title: spinal cord, 1 week post transection 1 (ATAC-seq)


title: spinal cord, sham 2 (ATAC-seq)

status: Public on Jul 18 2023

type: SRA

city: Madison

first: jianhong

last: ou

state: WI

address: 330 N Orchard Street

country: USA

institute: Morgridge institute for research

library_source: genomic

data_processing:
Sequences were aligned to the zebrafish genome (danRer10) using Bowtie2 (v 2.2.5)
The mapped reads were filtered by samtools (v 1.3.1, with parameter -q 30) and duplicates were removed by picard (v 1.91)
Peak calls were determined using MACS2 (v 2.1.0, with parameter -f BAM -g 1.5e9 -q 0.05 --nomodel --shift 37 --extsize 73), and csaw(v 1.20.0, cutoff P value <0.05).
DiffBind(v 2.14.0) was used to call differential accessible sites.
Supplementary_files_format_and_content: bigwig files were generated using deeptools (v 3.1.3) Scores represent count per million reads

molecule: genomic DNA

organism: Danio rerio

source_name: spinal cord, sham

extract_protocol:
Sham injured and injured (2 mm rostral and caudal to the lesion site) spinal cords were dissected into a single cell suspension using 0.25% trypsin-EDTA; dissociated cells were processed for FACS sorting using an Astrios sorter, to collect live and single cells. 50.000 cells were processed for ATAC-seq.
Library preparation as described in Buenrostro et al., 2015
Libraries were sequenced on the Illumina HiSeq 4000 platform, with over 40 million 150 bp paired-end reads obtained for each library.

tag: treatment

value: uninjured

tag: tissue

value: spinal cord


title: spinal cord, sham 1 (ATAC-seq)


title: Lung_DQ12_Control_Day1_rep2

status: Public on Jul 19 2023

type: RNA

city: Vandoeuvre les Nancy

first: Carole

last: Seidel

address: Rue du Morvan

country: France

institute: INRS

description: Gene expression in lung of control rat (vehicule instillation) 1 days post exposure

hyb_protocol: 600 ng of Cy3-CTP-labelled cRNA (Specific Activity > 6 pmol Cy3 per µg cRNA) were fragmented at 60°C for 30 min in a reaction volume of 25 µL containing 25X Agilent Fragmentation Buffer and 10X Agilent Blocking Agent following the manufacturer’s instructions. On cRNA fragmentation completion, 25 µL of 2X Agilent Hybridization Buffer were added to the fragmentation mixture. The subsequent purified labelled cRNAs were hybridized to Agilent G4853A SurePrint G3 Rat v2 GE 8*60K microarrays (Agilent Technologies) at 65°C overnight (17h) in a rotating hybridization oven. After hybridization, microarrays were washed 1 min at room temperature with Agilent Gene Expression Wash Buffer 1 and 1 min with 37°C Agilent Gene Expression Wash buffer 2.

scan_protocol: Slides were scanned within 3 hours after washing using Agilent high-resolution scanner (G2505C) by setting: (i) one color scan channel for 8x60k array slides, (ii) scan area of 61x21.6 mm, (iii) scan resolution of 3 µm, (iv) dye channel to Green, (v) Tiff file dynamic range of 20 bits and (vi) Green PMT to 100 %.

data_processing: Agilent Feature Extraction Software (v 12.0.1.1) was used for background subtraction and data were normalized using the GeneSpring software (v 14.9)

molecule: total RNA

organism: Rattus norvegicus

source_name: Rat, Lung, DQ12, Control, Day 1, replicate 2

label_protocol: For each of the 36 samples (6 control and 6 exposed rats per time group), 100 ng of RNA were labelled with Cyanine 3-CTP using Low Input Quick Amp Labelling kits (One-Color Microarray-Based Gene Expression Analysis, version 6.7, Agilent Technologies) and purified (RNeasy Mini kit, QIAGEN) according to the manufacturer's instruction . Dye incorporation and cRNA yield and quality were checked by spectrophotometry.

growth_protocol: Accessory lobe of rat lungs were stored in RNA later at -20°C before use

extract_protocol: Total RNA were disrupted using gentleMACS™ Dissociator (Miltenyi Biotech) and extracted from accessory lobe of lungs with Nucleospin® RNA midi kit (Macherey-Nagel) according to the manufacturer’s instructions. RNA quality was determined by spectrophotometry (A260nm/A280nm > 1.8) and by capillary electrophoresis using Agilent 2100 Bioanalyser (RIN > 6.6, Agilent RNA 6000 NanoRNA 6000 Nano® Kit, Santa Clara, CA, USA).

treatment_protocol: 13 week old female Sprague Dawley rats were exposed to DQ-12 (10 mg/rat) by endotracheal instillation.

tag: strain

value: Sprague Dawley

value: accessory lobe of lung

tag: gender

value: female

tag: age

value: 13 weeks-old (at the onset of instillation)


title: sham 3

data_processing:
Sequences were aligned to the zebrafish genome (danRer10) using Bowtie2 (v 2.2.5)
The mapped reads were filtered by samtools (v 1.3.1, with parameter -q 30) and duplicates were removed by picard (v 1.91)
Peak calls were determined using MACS2 (v 2.1.0, with parameter -f BAM -g 1.5e9 -q 0.05 --nomodel --shift 37 --extsize 73), and csaw(v 1.20.0, cutoff P value <0.05).
DiffBind(v 2.14.0) was used to call differential accessible sites.
Supplementary_files_format_and_content: bigwig files were generated by deeptools::bamCoverage (v 2.1.0) and normalized to 1x sequencing depth by ignore chrX for extaned reads

source_name: spinal cord

value: sham


title: Slr1p IP, AB2756, biol repl 2

city: Toronto

first: Farnaz

last: Mansouri-Noori

state: ON

address: 4700 Keele Street

department: Biology

country: Canada

institute: York University

description: PE 2x50bp reads

library_source: transcriptomic

data_processing:
Sequencing and analysis were performed by The Centre for Applied Genomics (TCAG, Toronto, Canada).
The untrimmed reads in FASTQ format were generated using bcl2fastq2 v2.20. The quality of the data was assessed using FastQC v.0.11.5.
Adaptors were trimmed using Trim Galore, the quality of the trimmed reads was re-assessed with FastQC. The trimmed reads were also screened for presence of rRNA and mtRNA sequences using FastQ-Screen v.0.10.0.
The raw trimmed reads were aligned to the reference genome using the STAR aligner, v.2.6.0c.
The filtered STAR alignments were processed to extract raw read counts for genes using htseq-count v.0.6.1p2.
Assembly: Schizosaccharomyces pombe(972h-)
Supplementary files format and content: Tab delimited text files include raw counts for each sample.

organism: Schizosaccharomyces pombe

growth_protocol: YES medium, 32°C, 200 rpm

extract_protocol:
1 μg/μl final concentration of proteinase K (Invitrogen) solution and 0.125% final concentration of SDS solution (Bioshop) was added to immunoprecipitated RNA. Samples were then incubated at 37°C for 1 hour to digest immunoprecipitated proteins first, and 65°C for another hour to reverse crosslinking. This was followed by phenol-chloroform extraction of RNA and ethanol precipitation. Equal volumes of acidic phenol pH 4.3 (Fisher) was added to each sample which was vortexed to mix and centrifuged at 21000xg for 10 minutes at 4°C. The top aqueous layer was removed to a new tube to which equal volumes of Phenol/Chloroform/Isoamyl Alcohol (25:24:1 mixture, Fisher) was added following by vortexing and centrifugation at 21000xg for 10 minutes at 4°C. The top aqueous layer was removed to a new tube again and to this, equal volumes of Chloroform/Isoamyl Alcohol (24:1 mixture, Sigma) was added. The centrifugation step above was repeated and the top layer was removed to a new tube again. Finally, 20 μg glycogen (Sigma), 1/10th of the volume 3M NaOAc pH 5.2 (Sigma) and 1 mL ice-cold 100% absolute ethanol (Greenfield Global) was added to each RNA sample which was precipitated next at -80°C until sequencing. Input RNA samples were extracted using the hot phenol RNA extraction method and precipitated as described above until sequencing.
The NEBNext Ultra II Directional RNA Library Prep Kit for Illumina was used for library preparations following manufacturer's protocol.

treatment_protocol: Formaldehyde cross-link

tag: cell line

tag: cell type

value: fission yeast

tag: genotype

value: WT

value: formaldehyde cross-link

tag: antibody


title: Hot phenol total RNA input, biol repl 2

description: PE 2x50bp reads


title: Hot phenol total RNA input, biol repl 1

description: PE 2x50bp reads


title: Slr1p IP, AB2756, biol repl 1

description: PE 2x50bp reads


title: Non-immune rabbit IgG IP

description: PE 2x50bp reads

value: IgG


title: Serum, inulin 2

city: Beijing

first: Wanjie

last: Yu

address: No. 2 Yuanmingyuan West Road

country: China

institute: Institute of Animal Science, Chinese Academy of Agricultural Sciences

data_processing:
Non-coding RNAs were annotated as rRNAs, tRNAs, small nuclear RNAs (snRNAs), and small nucleolar RNAs (snoRNAs) and subjected to the BLAST search against Rfam v.10.1 and GenBank databases. The known miRNAs were identified by aligning them against miRBase v.21 database , and known miRNA expression patterns were analyzed. Novel miRNAs were predicted by mirdeep2 and RNAfold (http://rna.tbi.univie.ac.at/cgi-bin/RNAWebSuite/RNAfold.cgi).
Assembly: Rfam (version 10.0)
Supplementary files format and content: counts for each sample

organism: Bos taurus

source_name: serum

extract_protocol:
The RNeasy Mini Kit (cat. No. 74104, QIAGEN, Germany) was used to isolate RNAs from the serum EVs.
The small RNA sequencing was conducted by OE biotech Co., Ltd. (Shanghai, China), using the Illumina Hiseq X Ten, PE150. Briefly, 3’ and 5’ adapters were ligated to the end of the RNA molecules with T4 RNA Ligase (catalog no. LR2D1132K, Epicentre, US). Then, the libraries were reverse transcribed by the SuperScript II Reverse Transcriptase kit (catalog no.18064-014, Invitrogen, US), and a polymerase chain reaction was performed to amplify them. The cDNA constructs were purified and recovered, and the libraries were checked by using the Agilent Technologies 2100 Bioanalyze and eventually normalized.

value: serum

tag: condition

value: subclinical mastitis

value: inulin


title: Serum, inulin 3


title: Serum, inulin 4


title: Serum, inulin 1


title: Serum, Control 5

value: control


title: Serum, Control 4


title: Serum, Control 1


title: spinal cord, 1 week post transection 3 (ATAC-seq)

source_name: spinal cord, 1 week post transection

value: injured


title: Serum, Control 3


title: spinal cord, sham 3 (ATAC-seq)


title: PLDF_3m_RNA_rep1

city: Tianjin

first: Jiayuan

last: Chen

state: State...

address: Heping

institute: Tianjin Medical University

data_processing:
Sequence reads were aligned to the mm10 reference genome sequence using STAR (2.7.4a).
The aligned reads were sorted using samtools (1.12).
Read counts per gene were obtained from mapped reads using FeatureCount (1.6.0).
Differentially expressed genes were identified by DESeq2 (1.26.0) algorithms.
Assembly: mm10
Supplementary files format and content: FPKM

molecule: polyA RNA

organism: Mus musculus

source_name: Liver

extract_protocol:
Total RNAs were extracted from primary cholangiocytes using TRIzol (Invitrogen, 15596018) according to the manufacturer’s instructions.
For RNA samples from female mice, libraries were constructed and sequenced on the Illumina NovaSeq platform.

value: Liver

value: primary cholangiocytes

value: PLD


title: PLDF_3m_RNA_rep2


title: WTF_3m_RNA_rep2


title: WTF_H3K9ac_rep2

data_processing:
Paired-end reads from ATAC-seq were aligned by the Bowtie2 (2.3.5.1) algorithm against the mouse reference genome mm10.
Picard “mark duplicates” (2.25.1) command was applied to remove PCR duplicates and reads aligned to mtDNA were removed.
Deeptools (3.4.3) was used for generating bigWig file.
Assembly: mm10
Supplementary files format and content: bigWig

extract_protocol:
Briefly, primary cholangiocytes were divided into 100,000 cells per tube, and the samples were kept on ice or at 4°C. Cells were lysed in 19 μL lysis buffer (0.5% NP-40, 0.5% Tween-20, 0.1% SDS and cOmplete Protease Inhibitor Cocktail), and then incubated with 19 μL MNase buffer (100 mM Tris-HCl pH 8.0 and 2 mM CaCl2) containing 0.02 U MNase (Sigma, N3755) at 37°C for 5 min. Digestion was terminated by adding 5 μL stop buffer (110 mM Tris-HCl pH 8.0 and 55 mM EDTA). Each sample was incubated with 45 μL 2x RIPA buffer (280 mM NaCl, 1% Triton X-100, 0.1% SDS, 0.2% sodium deoxycholate, 5 mM EGTA and cOmplete Protease Inhibitor Cocktail) for 10 min before centrifuged at 14500 rpm for 15 min. The supernatant was transferred to a new tube, and then added with 40 μL RIPA buffer (10 mM Tris-HCl pH 8.0, 140 mM NaCl, 1% Triton X-100, 0.1% SDS, 0.1% sodium deoxycholate and 1 mM EDTA). For IP samples, each sample was incubated overnight with 1 μg antibody of H3K9ac (Abcam, ab4441), H3K9me3 (Abcam, ab8898), H3K4me3 (Millipore, 05-745R), H3K4me1 (Abcam, ab8895) or H3K27ac (Abcam, ab4729), and followed by immunoprecipitation with Dynabeads Protein G (Thermo Fisher Scientific, 10004D). And then samples were centrifuged and the collected-beads were washed five times with 150 μL RIPA buffer and rinsed once with 150 μL LiCl buffer (10 mM Tris-HCl pH 8.0, 0.5% NP-40, 1 mM EDTA, 0.5% sodium deoxycholate and 250 mM LiCl). Beads were finally resuspended with 30 μL elution buffer containing 1 μL proteinase K (TransGen Biotech, GE201-01), and followed by shaking at 55°C for 90 min. The supernatant was transferred to a new tube, and proteinase K was inactivated by heated at 72°C for 40 min. For Input samples, each sample was treated with 1 μL proteinase K, followed by shaking at 55°C for 90 min, and then DNA was purified using DNA Extraction Reagent (Solarbio, P1012).
Library construction was performed using a VAHTS Universal DNA Library Prep Kit for Illumina V3 (Vazyme, ND607). Sequencing was performed on the Illumina platform.

tag: chip antibody

value: H3K9ac (Abcam, #ab4441)


title: WTF_Input_rep2


title: WTF_H3K9ac_rep1


title: WTF_H3K9me3_rep2

value: H3K9me3 (Abcam, #ab8898)


title: Serum, inulin 5


title: WTF_H3K27ac_rep2

value: H3K27ac (Abcam, #ab4729)


title: WTF_H3K9me3_rep1


title: WTF_Input_rep1


title: WTF_H3K27ac_rep1


title: PLDF_Input_rep2


title: PLDF_Input_rep1


title: PLDF_H3K9ac_rep1


title: PLDF_H3K9me3_rep1


title: PLDF_H3K9ac_rep2


title: PLDF_H3K9me3_rep2


title: PLDF_H3K27ac_rep2


title: PLDF_3m_ATAC_rep2

data_processing:
Paired-end reads from ATAC-seq were aligned by the Bowtie2 (2.3.5.1) algorithm against the mouse reference genome mm10.
Picard “mark duplicates” (2.25.1) command was applied to remove PCR duplicates and reads aligned to mtDNA were removed.
MACS3 (3.0.0a4) was used for each sample using fragment sizes obtained from the alignments and a p-value cutoff of 0.05.
Then IDR (2.0.4.2) was applied to identify reproducible peaks between biological replicates of the same condition. The IDR passed peaks were used for further analysis.
Deeptools (3.4.3) was used for generating bigWig file.
Assembly: mm10
Supplementary files format and content: bigWig

extract_protocol:
100,000 primary cholangiocytes were lysed in cold ATAC lysis buffer (10 mM Tris–HCl pH 7.5, 10 mM NaCl, 3 mM MgCl2, 0.1% (v/v) igepal CA-630) for 20 min on ice before centrifuged at 500 g for 10 min. The cell nuclei were collected and incubated with 50 μL transposition reaction buffer (3 μL TruePrep Tagment Enzyme, 10 μL TruePrep Tagment Buffer L from Vazyme TD501) at 37°C for 60 min.
DNA was purified using the QIAquick PCR Purification Kit (QIAGEN, 28106) according to the manufacturer’s instructions. After DNA fragmentation and purification, library construction was performed with TruePrepTM DNA Library Prep Kit V2 for Illumina (Vazyme, TD501) according to the manufacturer’s instructions.


title: PLDF_H3K27ac_rep1


title: WTF_3m_ATAC_rep2


title: Serum, Control 2


title: PLDF_3m_ATAC_rep1


title: 9C_M_997

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

data_processing:
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted mm10 reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Assembly: mm10
Supplementary files format and content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column
Library strategy: snmC-seq2

source_name: C57BL/6J Male P56 Mouse Brain

growth_protocol: All mice are C57BL/6J Male, brain dissected in P56

extract_protocol:
the brain of P56 male C57BL/6J mouse will be removed and cut into 600 microns thick coronal sections using a tissue matrix. Then each region will be microdissected from the coronal tissue sections based on identified landmarks and brain atlas coordinates, as defined in Allen brain atlas CCF3 (Avaliable at: http://atlas.brain-map.org). For each dissection region, the tissue from several littermate mice will be combined together into to separate replicate groups. The number of animals in a replicate depends on the size of the tissue. Nuclei preparation will be stained with the fluorescently labeled anti-NeuN body and nucleic acid stain Hoechst 33342.
Library prepared following protocol discribed in Luo, Chongyuan, Angeline Rivkin, Jingtian Zhou, Justin P. Sandoval, Laurie Kurihara, Jacinta Lucero, Rosa Castanon, et al. 2018. “Robust Single-Cell DNA Methylome Profiling with snmC-seq2.” Nature Communications 9 (1): 3824.

tag: brain region


title: 9C_M_999


title: 9C_M_998


title: 9C_M_994


title: 9C_M_993


title: 9C_M_996


title: 9C_M_992


title: 9C_M_995


title: 9C_M_990


title: 9C_M_986


title: 9C_M_984


title: 9C_M_99


title: 9C_M_985


title: 9C_M_987


title: WTF_3m_RNA_rep1


title: 9C_M_983


title: WTF_3m_ATAC_rep1


title: 9C_M_980


title: 9C_M_977


title: 9C_M_979


title: 9C_M_982


title: 9C_M_98


title: 9C_M_976


title: 9C_M_973


title: 9C_M_972


title: 9C_M_975


title: 9C_M_970


title: 9C_M_991


title: 9C_M_969


title: 9C_M_966


title: 9C_M_965


title: 9C_M_968


title: 9C_M_963


title: 9C_M_962


title: 9C_M_958


title: 9C_M_96


title: 9C_M_961


title: 9C_M_959


title: 9C_M_981


title: 9C_M_956


title: 9C_M_955


title: 9C_M_954


title: 9C_M_97


title: 9C_M_952


title: 9C_M_950


title: 9C_M_951


title: 9C_M_949


title: 9C_M_964


title: 9C_M_947


title: 9C_M_95


title: 9C_M_971


title: 9C_M_945


title: 9C_M_944


title: 9C_M_946


title: 9C_M_943


title: 9C_M_948


title: 9C_M_953


title: 9C_M_957


title: 9C_M_94


title: 9C_M_941


title: 9C_M_940


title: 9C_M_938


title: 9C_M_937


title: 9C_M_934


title: 9C_M_932


title: 9C_M_931


title: 9C_M_933


title: 9C_M_935


title: 9C_M_930


title: 9C_M_93


title: 9C_M_928


title: 9C_M_926


title: 9C_M_925


title: 9C_M_924


title: 9C_M_927


title: 9C_M_921


title: 9C_M_942


title: 9C_M_923


title: 9C_M_922


title: 9C_M_92


title: 9C_M_920


title: 9C_M_918


title: 9C_M_919


title: 9C_M_936


title: 9C_M_914


title: 9C_M_915


title: 9C_M_917


title: 9C_M_912


title: 9C_M_913


title: 9C_M_911


title: 9C_M_910


title: 9C_M_908


title: 9C_M_91


title: 9C_M_909


title: 9C_M_907


title: 9C_M_906


title: 9C_M_929


title: 9C_M_904


title: 9C_M_905


title: 9C_M_902


title: 9C_M_899


title: 9C_M_898


title: 9C_M_901


title: 9C_M_9


title: 9C_M_896


title: 9C_M_900


title: 9C_M_897


title: 9C_M_893


title: 9C_M_892


title: 9C_M_890


title: 9C_M_895


title: 9C_M_889


title: 9C_M_888


title: 9C_M_886


title: 9C_M_894


title: 9C_M_885


title: 9C_M_882


title: 9C_M_883


title: 9C_M_879


title: 9C_M_880


title: 9C_M_877


title: 9C_M_88


title: 9C_M_876


title: 9C_M_873


title: 9C_M_903


title: 9C_M_875


title: 9C_M_884


title: 9C_M_870


title: 9C_M_87


title: 9C_M_869


title: 9C_M_874


title: 9C_M_868


title: 9C_M_864


title: 9C_M_863


title: 9C_M_867


title: 9C_M_866


title: 9C_M_860


title: 9C_M_865


title: 9C_M_861


title: 9C_M_862


title: 9C_M_86


title: 9C_M_857


title: 9C_M_858


title: 9C_M_859


title: 9C_M_853


title: 9C_M_854


title: 9C_M_852


title: 9C_M_856


title: 9C_M_872


title: 9C_M_855


title: 9C_M_851


title: 9C_M_871


title: 9C_M_849


title: 9C_M_847


title: 9C_M_85


title: 9C_M_848


title: 9C_M_846


title: 9C_M_845


title: 9C_M_840


title: 9C_M_84


title: 9C_M_839


title: 9C_M_837


title: 9C_M_838


title: 9C_M_841


title: 9C_M_832


title: 9C_M_834


title: 9C_M_835


title: 9C_M_83


title: 9C_M_988


title: 9C_M_828


title: 9C_M_829


title: 9C_M_827


title: 9C_M_825


title: 9C_M_826


title: 9C_M_824


title: 9C_M_823


title: 9C_M_821


title: 9C_M_842


title: 9C_M_82


title: 9C_M_817


title: 9C_M_820


title: 9C_M_818


title: 9C_M_819


title: 9C_M_816


title: 9C_M_833


title: 9C_M_831


title: 9C_M_815


title: 9C_M_808


title: 9C_M_811


title: 9C_M_805


title: 9C_M_814


title: 9C_M_810


title: 9C_M_830


title: 9C_M_806


title: 9C_M_822


title: 9C_M_803


title: 9C_M_802


title: 9C_M_801


title: 9C_M_80


title: 9C_M_800


title: 9C_M_8


title: 9C_M_812


title: 9C_M_797


title: 9C_M_795


title: 9C_M_798


title: 9C_M_796


title: 9C_M_793


title: 9C_M_792


title: 9C_M_794


title: 9C_M_799


title: 9C_M_791


title: 9C_M_79


title: 9C_M_789


title: 9C_M_790


title: 9C_M_807


title: 9C_M_785


title: 9C_M_784


title: 9C_M_786


title: 9C_M_788


title: 9C_M_787


title: 9C_M_783


title: 9C_M_804


title: 9C_M_782


title: 9C_M_780


title: 9C_M_779


title: 9C_M_78


title: 9C_M_776


title: 9C_M_778


title: 9C_M_775


title: 9C_M_774


title: 9C_M_769


title: 9C_M_773


title: 9C_M_772


title: 9C_M_770


title: 9C_M_767


title: 9C_M_77


title: 9C_M_768


title: 9C_M_766


title: 9C_M_771


title: 9C_M_763


title: 9C_M_762


title: 9C_M_765


title: 9C_M_764


title: 9C_M_781


title: 9C_M_76


title: 9C_M_761


title: 9C_M_757


title: 9C_M_756


title: 9C_M_758


title: 9C_M_777


title: 9C_M_753


title: 9C_M_755


title: 9C_M_754


title: 9C_M_747


title: 9C_M_748


title: 9C_M_744


title: 9C_M_751


title: 9C_M_745


title: 9C_M_752


title: 9C_M_742


title: 9C_M_743


title: 9C_M_759


title: 9C_M_75


title: 9C_M_741


title: 9C_M_740


title: 9C_M_74


title: 9C_M_736


title: 9C_M_739


title: 9C_M_737


title: 9C_M_738


title: 9C_M_734


title: 9C_M_735


title: 9C_M_750


title: 9C_M_749


title: 9C_M_727


title: 9C_M_728


title: 9C_M_730


title: 9C_M_731


title: 9C_M_732


title: 9C_M_729


title: 9C_M_726


title: 9C_M_73


title: 9C_M_725


title: 9C_M_721


title: 9C_M_72


title: 9C_M_722


title: 9C_M_720


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title: 9B_M_1054


title: 9B_M_1068


title: 9B_M_1051


title: 9B_M_1052


title: 9B_M_1050


title: 9B_M_105


title: 9B_M_1046


title: 9B_M_1049


title: 9B_M_1047


title: 9B_M_1060


title: 9B_M_1042


title: 9B_M_1059


title: 9B_M_1040


title: 9B_M_1043


title: 9B_M_1041


title: 9B_M_1036


title: 9B_M_1037


title: 9B_M_1034


title: 9B_M_104


title: 9B_M_1035


title: 9B_M_1033


title: 9B_M_1031


title: 9B_M_1032


title: 9B_M_1038


title: 9B_M_1030


title: 9B_M_1053


title: 9B_M_103


title: 9B_M_1048


title: 9B_M_1045


title: 9B_M_1028


title: 9B_M_1029


title: 9B_M_1027


title: 9B_M_1026


title: 9B_M_1025


title: 9B_M_1024


title: 9B_M_1023


title: 9B_M_1039


title: 9B_M_1021


title: 9B_M_1020


title: 9B_M_102


title: 9B_M_1018


title: 9B_M_1019


title: 9B_M_1017


title: 9B_M_1014


title: 9B_M_1015


title: 9B_M_1013


title: 9B_M_1011


title: 9B_M_1012


title: 9B_M_1010


title: 9B_M_101


title: 9B_M_1009


title: 9B_M_1008


title: 9B_M_1007


title: 9B_M_1006


title: 9B_M_1005


title: 9B_M_1003


title: 9B_M_1002


title: 9B_M_1004


title: 9B_M_1000


title: 9B_M_1001


title: 9B_M_10


title: 9B_M_0


title: 9A_M_2947


title: 9A_M_2946


title: 9A_M_2945


title: 9A_M_2944


title: 9A_M_2943


title: 9A_M_2941


title: 9A_M_2940


title: 9A_M_2939


title: 9A_M_2938


title: 9A_M_2937


title: 9A_M_2936


title: 9A_M_2935


title: 9A_M_2933


title: 9B_M_1


title: 9A_M_2928


title: 9A_M_2929


title: 9A_M_2927


title: 9A_M_2931


title: 9A_M_2923


title: 9A_M_2922


title: 9A_M_2926


title: 9A_M_2925


title: 9A_M_2920


title: 9A_M_2921


title: 9A_M_2919


title: 9A_M_2918


title: 9A_M_2917


title: 9A_M_2942


title: 9A_M_2916


title: 9A_M_2915


title: 9A_M_2914


title: 9A_M_2913


title: 9A_M_2934


title: 9A_M_2932


title: 9A_M_2910


title: 9A_M_2912


title: 9A_M_2908


title: 9A_M_2909


title: 9A_M_2906


title: 9A_M_2907


title: 9A_M_2903


title: 9A_M_2902


title: 9A_M_2899


title: 9A_M_2901


title: 9A_M_2893


title: 9A_M_2895


title: 9A_M_2892


title: 9A_M_2898


title: 9A_M_2891


title: 9A_M_2890


title: 9A_M_2889


title: 9A_M_2886


title: 9A_M_2887


title: 9A_M_2885


title: 9A_M_2888


title: 9A_M_2884


title: 9A_M_2883


title: 9A_M_2882


title: 9A_M_2905


title: 9A_M_2879


title: 9A_M_2900


title: 9A_M_2881


title: 9A_M_2877


title: 9A_M_2896


title: 9A_M_2875


title: 9A_M_2873


title: 9A_M_2874


title: 9A_M_2872


title: 9A_M_2871


title: 9A_M_2868


title: 9A_M_2866


title: 9A_M_2865


title: 9A_M_2863


title: 9A_M_2870


title: 9A_M_2869


title: 9A_M_2862


title: 9A_M_2860


title: 9A_M_2864


title: 9A_M_2859


title: 9A_M_2878


title: 9A_M_2858


title: 9A_M_2856


title: 9A_M_2857


title: 9A_M_2876


title: 9A_M_2855


title: 9A_M_2850


title: 9A_M_2852


title: 9A_M_2851


title: 9A_M_2847


title: 9A_M_2854


title: 9A_M_2848


title: 9A_M_2849


title: 9A_M_2843


title: 9A_M_2846


title: 9B_M_1055


title: 9A_M_2867


title: 9A_M_2844


title: 9A_M_2840


title: 9A_M_2841


title: 9A_M_2842


title: 9A_M_2839


title: 9A_M_2838


title: 9A_M_2836


title: 9A_M_2835


title: 9A_M_2837


title: 9A_M_2834


title: 9A_M_2833


title: 9A_M_2832


title: 9A_M_2831


title: 9A_M_2829


title: 9A_M_2826


title: 9A_M_2825


title: 9A_M_2827


title: 9A_M_2823


title: 9A_M_2822


title: 9A_M_2824


title: 9A_M_2845


title: 9A_M_2820


title: 9A_M_2828


title: 9B_M_106


title: 9A_M_2821


title: 9A_M_2819


title: 9A_M_2818


title: 9A_M_2817


title: 9A_M_2815


title: 9A_M_2810


title: 9A_M_2813


title: 9A_M_2809


title: 9A_M_2807


title: 9A_M_2808


title: 9A_M_2830


title: 9A_M_2806


title: 9A_M_2814


title: 9A_M_2802


title: 9A_M_2801


title: 9A_M_2799


title: 9A_M_2805


title: 9A_M_2798


title: 9A_M_2797


title: 9A_M_2793


title: 9A_M_2791


title: 9A_M_2796


title: 9A_M_2792


title: 9A_M_2790


title: 9A_M_2795


title: 9A_M_2788


title: 9A_M_2794


title: 9A_M_2785


title: 9A_M_2787


title: 9A_M_2816


title: 9A_M_2784


title: 9A_M_2786


title: 9A_M_2804


title: 9A_M_2783


title: 9A_M_2803


title: 9A_M_2780


title: 9A_M_2782


title: 9A_M_2777


title: 9A_M_2776


title: 9A_M_2773


title: 9A_M_2778


title: 9A_M_2789


title: 9A_M_2772


title: 9A_M_2769


title: 9A_M_2766


title: 9A_M_2771


title: 9A_M_2765


title: 9A_M_2761


title: 9A_M_2762


title: 9A_M_2759


title: 9A_M_2760


title: 9A_M_2764


title: 9A_M_2756


title: 9A_M_2755


title: 9A_M_2754


title: 9A_M_2758


title: 9A_M_2779


title: 9A_M_2753


title: 9A_M_2752


title: 9A_M_2751


title: 9A_M_2748


title: 9A_M_2763


title: 9A_M_2747


title: 9A_M_2745


title: 9A_M_2781


title: 9A_M_2746


title: 9A_M_2742


title: 9A_M_2743


title: 9A_M_2744


title: 9A_M_2768


title: 9A_M_2770


title: 9A_M_2740


title: 9A_M_2739


title: 9A_M_2738


title: 9A_M_2737


title: 9A_M_2736


title: 9A_M_2734


title: 9A_M_2731


title: 9A_M_2733


title: 9A_M_2741


title: 9A_M_2732


title: 9A_M_2726


title: 9A_M_2727


title: 9A_M_2729


title: 9A_M_2728


title: 9A_M_2724


title: 9A_M_2725


title: 9A_M_2722


title: 9A_M_2723


title: 9A_M_2719


title: 9A_M_2720


title: 9A_M_2721


title: 9A_M_2718


title: 9A_M_2717


title: 9A_M_2716


title: 9A_M_2714


title: 9A_M_2711


title: 9A_M_2710


title: 9A_M_2735


title: 9A_M_2712


title: 9A_M_2708


title: 9A_M_2707


title: 9A_M_2709


title: 9A_M_2704


title: 9A_M_2703


title: 9A_M_2705


title: 9A_M_2702


title: 9A_M_2730


title: 9A_M_2699


title: 9A_M_2701


title: 9A_M_2698


title: 9A_M_2697


title: 9A_M_2695


title: 9A_M_2713


title: 9A_M_2696


title: 9A_M_2700


title: 9A_M_2694


title: 9A_M_2693


title: 9A_M_2689


title: 9A_M_2686


title: 9A_M_2692


title: 9A_M_2687


title: 9A_M_2688


title: 9A_M_2683


title: 9A_M_2685


title: 9A_M_2680


title: 9A_M_2682


title: 9A_M_2681


title: 9A_M_2678


title: 9A_M_2706


title: 9A_M_2684


title: 9A_M_2675


title: 9A_M_2674


title: 9A_M_2677


title: 9A_M_2676


title: 9A_M_2673


title: 9A_M_2672


title: 9A_M_2691


title: 9A_M_2667


title: 9A_M_2671


title: 9A_M_2668


title: 9A_M_2665


title: 9A_M_2661


title: 9A_M_2662


title: 9A_M_2666


title: 9A_M_2660


title: 9A_M_2670


title: 9A_M_2658


title: 9A_M_2664


title: 9A_M_2655


title: 9A_M_2653


title: 9A_M_2679


title: 9A_M_2650


title: 9A_M_2646


title: 9A_M_2649


title: 9A_M_2651


title: 9A_M_2643


title: 9A_M_2644


title: 9A_M_2654


title: 9A_M_2663


title: 9A_M_2642


title: 9A_M_2659


title: 9A_M_2641


title: 9A_M_2640


title: 9A_M_2669


title: 9A_M_2645


title: 9A_M_2657


title: 9A_M_2639


title: 9A_M_2635


title: 9A_M_2638


title: 9A_M_2632


title: 9A_M_2636


title: 9A_M_2630


title: 9A_M_2633


title: 9A_M_2634


title: 9A_M_2637


title: 9A_M_2628


title: 9A_M_2631


title: 9A_M_2629


title: 9A_M_2626


title: 9A_M_2625


title: 9A_M_2627


title: 9A_M_2624


title: 9A_M_2623


title: 9A_M_2622


title: 9A_M_2619


title: 9A_M_2621


title: 9A_M_2620


title: 9A_M_2618


title: 9A_M_2609


title: 9A_M_2610


title: 9A_M_2615


title: 9A_M_2602


title: 9A_M_2606


title: 9A_M_2605


title: 9A_M_2607


title: 9A_M_2608


title: 9A_M_2599


title: 9A_M_2601


title: 9A_M_2598


title: 9A_M_2612


title: 9A_M_2600


title: 9A_M_2595


title: 9A_M_2596


title: 9A_M_2617


title: 9A_M_2594


title: 9A_M_2614


title: 9A_M_2592


title: 9A_M_2611


title: 9A_M_2588


title: 9A_M_2587


title: 9A_M_2585


title: 9A_M_2586


title: 9A_M_2603


title: 9A_M_2583


title: 9A_M_2581


title: 9A_M_2579


title: 9A_M_2580


title: 9A_M_2597


title: 9A_M_2578


title: 9A_M_2577


title: 9A_M_2572


title: 9A_M_2575


title: 9A_M_2571


title: 9A_M_2574


title: 9A_M_2570


title: 9A_M_2573


title: 9A_M_2576


title: 9A_M_2604


title: 9A_M_2569


title: 9A_M_2590


title: 9A_M_2567


title: 9A_M_2568


title: 9A_M_2564


title: 9A_M_2565


title: 9A_M_2584


title: 9A_M_2566


title: 9A_M_2563


title: 9A_M_2561


title: 9A_M_2560


title: 9A_M_2562


title: 9A_M_2558


title: 9A_M_2557


title: 9A_M_2559


title: 9A_M_2553


title: 9A_M_2551


title: 9A_M_2550


title: 9A_M_2548


title: 9A_M_2545


title: 9A_M_2544


title: 9A_M_2542


title: 9A_M_2546


title: 9A_M_2547


title: 9A_M_2549


title: 9A_M_2540


title: 9A_M_2535


title: 9A_M_2532


title: 9A_M_2534


title: 9A_M_2539


title: 9A_M_2538


title: 9A_M_2533


title: 9A_M_2531


title: 9A_M_2529


title: 9A_M_2536


title: 9A_M_2528


title: 9A_M_2556


title: 9A_M_2554


title: 9A_M_2527


title: 9A_M_2525


title: 9A_M_2526


title: 9A_M_2524


title: 9A_M_2522


title: 9A_M_2555


title: 9A_M_2523


title: 9A_M_2521


title: 9A_M_2520


title: 9A_M_2519


title: 9A_M_2530


title: 9A_M_2518


title: 9A_M_2513


title: 9A_M_2512


title: 9A_M_2515


title: 9A_M_2517


title: 9A_M_2511


title: 9A_M_2516


title: 9A_M_2514


title: 9A_M_2506


title: 9A_M_2505


title: 9A_M_2507


title: 9A_M_2504


title: 9A_M_2508


title: 9A_M_2510


title: 9A_M_2498


title: 9A_M_2499


title: 9A_M_2503


title: 9A_M_2502


title: 9A_M_2509


title: 9A_M_2501


title: 9A_M_2500


title: 9A_M_2497


title: 9A_M_2494


title: 9A_M_2496


title: 9A_M_2493


title: C. elegans, raga-1::AID; Somatic::TIR1, no auxin, Day 3 adult, biol rep 3

city: Boston

first: Hannah

middle: Josephine

last: Smith

state: MA

address: 665 Huntington Avenue, Building 1, Room 512

department: Molecular Metabolism

institute: Harvard University T.H. Chan School of Public Health

description: Somatic RAGA-1 strain untreated

data_processing:
Raw reads were examined for quality using FastQC(v0.11.5)
To perform additonal quality checks, all reads were aligned to Ensembl assembly of the C. elegans (PRJNA13758) genome WBcel235_release104 using STAR (v.2.7.0)
Alignments were checked for biases, evenness of coverage, rRNA content, genomic content of alignments, complexity and other quality checks using a combination of FastQC, Qualimap, and MultiQC
To quantify the abundance of reads corresponding to each transcript, alignment and quantification was performed using Salmon (1.4.0)
In R (version 4.1.2) counts were normalized and pairwise comparisons of the differential gene expression between the various conditions was performed using DESeq2_1.34.0 from tximport with a p-vaule cutoff of 0.01
Assembly: Ensembl assembly of the C. elegans (PRJNA13758) genome WBcel235_release104
Supplementary files format and content: Excel file contains normalized counts for all genes for all samples.
Supplementary files format and content: Gene names are listed as WormBase IDs.

organism: Caenorhabditis elegans

source_name: lysate from ~400 whole nematodes

growth_protocol: C. elegans were maintained on 6 cm NGM plates with Carbenicillin at 20 degrees celsius.

extract_protocol:
On Day 3, animals were snap frozen in Qiazol Lysis Reagent and RNA was extracted using the Qiagen RNeasy Mini Kit.
Libraries were prepared using a SciClone G3 NGSx workstation (Perkin Elmer) using the Kapa mRNA HyperPrep kit (Roche Applied Science)

treatment_protocol: At day 1 of adulthood (3 days after hatch), animals were either transferred to plates with 0.15 mM auxin or "control" plates containing an equivalent amount of ethanol (the auxin solvent)

value: lysate from ~400 whole nematodes

value: raga-1(wbm40) [raga-1::AID::EmGFP], ieSi57 [eft-3p::TIR1::mRuby::unc-54 3'UTR + Cbr-unc-119(+)] II

value: no auxin

tag: time

value: Day 3 of adulthood


title: C. elegans, raga-1::AID; Somatic::TIR1, no auxin, Day 3 adult, biol rep 2

description: Somatic RAGA-1 strain untreated


title: C. elegans, raga-1::AID; Somatic::TIR1, no auxin, Day 3 adult, biol rep 4

description: Somatic RAGA-1 strain untreated


title: C. elegans, raga-1::AID; Somatic::TIR1, auxin at Day 1, Day 3 adult, biol rep 3

description: Somatic RAGA-1 knockdown

value: auxin from Day 1 adulthood onwards, somatic RAGA-1 degradation


title: C. elegans, raga-1::AID; Somatic::TIR1, auxin at Day 1, Day 3 adult, biol rep 4

description: Somatic RAGA-1 knockdown


title: C. elegans, raga-1::AID; Somatic::TIR1, auxin at Day 1, Day 3 adult, biol rep 2

description: Somatic RAGA-1 knockdown


title: C. elegans, raga-1::AID; Somatic::TIR1, auxin at Day 1, Day 3 adult, biol rep 1

description: Somatic RAGA-1 knockdown


title: C. elegans, raga-1::AID; Neuronal::TIR1, no auxin, Day 3 adult, biol rep 3

description: Neuronal RAGA-1 strain untreated

value: raga-1(wbm40) [raga-1::degron::EmGFP] II; wbmIs83 [rab-3p::3xflag::TIR1::rab-3 3'UTR *wbmIs66] IV


title: C. elegans, raga-1::AID, Neuronal::TIR1, auxin at Day 1, Day 3 adult, biol rep 1

description: Neuronal RAGA-1 knockdown

value: auxin from Day 1 adulthood onwards, neuronal RAGA-1 degradation


title: C. elegans, raga-1::AID, Neuronal::TIR1, auxin at Day 1, Day 3 adult, biol rep 4

description: Neuronal RAGA-1 knockdown


title: C. elegans, wild type, auxin at Day 1, Day 3 adult, biol rep 3

description: Wild type with auxin

value: N2 Bristol

value: wild type

value: auxin from Day 1 adulthood onwards


title: C. elegans, raga-1::AID; Neuronal::TIR1, no auxin, Day 3 adult, biol rep 2

description: Neuronal RAGA-1 strain untreated


title: C. elegans, raga-1::AID, Neuronal::TIR1, auxin at Day 1, Day 3 adult, biol rep 2

description: Neuronal RAGA-1 knockdown


title: C. elegans, raga-1::AID, Neuronal::TIR1, auxin at Day 1, Day 3 adult, biol rep 3

description: Neuronal RAGA-1 knockdown


title: C. elegans, raga-1::AID; Somatic::TIR1, no auxin, Day 3 adult, biol rep 1

description: Somatic RAGA-1 strain untreated


title: C. elegans, raga-1::AID; Neuronal::TIR1, no auxin, Day 3 adult, biol rep 4

description: Neuronal RAGA-1 strain untreated


title: C. elegans, raga-1::AID; Neuronal::TIR1, no auxin, Day 3 adult, biol rep 1

description: Neuronal RAGA-1 strain untreated


title: 9A_M_2495


title: C. elegans, wild type, auxin at Day 1, Day 3 adult, biol rep 4

description: Wild type with auxin


title: C. elegans, wild type, auxin at Day 1, Day 3 adult, biol rep 1

description: Wild type with auxin


title: C. elegans, wild type, no auxin, Day 3 adult, biol rep 3

description: Wild type


title: C. elegans, wild type, no auxin, Day 3 adult, biol rep 4

description: Wild type


title: C. elegans, wild type, no auxin, Day 3 adult, biol rep 2

description: Wild type


title: 9A_M_2492


title: C. elegans, wild type, no auxin, Day 3 adult, biol rep 1

description: Wild type


title: 9A_M_2543


title: 37CAF_microRNA

city: Akita City

first: Sei

last: Kuriyama

department: Molecular Medicine & Biochemistry

country: Japan

institute: Akita University

description: 37 CAF

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: Raw data was processed by company Filgen Co

label: biotin

organism: Homo sapiens

source_name: MicroRNA expression data from Stomach cancer asoociated fibroblasts

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix)

growth_protocol: 10% fetal bovine serum-added high concentration glucose containing DMEM

extract_protocol: MicroRNA was obtained with Qiagen microRNA preparation kit

treatment_protocol: Normal culture condition

value: Stomach cancer asoociated fibroblasts

tag: molecule type

value: micro RNA


title: C. elegans, wild type, auxin at Day 1, Day 3 adult, biol rep 2

description: Wild type with auxin


title: 37NF_microRNA

description: 37 NF

source_name: MicroRNA expression data from Normal fibroblasts of same patient of CAF


title: Sample S27: Placebo administered (refed3.FPKM.S27)

city: Bethesda

first: Komudi

last: Singh

address: Building 10

institute: NIH

data_processing:
QC performed usinf fastQC
Trmming applied using trimmomatic
Alignment performed using HISAT2
Gene expression quantification with Stringtie
Assembly: GrCh38
Supplementary files format and content: Gene Expression FPKM matrix

source_name: Primary CD4 T cells

growth_protocol: Primary peripheral blood mononuclear cells (PBMCs) were isolated from human blood by density centrifugation using Lymphocyte Separation Medium (MP Biomedicals). CD4+ T cells were negatively selected from PBMCs using the CD4+ T Cell Isolation Kit (Miltenyi Biotec) and cultured in RPMI 1640 media supplemented with 25 mM HEPES, 10% heat-inactivated FBS, and Penicillin/Streptomycin.

extract_protocol:
Total RNA from CD4+ T cells was extracted with the miRNeasy Micro Kit (Qiagen) and RNA quality and integrity was assessed by Qubit 3.0 fluorometer (Thermo Fisher Scientific) and Agilent Bioanalyzer (Agilent Technologies).
Libraries were prepared using TruSeq stranded Total RNA HT kit (Illumina) and sequenced in a HISeq 3000 (Illumina) by the DNA Sequencing and Genomics Core at NHLBI.

treatment_protocol: Double-blinded clinical trial on healthy participants either consuming NR or placebo

value: Primary CD4 T cells

value: CD4 T cells

tag: disease state

value: Healthy donor

value: placebo


title: Sample S39: NR administered (refed3NR.FPKM.S39)

value: NR


title: Sample S16: Placebo administered (refed3.FPKM.S16)


title: Sample S47: NR administered (refed3NR.FPKM.S47)


title: Sample S4: Placebo administered (refed3.FPKM.S4)


title: Sample S51: NR administered (refed3NR.FPKM.S51)


title: Sample S12: Placebo administered (refed3.FPKM.S12)


title: Sample S23: Placebo administered (refed3.FPKM.S23)


title: Sample S43: NR administered (refed3NR.FPKM.S43)


title: Sample S45: Psoriasis CD4 T cells treated with NR

data_processing:
QC performed usinf fastQC
Trmming applied using trimmomatic
Alignment performed using STAR
Gene expression quantification with featureCounts
Assembly: GrCh38
Supplementary files format and content: Gene Expression Counts matrix
Supplementary files format and content: Sample ID and treatment

treatment_protocol: CD4+ Cells were treated with NR (0.5 mM from ChromaDex) during TCR activation.

value: Psoriasis


title: Sample S35: NR administered (refed3NR.FPKM.S35)


title: Sample S8: Healthy CD4 T cells treated with vehicle

value: Vehicle

value: Healthy


title: Sample S41: Psoriasis CD4 T cells treated with vehicle


title: Sample S59: NR administered (refed3NR.FPKM.S59)


title: Sample S48: Psoriasis CD4 T cells treated with NR


title: Sample S42: Psoriasis CD4 T cells treated with NR


title: Sample S6: Healthy CD4 T cells treated with NR


title: Sample S9: Healthy CD4 T cells treated with NR


title: Sample S44: Psoriasis CD4 T cells treated with vehicle


title: Sample S39: Psoriasis CD4 T cells treated with NR


title: Sample S5: Healthy CD4 T cells treated with vehicle


title: Sample S31: Placebo administered (refed3.FPKM.S31)


title: Sample S47: Psoriasis CD4 T cells treated with vehicle


title: Sample S38: Psoriasis CD4 T cells treated with vehicle


title: Sample S8: Placebo administered (refed3.FPKM.S8)


title: Sample S55: NR administered (refed3NR.FPKM.S55)


title: Sample S35: Psoriasis CD4 T cells treated with vehicle


title: Sample S36: Psoriasis CD4 T cells treated with NR


title: Sample S33: Psoriasis CD4 T cells treated with NR


title: Sample S19: Placebo administered (refed3.FPKM.S19)


title: Sample S32: Psoriasis CD4 T cells treated with vehicle


title: Sample S3: Healthy CD4 T cells treated with NR


title: Sample S30: Psoriasis CD4 T cells treated with NR


title: Sample S26: Psoriasis CD4 T cells treated with vehicle