]


title: WT-1_S1

description: WT rep1

value: Liver


title: S5_3

source_name: Exponentially growing pneumococcal cells in C+Y

value: C+Y


title: S5_2


title: S5_1


title: S4_3

source_name: Exponentially growing pneumococcal cells in fever mimicking condition (FEVER)

value: Fever mimicking condition (FEVER)


title: S4_2


title: FP_F29_006V2

value: Fungiform papillae


title: FP_F29_037V3

value: Female


title: S4_1


title: S3_2

source_name: Exponentially growing pneumococcal cells in CSF-mimicking condition (CSFMC)

value: CSF-mimicking condition (CSFMC)


title: Animal 11641, motor cortex, index  CGATGT, 2nd run [B1_MC]

value: motor cortex


title: Animal 11641, motor cortex, index  CGATGT, 1st run [B1_MC]


title: FP_F28_103V1


title: S3_3


title: S3_1


title: S2_3

source_name: Exponentially growing pneumococcal cells in lung-mimicking condition (LMC)

value: Lung-mimicking condition (LMC)


title: S2_2


title: S1_3

source_name: Exponentially growing pneumococcal cells in nose-mimicking condition (NMC)

value: Nose-mimicking condition (NMC)


title: S6_1


title: S2_1


title: Animal 11641, entorhinal cortex, index  ATCACG, 1st run [B1_EC]

value: entorhinal cortex


title: Animal 11641, entorhinal cortex, index  ATCACG, 2nd run [B1_EC]


title: S1_1

value: strain D39V


title: YUJASMIN, scRNA-seq

city: New Haven

first: Ruth

last: Halaban

state: CT

address: 15 York St.

department: Dermatology

institute: Yale University

data_processing:
Single-cell RNA-seq reads from four acral melanoma patients were mapped to the GRCh38 human reference assembly and barcode-deduplicated using Cell Ranger (version 3.0.2 and 5.0.1).
The resulting data were imported into Seurat116 (version 4.0.4) and quality-control filtered for the number of expressed genes per cell and the fraction of reads mapped to mitochondrial genes.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include counts for each cell per gene

source_name: Tumor

extract_protocol:
For YUJASMIN, cryopreserved tumor cell suspension was sorted for viable singlets to target 10,000 cells. Cells were sorted in the following ratios prior to library preparation: 50% CD3+CD45+ T cells: 25% CD3–CD45+ non-T immune cells: 25% CD45– stromal/cancer cells. Cell viability was assessed by the LIVE/DEAD™ Fixable Red Dead Cell Stain Kit (catalog #L34971, Thermo Fisher). The following antibodies were used: Alexa Fluor® 488 anti-human CD45 antibody (clone H130, catalog #304019, BioLegend); APC anti-human CD3 antibody (clone HIT3a, catalog #300319, BioLegend). For the other three tumors,  cryopreserved tumor cell suspensions were used.
For YUJASMIN, the 10x Chromium 5’ expression profiling platform with V1 chemistry was applied  and  the 10x library was sequenced on an Illumina HiSeq 2500 instrument. For the other three tumors, the 10x Chromium 5’ assay with V2 chemistry was applied to cryopreserved tumor cell suspensions and sequenced on an Illumina NovaSeq 6000 instrument.

tag: individual

value: patient YUJASMIN

tag: disease state

value: acral melanoma

value: acral melanoma tumor

tag: 22q11.21 amplified

value: yes


title: ZS-2

data_processing:
Raw RNA-seq reads were aligned with Salmon101 (version 0.99) to the GENCODE v.25102 reference transcript assembly.
Subsequently, the tximport103 was used to generate an expression matrix normalized to transcripts per million (TPM).
Protein-coding genes were determined using Ensembl release 92 human annotation 104 (GRCh38.p12, Apr 2018), extracted by biomaRt105 (version 2.40.5) and non-protein-coding genes were omitted. Expression values were renormalized to TPM after this step.
For batch normalization, we applied ComBat from sva106 using a parametric adjustment for sequencing center and year of sequencing. Following batch correction, negative values were replaced with zero and the expression matrix was log2-transformed after adding a pseudo-count of 1.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited gene expression values

source_name: Melanoma

extract_protocol:
Melanomas were sequenced from snap-frozen tumors (Yale and CSU cohorts) or low passage cell cultures (<4). High melanin content was removed with OneStep™ PCR Inhibitor Removal Kit (Zymo Research Corporation, Irvine, CA). Direct-zol™ RNA MiniPrep w/ Zymo-Spin™ IIC Columns (Zymo cat # D4019) were used to extract RNA from tumors, and the RNeasy PowerLyzer Tissue & Cells Kit (Qiagen, CAT # 15055-50) was used to extract RNA from peripheral blood mononuclear cells (PBMCs) and melanoma cells.
For the CSU cohort, total RNA was depleted of rRNA using the Ribo-Zero rRNA removal kit, namely,1 μg of total RNA was used as input for rRNA removal. Sequencing libraries were generated using the TruSeq RNA sample prep kit (Illumina). The libraries were sequenced as 151 bp paired-end reads using an Illumina HiSeq X Ten platform. For the Yale cohort, rRNA was depleted starting from 25-1000ng of total RNA using the Kapa RNA HyperPrep Kit with RiboErase (KR1351). Indexed libraries that met appropriate cut-offs for both quantity and quality were quantified by qRT-PCR using a commercially available kit (KAPA Biosystems) and insert size distribution was determined with the LabChip GX or Agilent Bioanalyzer. Samples with a yield of ≥0.5 ng/ul were used for sequencing. Samples were run on a combination of Illumina HiSeq 2500, HiSeq 4000, and NovaSeq instruments, and multiplexed using unique dual barcode indexes (to avoid sample contamination or barcode hopping).

value: M

tag: age at diagnosis (years)

tag: mutation category

tag: subtype

value: Acral

tag: primary tumor location

value: foot

tag: cohort center

value: CSU

tag: site of tumor sampling

value: Primary

tag: ethnicity

value: Asian

tag: ajcc stage

tag: number of positive lymph nodes

tag: n stage

tag: overall survival event

tag: overall survival period from diagnosis date (year)

tag: overall survival period from resection date (year)

tag: tumor purity (loh based)


title: ZS-5

tag: gender

value: left foot


title: ZS-3

value: right foot


title: Animal 11641, hippocampus, index  CAGATC, 1st run [B1_HDG]

source_name: Animal 11641, hippocampus, index  CAGATC

tag: tissue

value: hippocampus

tag: animal id

value: Animal 11641

tag: molecule

value: miRNA


title: ZIRG

tag: age at diagnosis (years)

tag: mutation category

value: WT

value: SunExposed

value: left arm

value: Yale

value: Caucasian


title: ZACK

tag: subtype

tag: primary tumor location

value: left toe nail

value: Metastatic


title: S1_2

tag: strain

value: strain D39V

tag: genotype

value: wildtype

tag: condition

value: Nose-mimicking condition (NMC)


title: Animal 11641, occipital cortex, index  ACTTGA, 1st run [B1_OC]

value: occipital cortex


title: XY-8

value: F

value: Acral

value: left heel

tag: cohort center

value: CSU

tag: site of tumor sampling

value: Primary

tag: ethnicity

value: Asian

tag: ajcc stage

tag: number of positive lymph nodes


title: Animal 11641, cerebellum, index  GCCAAT, 1st run [B1_Cb]

source_name: Animal 11641, cerebellum, index  GCCAAT

value: cerebellum

value: Animal 11641

value: miRNA


title: Animal 11641, PBMC, index  ACAGTG, 2nd run [B1_PBMC]

source_name: Animal 11641, PBMC, index  ACAGTG

value: PBMC


title: Animal 11641, posterior parietal cortex, index  TTAGGC, 1st run [B1_PPC]

value: posterior parietal cortex


title: XY-4

value: M

value: right heel

tag: n stage

tag: overall survival event

tag: overall survival period from diagnosis date (year)

tag: overall survival period from resection date (year)

tag: tumor purity (loh based)


title: Animal 11641, PBMC, index  ACAGTG, 1st run [B1_PBMC]

tag: tissue

tag: animal id

tag: molecule


title: XY-18

tag: gender

tag: age at diagnosis (years)

tag: mutation category

tag: subtype

tag: primary tumor location

value: left plantar foot


title: XY-12

value: right plantar foot

tag: cohort center

tag: site of tumor sampling


title: XY-1

tag: ethnicity

tag: ajcc stage


title: XY-23

tag: number of positive lymph nodes

tag: n stage


title: Animal 11641, hippocampus, index  CAGATC, 2nd run [B1_HDG]

value: hippocampus


title: WW165

value: BRAF

value: SunExposed

value: back

value: Yale

value: Caucasian

tag: overall survival event

tag: overall survival period from diagnosis date (year)


title: Animal 11641, occipital cortex, index  ACTTGA, 2nd run [B1_OC]

value: occipital cortex


title: ZS-4

value: Acral

value: right foot

value: CSU

value: Primary

value: Asian

tag: overall survival period from resection date (year)

tag: tumor purity (loh based)


title: WERA

value: F

value: WT


title: VOCI

value: M

value: RAS

value: left medial ankle

value: Metastatic


title: WAPO

value: left dorsal foot


title: Animal 11641, cerebellum, index  GCCAAT, 2nd run [B1_Cb]

tag: tissue

value: cerebellum

tag: animal id

value: Animal 11641

value: miRNA


title: TOV

tag: gender

value: BRAF

value: SunExposed

value: left distal inner thigh

value: Yale

value: Caucasian


title: TOK

tag: age at diagnosis (years)

value: Acral

value: big toe primary, acral

value: Primary

value: Hispanic


title: TAUR

value: M

tag: mutation category

value: right foot


title: VERDE

value: WT

tag: subtype

value: mid forehead


title: 8d_GSK3i_L_2_WGBS

city: Cambridge

first: Felix

last: Krueger

address: Granta Park

department: Bioinformatics

country: United Kingdom

institute: Altos Labs

library_source: genomic

data_processing:
Raw sequence WGBS paired-end reads were trimmed to remove both poor quality calls and adapters using Trim Galore (v.0.6.5). Sequences were mapped to the mouse GRCm38 genome assembly using Bismark (v0.22.3), deduplicated with deduplicate_bismark, then CpG methylation calls were extracted and analysed with SeqMonk.
Raw, single-end RNA-seq reads were trimmed using Trim Galore (v.0.6.5) with default settings. Trimmed reads were mapped to the mouse GRCm38 genome assembly using HISAT2, and mappings with MAPQ scores <20 were discarded. Mapped RNA-seq data was quantitated over strand-specific mRNA probes using the Seqmonk RNA-seq Quantitation Pipeline to generate log2 RPM (reads per million mapped reads of library) expression values.
Genome_build: GRCm38
RNA-seq report: Tab-delimited text file of log2RPM values for each replicate sample individually (SeqMonk Annotated Probe report).
Bismark coverage report: A Bismark coverage file specific for either the top (OT) or bottom (OB) strand.

molecule: genomic DNA

growth_protocol: E14 (XY) mouse embryonic stem cells (mESCs) were cultured feeder-free in normoxia on 0.1% gelatin-coated plates. 1.5 million cells were plated per 10cm plate in S/L media (DMEM supplemented with 15% fetal bovine serum, 1% Penicillin-Streptomycin, 1% MEM non-essential amino acids, 1% Glutamax, 50 μM β-mercaptoethanol [all Gibco] and 10^3 U LIF [Cambridge Stem Cell Institute]). The following day, cells were washed twice with PBS and the media changed to S/L, 2i/L, GSK3i/L or MEKi/L media. 2i/L, GSK3i/L and MEKi/L media had in common the basal N2B27 media with LIF (1:1 ratio DMEM/F12 to neurobasal medium, 0.5% 100X N-2 supplement, 1% 50X B-27 supplement without Vitamin A, 1% Glutamax, 1% Penicillin- Streptomycin, 50 μM β-mercaptoethanol [all Gibco] and 10^3 U LIF). 2i/L media was supplemented with 1μM PD03259010 and 3μM CHIR99021 (both Cambridge Stem Cell Institute), GSK3i/L media with 3μM CHIR99021 only, and MEKi/L with 1μM PD03259010 only. Cells were passaged every 2 days using TrypLE Express (Gibco), and 3 million cells were plated per 10cm plate.

extract_protocol:
For collection at designated time points for DNA and RNA extraction, cells were washed twice with cold PBS and then scraped from plates in RLT plus buffer (Qiagen). DNA and RNA was extracted using the DNA/RNA mini kit (Qiagen). RNA was subsequently DNase treated using the TURBO DNA-free kit ’Rigorous DNase treatment’ protocol.
For whole genome Bisulfite-Seq, DNA was fragmented to an average of 400bp using a Covaris sonicator, and 50ng of sonicated DNA together with a spike-in of 8ng lambda DNA was used for library preparation. Methylated adaptors were added using NEBNext Ultra II DNA Library Prep reagents, then samples were bisulfite converted using the Zymo EZ Methylation-Direct kit. Libraries were amplified using KAPA HiFi Uracil+ then analysed on a Bioanalyzer and by KAPA quantification. A 10nM pool of 26 duplicate samples was 100bp paired-end sequenced over two lanes of a NovaSeq S1 flowcell.
RNA-seq libraries were made using the NEBNext Poly(A) mRNA Magnetic Isolation Module combined with the NEBNext Ultra II Directional Library Prep Kit for Illumina. Final libraries were KAPA quantified and the library quality assessed with the Agilent Bioanalyser DNA High Sensitivity Kit. A 20nM pool of 17 libraries was sequenced over two lanes of HiSeq2500-RapidRun 50bp Single End.

tag: cell type

value: Embryonic stem cells

tag: cell line

tag: treatment

value: 8 days GSK3i/L


title: 8d_S_L_3_WGBS

value: 8d S/L


title: SUSA

value: F

tag: primary tumor location

value: thumb bed nail

tag: cohort center

tag: site of tumor sampling

value: Metastatic

tag: ethnicity


title: TAS

value: BRAF

value: SunExposed

value: upper thigh

tag: ajcc stage

tag: number of positive lymph nodes

tag: n stage

tag: overall survival event


title: 8d_GSK3i_L_3_WGBS


title: SUBA

value: left infraclavicular chest

value: Yale

value: Caucasian

tag: overall survival period from diagnosis date (year)

tag: overall survival period from resection date (year)

tag: tumor purity (loh based)


title: 8d_S_L_2_WGBS


title: SIV

tag: gender

tag: age at diagnosis (years)

value: Right lower back


title: SOP

tag: mutation category

tag: subtype

value: unknown


title: SIK

value: right thigh


title: SEEP

value: M

value: WT

value: Acral

value: left heel

value: Primary


title: 8d_2i_L_2_WGBS

tag: cell type

value: Embryonic stem cells

tag: cell line

value: 8 days 2i/L


title: SMILE

tag: primary tumor location

value: right cheek, desmoplastic


title: 8d_1uM_MEKi_L_2_WGBS

tag: treatment

value: 8 days 1uM MEKi/L


title: RUDY

value: SunExposed

value: left forehead

tag: cohort center

tag: site of tumor sampling


title: ROL

value: recurrence right posterior thigh

value: Metastatic

tag: ethnicity

tag: ajcc stage


title: 8d_0.8uM_MEKi_L_3_WGBS

value: 8 days 0.8uM MEKi/L


title: 8d_0.8uM_MEKi_L_2_WGBS


title: RIDA

value: RAS

value: left neck

value: Yale

value: Caucasian

tag: number of positive lymph nodes

tag: n stage


title: REIL

value: F

value: WT

value: scalp, primary

tag: overall survival event

tag: overall survival period from diagnosis date (year)


title: 8d_2i_L_3_WGBS


title: 8d_0.6uM_MEKi_L_3_WGBS

value: 8 days 0.6uM MEKi/L


title: RIF

value: M

value: BRAF

value: right thigh

tag: overall survival period from resection date (year)

tag: tumor purity (loh based)


title: 8d_1uM_MEKi_L_3_WGBS

value: Embryonic stem cells

value: 8 days 1uM MEKi/L


title: QALE

tag: gender

tag: age at diagnosis (years)

value: SunExposed

value: left upper back


title: RAISE

tag: mutation category

tag: subtype

value: right calf

value: Metastatic


title: SEGI

value: left forearm; melanoma in situ in 8/2004 of the L neck and another scalp melanoma on L scalp in 1998)


title: SCH

value: Acral

value: right thumbnail


title: 8d_0.6uM_MEKi_L_2_WGBS

tag: cell type

tag: cell line


title: PRETE

tag: primary tumor location

value: left big toe

value: Yale

value: African American


title: QUANT

value: F

value: WT

value: right heel acral

tag: cohort center

value: Hispanic


title: 8d_0.4uM_MEKi_L_2_WGBS

tag: treatment

value: 8 days 0.4uM MEKi/L


title: 8d_0.2uM_MEKi_L_3_WGBS

value: Embryonic stem cells

value: 8 days 0.2uM MEKi/L


title: NUVO

value: M

value: left foot

tag: site of tumor sampling

value: Primary

tag: ethnicity

value: Caucasian


title: OFER

value: SunExposed

value: ear

tag: ajcc stage

tag: number of positive lymph nodes


title: 6d_1uM_MEKi_L_3_WGBS

value: 6 days 1uM MEKi/L


title: NP-59

value: Acral

value: left  great toe nail

value: CSU

value: Asian

tag: n stage

tag: overall survival event


title: NP-58

value: plantar area of the 3rd toe of his right foot

tag: overall survival period from diagnosis date (year)

tag: overall survival period from resection date (year)


title: NP-41

tag: gender

value: right heel

tag: tumor purity (loh based)


title: 8d_0.4uM_MEKi_L_3_WGBS


title: 6d_1uM_MEKi_L_2_WGBS


title: PER

tag: age at diagnosis (years)

tag: mutation category

value: BRAF

value: right thigh (mid sternal/xiphoid area)

value: Yale

value: Metastatic


title: NP-57

value: M

tag: subtype

value: right great  toe nail


title: POME

value: F

value: RAS

value: uppear thigh (left leg)


title: 8d_0.2uM_MEKi_L_2_WGBS

tag: cell type

value: Embryonic stem cells

tag: cell line

value: 8 days 0.2uM MEKi/L


title: NP-26

value: Acral

tag: primary tumor location

value: right toe nail

tag: cohort center

value: Primary


title: NP-33

value: left plantar foot

value: CSU

tag: site of tumor sampling

value: Asian


title: RDE

value: BRAF

value: SunExposed

value: right lower back

tag: ethnicity

value: Caucasian


title: 4d_1uM_MEKi_L_3_WGBS

tag: treatment

value: 4 days 1uM MEKi/L


title: NP-116

tag: ajcc stage

tag: number of positive lymph nodes


title: NP-123

tag: n stage

tag: overall survival event


title: NOL

value: M

value: WT

value: right cheek

value: Yale

value: Metastatic

tag: overall survival period from diagnosis date (year)

tag: overall survival period from resection date (year)


title: NIS

tag: gender

value: F

value: RAS

value: left foot

tag: tumor purity (loh based)


title: NIBO

tag: age at diagnosis (years)

tag: mutation category

value: mid back

value: Primary


title: NIGE

tag: subtype

value: left arm


title: MORF

value: left lower abdomen primary


title: 2d_1uM_MEKi_L_2_WGBS

tag: cell type

value: Embryonic stem cells

tag: cell line

value: 2 days 1uM MEKi/L


title: 2d_1uM_MEKi_L_3_WGBS


title: 24d_GSK3i_L_3_WGBS

value: 24 days GSK3i/L


title: MYNA

value: BRAF

value: SunExposed

tag: primary tumor location

value: right shoulder

tag: cohort center

value: Caucasian


title: LENIO

value: right uppear back

tag: site of tumor sampling

tag: ethnicity


title: Tx4w3

city: Philadelphia

first: Hoang

last: Nguyen

state: PA

address: 3400 Civic Center Boulevard

institute: University of Pennsylvania Perelman School of Medicine

data_processing:
Genome alignment single read: STAR --genomeDir ~/STAR_GENOME_DIR --runThreadN 20 --readFilesIn $i --outFileNamePrefix ${i/.fastq.gz/}_ --outFilterMultimapNmax 1 --outSAMtype BAM SortedByCoordinate --readFilesCommand zcat --outSAMstrandField intronMotif
Counting reads: featureCounts -t exon -g gene_id -a ~/genes.gtf -T 20
DGE with DESeq2.
Genome_build: hg38 (GRCh38) and mm10 (GRCm38)
Supplementary_files_format_and_content: *_SGS_counts.txt: featureCounts read counts for all samples.

source_name: explanted trachea

extract_protocol:
Tracheal tissues were placed in a vial 5ml conical tube containing RNAlater immediately after collection from the operating room. The tubes were vortex-mixed for 30 seconds, patties were removed, and the RNAlater solution decanted following 15 min of centrifugation at 16,000 x g. This step ensured maximum recovery of epithelial cells. The decanted RNAlater was collected in a fresh tube and centrifuged at 2,000 x g for 5 minutes. Pellets were resuspended in 500 μL of TRIzol. Samples were incubated for 1 hour at room temperature, before lysing the cells by repeated passage through a 29-G syringe. We then proceeded with the TRIzol RNA extraction protocol as suggested by the manufacturer’s instructions.
RNA libraries were prepared for sequencing per NEB protocol.

tag: strain

tag: age

value: 8 weeks

tag: time point

value: 4 weeks post laryngotracheal injury

tag: tissue

value: Explanted trachea


title: Tx4w5


title: LOVY

value: F

value: RAS

value: right medial calf

value: Yale

tag: ajcc stage

tag: number of positive lymph nodes

tag: n stage

tag: overall survival event

tag: overall survival period from diagnosis date (year)


title: Tx4w4


title: KLON

tag: gender

value: M

tag: age at diagnosis (years)

tag: mutation category

value: WT

value: cheek

value: Metastatic

tag: overall survival period from resection date (year)

tag: tumor purity (loh based)


title: 24d_GSK3i_L_2_WGBS

tag: cell type

value: Embryonic stem cells

tag: cell line

tag: treatment

value: 24 days GSK3i/L


title: MIFT

tag: subtype

value: Acral

tag: primary tumor location

value: left heel

tag: cohort center

tag: site of tumor sampling

tag: ethnicity


title: KSI

value: BRAF

value: SunExposed

value: scalp

value: Caucasian

tag: ajcc stage

tag: number of positive lymph nodes


title: LETA

value: right leg

tag: n stage

tag: overall survival event


title: LEKI

tag: gender

value: Primary

tag: overall survival period from diagnosis date (year)


title: KIVA

value: F

tag: age at diagnosis (years)

tag: mutation category

value: right gluteal (back)


title: KIM

value: RAS

value: left scapular area

value: Yale

tag: overall survival period from resection date (year)

tag: tumor purity (loh based)


title: 4d_1uM_MEKi_L_2_WGBS

tag: cell type

tag: cell line

value: 4 days 1uM MEKi/L


title: Tx4w2

tag: strain

tag: age

value: 8 weeks

tag: time point

value: 4 weeks post laryngotracheal injury

tag: tissue

value: Explanted trachea


title: KIL

value: M

tag: subtype

tag: primary tumor location

value: right neck

tag: cohort center

tag: site of tumor sampling

value: Metastatic

tag: ethnicity


title: Tx4w1


title: KADI

tag: gender

value: BRAF

value: SunExposed

value: right shoulder

tag: ajcc stage

tag: number of positive lymph nodes

tag: n stage

tag: overall survival event


title: JOIN

tag: age at diagnosis (years)

tag: mutation category

value: left chest

value: Caucasian

tag: overall survival period from diagnosis date (year)

tag: overall survival period from resection date (year)

tag: tumor purity (loh based)


title: Tx3w6

tag: strain

tag: age

tag: time point

value: 3 weeks post laryngotracheal injury


title: MUL

tag: subtype

tag: primary tumor location

value: right thigh


title: MUT

value: right upper back

tag: cohort center

tag: site of tumor sampling


title: JASMIN

tag: gender

value: WT

value: Acral

value: right foot, acral

tag: ethnicity


title: Tx3w5

value: 8 weeks

tag: tissue


title: HT-4

value: right thumb nail

value: CSU

value: Primary

value: Asian

tag: ajcc stage

tag: number of positive lymph nodes

tag: n stage


title: HT-2

value: M

tag: age at diagnosis (years)

tag: mutation category

value: left plantar foot

value: Metastatic

tag: overall survival event


title: HT-12

value: right  heel

tag: overall survival period from diagnosis date (year)

tag: overall survival period from resection date (year)

tag: tumor purity (loh based)


title: Tx3w4

tag: strain

tag: age

tag: time point

value: Explanted trachea


title: HT-18

value: F

tag: subtype

tag: primary tumor location

value: between the 4th and 5th toes of the left foot

tag: cohort center


title: HT-10

tag: gender

tag: site of tumor sampling

tag: ethnicity


title: HEF

value: SunExposed

value: scalp

value: Yale

value: Caucasian

tag: ajcc stage

tag: number of positive lymph nodes


title: Tx3w3

value: 3 weeks post laryngotracheal injury

tag: tissue


title: HIMO

tag: age at diagnosis (years)

tag: mutation category

value: WT

value: Acral

value: posterior right heel

tag: n stage


title: GLORY

value: left foot (acral)

value: Primary

tag: overall survival event

tag: overall survival period from diagnosis date (year)

tag: overall survival period from resection date (year)


title: Tx3w1

tag: strain

tag: age

value: 8 weeks


title: Tx3w2

tag: time point


title: GAFFE

value: M

value: BRAF

tag: subtype

tag: primary tumor location

value: back of left ear (neck)

tag: tumor purity (loh based)


title: Tx1w3

value: 1 week post laryngotracheal injury

value: Explanted trachea


title: Tx1w5


title: GAVE

tag: gender

value: back

tag: cohort center

tag: site of tumor sampling

value: Metastatic


title: FIG

value: F

value: RAS

value: SunExposed

value: left uppear leg

tag: ethnicity

tag: ajcc stage

tag: number of positive lymph nodes


title: FARM

tag: age at diagnosis (years)

tag: mutation category

value: plantar area of the 3rd toe of her left foot

value: Yale

value: Caucasian


title: FAND

value: right ear primary

tag: n stage

tag: overall survival event


title: FRESA

value: WT

value: right upper arm

tag: overall survival period from diagnosis date (year)

tag: overall survival period from resection date (year)


title: EPIC

value: M

value: scalp primary

value: Primary


title: Tx1w4

tag: strain

tag: age

value: 8 weeks

value: 1 week post laryngotracheal injury

tag: tissue


title: ECO

tag: subtype

value: Acral

tag: primary tumor location

value: plantar foot, acral


title: Tx1w2

tag: time point

value: Explanted trachea


title: DOLE

tag: gender

value: RAS

value: right ear

tag: cohort center

value: Metastatic

tag: tumor purity (loh based)


title: Tx1w1


title: DOSO

value: SunExposed

value: left abdomen

tag: site of tumor sampling

tag: ethnicity

tag: ajcc stage


title: CRATE

value: F

tag: age at diagnosis (years)

tag: mutation category

value: BRAF

value: plantar left foot

value: Yale

value: Hispanic

tag: number of positive lymph nodes


title: Tx0w3

value: Immediately post laryngotracheal injury


title: COT

value: right neck

value: Caucasian

tag: n stage

tag: overall survival event

tag: overall survival period from diagnosis date (year)


title: COSMIC

value: right bicep

tag: overall survival period from resection date (year)


title: Tx0w1

tag: strain

tag: age

value: 8 weeks

tag: tissue


title: COB

value: WT

tag: subtype

value: Acral

tag: primary tumor location

value: right foot


title: polyA Enriched RNA-sequencing_ATMPARP_1_CTX

city: Memphis

first: Peter

middle: J

last: McKinnon

state: Tennessee

address: 262 Danny Thomas Place

department: Center for Pediatric Neurological Disease Research

institute: St. Jude Children's Research Hospital

description: polyA enriched RNA

data_processing:
FASTQ sequences are mapped to the University of California Santa Cruz mouse reference genome (mm9)
RNA-seq reads were mapped by our in-house mapping pipeline STRONGARM developed for the PCGP (Downing et al., 2012).
Reads were aligned to four different databases using BWA (0.5.10): (i) the mouse MGSCv37 reference sequence; (ii) RefSeq; (iii) a sequence file representing all possible combinations of non-sequential pairs in RefSeq exons; and (iv) the AceView database flat file downloaded from the UCSC Genome Browser, representing transcripts constructed from mouse ESTs
Genome_build: mm9
Supplementary_files_format_and_content: BigWig

molecule: polyA RNA

source_name: Whole Cortex_Atm Nes-cre; Parp1-/-

extract_protocol:
Total RNA was isolated from mouse brain tissue with TRIzol (Invitrogen)
From total RNA, poly-A RNA was purified by removing rRNA using Epicentre’s Ribo-Zero rRNA Removal kit (Cat# RZH11042). library preparation using TruSeq Standed Total RNA Kit (Illumina): Double stranded cDNA fragments are ligated with Illumina paired end adaptors, followed by size selection (~200bp). need confirmation by Scott Olson

tag: genotype

value: Atm Nes-cre; Parp1-/-

tag: tissue type

value: Cortex


title: COLA

tag: gender

value: SunExposed

tag: cohort center

tag: site of tumor sampling

value: Metastatic

tag: tumor purity (loh based)


title: Tx0w2

tag: time point

value: Explanted trachea


title: polyA Enriched RNA-sequencing_ATMPARP_2_CTX

description: polyA enriched RNA


title: CLUE

value: M

tag: age at diagnosis (years)

tag: mutation category

value: BRAF

value: right fourth toe

tag: ethnicity

tag: ajcc stage

tag: number of positive lymph nodes


title: Ctrl3

tag: strain

value: No injury control


title: polyA Enriched RNA-sequencing_ATMAPTX_3_CTX

description: polyA enriched RNA

source_name: Whole Cortex_Atm Nes-cre; Aptx-/-

value: Atm Nes-cre; Aptx-/-


title: polyA Enriched RNA-sequencing_ATMAPTX_4_CTX

description: polyA enriched RNA


title: BROT

value: right shoulder

value: Yale

tag: n stage

tag: overall survival event

tag: overall survival period from diagnosis date (year)

tag: overall survival period from resection date (year)


title: CHER

value: RAS

tag: subtype

tag: primary tumor location

value: right arm

value: Caucasian


title: ELSA

tag: gender

value: WT

value: Acral

value: right toe, acral


title: BAIX

value: right occipital lobe (scalp)

tag: cohort center


title: Ctrl2

tag: age

value: 8 weeks

tag: tissue


title: Ctrl1

tag: time point


title: BILI

tag: age at diagnosis (years)

value: SunExposed

value: left ear (tragus)

tag: site of tumor sampling

value: Metastatic

tag: tumor purity (loh based)


title: polyA Enriched RNA-sequencing_ATMAPTX_2_CTX

description: polyA enriched RNA

tag: genotype

tag: tissue type

value: Cortex


title: polyA Enriched RNA-sequencing_ATMAPTX_1_CTX

description: polyA enriched RNA


title: COVE

value: F

tag: mutation category

value: BRAF

value: scalp

tag: ethnicity

tag: ajcc stage

tag: number of positive lymph nodes


title: polyA Enriched RNA-sequencing_Control_2_CTX

description: polyA enriched RNA

source_name: Whole Cortex_Control

value: Control


title: polyA Enriched RNA-sequencing_Conrol_1_CTX

description: polyA enriched RNA


title: CHIPS

value: right temple

value: Yale

tag: n stage

tag: overall survival event

tag: overall survival period from diagnosis date (year)

tag: overall survival period from resection date (year)


title: SLAM iTreg-ASC-JQ1, Replicate2

first: Beisi

last: Xu

address: 262 Danny Thomas Pl

department: Center for Applied Bioinformatics

institute: St Jude Children's Research Hosipital

data_processing:
Library strategy: SLAM-Seq
Single-end reads of 100bp were first trimmed by cutadapt (version 1.9, default parameter with “ -m 25 -O 6 ”) (Martin, 2011) and then aligned to mouse genome mm9 (MGSCv37 from Sanger) by SLAMDUNK (version 0.4.0, parameters “-5 12 -n 100 -c 2 -mv 0.2 -m -rl 100”) (Neumann et al., 2019).
3’UTR bed files from Gencode vM17 (liftOver from mm9, regions were merged, and 3’UTRs from different isoforms were overlaid) (Harrow et al., 2012) were used for reads counting and gene-based counting (SLAMDUNK collapse function). All samples achieved more than 100M reads (median 120M) and at least 98.4% mapping rate. Quality control results from SLAMDUNK (alleyoop function, all default parameters except “-mq 2” for rates subfunction) were comparable to those from published SLAM-seq data (Muhar et al., 2018).
We took the results table from SLAMDUNK and first filtered genes that required at least 10 “readCount”, 2 “tcReadCount”, and counts per million (CPM) > 1. For each comparison, we performed two differential expression analyses using two normalization methods. For nascent RNA analysis (new mRNA), we normalized nascent RNA with “tcReadCount” and trimmed mean of M-values normalization method (TMM). For normalized nascent RNA analysis (normalized new mRNA), we normalized nascent RNA with total “readCount”. We then applied Empirical Bayes Statistics test to “tcReadCount” after linear fitting from voom packge (R 3.23, edgeR 3.12.1, limma 3.26.9) (Law et al., 2014).
Genome_build: mm9(MGSCv37)
Supplementary_files_format_and_content: gene-based raw total counts, TC counts, et.al from SLAMDUNK

source_name: In vitro induced wild-type regulatory T cells (ascorbic acid treated)

growth_protocol: CD4 naïve T cells from male Foxp3-gfp mice were sorted to induce regulatory T cells in vitro (iTreg) by plate-bound anti-CD3 and anti-CD28 antibodies, recombinant Interleukin-2 (IL-2), TGF-beta, and with or without ascorbic acid. After 4 days of induction, live GFP+ cells were FACS sorted.

extract_protocol:
Cells were lysed with the TRIzol reagent and stored at -80C. Total RNA extraction, sequencing library preparation, and deep sequencing were conducted by the Hartwell Center at St. Jude Children’s Research Hospital according to standard protocols.
Libraries were constructed by the Hartwell Center at St. Jude Children’s Research Hospital according to standard protocols for RNA sequencing.
Squencing libraries were constructed according to TruSeq Stranded mRNA Library Prep Kit

treatment_protocol: Sorted iTreg cells reseeded onto 12-well plates precoated with anti-CD3 and anti-CD28 antibodies (1µg/mL in PBS) at 2 × 106 cells per well with complete RPMI supplemented with 100 U/mL IL-2, 5 µM JQ1 or DMSO. 1 h later, 100 µM 4sU was added to culture medium for 4 h to label newly synthesized RNA.

tag: strain

tag: cell type

value: In vitro induced regulatory T cells

value: wild-type

tag: treatment

value: Treated with 0.25 mM ascorbic acid-2-phosphate (AA2P) during iTreg induction and 5 hours of JQ1 before harvest


title: SLAM iTreg-Mock-JQ1, Replicate2

source_name: In vitro induced wild-type regulatory T cells (control)

value: Mock treated during induction and 5 hours of JQ1 before harvest


title: SLAM iTreg-ASC-JQ1, Replicate1


title: BAY

tag: gender

value: M

value: WT

tag: subtype

tag: primary tumor location

value: right lateral arm

tag: cohort center

value: Caucasian


title: polyA Enriched RNA-sequencing_ATMPARP_1_CB

description: polyA enriched RNA

source_name: Whole Cerebellum_Atm Nes-cre; Parp1-/-

tag: genotype

value: Atm Nes-cre; Parp1-/-

value: Cerebellum


title: polyA Enriched RNA-sequencing_ATMPARP_2_CB

description: polyA enriched RNA

tag: tissue type


title: polyA Enriched RNA-sequencing_Control_3_CTX

description: polyA enriched RNA

value: Cortex


title: polyA Enriched RNA-sequencing_ATMAPTX_4_CB

description: polyA enriched RNA

source_name: Whole Cerebellum_Atm Nes-cre; Aptx-/-

value: Atm Nes-cre; Aptx-/-


title: SLAM iTreg-ASC-DMSO, Replicate1

value: Treated with 0.25 mM ascorbic acid-2-phosphate (AA2P) during iTreg induction and 5 hours of DMSO before harvest


title: SLAM iTreg-ASC-DMSO, Replicate2


title: Control 4

city: New Delhi

first: Vaishali

last: Suri

state: Delhi

address: Sri Aurobindo Marg, Ansari Nagar, Ansari Nagar East

department: Pathology

country: India

institute: AIIMS

description: Gene Expression_Control  4

hyb_protocol: Cy3-labeled cRNA samples were hybridized onto whole human genome SurePrint G3 8X60K arrays using Agilent’s Surehyb Chambers in an Agilent hybridization oven set at 65°C for 17 hours.

scan_protocol: The slides were then washed and subsequently scanned by an Agilent G4900DA SureScan Microarray Scanner (Agilent Technologies).

data_processing: Images from the scanned array were analyzed using Agilent’s Feature Extraction software, version 11.5.1.1 and further analyzed for statistical evaluations using GeneSpring GX version-13.0 software (Agilent Technologies).

source_name: Commercial RNA_HA total

label_protocol: Expression profiling was performed using a low-input QuickAmp labeling kit and human SurePrint G3 8x60K microarrays (Agilent Technologies, Santa Clara, CA). Briefly, 100 ng quality-checked total RNA was reverse transcribed using a Low Input Quick Amp labeling kit and then transcribed to Cy3-labeled cRNA according to the manufacturer’s protocol.

extract_protocol: RNA from the formalin-fixed paraffin-embedded (FFPE) blocks was extracted using the manufacturer’s protocol (RecoverAll™ Total Nucleic Acid Isolation Kit, Thermo Scientific). The extent of RNA fragmentation or quality and concentration were assessed via capillary chip electrophoresis using the RNA 6000 Nano Chip kit on Agilent 2100 Bioanalyzer (Agilent Technologies). RNA samples with an integrity number above 5 were used for the further analysis.

treatment_protocol: Genome-wide expression profiling of 14 PXA and 6 APXAs was performed by microarray. Amongst differentially expressed genes ( DEGs), Cyclin Dependent Kinase 14 (CDK 14)  and Mitochondrial Fission Process 1  (MTFP 1) were validated by qRT-PCR.

tag: tissue

value: Commercial RNA

tag: age

value: Not Avaialble


title: polyA Enriched RNA-sequencing_ATMAPTX_3_CB

description: polyA enriched RNA


title: SLAM iTreg-Mock-DMSO, Replicate2

value: Mock treated during induction and 5 hours of DMSO before harvest


title: Control 2

description: Gene Expression_Control  2

source_name: Commercial RNA_BFL


title: SLAM iTreg-Mock-JQ1, Replicate1


title: polyA Enriched RNA-sequencing_ATMAPTX_2_CB

description: polyA enriched RNA


title: Control 3

description: Gene Expression_Control  3

source_name: Commercial RNA_BTL


title: Case 15: Brain tumour_PXA

description: Gene Expression_PXA

source_name: Tumour tissue_FFPE_PXA

value: Formalin Fixed Paraffin Embedded

value: male


title: Case 16-R: Brain tumour_PXA

description: Gene Expression_PXA

value: female


title: polyA Enriched RNA-sequencing_ATMAPTX_1_CB

description: polyA enriched RNA


title: ATAC CNS2KO iTr-AA2P, Replicate2

description: ATAC-YF_2KO-iTr-wAA2P-Rep2-2199049.free.bw

data_processing:
2x100bp paired-end reads obtained from all samples were trimming for Nextera adapter by cutadapt(version 1.9, paired-end mode, default parameter with “ -m 25 -O 6 ”) and aligned to mouse genome mm9 (MGSCv37 from Sanger) by BWA (version 0.7.12-r1039, default parameter) , duplicated reads were then marked with biobambam2(version v2.0.87) and only non-duplicated proper paired reads have been kept by samtools (parameter “-q 1 -F 1804” version 1.2).
We also confirmed good reproducibility. All cell types have more than 15M nucleosome free reads after merge so we consider all important nucleosome free regions should be called.
At last, we merge replicates and adjust Tn5 shift (reads were offset were offset by +4 bp for the sense strand and -5 bp for the antisense strand) and we separated reads into nucleosome free, mononucleosome, dinucleosome, trinucleosome as described in Buenrostro et.al by fragment size and generated bigwig files by using the center 80bp of fragments and scale to 20 million nucleosome free reads. We observed good pattern that nucleosome tracks surrounding nucleosome free tracks and only provide nucleosome free tracks here.
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: bigwig

source_name: In vitro induced CNS2KO regulatory T cells (ascorbic acid treated)

growth_protocol: Tn cells were sorted from the lymphocytes isolated from male mice by CD4+GFP- CD25-CD44loCD62Lhi, then induced to iTreg cells with TCR agonists, IL-2, TGF-beta for 4 days in the presence or absence of 0.25mM ascorbic acid 2-phosphate. At the end of induction, live GFP+ cells were FACS sorted.

extract_protocol:
Sorted cells were harvested by centrifugation before being permeabilized for Tn5 transposition according to published protocols (PMID: 25559105).
Library was constructed according to published protocols (PMID: 25559105).

treatment_protocol: iTreg cells were treated with or without 0.25mM ascorbic acid 2-phosphate for 4 days during Treg induction.

tag: Sex

value: Ascorbic Acid


title: Case 14: Brain tumour_PXA

description: Gene Expression_PXA


title: Case 31: Brain tumour_PXA

description: Gene Expression_PXA


title: Case 29: Brain tumour_PXA

description: Gene Expression_PXA


title: ATAC CNS2KO iTr-AA2P, Replicate1

description: ATAC-YF_2KO-iTr-wAA2P-Rep1-2199048.free.bw

value: In vitro induced CNS2KO regulatory T cells


title: polyA Enriched RNA-sequencing_Control_3_CB

description: polyA enriched RNA

source_name: Whole Cerebellum_Control

value: Control


title: ATAC CNS2KO iTr-noAA2P, Replicate2

description: ATAC-YF_2KO-iTr-noAA2P-Rep2-2199047.free.bw

source_name: In vitro induced CNS2KO regulatory T cells (control)

value: Mock


title: Case 23: Brain tumour_PXA

description: Gene Expression_PXA


title: Control 1

description: Gene Expression_Control  1

source_name: Commercial RNA_BCC


title: Case 19B: Brain tumour_PXA

description: Gene Expression_PXA


title: Case 57: Brain tumour_PXA

description: Gene Expression_PXA


title: Case 20: Brain tumour_PXA

description: Gene Expression_PXA


title: ATAC CNS2KO iTr-noAA2P, Replicate1

description: ATAC-YF_2KO-iTr-noAA2P-Rep1-2199046.free.bw


title: polyA Enriched RNA-sequencing_Control_2_CB

description: polyA enriched RNA


title: Case 34: Brain tumour_APXA

description: Gene Expression_APXA

source_name: Tumour tissue_FFPE_APXA


title: SLAM iTreg-Mock-DMSO, Replicate1

value: In vitro induced regulatory T cells

value: wild-type


title: Case 56: Brain tumour_APXA

description: Gene Expression_APXA


title: Case 27: Brain tumour_APXA

description: Gene Expression_APXA


title: Case 25: Brain tumour_PXA

description: Gene Expression_PXA


title: Case 18: Brain tumour_PXA

description: Gene Expression_PXA


title: Case 19A: Brain tumour_PXA

description: Gene Expression_PXA


title: Case 21: Brain tumour_PXA

description: Gene Expression_PXA


title: LL17LL

first: Micha Sam

middle: Brickman

last: Raredon

state: Connecticut

address: 10 Amistad Street

department: Biomedical Engineering

description: Bulk RNAseq

data_processing:
For scRNAseq, FASTQ read 2 sequences were trimmed of the reverse complement sequence of the template switch oligo, as well as for poly(A) contaminants. Paired reads with a trimmed read 2 less than 30 bp long were discarded.
For scRNAseq, downstream processing was conducted with Cellranger 3.0.2 with the default parameters.
For scRNAseq, cells were accepted with greater than 500 and fewer than 10000 unique mapped genes, and fewer than 100000 gene transcripts. Analysis was performed on cells with less than 5% mitochondrial mapping for P4PMEC, Engineered lung, Preseeded iPSC, and iPSC-ECFC lung samples and less than 20% for the P7native sample.
Genome_build: Reads were aligned to rat reference genome Ensembl Rnor6.0 release 95 an human reference genome GRCh38 release 31 (GRCh38.p12), respectively.
Supplementary_files_format_and_content: *.mtx: sparse matrix file of raw counts, *genes.tsv: genelist (rownames for .mtx file), *barcodes.tsv: barcodes (column names for .mtx file), *.idents.tsv: celltype idents (metadata)

organism: Rattus norvegicus

source_name: Lung Endothelium

growth_protocol: Rodent pulmonary microvascular endothelial cells were isolated from postnatal day 7 rat lungs. The isolated cells were cultured on fibronectin-coated 6 well-plate at a density of 5000 cells/cm2 in endothelial culture medium (Vasculife (VEGF) medium (Lifeline cell technology) supplemented with 10 % FBS and 1.5% antibiotic/antimycotic (A/A)) for 7 days with daily complete medium change.  Human iPSC-derived endothelial colony forming cells were cultured on collagen I-coated flasks (50 μg/mL) in endothelial culture medium.

extract_protocol:
Lungs were extracted from the animals and transferred into 60mm petri dish. A syringe fitted with 25G needle was injected into lung pieces with enzyme solution (DMEM (low glucose) + 1 mg/mL Collagenase/Dispase + 3 U/mL Elastase + 20 U/mL DNAse).  The tissue pieces were minces into small pieces and transfered to a 50 mL conical tube. Incubate the tissue pieces at 37C for 20 minutes at a agitation of ~75rpm. The tissue was dissociated through a wire mesh strainer and rinsed with medium, followed by centrifugation and filtration. The number of cells was counted and the cell solution was diluted to a final concentration of 1M cells/mL in 0.01% BSA in PBS.
scRNAseq libraries were generated with the Chromium Single Cell 3’ assay (10x Genomics). Samples were diluted for an expected cell recovery population of 10,000 cells per lane. Bulk RNAseq libraries were prepared using the Pair End Sequencing Prep Kit.
For scRNAseq, libraries sequenced on the HiSeq4000 platform to a depth of 180 to 500 million reads per library. Downstream processing was conducted with Cellranger 3.0.2 with the default parameters. For bulk RNAseq, libraries were sequenced through NovaSeq with sequencing read length of 100 base pairs (bp).

value: Lung Endothelium

value: Postnatal day 7


title: polyA Enriched RNA-sequencing_Control_1_CB

description: polyA enriched RNA

value: Cerebellum


title: Total Stranded RNA-sequencing_CNTRL_CTX_4

description:
TS07_C1_CNTRL_CTX_4
processed data file: TotalStranded_FPKM_Cortex.xlsx

data_processing:
FASTQ sequences are mapped to the University of California Santa Cruz mouse reference genome (mm9)
RNA-seq reads were mapped by our in-house mapping pipeline STRONGARM developed for the PCGP (Downing et al., 2012).
Reads were aligned to four different databases using BWA (0.5.10): (i) the mouse MGSCv37 reference sequence; (ii) RefSeq; (iii) a sequence file representing all possible combinations of non-sequential pairs in RefSeq exons; and (iv) the AceView database flat file downloaded from the UCSC Genome Browser, representing transcripts constructed from mouse ESTs
Mapped reads were counted with HTseq and normalized to FPKM (fragments per kilobase of transcript per million mapped reads).
Genome_build: mm9
Supplementary_files_format_and_content: FPKM

extract_protocol:
Total RNA was isolated from mouse brain tissue with TRIzol (Invitrogen)
TruSeq Standed Total RNA Kit (Illumina) is used for library preparation: Double stranded cDNA fragments are ligated with Illumina paired end adaptors, followed by size selection (~200bp).

value: Cortex


title: Total Stranded RNA-sequencing_CNTRL_CTX_3

description:
TS05_C1_CNTRL_CTX_3
processed data file: TotalStranded_FPKM_Cortex.xlsx


title: Total Stranded RNA-sequencing_CNTRL_CTX_2

description:
TS03_C1_CNTRL_CTX_2
processed data file: TotalStranded_FPKM_Cortex.xlsx


title: Rat

city: Ann Arbor

first: Martin

middle: G

last: Myers Jr

state: MI

address: 1000 Wall St

institute: University of Michigan

data_processing:
alignment, mapping, and demultiplexing with cellranger
Genome_build: Rnor_6.0 / GRCm38
Supplementary_files_format_and_content: sparse matrix of counts with associated barcodes and features

source_name: Mediobasal hypothalamus

growth_protocol: Chow with ad libitum food

extract_protocol:
Rats were euthanized, the hypothalamus was dissected, nuclei were isolated and cleaned using FACS, and submitted to 10x library preparating and sequencing
10x 3’ Gene Expression

value: mediobasal hypothalamic cells