title: Control_rep1

city: Los Angeles

first: Angela

last: Park

state: CA

address: 1501 San Pablo St, ZNI 521

department: Molecular Microbiology and Immunology

institute: University of Southern California

data_processing:
Raw sequencing files were filtered for short or poor quality reads, then aligned to the ferret genome using CLC Genomics Workbench Tool (v 11)
Differentially expressed genes were identified using CLC Genomics Workbench Tool. Two-tailed Wald Test was used to calculate the p value. Genes showing altered expression with p < 0.05 and more than 2 fold changes were considered differentially expressed.
The pathway and network analysis was performed using Ingenuity (IPA). IPA computes a score for each network according to the fit of the set of supplied focus genes.
The canonical pathways generated by IPA are the most significant for the uploaded data set.
Genome_build: Ferret genome from Ensembl (MusPutFur1.0)
Supplementary_files_format_and_content: Read counts and differential gene expression in .xlsx format

organism: Mustela putorius furo

source_name: PBMC

extract_protocol:
Total RNA was extracted from PBMCs of mock PBS control- and SFTSV CB1/2014-infected ferrets using RNeasy Micro Kit (Qiagen) according to the manufacturer’s protocol. RNA quantity was assessed by spectrophotometry using Nanodrop 1000 (Thermo Fisher Scientific).
RNA libraries were prepared using TruSeq Stranded mRNA Sample Prep Kit  (Illumina). About 50 millions of paired-end reads with 100-nucleotide length were generated for each sample and sequenced on Illumina Hi-Seq 2500 system

value: 20-24 months

value: PBMC

tag: infection status

value: mock


title: Control_rep2

status: Public on Oct 30 2018

type: SRA

country: USA

library_source: transcriptomic

molecule: total RNA

tag: age

tag: cell type


title: S. cerevisiae-WT-untreated-smRNA-rep3

city: Copenhagen N

first: Jeppe

last: Vinther

address: Ole Maaloes Vej 5

department: Biology

country: Denmark

institute: University of Copenhagen

description:
Small RNA libraries were prepared using “The NEBNext Multiplex Small RNA” kit according to manufactures protocol
yeast_tRNA_out.txt

data_processing:
Sequencing reads were processed with Cutadapt (version 1.14) to remove adapter sequences using the setting -a AGATCGGAAGAGCACACGTCT. For reads generated nextseq platform, the option --nextseq-trim=20” was included.
All samples (except small RNA-Seq experiments): The RNAProbR preprocessing.sh script (http://people.binf.ku.dk/~jvinther/data/rna_probing/) was used to remove the 7 base barcode from the sequencing read using the options “-b NNNNNNN -t 9”
Reads were aligned with bowtie2 (version 2.2.3) using high sensitivity options “--local -N 1 -D 20 -R 3 -L 15”
All samples (except small RNA-Seq experiments): Potential PCR duplicates among the sequencing reads were removed by discarding all but one of the reads having identical barcode and mapping to the same position using the collapse.sh script (available at http://people.binf.ku.dk/jvinther/data/RNA-seq).
The mapped reads for the control and NaBH4 treated samples were processed with the mpileup tool from the samtools package (version 1.7).
Genome_build: E. coli strain bw25113 (ensembl cDNA release 87), S. cerevisiae (ensembl cDNA release 84). rRNA sequences were obtained were obtained from the CRW database (http://www.rna.ccbb.utexas.edu). tRNA sequences were obtained from the genomic tRNA database (http://gtrnadb.ucsc.edu/index.html).
Supplementary_files_format_and_content: The mutation frequency file is the output from the GetFreq function (available at https://github.com/jeppevinther/m7g_map_seq) includes a number of statistics for each position, including coverage,  mutation frequency for the treated and control samples and the mutation rate difference between the treated and control samples. It includes p-values for the observed mutation rates being different in the treated and the control samples and for the replicate samples being different.

organism: Saccharomyces cerevisiae

source_name: yeast

extract_protocol:
Hot acid phenol extraction
RNA-seq: Methods in molecular biology, 1038, 213-231 (2013) with RNA fragmentation step included.  Small RNA-seq: NEBNext Multiplex Small RNA Kit.

tag: strain

tag: nabh4 treatment


title: 253G1 (II), biological rep3

type: RNA

city: Setagaya

first: Takuya

last: Kuroda

state: Tokyo

address: 1-18-1 Kamiyoga

department: Division of cell-based therapeutic products

country: Japan

institute: National Institute of Health and Sciences

hyb_protocol: Following fragmentation, 15 ug of aRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner 3000 7G.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The TGT value is 500.

label: biotin

organism: Homo sapiens

label_protocol: Biotinylated aRNA were prepared according to the standard Affymetrix protocol from 250 ng total RNA.

extract_protocol: Extraction of total RNA was performed according to the manufacturer's instructions (RNeasy  Mini Kit, Qiagen)

tag: cell line


title: 4dpi-Young_rep3

value: infected with SFTSV CB1/2014


title: 409B2 (II), biological rep3


title: HiPS-RIKEN-1A (II), biological rep1


title: input_3509

city: Toulouse

first: Delphine

last: Labourdette

address: Hall Gilbert Durand - Bio5 - 135 Avenue de Rangueil

department: LISBP

country: France

institute: INSA

description: Total reads :  4 980 168 ; average fragment size : 200

library_source: genomic

data_processing:
Basecalls and alignment performed using Torrent_Suite 5.0.4
ChIP-seq reads were aligned to the N16961 genome
Genome_build: Escherichia coli str. K-12 substr. MG1655 ASM584v2
Supplementary_files_format_and_content: The counting of reads over the genomic sequences was performed using bedtools 2.26.0 with the tool genomecov and the option –d and –fs

molecule: genomic DNA

organism: Escherichia coli

source_name: bacteria

growth_protocol: Samples were prepared from exponential growing phase cultures at 37°C in LB media (OD = 0.5) in the presence of IPTG (where indicated)

extract_protocol:
Lysates were clarified from sonicated cell and protein-DNA complexes were isolated with anti ParBF antibody
A maximum of 2 ng of ChIP DNA was used to synthetize the library as described in manufacturer’s instructions (Ion ChIP-Seq Library Preparation on the Ion Proton™ System - revision B - Step10). The last size selection was modified by a double size selection (0.55X/0.25X) of binding to AMPure® XP beads followed by a step of wash and elution. Then, qualification and quantification were made with the Bioanalyzer - Agilent, Santa Clara, CA

treatment_protocol: Cells were treated with formalhedyde (1 %)

tag: parsf location

value: E.coli xylE::parSF

tag: iptg induction (µm)

tag: parbf allele

value: wild type

tag: antibody

value: input


title: 253G1 (II), biological rep1


title: S. cerevisiae-WT-untreated-smRNA-rep2


title: 253G1 (II), biological rep2


title: 201B7 (II), biological rep2


title: IP_3508

description: Total reads :  18 532 537 ; average fragment size : 225

value: anti ParBF


title: EUB040

type: genomic

city: Paris

first: Lucas

middle: Theo

last: Husquin

state: --- Select a state ---

address: 28 rue du docteur Roux

department: Genetics and Genomics

institute: Institut Pasteur

description: SAMPLE 15

hyb_protocol: Bisulfite converted DNAs were hybridized to beadchips provided the Illumina Infinium MethylationEPIC BeadChip Kit

scan_protocol: Signal intensity is measured with the Illumina HiScan system to generate beta values, a measure of the degree of methylation at a locus

source_name: CD14+ Monocytes, resting cells

label_protocol: Sample barcoding and staining were carried out by following the instructions of Illumina provided in the Infinium MethylationEPIC BeadChip Kit

growth_protocol: Monocyte DNA samples were obtained from PBMCs frozen in 90% fetal calf serum (FCS) and 10% dimethyl sulfoxide  dimethyl sulfoxid

extract_protocol: Each DNA sample was extracted from 2x106 primary monocytes by a standard phenol/chloroform protocol followed by ethanol precipitation. Prior to DNA methylation profiling, DNAs were then bisulfite converted and processed using the Illumina Infinium MethylationEPIC BeadChip Kit, according to the manufacturer's instructions  followed by ethanol precipitation

treatment_protocol: Primary monocytes were positively selected with magnetic CD14 microbeads from Miltenyi Biotec, according to the manufacturer's instructions

tag: gender

value: Male

tag: batch

tag: ethnicity

value: European descent


title: S. cerevisiae-WT-untreated-smRNA-rep1


title: S. cerevisiae-WT-NaBH4 treated-mRNA-exp2-rep3

description:
Libraries were prepared from polyA enriched RNA. Briefly, after NaBH4/mock treatment the RNA was reverse transcribed to cDNA using a random primer with Illumina overhang, and an adapter was ligated to the 3'-end of the cDNA. The
yeast_mrna_rrna_out.txt

value: 0.3 M NaBH4, incubated at 0 C for 30 minutes in darkness


title: 2dpi-Young_rep1


title: S. cerevisiae-WT-NaBH4 treated-mRNA-exp2-rep2


title: input_3508

description: Total reads :  2 949 097 ; average fragment size : 200


title: 2dpi-Young_rep2


title: AFB041

description: SAMPLE 14

data_processing: Signal intensity is measured with the Illumina HiScan system to generate beta values, a measure of the degree of methylation at a locus

value: African descent


title: EUB199

description: SAMPLE 13


title: IP_2076

description: Total reads :  15 950 281 ; average fragment size : 205

value: E.coli xylE::parSF-rev


title: S. cerevisiae-WT-NaBH4 treated-exp2-mRNA-rep1


title: 4dpi-Old_rep3

value: 48-50 months


title: input_2076

description: Total reads : 4 687 017 ; average fragment size : 212


title: IP_3586

description: Total reads :  19 464 845 ; average fragment size : 217


title: EUB128

description: SAMPLE 16


title: 4dpi-Young_rep1


title: 4dpi-Young_rep2


title: S. cerevisiae-WT-untreated-mRNA-exp2-rep3


title: AFB205

description: SAMPLE 12


title: 4dpi-Old_rep2


title: AFB148

description: SAMPLE 11


title: 201B7 (II), biological rep3


title: 4dpi-Old_rep1


title: S. cerevisiae-WT-untreated-mRNA-exp2-rep2


title: input_3586

description: Total reads : 7 798 374 ; average fragment size : 219


title: zebrafish_heart_yap_sham_2

city: Wauwatosa

first: Michael

middle: Andrew

last: Flinn

state: WI

address: 8701 W Watertown Plank Rd

department: Physiology

institute: Medical College of Wisconsin

data_processing:
Primary sequencing data was conducted with a BGISEQ-500 50SE at 20M reads per sample.
Raw reads are subjected to quality control (QC) to determine if a resequencing step is needed. After QC, raw reads are filtered into clean reads which are aligned to the reference sequences.
"Dirty" raw reads are reads which contain the sequence of adaptor, high content of unknown bases and low quality reads, and are removed before analysis.
Bowtie2 was used to map clean reads to reference gene, and HISAT used to reference genome.
The Fragments Per Kilobase of transcript per Million mapped reads (FPKM)  method is used to calculated expression level.
Genome_build: GRCz11
Supplementary_files_format_and_content: Excel files containing FKPM values for expression levels.

organism: Danio rerio

source_name: 7 days post injury, sham, yap mutant zebrafish heart, replicate 2

growth_protocol: Zebrafish (Danio rerio) were maintained at 28.5C on an Aquatic Habitats recirculating filtered water system in reverse-osmosis purified water supplemented with Instant Ocean salts (60 mg/l) on a 14 h light:10 h dark lighting cycle and fed a standard diet.

extract_protocol:
RNA was extracted using Trizol (Thermo Fisher Scientific) phenol cholorform extraction.
RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low-input poly-A BGISEQ-500RSRNASeq(Transcriptome) protocol.

treatment_protocol: Zebrafish were anesthetized in 0.02% tricaine. An incision was made through the chest to gain access to the heart. Ventricles were exposed for roughly four seconds to a 0.5mm liquid nitrogen chilled stainless steel probe for cryoinjury or left alone for sham injury

tag: injury type

value: Sham Injured

tag: genotype

value: yap -/-


title: zebrafish_heart_yap_sham_3

source_name: 7 days post injury, sham, yap mutant zebrafish heart, replicate 3


title: 2dpi-Old_rep3


title: AFB139

description: SAMPLE 9


title: EUB077

description: SAMPLE 8


title: EUB136

description: SAMPLE 7


title: zebrafish_heart_yap_cryo_3

source_name: 7 days post injury, cryoinjury, yap mutant zebrafish heart, replicate 3

value: Cryoinjured


title: zebrafish_heart_yap_sham_1

source_name: 7 days post injury, sham, yap mutant zebrafish heart, replicate 1


title: AFB071

description: SAMPLE 17


title: EUB126

description: SAMPLE 6


title: 2dpi-Old_rep2


title: knockout3

city: Wuerzburg

first: Philip

last: Kruber

state: Bayern

address: Am Hubland

department: Physiological Chemistry

country: Germany

institute: University of Wuerzburg

data_processing:
Basecalls performed using CASAVA version 1.8
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using bowtie2
We use AASRA to map clean reads to reference genome and other sRNA database, except Rfam which was performanced by using cmsearch
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample

organism: Mus musculus

source_name: whole embryonal mouse kidney

extract_protocol:
kidneys were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent.
microRNA libraries were prepared for sequencing using standard BGI protocols

tag: developmental stage

value: embryonal stage 16.5

value: DROSHA knockout

tag: tissue

value: embryonal kidney


title: knockout2


title: zebrafish_heart_yap_cryo_1

source_name: 7 days post injury, cryoinjury, yap mutant zebrafish heart, replicate 1


title: Control_mOSE_2

city: Ottawa

first: David

last: Cook

state: ON

address: 501 Smyth Rd

department: Cancer Therapeutics Program

country: Canada

institute: Ottawa Hospital Research Institute

data_processing:
Pseudoalignment and transcript quantification performed with Kallisto (0.44.0) with -b 50
Differential expression analysis performed with Sleuth (0.30.0)
Genome_build: GRCm38
Supplementary_files_format_and_content: CSV file containing TPM values for each gene across all samples

source_name: Ovarian surface epithelial cells

growth_protocol: mOSE cells were cultured in media consisting of a-Minimum Essential Medium (Corning) supplemented with 4% FBS, 0.01mg/mL ITSS (Roche), 2ug/mL EGF (R&D Systems).

extract_protocol:
Total RNA was collected using the RNeasy Kit (Qiagen)
Libraries were generated from 250 ng of total RNA as following: mRNA enrichment was performed using the NEBNext Poly(A) Magnetic Isolation Module (New England BioLabs). cDNA synthesis was achieved with the NEBNext RNA First Strand Synthesis and NEBNext Ultra Directional RNA Second Strand Synthesis Modules (New England BioLabs). The remaining steps of library preparation were done using and the NEBNext Ultra II DNA Library Prep Kit for Illumina (New England BioLabs). Adapters and PCR primers were purchased from New England BioLabs. Libraries were quantified using the Quant-iT™ PicoGreen® dsDNA Assay Kit (Life Technologies) and the Kapa Illumina GA with Revised Primers-SYBR Fast Universal kit (Kapa Biosystems). Average size fragment was determined using a LabChip GX (PerkinElmer) instrument.

treatment_protocol: TGFB1-treated cells were treated with 10ng/mL TGFB1 (R&D Systems) for 4 days prior to RNA extraction

value: Ovarian surface epithelial cells

tag: treatment

value: Untreated


title: knockout1


title: EUB051

description: SAMPLE 5

tag: age


title: EUB085

description: SAMPLE 4


title: zebrafish_heart_wt_sham_3

source_name: 7 days post injury, sham, wildtype zebrafish heart, replicate 3

value: yap +/+


title: transgene3

value: DROSHA-E1147K transgene


title: EUB172

description: SAMPLE 3


title: AFB182

description: SAMPLE 10


title: S. cerevisiae-WT-untreated-mRNA-exp2-rep1


title: zebrafish_heart_wt_sham_2

source_name: 7 days post injury, sham, wildtype zebrafish heart, replicate 2


title: transgene2


title: AFB045

description: SAMPLE 2


title: zebrafish_heart_wt_sham_1

source_name: 7 days post injury, sham, wildtype zebrafish heart, replicate 1


title: AFB180

description: SAMPLE 1


title: 2dpi-Old_rep1

tag: cell type

value: PBMC

tag: infection status

value: infected with SFTSV CB1/2014


title: 201B7 (II), biological rep1


title: transgene1


title: zebrafish_heart_yap_cryo_2

source_name: 7 days post injury, cryoinjury, yap mutant zebrafish heart, replicate 2


title: 153-1

city: Kunming

first: Junjun

last: Hao

address: 32 Jiaochang Donglu Kunming

country: China

institute: Kunming Institute of Zoology

data_processing:
Basecalls performed using CASAVA version 1.8
Bowtie software was used for sequence alignment
Data were filtered using GSQCToolkitv2.3.3 with parameters –pe -cutOffReadLen4HQ 70 –cutOffQualScore 20 N 5.
Tophat2.10 software was used for sequence alignment
Cufflinks2.2.1 was used to calculate gene expression values
The upper quartile normalization method was used to calculate gene expression values for each sample
Genome_build: ref_TupChi_1.0 (http://www.treeshrewdb.org/)
Supplementary_files_format_and_content: Interpretable processed data were not provided for this study.

organism: Tupaia chinensis

source_name: pancreatic cancer sample

extract_protocol:
RNA extraction protocol not provided.
RNA-seq libraries were constructed using the mRNA-Seq Prep kit and were sequenced on the Illumina HiSeq 4000 platform in paired-end form with 150 bp

value: pancreatic cancer

tag: organ

value: pancreas


title: control3

value: wild type


title: zebrafish_heart_wt_cryo_2

source_name: 7 days post injury, cryoinjury, wildtype zebrafish heart, replicate 2


title: zebrafish_heart_wt_cryo_1

source_name: 7 days post injury, cryoinjury, wildtype zebrafish heart, replicate 1


title: control2


title: hPSC medium

city: Helsinki

first: Sippy

last: Kaur

address: PO Box 63

department: Oral and Maxillofacial Diseases

country: Finland

institute: University of Helsinki

data_processing:
Raw data was de-multiplexed and FASTQ files for each sample were generated using the bcl2fastq software (Illumina inc.).
Reads were mapped using Bowtie 2 software according to the Exiqon NGS Service microRNA/smallRNA pipeline. First, reads aligned to spike-ins or abundant sequences were discarded. Second, reads were aligned to miRBase 20. Third, unaligned reads were aligned to miRNA and smRNA loci in GRCh37 reference genome. Reads aligned to miRNA loci were combined with reads aligned to miRBase.
Genome_build: GRCh37
Supplementary_files_format_and_content: mirna_raw_counts.txt: tab-delimited text file including miRNA raw counts for all samples, smrna_raw_counts.txt: tab-delimited text file including other smRNA raw counts for all samples

organism: other sequences

source_name: Pluripotent stem cell culture medium

extract_protocol:
EVs were isolated from 3 ml conditioned cell culture media using miRCURY™ Exosome Isolation kit (Exiqon A/S) followed by RNA isolation using miRCURY™ RNA Isolation Kits - Cell & Plant (Exiqon A/S).
The library preparation was done using the NEBNext® Small RNA Library preparation kit (New England Biolabs). A total of 6 μl isolated RNA was converted into microRNA NGS libraries. Library preparation QC was performed using either Bioanalyzer 2100 (Agilent). Based on quality of the inserts and the concentration measurements the libraries were pooled in equimolar ratios. The pool was then size selected using the LabChip XT (PerkinElmer) aiming to select the fraction with the size corresponding to microRNA libraries (~ 145 nt). The library pool were then sequenced on a NextSeq 500 sequencing instrument according to the manufacturer instructions.

tag: sex/karyotype

tag: passage

tag: source/details


title: control1


title: 130-1


title: 149-1


title: Widetype in CuSO4 relicate3

status: Public on Oct 29 2018

city: Durham

first: John

middle: R.

last: Perfect

state: North Carolina

address: 303 Research Drive, Rm.337

department: Division of Infectious Diseases

institute: Duke University School of Medicine

data_processing:
The quality control of the reads was conducted with FastQC for each sample.
Reads with Illumina standard adapter sequences or with low-quality sequences (Phred quality score less than 30) were trimmed by Cutadapt. Reads with the length less than 50 bp were filtered after trimming.
The quality paired-end reads for each sample were aligned to the reference genome and transcriptome using Bowtie 2 and Tophat.
Read-count-per-gene measurements were estimated by htseq-count (HTSeq) to convert the mapped reads to read counts.
Gene expression differences were evaluated using a test based on a gamma generalized linear model (GLM), which was implemented in the R package edgeR.
Genome_build: CNA3
Supplementary_files_format_and_content: tab-delimited text files include normalized count values for each Sample for each H99 gene

organism: Cryptococcus neoformans H99

source_name: Yeast

growth_protocol: Overnight C. neoformans cultures of wild-type and cuf1Δ strains in synthetic complete (SC) medium (MP Biomedicals) were back-diluted to an OD600 of 0.2 in SC media and grown for three hours corresponding to ~one population doubling. At this time point, cells were treated as described below.

extract_protocol:
Cells were pelleted using bead beating tubes (Mo Bio) and lysed in a mini bead-beater (BioSpec). RNA was extracted using the RNeasy Mini Kit (Qiagen). RNA was eluted in 50 µl of RNAse free water, and DNAse treated using Turbo DNAse (Roche) as suggested by the manufacturer.
RNA samples for construction of the sequencing libraries for RNA-seq analysis were prepared using a TruSeq RNA sample preparation kit (Illumina) as standard Illumina protocols. The cDNA libraries were sequenced on an Illumina HiSeq 2000 instrument (Illumina). Approximately 0.9 - 1.8 × 107 paired-end, 75-bp reads were generated for each sample.

treatment_protocol: 1 mM CuSO4 or 1 mM BCS were added to the media and cells grown for three hours before harvesting.

tag: strain

tag: media

value: SC media with 1 mM CuSO4

value: wild-type


title: Widetype in CuSO4 relicate1


title: Widetype in CuSO4 relicate2


title: Widetype in BCS relicate2

value: SC media with 1 mM BathoCuproinediSulfonate


title: Widetype in BCS relicate3


title: CUF1 KO in CuSO4 relicate2


title: Widetype in BCS relicate1


title: CUF1 KO in CuSO4 relicate3


title: CUF1 KO in BCS relicate3


title: CUF1 KO in CuSO4 relicate1


title: CUF1 KO in BCS relicate1


title: Cu_Whole_Cell_Extract_replicate1

data_processing:
read alignment were performed by Bowtie2.
Reads were aligned to the C. neoformans var. grubii H99  reference genome using Bowtie 2. Approximately 75 – 83% reads aligned uniquely to the reference.
THOR tool was used to detect and analyze differential signal peaks between control and treated samples with replicates.
The Integrative Genomics Viewer were used to visualize and compare peak differences between control and treatment replicate samples.
Genome_build: CNA3
Supplementary_files_format_and_content: narrowPeak

growth_protocol: An overnight C. neoformans culture of a cuf1Δ complemented with Cuf1-2xFLAG strain in synthetic complete (SC) medium (MP Biomedicals) was back-diluted to an OD600 of 0.2 in a 50 ml volume of SC media and grown for three hours at 30˚C, corresponding to ~one population doubling. At this time point, cells were treated as described below.

extract_protocol:
After 3 hours of treatment, formaldehyde was added and cells incubated for 20 minutes for crosslinking and crosslinking quenched with glycine for 5 minutes. Cells were pelleted and washed once in 10 mL of PBS containing glycine. The washed pellets were resuspended in 1 mL ChIP lysis buffer and lysed by bead beating three times 1 minute with a Mini Bead Beater 16 (BioSpec). The lysate was aspirated added to a 15 ml conical tube with 1 ml of ChIP lysis buffer and sonicated 40 seconds, 20 seconds on, 20 seconds off. Lysates were cleared by two successive centrifugations for 10 minutes at 20,000 x g at 4˚C. The resulting supernatant is now the input for the ChIP experiment. 30 µl were transferred to a new tube as the Whole Cell Extract (WCE). To prepare immunoprecipitation samples 250 µl lysate was added to 250 µl ChIP lysis buffer and 120 µl 3.6 M NaCl. To these samples, protein A agarose beads (Protein A Plus Agarose, Pierce) were added and incubated for 1 hour at 4˚C with rotation to clear protein that non-specifically binds beads. Lysates with agarose beads were then centrifuged at 10,000 x g for 1 minute at 4˚C, the supernatant transferred to a new tube and FLAG antibody beads (EZview Red Anti-FLAG M2 Affinity Gel, Sigma) blocked in PBS with 5% milk for 1 hour and washed in ChIP lysis buffer were added to the lysates and incubated for 16 hours at 4˚C while rotating. After beads washed several times, The immunoprecipitated Cuf1-2xFLAG was eluted by adding 150 µl of ChIP elution buffer and incubated for 10 minutes at 65˚C, centrifuged at 10,000 x g for 1 minute and 125 µl of the supernatant was transferred to a new tube. 95 µl of ChIP elution buffer was added to 30 ul WCE. The IP and WCE tubes were incubated at 65˚C overnight to reverse formaldehyde crosslinks, treated with 5 µl of proteinase K (BioLine) at 37˚C for 90 minutes and samples purified using a Qiagen PCR purification kit as per manufacturer’s instructions and eluted in 50 µl of water.
Libraries were prepared using the Kapa BioSystem HyperPrep Library Kit. libraries were cleaned using SPRI beads, quantified using Qubit 2.0 and size checked using the Agilent Bioanalyzer. Four libraries of replicate 1 were pooled together and sequenced by Illumina HiSeq 2000 sequencer at 100 bp single end. the other eight files from replicate 2 and 3 were sequenced by Illumina HiSeq 4000 sequencer at 51 bp single end.

treatment_protocol: Cells were treated with 1 mM CuSO4 or 1 mM BCS for three hours at 30˚C.

value: Cuf1(del) complemented with Cuf1-2xFLAG

tag: chip antibody


title: CUF1 KO in BCS relicate2


title: zebrafish_heart_wt_cryo_3

source_name: 7 days post injury, cryoinjury, wildtype zebrafish heart, replicate 3

value: Cryoinjured


title: Cu_IP_Cuf1_replicate1

value: EZview Red Anti-FLAG (Sigma)


title: AT-MSC medium

source_name: Mesenchymal stem cell culture medium


title: BCS_IP_Cuf1_replicate1


title: Poly_rep3 [hTERTpolyEF]

city: Goettingen

first: Gabriela

last: Salinas

state: Lower-Saxony

address: Kreuzbergring 57

department: Department of Pathology

institute: Universitaetsmedizin Goettingen

description: r1056shTERTpolyEF_cj_rna_sr_DPZ_C_3_CAGATC_L005

data_processing:
Demultiplexing was performed using Illumina CASAVA-1.8.2
Quality check was performed using FastQC
Sequence Alignment was performed using star-2.3
Read counting was performed using featurecount
Differential gene expression analysis was performed using DESeq2_1.8.2
Genome_build: C_jacchus3.2.1
Supplementary_files_format_and_content: normalized counts and differential gene expression as indicated in the file names

organism: Callithrix jacchus

source_name: polyclonal hTERT-immortalized  marmoset fibroblasts

growth_protocol: All cells were grown on 10 cm tissue culture plates were coated with 0.1% gelatine. Medium used was DMEM high glucose supplemented with 10% FBS, GlutaMax, 1xNEAA, and Penicillin/Streptomycin.

extract_protocol:
RNA was isolated with TRIzol reagent. The RNA quality was assessed by measuring the RIN (RNA Integrity Number) using Agilent 2100 Bioanalyzer.
Library construction was performed using the TruSeq RNA Sample Preparation Kit (Illumina, Cat. N°RS-122–2002) starting from 500 ng of total RNA.

treatment_protocol: Immortalized cells were generated by transfection of piggyBac transposon carrying hTERT and puromycin resistance expression cassettes (pTT-PB-hTERT-Puro) and piggyBac transposase (pcA3-PBase-Tomato). The cells expressing hTERT were selected with puromycin.

value: newborn

tag: genotype/variation

value: hTERT

value: skin


title: Poly_rep2 [hTERTpolyCD]

description: r1056shTERTpolyCD_cj_rna_sr_DPZ_C_2_TGACCA_L005


title: Poly_rep1 [hTERTpolyAB]

description: r1056shTERTpolyAB_cj_rna_sr_DPZ_C_1_CGATGT_L005


title: K4_rep2 [HTERT-K4CD]

description: r1056sHTERT-K4CD_cj_rna_sr_DPZ_B_2_GCCAAT_L004

source_name: monoclonal hTERT-immortalized  marmoset fibroblasts


title: K1_rep3 [HTERT-K1EF]

description: r1056sHTERT-K1EF_cj_rna_sr_DPZ_A_3_CAGATC_L004


title: K4_rep1 [HTERT-K4AB]

description: r1056sHTERT-K4AB_cj_rna_sr_DPZ_B_1_CCGTCC_L004


title: WT_rep3 [37EF]

description: r1056s37EF_cj_rna_sr_DPZ_D_3_CTTGTA_L005

source_name: wild type marmoset fibroblasts


title: K1_rep2 [HTERT-K1CD]

description: r1056sHTERT-K1CD_cj_rna_sr_DPZ_A_2_TGACCA_L004


title: WT_rep1 [37AB]

description: r1056s37AB_cj_rna_sr_DPZ_D_1_CCGTCC_L005


title: K1_rep1 [HTERT-K1AB]

description: r1056sHTERT-K1AB_cj_rna_sr_DPZ_A_1_CGATGT_L004


title: K4_rep3 [HTERT-K4EF]

description: r1056sHTERT-K4EF_cj_rna_sr_DPZ_B_3_CTTGTA_L004


title: WT_rep2 [37CD]

description: r1056s37CD_cj_rna_sr_DPZ_D_2_GCCAAT_L005


title: Lungs_treatment_4

city: Burnaby

first: Amy

middle: H.

last: Lee

state: BC

address: 8888 University Drive

department: Molecular Biology and Biochemistry

institute: Simon Fraser University

data_processing:
Base-calling and de-multiplexing were performed on the Illumina instrument.
fastq file quality control was performed using FastQC v0.11.5 and MultiQC v0.8.dev0
FASTQ files were aligned to the Ensembl murine reference genome using STAR aligner (version 2.5.2B).
Read count tables were generated using HTSeq-count (version 0.6.1p1)
Genome_build: GRCm38.p5 (build 86)
Supplementary_files_format_and_content: The .count files were generated using HTSeq-count and represent read counts.

molecule: polyA RNA

source_name: Lung

extract_protocol:
Lung samples were collected in RNAlater (Qiagen) and blood samples were collected in RNAprotect animal blood tubes (Qiagen), both according to the manufacturer protocols. Total RNA was isolated using the RNAeasy Plus Mini kit (Qiagen). An enrichment with poly d(T) beads (New England Biolabs) was used to isolate polyA RNA. A KAPA Stranded Total RNA-Seq kit (Kapa Biosystems) was used to create the cDNA libraries.
The cDNA libraries were made according to the manufacturer protocol. In brief, first strand cDNA was synthesized, following by second strand synthesis and blunt-end formation. After 3’ adenylation, adapters (Bioo Scientific) for multiplexing were ligated, followed by amplification and then purification using Agencourt Ampure XP beads (Beckman Coulter).

value: lung


title: Lungs_treatment_5


title: BCS_Whole_Cell_Extract_replicate1


title: Lungs_treatment_3


title: Lungs_PA103_3


title: Lungs_IDR1002_5


title: Lungs_PA103_1


title: Lungs_treatment_1


title: Lungs_PA103_2


title: Lungs_PA103_4


title: Lungs_IDR1002_2


title: Lungs_treatment_2


title: Lungs_IDR1002_3


title: Lungs_control_5


title: Lungs_IDR1002_1


title: Lungs_control_3


title: Lungs_control_4


title: Lungs_control_2


title: Lungs_control_1


title: D72-L13: D.05.168

city: Grange

first: Carla

last: Surlis

state: meath

address: Dunsany

department: Animal Bioscience

country: Ireland

institute: Teagasc

description: Artificially fed 5% total body weight colostrum

data_processing:
Reads were quality-filtered and adapter-trimmed using cutadapt, trimming the first 13bp standard Illumina adapter, retaining reads with minimum base quality 30, minimum read length 20.
Quality assessment of the filtered data was performed by FastQC
Read alignment was performed using STAR.
Gene level read-counts were quantified using STAR's '--quantMode GeneCounts' parameter.
Analysis of the count data was performed using R's Bioconductor package DESeq2.
Genome_build: UMD3.1
Supplementary_files_format_and_content: First row contains the ENSEMBL gene IDs and second row the raw number of reads that map to each gene

organism: Bos taurus

source_name: Dairy calve

growth_protocol: Beef breed calves were allowed free access to dam from birth, with dairy calves artificially fed 5% total body weight colostrum

extract_protocol:
RNA was isolated from whole blood collected from dairy and beef calves using the tempus spin RNA isolation reagent kit following manufacturers guidelines (Applied Biosystems, USA).
Single-end mRNA-seq libraries were constructed using the Illumina Truseq sample prep kit.

treatment_protocol: Blood samples were collected from the calf via the jugular vein using a 10 mL serum vacutainer tube (BD, Oxford, UK), at 0, 48, 72, and 168 hour (h) post birth.

tag: calf breed

value: holstein friesian

tag: rna number

tag: tag number

value: Whole blood

tag: timepoint

value: 168 hours


title: D48-L1R: D.05.168

tag: tissue


title: D37-L2: D.05.168


title: D42-L16: D.05.168


title: D71-L6: D.05.072

value: 72 hours


title: D161-L5: D.05.168


title: D47-L16: D.05.072


title: D30-L7: D.05.168


title: Lungs_IDR1002_4

tag: treatment


title: D28-L10: D.05.048

value: 48 hours


title: D46-L11: D.05.048


title: D166-L11: D.05.072


title: D154-L11: D.05.072


title: D165-L4: D.05.048


title: D70-L8: D.05.048


title: D41-L7: D.05.072


title: D160-L14: D.05.072


title: D178-L12: D.05.072


title: D159-L7R: D.05.048


title: D153-L14: D.05.048


title: D40-L9: D.05.048


title: D177-L1R: D.05.048


title: D44-L5: D.05.000 Rep 7

value: 0 hours


title: D68-L9: D.05.000


title: D38-L4: D.05.000 Rep 6


title: D26-L2R: D.05.000 Rep 5


title: D175-L3: D.05.000 Rep 4


title: D31-L6: D.05.168


title: D163-L8: D.05.000 Rep 3


title: D179-L10: D.05.168


title: D157-L3: D.05.000 Rep 2


title: D151-L13: D.05.000 Rep 1


title: B125-L4: B.LF.168 Rep 5

description: Suckled from dam breed LF

source_name: Beef calve

value: limousin friesian


title: D29-L3: D.05.072


title: B130-L3: B.LF.168 Rep 6

description: Suckled from dam breed LF


title: B99-L13: B.LF.072 Rep 7

description: Suckled from dam breed LF


title: B110-L14: B.LF.168 Rep 3

description: Suckled from dam breed LF


title: B100-L7R: B.LF.168 Rep 1

description: Suckled from dam breed LF


title: B129-L8: B.LF.072 Rep 5

description: Suckled from dam breed LF


title: B115-L9: B.LF.168 Rep 4

description: Suckled from dam breed LF


title: B114-L10: B.LF.072 Rep 3

description: Suckled from dam breed LF


title: B109-L15: B.LF.072 Rep 2

description: Suckled from dam breed LF


title: B124-L9: B.LF.072 Rep 4

description: Suckled from dam breed LF


title: B65-L1: B.LF.168 Rep 7

description: Suckled from dam breed LF


title: B63-L7: B.LF.048 Rep 6

description: Suckled from dam breed LF


title: B98-L4: B.LF.048 Rep 7

description: Suckled from dam breed LF


title: B104-L1: B.LF.072 Rep 1

description: Suckled from dam breed LF


title: B105-L8: B.LF.168 Rep 2

description: Suckled from dam breed LF


title: B64-L10: B.LF.072 Rep 6

description: Suckled from dam breed LF


title: S50_Yes.sb

city: Boston

first: Minseok

last: Seo

state: MA

address: 181 longwood ave.

department: Channing Division of Network Medicine

institute: Brigham & Women's Hospital and Harvard Medical School

description:
COPD patient
SAMPLE 50

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were quantile normalized using lumi package in R

source_name: Blood

label_protocol: cDNA was labeled using an Ambion labeling kit (Ambion)

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

tag: oxygen therapy

value: Yes

tag: time-point

value: sb


title: B128-L3: B.LF.048 Rep 5

description: Suckled from dam breed LF


title: S48_Yes.sb

description:
COPD patient
SAMPLE 48


title: B123-L2: B.LF.048 Rep 4

description: Suckled from dam breed LF


title: S42_Yes.f12

description:
COPD patient
SAMPLE 42


title: B113-L12: B.LF.048 Rep 3

description: Suckled from dam breed LF


title: S46_No.f12

description:
COPD patient
SAMPLE 46

value: No


title: B108-L13: B.LF.048 Rep 2

description: Suckled from dam breed LF


title: S49_No.sb

description:
COPD patient
SAMPLE 49


title: S47_No.sb

description:
COPD patient
SAMPLE 47


title: S43_No.sb

description:
COPD patient
SAMPLE 43


title: S51_No.sb

description:
COPD patient
SAMPLE 51


title: B103-L14: B.LF.048 Rep 1

description: Suckled from dam breed LF


title: hESC Mesoderm

city: Macau

first: Ren

last: Zhili

address: Avenida da Universidade

institute: University of Macau

hyb_protocol: cRNA was hybridized onto HumanHT-12 v4 Expression BeadChip (Illumina) using standerd protocol.

scan_protocol: BeadChips were scanned with the iScanner (Illumina).

data_processing: Data was normalized by quantile normalization.

source_name: Human embryonic stem cell H9

label_protocol: RNA was converted to cRNA using the TargetAmp™-Nano Labeling Kit for Illumina Expression BeadChip (Epibio).

growth_protocol: Human ESCs (H1) were maintained in E8 medium on matrigel-coated plates with daily medium change. Cell culture of <70% confluence is designated as low density, and >90% confluence as high density.

extract_protocol: Total RNA was isolated by RNAiso Plus.

treatment_protocol: E8 24 hrs: normal E8 medium. Nam 24 hrs: E8 medium supplemented with 10 mM nicotinamide for 24 hours. ROCKi 24 hrs: E8 medium supplemented with 10 μM ROCK inhibitor Y27632 treatment for 24 hours. Mesoderm: E8 medium supplemented with BMP4 for 6 days.

tag: cell line

tag: cell type

value: human embryonic stem cell (hESC)


title: hESC E8 24 hrs


title: hESC Nam 24 hrs


title: S45_No.sb

description:
COPD patient
SAMPLE 45


title: S44_No.sb

description:
COPD patient
SAMPLE 44


title: S41_Yes.sb

description:
COPD patient
SAMPLE 41


title: hESC ROCKi 24 hrs


title: S39_Yes.f12

description:
COPD patient
SAMPLE 39


title: S36_No.sb

description:
COPD patient
SAMPLE 36


title: S37_Yes.sb

description:
COPD patient
SAMPLE 37


title: B61-L16: B.LF.000 Rep 6

description: Suckled from dam breed LF


title: S40_Yes.sb

description:
COPD patient
SAMPLE 40


title: B96-L10: B.LF.000 Rep 7

description: Suckled from dam breed LF


title: B126-L11: B.LF.000 Rep 5

description: Suckled from dam breed LF


title: S38_Yes.sb

description:
COPD patient
SAMPLE 38


title: B111-L14: B.LF.000 Rep 3

description: Suckled from dam breed LF


title: S35_Yes.f12

description:
COPD patient
SAMPLE 35


title: B106-L6: B.LF.000 Rep 2

description: Suckled from dam breed LF


title: B95-L10R: B.CL.168 Rep 7

description: Suckled from dam breed CL

value: charolais limousin


title: B55-L13: B.CL.168 Rep 6

description: Suckled from dam breed CL


title: S33_No.sb

description:
COPD patient
SAMPLE 33


title: B40-L12: B.CL.168 Rep 4

description: Suckled from dam breed CL


title: B50-L15R: B.CL.168 Rep 5

description: Suckled from dam breed CL


title: B121-L5: B.LF.000 Rep 4

description: Suckled from dam breed LF


title: B30-L11: B.CL.168 Rep 2

description: Suckled from dam breed CL


title: B35-L15: B.CL.168 Rep 3

description: Suckled from dam breed CL


title: B135-L6: B.CL.168 Rep 1

description: Suckled from dam breed CL


title: B94-L2: B.CL.072 Rep 7

description: Suckled from dam breed CL


title: B101-L14: B.LF.000 Rep 1

description: Suckled from dam breed LF


title: B54-L4: B.CL.072 Rep 6

description: Suckled from dam breed CL


title: B49-L2: B.CL.072 Rep 5

description: Suckled from dam breed CL


title: S31_No.f12

description:
COPD patient
SAMPLE 31


title: S30_Yes.f12

description:
COPD patient
SAMPLE 30


title: S26_No.sb

description:
COPD patient
SAMPLE 26


title: S32_No.f12

description:
COPD patient
SAMPLE 32


title: S34_No.sb

description:
COPD patient
SAMPLE 34


title: S29_No.f12

description:
COPD patient
SAMPLE 29


title: S25_Yes.f12

description:
COPD patient
SAMPLE 25


title: S22_Yes.sb

description:
COPD patient
SAMPLE 22


title: B39-L6: B.CL.072 Rep 4

description: Suckled from dam breed CL


title: S24_No.f12

description:
COPD patient
SAMPLE 24


title: B34-L16R: B.CL.072 Rep 3

description: Suckled from dam breed CL


title: B29-L9: B.CL.072 Rep 2

description: Suckled from dam breed CL


title: S28_No.f12

description:
COPD patient
SAMPLE 28


title: B134-L13: B.CL.072 Rep 1

description: Suckled from dam breed CL


title: S27_Yes.sb

description:
COPD patient
SAMPLE 27


title: B48-L6: B.CL.048 Rep 5

description: Suckled from dam breed CL


title: B53-L8: B.CL.048 Rep 6

description: Suckled from dam breed CL


title: B38-L3: B.CL.048 Rep 4

description: Suckled from dam breed CL


title: S19_No.f12

description:
COPD patient
SAMPLE 19


title: B28-L11: B.CL.048 Rep 2

description: Suckled from dam breed CL


title: B93-L5R: B.CL.048 Rep 6

description: Suckled from dam breed CL


title: B133-L15: B.CL.048 Rep 1

description: Suckled from dam breed CL


title: B91-L9: B.CL.000 Rep 7

description: Suckled from dam breed CL


title: B51-L1: B.CL.000 Rep 6

description: Suckled from dam breed CL


title: B46-L7: B.CL.000 Rep 5

description: Suckled from dam breed CL


title: B36-L12: B.CL.000 Rep 4

description: Suckled from dam breed CL


title: B31-L1: B.CL.000 Rep 3

description: Suckled from dam breed CL


title: B33-L16: B.CL.048 Rep 3

description: Suckled from dam breed CL


title: B131-L8: B.CL.000 Rep 1

description: Suckled from dam breed CL


title: B26-L12: B.CL.000 Rep 2

description: Suckled from dam breed CL


title: S21_Yes.f12

description:
COPD patient
SAMPLE 21


title: S23_No.sb

description:
COPD patient
SAMPLE 23


title: S17_Yes.sb

description:
COPD patient
SAMPLE 17


title: S15_No.f12

description:
COPD patient
SAMPLE 15


title: S8_Yes.f12

description:
COPD patient
SAMPLE 8


title: S16_No.f12

description:
COPD patient
SAMPLE 16


title: S6_No.sb

description:
COPD patient
SAMPLE 6


title: S18_Yes.sb

description:
COPD patient
SAMPLE 18


title: S14_Yes.sb

description:
COPD patient
SAMPLE 14


title: KO (MoGene-2_0-st) 3

city: Tianjin

first: Xiaoming

last: Feng

address: 288 Nanjing Road

institute: Institute of Hematology and Hospital of Blood Disease, Chinese Academy of Medical Sciences

description: KO (MoGene-2_0-st) 3

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

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

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

source_name: DCs sorted from spleen of Cd11cCreLkb1f/f  mice

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

growth_protocol: Lkb1f/f mice were crossed with Cd11cCre mice to generate Cd11cCreLkb1f/f,

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

treatment_protocol: DCs were sorted from spleen of Lkb1f/f mice, LPS-treated mice (overnight), Cd11cCreLkb1f/f mice, and placed on ice in the Trizol solution (GibcoBRL).

tag: strain background

tag: age

value: spleen

value: dendritic cells (DCs)


title: Control_(MoGene-2_0-st)

source_name: DCs sorted from spleen of C57BL/6 mice

value: wild type


title: S3_No.f12

description:
COPD patient
SAMPLE 3


title: WT (MoGene-2_0-st) 3

description: WT (MoGene-2_0-st) 3

source_name: DCs sorted from spleen of Lkb1f/f mice


title: S13_No.sb

description:
COPD patient
SAMPLE 13


title: S7_Yes.f12

description:
COPD patient
SAMPLE 7


title: LPS_(MoGene-2_0-st)

source_name: DCs sorted from spleen of C57BL/6 mice treated with LPS over night

value: LPS


title: S1_Yes.sb

description:
COPD patient
SAMPLE 1


title: S4_No.sb

description:
COPD patient
SAMPLE 4


title: WT (MoGene-2_0-st) 1

description: WT (MoGene-2_0-st) 1


title: S10_No.sb

description:
COPD patient
SAMPLE 10


title: S20_Yes.f12

description:
COPD patient
SAMPLE 20


title: S11_Yes.f12

description:
COPD patient
SAMPLE 11


title: S5_Yes.sb

description:
COPD patient
SAMPLE 5


title: KO (MoGene-2_0-st) 1

description: KO (MoGene-2_0-st) 1


title: S9_No.sb

description:
COPD patient
SAMPLE 9


title: KO (MoGene-2_0-st) 2

description: KO (MoGene-2_0-st) 2


title: WT (MoGene-2_0-st) 2

description: WT (MoGene-2_0-st) 2


title: S2_Yes.sb

description:
COPD patient
SAMPLE 2


title: S12_Yes.f12

description:
COPD patient
SAMPLE 12


title: HEL-iMKL1 Dox+TPA treated cells rep2

city: New Haven

first: Vince

last: Schulz

state: CT

address: 333 Cedar St. LMP 4085

department: Department of Pediatrics

institute: Yale University

description:
Krause_SRF_RNAseq_RPKM.txt
Krause_SRF_RNAseq_ReadCount.txt

data_processing:
RNA-sequencing reads were mapped to the hg19 human genome using TopHat2 (version 2.0.13)  utilizing UCSC genome database refFlat transcript information.
Reads were counted for each human gene using Rsubread featureCounts, with default parameters.
Differentially expressed genes were identified using the EdgeR package (version 3.14.0). Genes with less than two samples with more than 1 count per million reads were excluded from analysis.  Normalization factors were calculated using the trimmed mean of M-values method. EdgeR was used to estimate common dispersion, trended dispersions, and tagwise dispersions, and then to identify differentially expressed genes using the generalized linear model likelihood ratio test.
Reads Per Kilobase of transcript per Million mapped reads (RPKM) values from Trimmed Mean of M-values (TMM) normalized read counts were obtained using the EdgeR package, and the values of replicate biological replicates were averaged for heatmaps and other analysis.  Exploratory data and quality control analysis was performed using principal components, multidimensional scaling and hierarchical clustering analysis.
Genome_build: hg19
Supplementary_files_format_and_content: Read count per gene. RPKM with trimmed median of means normalization

source_name: HEL-iMKL1 cells

growth_protocol: HEL cells were cultured in RPMI with 10% Tet-free FBS, supplemented with L-glutamine and Pen/Strep. Cultures were maintained at a confluence of 0.5-2million cells per ml. Cells were always incubated in a 37degrees Celsius incubator with 5% CO2.

extract_protocol:
RNA was extracted with Trizol. The RNA layer was then purified using the RNeasy Mini Kit columns from Qiagen (Hilden, Germany). RNA was eluted in a total of 20µl TE buffer, and quantified using a standard Nanodrop device.
Single-end RNA libraries were prepared for sequencing using standard Illumina protocols at the Yale Stem Cell Center Genomics Core

treatment_protocol: HEL cells were either left untreated, or treated with 10ng/ml of Doxycycline for 24 hours, or treated with 15nM TPA for 24 hours, or treated with both Dox and TPA (same concentrations as before) for 24 hours.

value: Treated with 10ng/ml Dox & 15nM TPA for 24 horus

tag: mkl overexpression

value: Overexpressed

tag: tpa treatment

value: TPA


title: HEL-iMKL1 TPA treated cells rep1

value: Treated with 15nM TPA for 24 hours

value: Not overexpressed


title: HEL-iMKL1 TPA treated cells rep2


title: HEL-iMKL1 Dox+TPA treated cells rep1


title: HEL-iMKL1 Dox treated cells rep2

value: Treated with 10ng/ml Dox for 24 hours

value: No TPA


title: HEL-iMKL1 untreated cells rep1

value: No treatment


title: HEL-iMKL1 Dox treated cells rep1


title: HEL-iMKL1 untreated cells rep2


title: HEL-iMKL1 TPA treated cells input rep2

data_processing:
ChIP-sequencing reads were mapped to the hg19 human genome using Bowtie version 1.1.2 and parameters -m 1 -v 3 --best –strata. Reads mapping to the ENCODE project blacklist of repetitive regions were removed .
Regions of SRF binding were identified using the MACS2 version 2.1.0.20150420 software and a matched total input control using default parameters. Read counts for enriched regions in all samples were obtained using the DiffBind version 2.0.7 package with DESEQ2 normalization utilizing read counts in analyzed regions (parameter: bFullLibrarySize=FALSE). Statistically significant differentially bound regions were identified by DiffBind using the DESEQ2 method with default parameters.
Genome_build: hg19
Supplementary_files_format_and_content: bigwig and narrowPeak

extract_protocol:
Cells were first fixed in 1% formaldehyde with shaking for 10 minutes at room temperature. After PBS wash, they were sonicated at 4degrees Celsius in a BioRuptor, to obtain 200-300bp fragment sizes. They were pre-cleaned by incubating with Millipore Protein A Salmon-Sperm DNA coated beads, with shaking for 1 hour at 4degrees Celsius. Fixed chromatin was then incubated overnight with either anti-SRF or anti-IgG antibody, followed by 1-hour incubation with coated beads the following morning. DNA was eluted from the beads using high to low salt solutions, with the final elute in freshly made Tris-EDTA (TE) buffer. The DNA was then treated with Proteinase K and reverse cross-linked with 5M NaCl, before being sent for sequencing.
Single end DNA libraries were prepared for sequencing using standard Illumina protocols at the Yale Stem Cell Center Genomics Core

tag: ChIP

value: Total Input Control


title: HEL-iMKL1 untreated cells ChIP rep1

value: SRF


title: HEL-iMKL1 Dox+TPA treated cells input rep2


title: HEL-iMKL1 TPA treated cells ChIP rep1


title: HEL-iMKL1 untreated cells input rep1


title: HEL-iMKL1 Dox+TPA treated cells input rep1


title: HEL-iMKL1 Dox+TPA treated cells ChIP rep1


title: HEL-iMKL1 TPA treated cells ChIP rep2


title: HEL-iMKL1 Dox treated cells input rep1


title: HEL-iMKL1 TPA treated cells input rep1


title: HEL-iMKL1 Dox treated cells ChIP rep2


title: HEL-iMKL1 untreated cells ChIP rep2


title: CD63+ cells from DDC injury_rep3

city: Shanghai

first: Kunshan

last: Zhang

address: 389 Xincun Road

department: Stem cell Translational Research center

institute: Tongji Hospital, Tongji University

hyb_protocol: The Labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000. 1 μg of each labeled cRNA was fragmented by adding 11 μl 10 × Blocking Agent and 2.2 μl of 25×Fragmentation Buffer, then heated at 60 °C for 30 min, and finally 55 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 100 μl of hybridization solution was dispensed into the gasket slide and assembled to the gene expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2505C).

data_processing: Raw data were normalized by the quantile normalization method using the ‘‘normalizeBetweenArrays’’ function in the LIMMA

source_name: Adult mouse liver

label_protocol: Sample labeling and array hybridization were performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology). Briefly, total RNA from each sample was linearly amplified and labeled with Cy3-UTP.

growth_protocol: Sorted cells were cultured in our stem cell cultured medium named ScmA by supplemented with 10% fetal bovine serum (HyClone), 1% penicillin/streptomycin, 0.1 mmol/l 2-mercaptoethanol (both from GIBCO), 10 ng/ml HGF, 10 ng/ml EGF (both from R&D Systems), insulin-transferrin-selenium (ITS), 10-7 mol/l dexamethasone, 10 ng/ml nicotinamide, and 50 mg/ml gentamicin (all from Sigma-Aldrich) in DMEM/F12 (Gibco)

extract_protocol: Total RNA was extracted using Trizol reagent (Invitrogen). RNA quantity and quality were measured by NanoDrop ND-1000. RNA integrity was assessed by standard denaturing agarose gel electrophoresis.The Whole Mouse Genome Oligo Microarray was a broad view that represents all known genes and transcripts in the mouse genome. Sequences were compiled from a broad source survey, and then verified and optimized by alignment to the assembled mouse genome.

treatment_protocol: Cultre medium ScmA was added with growth factor VEGF and bFGF in the P6, P7 and P9 group

tag: liver injury

value: DDC induced liver injury


title: CD63+ cells from non-injury_rep1

value: no Injury


title: HEL-iMKL1 Dox treated cells input rep2


title: HEL-iMKL1 Dox treated cells ChIP rep1


title: CD63+ cells from non-injury_rep3


title: CD63+ cells from non-injury_rep2


title: CD63+ cells from DDC injury_rep2


title: CD63+ cells from DDC injury_rep1


title: HEL-iMKL1 untreated cells input rep2


title: U2OS input

city: München

first: Caroline

last: Friedel

address: Amalienstr. 17

department: Institut für Informatik

institute: Ludwig-Maximilians-Universität München

data_processing:
Raw sequencing reads were aligned to the human genome (GRCh38) using BWA.
Sequence reads with an alignment score < 30 for paired-end reads and <20 for single-end reads were discarded
Peak calling was performed using GEM in GPS mode and with a q-value cutoff of 0.01
Genome_build: GRCh38
Supplementary_files_format_and_content: BED

source_name: U2OS cells

growth_protocol: U2OS osteosarcoma cells were cultured in Dulbecco's modified Eagle's medium (DMEM, Gibco) and Raji B-cells in RPMI 1640 medium (Gibco) supplemented with 10% fetal calf serum (FCS, Bio&Sell), 2 mM L-glutamine (Gibco), 100 U/mL penicillin (Gibco), and 100 µg/mL streptomycin (Gibco) at 37°C at 8% or 5% CO2, respectively.

extract_protocol:
Chromatin immunoprecipitation for ChIP-seq: Cells were crosslinked using a formaldehyde containing solution (10mM NaCl, 0,1mM EDTA pH 8, 0,05mM EGTA pH 8, 5mM HEPES pH 7.8 and 1% formaldehyde) for 10 minutes at 20°C, the reaction was quenched by the addition of glycin to a final concentration of 250uM for 5 minutes. Crosslinked cells were collected and washed twice with PBS before snap freezing in liquid nitrogen and storage at -80°C until subsequent use. Prior to sonication, the crosslinked cells were resuspended in lysis buffer (50mM Hepes pH 7.5, 140mM NaCl, 1mM EDTA pH 8, 10% glycerol, 0.75% NP-40, 0.25% Triton X-100, 1X protease inhibitor cocktail) at 4°C for 20 minutes. Nuclei were collected by centrifugation and washed in a second buffer (200mM NaCl, 1mM EDTA pH 8, 0.5mM EGTA pH 8, 10mM Tris pH 8, 1X protease inhibitor cocktail) for 10 minutes at 4°C then collected by centrifugation and resuspended in the shearing buffer (1mM EDTA pH 8, 0.5mM EGTA pH 8, 10mM Tris pH 8, 100mM NaCl, 0.1% Na-Deoxycholate, 0.5% N-lauroylsarcosine, 1X protease inhibitor cocktail). Sonication was carried out in a Bioruptor Pico ultrasounds water bath (Diagenode B01060001) for 30 cycles of 30 sec ON and 30 sec OFF pulses in 4°C water. Sonicated extracts were centrifuged at high speed in the presence of 0,1% of Triton X-100 and snap frozen in liquid nitrogen then stored at -80°C until subsequent use. Prior to ChIP, the ZNF768 mAb was coupled to protein-G coated magnetic beads (Dynabeads, life technologies) by incubation in 0,5% BSA PBS overnight at 4°C. Pre-coated beads were then washed and incubated with the sonicated chromatin extracts, the ChIP was carried out overnight at 4°C on a rotating wheel. The equivalent of 10 × 107 cells sonicated extract was used for each ZNF ChIP experiment for both cell lines. After incubation, the beads were washed 7 times with Wash buffer (50mM Hepes pH 7.6, 500mM LiCl, 1mM EDTA pH 8, 1% NP-40, 0.7% Na-Deoxycholate, 1X protease inhibitor cocktail) followed by one wash with TE-NaCl buffer (10mM Tris pH 8 and 1mM EDTA pH 8, 50mM NaCl). Immunoprecipitated chromatine was eluted by two sequential incubations with 100µl Elution buffer (50mM Tris pH 8, 10mM EDTA pH 8, 1% SDS) at 65°C for 15 minutes. The two eluates were pooled and incubated at 65°C for 12 hours to reverse-crosslink the chromatin followed by treatment with RNase A (0.2µg/mL) at 37°C for two hours and Proteinase K (0.2µg/mL) at 55°C for two hours. The DNA was isolated by phenol:chloroform: isoamylalcohol (25:24:1 pH 8) extranction followed by Qiaquick PCR Purification (Qiagen, Germany) and quantified with Qubit DS DNA HS Assay (ThermoFisher Scientific, USA).
At least 1ng of ChIP DNA was used to prepare sequencing library with Illumina ChIP Sample Library Prep Kit (Illumina, USA) with a few optimizations to the protocol. The ChIP DNA was size selected using Ampure beads (Life technologies) to enrich for fragments < 400Bp prior to end-repair, 3’end adenylation and adapter ligation. Library fragments were then directly amplified by 10 cycles of PCR.

tag: chip antibody

value: no antibody


title: U2OS ZNF768 ChIP-seq (rep. 1)

value: ZNF768 mAb 7D6


title: Raji input

source_name: Raji cells


title: U2OS ZNF768 ChIP-seq (rep. 2)


title: HEL-iMKL1 Dox+TPA treated cells ChIP rep2


title: Raji ZNF768 ChIP-seq (rep. 2)


title: Raji ZNF768 ChIP-seq (rep. 1)


title: Smchd1GFP/GFP No Crosslink 3

city: Parkville

first: Marnie

last: Blewitt

state: Victoria

address: 1G Royal Parade

country: Australia

institute: Walter and Eliza Hall Institute

description:
PAR-CLIP library
Smchd1GFP_PARCLIP_clusters.txt

data_processing:
Base calling using Real-Time Analysis v2.4.6
Demultiplexing and fastq.gz file generation and de-multiplexing using bcl2fastq conversion software v2.15.0.4
Tophat v2.1.0 (--read mismatches 5 --read-edit-dist 5)
PARalyzer v1.5 was used to call PAR-CLIP clusters
Genome_build: mm10
Supplementary_files_format_and_content: a text file containing coordinates and reads for PARalyzer clusters called on Smchd1-GFP PAR-CLIP samples

source_name: Neural stem cells

growth_protocol: Neural stem cells were generated from Smchd1GFP/GFP or Smchd1+/+ E14.5 embryos, as previously described (Chen et al., 2015 PNAS).

extract_protocol:
Cells were scraped from the tissue culture plate, and put stright into the PAR-CLIP library construction protocol.
Libraries were prepared according to Hafner et al., Cell, (2010).

treatment_protocol: Cells were treated with 100µM 4-thiouridine for 24-hours, then irradiated with 0.15J/cm2 light at 365nm before being harvested for RNA extraction.

tag: strain

tag: Sex

value: Female

tag: genotype


title: Smchd1GFP/GFP No Crosslink 4


title: Smchd1+/+ 3


title: Smchd1GFP/GFP No Crosslink 1


title: Smchd1+/+ 4


title: Smchd1+/+ 2


title: Smchd1GFP/GFP No Crosslink 2


title: A375-G10, catalase transfected, biological rep3

city: San Martín

first: Hebe

last: Durán

state: Buenos Aires

address: Av. Gral. Paz 1499

department: Departamento de Micro y Nanotecnología

country: Argentina

institute: Comisión Nacional de Energía Atómica

description: Gene expression data from A375 human melanoma cells transfected with pcDNA3 containing cDNA of human catalase, clone G10

hyb_protocol: Hybridisation during 16 h at 45ºC on Affymetrix Human Genome Chip (GeneChip® Human Gene 1.0 ST) was performed.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.

data_processing: The data were analysed by using the R programming language (2.12.0) and different tools of Bioconductor. Background correction and normalization of data were performed by Robust Multi-array Average (rma) both for probe set and core. Differential gene expression was evaluated by Limma package (Linear Models for Microarray Data).

source_name: A375 cells transfected with catalase, clone G10

label_protocol: Biotin-labeled cRNA was generated following the standard Affymetrix protocol from 5 mg total RNA samples (500 ng/ml)

growth_protocol: Cells were cultured in Dulbecco's Modified Eagle Medium-Ham-F12 (DMEM/F-12) 1:1 supplemented with ascorbic acid (17.6 mg/ml), pyruvic acid (150 mg/ml), galactose (300 mg/ml), insulin (5 mg/ml), fetal bovine serum (10%), penicillin (50 U/ml) and streptomycin (50 mg/ml). Cells were grown at 37ºC in a humidified atmosphere with 5%CO2. Stable transfected cells were grown in presence of geneticin (700 µg/ml).

extract_protocol: Total RNA were isolated from cultured cells using RNAspin Mini RNA Isolation Kit (GE Healthcare), following manufacturer instructions. RNA quantity and quality were determined by NanoDrop2000 photometer (Thermo). RNA integrity was assessed evaluating the 2:1 ratio of 28S:18S bands in 1% agarose gel electrophoresis.

treatment_protocol: A375 cells were transfected with pcDNA3 vector harboring the human catalase cDNA using Lipofectamine 2000 (Invitrogen). Stable transfectants were selected in medium with 1500 µg/ml geneticin. The resistant clones A375-A7 and A375-G10 were obtained by clonal dilution. Non transfected A375 cells and transfected cells with empty vector were used as negative control (A375-PCDNA3). Cells were cultured until subconfluence for total RNA extraction.

value: human melanoma


title: A375-G10, catalase transfected, biological rep2


title: A375-G10, catalase transfected, biological rep4


title: Smchd1+/+ 1


title: A375-A7, catalase transfected, biological rep1

description: Gene expression data from A375 human melanoma cells transfected with pcDNA3 containing cDNA of human catalase, clone A7

source_name: A375 cells transfected with catalase, clone A7


title: A375-G10, catalase transfected, biological rep1


title: A375-A7, catalase transfected, biological rep2


title: A375, control, biological rep2

description: Gene expression data from A375 human melanoma cells

source_name: A375 cells


title: A375-A7, catalase transfected, biological rep4


title: Healthy control (off season) [264]

city: Munich

first: Ulrich

middle: M

last: Zissler

address: Biedersteiner Str. 29

department: Center of Allergy & Environment (ZAUM)

institute: Technical University of Munich & Helmholtz Center Munich

description:
264
ex-vivo brushing

hyb_protocol: 0.6 ug of Cy3-labelled cRNA (specific activity >6.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25µl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer's instructions. On completion of the fragmentation reaction, 25µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3µm, Dye channel is set to Green and 20 bit Tiff).

data_processing: The scanned images were analyzed with Feature Extraction Software 11.0.1.1 (Agilent) using default parameters (protocol GE1_1100_Jul11 and Grid: 072363_D_F_20150612) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded. Agilent.SingleColor.28004 microarray, Software GeneSpring 14.5; Threshold: 1.0, Logbase: 2; Normalization: Quantile; Baseline Transformation: None; Filtered on Expression (20.0-100.0); Filtered on Flags (Detected, Not Detected); T test unpaired , P<=:0.05, FC>=1.5.

source_name: nasal brushing

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 17 ng RNA using the One-Color Agilent Low Input Quick Amp Labeling Kit (Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN, Hilden, GER). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Freshly brushed cells were directly transferred into RNAcell protect reagent (Qiagen) and stored at -80°C until RNA extraction. Total RNA was extracted using RNeasy Mini Kit (Cat.-No. 74104, Qiagen, Hilden, Germany) with on-column DNase digestion (Cat.-No. 79254, DNase-Free DNase Set, Qiagen) for avoiding DNA contaminations {Zissler, 2016 #317}. RNA quantification was performed by ultraviolet–visible spectrophotometry (Nanodrop Technologies, Wilmington, DE, USA), for assessment of the RNA integrity by the RNA 6000 Nano Chip Kit with the Agilent 2100 Bioanalyzer (Agilent Technologies, Waldbronn, Germany).

value: nasal brushing

tag: disease status

value: healthy

tag: grass pollen season

value: off season

tag: ait treatment

value: no

tag: patient id


title: A375, control, biological rep3


title: A375, control, biological rep4


title: A375-PCDNA3, control, biological rep4

description: Gene expression data from A375 human melanoma cells transfected with pcDNA3 vector

source_name: A375 cells transfected with pcDNA3 vector


title: A375-PCDNA3, control, biological rep1


title: Allergic Rhinitis [151e]

description:
151e
ex-vivo brushing

tag: tissue

value: allergic rhinitis

value: yes

tag: timepoint

value: 6h after last topdose (T4)


title: Smchd1GFP/GFP 4


title: F114#1_3_A8918

city: Bethesda

first: Timothy

middle: G

last: Myers

state: MD

address: 50 South Drive, Room 5509

department: Research Technologies Branch

institute: National Institute of Allergy and Infectious Diseases

description: spleen RNA 24 hr post infection with strain F114#1,mouse replicate 3, RNAsampleID=A8918

scan_protocol: Standard Illumina scanning protocol using HiScan-SQ

data_processing: Raw data filtered to include only probes detected in at least two arrays, using the detection_pvalue parameter output from Genome Studio, cutoff is 0.1; Each array normalized using quantile normalization of bead_average intensity, performed using JMP/Genomics software.

source_name: spleen

label_protocol: Biotinylated cRNA were prepared with the Ambion TotalPrep kit for Illumina arrays

growth_protocol: Inbred female C57BL/6 mice, aged 6–8 weeks, were purchased from Charles River Laboratory.

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyzer or TapeStation.

treatment_protocol: An inoculum containing 10×106 iRBC suspended in 100 ml of phosphate-buffered saline, pH 7.4, from donor mice was injected intravenously into each experimental C57BL/6 mouse to initiate infection. Naive mice receiving an equivalent number of uninfected RBCs served as a negative control group. Three to six mice as a group were infected with each parasite, and parasitemia were monitored by microscopic examination of Giemsa-stained thin tail blood smears.

value: spleen

value: female

tag: parasite strain

tag: replicate mouse

tag: rna sample id


title: Allergic Rhinitis [23k]

description:
23k
ex-vivo brushing

value: after three years of AIT (T9)


title: A375-PCDNA3, control, biological rep2

tag: cell line

tag: cell type


title: Smchd1GFP/GFP 3


title: Smchd1GFP/GFP 2


title: A375-PCDNA3, control, biological rep3


title: IL-10-producing CD4 T cells

city: Chicago

first: Weiguo

last: Cui

state: IL

address: 303 E Chicago Ave

department: Pathology

institute: Northwestern University

data_processing:
Demultiplexing was performed using the mkfastq function in Cell Ranger (version 1.3.1) (10x Genomics)
Alignment and generation of gene-barcode matrix was performed using the count function in Cell Ranger (version 1.3.1) (10x Genomics)
Genome_build: mm10
Supplementary_files_format_and_content: barcodes.tsv, genes.tsv, and matrix.mtx: filtered gene-barcode matrix in MEX format

extract_protocol:
IL-10-producing (Thy1.1+) CD4 T cells were sorted by flow cytometry, then single cell libraries were prepared according the the 10x Genomics Chromium Single Cell 3' Reagent Kit protocol.
IL-10-producing (Thy1.1+) CD4 T cells were sorted by flow cytometry, then single cell libraries were prepared according the the 10x Genomics Chromium Single Cell 3' Reagent Kit protocol.

tag: strain background

tag: genotype/variation

value: 10BiT IL-21-tRFP

tag: time point

value: day 16 p.i. with LCMV Cl13

value: CD4 T cell

tag: cell subset


title: Allergic Rhinitis [23a]

description:
23a
ex-vivo brushing

value: baseline (T0)


title: A375-A7, catalase transfected, biological rep3


title: Tfh_IL21IL10_DP_2

data_processing:
Reads were aligned to the mouse reference genome (mm9) using Tophat (version 2.1.1)
Expression values for each gene were quantified and differential gene expression analysis was carried out using Cuffdiff (Cufflinks version 2.2.2)
Genome_build: mm9
Supplementary_files_format_and_content: genes.read_group_tracking contains the FPKM values for each gene in each replicate

extract_protocol:
Splenic CD4 T cells from 10Bit IL-21-tRFP mice on day 18 p.i. with LCMV Cl13 were sorted for each of the three groups (naive, Tfh IL21+ IL10-, Tfh IL21+ IL10+) directly into lysis buffer (Picelli et al., Nature Protocols 2014). About 500 cells were used per sample
Libraries were constructed using Smart-seq2 protocol (Picelli et al, Nature Protocols 2014)

value: day 18 p.i. with LCMV Cl13

value: Tfh IL-21+ IL-10+ double producers (CD44hi CXCR5+ PD-1hi tRFP+ Thy1.1+)


title: A375, control, biological rep1

value: human melanoma


title: Allergic Rhinitis [21e]

description:
21e
ex-vivo brushing

value: nasal brushing


title: G055#3_1_A8913

description: spleen RNA 24 hr post infection with strain G055#3,mouse replicate 1, RNAsampleID=A8913

tag: Sex

tag: strain


title: Tfh_IL21IL10_DP_1


title: Smchd1GFP/GFP 1

value: Female

tag: genotype


title: Tfh_IL21_SP_3

value: Tfh IL-21+ single producers (CD44hi CXCR5+ PD-1hi tRFP+ Thy1.1-)


title: Allergic Rhinitis [20k]

description:
20k
ex-vivo brushing

tag: disease status


title: F114#1_1_A8916

description: spleen RNA 24 hr post infection with strain F114#1,mouse replicate 1, RNAsampleID=A8916


title: Allergic Rhinitis [20a]

description:
20a
ex-vivo brushing

tag: ait treatment

value: no


title: F114#1_2_A8917

description: spleen RNA 24 hr post infection with strain F114#1,mouse replicate 2, RNAsampleID=A8917


title: Allergic Rhinitis [20e]

description:
20e
ex-vivo brushing

value: allergic rhinitis

tag: patient id


title: N67_1_A8952_4

description: spleen RNA 24 hr post infection with strain N67,mouse replicate 1, RNAsampleID=A8952

tag: tissue


title: F117#2_1_A8910

description: spleen RNA 24 hr post infection with strain F117#2,mouse replicate 1, RNAsampleID=A8910


title: G055#3_2_A8914

description: spleen RNA 24 hr post infection with strain G055#3,mouse replicate 2, RNAsampleID=A8914


title: F117#2_2_A8911

description: spleen RNA 24 hr post infection with strain F117#2,mouse replicate 2, RNAsampleID=A8911


title: naive_1_A8955_4

description: spleen RNA 24 hr post infection with strain naive,mouse replicate 1, RNAsampleID=A8955

value: naive


title: Allergic Rhinitis [155a]

description:
155a
ex-vivo brushing

tag: timepoint


title: Allergic Rhinitis [155k]

description:
155k
ex-vivo brushing

value: yes


title: Tfh_IL21_SP_2


title: F239#4_2_A8944

description: spleen RNA 24 hr post infection with strain F239#4,mouse replicate 2, RNAsampleID=A8944

value: spleen

tag: parasite strain


title: F239#4_1_A8943

description: spleen RNA 24 hr post infection with strain F239#4,mouse replicate 1, RNAsampleID=A8943

value: female

tag: replicate mouse


title: Tfh_IL21_SP_1


title: G055#3_3_A8915

description: spleen RNA 24 hr post infection with strain G055#3,mouse replicate 3, RNAsampleID=A8915

tag: rna sample id


title: F239#4_3_A8945

description: spleen RNA 24 hr post infection with strain F239#4,mouse replicate 3, RNAsampleID=A8945


title: F117#2_3_A8912

description: spleen RNA 24 hr post infection with strain F117#2,mouse replicate 3, RNAsampleID=A8912


title: Naive_3

source_name: Naive

value: Naive (CD44lo)


title: F996#5_2_A8941

description: spleen RNA 24 hr post infection with strain F996#5,mouse replicate 2, RNAsampleID=A8941


title: F245#1_1_A8937

description: spleen RNA 24 hr post infection with strain F245#1,mouse replicate 1, RNAsampleID=A8937


title: F996#5_3_A8942

description: spleen RNA 24 hr post infection with strain F996#5,mouse replicate 3, RNAsampleID=A8942


title: Naive_1

value: 10BiT IL-21-tRFP


title: Naive_2


title: Allergic Rhinitis [15k]

description:
15k
ex-vivo brushing

value: after three years of AIT (T9)


title: N67_1_A8952_3


title: F996#5_1_A8940

description: spleen RNA 24 hr post infection with strain F996#5,mouse replicate 1, RNAsampleID=A8940


title: F245#1_2_A8938

description: spleen RNA 24 hr post infection with strain F245#1,mouse replicate 2, RNAsampleID=A8938


title: Allergic Rhinitis [15e]

description:
15e
ex-vivo brushing

value: 6h after last topdose (T4)


title: 17XNL_1_A8949_3

description: spleen RNA 24 hr post infection with strain 17XNL,mouse replicate 1, RNAsampleID=A8949


title: Allergic Rhinitis [15a]

description:
15a
ex-vivo brushing

value: baseline (T0)


title: naive_1_A8955_3


title: F245#1_3_A8939

description: spleen RNA 24 hr post infection with strain F245#1,mouse replicate 3, RNAsampleID=A8939


title: Allergic Rhinitis [14k]

description:
14k
ex-vivo brushing


title: G001#4_3_A8936

description: spleen RNA 24 hr post infection with strain G001#4,mouse replicate 3, RNAsampleID=A8936


title: 17XNL_1_A8949_4


title: G001#4_1_A8934

description: spleen RNA 24 hr post infection with strain G001#4,mouse replicate 1, RNAsampleID=A8934


title: Allergic Rhinitis [14e]

description:
14e
ex-vivo brushing


title: Allergic Rhinitis [155e]

description:
155e
ex-vivo brushing


title: G013#3_3_A8933

description: spleen RNA 24 hr post infection with strain G013#3,mouse replicate 3, RNAsampleID=A8933


title: Healthy control (off season) [267]

description:
267
ex-vivo brushing

value: healthy

tag: grass pollen season

value: off season


title: G013#3_1_A8931

description: spleen RNA 24 hr post infection with strain G013#3,mouse replicate 1, RNAsampleID=A8931


title: G013#3_2_A8932

description: spleen RNA 24 hr post infection with strain G013#3,mouse replicate 2, RNAsampleID=A8932


title: F996#1_3_A8930

description: spleen RNA 24 hr post infection with strain F996#1,mouse replicate 3, RNAsampleID=A8930


title: G001#4_2_A8935

description: spleen RNA 24 hr post infection with strain G001#4,mouse replicate 2, RNAsampleID=A8935


title: essential thrombocythemia, biological rep1

city: Aachen

first: Bernd

last: Denecke

state: NRW

address: Pauwelsstrasse 30

department: IZKF Aachen

institute: RWTH Aachen University

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials according to the manufacturers instructions: hybridization 45°C for 16 hours at 60 rpm; Fluidics Station Program FS_450_0001

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G.

data_processing: Raw image data were analysed with Affymetrix® Expression Console™ Software (Affymetrix, USA), and gene expression intensities were normalized and summarized with SST robust multiarray average algorithm (Affymetrix): SST-RMA. Further analyses was performed using the Transcriptome Analysis Console (TAC) Software of Affymetrix.

source_name: MPN patients

label_protocol: Fragmented, biotinylated cDNAs were prepared from 6.6 ng total RNA using  the Affymetrix WT Pico Reagent Kit according to the manufacturers instructions.

extract_protocol: Blood and bone marrow mononuclear cells from MPN patients were isolated using Ficoll density gradient centrifugation. Enrichment of the CD34+ cell population was performed by magnetic cell separation (MACS) with the CD34 MicroBead Kit, human (Miltenyi). RNA was isolated using the RNeasy Micro Kit (QIAGEN).

tag: disease state

value: essential thrombocythemia

tag: cell type

value: CD34+ BMMCs

value: bone marrow

value: JAK2V617F positive


title: Allergic Rhinitis [186e]

description:
186e
ex-vivo brushing

value: nasal brushing


title: Healthy control (off season) [265]

description:
265
ex-vivo brushing

value: no


title: N67_3_A8954_3

description: spleen RNA 24 hr post infection with strain N67,mouse replicate 3, RNAsampleID=A8954


title: post-PV-myelofibrosis, biological rep2

value: post-PV-myelofibrosis


title: F996#1_2_A8929

description: spleen RNA 24 hr post infection with strain F996#1,mouse replicate 2, RNAsampleID=A8929


title: naive_3_A8957_3

description: spleen RNA 24 hr post infection with strain naive,mouse replicate 3, RNAsampleID=A8957

value: naive


title: EUHSR Rapamycin (4h, ECM33i overexpression)

city: Cambridge

first: Jeffrey

middle: T

last: Morgan

address: 455 Main Street

institute: Whitehead Institute

data_processing:
Reads were trimmed of adaptor sequence using cutadapt (v1.8) (5prime adaptor: 5 GTTCAGAGTTCTACAGTCCGACGATCNNNNNNNN 3; 3prime adaptor: 5 TCGTATGCCGTCTTCTGCTTGddC 3). See http://bartellab.wi.mit.edu/protocols.html for further adaptor information. Trimmed shorter than 10 nucleotides were discarded.
Trimmed reads were aligned to the S. cerevisiae genome (R64-1-1, downloaded from www.yeastgenome.org) using STAR (v2.4) with the parameters “--alignIntronMax 1000 --sjdbOverhang 31 --outSAMtype BAM SortedByCoordinate --quantMode GeneCounts” and with “--sjdbGTFfile” supplied with transcript annotations. Intron annotations were constructed from the UCSC Genome browser and the Ares lab yeast intron database (http://intron.ucsc.edu/yeast4.3/).
TPMs were calculated based on reads mapping to mRNAs, spliceosomal introns, and SNR17A/B (ncRNAs that contain spliceosomal introns).
Genome_build: sacCer3 (R64-1-1)
Supplementary_files_format_and_content: The processed data files contain abundance measurements for genes and introns

source_name: saccharomyces cerevisiae cells

growth_protocol: Yeast were grown at 30°C and in accordance with standard protocols.

extract_protocol:
All cultures were rapidly harvested by vacuum filtration and flash frozen in liquid nitrogen as described in Weinberg et al., 2016 (GSE53268). Frozen pellets were mechanically lysed using a Sample Prep 6870 Freezer/Mill (Spex SamplePrep; 10 cycles of 2 min on, 2 min off at setting 10). Lysate powder was aliquoted and stored at –80°C.
Total RNA was extracted using TRI Reagent (Ambion) according to the manufacturer’s protocol. rRNA was depleted from 5 μg of total RNA using the Ribo-Zero Gold Yeast rRNA Removal Kit (Illumina) according to the manufacturer’s protocol. RNA was randomly fragmented by partial alkaline hydrolysis and then 27- to 40-nucleotide RNA fragments were size-selected and used for library preparation. RNA-seq libraries were prepared as described in Subtelny et al. 2014 (GSE52809) and sequenced on the Illumina HiSeq platform using 40 bp single reads.

value: BY4741 ecm33-delta-intron ubc4-delta-intron hnt1-delta-intron sac6-delta-intron rfa2-delta-intron

tag: growth condition

value: Culture was seeded at OD600 0.2 from overnight culture, allowed to grow to early log phase (4h), collected by vacuum filtration, resuspended in fresh media supplemented with 100 nM rapamycin, and harvested after 4h.

tag: treatment

value: pre-growth in SC-Ura, growth in SC-Ura+rapamycin (100 nM)


title: EUHSR Rapamycin (4h, ACT1i overexpression)


title: EUHSR Rapamycin (4h)

value: pre-growth in SC, growth in SC+rapamycin (100 nM)


title: WT Saturated (replicate 2)

value: Culture was seeded at OD600 0.2 from overnight cultures (typically OD600 ~6), and was harvested after reaching saturation.

value: SC media


title: F996#1_1_A8928

description: spleen RNA 24 hr post infection with strain F996#1,mouse replicate 1, RNAsampleID=A8928

value: spleen

value: female


title: WT Lawn

value: Culture was seeded at OD600 0.2 from overnight cultures (typically OD600 ~6), and spread on 10-cm plates. Yeast were grown for 3 days until lawn had formed.

value: SC plates


title: WT Log-phase (replicate 2)

value: Culture was seeded at OD600 0.2 from overnight cultures (typically OD600 ~6), and was harvested during early log phase at OD600 0.5.


title: primary myelofibrosis, biological rep10

value: primary myelofibrosis

value: CD34+ BMMCs

value: bone marrow


title: Allergic Rhinitis [186k]

description:
186k
ex-vivo brushing

value: nasal brushing

value: allergic rhinitis

value: yes

value: after three years of AIT (T9)


title: Allergic Rhinitis [186a]

description:
186a
ex-vivo brushing

value: no

value: baseline (T0)


title: F118#4_3_A8927

description: spleen RNA 24 hr post infection with strain F118#4,mouse replicate 3, RNAsampleID=A8927


title: primary myelofibrosis, biological rep5

value: JAK2V617F positive


title: primary myelofibrosis, biological rep7


title: primary myelofibrosis, biological rep1


title: 17XNL_3_A8951_3

description: spleen RNA 24 hr post infection with strain 17XNL,mouse replicate 3, RNAsampleID=A8951


title: Allergic Rhinitis [177k]

description:
177k
ex-vivo brushing


title: primary myelofibrosis, biological rep3

value: CD34+ PBMCs

value: peripheral blood


title: Healthy Control_in season [226]

description:
226
ex-vivo brushing

value: healthy

value: in season


title: WT Rapamycin (4h)

value: Culture was seeded at OD600 0.2 from overnight culture, allowed to grow to early log phase (4h), collected by vacuum filtration, resuspended in fresh media supplemented with 100 nM rapamycin, and harvested after 4h.

value: pre-growth in SC, growth in SC+rapamycin (100 nM)


title: WT Rapamycin (1h)

value: Culture was seeded at OD600 0.2 from overnight culture, allowed to grow to early log phase (4h), collected by vacuum filtration, resuspended in fresh media supplemented with 100 nM rapamycin, and harvested after 1h.


title: Healthy Control_in season [246]

description:
246
ex-vivo brushing


title: Allergic Rhinitis [177a]

description:
177a
ex-vivo brushing


title: WT Saturated

value: Culture was seeded at OD600 0.2 from overnight cultures (typically OD600 ~6), and was harvested after reaching saturation.

value: SC media


title: WT Log-phase

value: Culture was seeded at OD600 0.2 from overnight cultures (typically OD600 ~6), and was harvested during early log phase at OD600 0.5.


title: Col-0 x Cvi endosperm 7 DAP rep 3

first: Mary

last: Gehring

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

data_processing:
Reads were trimmed for QC with Trim_galore v 0.4.1 using the command " trim_galore -q 25 --phred64   --fastqc  --stringency 5 --length 18"
Aligned to TAIR10 genome with TOPHAT v2.1.1 using the command tophat  "-i 30 -I 3000 --b2-very-sensitive --solexa1.3-quals -p 5 --segment-mismatches 1 --segment-length 18 "
Cuffdiff v 2.2.1 was used with default settings to identify differentially expressed genes. The ARAPORT11 genome annotation was used. BAM files were the input for CuffDiff.
Genome_build: TAIR10

organism: Arabidopsis thaliana

source_name: endosperm at 7 days after pollination

growth_protocol: Plants were grown in a greenhouse with a controlled 16 hour light cycle at ~22C.

extract_protocol:
Seeds from crosses 7 days after pollination were dissected to isolate endosperm. RNA was isolated from endosperm using the Ambion RNAaqueous Micro Kit. RNA was treated with DNase and was submitted for library preparation at the Genome Technology Core of The Whitehead Institute.
SMARTerUltra-lowPOLYA-V4

value: Col-0 x Cvi F1

value: endosperm

tag: developmental stage

value: 7 days after pollination


title: hdg3-1 Col-0 endosperm 7 DAP rep 1

value: hdg3-1 Col-0 mutant


title: hdg3-1 Col-0 endosperm 7 DAP rep 3


title: hdg3-1 Col-0 endosperm 7 DAP rep 2


title: DA#8

city: San Francisco

first: Joel

last: Hrit

state: CA

address: 600 16th Street

department: Biochemistry and Biophysics

institute: University of California San Francisco

data_processing:
Basecalls performed using RTA 2.7.7
Sequenced reads were trimmed for adaptor sequence with cutadapt 1.16, -q 20, -u 10, -m 50
The trimmed bisulfite treated reads were mapped to mm10 with Bismark v0.19.0 --pbat
Individual CG methylation state is processed with methylpy 1.3.4 , call-methylation-state and merged both strand to increase coverages at each CG sites
Differentially methylated regions (DMRs) were defined by the DMRfind function in methylpy 1.3.4 by joining at least two DMSs within 250bp, FDR < 0.01 for each DMSs.
Genome_build: mm10

source_name: Tet1 D2018A mutant knock in mouse stem cells

extract_protocol:
The genomic DNA is extracted from 1 million mouse stem cells (Two biological replicates each for wild type and Tet1 D2018A mutant) by using the DNeasy kit from Qiagen following the manufacturer's protocol.
Then Methyl-Seq libraries were prepared using Accel-NGS® Methyl-Seq DNA Library Kit with 30 ng gDNA for each sample. Briefly, the single-stranded DNA fragments were end repaired, tailed of 3’ ends and ligated with adapter. After adapter ligation DNA was PCR amplified with Illumina Truseq primers for 8 cycles. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on Illumina HiSeq 4000 with 150 bases pair-ended reads.

value: Tet1 D2018A


title: primary myelofibrosis, biological rep4

value: primary myelofibrosis

value: CALR mut


title: Col-0 x Cvi endosperm 7 DAP rep 2


title: Healthy Control_in season [224]

description:
224
ex-vivo brushing

value: nasal brushing

value: no


title: pre-myelofibrosis, biological rep1

value: pre-myelofibrosis

value: CD34+ PBMCs

value: peripheral blood


title: DA#7


title: E982#1_1_A8922

description: spleen RNA 24 hr post infection with strain E982#1,mouse replicate 1, RNAsampleID=A8922

value: spleen

tag: Sex

value: female


title: Col-0 x Cvi endosperm 7 DAP rep 1


title: Allergic Rhinitis_in season [213]

description:
213
ex-vivo brushing

value: allergic rhinitis

value: in season


title: WT#5

source_name: wild type mouse stem cells

value: wild type


title: E982#1_2_A8923

description: spleen RNA 24 hr post infection with strain E982#1,mouse replicate 2, RNAsampleID=A8923

tag: strain


title: F118#4_2_A8926

description: spleen RNA 24 hr post infection with strain F118#4,mouse replicate 2, RNAsampleID=A8926


title: essential thrombocythemia, biological rep4

value: essential thrombocythemia

value: CD34+ BMMCs

value: bone marrow

tag: genotype


title: G007#3_1_A8919

description: spleen RNA 24 hr post infection with strain G007#3,mouse replicate 1, RNAsampleID=A8919


title: F118#4_1_A8925

description: spleen RNA 24 hr post infection with strain F118#4,mouse replicate 1, RNAsampleID=A8925


title: Allergic Rhinitis_in season [204]

description:
204
ex-vivo brushing

tag: disease status


title: G007#3_3_A8921

description: spleen RNA 24 hr post infection with strain G007#3,mouse replicate 3, RNAsampleID=A8921


title: E982#1_3_A8924

description: spleen RNA 24 hr post infection with strain E982#1,mouse replicate 3, RNAsampleID=A8924


title: Allergic Rhinitis_in season [250]

description:
250
ex-vivo brushing

tag: ait treatment


title: post-ET-myelofibrosis, biological rep3

value: post-ET-myelofibrosis


title: Allergic Rhinitis_in season [201]

description:
201
ex-vivo brushing

tag: patient id


title: G007#3_2_A8920

description: spleen RNA 24 hr post infection with strain G007#3,mouse replicate 2, RNAsampleID=A8920

tag: tissue


title: D2018A line #8 replicate #1

data_processing:
Data was collected on an Illumina HiSeq 4000 machine
Reads were aligned and gene counts were generated using STAR_2.5.3a
Normalized counts and differential expression analysis was performed using DESeq2 v1.20.0
Genome_build: Ensembl Mouse GRCm38.p6

source_name: embryonic stem cells

growth_protocol: embryonic stem cells were passaged in LIF containing embryonic stem cells media (10% FBS)

extract_protocol:
mRNA was isolated using Trizol and Direct-zol RNA miniprep kit
library was constructed using Lexogen SENSE total RNA-seq library prep kit according to manufacturer's instructions

value: TET1 mutation, D2018A

tag: cell line

tag: tag

value: C-terminal FLAG tag on TET1


title: D2018A line #7 replicate #2


title: Col-0 endosperm 7 DAP rep 1

value: endosperm

value: 7 days after pollination


title: small RNA sequencing data of clsy1234

city: Nanjing

first: Dong-Lei

last: Yang

state: Jiangsu Province

address: Weigang 1

department: Agriculture College

institute: Nanjing Agricultural University

description: small RNA

data_processing:
Adapter sequences were trimed and clean reads with sizes ranging from 18 to 35 were mapped to TAIR10 using Bowtie with parameter -v 0 -k 10.
Annotated structure RNAs were excluded.
Read counts were normalized to RPTM.
Genome_build: TAIR10
Supplementary_files_format_and_content: file with read count and sequence

source_name: 2-week-old seedlings

growth_protocol: Arabdopsis plants grown in 1/2MS solid medium under the condition of 16h light/8h dark.

extract_protocol:
RNA was extrated using TRIzol method.
18-35nt small RNA was cut from PAGE gel.

tag: genetic background ecotype

value: seedling

tag: age


title: WT#2


title: Allergic Rhinitis_in season [241]

description:
241
ex-vivo brushing

value: nasal brushing

tag: grass pollen season

value: no


title: small RNA sequencing data of Col-0

description: small RNA


title: D2018A line #8 replicate #2


title: D2018A line #7 replicate #1


title: Wild type line #5 replicate #2


title: Col-0 wild type BS-seq

description: Col-0 wild type Bs-seq

data_processing:
Low-quality sequences(q<20) and adapters were trimmed using trimmomatic.
Reads were mapped to TAIR10 using MSMAP 2.87 with parameters -g 1
methratio.py pathon script of BSMAP was used to extrac methylation ratios from BSMAP results with parameters -z and -r
Genome_build: TAIR10
Supplementary_files_format_and_content: wig or tdf

source_name: 2-week-old seedling

extract_protocol:
genomic DNA was extracted using CTAB method.
Genomic DNA was sonicated and then end-repaired with End repair Enzyme Mix. The blunt-ended DNA were treated with Klenow fragment and dATP to yield a proruding3-"A" and cytosine-methylated adaptors from Illumina were ligated according to manufacture's instructions.

value: Col-0 wild type


title: Col-0 endosperm 7 DAP rep 3


title: Wild type line #5 replicate #1


title: clsy1234 BS-seq

description: clsy1234 Bs-seq


title: Wild type line #2 replicate #2


title: clsy234 BS-seq

description: clsy234 Bs-seq


title: clsy134 BS-seq

description: clsy134 Bs-seq


title: N67_2_A8953_3

description: spleen RNA 24 hr post infection with strain N67,mouse replicate 2, RNAsampleID=A8953

value: spleen

tag: parasite strain

tag: replicate mouse

tag: rna sample id


title: F115#5_2_A8899

description: spleen RNA 24 hr post infection with strain F115#5,mouse replicate 2, RNAsampleID=A8899

value: female


title: 17XNL_2_A8950_3

description: spleen RNA 24 hr post infection with strain 17XNL,mouse replicate 2, RNAsampleID=A8950


title: naive_2_A8956_3

description: spleen RNA 24 hr post infection with strain naive,mouse replicate 2, RNAsampleID=A8956

value: naive


title: F115#5_3_A8900

description: spleen RNA 24 hr post infection with strain F115#5,mouse replicate 3, RNAsampleID=A8900


title: F122#2_3_A8897

description: spleen RNA 24 hr post infection with strain F122#2,mouse replicate 3, RNAsampleID=A8897


title: Wild type line #2 replicate #1


title: F115#5_1_A8898

description: spleen RNA 24 hr post infection with strain F115#5,mouse replicate 1, RNAsampleID=A8898


title: F122#2_2_A8896

description: spleen RNA 24 hr post infection with strain F122#2,mouse replicate 2, RNAsampleID=A8896


title: clsy123 BS-seq

description: clsy123 Bs-seq


title: E986#4_3_A8894

description: spleen RNA 24 hr post infection with strain E986#4,mouse replicate 3, RNAsampleID=A8894


title: clsy4nrpd1 BS-seq

description: clsy4nrpd1 Bs-seq


title: E986#4_2_A8893

description: spleen RNA 24 hr post infection with strain E986#4,mouse replicate 2, RNAsampleID=A8893


title: clsy3 BS-seq

description: clsy3 Bs-seq


title: ECKO-2

city: Boulder

first: Harald

last: Junge

state: Colorado

address: 347 UCB

institute: University of Colorado at Boulder

data_processing:
Raw reads were mapped to the mouse C57BL6J reference genome using DNASTAR SeqMan Ngen 15.0.1
RPKM values, differential expression (fold change), stasticial significance, and gene ontology were analyzed using DNASTAR Arraystar version 15.0.1
Genome_build: GRCm38.p4
Supplementary_files_format_and_content: A TXT file with mapped and RPKM determined using DNASTAR, table shows all genes in alphabetical order

source_name: Whole retina

extract_protocol:
Total RNA was purified from freshly dissected retinas. Retinas were homogenized in Trizol (Invitrogen) and total RNA was isolated. RNA was treated with Turbo DNAse (Ambion) in the presence of RNAse inhibitor (Qiagen)
RNA was ribodepleted and libraries were generated using the Illumina TruSeq stranded total RNA kit (RS-122-2202). 300 bp fragments were isolated.

treatment_protocol: 100 µl of 20 mg/ml tamoxifen in corn oil was administered to mice in four i.p. injections spaced two days apart, starting at P28

value: 7 month

value: Tspan12 flox/-; CDH5CreERTII

value: total retina


title: ECKO-1


title: ECKO-4


title: clsy4 BS-seq

description: clsy4 Bs-seq


title: Control-4

value: Tspan12 flox/+; CDH5CreERTII


title: clsy2 BS-seq

description: clsy2 Bs-seq


title: clsy1 BS-seq

description: clsy1 Bs-seq


title: Control-3


title: Intermediate subiculum_i5_2

city: Vancouver

first: Mark

middle: Steven

last: Cembrowski

address: 2350 Health Sciences Mall

department: Cellular and Physiological Sciences

institute: University of British Columbia

data_processing:
Trim input file and remove adapters.
Tag reads with cell barcode and UMI
Align reads to PhiX, then to mouse.
Aggregate reads and de-duplicate UMIs.
Post-processing in R with custom scripts and Seurat.
Genome_build: NCBIM37
Supplementary_files_format_and_content: Tab delimited file containing count values.

source_name: Intermediate subiculum

extract_protocol:
Microdissect and dissociate cells from acute brain slices in B6 mice
As in Cembrowski et al., Cell 173, 1-13

value: brain (slices)

tag: tissue subtype

value: Intermediate subiculum

tag: cell type

value: subiculum pyramidal cell


title: Control-2

tag: developmental stage


title: ECKO-3

tag: strain


title: Intermediate subiculum_i5_1


title: Control-1

tag: genotype


title: N67_2_A8953-2

tag: Sex


title: Intermediate subiculum_i4_2


title: F122#2_1_A8895

description: spleen RNA 24 hr post infection with strain F122#2,mouse replicate 1, RNAsampleID=A8895


title: naive_2_A8956_2


title: G008#2_3_A8891

description: spleen RNA 24 hr post infection with strain G008#2,mouse replicate 3, RNAsampleID=A8891


title: E986#4_1_A8892

description: spleen RNA 24 hr post infection with strain E986#4,mouse replicate 1, RNAsampleID=A8892


title: 17XNL_2_A8950_2


title: Intermediate subiculum_i4_1


title: G008#2_1_A8889

description: spleen RNA 24 hr post infection with strain G008#2,mouse replicate 1, RNAsampleID=A8889


title: G008#2_2_A8890

description: spleen RNA 24 hr post infection with strain G008#2,mouse replicate 2, RNAsampleID=A8890