title: memory_gen1-2

data_processing:
Trimmed data provided by BGI-Tech (Shenzhen, China) were used for the downstream processing
Small RNA-seq data were aligned to the Arabidopsis thaliana genome assembly (version TAIR10) using ShortStack (version 3.8.3; https://github.com/MikeAxtell/ShortStack/releases; Johnson et al., 2016) with default parameters except that the 'align-only' switch was activated
Each library was individually aligned, followed by merging the resultant bam files using samtools merge (Li et al., 2009)
Resulting clusters were used for control and treatment comparison
Genome_build: Arabidopsis thaliana genome assembly (version TAIR10)
Supplementary_files_format_and_content: tab-delimited file, <seqnames/chromosome>  <start position>  <end position> <strand> <name/cluster name>  <counts>

source_name: Arabidopsis thaliana Col-0

extract_protocol:
sRNA extraction using NucleoSpin miRNA Plant Kit (Macherey-Nagel, Germany)
sRNA-seq libraries were constructed using the Illumina TruSeq Small RNA Sample Preparation Kit and sequenced on a BGISEQ-500 with a single-end 50-bp run length

treatment_protocol: Two memory plants, and four Col-0 wild-type plants were used. Leaves at bolting were flash freezed in liquid nitrogen.  Tissues were ground by motor and pestle in liquid nitrogen.

value: biological rep 2

tag: ecotype

tag: genotype/variation

value: memory line


title: M-2-2 [BiSulfite-seq]

status: Public on Apr 03 2020

type: SRA

city: University Park

first: Hardik

last: Kundariya

state: PA

address: 361 N. Frear

country: USA

institute: The Pennsylvania State University

description: Generation 2 memory line

library_source: genomic

data_processing:
Illumina for basecalling
Raw sequencing reads were quality controlled with FastQC (version 0.11.5), trimmed with TrimGalore! (version 0.4.1) and Cutadapt (version 1.15).
aligned to the TAIR10 reference genome using Bismark (version 0.19.0)33 along with bowtie2 (version 2.3.3.1).
Methylated Cs (COV files) were acquired from Bismark methylation extractor with default parameters
Genome_build: TAIR 10
Supplementary_files_format_and_content: tab-delimited file, 1-based genomic coords with <chromosome>  <position>  <strand>  <count methylated>  <count unmethylated>  <C-context> <trinucleotide context> fields

molecule: genomic DNA

organism: Arabidopsis thaliana

growth_protocol: Seeds were sown on peat mix in square pots in reach-in chambers at 12hrs daylenght (22 °C, 120-150 μmol/(m^2*s) light)

extract_protocol:
genomic DNA extraction using DNeasy Plant kit (Qiagen, Germany).
Genomic DNA Sonicated to 100-300 bp fragments and purified with MiniElute PCR Purification Kit (Qiagen, Germany), incubated at 20 ℃ after add End Repair Mix. Then purified and added a single ‘A’ nucleotide to the 3’ ends of the blunt fragments, purified again and add Methylated Adapter to the 5’ and 3’ ends of each fragment. Then fragments with 300bp-400bp size-range were purified with QIAquick Gel Extraction kit (Qiagen, Germany) and subjected to bisulfite treatment by using Methylation-Gold kit (ZYMO). Followed with PCR and gel purification (350bp-400bp range fragments were selected). Qualified libraries sequenced pair end on the HiSeq X-ten system.

treatment_protocol: Five memory plants, four non-memory plants, and four Col-0 wild-type plants were sequenced were used. Leaves at bolting were flash freezed in liquid nitrogen.  Tissues were ground by motor and pestle in liquid nitrogen.

tag: replicate type

tag: tissue

value: rosette leaves

tag: sample type

value: Generation 2 memory line


title: Leaf, S1C2

city: Cordoba

first: Victor

middle: Manuel

last: Guerrero-Sanchez

state: Spain

address: Medina Azahara

department: Biochemistry and Molecular Biology

country: Spain

institute: University of Cordoba

library_source: transcriptomic

data_processing:
Sequenced reads were trimmed for adaptor sequence
Ambigous nucleotides and low quality sequences (first 12 bp of each read) were removed using Cutadapt v1.9
The trimmed reads were mapped to the Quercus ilex transcriptome using RSEM
Genome_build: qilextranscriptomeV3a.fa
Supplementary_files_format_and_content: tab-delimited text files include the quantification values for each Sample

molecule: total RNA

organism: Quercus ilex

source_name: Leaf

growth_protocol: Germinated acorns as previously reported in Simova-Stoilova et al. 2015

extract_protocol:
Leaves were taken from the biological replicates and total mRNA was extracted according to Echevarria-Zomeno et al. 2012
Illumina's TruSeq Stranded mRNA Library Prep Kit

treatment_protocol: Drought was imposed by water withholding for 25 days

tag: age

value: 6 months

tag: stress

value: Control (well watered)

tag: time

value: 20 days

value: Leaf


title: WT-4

value: biological rep 4

value: Wild-type control


title: MMD_CSF_03

type: RNA

city: Guangzhou

first: Gang

last: Wang

state: Guangdong

address: 1023 Guangzhou Avenue North

department: Neurosurgery

country: China

institute: Nanfang Hospital of Southern Medical University

description: miRNA expression in cerebrospinal fluid with moyamoya disease

hyb_protocol: Samples were labeled and hybridized with Agilent's miRNA Complete Labeling and Hyb Kit (P/N 5190-0456).

scan_protocol: Chips were scanned with Agilent Scan Control Software. For 8x60k chips, AgilentG3_miRNA mode (of resolution 3 microns) was selected.

data_processing: Data from scanning was analyzed using Agilent Feature Extraction(AFE) Software (version 10.7.1.1).

organism: Homo sapiens

source_name: cerebrospinal fluid

extract_protocol: With informed consent of each patient, 10ml cerebrospinal fluid was attained from lumbar puncture while following aseptic principles, and then quickly stored in a condition of -80°C. Then total RNA was extracted using miRNeasy Mini Kit (Qiagen, P/N 217004), after which quality check was performed with NanoDrop ND-2000 and Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, US).

value: cerebrospinal fluid

tag: disease

value: moyamoya


title: WT-3

value: biological rep 3


title: C8, C1D1

city: Bern

first: Carsten

last: Riether

address: Murtenstrasse 35

department: Department for BioMedical Research

country: Switzerland

institute: University of Bern

data_processing:
bcl2fastq v2.20.0.422
cellranger count v. 3.0.2
Genome_build: GRCh38
Supplementary_files_format_and_content: feature-barcode matrices from cellranger count. Each element of the matrix is the number of UMIs associated with a feature (row) and a barcode (column). Filtered to remove background and retain only cellular barcodes.

molecule: polyA RNA

source_name: blood

extract_protocol:
CD34+ AML stem/progenitor cells were FACS-purfied. Barcoded cDNA from lineage-negative CD34+ cells from patients C8 and C10 was prepared using the Chromium Single Cell 3′ Library (v2 Chemistry) & Gel Bead Kit on a Chromium Controller  (10XGenomics).
10X single cell RNA

tag: timepoint

value: after cusatzumab monotherapy

tag: cell type

value: CD34+ stem/progenitor cells

tag: disease state

value: AML


title: WT-2


title: glp-1(e2144) Caenorhabditis elegans vs. dcr-1(mg375) glp-1(e2144) Caenorhabditis elegans [WIS_252018610642_1_4]

city: Ramat-Gan

first: Hiba

last: Waldman Ben-Asher

address: Ramat-Gan

department: Life-Sciences

country: Israel

institute: Bar-Ilan University

hyb_protocol: Equal amounts of labeled RNA were then hybridized on the chip, per the Agilent protocol, at 60 degrees overnight. The hybridization mixes were prepared using the Gene Expression Hybridization Kit from Agilent following the manufacturer’s protocol. After hybridization, the slide was washed first with Gene Expression Wash Buffer 1(Agilent) and then Gene Expression Wash Buffer 2(Agilent). This was followed by a acetonitrile wash and finally the slides were placed in Stabilization& Drying Solution (Agilent). The washed slides were scanned on on an Agilent G2565BA scanner. Feature extraction was performed using the Feature extraction software from Agilent

scan_protocol: Scanned on an Agilent G2565BA microarray scanner

data_processing: The data from all arrays were first subjected to background correction and LOESS within-array normalization using Agilent Feature Extraction software (version 9.5.1.1 Agilent Technologies, Santa Clara, CA). The rest of the analysis was performed in Partek® Genomics Suite software, version 6.6 Copyright © 2012 Partek Inc., St. Louis, MO, USA.The log expression ratios that were produced during the normalization step were analyzed.

organism: Caenorhabditis elegans

label_protocol: 200 ng of total RNA, in the presence of control RNAs (RNA spike-in kit; Agilent), for each sample was labeled with either Cy-3 or Cy-5 using the Low Input Quick Amp Labeling Kit, two-color (Agilent) following the manufacturer’s protocol.

growth_protocol: Wild type or dcr-1(mg375) or glp-1(e2144) or dcr-1(mg375) glp-1(e2144) eggs were incubated at 25°C for 50 hours to day-1 stage.

extract_protocol: Total RNA extracted using Trizol

tag: genotype

tag: temperature

value: 25°C from the egg level

source_name: glp


title: Wild type (N2) Caenorhabditis elegans vs. dcr-1(mg375) Caenorhabditis elegans [WIS_252018610642_1_2]

source_name: dcr

value: Wild type


title: shRNA2

status: Public on Apr 02 2020

city: Pittsburgh

first: Yue

state: Pennsylvania

address: 5607 Baum Blvd

institute: UNIVERSITY OF PITTSBURGH

data_processing:
STAR and RSEM was used to profile RNA-seq data of T47D cell lines after ERINA knockdown.
The gene expression was quantified in log2-transformed FPKM and annotated based on the human reference genome GRCh38
Genome_build: GRCh38
Supplementary_files_format_and_content: Quantified expression files are generated by RSEM.

growth_protocol: ERINA and shRNA expressing vectors were separately co-transfected with psPAX2 and Pmd2G vectors into cells. Supernatant was collected at 48 hours post-transfection. The culture medium containing the lentiviruses was filtered through a 0.45 μm filter. Target cells were infected with viruses in the presence of polybrene and selected using puromycin to establish stable cells.

extract_protocol:
Total RNA was extracted using the RNAeasy mini Kit (Qiagen, 74104).
Reverse transcription from 1 µg RNA to cDNA was performed using the High-capacity cDNA reverse transcription kit (Applied Biosystems, 4368813). Real-time PCR was performed with Power SYBR Green PCR Master Mix (Applied Biosystems, 4367659) on a QuantStudio 6 Flex Real-Time PCR System (Applied Biosystems).

tag: cell line

value: breast cancer cell line

value: ERINA knockdown

tag: shRNA


title: 6h_DMSO_Rep1a

city: Boston

first: Zhi-Wei

last: Tan

state: Massachusetts

address: Dept. of Microbiology, Harvard Medical School HIM, Room 1018D, 4 Blackfan Circle Boston, MA 02115

institute: Harvard University

data_processing:
Basecalls were performed by sequencing facility, biopolymers in Harvard
Sequenced reads were trimmed for adaptor sequence,  then mapped to hg19 whole genome using Star Align with the following configurations: --runMode alignReads \  --genomeDir hg19_genome \  --readFilesIn files_R1, files_R2 \  --twopassMode Basic \  --sjdbOverhang 74 \  --outFileNamePrefix $HOME/RNA-seq/6h_T_c \  --outSAMtype BAM SortedByCoordinate \  --outFilterMultimapNmax 20 \  --outFilterMismatchNmax 999 \  --outFilterMismatchNoverLmax 0.04 \  --alignIntronMin 70 \  --alignIntronMax 500000 \  --alignMatesGapMax 500000 \  --alignSJoverhangMin 8 \  --alignSJDBoverhangMin 1 \  --outSAMstrandField intronMotif \  --outFilterType BySJout
After mapping, junction spanning reads were input into custom software to generate exon coordinate and classification information (see Boutz et al., Genes Dev). Mapped reads generated from Star Aligner were assigned to the generated gff and counted, and processed by DEXSeq to provide exon counts. DIfferential expression at the non-overlapping exon part level comparing DMSO/OSMI2 or DMSO/TMG was performed using standard DEXseq differential expression analysis.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files including exon parts genomic coordinates and differential expression analysis by DEXseq

source_name: Human embryonic kidney

growth_protocol: HEK293T cells grown on 6 well plates to around 80% confluence. Media changed fresh for 3 h befor treatment. Treated with DMSO or compounds for indicated time point.

extract_protocol:
HEK293T cells were scrapped, flash frozen on dry ice, and RNA was harvested using Trizol reagent or Rneasy plus kit.. Illumina TruSeq Stranded mRNA Library Preparation Kit Set A (Cat#RS-122-2101) was used with 2 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard illumina methods

treatment_protocol: Treated with 10 uM OSMI-2 (OGT inhibitor) or 5 uM TMG (OGA/MGEA5 inhibitor)

tag: treatment

value: DMSO


title: C10, day -14

value: at diagnosis


title: Wild type (N2) Caenorhabditis elegans vs. dcr-1(mg375) Caenorhabditis elegans [WIS_252018610642_1_1]


title: C10, C1D1


title: Healthy 4

city: Bethesda

first: Sivaranjani

last: Namasivayam

state: Maryland

address: 33 North Drive

institute: National Institutes of Health

description: Gene expression data from blood of an healthy subject

hyb_protocol: Microarray hybridization was performed using human Affymetrix Clariom D (Applied Biosystem Inc., Foster Coty, USA).

scan_protocol: Per Affymetrix protocol.

data_processing: Microarray gene expression data was analyzed using the Partek Genomics Suite 7.0.1 (Partek Ink. St. Louis, MO, USA). Raw data were normalized using the robust multi-array average (RMA) approach.

label: biotin

source_name: Blood from a healthy subject

label_protocol: Per Affymetrix protocol.

extract_protocol: RNA was isolated from peripheral blood collected in PAXgene blood RNA tubes (PreAnalytiX, Hombrechtikon, Switzerland) using a QIAamp RNA Blood extraction Kit (QIAGEN Inc., Germantown, USA).

value: Blood

tag: disease status

value: Healthy


title: Wild type (N2) Caenorhabditis elegans vs. dcr-1(mg375) glp-1(e2144) Caenorhabditis elegans [WIS_252018610640_1_4]


title: WT-1

value: biological rep 1

value: rosette leaves

tag: ecotype

tag: genotype/variation


title: glp-1(e2144) Caenorhabditis elegans vs. dcr-1(mg375) glp-1(e2144) Caenorhabditis elegans [WIS_252018610642_1_3]


title: glp-1(e2144) Caenorhabditis elegans vs. dcr-1(mg375) Caenorhabditis elegans [WIS_252018610640_1_3]


title: memory_gen1-1

tag: replicate type

tag: tissue

value: memory line


title: E5_CHIRP

city: New York

first: Aarthi

last: Ramakrishnan

state: New York

address: 1425 Madison Avenue

department: Neuroscience

institute: Icahn School of Medicine at Mount Sinai

description:
10_F_input
E5_CHIRP

data_processing:
library strategy: CHIRP-seq
For RNA-seq differential expression analysis, raw reads were aligned to the mouse genome (mm10) or the human genome (hg38) for NPC data using HISAT2.
Normalization and differential expression analysis were performed using DESeq2
For ChIRP-seq, raw sequencing reads were aligned to the human hg19 genome using default settings of Bowtie. Peak-calling was performed using MACS with a FDR cutoff of 0.05.
Genome_build: mm10, hg19
Supplementary_files_format_and_content: Tab-delimited text files

source_name: Cells

extract_protocol:
For in vivo samples, mice were cervically dislocated and the brains were rapidly removed. Bilateral 1 mm-thick 14 g microdissections of mPFC were taken from fresh slices and flash-frozen on dry ice. Total RNA was isolated with TriZol reagent (Invitrogen) and purified with RNeasy Micro Kits (Qiagen). For cell culture samples, a RNAeasy kit mini (Qiagen) was used for total RNA. Samples used for RNA-seq were analyzed using a bioanalyzer RNA Nano chip (Agilent) for integrity.
RNA libraries were prepared separately from female mouse mPFC infected with linc00473 or GFP, and from male and female NPCs transfected with linc00473 ASO or control ASO. The successful manipulation of linc00473 was confirmed in the samples used for sequencing. Libraries were made using 1 µg of purified RNA using the ScriptSeq Complete Kit (Epicentre). Briefly, the cDNA was synthesized from ribosomal depleted RNA and then fragmented total RNA using random hexamers, followed by terminal tagging. The libraries were PCR amplified and then purified using AMPure XP beads (Beckman Coulter, Brea, CA). Barcode bases (6 bp) were introduced at one end of the adaptors during PCR amplification steps. Quality and concentration of libraries were confirmed on a Bioanalyzer (Agilent) and libraries were sequenced on an Illumina Hi-seq machine with 150-bp paired-end reads in Genewiz. Samples were multiplexed to produce >40 million reads per sample. Sample size was n=3-5 independent samples per group. ChIRP-seq libraries were prepared from samples from DMSO- or forskolin-treated SH-SY5Y cells purified with two sets of probes (‘odd’ and ‘even’) for linc00473 or LacZ and input samples. The libraries were made using the entire precipitation product with the NEBNext Ultra DNA Library Prep kit for Illumina (New England BioLabs), without size selection, as recommended for low-input samples. Barcodes were used to multiplex samples to achieve >60 million reads/sample. Library size and quality were assessed on a BioAnalyzer prior to sequencing on an Illumina Hi-seq machine with 150-bp paired-end reads at Genewiz.


title: D5_CHIRP

description:
8_F_Lacz even
D5_CHIRP

value: transfected with control ASO

value: forskolin


title: C8, day -14


title: Healthy 2


title: shRNA1


title: Control

description: shCtrl

value: control


title: W-4-1 [BiSulfite-seq]

description: Generation 4 WT control

tag: sample type

value: Generation 4 WT control


title: C5_CHIRP

description:
6_F_473 even
C5_CHIRP

value: transfected with linc00473 ASO


title: D3_CHIRP

description:
7_F_LacZ odd
D3_CHIRP


title: Wild type (N2) Caenorhabditis elegans vs. dcr-1(mg375) glp-1(e2144) Caenorhabditis elegans [WIS_252018610640_1_2]

tag: age


title: B5_CHIRP

description:
4_D_Lacz even
B5_CHIRP


title: B3_CHIRP

description:
3_D_LacZ odd
B3_CHIRP


title: A5_CHIRP

description:
2_D_473 even
A5_CHIRP


title: E3

data_processing:
For RNA-seq differential expression analysis, raw reads were aligned to the mouse genome (mm10) or the human genome (hg38) for NPC data using HISAT2.
Normalization and differential expression analysis were performed using DESeq2
For ChIRP-seq, raw sequencing reads were aligned to the human hg19 genome using default settings of Bowtie. Peak-calling was performed using MACS with a FDR cutoff of 0.05.
Genome_build: mm10, hg19
Supplementary_files_format_and_content: Tab-delimited text files

tag: Sex

value: male

value: NPCs


title: glp-1(e2144) Caenorhabditis elegans vs. dcr-1(mg375) Caenorhabditis elegans [WIS_252018610640_1_1]

value: 25°C from the egg level


title: B3

value: knockdown of linc00473


title: C3


title: H9

value: female


title: E7


title: D9


title: F9


title: B9


title: B7


title: Normal_CD117+NKp44+

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

country: Japan

institute: Osaka univ.

description: Normal_CD117+NKp44+ from human normal colon

data_processing:
Sequencing was performed on an Illumina HiSeq 2500 platform in a 75-base single-end mode.
Illumina Casava1.8.2 software used for basecalling.
Sequenced reads were mapped to the human reference genome sequences (gh19) using TopHat v2.0.13 in combination with Bowtie2 ver. 2.2.3 and SAMtools ver. 0.1.19.
The fragments per kilobase of exon per million mapped fragments (FPKMs) was calculated using Cufflinks version 2.2.1.
Genome_build: hg19

source_name: Normal CD117+NKp44+

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer’s protocol.
Full-length cDNA was generated using a SMART-Seq HT Kit (Takara Bio, Mountain View, CA) according to the manufacturer’s instructions. An Illumina library was prepared using a Nextera DNA Library Preparation Kit (Illumina, San Diego, CA) according to SMARTer kit instructions.

value: Innate lymphoid cells


title: C3_CHIRP

description:
5_F_473 odd
C3_CHIRP


title: GFP1

city: Fuzhou

first: Yajuan

last: Fu

state: Fujian

address: Fujian Normal University,Qishan Campus, No.1 Keji Road, Shangjie, Minhou

department: Biomedical Research Center of South China

institute: Fujian Normal University

data_processing:
Bowtie2 (version:2.2.5, parameters: -q --phred64 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -p 16 -k 200)
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Mus_musculus reference genome (Mus musculus GRCm38.p5) using bowtie2
The expression levels for each of the genes were normalized to fragments per kilobase of exon model per million mapped reads (FPKM) using RNA-seq by Expectation Maximization (RSEM) (version:1.2.12, default parameters).
For the identification of differentially expressed genes (DEGs), we used PossionDis, which is developed by BGI Genomics, implementing the passion distribution method
A false discovery rate (FDR) cutoff of 0.001 and a log-fold change (LogFC) threshold of 2 were implemented to filter the significantly different genes. The genes with logFC ≥ 2 and logFC ≤ -2 with FDR ≤ 0.001 between two treatment conditions were determined to be up-regulated and down-regulated genes. DEGs was used for GO enrichment analysis by culsterProfiler (R version: 3.4.4 , culsterProfiler version: 3.6.0)
Genome_build: Mus_musculus reference genome (Mus musculus GRCm38.p5)
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample …

organism: Mus musculus

source_name: mouse fibroblast cells

extract_protocol:
L929 cells were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent.
cDNA library construction and sequencing were performed by BGI Genomics (BGI-SHENZHEN, China) using BGISEQ-500 platform

treatment_protocol: L929 cells were pretreated with DMSO or 0.5 uM BX795 for one hour, then transfected with pEGFP-N1 plasmid for 6 hours.

value: subcutaneous connective tissue; areolar and adipose

value: fibroblast

tag: strain

tag: agent

value: GFP


title: Normal_CD117-

description: Normal_CD117- from human normal colon

source_name: Normal CD117-

tag: cell type


title: BX795GFP2


title: Normal_CD117+NKp44-

description: Normal_CD117+NKp44- from human normal colon

source_name: Normal CD117+NKp44-


title: F3


title: A3


title: Th1_WT2 (RNA-seq)

city: Vienna

first: Wilfried

last: Ellmeier

address: Lazarettgase 19

department: Institute of Immunology

country: Austria

institute: Medical University of Vienna

data_processing:
Illumina HiSeq Control Software (HCS) HD 3.4.0.38 was used for the data acquistion on the sequencing instrument.
Basecalling was performed with the Illumina Real-Time Analysis (RTA) software 2.7.7.
BCL to BAM file conversion and demultiplexing was performed with custom programs based on Picard tools (v2.18.11, http://broadinstitute.github.io/picard/).
The transcriptome analysis was performed using the Tuxedo suite. TopHat2 (v2.1.1, http://genomebiology.com/2013/14/4/R36/abstract) was supplied with reads passing vendor quality filtering (PF reads) and the Ensembl transcript set (Homo sapiens, e87, December 2016) as reference. Tophat2 spliced alignments were run independently for each replicate.
Cufflinks (v2.2.1, http://www.nature.com/nbt/journal/v31/n1/full/nbt.2450.html) was then used to assemble transcripts from spliced read alignments, again using the Ensembl e87 transcriptome as the reference, preventing de novo assembly of transcript models.
Transcriptome sets of all replicates for each sample group were combined with Cuffmerge.
Differential expression was assessed with Cuffdiff v2.2.1 (http://www.nature.com/nbt/journal/v28/n5/full/nbt.1621.html).
The Bioconductor cummeRbund (http://www.bioconductor.org/packages/release/bioc/html/cummeRbund.html) pckage was used in combination with custom R scripts to perform quality assessment and further refine analysis results.
Genome_build: GRCm38 (UCSC mm10)
Supplementary_files_format_and_content: tab-separated value files of FPKM estimates obtained from Cufflinks, enriched with Ensembl transcrit annotation.

source_name: spleen, lymph nodes

extract_protocol:
Total RNA was prepared from 3x10^6 viable WT and NCOR1f/f,Cd4Cre in vitro-generated Th1 cells with QIAshredder, RNaeasy Mini Kit and RNase-Free DNase Set (Qiagen) according to manufacturer's protocol.
RNA-seq libraries were prepared with TruSeq Stranded mRNA LT sample preparation kit (Illumina) using Sciclone and Zephyr liquid handling robotics (PerkinElmer). Library amounts were quantified using Qubit 2.0 Fluorometric Quantitation system (Life Technologies) and the size distribution was assessed using Experion Automated Electrophoresis System (Bio-Rad). For sequencing, libraries were pooled, diluted and sequenced on an Illumina HiSeq 3000 instrument using 50 bp single-read chemistry.

value: in vitro-generated Th1 cells

tag: culture time

value: 3 days

value: wild-type


title: wild type replicate 1 of P14

city: Ottawa

first: Ziying

last: Liu

state: ON

address: 1200 Montreal Road

country: Canada

institute: National Research Council, Canada

description:
control group postnatal day (P) 14
P14-WT1_S1

data_processing:
RNA-seq reads were preprocessed by trimming the adaptor sequences, filtering low-quality reads (Phred Score <=20 [Phred]) and eliminating short reads (length <= 20 bps) using software package FASTX-toolkit [http://hannonlab.cshl.edu/fastx_toolkit/].
STAR (v2.5.3a) was used for alignment of the reads to the reference genome and to generate gene-level read counts.
R package DESeq2 was used for data normalization and differentially expressed gene identification for each pair-wise comparison
Genome_build: Mus musculus reference genome version GRCm38.p5
Supplementary_files_format_and_content: In excel file format, including Raw read counts data; Normalized read counts data; Alignment summary; DEGs

source_name: Cortical tissue

growth_protocol: Mice cortical ECs (cECs) were isolated by incubation with CD31-coated magnetic microbeads (130-097-418, Miltenyi Biotec) and placed in the magnetic MACS separator for positive selection. Then cECs were cultured in an endothelial cell culture medium (MV2, PromoCell) replaced 24 hrs post-seeding and every 48 hrs until appropriate level of confluence is reached (30-40% for ICC; 90-100% for matrigel experiments). ECs were isolated as above, but with additional steps to deplete myelin (Myelin removal beads II, Miltenyi Biotec) and CD45-positive cells (CD45 microbeads, 130-052-  301, Miltenyi Biotec) to obtain a pure CD31-positive cell suspension. Cell suspensions from two animals were pooled in one biological replicate.

extract_protocol:
RNA was acutely extracted using this suspension (E.Z.N.A. HP Total RNA kit, OMEGA bio-tek), with additional DNase step (E1091, OMEGA bio-tek) following the manufacturer’s protocol. Total cEC RNA was extracted as for RNA sequencing. RNA was converted to cDNA  using the High-Capacity cDNA Reverse Transcription kit (Life Technologies) with 200-500 ng  starting material per reaction. qPCR was performed using an ABI Prism 7000 Sequence Detection  System with SYBR Advantage qPCR Premix (Cedarlane). Amplicons were separated by agarose  gel (1%) electrophoresis. Primers used were: 5′-CAACGCTACCACGAGGACATT-3′ (forward)  and 5′-CTCCTGCAAAGAAAAGCTCTGG-3′ (reverse) for eNOS; 5'-  CTGCCAGTCCGAAAATGGAAC-3' (forward) and 5'-CTTCATCCACCGGGGCTATC-3'  (reverse) for CD31; 5'-CTCATGTCTGAACTCAAGATCC-3' (forward) and 5'-  CCAGAATCCTCTTCCATGCTCA-3' (reverse) for VEGFR2; 5'-  GGCAAATTCAACGGCACAGT-3' (forward) and 5'-AGATGGTGATGGGCTTCCC-3'  (reverse) for GAPDH. A no reverse transcriptase control (NRT) was used by carrying out the  reverse transcription step of the qRT-PCR experiment in the absence of reverse transcriptase in  order to assess the amount of DNA contamination present in an RNA preparation.
RNA-Seq Libraries were generated using the TruSeq strand mRNA kit (Illumina). The RNA-Seq libraries were quantified by Qbit and qPCR according to the Illumina Sequencing Library qPCR Quantification Guide and the quality of the libraries was evaluated on Agilent Bioanalyzer 2100 using the Agilent DNA-100 chip. The RNA-Seq library sequencing was performed using Illumina Next-Seq500.

treatment_protocol: Males 16p11.2df/+ (Jackson laboratory, stock #013128; mixed B6/129 background) were crossed with WT females of the same background (Jackson laboratory, stock #101043) to obtain hemizygous 16p11.2df/+ offspring and WT littermates. Conditional Cdh5- Cretg/+;16p11.2flox/+ mutants (i.e. ‘16p11.2DEC’; mixed B6/129 background) and littermate controls were obtained from breeding between Cdh5-Cretg/+ males (Jackson laboratory, stock #006137, B6 background) and 16p11.2flox/+ females (Jackson laboratory, stock #025330; 129 background). As recommended by Jackson Laboratory to improve 16p11.2df/+ pup survival, breeding cages (both constitutive and conditional mutants) were supplemented with breeding chow (#2019, Envigo Teklad) and DietGel (#76A, ClearH2O) up to weaning age. To assess astrocyte coverage/number in 16p11.2 hemizygous mice, 16p11.2df/+ males were crossed with Aldh1l1-eGFP (BAC) females (Jackson laboratory, stock #026033; B6 background).

value: Cortical endothelial cells

tag: disease state

value: control group

value: postnatal day (P) 14


title: PatID:10466064014, Tissue:LS, Visit:W12, Treatment:Ustekinumab

first: Mayte

last: Suarez-Farinas

state: NY

address: 1425 Madison Ave, L2-70C, Box 1077,

institute: Mount SinaiSchool of Medicine

hyb_protocol: GeneChip Affymetrix protocol

scan_protocol: Hewlett ÐPackard Gene Array Scanner

data_processing: GCRMA (using gcrma package from R/Bioconductor).

label_protocol: GeneChip Affymetrix protocol

extract_protocol: QIAGEN Rneasy Kit

tag: patientid

value: lesional skin

tag: visit

value: Ustekinumab

tag: pasi

tag: bmi

tag: race

value: WHITE

tag: weight


title: PatID:10466064018, Tissue:NL, Visit:W12, Treatment:Brodalumab 140 mg Q2W

value: non-lesional skin

tag: treatment

value: Brodalumab 140 mg Q2W


title: PatID:10466064014, Tissue:NL, Visit:W12, Treatment:Ustekinumab


title: PatID:10466064018, Tissue:LS, Visit:W4, Treatment:Brodalumab 140 mg Q2W


title: PatID:10466064007, Tissue:LS, Visit:W12, Treatment:Brodalumab 140 mg Q2W


title: PatID:10466064018, Tissue:LS, Visit:W12, Treatment:Brodalumab 140 mg Q2W


title: PatID:10466064018, Tissue:NL, Visit:BL, Treatment:Brodalumab 140 mg Q2W

value: BL


title: PatID:10466064007, Tissue:NL, Visit:BL, Treatment:Brodalumab 140 mg Q2W


title: PatID:10466064014, Tissue:LS, Visit:BL, Treatment:Ustekinumab


title: PatID:10466064006, Tissue:LS, Visit:BL, Treatment:Brodalumab 140 mg Q2W


title: PatID:10466064006, Tissue:LS, Visit:W12, Treatment:Brodalumab 140 mg Q2W


title: PatID:10466064007, Tissue:LS, Visit:W4, Treatment:Brodalumab 140 mg Q2W


title: PatID:10466064014, Tissue:LS, Visit:W4, Treatment:Ustekinumab


title: PatID:10466064005, Tissue:NL, Visit:W12, Treatment:Brodalumab 210 mg Q2W

value: Brodalumab 210 mg Q2W


title: PatID:10466064007, Tissue:LS, Visit:BL, Treatment:Brodalumab 140 mg Q2W


title: PatID:10466064005, Tissue:LS, Visit:W4, Treatment:Brodalumab 210 mg Q2W


title: 6h_OSMI2_Rep1a

tag: cell line

value: OGT inhibitor


title: PatID:10466064006, Tissue:LS, Visit:W4, Treatment:Brodalumab 140 mg Q2W

tag: tissue


title: PatID:10466064018, Tissue:LS, Visit:BL, Treatment:Brodalumab 140 mg Q2W


title: PatID:10466064014, Tissue:NL, Visit:BL, Treatment:Ustekinumab


title: PatID:10466064006, Tissue:NL, Visit:BL, Treatment:Brodalumab 140 mg Q2W


title: PatID:10466064006, Tissue:NL, Visit:W12, Treatment:Brodalumab 140 mg Q2W


title: PatID:10466064004, Tissue:LS, Visit:W4, Treatment:Brodalumab 140 mg Q2W


title: PatID:10466064005, Tissue:LS, Visit:BL, Treatment:Brodalumab 210 mg Q2W


title: PatID:10466064005, Tissue:NL, Visit:BL, Treatment:Brodalumab 210 mg Q2W


title: PatID:10466064007, Tissue:NL, Visit:W12, Treatment:Brodalumab 140 mg Q2W


title: PatID:10466064003, Tissue:LS, Visit:W4, Treatment:Ustekinumab


title: PatID:10466064004, Tissue:LS, Visit:W12, Treatment:Brodalumab 140 mg Q2W


title: PatID:10466064003, Tissue:NL, Visit:W12, Treatment:Ustekinumab


title: PatID:10466064004, Tissue:NL, Visit:W12, Treatment:Brodalumab 140 mg Q2W


title: PatID:10466064004, Tissue:NL, Visit:BL, Treatment:Brodalumab 140 mg Q2W


title: PatID:10466064003, Tissue:NL, Visit:BL, Treatment:Ustekinumab


title: PatID:10466064003, Tissue:LS, Visit:W12, Treatment:Ustekinumab


title: PatID:10466064001, Tissue:LS, Visit:W12, Treatment:Placebo

value: Placebo


title: PatID:10466064003, Tissue:LS, Visit:BL, Treatment:Ustekinumab


title: PatID:10466064001, Tissue:NL, Visit:BL, Treatment:Placebo


title: PatID:10466045002, Tissue:NL, Visit:BL, Treatment:Brodalumab 140 mg Q2W


title: PatID:10466040029, Tissue:LS, Visit:BL, Treatment:Brodalumab 210 mg Q2W


title: PatID:10466040016, Tissue:LS, Visit:W4, Treatment:Brodalumab 210 mg Q2W


title: PatID:10466064001, Tissue:LS, Visit:BL, Treatment:Placebo


title: PatID:10466045003, Tissue:LS, Visit:W4, Treatment:Brodalumab 140 mg Q2W


title: PatID:10466045002, Tissue:LS, Visit:W4, Treatment:Brodalumab 140 mg Q2W


title: PatID:10466045002, Tissue:LS, Visit:BL, Treatment:Brodalumab 140 mg Q2W


title: PatID:10466045003, Tissue:NL, Visit:BL, Treatment:Brodalumab 140 mg Q2W


title: PatID:10466040029, Tissue:NL, Visit:BL, Treatment:Brodalumab 210 mg Q2W


title: PatID:10466045003, Tissue:LS, Visit:BL, Treatment:Brodalumab 140 mg Q2W


title: PatID:10466040016, Tissue:LS, Visit:BL, Treatment:Brodalumab 210 mg Q2W


title: E3_CHIRP

description:
9_D_input
E3_CHIRP


title: PatID:10466040016, Tissue:LS, Visit:W12, Treatment:Brodalumab 210 mg Q2W


title: PatID:10466040014, Tissue:LS, Visit:W4, Treatment:Brodalumab 210 mg Q2W


title: PatID:10466040016, Tissue:NL, Visit:BL, Treatment:Brodalumab 210 mg Q2W


title: PatID:10466040014, Tissue:NL, Visit:BL, Treatment:Brodalumab 210 mg Q2W


title: PatID:10466040014, Tissue:NL, Visit:W12, Treatment:Brodalumab 210 mg Q2W


title: PatID:10466040014, Tissue:LS, Visit:W12, Treatment:Brodalumab 210 mg Q2W


title: PatID:10466040012, Tissue:NL, Visit:W12, Treatment:Ustekinumab

value: BLACK OR AFRICAN AMERICAN


title: PatID:10466040014, Tissue:LS, Visit:BL, Treatment:Brodalumab 210 mg Q2W


title: PatID:10466040012, Tissue:LS, Visit:W4, Treatment:Ustekinumab


title: PatID:10466040008, Tissue:NL, Visit:BL, Treatment:Brodalumab 210 mg Q2W


title: PatID:10466040007, Tissue:NL, Visit:W12, Treatment:Ustekinumab


title: PatID:10466040029, Tissue:LS, Visit:W4, Treatment:Brodalumab 210 mg Q2W


title: PatID:10466037003, Tissue:NL, Visit:BL, Treatment:Brodalumab 140 mg Q2W


title: PatID:10466040007, Tissue:LS, Visit:BL, Treatment:Ustekinumab


title: PatID:10466040007, Tissue:LS, Visit:W12, Treatment:Ustekinumab


title: PatID:10466037003, Tissue:LS, Visit:BL, Treatment:Brodalumab 140 mg Q2W


title: PatID:10466040007, Tissue:NL, Visit:BL, Treatment:Ustekinumab


title: PatID:10466064005, Tissue:LS, Visit:W12, Treatment:Brodalumab 210 mg Q2W


title: PatID:10466040012, Tissue:LS, Visit:BL, Treatment:Ustekinumab


title: PatID:10466040012, Tissue:NL, Visit:BL, Treatment:Ustekinumab


title: PatID:10466040008, Tissue:LS, Visit:BL, Treatment:Brodalumab 210 mg Q2W


title: PatID:10466031007, Tissue:NL, Visit:W12, Treatment:Placebo


title: PatID:10466037003, Tissue:NL, Visit:W12, Treatment:Brodalumab 140 mg Q2W


title: PatID:10466040012, Tissue:LS, Visit:W12, Treatment:Ustekinumab


title: PatID:10466031007, Tissue:LS, Visit:W4, Treatment:Placebo


title: PatID:10466031007, Tissue:LS, Visit:W12, Treatment:Placebo


title: PatID:10466031007, Tissue:NL, Visit:BL, Treatment:Placebo


title: PatID:10466031007, Tissue:LS, Visit:BL, Treatment:Placebo


title: PatID:10466037003, Tissue:LS, Visit:W12, Treatment:Brodalumab 140 mg Q2W


title: PatID:10466037003, Tissue:LS, Visit:W4, Treatment:Brodalumab 140 mg Q2W


title: A3_CHIRP

description:
1_D_473 odd
A3_CHIRP

tag: genotype/variation

value: transfected with linc00473 ASO

value: DMSO


title: PatID:10466031006, Tissue:NL, Visit:BL, Treatment:Brodalumab 210 mg Q2W

tag: age


title: PatID:10466031002, Tissue:NL, Visit:W12, Treatment:Brodalumab 210 mg Q2W


title: PatID:10466031002, Tissue:LS, Visit:W12, Treatment:Brodalumab 210 mg Q2W


title: PatID:10466031002, Tissue:LS, Visit:W4, Treatment:Brodalumab 210 mg Q2W


title: PatID:10466031002, Tissue:LS, Visit:BL, Treatment:Brodalumab 210 mg Q2W


title: PatID:10466031001, Tissue:NL, Visit:W12, Treatment:Brodalumab 140 mg Q2W


title: PatID:10466031002, Tissue:NL, Visit:BL, Treatment:Brodalumab 210 mg Q2W


title: PatID:10466040016, Tissue:NL, Visit:W12, Treatment:Brodalumab 210 mg Q2W


title: PatID:10466031001, Tissue:LS, Visit:W4, Treatment:Brodalumab 140 mg Q2W


title: PatID:10466024017, Tissue:LS, Visit:W4, Treatment:Brodalumab 210 mg Q2W


title: PatID:10466024017, Tissue:LS, Visit:W12, Treatment:Brodalumab 210 mg Q2W


title: PatID:10466031006, Tissue:LS, Visit:BL, Treatment:Brodalumab 210 mg Q2W


title: PatID:10466064004, Tissue:LS, Visit:BL, Treatment:Brodalumab 140 mg Q2W


title: PatID:10466024016, Tissue:LS, Visit:W12, Treatment:Brodalumab 140 mg Q2W


title: PatID:10466031001, Tissue:LS, Visit:BL, Treatment:Brodalumab 140 mg Q2W


title: PatID:10466024017, Tissue:NL, Visit:BL, Treatment:Brodalumab 210 mg Q2W


title: PatID:10466031001, Tissue:LS, Visit:W12, Treatment:Brodalumab 140 mg Q2W


title: PatID:10466024014, Tissue:NL, Visit:W12, Treatment:Placebo


title: PatID:10466024017, Tissue:LS, Visit:BL, Treatment:Brodalumab 210 mg Q2W


title: PatID:10466024016, Tissue:NL, Visit:W12, Treatment:Brodalumab 140 mg Q2W


title: PatID:10466024016, Tissue:LS, Visit:W4, Treatment:Brodalumab 140 mg Q2W


title: PatID:10466024014, Tissue:NL, Visit:BL, Treatment:Placebo


title: PatID:10466024014, Tissue:LS, Visit:BL, Treatment:Placebo


title: PatID:10466024014, Tissue:LS, Visit:W4, Treatment:Placebo


title: PatID:10466024012, Tissue:LS, Visit:W4, Treatment:Brodalumab 210 mg Q2W

value: OTHER


title: PatID:10466024016, Tissue:LS, Visit:BL, Treatment:Brodalumab 140 mg Q2W


title: PatID:10466024017, Tissue:NL, Visit:W12, Treatment:Brodalumab 210 mg Q2W


title: PatID:10466024012, Tissue:LS, Visit:W12, Treatment:Brodalumab 210 mg Q2W


title: PatID:10466024014, Tissue:LS, Visit:W12, Treatment:Placebo


title: PatID:10466024012, Tissue:NL, Visit:W12, Treatment:Brodalumab 210 mg Q2W


title: PatID:10466024012, Tissue:NL, Visit:BL, Treatment:Brodalumab 210 mg Q2W


title: PatID:10466024016, Tissue:NL, Visit:BL, Treatment:Brodalumab 140 mg Q2W


title: PatID:10466024012, Tissue:LS, Visit:BL, Treatment:Brodalumab 210 mg Q2W


title: PatID:10466024010, Tissue:LS, Visit:W12, Treatment:Brodalumab 210 mg Q2W


title: PatID:10466024010, Tissue:NL, Visit:BL, Treatment:Brodalumab 210 mg Q2W


title: PatID:10466024010, Tissue:NL, Visit:W12, Treatment:Brodalumab 210 mg Q2W


title: PatID:10466024010, Tissue:LS, Visit:BL, Treatment:Brodalumab 210 mg Q2W


title: PatID:10466024010, Tissue:LS, Visit:W4, Treatment:Brodalumab 210 mg Q2W


title: PatID:10466024009, Tissue:LS, Visit:W4, Treatment:Brodalumab 140 mg Q2W


title: PatID:10466024009, Tissue:NL, Visit:W12, Treatment:Brodalumab 140 mg Q2W


title: PatID:10466024009, Tissue:NL, Visit:BL, Treatment:Brodalumab 140 mg Q2W


title: PatID:10466024009, Tissue:LS, Visit:W12, Treatment:Brodalumab 140 mg Q2W


title: PatID:10466024006, Tissue:LS, Visit:W4, Treatment:Brodalumab 140 mg Q2W


title: PatID:10466024006, Tissue:NL, Visit:W12, Treatment:Brodalumab 140 mg Q2W


title: PatID:10466024007, Tissue:LS, Visit:W4, Treatment:Brodalumab 210 mg Q2W


title: PatID:10466024005, Tissue:NL, Visit:W12, Treatment:Brodalumab 140 mg Q2W


title: PatID:10466024006, Tissue:LS, Visit:BL, Treatment:Brodalumab 140 mg Q2W


title: PatID:10466024007, Tissue:LS, Visit:BL, Treatment:Brodalumab 210 mg Q2W


title: PatID:10466024006, Tissue:LS, Visit:W12, Treatment:Brodalumab 140 mg Q2W


title: PatID:10466024006, Tissue:NL, Visit:BL, Treatment:Brodalumab 140 mg Q2W


title: PatID:10466024005, Tissue:LS, Visit:W12, Treatment:Brodalumab 140 mg Q2W


title: PatID:10466024005, Tissue:LS, Visit:BL, Treatment:Brodalumab 140 mg Q2W


title: PatID:10466024007, Tissue:NL, Visit:W12, Treatment:Brodalumab 210 mg Q2W


title: PatID:10466024007, Tissue:LS, Visit:W12, Treatment:Brodalumab 210 mg Q2W


title: PatID:10466031001, Tissue:NL, Visit:BL, Treatment:Brodalumab 140 mg Q2W


title: PatID:10466024007, Tissue:NL, Visit:BL, Treatment:Brodalumab 210 mg Q2W


title: PatID:10466024004, Tissue:LS, Visit:W12, Treatment:Brodalumab 140 mg Q2W


title: PatID:10466024009, Tissue:LS, Visit:BL, Treatment:Brodalumab 140 mg Q2W


title: PatID:10466024004, Tissue:NL, Visit:W12, Treatment:Brodalumab 140 mg Q2W


title: PatID:10466024004, Tissue:LS, Visit:W4, Treatment:Brodalumab 140 mg Q2W


title: PatID:10466024004, Tissue:NL, Visit:BL, Treatment:Brodalumab 140 mg Q2W


title: PatID:10466024005, Tissue:LS, Visit:W4, Treatment:Brodalumab 140 mg Q2W


title: PatID:10466014008, Tissue:LS, Visit:W4, Treatment:Brodalumab 140 mg Q2W


title: PatID:10466024004, Tissue:LS, Visit:BL, Treatment:Brodalumab 140 mg Q2W


title: PatID:10466024001, Tissue:NL, Visit:W12, Treatment:Brodalumab 140 mg Q2W


title: PatID:10466014008, Tissue:NL, Visit:W12, Treatment:Brodalumab 140 mg Q2W


title: PatID:10466024001, Tissue:NL, Visit:BL, Treatment:Brodalumab 140 mg Q2W


title: PatID:10466014008, Tissue:LS, Visit:BL, Treatment:Brodalumab 140 mg Q2W


title: PatID:10466014008, Tissue:LS, Visit:W12, Treatment:Brodalumab 140 mg Q2W


title: PatID:10466014003, Tissue:LS, Visit:W4, Treatment:Placebo


title: PatID:10466024001, Tissue:LS, Visit:BL, Treatment:Brodalumab 140 mg Q2W


title: PatID:10466014003, Tissue:NL, Visit:W12, Treatment:Placebo


title: PatID:10466014003, Tissue:NL, Visit:BL, Treatment:Placebo


title: PatID:10466014008, Tissue:NL, Visit:BL, Treatment:Brodalumab 140 mg Q2W


title: PatID:10466014003, Tissue:LS, Visit:BL, Treatment:Placebo


title: PatID:10448010058, Tissue:LS, Visit:W4, Treatment:Brodalumab 140 mg Q2W


title: PatID:10448010058, Tissue:LS, Visit:W12, Treatment:Brodalumab 140 mg Q2W


title: PatID:10448010058, Tissue:NL, Visit:BL, Treatment:Brodalumab 140 mg Q2W


title: PatID:10466024001, Tissue:LS, Visit:W12, Treatment:Brodalumab 140 mg Q2W


title: PatID:10448010058, Tissue:NL, Visit:W12, Treatment:Brodalumab 140 mg Q2W


title: PatID:10466014003, Tissue:LS, Visit:W12, Treatment:Placebo


title: PatID:10448010055, Tissue:LS, Visit:W4, Treatment:Brodalumab 140 mg Q2W


title: PatID:10448010053, Tissue:LS, Visit:W12, Treatment:Placebo


title: PatID:10448010055, Tissue:LS, Visit:W12, Treatment:Brodalumab 140 mg Q2W


title: PatID:10448010055, Tissue:LS, Visit:BL, Treatment:Brodalumab 140 mg Q2W


title: PatID:10448010055, Tissue:NL, Visit:W12, Treatment:Brodalumab 140 mg Q2W


title: PatID:10448010053, Tissue:LS, Visit:W4, Treatment:Placebo


title: PatID:10448010053, Tissue:NL, Visit:BL, Treatment:Placebo


title: PatID:10448010053, Tissue:NL, Visit:W12, Treatment:Placebo


title: PatID:10448010052, Tissue:LS, Visit:W12, Treatment:Brodalumab 210 mg Q2W


title: PatID:10448010050, Tissue:LS, Visit:W4, Treatment:Brodalumab 210 mg Q2W


title: PatID:10448010052, Tissue:NL, Visit:W12, Treatment:Brodalumab 210 mg Q2W


title: PatID:10448010053, Tissue:LS, Visit:BL, Treatment:Placebo


title: PatID:10448010049, Tissue:NL, Visit:BL, Treatment:Brodalumab 140 mg Q2W


title: PatID:10448010052, Tissue:LS, Visit:W4, Treatment:Brodalumab 210 mg Q2W


title: PatID:10448010050, Tissue:LS, Visit:W12, Treatment:Brodalumab 210 mg Q2W


title: PatID:10448010052, Tissue:LS, Visit:BL, Treatment:Brodalumab 210 mg Q2W


title: PatID:10448010049, Tissue:LS, Visit:W12, Treatment:Brodalumab 140 mg Q2W


title: PatID:10448010052, Tissue:NL, Visit:BL, Treatment:Brodalumab 210 mg Q2W


title: PatID:10448010049, Tissue:LS, Visit:W4, Treatment:Brodalumab 140 mg Q2W


title: PatID:10448010049, Tissue:NL, Visit:W12, Treatment:Brodalumab 140 mg Q2W


title: PatID:10448010049, Tissue:LS, Visit:BL, Treatment:Brodalumab 140 mg Q2W


title: PatID:10448010050, Tissue:NL, Visit:BL, Treatment:Brodalumab 210 mg Q2W


title: PatID:10448010050, Tissue:NL, Visit:W12, Treatment:Brodalumab 210 mg Q2W


title: PatID:10448010050, Tissue:LS, Visit:BL, Treatment:Brodalumab 210 mg Q2W


title: PatID:10448010044, Tissue:LS, Visit:W4, Treatment:Brodalumab 140 mg Q2W


title: PatID:10448010045, Tissue:LS, Visit:BL, Treatment:Placebo


title: PatID:10448010045, Tissue:LS, Visit:W12, Treatment:Placebo


title: PatID:10448010045, Tissue:NL, Visit:W12, Treatment:Placebo


title: PatID:10448010044, Tissue:LS, Visit:BL, Treatment:Brodalumab 140 mg Q2W


title: PatID:10448010045, Tissue:NL, Visit:BL, Treatment:Placebo


title: PatID:10448010044, Tissue:NL, Visit:W12, Treatment:Brodalumab 140 mg Q2W


title: PatID:10448010044, Tissue:LS, Visit:W12, Treatment:Brodalumab 140 mg Q2W


title: PatID:10448010043, Tissue:LS, Visit:W4, Treatment:Ustekinumab


title: PatID:10466024001, Tissue:LS, Visit:W4, Treatment:Brodalumab 140 mg Q2W


title: PatID:10448010044, Tissue:NL, Visit:BL, Treatment:Brodalumab 140 mg Q2W


title: PatID:10448010039, Tissue:LS, Visit:W4, Treatment:Ustekinumab


title: PatID:10448010043, Tissue:LS, Visit:BL, Treatment:Ustekinumab


title: PatID:10448010043, Tissue:LS, Visit:W12, Treatment:Ustekinumab


title: PatID:10448010039, Tissue:NL, Visit:BL, Treatment:Ustekinumab


title: PatID:10448010039, Tissue:LS, Visit:W12, Treatment:Ustekinumab


title: PatID:10448010043, Tissue:NL, Visit:W12, Treatment:Ustekinumab


title: PatID:10448010039, Tissue:NL, Visit:W12, Treatment:Ustekinumab


title: PatID:10448010038, Tissue:LS, Visit:W4, Treatment:Brodalumab 210 mg Q2W


title: PatID:10448010039, Tissue:LS, Visit:BL, Treatment:Ustekinumab


title: PatID:10448010043, Tissue:NL, Visit:BL, Treatment:Ustekinumab


title: PatID:10448010038, Tissue:NL, Visit:W12, Treatment:Brodalumab 210 mg Q2W


title: PatID:10448010037, Tissue:LS, Visit:W4, Treatment:Brodalumab 210 mg Q2W


title: PatID:10466024005, Tissue:NL, Visit:BL, Treatment:Brodalumab 140 mg Q2W


title: PatID:10448010038, Tissue:LS, Visit:W12, Treatment:Brodalumab 210 mg Q2W


title: PatID:10448010037, Tissue:LS, Visit:W12, Treatment:Brodalumab 210 mg Q2W


title: PatID:10448010037, Tissue:LS, Visit:BL, Treatment:Brodalumab 210 mg Q2W


title: PatID:10448010038, Tissue:LS, Visit:BL, Treatment:Brodalumab 210 mg Q2W


title: PatID:10448010033, Tissue:LS, Visit:W4, Treatment:Ustekinumab


title: PatID:10448010033, Tissue:NL, Visit:W12, Treatment:Ustekinumab


title: PatID:10448010035, Tissue:LS, Visit:W12, Treatment:Brodalumab 140 mg Q2W


title: PatID:10448010035, Tissue:NL, Visit:BL, Treatment:Brodalumab 140 mg Q2W


title: PatID:10448010037, Tissue:NL, Visit:BL, Treatment:Brodalumab 210 mg Q2W


title: PatID:10448010033, Tissue:LS, Visit:W12, Treatment:Ustekinumab


title: PatID:10448010035, Tissue:LS, Visit:W4, Treatment:Brodalumab 140 mg Q2W


title: PatID:10448010038, Tissue:NL, Visit:BL, Treatment:Brodalumab 210 mg Q2W


title: PatID:10448010033, Tissue:LS, Visit:BL, Treatment:Ustekinumab


title: PatID:10448010032, Tissue:LS, Visit:BL, Treatment:Ustekinumab


title: PatID:10448010032, Tissue:NL, Visit:W12, Treatment:Ustekinumab


title: PatID:10448010035, Tissue:LS, Visit:BL, Treatment:Brodalumab 140 mg Q2W


title: PatID:10448010035, Tissue:NL, Visit:W12, Treatment:Brodalumab 140 mg Q2W


title: PatID:10448010032, Tissue:LS, Visit:W12, Treatment:Ustekinumab


title: PatID:10448010032, Tissue:NL, Visit:BL, Treatment:Ustekinumab


title: PatID:10448010033, Tissue:NL, Visit:BL, Treatment:Ustekinumab


title: PatID:10448010030, Tissue:NL, Visit:W12, Treatment:Ustekinumab


title: PatID:10448010032, Tissue:LS, Visit:W4, Treatment:Ustekinumab


title: PatID:10448010030, Tissue:LS, Visit:W12, Treatment:Ustekinumab


title: PatID:10448010030, Tissue:NL, Visit:BL, Treatment:Ustekinumab


title: PatID:10448010027, Tissue:LS, Visit:W12, Treatment:Brodalumab 210 mg Q2W


title: PatID:10448010030, Tissue:LS, Visit:BL, Treatment:Ustekinumab


title: PatID:10448010027, Tissue:NL, Visit:W12, Treatment:Brodalumab 210 mg Q2W


title: PatID:10448010055, Tissue:NL, Visit:BL, Treatment:Brodalumab 140 mg Q2W


title: PatID:10448010045, Tissue:LS, Visit:W4, Treatment:Placebo


title: PatID:10448010058, Tissue:LS, Visit:BL, Treatment:Brodalumab 140 mg Q2W


title: PatID:10448010027, Tissue:NL, Visit:BL, Treatment:Brodalumab 210 mg Q2W


title: PatID:10448010025, Tissue:NL, Visit:W12, Treatment:Brodalumab 210 mg Q2W


title: PatID:10448010023, Tissue:NL, Visit:W12, Treatment:Brodalumab 140 mg Q2W


title: PatID:10448010025, Tissue:LS, Visit:W4, Treatment:Brodalumab 210 mg Q2W


title: PatID:10448010026, Tissue:NL, Visit:BL, Treatment:Brodalumab 140 mg Q2W


title: PatID:10448010025, Tissue:LS, Visit:BL, Treatment:Brodalumab 210 mg Q2W


title: PatID:10448010023, Tissue:NL, Visit:BL, Treatment:Brodalumab 140 mg Q2W


title: PatID:10448010021, Tissue:NL, Visit:W12, Treatment:Ustekinumab


title: PatID:10448010026, Tissue:NL, Visit:W12, Treatment:Brodalumab 140 mg Q2W


title: PatID:10448010021, Tissue:LS, Visit:W12, Treatment:Ustekinumab


title: PatID:10448010023, Tissue:LS, Visit:BL, Treatment:Brodalumab 140 mg Q2W


title: PatID:10448010017, Tissue:NL, Visit:W12, Treatment:Brodalumab 140 mg Q2W


title: PatID:10448010026, Tissue:LS, Visit:W12, Treatment:Brodalumab 140 mg Q2W


title: PatID:10448010025, Tissue:LS, Visit:W12, Treatment:Brodalumab 210 mg Q2W


title: PatID:10448010017, Tissue:LS, Visit:W4, Treatment:Brodalumab 140 mg Q2W


title: PatID:10448010025, Tissue:NL, Visit:BL, Treatment:Brodalumab 210 mg Q2W


title: PatID:10448010021, Tissue:LS, Visit:BL, Treatment:Ustekinumab


title: PatID:10448010021, Tissue:NL, Visit:BL, Treatment:Ustekinumab


title: PatID:10448010017, Tissue:NL, Visit:BL, Treatment:Brodalumab 140 mg Q2W


title: PatID:10448010026, Tissue:LS, Visit:W4, Treatment:Brodalumab 140 mg Q2W


title: PatID:10448010026, Tissue:LS, Visit:BL, Treatment:Brodalumab 140 mg Q2W


title: PatID:10448010017, Tissue:LS, Visit:BL, Treatment:Brodalumab 140 mg Q2W


title: PatID:10448010021, Tissue:LS, Visit:W4, Treatment:Ustekinumab


title: PatID:10448010027, Tissue:LS, Visit:BL, Treatment:Brodalumab 210 mg Q2W


title: PatID:10448010017, Tissue:LS, Visit:W12, Treatment:Brodalumab 140 mg Q2W


title: PatID:10448010023, Tissue:LS, Visit:W12, Treatment:Brodalumab 140 mg Q2W


title: PatID:10448008048, Tissue:NL, Visit:W12, Treatment:Placebo


title: PatID:10448008048, Tissue:NL, Visit:BL, Treatment:Placebo


title: PatID:10448008048, Tissue:LS, Visit:W12, Treatment:Placebo


title: PatID:10448008048, Tissue:LS, Visit:BL, Treatment:Placebo


title: PatID:10448008048, Tissue:LS, Visit:W4, Treatment:Placebo


title: PatID:10448008041, Tissue:LS, Visit:W4, Treatment:Brodalumab 210 mg Q2W


title: PatID:10448008041, Tissue:LS, Visit:W12, Treatment:Brodalumab 210 mg Q2W


title: PatID:10448008041, Tissue:NL, Visit:W12, Treatment:Brodalumab 210 mg Q2W


title: PatID:10448006002, Tissue:LS, Visit:BL, Treatment:Ustekinumab


title: PatID:10425008007, Tissue:LS, Visit:BL, Treatment:Brodalumab 210 mg Q2W


title: PatID:10425001057, Tissue:LS, Visit:BL, Treatment:Ustekinumab


title: PatID:10425001057, Tissue:LS, Visit:W4, Treatment:Ustekinumab


title: PatID:10425008002, Tissue:LS, Visit:BL, Treatment:Brodalumab 140 mg Q2W


title: PatID:10425001057, Tissue:NL, Visit:BL, Treatment:Ustekinumab


title: PatID:10425001049, Tissue:NL, Visit:BL, Treatment:Brodalumab 210 mg Q2W


title: PatID:10448006002, Tissue:NL, Visit:BL, Treatment:Ustekinumab


title: PatID:10425008002, Tissue:NL, Visit:BL, Treatment:Brodalumab 140 mg Q2W


title: PatID:10425001049, Tissue:LS, Visit:W12, Treatment:Brodalumab 210 mg Q2W


title: PatID:10448008041, Tissue:NL, Visit:BL, Treatment:Brodalumab 210 mg Q2W


title: PatID:10425001057, Tissue:LS, Visit:W12, Treatment:Ustekinumab


title: PatID:10425001019, Tissue:NL, Visit:BL, Treatment:Placebo


title: PatID:10425001019, Tissue:LS, Visit:W12, Treatment:Placebo


title: PatID:10425001004, Tissue:LS, Visit:W4, Treatment:Placebo


title: PatID:10425001049, Tissue:NL, Visit:W12, Treatment:Brodalumab 210 mg Q2W


title: PatID:10425001049, Tissue:LS, Visit:BL, Treatment:Brodalumab 210 mg Q2W


title: PatID:10425001019, Tissue:LS, Visit:BL, Treatment:Placebo


title: PatID:10425001019, Tissue:LS, Visit:W4, Treatment:Placebo


title: PatID:10425001049, Tissue:LS, Visit:W4, Treatment:Brodalumab 210 mg Q2W


title: PatID:10425001004, Tissue:NL, Visit:W12, Treatment:Placebo


title: PatID:10425001019, Tissue:NL, Visit:W12, Treatment:Placebo


title: PatID:10366064004, Tissue:LS, Visit:W4, Treatment:Brodalumab 140 mg Q2W


title: PatID:10425001004, Tissue:LS, Visit:BL, Treatment:Placebo


title: PatID:10448010037, Tissue:NL, Visit:W12, Treatment:Brodalumab 210 mg Q2W


title: PatID:10366064004, Tissue:LS, Visit:W12, Treatment:Brodalumab 140 mg Q2W


title: PatID:10366043004, Tissue:LS, Visit:W4, Treatment:Brodalumab 140 mg Q2W


title: PatID:10366064004, Tissue:NL, Visit:W12, Treatment:Brodalumab 140 mg Q2W


title: PatID:10366043004, Tissue:NL, Visit:W12, Treatment:Brodalumab 140 mg Q2W


title: PatID:10366043004, Tissue:NL, Visit:BL, Treatment:Brodalumab 140 mg Q2W


title: PatID:10425001004, Tissue:LS, Visit:W12, Treatment:Placebo


title: PatID:10366043004, Tissue:LS, Visit:BL, Treatment:Brodalumab 140 mg Q2W


title: PatID:10366018015, Tissue:LS, Visit:W4, Treatment:Brodalumab 140 mg Q2W


title: PatID:10366064004, Tissue:NL, Visit:BL, Treatment:Brodalumab 140 mg Q2W


title: PatID:10366064004, Tissue:LS, Visit:BL, Treatment:Brodalumab 140 mg Q2W


title: PatID:10366018015, Tissue:LS, Visit:W12, Treatment:Brodalumab 140 mg Q2W


title: PatID:10366018001, Tissue:LS, Visit:W12, Treatment:Brodalumab 210 mg Q2W

value: MULTIPLE


title: PatID:10366018001, Tissue:LS, Visit:W4, Treatment:Brodalumab 210 mg Q2W


title: PatID:10366018015, Tissue:NL, Visit:W12, Treatment:Brodalumab 140 mg Q2W


title: PatID:10366018001, Tissue:NL, Visit:BL, Treatment:Brodalumab 210 mg Q2W


title: PatID:10366018001, Tissue:NL, Visit:W12, Treatment:Brodalumab 210 mg Q2W


title: PatID:10366010015, Tissue:LS, Visit:W4, Treatment:Brodalumab 210 mg Q2W


title: PatID:10366018015, Tissue:LS, Visit:BL, Treatment:Brodalumab 140 mg Q2W


title: PatID:10366018015, Tissue:NL, Visit:BL, Treatment:Brodalumab 140 mg Q2W


title: PatID:10366010015, Tissue:LS, Visit:W12, Treatment:Brodalumab 210 mg Q2W


title: PatID:10366010015, Tissue:LS, Visit:BL, Treatment:Brodalumab 210 mg Q2W


title: PatID:10366043004, Tissue:LS, Visit:W12, Treatment:Brodalumab 140 mg Q2W


title: PatID:10366010015, Tissue:NL, Visit:BL, Treatment:Brodalumab 210 mg Q2W


title: PatID:10366010013, Tissue:NL, Visit:W12, Treatment:Brodalumab 140 mg Q2W


title: PatID:10366010015, Tissue:NL, Visit:W12, Treatment:Brodalumab 210 mg Q2W


title: PatID:10366010013, Tissue:LS, Visit:W4, Treatment:Brodalumab 140 mg Q2W


title: PatID:10366010013, Tissue:LS, Visit:BL, Treatment:Brodalumab 140 mg Q2W


title: PatID:10366010007, Tissue:LS, Visit:BL, Treatment:Brodalumab 140 mg Q2W


title: PatID:10366010005, Tissue:LS, Visit:W4, Treatment:Placebo


title: PatID:10366010007, Tissue:NL, Visit:BL, Treatment:Brodalumab 140 mg Q2W


title: PatID:10366010007, Tissue:LS, Visit:W12, Treatment:Brodalumab 140 mg Q2W


title: PatID:10366010013, Tissue:NL, Visit:BL, Treatment:Brodalumab 140 mg Q2W


title: PatID:10366010007, Tissue:LS, Visit:W4, Treatment:Brodalumab 140 mg Q2W


title: PatID:10366010005, Tissue:LS, Visit:W12, Treatment:Placebo


title: PatID:10366010013, Tissue:LS, Visit:W12, Treatment:Brodalumab 140 mg Q2W


title: PatID:10366010005, Tissue:NL, Visit:BL, Treatment:Placebo


title: PatID:10366006034, Tissue:LS, Visit:W4, Treatment:Brodalumab 210 mg Q2W


title: PatID:10366010007, Tissue:NL, Visit:W12, Treatment:Brodalumab 140 mg Q2W


title: PatID:10366006034, Tissue:LS, Visit:W12, Treatment:Brodalumab 210 mg Q2W


title: PatID:10366006034, Tissue:NL, Visit:W12, Treatment:Brodalumab 210 mg Q2W


title: PatID:10366010005, Tissue:NL, Visit:W12, Treatment:Placebo


title: PatID:10366006034, Tissue:NL, Visit:BL, Treatment:Brodalumab 210 mg Q2W


title: PatID:10366006034, Tissue:LS, Visit:BL, Treatment:Brodalumab 210 mg Q2W


title: PatID:10348004001, Tissue:LS, Visit:W4, Treatment:Brodalumab 140 mg Q2W


title: PatID:10348004001, Tissue:NL, Visit:W12, Treatment:Brodalumab 140 mg Q2W


title: PatID:10321006014, Tissue:LS, Visit:W4, Treatment:Brodalumab 140 mg Q2W


title: PatID:10366010005, Tissue:LS, Visit:BL, Treatment:Placebo


title: PatID:10348004001, Tissue:LS, Visit:BL, Treatment:Brodalumab 140 mg Q2W


title: PatID:10348004001, Tissue:LS, Visit:W12, Treatment:Brodalumab 140 mg Q2W


title: PatID:10348004001, Tissue:NL, Visit:BL, Treatment:Brodalumab 140 mg Q2W


title: PatID:10321006014, Tissue:LS, Visit:W12, Treatment:Brodalumab 140 mg Q2W


title: PatID:10321006014, Tissue:NL, Visit:W12, Treatment:Brodalumab 140 mg Q2W


title: PatID:10321006014, Tissue:LS, Visit:BL, Treatment:Brodalumab 140 mg Q2W


title: PatID:10321006009, Tissue:LS, Visit:W4, Treatment:Ustekinumab


title: PatID:10321006009, Tissue:NL, Visit:W12, Treatment:Ustekinumab


title: Control2

city: Dalseonggun, Daegu

first: Yongcheol

last: Cho

state: Daegu

address: 333, Techno jungang-daero, Hyeonpung-eup, Dalseong-gun

department: Department of Brain Sciences

country: South Korea

institute: DGIST

description: mDRG(cont_vs_CD133)_RNA-Seq_CHI_092818.xlsx

data_processing:
The de-multiplexed sequencing reads (obtained by using CASAVA; Illumina) were aligned to the mouse genome (mm9) using TopHat2 (tophat2 -a 4 -g 1 --b2-sensitive -r 100 --mate-std-dev=50 --library-type fr-firststrand) under a supply of RefSeq gene annotations. (Huang et al., 2009a,b). Enriched biological process terms (P<0.001) were visualized by using REVIGO (http://revigo.irb.hr/) in semantic space as cluster representatives, after reduction of the redundant terms. Functional protein association was analyzed by STRING (https://string-db.org/).
Genome_build: mm9
Supplementary_files_format_and_content: Excel file, Differential expression list

source_name: E13.5 embryonic DRG neuron culture

growth_protocol: Embryonic DRG cultures were generated as previously described. Embryonic DRG collected from embryonic day 13.5 mice were dissociated in 0.05% trypsin-EDTA and plated on poly-D-lysine/laminin-coated dishes in Neurobasal medium (Gibco) supplemented with 2% B-27 (Gibco), 1% Glutamax, 1 μM 5-fluoro-2'-deoxyuridine (Sigma), 1 μM uridine (Sigma), 1% penicillin-streptomycin, and 50 ng/ml 2.5S nerve growth factor (Envigo, BT-5017).

extract_protocol:
RNA extraction and analysis procedures were performed with RNAqueous Total RNA isolation kit (Thermo, AM1931), RevertAid Reverse Transcriptase (Thermo, EP0441), and PowerUP SYBR green master mix (Thermo, A25918) from L4-5 DRG tissues or cultured embryonic neurons (E13, DIV 5), following the manufacturer’s instructions. The transcript levels were compared between conditions by the ΔΔCt method, using Gapdh transcript levels as an internal control.
RNA-Seq libraries were generated by using strand-displacement stop/ligation method from cultured embryonic DRG neurons (E13) transduced with either control or human PROM1-overexpressing lentivirus. From 1.5μg of large RNA (>200nt, extracted by RNeasy Mini Kit; Qiagen), polyadenylated mRNA was purified by using 10μl of Dynabead Oligo(dT)25 (Invitrogen) according to protocol provided by manufacturer. Then, 10ng of the purified mRNA was subjected to prepare RNA-Seq library by using SENSE Total RNA-Seq Library Kit (Lexogen) as instructed by manufacturer. After the libraries were produced, they were amplified by PCR with the lowest optimal cycle, which was determined by comparing results from different cycles. The quality of the amplified library was checked by using Fragment Analyzer (Advanced analytical) for its size distribution and quantity. Finally, the prepared multiplexed library was precisely quantitated by using both Qubit RNA HS assay kit (Thermo Fisher) and Fragment Analyzer, applied to be sequenced by HiSeq 2500 system (Illumina) as 50 single-end reads.

treatment_protocol: For lentiviral transduction, lentivirus was added to the culture at DIV 2. For re-plating assay using the embryonic DRG cultures, neurons were re-plated at DIV 5. Briefly, cultures were incubated in DMEM/0.05% Trypsin-EDTA mixture (1:1) for 5 min at 37°C, 5% CO2 and rinsed with culture medium described above. Cells were then dissociated by gentle pipetting and transferred to new culture plates coated with poly-D-lysine/laminin. Re-plated Neurons were incubated over night at 37°C with 5% CO2.

tag: tag

tag: lentivirus

value: control pLKO

value: pLKO


title: PatID:10321006014, Tissue:NL, Visit:BL, Treatment:Brodalumab 140 mg Q2W


title: CD133_1

value: human PROM1 overexpression


title: CD133_2


title: PatID:10321006009, Tissue:NL, Visit:BL, Treatment:Ustekinumab


title: 48hour post infection OT1 TLN rep2

city: La Jolla

first: Susan

last: Kaech

state: CA

address: 10010 N Torrey Pines Rd

institute: Salk Institute

data_processing:
STAR Aligner
HTSeq
DESeq2
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: mediastinal LN memory T cells

extract_protocol: cells were sorted based on gating strategy mentioned,directly into Trizol. RNA was isolated in combination with Qiagen RNeasy Plus Kit

tag: hours post infection

value: mediastinal LN

value: CD8+ P14+ CD8b- CD98hi


title: 168hour post infection P14 Trm rep1

source_name: Lung Trm cells

value: Lung

tag: cell type


title: 48hour post infection OT1 TLN rep1


title: 48hour post infection OT1 Trm rep2


title: 168hour post infection P14 Trm rep2


title: Control1


title: 48hour post infection OT1 Trm rep1


title: PatID:10448008041, Tissue:LS, Visit:BL, Treatment:Brodalumab 210 mg Q2W

value: lesional skin

value: WHITE


title: PatID:10321006006, Tissue:LS, Visit:W12, Treatment:Brodalumab 210 mg Q2W


title: PatID:10321006006, Tissue:LS, Visit:BL, Treatment:Brodalumab 210 mg Q2W

value: BL


title: 48hour post infection P14 TLN rep2


title: PatID:10321006009, Tissue:LS, Visit:W12, Treatment:Ustekinumab

value: Ustekinumab


title: PatID:10321006006, Tissue:NL, Visit:BL, Treatment:Brodalumab 210 mg Q2W

value: non-lesional skin

value: Brodalumab 210 mg Q2W


title: PatID:10321006009, Tissue:LS, Visit:BL, Treatment:Ustekinumab


title: PatID:10321006006, Tissue:LS, Visit:W4, Treatment:Brodalumab 210 mg Q2W


title: PatID:10321006005, Tissue:LS, Visit:W4, Treatment:Placebo

value: Placebo


title: 48hour post infection P14 Trm Nur77-negative rep2


title: 48hour post infection P14 TLN rep1


title: 48hour post infection P14 Trm rep1


title: 48hour post infection P14 Trm Nur77-negative rep1


title: 48hour post infection P14 Trm rep2


title: PatID:10321006006, Tissue:NL, Visit:W12, Treatment:Brodalumab 210 mg Q2W


title: 24hour post infection P14 TLN rep2


title: 24hour post infection P14 TLN rep1


title: 24hour post infection P14 Trm rep2


title: PatID:10321006005, Tissue:NL, Visit:BL, Treatment:Placebo


title: 0hour post infection OT1 Trm rep2


title: 0hour post infection P14 TLN rep2


title: 0hour post infection OT1 Trm rep1


title: 0hour post infection P14 TLN rep1


title: PatID:10321006004, Tissue:LS, Visit:BL, Treatment:Brodalumab 140 mg Q2W

value: Brodalumab 140 mg Q2W


title: PatID:10321006005, Tissue:NL, Visit:W12, Treatment:Placebo


title: PatID:10316006025, Tissue:NL, Visit:W12, Treatment:Ustekinumab


title: PatID:10316006025, Tissue:LS, Visit:W4, Treatment:Ustekinumab


title: PatID:10321006004, Tissue:NL, Visit:W12, Treatment:Brodalumab 140 mg Q2W


title: PatID:10321006005, Tissue:LS, Visit:W12, Treatment:Placebo


title: PatID:10321006004, Tissue:LS, Visit:W12, Treatment:Brodalumab 140 mg Q2W


title: PatID:10321006005, Tissue:LS, Visit:BL, Treatment:Placebo


title: PatID:10321006004, Tissue:LS, Visit:W4, Treatment:Brodalumab 140 mg Q2W


title: 0hour post infection P14 Trm rep2


title: PatID:10366018001, Tissue:LS, Visit:BL, Treatment:Brodalumab 210 mg Q2W


title: PatID:10316006025, Tissue:LS, Visit:BL, Treatment:Ustekinumab


title: PatID:10316006025, Tissue:NL, Visit:BL, Treatment:Ustekinumab


title: WT_24hour post infection P14 Trm rep1

data_processing:
STAR Aligner
HTSeq
DESeq2
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: tab-delimited text files include HT-seq counts for each Sample

tag: bm donor

value: WT

tag: irradiated recipient

tag: gating strategy


title: PatID:10316006025, Tissue:LS, Visit:W12, Treatment:Ustekinumab

tag: patientid

tag: visit


title: WT_24hour post infection P14 Trm rep2


title: PatID:10321006004, Tissue:NL, Visit:BL, Treatment:Brodalumab 140 mg Q2W

tag: pasi

tag: bmi


title: PatID:10316006014, Tissue:LS, Visit:W4, Treatment:Ustekinumab

tag: race

tag: weight


title: TAPKOnonhemo_24hour post infection P14 Trm rep3


title: TAPKOnonhemo_24hour post infection P14 Trm rep2


title: WT_24hour post infection P14 Trm rep3


title: TAPKOnonhemo_24hour post infection P14 Trm rep1


title: TAPKOBM_24hour post infection P14 Trm rep3


title: TAPKOBM_24hour post infection P14 Trm rep2


title: PatID:10316006014, Tissue:LS, Visit:BL, Treatment:Ustekinumab

tag: treatment


title: TAPKOBM_24hour post infection P14 Trm rep1


title: PatID:10316006014, Tissue:NL, Visit:W12, Treatment:Ustekinumab

tag: tissue


title: PatID:10316006008, Tissue:LS, Visit:W4, Treatment:Brodalumab 140 mg Q2W


title: PatID:10316006014, Tissue:LS, Visit:W12, Treatment:Ustekinumab


title: PatID:10316006014, Tissue:NL, Visit:BL, Treatment:Ustekinumab


title: PatID:10316006008, Tissue:NL, Visit:W12, Treatment:Brodalumab 140 mg Q2W


title: PatID:10316006008, Tissue:NL, Visit:BL, Treatment:Brodalumab 140 mg Q2W


title: PatID:10316006008, Tissue:LS, Visit:W12, Treatment:Brodalumab 140 mg Q2W


title: 4T1 Kras-G12D-myc sample C

first: Maxwell

last: Lee

state: MD

address: Building 37, Room 5120

department: CCR

institute: National Cancer Institute, NIH

data_processing:
quantile normalized
Samples were trimmed of adapters using Trimmomatic software (0.39)
The trimmed reads were aligned to 316 the mm10 reference mouse genome using BWA (0.7.17) or Bowtie (2-2.3.5.1) mapping software
SAMtools (1.9) mpileup, 317 GATK (3.8-1) Mutect2, and Strelka (2.7.1) were used to identify potential variants and the variants were filtered for known 318 polymorphisms from mgp.v5 (ftp://ftp-mouse.sanger.ac.uk/current_snps /mgp.v5.merged.snps_ all.dbSNP142 .vcf.gz) and 319 variants with Phred-scaled quality score of < 30 were removed
Annotation was performed by Annovar (2018-04-16).
High probability SNVs were identified after reads were visualized in IGV and false positives were removed from the data. Select SNVs validated by Sanger sequencing performed by the CCR Genomics Core.
Genome_build: mouse mm10
Supplementary_files_format_and_content: vcf files include variants for each sample

source_name: 4T1 cell line

extract_protocol:
Mice were bred and allowed to age until a humane endpoint was reached. Primary tumors and lung metastases were isolated and snap frozen in cryo vials using liquid nitrogen. Tissue was stored at -80 and gDNA was later isolated using the gDNA purification using ZR-Duet DNA/RNA MiniPrep kit from Zymo Research.  (cat.no. D7001)
Whole genome sequencing library preparation was performed using the TruSeq DNA Sample Prep kit FC-121-1001.  Samples were barcoded, pooled and sequenced on an Illumina HiSeq4000 to a depth of ~10x per sample. For RNA sequencing, the preparation of mRNA libraries and mRNA sequencing was performed by the Sequencing Facility using the HiSeq2500 instrument with Illumina TruSeq v4 chemistry.

treatment_protocol: genetically engineered mice were allowed to age until a humane endpoint was reached, no treatment was applied

value: 4T1 cell line

tag: oncogenic driver

value: Spontaneous / unknown

tag: model

value: cell line lentivirally transduced with pDest Kras-G12D-myc

tag: strain

value: Balb/cJ x FVBn/J

tag: mouse id

value: Sample C


title: 4T1 Kras-wildtype-myc sample C

value: cell line lentivirally transduced with pDest Kras wildtype-myc


title: 4T1 Kras-G12D-myc sample B

value: Sample B


title: 4T1 Kras-G12D-myc sample A

value: Sample A


title: 4T1 Kras-wildtype-myc sample B


title: PatID:10316006007, Tissue:LS, Visit:W4, Treatment:Brodalumab 210 mg Q2W

value: lesional skin

tag: age


title: Single-cell RNA-seq of healthy and dystrophic murine skeletal muscle

city: Berlin

first: Jordi

last: Camps

address: Müllerstraße 178

country: Germany

institute: Bayer AG

data_processing:
Fastq files contained 50-bp-long single-end sequenced tags (reads) from 384 cells each were trimmed with cutadapt 1.5 with the parameters ‘-q 20,20 --minimum-length 35‘ and the Nextera adapter sequence. The retained tags were aligned to the Ensembl 84 gene annotation of the NCBI38/mm10 mouse genome using STAR 2.4.0 with the parameters ‘--outSAMunmapped Within --runThreadN 8 --genomeDir {reference_genome} --readFilesCommand zcat --outSAMtype BAM SortedByCoordinate’. The number of tags per gene was calculated using htseq-count 0.6.0 with the parameters –’format=bam --order=pos --mode=intersection-strict --stranded=no --type=exon --idattr=gene_id {input.bam} {reference_gtf} > {output.count}’. Quality control on alignment and counting was done with ngsplot with parameters ‘-G mm10 -R genebody -C {input.bam} -O {results_dir}/genecoverage/{wildcards.sample}.gene -F rnaseq’ and multiqc
Genome_build: mm10
Supplementary_files_format_and_content: csv format contains raw count reads and metadata relating to the experiment

source_name: 384 single cells from muscle

extract_protocol:
all hindlimb muscles were isolated by surgical dissection and finely minced. Minced muscles were digested with Collagenase II (Sigma-Aldrich #234155, 700-800 U/ml in PBS) supplemented with 10 per cent horse serum (HS, Gibco #26050088), 25 mM CaCl2 and 100 U/ml penicillin-streptomycin (Gibco #15140122), for 90 min at 37 °C in a warm water bath with agitation (60-70 rpm). At 60 and 90 min, the tissue was homogenised with an 18 and 20-gauge needle respectively. Next, a red blood cell lysis was performed by incubating the cell pellet in the red blood cell lysis buffer (154 mM NH4Cl, 10 mM KHCO3, 0.1 mM EDTA) for 5 min, followed by a PBS wash, filtration through a 40 µm cell strainer (Corning #352340) and centrifugation for 5 min at 400 g at 4 °C. CD31-CD45- muscle cells were sorted single-cell by FACS in 96 well plates
SMART-seq2

value: Hindlimb muscle

tag: cell markers

value: CD45-negative and CD31-negative

tag: genotype

value: mixed sample (wildtype and Sgcb-null)

tag: disease state

value: mixed sample (healthy and dystrophic)


title: 4T1 empty vector sample C

value: cell line lentivirally transduced with pDest empty vector


title: PatID:10316006008, Tissue:LS, Visit:BL, Treatment:Brodalumab 140 mg Q2W

value: BL

value: WHITE


title: PatID:10316006007, Tissue:NL, Visit:BL, Treatment:Brodalumab 210 mg Q2W

value: non-lesional skin

value: Brodalumab 210 mg Q2W


title: PatID:10316006007, Tissue:LS, Visit:BL, Treatment:Brodalumab 210 mg Q2W


title: PatID:10316006006, Tissue:LS, Visit:W4, Treatment:Ustekinumab

value: Ustekinumab


title: 4T1 empty vector sample A

value: 4T1 cell line

value: Spontaneous / unknown


title: 4T1 empty vector sample B

value: Balb/cJ x FVBn/J


title: PatID:10316006006, Tissue:NL, Visit:W12, Treatment:Ustekinumab


title: PatID:10316006007, Tissue:NL, Visit:W12, Treatment:Brodalumab 210 mg Q2W


title: PatID:10316006007, Tissue:LS, Visit:W12, Treatment:Brodalumab 210 mg Q2W


title: PatID:10316006006, Tissue:LS, Visit:W12, Treatment:Ustekinumab


title: PatID:10316006006, Tissue:LS, Visit:BL, Treatment:Ustekinumab


title: PatID:10316006006, Tissue:NL, Visit:BL, Treatment:Ustekinumab


title: Ring1B_dSuz12_G7_+Aux

first: Thomas

middle: Rainer

last: Burkard

address: Dr. Bohrgasse 7

institute: IMBA

data_processing:
For ChIP-seq experiment, after standard quality control, the raw reads were mapped to the mm10 genome using bowtie2 (Langmead et al., 2012) and BAM files were obtained as output. To correct the GC-bias in our samples, we first quantified the bias using the computeGCBias function in deepTools (Ramirez F et al., 2016) excluding called peaks, so that the calculated GC bias reflects the technical biases rather than the CpG islands (CGIs) enriched by PcG proteins and histone modifications during the ChIP reaction. Then, GC-bias file and GC-corrected BAM files were generated from the original BAM files. Finally, biological replicates were merged using SAMtools (Li H et al., 2009).
Genome_build: mm10
Supplementary_files_format_and_content: *.bw files: bigWig Track format of read density coverage in reads per million after extension to 200 base pairs

source_name: mouse embryonic stem cell

growth_protocol: Mouse embryonic stem (mES) cells were cultivated feeder-free in base medium composed of high-glucose-DMEM supplemented with 13.5% fetal bovine serum (Sigma), 10 mM HEPES pH 7.4, 2 mM GlutaMAX (Gibco), 1 mM sodium pyruvate (Sigma), 100 U penicillin/ml (Sigma), 0.1 mg streptomycin/ml (Sigma), 1x non-essential amino acids (Sigma), 50 mM beta-mercaptoethanol (Gibco) and supplemented with 10% FBS (Sigma) and recombinant Leukemia Inhibitory Factor (LIF – produced in-house). Cells were maintained at 37°C with 5% CO2 and passaged every second day.

extract_protocol:
For ChIP-Seq samples: phenol-chloroform extraction
For ChIP-Seq samples: Libraries were prepared using the NEXTflex ChIP-Seq kit (Bio Scientific) following the “No size-selection cleanup” protocol.

treatment_protocol: Mouse embryonic stem cells (mES cells) were cultivated in regular mESC medium (untreated), or treated with 250 μM IAA for the indicated duration of time.

tag: antibodies

value: Cell Signaling (D22F2) #5694


title: Ring1B_dSuz12_G7

value: untreated


title: 4T1 Kras-wildtype-myc sample A

value: cell line lentivirally transduced with pDest Kras wildtype-myc

value: Sample A


title: Ring1B_Pcgf1_null_dSuz12_A3_+Aux


title: Ring1B_dSuz12_D8_+Aux


title: Ring1B_dSuz12_D8


title: Ring1B_Pcgf1_null_dSuz12_A3


title: Ring1B_Pcgf1_null_dSuz12_A2


title: H2A_dSuz12_G7_+Aux

value: Cell Signaling (D27C4) #8240


title: H2A_dSuz12_G7


title: PatID:10316006004, Tissue:LS, Visit:W4, Treatment:Brodalumab 140 mg Q2W

tag: patientid

value: lesional skin

value: Brodalumab 140 mg Q2W


title: PatID:10316006004, Tissue:NL, Visit:W12, Treatment:Brodalumab 140 mg Q2W

tag: visit


title: H2A_dSuz12_D8


title: PatID:10316006001, Tissue:LS, Visit:W4, Treatment:Brodalumab 140 mg Q2W

tag: pasi


title: PatID:10316006004, Tissue:LS, Visit:W12, Treatment:Brodalumab 140 mg Q2W

tag: bmi


title: H2A_Pcgf1_null_dSuz12_A3_+Aux


title: Ring1B_Pcgf1_null_dSuz12_A2_+Aux


title: H2A_Pcgf1_null_dSuz12_A3


title: PatID:10316006001, Tissue:NL, Visit:BL, Treatment:Brodalumab 140 mg Q2W

tag: race


title: PatID:10316006001, Tissue:NL, Visit:W12, Treatment:Brodalumab 140 mg Q2W

tag: weight


title: PatID:10316006001, Tissue:LS, Visit:W12, Treatment:Brodalumab 140 mg Q2W

tag: treatment


title: PatID:10316006004, Tissue:NL, Visit:BL, Treatment:Brodalumab 140 mg Q2W

tag: tissue


title: PatID:10316006004, Tissue:LS, Visit:BL, Treatment:Brodalumab 140 mg Q2W


title: PatID:10316001002, Tissue:LS, Visit:W4, Treatment:Brodalumab 210 mg Q2W

value: OTHER


title: PatID:10316006001, Tissue:LS, Visit:BL, Treatment:Brodalumab 140 mg Q2W


title: H2A_Pcgf1_null_dSuz12_A2_+Aux


title: H7_S17

data_processing:
NA
For RNA-seq differential expression analysis, raw reads were aligned to the mouse genome (mm10) or the human genome (hg38) for NPC data using HISAT2.
Normalization and differential expression analysis were performed using DESeq2
For ChIRP-seq, raw sequencing reads were aligned to the human hg19 genome using default settings of Bowtie. Peak-calling was performed using MACS with a FDR cutoff of 0.05.
Genome_build: mm10, hg19
Supplementary_files_format_and_content: Tab-delimited text files

source_name: Brain

tag: Sex

value: female

tag: genotype/variation

value: expressing GFP

tag: stress

value: CVS (chronic variable stress)

value: Brain

tag: cell type

value: prefrontal cortex neurons


title: H2A_Pcgf1_null_dSuz12_A2


title: H2A_dSuz12_D8_+Aux


title: PatID:10316001002, Tissue:LS, Visit:W12, Treatment:Brodalumab 210 mg Q2W

value: Brodalumab 210 mg Q2W

tag: age


title: PatID:10316001002, Tissue:NL, Visit:W12, Treatment:Brodalumab 210 mg Q2W

value: non-lesional skin


title: PatID:10316001002, Tissue:LS, Visit:BL, Treatment:Brodalumab 210 mg Q2W

value: BL


title: H3_S25


title: PatID:10266043004, Tissue:NL, Visit:BL, Treatment:Placebo

value: Placebo

value: WHITE


title: PatID:10316001002, Tissue:NL, Visit:BL, Treatment:Brodalumab 210 mg Q2W


title: PatID:10266043003, Tissue:LS, Visit:BL, Treatment:Brodalumab 210 mg Q2W

value: BLACK OR AFRICAN AMERICAN


title: G5_S14

value: expressing linc00473


title: PatID:10266043004, Tissue:LS, Visit:BL, Treatment:Placebo


title: PatID:10266043003, Tissue:NL, Visit:BL, Treatment:Brodalumab 210 mg Q2W


title: F5_S13


title: F7_S22

value: no; baseline


title: PatID:10266043002, Tissue:NL, Visit:W12, Treatment:Brodalumab 140 mg Q2W


title: 24hour post infection P14 Trm rep1

tag: hours post infection

value: Lung


title: E7_S21


title: D7_S16


title: E5_S19


title: PatID:10266043002, Tissue:LS, Visit:W12, Treatment:Brodalumab 140 mg Q2W

value: lesional skin


title: G7_S23


title: D5_S18


title: C7_S15


title: C5_S12


title: B5_S11


title: G3_S24


title: PatID:10266043002, Tissue:NL, Visit:BL, Treatment:Brodalumab 140 mg Q2W

value: Brodalumab 140 mg Q2W


title: PatID:10266017003, Tissue:LS, Visit:BL, Treatment:Brodalumab 210 mg Q2W


title: PatID:10266043002, Tissue:LS, Visit:BL, Treatment:Brodalumab 140 mg Q2W


title: PatID:10266017002, Tissue:LS, Visit:BL, Treatment:Brodalumab 140 mg Q2W


title: PatID:10266017001, Tissue:NL, Visit:W12, Treatment:Placebo


title: PatID:10266017002, Tissue:LS, Visit:W12, Treatment:Brodalumab 140 mg Q2W


title: PatID:10266017003, Tissue:NL, Visit:BL, Treatment:Brodalumab 210 mg Q2W


title: A7_S20


title: PatID:10266017001, Tissue:LS, Visit:W12, Treatment:Placebo


title: PatID:10266017001, Tissue:NL, Visit:BL, Treatment:Placebo


title: A5_S10


title: PatID:10266017001, Tissue:LS, Visit:BL, Treatment:Placebo


title: 59317 dRnf2_Ring1-null IAA-48h Rep2

description:
dRnf2_Ring1-null IAA-48h Rep2
59317_Ring1A-KO_AID-Ring1B-C2_48-hrs_Auxin_B.tsv

data_processing:
For ChIP-seq experiment, after standard quality control, the raw reads were mapped to the mm10 genome using bowtie2 (Langmead et al., 2012) and BAM files were obtained as output. For each ChIP-seq sample, we called the peaks using MACS2 (Zhang et al., 2008) with parameter -broad and default q-value cutoff 0.1. In particular, peaks of H2AK119ub1 and H3K27me3 were merged when closer than 5 kilobases; for other ChIP-seq samples,  peaks closer than 2 kilobases were merged. To correct the GC-bias in our samples, we first quantified the bias using the computeGCBias function in deepTools (Ramirez F et al., 2016) excluding called peaks, so that the calculated GC bias reflects the technical biases rather than the CpG islands (CGIs) enriched by PcG proteins and histone modifications during the ChIP reaction. Then, GC-bias file and GC-corrected BAM files were generated from the original BAM files. Finally, biological replicates were merged using SAMtools (Li H et al., 2009).
For RNA-seq experiment, after standard quality control, SlamDunk (Herzog et al., 2017, http://t-neumann.github.io/slamdunk/docs.html) was used to map the raw reads to the mm10 genome and count tables were generated. Two bed files with custom annotations of the 3’ UTR coordinates of AN3-12 mESCs, one for mapping, and one to filter multi-mappers, were kindly provided by Veronika Herzog (Ameres Lab) to improve mapping and counting of the reads. To do differential Expression analysis, the count tables were loaded into R and the DESeq2 package (Love M et al., 2014) was used to calculate pairwise differential expression between different conditions, always using all three replicates per condition.
Genome_build: mm10
Supplementary_files_format_and_content: *.bw files: bigWig Track format of read density coverage in reads per million after extension to 150 base pairs;  *.tsv files: Count file output from SLAMdunk containing the chromosomal coordinates, Gene Name and Strand of the counting windows, T>C conversion rate, Expression (ReadsCPM), T content of the counting window, Coverage on Ts within counting window, T>C Conversion Rate on Ts, Read Count, T>C Read Count and Multimap Counts

source_name: mouse embryonic stem cells D10B3C10-C2

extract_protocol:
For ChIP-Seq samples: phenol-chloroform extraction
For RNA-Seq samples: RNeasy kit (Qiagen) following the on-column DNase digestion protocol.
For ChIP-Seq samples: Libraries were prepared using the NEXTflex ChIP-Seq kit (Bio Scientific) following the “No size-selection cleanup” protocol.
For RNA-Seq samples: Total RNA was subjected to mRNA 3ʹ end sequencing library preparation (QuantSeq, Lexogen).

tag: genotype


title: 59316 dRnf2_Ring1-null IAA-48h Rep1

description:
dRnf2_Ring1-null IAA-48h Rep1
59316_Ring1A-KO_AID-Ring1B-C2_48-hrs_Auxin_A.tsv


title: 59318 dRnf2_Ring1-null IAA-48h Rep3

description:
dRnf2_Ring1-null IAA-48h Rep3
59318_Ring1A-KO_AID-Ring1B-C2_48-hrs_Auxin_C.tsv


title: 59315 dRnf2_Ring1-null IAA-48h Rep3

description:
dRnf2_Ring1-null IAA-48h Rep3
59315_Ring1A-KO_AID-Ring1B-B10_48-hrs_Auxin_C.tsv

source_name: mouse embryonic stem cells D10B3C10-B10


title: 59314 dRnf2_Ring1-null IAA-48h Rep2

description:
dRnf2_Ring1-null IAA-48h Rep2
59314_Ring1A-KO_AID-Ring1B-B10_48-hrs_Auxin_B.tsv


title: 59311 dRnf2_Ring1-null IAA-24h Rep2

description:
dRnf2_Ring1-null IAA-24h Rep2
59311_Ring1A-KO_AID-Ring1B-C2_24-hrs_Auxin_B.tsv


title: 59312 dRnf2_Ring1-null IAA-24h Rep3

description:
dRnf2_Ring1-null IAA-24h Rep3
59312_Ring1A-KO_AID-Ring1B-C2_24-hrs_Auxin_C.tsv


title: 59313 dRnf2_Ring1-null IAA-48h Rep1

description:
dRnf2_Ring1-null IAA-48h Rep1
59313_Ring1A-KO_AID-Ring1B-B10_48-hrs_Auxin_A.tsv


title: 59310 dRnf2_Ring1-null IAA-24h Rep1

description:
dRnf2_Ring1-null IAA-24h Rep1
59310_Ring1A-KO_AID-Ring1B-C2_24-hrs_Auxin_A.tsv


title: 59308 dRnf2_Ring1-null IAA-24h Rep2

description:
dRnf2_Ring1-null IAA-24h Rep2
59308_Ring1A-KO_AID-Ring1B-B10_24-hrs_Auxin_B.tsv


title: 59309 dRnf2_Ring1-null IAA-24h Rep3

description:
dRnf2_Ring1-null IAA-24h Rep3
59309_Ring1A-KO_AID-Ring1B-B10_24-hrs_Auxin_C.tsv


title: 59307 dRnf2_Ring1-null IAA-24h Rep1

description:
dRnf2_Ring1-null IAA-24h Rep1
59307_Ring1A-KO_AID-Ring1B-B10_24-hrs_Auxin_A.tsv


title: PatID:10266017002, Tissue:NL, Visit:W12, Treatment:Brodalumab 140 mg Q2W


title: 59306 dRnf2_Ring1-null IAA-6h Rep3

description:
dRnf2_Ring1-null IAA-6h Rep3
59306_Ring1A-KO_AID-Ring1B-C2_6-hrs_Auxin_C.tsv


title: PatID:10266009025, Tissue:NL, Visit:BL, Treatment:Placebo


title: PatID:10266009020, Tissue:NL, Visit:BL, Treatment:Brodalumab 210 mg Q2W


title: PatID:10266009025, Tissue:NL, Visit:W12, Treatment:Placebo


title: PatID:10266009025, Tissue:LS, Visit:W12, Treatment:Placebo


title: PatID:10266014010, Tissue:NL, Visit:BL, Treatment:Brodalumab 210 mg Q2W


title: PatID:10266009025, Tissue:LS, Visit:BL, Treatment:Placebo


title: 59305 dRnf2_Ring1-null IAA-6h Rep2

description:
dRnf2_Ring1-null IAA-6h Rep2
59305_Ring1A-KO_AID-Ring1B-C2_6-hrs_Auxin_B.tsv


title: PatID:10266009020, Tissue:LS, Visit:BL, Treatment:Brodalumab 210 mg Q2W


title: PatID:10266009018, Tissue:NL, Visit:BL, Treatment:Brodalumab 140 mg Q2W


title: 59303 dRnf2_Ring1-null IAA-6h Rep3

description:
dRnf2_Ring1-null IAA-6h Rep3
59303_Ring1A-KO_AID-Ring1B-B10_6-hrs_Auxin_C.tsv


title: PatID:10266009020, Tissue:LS, Visit:W12, Treatment:Brodalumab 210 mg Q2W


title: 59301 dRnf2_Ring1-null IAA-6h Rep1

description:
dRnf2_Ring1-null IAA-6h Rep1
59301_Ring1A-KO_AID-Ring1B-B10_6-hrs_Auxin_A.tsv


title: PatID:10266009020, Tissue:NL, Visit:W12, Treatment:Brodalumab 210 mg Q2W


title: PatID:10266014010, Tissue:NL, Visit:W12, Treatment:Brodalumab 210 mg Q2W


title: 59302 dRnf2_Ring1-null IAA-6h Rep2

description:
dRnf2_Ring1-null IAA-6h Rep2
59302_Ring1A-KO_AID-Ring1B-B10_6-hrs_Auxin_B.tsv


title: PatID:10266009014, Tissue:NL, Visit:BL, Treatment:Brodalumab 210 mg Q2W


title: 59304 dRnf2_Ring1-null IAA-6h Rep1

description:
dRnf2_Ring1-null IAA-6h Rep1
59304_Ring1A-KO_AID-Ring1B-C2_6-hrs_Auxin_A.tsv


title: PatID:10266014010, Tissue:LS, Visit:W12, Treatment:Brodalumab 210 mg Q2W


title: 59300 dRnf2_Ring1-null untreated Rep3

description:
dRnf2_Ring1-null untreated Rep3
59300_Ring1A-KO_AID-Ring1B-C2_0-hrs_Auxin_C.tsv

value: untreated


title: 59299 dRnf2_Ring1-null untreated Rep2

description:
dRnf2_Ring1-null untreated Rep2
59299_Ring1A-KO_AID-Ring1B-C2_0-hrs_Auxin_B.tsv


title: PatID:10266009008, Tissue:LS, Visit:W12, Treatment:Placebo


title: PatID:10266009014, Tissue:LS, Visit:BL, Treatment:Brodalumab 210 mg Q2W


title: PatID:10266009008, Tissue:NL, Visit:BL, Treatment:Placebo


title: PatID:10266009018, Tissue:LS, Visit:BL, Treatment:Brodalumab 140 mg Q2W


title: PatID:10266009008, Tissue:LS, Visit:BL, Treatment:Placebo


title: PatID:10266009008, Tissue:NL, Visit:W12, Treatment:Placebo


title: 59297 dRnf2_Ring1-null untreated Rep3

description:
dRnf2_Ring1-null untreated Rep3
59297_Ring1A-KO_AID-Ring1B-B10_0-hrs_Auxin_C.tsv


title: PatID:10266009007, Tissue:LS, Visit:W12, Treatment:Placebo


title: 59294 dSuz12_Rybp-null IAA-48h Rep3

description:
dSuz12_Rybp-null IAA-48h Rep3
59294_Rybp-KO_Suz12-AID-B11_48-hrs_Auxin_C.tsv

source_name: mouse embryonic stem cells AN3E9-B11


title: PatID:10266009007, Tissue:NL, Visit:BL, Treatment:Placebo


title: 59293 dSuz12_Rybp-null IAA-48h Rep2

description:
dSuz12_Rybp-null IAA-48h Rep2
59293_Rybp-KO_Suz12-AID-B11_48-hrs_Auxin_B.tsv


title: PatID:10266009007, Tissue:NL, Visit:W12, Treatment:Placebo


title: 59292 dSuz12_Rybp-null IAA-48h Rep1

description:
dSuz12_Rybp-null IAA-48h Rep1
59292_Rybp-KO_Suz12-AID-B11_48-hrs_Auxin_A.tsv


title: PatID:10266009007, Tissue:LS, Visit:BL, Treatment:Placebo


title: 59295 dRnf2_Ring1-null untreated Rep1

description:
dRnf2_Ring1-null untreated Rep1
59295_Ring1A-KO_AID-Ring1B-B10_0-hrs_Auxin_A.tsv


title: PatID:10266009005, Tissue:NL, Visit:W12, Treatment:Placebo


title: PatID:10266009005, Tissue:LS, Visit:W12, Treatment:Placebo


title: 59291 dSuz12_Rybp-null IAA-48h Rep3

description:
dSuz12_Rybp-null IAA-48h Rep3
59291_Rybp-KO_Suz12-AID-A8_48-hrs_Auxin_C.tsv

source_name: mouse embryonic stem cells AN3E9-A8


title: 59290 dSuz12_Rybp-null IAA-48h Rep2

description:
dSuz12_Rybp-null IAA-48h Rep2
59290_Rybp-KO_Suz12-AID-A8_48-hrs_Auxin_B.tsv


title: 59289 dSuz12_Rybp-null IAA-48h Rep1

description:
dSuz12_Rybp-null IAA-48h Rep1
59289_Rybp-KO_Suz12-AID-A8_48-hrs_Auxin_A.tsv


title: 59288 dSuz12_Rybp-null IAA-24h Rep3

description:
dSuz12_Rybp-null IAA-24h Rep3
59288_Rybp-KO_Suz12-AID-B11_24-hrs_Auxin_C.tsv


title: 59287 dSuz12_Rybp-null IAA-24h Rep2

description:
dSuz12_Rybp-null IAA-24h Rep2
59287_Rybp-KO_Suz12-AID-B11_24-hrs_Auxin_B.tsv


title: 59286 dSuz12_Rybp-null IAA-24h Rep1

description:
dSuz12_Rybp-null IAA-24h Rep1
59286_Rybp-KO_Suz12-AID-B11_24-hrs_Auxin_A.tsv


title: PatID:10266009005, Tissue:NL, Visit:BL, Treatment:Placebo


title: PatID:10266009005, Tissue:LS, Visit:BL, Treatment:Placebo


title: PatID:10266009004, Tissue:LS, Visit:W12, Treatment:Placebo


title: 59285 dSuz12_Rybp-null IAA-24h Rep3

description:
dSuz12_Rybp-null IAA-24h Rep3
59285_Rybp-KO_Suz12-AID-A8_24-hrs_Auxin_C.tsv


title: PatID:10266009004, Tissue:NL, Visit:BL, Treatment:Placebo


title: 59284 dSuz12_Rybp-null IAA-24h Rep2

description:
dSuz12_Rybp-null IAA-24h Rep2
59284_Rybp-KO_Suz12-AID-A8_24-hrs_Auxin_B.tsv


title: PatID:10266009004, Tissue:NL, Visit:W12, Treatment:Placebo


title: PatID:10266009004, Tissue:LS, Visit:BL, Treatment:Placebo


title: PatID:10266009003, Tissue:LS, Visit:W12, Treatment:Brodalumab 140 mg Q2W


title: PatID:10266009003, Tissue:LS, Visit:BL, Treatment:Brodalumab 140 mg Q2W


title: PatID:10266009003, Tissue:NL, Visit:BL, Treatment:Brodalumab 140 mg Q2W


title: 59281 dSuz12_Rybp-null IAA-6h Rep2

description:
dSuz12_Rybp-null IAA-6h Rep2
59281_Rybp-KO_Suz12-AID-B11_6-hrs_Auxin_B.tsv


title: 59280 dSuz12_Rybp-null IAA-6h Rep1

description:
dSuz12_Rybp-null IAA-6h Rep1
59280_Rybp-KO_Suz12-AID-B11_6-hrs_Auxin_A.tsv


title: 59283 dSuz12_Rybp-null IAA-24h Rep1

description:
dSuz12_Rybp-null IAA-24h Rep1
59283_Rybp-KO_Suz12-AID-A8_24-hrs_Auxin_A.tsv


title: PatID:10266009003, Tissue:NL, Visit:W12, Treatment:Brodalumab 140 mg Q2W


title: PatID:10266009002, Tissue:NL, Visit:W12, Treatment:Brodalumab 210 mg Q2W


title: 59277 dSuz12_Rybp-null IAA-6h Rep1

description:
dSuz12_Rybp-null IAA-6h Rep1
59277_Rybp-KO_Suz12-AID-A8_6-hrs_Auxin_A.tsv


title: 59279 dSuz12_Rybp-null IAA-6h Rep3

description:
dSuz12_Rybp-null IAA-6h Rep3
59279_Rybp-KO_Suz12-AID-A8_6-hrs_Auxin_C.tsv


title: 59278 dSuz12_Rybp-null IAA-6h Rep2

description:
dSuz12_Rybp-null IAA-6h Rep2
59278_Rybp-KO_Suz12-AID-A8_6-hrs_Auxin_B.tsv


title: 59276 dSuz12_Rybp-null untreated Rep3

description:
dSuz12_Rybp-null untreated Rep3
59276_Rybp-KO_Suz12-AID-B11_0-hrs_Auxin_C.tsv


title: 59282 dSuz12_Rybp-null IAA-6h Rep3

description:
dSuz12_Rybp-null IAA-6h Rep3
59282_Rybp-KO_Suz12-AID-B11_6-hrs_Auxin_C.tsv


title: 59275 dSuz12_Rybp-null untreated Rep2

description:
dSuz12_Rybp-null untreated Rep2
59275_Rybp-KO_Suz12-AID-B11_0-hrs_Auxin_B.tsv


title: 59296 dRnf2_Ring1-null untreated Rep2

description:
dRnf2_Ring1-null untreated Rep2
59296_Ring1A-KO_AID-Ring1B-B10_0-hrs_Auxin_B.tsv


title: 59274 dSuz12_Rybp-null untreated Rep1

description:
dSuz12_Rybp-null untreated Rep1
59274_Rybp-KO_Suz12-AID-B11_0-hrs_Auxin_A.tsv


title: PatID:10266009002, Tissue:NL, Visit:BL, Treatment:Brodalumab 210 mg Q2W


title: PatID:10266009002, Tissue:LS, Visit:W12, Treatment:Brodalumab 210 mg Q2W


title: PatID:10260002003, Tissue:NL, Visit:BL, Treatment:Brodalumab 210 mg Q2W


title: PatID:10260002003, Tissue:LS, Visit:W12, Treatment:Brodalumab 210 mg Q2W


title: PatID:10260002003, Tissue:LS, Visit:BL, Treatment:Brodalumab 210 mg Q2W


title: 59273 dSuz12_Rybp-null untreated Rep3

description:
dSuz12_Rybp-null untreated Rep3
59273_Rybp-KO_Suz12-AID-A8_0-hrs_Auxin_C.tsv


title: PatID:10248014009, Tissue:LS, Visit:W12, Treatment:Brodalumab 210 mg Q2W


title: PatID:10226008006, Tissue:NL, Visit:W12, Treatment:Placebo


title: PatID:10248014009, Tissue:LS, Visit:BL, Treatment:Brodalumab 210 mg Q2W


title: 59268 dRybp_Eed-null IAA-48h Rep1

description:
dRybp_Eed-null IAA-48h Rep1
59268_Eed-KO_Rybp-AID-C3_48-hrs_Auxin_A.tsv

source_name: mouse embryonic stem cells 515D10-C3


title: PatID:10226008006, Tissue:NL, Visit:BL, Treatment:Placebo


title: 59267 dRybp_Eed-null IAA-48h Rep3

description:
dRybp_Eed-null IAA-48h Rep3
59267_Eed-KO_Rybp-AID-A12_48-hrs_Auxin_C.tsv

source_name: mouse embryonic stem cells 515D10-A12


title: 59269 dRybp_Eed-null IAA-48h Rep2

description:
dRybp_Eed-null IAA-48h Rep2
59269_Eed-KO_Rybp-AID-C3_48-hrs_Auxin_B.tsv


title: PatID:10248014009, Tissue:NL, Visit:W12, Treatment:Brodalumab 210 mg Q2W


title: 59266 dRybp_Eed-null IAA-48h Rep2

description:
dRybp_Eed-null IAA-48h Rep2
59266_Eed-KO_Rybp-AID-A12_48-hrs_Auxin_B.tsv


title: 59272 dSuz12_Rybp-null untreated Rep2

description:
dSuz12_Rybp-null untreated Rep2
59272_Rybp-KO_Suz12-AID-A8_0-hrs_Auxin_B.tsv


title: 59265 dRybp_Eed-null IAA-48h Rep1

description:
dRybp_Eed-null IAA-48h Rep1
59265_Eed-KO_Rybp-AID-A12_48-hrs_Auxin_A.tsv


title: PatID:10226008004, Tissue:NL, Visit:BL, Treatment:Placebo


title: PatID:10226008004, Tissue:NL, Visit:W12, Treatment:Placebo


title: PatID:10226008006, Tissue:LS, Visit:W12, Treatment:Placebo


title: PatID:10226008004, Tissue:LS, Visit:W12, Treatment:Placebo


title: PatID:10226008004, Tissue:LS, Visit:BL, Treatment:Placebo


title: 59271 dSuz12_Rybp-null untreated Rep1

description:
dSuz12_Rybp-null untreated Rep1
59271_Rybp-KO_Suz12-AID-A8_0-hrs_Auxin_A.tsv


title: PatID:10248014009, Tissue:NL, Visit:BL, Treatment:Brodalumab 210 mg Q2W


title: PatID:10225001009, Tissue:NL, Visit:W12, Treatment:Placebo


title: 59264 dRybp_Eed-null IAA-24h Rep3

description:
dRybp_Eed-null IAA-24h Rep3
59264_Eed-KO_Rybp-AID-C3_24-hrs_Auxin_C.tsv


title: 59262 dRybp_Eed-null IAA-24h Rep1

description:
dRybp_Eed-null IAA-24h Rep1
59262_Eed-KO_Rybp-AID-C3_24-hrs_Auxin_A.tsv


title: 59263 dRybp_Eed-null IAA-24h Rep2

description:
dRybp_Eed-null IAA-24h Rep2
59263_Eed-KO_Rybp-AID-C3_24-hrs_Auxin_B.tsv


title: PatID:10225001009, Tissue:LS, Visit:W12, Treatment:Placebo


title: 59270 dRybp_Eed-null IAA-48h Rep3

description:
dRybp_Eed-null IAA-48h Rep3
59270_Eed-KO_Rybp-AID-C3_48-hrs_Auxin_C.tsv


title: 59260 dRybp_Eed-null IAA-24h Rep2

description:
dRybp_Eed-null IAA-24h Rep2
59260_Eed-KO_Rybp-AID-A12_24-hrs_Auxin_B.tsv


title: 59261 dRybp_Eed-null IAA-24h Rep3

description:
dRybp_Eed-null IAA-24h Rep3
59261_Eed-KO_Rybp-AID-A12_24-hrs_Auxin_C.tsv


title: PatID:10225001007, Tissue:NL, Visit:W12, Treatment:Brodalumab 210 mg Q2W


title: PatID:10225001009, Tissue:NL, Visit:BL, Treatment:Placebo


title: PatID:10225001009, Tissue:LS, Visit:BL, Treatment:Placebo


title: PatID:10225001007, Tissue:LS, Visit:W12, Treatment:Brodalumab 210 mg Q2W


title: 59259 dRybp_Eed-null IAA-24h Rep1

description:
dRybp_Eed-null IAA-24h Rep1
59259_Eed-KO_Rybp-AID-A12_24-hrs_Auxin_A.tsv


title: ok3062_starvation_rep4

city: Baltimore

first: Jiou

address: 615 N. Wolfe Street

institute: The Johns Hopkins University

description: C.elegans were incubated in M9 buffer away from food with gentle rocking for 6 hours prior to freezing at -80℃ and RNA extraction

hyb_protocol: 17hrs at 45° C with rotation (60rpm) as described by Affymetrix in their GeneChip Expression Analysis Technical Manual

scan_protocol: Using Affymetrix’ GeneChip Scanner 3000 7G and default parameters described by the manufacturer in their GeneChip Expression Analysis Technical Manual

data_processing: Affymetrix CEL files were extracted and their data RMA normalized with the Partek GS 6.6 platform.  Partek's Meta-Probeset set was used with RMA normalization to create quantile-normalized gene-level log2 transcript signal values, which were used in subsequent ANOVA analyses.

source_name: entire C. elegans IW314

label_protocol: The Ambion Expression WT kit was used as described in the manufacturer's manual.

growth_protocol: C.elegans were maintained at 20℃ on standard NGM plates with OP50 E.coli prior to experimentaion

extract_protocol: C.elegans were freeze-thawed at -80℃ and total RNA was extracted using RNeasy MiniPrep Kit (Qiagen)

treatment_protocol: C.elegans were incubated in M9 buffer with gentle rocking for 6 hours prior to freezing.  Control animals had food whereas food was withheld from starvation animals.

value: without food 6 hours

tag: strain


title: ok3062_starvation_rep3


title: PatID:10225001007, Tissue:NL, Visit:BL, Treatment:Brodalumab 210 mg Q2W


title: PatID:10225001007, Tissue:LS, Visit:BL, Treatment:Brodalumab 210 mg Q2W


title: 59256 dRybp_Eed-null IAA-6h Rep1

description:
dRybp_Eed-null IAA-6h Rep1
59256_Eed-KO_Rybp-AID-C3_6-hrs_Auxin_A.tsv


title: 59257 dRybp_Eed-null IAA-6h Rep2

description:
dRybp_Eed-null IAA-6h Rep2
59257_Eed-KO_Rybp-AID-C3_6-hrs_Auxin_B.tsv


title: 59258 dRybp_Eed-null IAA-6h Rep3

description:
dRybp_Eed-null IAA-6h Rep3
59258_Eed-KO_Rybp-AID-C3_6-hrs_Auxin_C.tsv


title: 59254 dRybp_Eed-null IAA-6h Rep2

description:
dRybp_Eed-null IAA-6h Rep2
59254_Eed-KO_Rybp-AID-A12_6-hrs_Auxin_B.tsv


title: ok3062_starvation_rep1


title: ok3062_starvation_rep2


title: ok3062_control_rep2

description: C.elegans were incubated in M9 buffer containing food with gentle rocking for 6 hours prior to freezing at -80℃ and RNA extraction

value: with food


title: ok3062_control_rep1


title: ok3062_control_rep3


title: PatID:10225001006, Tissue:LS, Visit:W12, Treatment:Brodalumab 140 mg Q2W


title: PatID:10225001006, Tissue:LS, Visit:BL, Treatment:Brodalumab 140 mg Q2W


title: PatID:10225001006, Tissue:NL, Visit:BL, Treatment:Brodalumab 140 mg Q2W


title: 59253 dRybp_Eed-null IAA-6h Rep1

description:
dRybp_Eed-null IAA-6h Rep1
59253_Eed-KO_Rybp-AID-A12_6-hrs_Auxin_A.tsv


title: N2_starvation_rep4

value: Wild Type


title: ok3062_control_rep4


title: 59298 dRnf2_Ring1-null untreated Rep1

description:
dRnf2_Ring1-null untreated Rep1
59298_Ring1A-KO_AID-Ring1B-C2_0-hrs_Auxin_A.tsv


title: N2_control_rep4


title: 59252 dRybp_Eed-null untreated Rep3

description:
dRybp_Eed-null untreated Rep3
59252_Eed-KO_Rybp-AID-C3_0-hrs_Auxin_C.tsv


title: N2_starvation_rep2


title: 59255 dRybp_Eed-null IAA-6h Rep3

description:
dRybp_Eed-null IAA-6h Rep3
59255_Eed-KO_Rybp-AID-A12_6-hrs_Auxin_C.tsv


title: N2_control_rep3


title: PatID:10225001005, Tissue:LS, Visit:W12, Treatment:Placebo