title: mouse54_skeletal_60sec_RiboSeq

description: processed data file:

data_processing:
library strategy: Ribo-seq
To remove illumina adapter from Ribo-seq libraries run "cutadapt -u 1 -m 23 -a AGATCGGAAGAGCACACGTCT --discard-untrimmed -o output.fastq input.fastq"
mRNA-seq sequences were aligned with TopHat 2.1.0 using following settings: tophat --transcriptome-index --no-discordant --no-mixed --no-novel-juncs
The NCBI mouse genome build GRCm38.p3 and the Mus musculus Annotation Release 105 were used as a reference. When aligning mRNA-seq and ribosome profiling reads for expression and translation efficiency estimation we used the following strategy. Only full chromosomes were left and all non-chromosomal and mitochondrial records removed. Furthermore, only RefSeq and BestRefSeq records were left in the transcriptome annotation, while Gnomon predictions were discarded along with pseudogenes. Read count per gene was accessed by HTseq-count software
To plot time-dependent ribosome occupancy, we employed a different strategy. First, using a gene bank (gbk) file, which comes in a package with the genome assembly and annotation, we extracted RefSeq and BestRefSeq records for every gene including CDS, 5’-UTR and 3’-UTR lengths and sequences. Among them, we identified the longest isoform for every gene, prioritized as CDS > 5’UTR > 3’UTR. 5’-UTRs were trimmed by 100 nucleotides. If either or UTRs were shorter than 100 nucleotides, we filled it with up to 100 based on genomic coordinates. The full list of sequences is collected in the mRNA_100.fna file. To prepare a list of non-redundant genes, we run blast of all vs. all (blastall -p blastn -m 8 -b 500 -v 500 -e 0.001). Gene pairs that are too similar at the level of nucleotide sequence were excluded. In addition to the e-score, we enforced a requirement of the high-homology stretch being at least 50 nt long, and if it was longer, the similarity had to be at least 90% to treat these genes as homologous and redundant. A total of 13,685 genes passed every threshold. This reference set ensured unambiguous alignment of ribosome footprints. Resulting sequences are collected in the mRNA_100unique.fna file.
Custom Perl and R scripts were used to calculate the footprint coverage profiles of individual genes.
Genome_build: GRCm38
Supplementary_files_format_and_content: read counts contain raw read count of individual genes; footprint coverage contains gene coverage profiles

extract_protocol:
Frozen tissue was pulverized in a ceramic mortar-pestle filled with liquid nitrogen, then lysed a glass-Teflon Dounce homogenizer: 20 mM Tris-HCl pH 7.5, 100 mM KCl, 5 mM MgCl2, 5 mM CaCl2, 1 mM DTT, 1% Tween-20, 0.25% Deoxycholate, 0.1 mg/ml cycloheximide. The lysate was incubated with 4:1 mixture of ribonucleases T1 and S7 for 30 min at room temperature with gentle agitation. Lysate fractionation was performed by ultracentrifugation for 3 h at 35.000 rpm in an SW41 rotor (Beckman, Optima L-20K) at 4⁰ C in 10-50% sucrose, 20 mM Tris-HCl pH 7.5, 100 mM KCl, 10 mM MgCl2, 1 mM DTT, 0.1 mg/ml cycloheximide. After the centrifugation, gradients were passed through a UV detector (Bio-Rad) and the absorption at 254 nm was recorded. The fraction containing monosomes was collected in a single tube. The volume of the sample was brought to 50 ul by concentrating it using 100 kDa filters (Amicon Ultra, Millipore). Then, the sample was diluted to 500 ul with a buffer containing 10 mM Tris-HCl pH 7.5, 2 mM EDTA, 1% SDS. RNA was extracted by hot acid phenol (Ambion) and precipitated by the glycogen-ethanol method (1/10 volume of 3 M sodium acetate, 1/100 volume of glycogen, 2.5 volumes of pure ethanol, 1-hour incubation at -20 followed by centrifugation). RNA was loaded on a 15% polyacrylamide TBE-urea gel and the band containing ribosomal footprints around 28-30 nucleotides was cut.
DNA adapter (rApp-AGATCGGAAGAGCACACGTCT- ddC) was ligated to the 3' end of RNA footprint. Illumina flanking sequences were added through reverse transcription and consequent Circligation technique.

tag: internal animal id

value: 15 weeks old mouse

tag: inhibitors

value: harringtonine 60 sec cycloheximide

tag: injection route

value: tail-vein

value: skeletal muscle

value: ribosome footprints


title: mouse54_kidney_60sec_RiboSeq

status: Public on Dec 31 2018

type: SRA

city: Boston

first: Maxim

last: Gerashchenko

state: Massachusetts

address: 77 Louis Pasteur Ave, NRB 435

department: Medicine

country: USA

institute: Brigham and Women's Hospital

description: processed data file:

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

extract_protocol:
Frozen tissue was lysed a glass-Teflon Dounce homogenizer: 20 mM Tris-HCl pH 7.5, 100 mM KCl, 5 mM MgCl2, 5 mM CaCl2, 1 mM DTT, 1% Triton-X100, 0.1 mg/ml cycloheximide. The lysate was incubated with 4:1 mixture of ribonucleases T1 and S7 for 30 min at room temperature with gentle agitation. Lysate fractionation was performed by ultracentrifugation for 3 h at 35.000 rpm in an SW41 rotor (Beckman, Optima L-20K) at 4⁰ C in 10-50% sucrose, 20 mM Tris-HCl pH 7.5, 100 mM KCl, 10 mM MgCl2, 1 mM DTT, 0.1 mg/ml cycloheximide. After the centrifugation, gradients were passed through a UV detector (Bio-Rad) and the absorption at 254 nm was recorded. The fraction containing monosomes was collected in a single tube. The volume of the sample was brought to 50 ul by concentrating it using 100 kDa filters (Amicon Ultra, Millipore). Then, the sample was diluted to 500 ul with a buffer containing 10 mM Tris-HCl pH 7.5, 2 mM EDTA, 1% SDS. RNA was extracted by hot acid phenol (Ambion) and precipitated by the glycogen-ethanol method (1/10 volume of 3 M sodium acetate, 1/100 volume of glycogen, 2.5 volumes of pure ethanol, 1-hour incubation at -20 followed by centrifugation). RNA was loaded on a 15% polyacrylamide TBE-urea gel and the band containing ribosomal footprints around 28-30 nucleotides was cut.
DNA adapter (rApp-AGATCGGAAGAGCACACGTCT- ddC) was ligated to the 3' end of RNA footprint. Illumina flanking sequences were added through reverse transcription and consequent Circligation technique.

tag: strain

tag: age

tag: tissue

value: kidney

tag: molecule subtype


title: mouse45_liver_60sec_RiboSeq

description: processed data file:

value: 14 weeks old mouse

value: liver


title: F3.1001200127

city: Stanford

first: Qingyun

last: Li

state: CA

address: 299 Campus Drive

department: Neurobiology

institute: Stanford University

description: Single_myeloid_1922_cells_processed_data.csv

data_processing:
Prinseq (version 0.20.4) was first used to filter sequencing reads shorter than 30 bp (-min_len 30), trim the first 10 bp at the 5’-end (-trim_left 10) of the reads, trim reads with low quality from the 3’-end (-trim_qual_right 25) and remove low complexity reads (-lc_method entropy, -lc_threshold 65).
Trim Galore (version 0.4.3) was applied to trimmed the Nextera adapters (--stringency 1).
The remaining reads were aligned to the mm10 genome by calling STAR (version 2.5.3a) with the following options: --outFilterType BySJout, --outFilterMultimapNmax 20, --alignSJoverhangMin 8, --alignSJDBoverhangMin 1, --outFilterMismatchNmax 999, --outFilterMismatchNoverLmax 0.04, --alignIntronMin 20, --alignIntronMax 1000000, --alignMatesGapMax 1000000, --outSAMstrandField intronMotif.
Picard was then used to remove the duplicate reads (VALIDATION_STRINGENCY=LENIENT, REMOVE_DUPLICATES=true).
The aligned reads were converted to counts for each gene by using HTSeq (-m intersection-nonempty, -s no)
To filter out cells with low sequencing quality, three criteria, namely the number of total reads, the number of total detected genes and correlation coefficient between ERCC spike-ins input and corresponding read counts, were each evaluated based on the distributions of the data. The distribution of the total reads (in logarithmic scale) was fitted by a truncated Cauchy distribution, and data points in two tails of the estimated distribution were considered as outliers and eliminated. Fitting and elimination were then applied to the remaining data. This process was run iteratively until the estimated distribution became stable. The threshold was set to the value where the cumulative distribution function of the estimated distribution reaches 0.05. Similarly, cells with small numbers of detected genes, and poor correlation coefficients for ERCC (low sequencing accuracy) were dropped. After filtering, 1816 cells, out of 1922, were retained.
Genome_build: mm10
Supplementary_files_format_and_content: Common delimited file (csv) containing all 1922 cells and mapped gene counts (including counts for ERCC spike-ins)

source_name: Brain myeloid cell

extract_protocol:
For the E14.5 stage, whole brains were dissected out from timed embryos, and collected into 1ml PBS with 1% fetal bovine serum (added 10ul Ambion DNase I, 2ul RNase inhibitor) on ice. The sample was passed through a 26G needle 5-10 times to create single cell suspension. Cells were spun down (500g) at 4˚C for 5min, and suspended in 1ml PBS for FACS staining. Single live cells in the cKit-CD45+ gate were sorted into 96-well plates for library preparation.  For P7 and P60 stages, cortex (CTX), cerebellum (CB), hippocampus (HIP), striatum (STR), olfactory bulb (OB) and choroid plexus (CP) were dissected out. Tissues from the same region were pooled from multiple mice (3-8 depending on the ages and regions) into a 6cm petri dish with 200ul cold medium A on ice (15mM HEPES, 0.5% glucose in 1 X Hanks' Balanced Salt Solution (HBSS without phenol red)). Microglia (myeloid cells) extraction was carried out on ice following a published protocol (Bennett et al. PNAS. 2016) through douncing, MACS myelin removal and FACS staining. Single live cells in the CD45lowCD11b+ (microglia) or CD45hiCD11b+ (myeloid cells) gate were sorted into 96-well plates for library preparation.
Sequencing libraries were prepared following the published Smart-seq2 protocol with the aid of liquid handling robotics (Picelli et al. Nature Protocols. 2014). Briefly, plates with sorted cells were thawed on ice and incubated at 72˚C for 3 min in order to anneal RNAs to the Oligo-dT30VN primer. After that, 6ul reverse transcription mixture (95U SMARTScribe™ Reverse Transcriptase (100U/ul, Clontech 639538), 10U RNase inhibitor (40U/ul), 1XFirst-Strand buffer, 5mM DTT, 1M Betaine, 6mM MgCl2, 1uM TSO (Exiqon, Rnase free HPLC purified)) was added into each well, and RT was performed at 42˚C for 90 min, followed by 70˚C, 5 min. To amplify cDNA, 15ul PCR amplification mix (1X KAPA HIFI Hotstart Master Mix (Kapa Biosciences KK2602), 0.1uM ISPCR Oligo (AAGCAGTGGTATCAACGCAGAGT), 0.56U Lambda Exonuclease (5U/ul, New England BioLabs M0262S)) was added, and the following PCR program was used: (1) 37˚C 30 min; (2)95˚C 3 min; (3) 21 cycles of 98˚C 20 sec, 67˚C 15 sec, 72˚C 4 min; (4) 72˚C 5 min. Amplified cDNA samples were then purified with PCRClean DX beads (0.7:1 ratio, Aline C-1003-50), and resuspended in 20ul EB buffer. cDNA quality was examined with a Fragment Analyzer (AATI, High Sensitivity NGS Fragment Analysis Kit:1 bp - 6000 bp) following the manufacture’s instruction. Samples with sufficient amount of cDNA content (>0.05ng/ul) and normal peaks on the quantification graphs were retained for library preparation. To make libraries, all samples were first diluted down to 0.15ng/ul (only if higher than 0.15ng/ul) in 384-well plates using Mantis Liquid Handler (Formulatrix) and Mosquito X1 (TTP Labtech) with customized scripts. Nextera XT DNA Sample Prep Kit (Illumina FC-131-1096) was used at 1/10 of recommendation volume, with the help of a Mosquito HTS robot for liquid transfer. Specifically, tagmentation was done in 1.6ul (1.2ul Tagment enzyme mix, 0.4ul diluted cDNA) at 55˚C, 10 min. Neutralization buffer was added 0.4ul per well and incubated at room temperature for 5 min to stop the reaction. Then 0.8ul Illumina Nextera XT 384 Indexes (0.4ul each, 5uM from 4 sets of 96 indexes) and 1.2ul PCR master mix were added to amplify whole transcriptomes using the following program: (1) 72˚C 3 min; (2) 95˚C 30 sec; (3) 10 cycles of 95˚C 10 sec, 55˚C 30 sec, 72˚C 1 min; (4) 72˚C 5 min. Libraries from a single 384 plate were pooled together in an Eppendorf tube and purified twice with PCRClean DX beads. The quality and concentrations of the final mixed libraries were measured with Bioanalyzer and Qubit, respectively, before Illumina Nextseq sequencing.

tag: genotype

value: wild type

value: STR

tag: gate

value: Y


title: mouse45_kidney_60sec_RiboSeq

description: processed data file:


title: mouse78_skeletal_60sec_RiboSeq

description: processed data file:


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_GGAGCTAC-TCGCATAA

city: Atlanta

first: Steven

last: Sloan

state: GA

address: 615 Michael Street, Whitehead Building Room 375

department: Human Genetics

institute: Emory University

description: Single cell

data_processing:
Read alignment: reads were aligned to the hg38 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ).
Per-gene read assignement: aligned reads were converted to counts for every gene using FeatureCounts (-p -t exon -g gene_id -a ).
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample

molecule: polyA RNA

organism: Homo sapiens

source_name: human oligodendrocyte spheroids

growth_protocol: Human induced pluripotent stem cells (hiPSCs) grown in feeder free conditions were enzymatically dissociated and plated in microwells to form spheroids. The following day the spheroids were flushed from the microwellsand transferred into ultra-low attachment plastic dishes (Thermo Fisher Scientific) in EssentialTM 6 medium (Thermo Fisher Scientific) supplemented with two SMAD pathway inhibitors– dorsomorphin (DM, 2.5 μM, Sigma-Aldrich, P5499-CONF) and SB-431542 (10 μM, R&D systems, 1614) for five days. On day 6 in suspension the spheroids were transferred to differentiation and maintenance medium (DMM) containing DMEM/F12 (Thermo Fisher Scientific), B-27 Supplement without vitamin A (Thermo Fisher Scientific), N-2 Supplement (Thermo Fisher Scientific), MEM Non-Essential Amino Acids (1:100, Thermo Fisher Scientific), GlutaMax (1:100, Thermo Fisher Scientific), human insulin (25 μg/mL, Sigma-Aldrich), and penicillin-streptomycin (1:100, Thermo Fisher Scientific). The DMM medium was supplemented with 20 ng/ml EGF (R&D Systems) and 20 ng/ml bFGF (Peprotech) for 19 days. IWP-2 (5 μM, Selleckchem) was added from day 4 until day 24, and SAG (1 μM, Millipore Sigma) was added from day 12 to day 24. From day 25 to day 36, hOLS were cultured in DMM supplemented with T3 (60 ng/mL, Sigma Aldrich), biotin (100 ng/mL, Sigma Aldrich), NT-3 (20 ng/mL, Peprotech), BDNF (20 ng/mL, Peprotech), cAMP (1 μM, Sigma Aldrich), HGF (5 ng/mL, Peprotech), IGF-1 (10 ng/mL, VWR), and PDGFaa (10 ng/mL, R&D Systems). From day 37 onwards, hOLs were cultured in complete DMM (DMM supplemented with T3, biotin, cAMP, and ascorbic acid (AA, 20 μg/mL, Wako Pure Chemical).

extract_protocol:
Single cells were sorted into lysis buffer according to a published Smartseq2  protocol (Picelli, S. et al. 2014). ERCC RNA Spike-In Mix was added at 1: 2.4X10^7  dilution in the buffer.
Sorted cells in 96-well plates were used for library preparation following the  Smartseq2 protocol (Picelli, S. et al. 2014) with modifications. Briefly, plates were  incubated at 72˚C, 3 min for annealing with Oligo-dT 30 VN. Reverse transcription  mixture was added 6ul per well, and RT was performed at 42˚C for 90 min, followed  by 70˚C, 5 min. To amplify the whole transcriptome, 15ul of DNA amplification  mixture was added and cDNA was amplified for 21 cycles. Amplified cDNA was then  purified using PCRClean DX beads. cDNA quality and quantity were assessed using a  Fragment Analyzer (AATI, High Sensitivity NGS Fragment Analysis Kit:1 bp - 6000  bp), and samples with concentrations below 0.08ng/ul or abnormal peak patterns  were filtered out. A total of 295 cDNA samples (retaining 88.9% of initially sorted)  were diluted down to 0.15ng/ul (only if above it) and consolidated into a 384-well  plate using a Mosquito X1 (TTP Labtech). Library preparation was performed using  Nextera XT DNA Sample Prep Kit (Illumina, Cat: FC-131-1096) and Nextera XT 384  dual index primers, with the help of a Mosquito HTS machine for liquid transfer.  Tagmentation was performed in 1.2ul at 55˚C for 10 min and amplification was  performed in 4ul system, 10 cycles. In the end, all samples were pooled (0.5ul each)  together into a 1.5ml Eppendorf tube, and the mixed libraries were purified twice  with PCRClean DX beads. The final sample was reconstituted in 50ul EB buffer, and  the concentration and peaks were measured by Qubit and Bioanalyzer before  Illumina sequencing (Hiseq).
Single cell RNA-seq

tag: plate id

value: plate 3

value: Day 333

tag: line


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_GTAGAGGA-AGAGGATA

description: Single cell

value: plate 2

value: Day 336


title: mouse53_skeletal_45sec_RiboSeq

description: processed data file:

value: harringtonine 45 sec cycloheximide


title: H1.1001200122

value: OB


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_GGAGCTAC-TCTTACGC

description: Single cell

value: Day 334


title: mouse45_skeletal_60sec_RiboSeq

description: processed data file:

value: harringtonine 60 sec cycloheximide


title: mouse53_kidney_45sec_RiboSeq

description: processed data file:

value: 15 weeks old mouse

value: tail-vein


title: mouse77_skeletal_45sec_RiboSeq

description: processed data file:

value: skeletal muscle

value: ribosome footprints


title: WT IN Treated 3

city: Cincinnati

first: Mei-Ling

last: Bermudez

state: Ohio

address: 160 Panzeca Way

department: Environmental Health

institute: University of Cincinnati

data_processing:
none provided by the submitter
Supplementary_files_format_and_content: entrez gene ID and counts

source_name: Midbrain

extract_protocol:
RNA was extracted using the mirVana miRNA Isolation Kit  following the manufacturer’s protocol for total RNA extraction
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Two months old WT and TG mice were treated for 2-months

tag: treatment

value: carnosine


title: G11.1001200126

value: CTX


title: WT Control 2

value: control


title: mouse53_liver_45sec_RiboSeq

description: processed data file:

value: liver


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_GGAGCTAC-TATGCAGT

description: Single cell

value: Day 332


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_GTAGAGGA-AGGCTTAG

description: Single cell

value: Day 338


title: G10.1001200124

value: wild type

value: CB

value: Y


title: mouse44_liver_45sec_RiboSeq

description: processed data file:

value: 14 weeks old mouse

value: harringtonine 45 sec cycloheximide


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_GGAGCTAC-TACTCCTT

description: Single cell

value: plate 3

value: Day 331


title: A6.1001200127

value: STR


title: mouse72_skeletal_30sec_RiboSeq

description: processed data file:

value: 15 weeks old mouse

value: harringtonine 30 sec cycloheximide

value: tail-vein


title: H3.1001200123

value: OB


title: mouse52_skeletal_30sec_RiboSeq

description: processed data file:

value: skeletal muscle

value: ribosome footprints


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_GGAGCTAC-TAAGGCTC

description: Single cell

value: Day 330


title: B4.1001200126

value: CTX


title: mouse43_skeletal_30sec_RiboSeq

description: processed data file:


title: mouse52_liver_30sec_RiboSeq

description: processed data file:

value: liver


title: mouse43_liver_30sec_RiboSeq

description: processed data file:


title: mouse43_kidney_30sec_RiboSeq

description: processed data file:

value: kidney


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_GGAGCTAC-CTAGTCGA

description: Single cell

value: Day 327


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_GGAGCTAC-CGGAGAGA

description: Single cell

value: Day 326


title: H2.1001200126

value: wild type

value: Y


title: mouse51_skeletal_15sec_RiboSeq

description: processed data file:

value: harringtonine 15 sec cycloheximide


title: mouse44_kidney_45sec_RiboSeq

description: processed data file:

value: 14 weeks old mouse

value: harringtonine 45 sec cycloheximide


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_GGAGCTAC-CTTAATAG

description: Single cell

value: plate 3

value: Day 329


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_GGAGCTAC-CTCCTTAC

description: Single cell

value: Day 328


title: B7.1001200124

value: CB


title: mouse52_kidney_30sec_RiboSeq

description: processed data file:

value: 15 weeks old mouse

value: harringtonine 30 sec cycloheximide

value: tail-vein


title: mouse70_skeletal_15sec_RiboSeq

description: processed data file:

value: 13 weeks old mouse

value: skeletal muscle

value: ribosome footprints


title: E7.1001200124

value: N


title: mouse71_skeletal_15sec_RiboSeq

description: processed data file:


title: mouse50_kidney_15sec_RiboSeq

description: processed data file:

value: kidney


title: D9.1001200124

value: wild type


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_GGAGCTAC-ATAGCCTT

description: Single cell

value: Day 324


title: mouse51_liver_15sec_RiboSeq

description: processed data file:

value: harringtonine 15 sec cycloheximide

value: liver


title: mouse50_liver_15sec_RiboSeq

description: processed data file:

value: 14 weeks old mouse


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_GGAGCTAC-ATTAGACG

description: Single cell

value: plate 3

value: Day 325


title: mouse51_kidney_15sec_RiboSeq

description: processed data file:


title: mouse23_brain_30min_RiboSeq

description: processed data file:

value: 16 weeks old muse

value: harringtonine 30 min

value: retro-orbital

value: brain


title: mouse29_spleen_RiboSeq

description:
processed data file:
organs_RiboSeq_count.txt

extract_protocol:
Frozen tissue was lysed a glass-Teflon Dounce homogenizer: 20 mM Tris-HCl pH 7.5, 100 mM KCl, 5 mM MgCl2, 1 mM DTT, 1% Tween-20, 0.25% deoxycholate, 0.1 mg/ml cycloheximide. The lysate was incubated with T1 ribonuclease for 30 min at room temperature with gentle agitation. Lysate fractionation was performed by ultracentrifugation for 3 h at 35.000 rpm in an SW41 rotor (Beckman, Optima L-20K) at 4⁰ C in 10-50% sucrose, 20 mM Tris-HCl pH 7.5, 100 mM KCl, 10 mM MgCl2, 1 mM DTT, 0.1 mg/ml cycloheximide. After the centrifugation, gradients were passed through a UV detector (Bio-Rad) and the absorption at 254 nm was recorded. The fraction containing monosomes was collected in a single tube. The volume of the sample was brought to 50 ul by concentrating it using 100 kDa filters (Amicon Ultra, Millipore). Then, the sample was diluted to 500 ul with a buffer containing 10 mM Tris-HCl pH 7.5, 2 mM EDTA, 1% SDS. RNA was extracted by hot acid phenol (Ambion) and precipitated by the glycogen-ethanol method (1/10 volume of 3 M sodium acetate, 1/100 volume of glycogen, 2.5 volumes of pure ethanol, 1-hour incubation at -20 followed by centrifugation). RNA was loaded on a 15% polyacrylamide TBE-urea gel and the band containing ribosomal footprints around 28-30 nucleotides was cut.
DNA adapter (rApp-AGATCGGAAGAGCACACGTCT- ddC) was ligated to the 3' end of RNA footprint. Illumina flanking sequences were added through reverse transcription and consequent Circligation technique.

value: spleen


title: mouse27_spleen_RiboSeq

value: 13 weeks old mouse


title: mouse26_spleen_RiboSeq


title: mouse15_pancreas_5min_RiboSeq

description:
processed data file:
mouse13-15_pancreas_5min_RiboSeq.coverage.txt

value: harringtonine 5 min

value: pancreas


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_GGAGCTAC-ATAGAGAG

description: Single cell

value: Day 323


title: mouse14_pancreas_5min_RiboSeq

value: ribosome footprints


title: mouse13_pancreas_5min_RiboSeq


title: mouse16_skeletal_5min_RiboSeq

description:
processed data file:
mouse13-16_skeletal_5min_RiboSeq.coverage.txt

value: skeletal muscle


title: mouse14_skeletal_5min_RiboSeq


title: mouse16_heart_5min_RiboSeq

description:
processed data file:
mouse13-16_heart_5min_RiboSeq.coverage.txt

value: heart


title: mouse13_skeletal_5min_RiboSeq


title: mouse15_heart_5min_RiboSeq


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_GGAGCTAC-AGGCTTAG

description: Single cell

value: Day 322


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_GGACTCCT-TCTTACGC

description: Single cell

value: Day 318


title: mouse14_heart_5min_RiboSeq


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_GGAGCTAC-ACTCTAGG

description: Single cell

value: Day 319


title: mouse15_skeletal_5min_RiboSeq


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_GGAGCTAC-AGCTAGAA

description: Single cell

value: plate 3

value: Day 321


title: mouse13_heart_5min_RiboSeq


title: mouse16_lung_5min_RiboSeq

description:
processed data file:
mouse14-16_lung_5min_RiboSeq.coverage.txt

value: lung


title: mouse15_lung_5min_RiboSeq


title: mouse24_testis_RiboSeq

description:
processed data file:
mouse23-25_testis_30min_RiboSeq.coverage.txt

value: 16 weeks old muse

value: harringtonine 30 min

value: testis


title: mouse14_lung_5min_RiboSeq

value: retro-orbital


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_GGACTCCT-TCGCATAA

description: Single cell

value: plate 1

value: Day 317


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_GGACTCCT-TACTCCTT

description: Single cell

value: Day 315


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_GGACTCCT-TAAGGCTC

description: Single cell

value: Day 314


title: mouse23_testis_RiboSeq

value: ribosome footprints


title: mouse25_testis_RiboSeq


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_GGACTCCT-CTTAATAG

description: Single cell

value: Day 313


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_GGAGCTAC-AGAGGATA

description: Single cell

value: Day 320


title: mouse27_testis_RiboSeq

value: 13 weeks old mouse


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_GGACTCCT-CTCCTTAC

description: Single cell

value: Day 312


title: mouse78_kidney_60sec_RiboSeq

description: processed data file:

value: 15 weeks old mouse

value: harringtonine 60 sec cycloheximide

value: tail-vein

value: kidney


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_GGACTCCT-CGGAGAGA

description: Single cell

value: Day 310


title: mouse26_pancreas_RiboSeq

value: pancreas


title: mouse74_kidney_60sec_RiboSeq

description: processed data file:


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_GGACTCCT-TATGCAGT

description: Single cell

value: Day 316


title: mouse27_skeletal_RiboSeq

value: skeletal muscle


title: mouse27_lung_RiboSeq

value: lung


title: mouse26_lung_RiboSeq


title: mouse28_heart_RiboSeq

value: heart


title: mouse27_pancreas_RiboSeq


title: mouse27_brain_RiboSeq

value: brain


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_GGACTCCT-ATTAGACG

description: Single cell

value: plate 1

value: Day 309


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_GGACTCCT-ATAGAGAG

description: Single cell

value: Day 307


title: mouse26_heart_RiboSeq

value: ribosome footprints


title: mouse26_testis_RiboSeq

value: 13 weeks old mouse

value: testis


title: mouse26_kidney_RiboSeq


title: mouse78_liver_60sec_RiboSeq

description: processed data file:

value: 15 weeks old mouse

value: liver


title: mouse26_skeletal_RiboSeq


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_GGACTCCT-ATAGCCTT

description: Single cell

value: Day 308


title: mouse29_liver_RiboSeq


title: mouse74_liver_60sec_RiboSeq

description: processed data file:

value: harringtonine 60 sec cycloheximide

value: tail-vein


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_GGACTCCT-AGGCTTAG

description: Single cell

value: Day 306


title: mouse28_liver_RiboSeq


title: mouse77_kidney_45sec_RiboSeq

description: processed data file:

value: harringtonine 45 sec cycloheximide

value: kidney


title: mouse27_liver_RiboSeq


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_GGACTCCT-AGCTAGAA

description: Single cell

value: Day 305


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_GGACTCCT-CTAGTCGA

description: Single cell

value: Day 311


title: mouse26_brain_RiboSeq

value: brain


title: mouse26_liver_RiboSeq


title: mouse77_liver_45sec_RiboSeq

description: processed data file:


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_GCTCATGA-TCTTACGC

description: Single cell

value: plate 1

value: Day 302


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_GGACTCCT-ACTCTAGG

description: Single cell

value: Day 303


title: mouse76_kidney_30sec_RiboSeq

description: processed data file:

value: harringtonine 30 sec cycloheximide

value: ribosome footprints


title: mouse27_kidney_RiboSeq

value: 13 weeks old mouse


title: mouse71_kidney_15sec_RiboSeq

description: processed data file:

value: 15 weeks old mouse

value: harringtonine 15 sec cycloheximide


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_GCTCATGA-TACTCCTT

description: Single cell

value: plate 3

value: Day 299


title: mouse72_liver_30sec_RiboSeq

description: processed data file:

value: tail-vein

value: liver


title: mouse72_kidney_30sec_RiboSeq

description: processed data file:


title: mouse71_liver_15sec_RiboSeq

description: processed data file:


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_GCTCATGA-CTTAATAG

description: Single cell

value: Day 297


title: mouse73_kidney_45sec_RiboSeq

description: processed data file:

value: harringtonine 45 sec cycloheximide

value: kidney


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_GCTCATGA-TAAGGCTC

description: Single cell

value: Day 298


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_GCTCATGA-TCGCATAA

description: Single cell

value: Day 301


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_GGACTCCT-AGAGGATA

description: Single cell

value: plate 1

value: Day 304


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_GCTCATGA-CGGAGAGA

description: Single cell

value: plate 2

value: Day 294


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_GCTCATGA-ATTAGACG

description: Single cell

value: Day 293


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_GCTCATGA-ATAGCCTT

description: Single cell

value: Day 292


title: mouse75_kidney_15sec_RiboSeq

description: processed data file:

value: 15 weeks old mouse

value: ribosome footprints


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_GCTCATGA-TATGCAGT

description: Single cell

value: plate 3

value: Day 300


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_GCTCATGA-ATAGAGAG

description: Single cell

value: Day 291


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_GCTCATGA-AGCTAGAA

description: Single cell

value: Day 289


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_GCTCATGA-CTCCTTAC

description: Single cell

value: Day 296


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_GCTCATGA-CTAGTCGA

description: Single cell

value: Day 295


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_GCTCATGA-AGAGGATA

description: Single cell

value: Day 288


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_GCTCATGA-ACTCTAGG

description: Single cell

value: Day 287


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_GCGTAGTA-TCTTACGC

description: Single cell

value: Day 286


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_GCGTAGTA-TATGCAGT

description: Single cell

value: Day 284


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_GCGTAGTA-TCGCATAA

description: Single cell

value: Day 285


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_GCTCATGA-AGGCTTAG

description: Single cell

value: plate 2

value: Day 290


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_GCGTAGTA-TAAGGCTC

description: Single cell

value: Day 282


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_GCGTAGTA-CTTAATAG

description: Single cell

value: Day 281


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_GCGTAGTA-CTAGTCGA

description: Single cell

value: Day 279


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_GCGTAGTA-TACTCCTT

description: Single cell

value: Day 283


title: BAL_IPF_Siena_49

type: RNA

city: Hannover

first: Antje

last: Prasse

address: Carl-Neubergstrasse 1

department: Pneumology

country: Germany

institute: Medical School Hannover

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 µl containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 ml of 2x GEx Agilent hybridization buffer HI-RPM was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays, 4x44K (Freiburg and Siena) or  8 x 60K (Leuven) 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.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA High Resolution Microarray Scanner (G2505C US45102918) using one color scan setting for 8 x 60K array slides (Freiburg and Siena) and  8 x 60K array slides (Leuven). Scan Area 61x21.6 mm, Scan resolution 5 μm, Tiff 20 bit, Dye channel is set to Green.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  Gene expression data was normalized to the geometric mean of all the IPF samples and controls using quantile normalization. Non-expressed and invariant transcripts were removed.  For statiscal analysis we used the average gene expression values of the replicated probes. After merging the datasets of the 3 cohorts we obtained a final dataset of 20330 transcript measurements across the 176 IPF samples and 20 healthy donor samples.

source_name: BAL cells

label_protocol: Labeling reactions were performed for each sample using Agilent Low Input Quick Amp Labeling, One-Color (Agilent Technologies, Santa Clara, CA). Briefly, with a starting concentration of 100 nanograms of total RNA, an initial cDNA strand was synthesized using a oligo(dT)24 primer containing a T7 RNA polymerase, this cDNA was then used as a template to generate Cy3 labeled cRNA by a reverse transcriptase enzyme. After the cRNA was obtained a purification step was performed using RNeasy Mini Kit (74104, Qiagen, Valencia, CA) followed by measurement of the yield and specific activity of each sample

extract_protocol:
[Isolation protocol] BAL cells were obtained by bronchoscopy, immediately isolated and 1 ml of TRIzol (15596018, life technologies, Darmstadt, Germany) was added to the cell pellet, which was then immediately snap frozen in -80 celsius.
Total RNA of TRIzol samples was extracted and purified using the RNeasy Mini Kit (217004, Qiagen, Valencia, CA), under fully automated sample preparation by the assistance of the QIAcube device (9001292, Qiagen, Valencia CA) following the manufacturer’s protocol. After extraction, total RNA yield and quality were evaluated using NanoDrop at 260 nm and the 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA)

tag: cell type

value: bronchoalveolar lavage (BAL) cells

tag: diagnosis

value: IPF

tag: cohort

value: SIENA

tag: sex (0=female, 1=male)

tag: time to death (days)

tag: survival status, 0 = censored, 1 = death

tag: gap


title: BAL_IPF_Siena_42


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_GCGTAGTA-CGGAGAGA

description: Single cell

value: plate 3

value: Day 278


title: BAL_IPF_Siena_50


title: BAL_IPF_Siena_37


title: BAL_IPF_Siena_41


title: BAL_IPF_Siena_31


title: BAL_IPF_Siena_34


title: BAL_IPF_Siena_47


title: BAL_IPF_Siena_35


title: BAL_IPF_Siena_43


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_GCGTAGTA-CTCCTTAC

description: Single cell

value: Day 280


title: BAL_IPF_Siena_30


title: BAL_IPF_Siena_48


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_GCGTAGTA-ATTAGACG

description: Single cell

value: Day 277


title: BAL_IPF_Siena_39


title: BAL_IPF_Siena_45


title: BAL_IPF_Siena_33


title: BAL_IPF_Siena_38


title: BAL_IPF_Siena_40


title: BAL_IPF_Siena_36


title: BAL_IPF_Siena_44


title: BAL_IPF_Siena_46


title: BAL_IPF_Siena_32


title: BAL_IPF_Siena_27


title: BAL_IPF_Siena_28


title: BAL_IPF_Siena_26


title: BAL_IPF_Siena_29


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_GCGTAGTA-ATAGCCTT

description: Single cell

value: Day 276


title: BAL_IPF_Siena_25


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_GCGTAGTA-ATAGAGAG

description: Single cell

value: Day 275


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_GCGTAGTA-AGGCTTAG

description: Single cell

value: Day 274


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_GCGTAGTA-AGAGGATA

description: Single cell

value: Day 272


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_GCGTAGTA-ACTCTAGG

description: Single cell

value: Day 271


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_GCGTAGTA-AGCTAGAA

description: Single cell

value: Day 273


title: BAL_IPF_Siena_24


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_CTCTCTAC-TCTTACGC

description: Single cell

value: Day 270


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_CTCTCTAC-TCGCATAA

description: Single cell

value: plate 2

value: Day 269


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_CTCTCTAC-TATGCAGT

description: Single cell

value: Day 268


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_CTCTCTAC-TACTCCTT

description: Single cell

value: Day 267


title: BAL_IPF_Siena_23

value: bronchoalveolar lavage (BAL) cells

value: IPF


title: BAL_IPF_Siena_22

value: SIENA


title: BAL_IPF_Siena_21


title: BAL_IPF_Siena_15


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_CTCTCTAC-TAAGGCTC

description: Single cell

value: Day 266


title: BAL_IPF_Siena_19


title: BAL_IPF_Siena_18


title: BAL_IPF_Siena_16


title: BAL_IPF_Siena_20


title: BAL_IPF_Siena_17


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_CTCTCTAC-CTTAATAG

description: Single cell

value: Day 265


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_CTCTCTAC-CTCCTTAC

description: Single cell

value: Day 264


title: BAL_IPF_Siena_14


title: BAL_IPF_Siena_9


title: BAL_IPF_Siena_10


title: BAL_IPF_Siena_13


title: BAL_IPF_Siena_12


title: BAL_IPF_Siena_6


title: BAL_IPF_Siena_11


title: BAL_IPF_Siena_5


title: BAL_IPF_Siena_8


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_CTCTCTAC-CTAGTCGA

description: Single cell

value: Day 263


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_CTCTCTAC-CGGAGAGA

description: Single cell

value: Day 262


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_CTCTCTAC-ATTAGACG

description: Single cell

value: Day 261


title: BAL_IPF_Freiburg_62

value: Freiburg


title: BAL_IPF_Siena_2


title: BAL_IPF_Siena_7


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_CTCTCTAC-ATAGCCTT

description: Single cell

value: Day 260


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_CTCTCTAC-ATAGAGAG

description: Single cell

value: Day 259


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_CTCTCTAC-AGCTAGAA

description: Single cell

value: Day 257


title: BAL_IPF_Siena_3


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_CTCTCTAC-AGAGGATA

description: Single cell

value: plate 2

value: Day 256


title: BAL_IPF_Siena_4


title: BAL_IPF_Freiburg_58


title: BAL_IPF_Freiburg_60


title: BAL_IPF_Freiburg_57


title: BAL_IPF_Siena_1


title: BAL_IPF_Freiburg_56


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_CTCTCTAC-ACTCTAGG

description: Single cell

value: Day 255


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_CGTACTAG-TCTTACGC

description: Single cell

value: Day 254


title: BAL_IPF_Freiburg_61

value: bronchoalveolar lavage (BAL) cells


title: BAL_IPF_Freiburg_53

value: IPF


title: BAL_IPF_Freiburg_52


title: BAL_IPF_Freiburg_55


title: BAL_IPF_Freiburg_51


title: BAL_IPF_Freiburg_54


title: BAL_IPF_Freiburg_48


title: BAL_IPF_Freiburg_49


title: BAL_IPF_Freiburg_50


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_CTCTCTAC-AGGCTTAG

description: Single cell

value: Day 258


title: BAL_IPF_Freiburg_59


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_CGTACTAG-TCGCATAA

description: Single cell

value: plate 1

value: Day 253


title: BAL_IPF_Freiburg_46


title: BAL_IPF_Freiburg_43


title: BAL_IPF_Freiburg_42


title: BAL_IPF_Freiburg_44


title: BAL_IPF_Freiburg_45


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_CGTACTAG-TATGCAGT

description: Single cell

value: Day 252


title: BAL_IPF_Freiburg_47


title: BAL_IPF_Freiburg_40


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_CGTACTAG-CTTAATAG

description: Single cell

value: Day 249


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_CGTACTAG-CTAGTCGA

description: Single cell

value: Day 247


title: BAL_IPF_Freiburg_37


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_CGTACTAG-CTCCTTAC

description: Single cell

value: Day 248


title: BAL_IPF_Freiburg_35

value: Freiburg


title: BAL_IPF_Freiburg_39


title: BAL_IPF_Freiburg_36


title: BAL_IPF_Freiburg_41


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_CGTACTAG-ATTAGACG

description: Single cell

value: Day 245


title: BAL_IPF_Freiburg_34


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_CGTACTAG-CGGAGAGA

description: Single cell

value: Day 246


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_CGTACTAG-TACTCCTT

description: Single cell

value: Day 251


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_CGTACTAG-TAAGGCTC

description: Single cell

value: Day 250


title: BAL_IPF_Freiburg_31


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_CGTACTAG-ATAGCCTT

description: Single cell

value: Day 244


title: BAL_IPF_Freiburg_38


title: BAL_IPF_Freiburg_29


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_CGTACTAG-ATAGAGAG

description: Single cell

value: Day 243


title: BAL_IPF_Freiburg_30


title: BAL_IPF_Freiburg_32


title: BAL_IPF_Freiburg_26


title: BAL_IPF_Freiburg_28


title: BAL_IPF_Freiburg_27


title: BAL_IPF_Freiburg_25


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_CGTACTAG-AGGCTTAG

description: Single cell

value: Day 242


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_CGTACTAG-AGCTAGAA

description: Single cell

value: Day 241


title: BAL_IPF_Freiburg_20

value: bronchoalveolar lavage (BAL) cells

value: IPF


title: BAL_IPF_Freiburg_21


title: BAL_IPF_Freiburg_23


title: BAL_IPF_Freiburg_22


title: BAL_IPF_Freiburg_19


title: BAL_IPF_Freiburg_33


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_CGTACTAG-AGAGGATA

description: Single cell

value: plate 1

value: Day 240


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_CGTACTAG-ACTCTAGG

description: Single cell

value: Day 239


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_CGGAGCCT-TCTTACGC

description: Single cell

value: Day 238


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_CGGAGCCT-TCGCATAA

description: Single cell

value: plate 3

value: Day 237


title: BAL_IPF_Freiburg_24

value: Freiburg


title: BAL_IPF_Freiburg_18


title: BAL_IPF_Freiburg_15


title: BAL_IPF_Freiburg_17


title: BAL_IPF_Freiburg_16


title: BAL_IPF_Freiburg_14


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_CGGAGCCT-TACTCCTT

description: Single cell

value: Day 235


title: BAL_IPF_Freiburg_12


title: HBP after coculture 2

city: Majadahonda

first: Laura

last: Sanz

state: Madrid

address: Joaquín Rodrigo 2

department: Molecular Immunology

country: Spain

institute: Hospital Puerta de Hierro

description: HBP cocul 2

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials in a GeneChip® Hybridization Oven 640

scan_protocol: Affymetrix GeneChip® 3000 scanner

data_processing: The CEL files generated from the scanning were converted to gene expression signals using RMA Algorithm in Affymetrix® Expression Console

label: SAPE

source_name: HBP after coculture

label_protocol: cDNA was labeled with Affymetrix WT terminal Labeling kit

growth_protocol: HBP were cultured in Pericyte Medium with 2% FBS, pericyte growth supplement and penicillin/streptomycin (all from ScienceCell, Carlsbad, CA, USA). HCT-116 cells, obtained from the ATCC (CCL-247), were grown in DMEM supplemented with 10% FBS. Cocultureswere maintained in supplemented  2% FBS Pericyte Medium.

extract_protocol: Total RNA was extracted using a Qiagen RNeasy Micro kit according to manufacturer´s instructions.

treatment_protocol: HBP and HCT-116 (5x105 each) were mixed and cocultured in 60 mm Petri dishes for 48h. Then, cells were harvested and sorted into PDGFR + (HBP) and PDGFR - (HCT-116) populations using a BD FACSAria II cell sorter to above 98% purity.

tag: tissue source

value: Brain

value: primary pericytes

tag: cocultured with


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_CGGAGCCT-TAAGGCTC

description: Single cell

tag: age

value: Day 234


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_CGGAGCCT-TATGCAGT

description: Single cell

value: plate 4

value: Day 236


title: BAL_IPF_Freiburg_8


title: BAL_IPF_Freiburg_11


title: BAL_IPF_Freiburg_9


title: HBP after coculture 1

description: HBP cocul 1


title: HBP after coculture 3

description: HBP cocul 3


title: BAL_IPF_Freiburg_10


title: HCT-116 after coculture 3

description: HCT cocul 3

source_name: HCT-116 after coculture

tag: cell line

value: Colon

value: colorectal cancer cell line


title: BAL_IPF_Freiburg_13

value: bronchoalveolar lavage (BAL) cells


title: BAL_IPF_Freiburg_7

value: IPF


title: HCT-116 after coculture 1

description: HCT cocul 1


title: HBP in monoculture 3

description: HBP mono 3

source_name: HBP in monoculture

value: none (monoculture)


title: BAL_IPF_Freiburg_5


title: HCT-116 after coculture 2

description: HCT cocul 2


title: BAL_IPF_Freiburg_6


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_CGGAGCCT-CTTAATAG

description: Single cell

value: Day 233


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_CGGAGCCT-CTCCTTAC

description: Single cell

value: Day 232


title: HBP in monoculture 1

description: HBP mono 1


title: BAL_IPF_Freiburg_4


title: BAL_IPF_Freiburg_3


title: HBP in monoculture 2

description: HBP mono 2


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_CGGAGCCT-CTAGTCGA

description: Single cell

value: Day 231


title: HCT-116 in monoculture 2

description: HCT mono 2

source_name: HCT-116 in monoculture


title: BAL_HD_Freiburg_20

value: healthy donor


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_CGGAGCCT-CGGAGAGA

description: Single cell

value: plate 3

value: Day 230


title: HCT-116 in monoculture 3

description: HCT mono 3


title: BAL_IPF_Freiburg_2

value: Freiburg


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_CGGAGCCT-ATTAGACG

description: Single cell

value: Day 229


title: BAL_IPF_Freiburg_1


title: BAL_HD_Freiburg_19


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_CGGAGCCT-ATAGAGAG

description: Single cell

value: Day 227


title: BAL_HD_Freiburg_18


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_CGGAGCCT-AGGCTTAG

description: Single cell

value: Day 226


title: HCT-116 in monoculture 1

description: HCT mono 1


title: BAL_HD_Freiburg_12


title: BAL_HD_Freiburg_13


title: BAL_HD_Freiburg_11


title: BAL_HD_Freiburg_16


title: BAL_HD_Freiburg_15


title: BAL_HD_Freiburg_17


title: BAL_HD_Freiburg_8


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_CGGAGCCT-ATAGCCTT

description: Single cell

value: plate 4

value: Day 228


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_CGGAGCCT-AGCTAGAA

description: Single cell

value: Day 225


title: BAL_HD_Freiburg_9


title: BAL_HD_Freiburg_10


title: IF + ZT21 + Feeding-replicate 3

city: Indianapolis

first: Leni

last: Moldovan

state: IN

address: 980 W Walnut St., Rm. C422

department: Ophthalmology

institute: Indiana University

description: gene expression data from liver of mice on intermittent fasting, feeding phase, night time

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix protocol

data_processing: Affymetrix Expression Console (RMA), Transcriptome Analysis Console, and R (version 2.15.3). A linear model with covariates of long-term IF effect, ZT time effect and feeding/fasting effect was built and the adequacy of fit was tested by likelihood ratio test. False discovery rate (FDR) correction was conducted to adjust for multiple testing

label: biotin

source_name: db/db mice, liver

label_protocol: Standard Affymetrix protocol

growth_protocol: Standard diet, strict 12h:12h light:dark cycle

extract_protocol: Total RNA was extracted using miRNeasy Mini kit (Qiagen, Valencia, CA) as per manufacturer protocol.

treatment_protocol: Mice were fed ad lib before the IF was initiated at 4 months of agethereafter they were divided in two groups, ad lib feeding (control) and IF, wherein the animals were fasted for 24 hours every other day for 7 months, beginning at night

tag: strain

tag: gender

value: male

tag: regimen

value: intermittent fasting

tag: time

value: night

tag: feeding phase

value: feeding


title: IF + ZT21 + Feeding-replicate 2


title: IF + ZT9 + Fasting-replicate 3

description: gene expression data from liver of mice on intermittent fasting, fasting phase, day time

value: day

value: fasting


title: IF + ZT21 + Feeding-replicate 1


title: BAL_HD_Freiburg_14

value: bronchoalveolar lavage (BAL) cells


title: IF + ZT9 + Fasting-replicate 2


title: BAL_HD_Freiburg_7

value: healthy donor


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_CGGAGCCT-ACTCTAGG

description: Single cell

tag: plate id

value: plate 3

value: Day 223

tag: line


title: BAL_HD_Freiburg_5

tag: cell type

tag: diagnosis

value: Freiburg


title: BAL_HD_Freiburg_2

tag: cohort

tag: sex (0=female, 1=male)


title: BAL_HD_Freiburg_4


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_CGGAGCCT-AGAGGATA

description: Single cell

value: Day 224


title: IF + ZT9 + Fasting-replicate 1


title: IF + ZT21 + Fasting-replicate 3

description: gene expression data from liver of mice on intermittent fasting, fasting phase, night time


title: BAL_HD_Freiburg_6


title: BAL_HD_Freiburg_1


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_CGAGGCTG-TCGCATAA

description: Single cell

value: plate 2

value: Day 221


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_CGAGGCTG-TATGCAGT

description: Single cell

value: Day 220


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_CGAGGCTG-TACTCCTT

description: Single cell

value: Day 219


title: alveolar macrophages from healthy donors_7

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 ml containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 ml of 2x GEx Agilent hybridization buffer HI-RPM was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112F) 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.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA High Resolution Microarray Scanner (G2505C US45102918) using one color scan setting for 8 x 60K array slides (Scan Area 61x21.6 mm, Scan resolution 5 μm, Tiff 20 bit, Dye channel is set to Green).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended. Processed Signal intensities.  Gene expression data was normalized to the geometric mean of all samples using quantile normalization. Non-expressed and invariant transcripts were removed.    A final dataset of 29271 transcript measurements across the 22 samples was obtained. For statistical analysis we used the average gene expression values of the replicated probes.

source_name: Alveolar macrophages

label_protocol: Labeling reactions were performed for each sample using Agilent Low RNA Input Linear Amplification Kit PLUS, One-Color ( Agilent Technologies, Santa Clara, CA). Briefly, with a starting concentration of 100 nanograms of total RNA, an initial cDNA strand was synthesized using a oligo(dT)24 primer containing a T7 RNA polymerase, this cDNA was then used as a template to generate Cy3 labeled cRNA by a reverse transcriptase enzyme. After the cRNA was obtained a purification step was performed using RNeasy Mini Kit (74104, Qiagen, Valencia, CA) followed by measurement of the yield and specific activity of each sample

extract_protocol:
[Isolation protocol] Bronchial epithelial cells were obtained by bronchial brushes during bronchoscopy. The brushs were immediately placed in RNA protect. To the cell pellets of alveolar macrophages and airway basal cells 1 ml of QIAzol (79306, Qiagen, Valencia, CA) was immediately added and they were snap frozen in -80 celsius.
Total RNA was extracted and purified using the miRNeasy Mini Kit (217004, Qiagen, Valencia, CA) under fully automated sample preparation by the assistance of the QIAcube device (9001292, Qiagen, Valencia CA) following the manufacturer’s protocol.After extraction, total RNA yield and quality were evaluated using NanoDrop at 260 nm and the 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA)

value: alveolar macrophages


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_CGAGGCTG-TCTTACGC

description: Single cell

value: Day 222


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_CGAGGCTG-TAAGGCTC

description: Single cell

value: Day 218


title: alveolar macrophages from healthy donors_6


title: BAL_HD_Freiburg_3


title: IF + ZT21 + Fasting-replicate 1

value: male

value: intermittent fasting

value: night


title: alveolar macrophages from healthy donors_5


title: alveolar macrophages from healthy donors_3


title: alveolar macrophages from healthy donors_1


title: alveolar macrophages from healthy donors_4


title: IF + ZT9 + Feeding-replicate 2

description: gene expression data from liver of mice on intermittent fasting, feeding phase, day time

value: day

value: feeding


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_CGAGGCTG-CTCCTTAC

description: Single cell

value: Day 216


title: alveolar macrophages from healthy donors_2

value: healthy donor


title: bronchial epithelial cells from healthy donor_3

source_name: Bronchial epithelial cells

value: bronchial epithelial cells


title: IF + ZT21 + Fasting-replicate 2

value: fasting


title: bronchial epithelial cells from healthy donor_4


title: IF + ZT9 + Feeding-replicate 1


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_CGAGGCTG-CTTAATAG

description: Single cell

value: Day 217


title: IF + ZT9 + Feeding-replicate 3


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_CGAGGCTG-CTAGTCGA

description: Single cell

value: plate 2

value: Day 215


title: ad lib + ZT21 + Feeding-replicate 3

description: gene expression data from liver of mice fed ad libitum, night time

value: ad libitum


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_CGAGGCTG-CGGAGAGA

description: Single cell

value: Day 214


title: airway basal cells from human healthy donor_11

source_name: Airway basal cells derived from bronchial brushes

value: airway basal cells


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_CGAGGCTG-ATTAGACG

description: Single cell

value: Day 213


title: ad lib + ZT9 + Feeding-replicate 3

description: gene expression data from liver of mice fed ad libitum, day time


title: bronchial epithelial cells from healthy donor_1


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_CGAGGCTG-ATAGAGAG

description: Single cell

value: Day 211


title: ad lib + ZT21 + Feeding-replicate 2

value: male


title: airway basal cells from human healthy donor_8


title: bronchial epithelial cells from healthy donor_2


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_CGAGGCTG-AGGCTTAG

description: Single cell

value: Day 210


title: airway basal cells from human healthy donor_9


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_CGAGGCTG-AGCTAGAA

description: Single cell

value: Day 209


title: airway basal cells from human healthy donor_10


title: ad lib + ZT21 + Feeding-replicate 1

value: night


title: airway basal cells from human healthy donor_6


title: ad lib + ZT9 + Feeding-replicate 2

value: day

value: feeding


title: airway basal cells from human healthy donor_5

value: healthy donor


title: airway basal cells from human healthy donor_7


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_CGAGGCTG-AGAGGATA

description: Single cell

value: Day 208


title: ad lib + ZT9 + Feeding-replicate 1


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_CGAGGCTG-ATAGCCTT

description: Single cell

value: Day 212


title: airway basal cells from human healthy donor_3


title: d18_H7N7_16

city: Braunschweig

first: Robert

last: Geffers

address: Inhoffenstr. 7

department: Dep. Molecular Bacteriology

institute: HCI - Helmholtz Centre for Infection Research

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml 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 65Â°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 37Â°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 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software10.5 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: hippocampus

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was prepared using Qiagen RNAeasy Kit. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Female mice of the age 8-10 weeks were anesthetized by intra-peritoneal injection of 0.9% (w/v) NaCl (Merck) ketamin-xylazine solution (85% NaCl (0.9%), 10% ketamine (100 mg/ml), 5% xylazine (20 mg/ml); 10mL per 1kg body weight) and then infected intra-nasally with a dose of 10 or 2x103 FFU (Focus Forming Units) of the respective virus in 20µL sterile phosphate-buffered saline (PBS). Body weight was monitored for two weeks. Mice showing more than 30% of body weight loss were euthanized.

tag: tissue

value: hippocampus

tag: virus

value: female


title: airway basal cells from human healthy donor_2


title: airway basal cells from human healthy donor_1


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_CGAGGCTG-ACTCTAGG

description: Single cell

value: plate 2

value: Day 207


title: d18_H7N7_17


title: d18_H7N7_18


title: d18_H3N2_11


title: d18_H3N2_13


title: d18_H3N2_12


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_ATGCGCAG-TCTTACGC

description: Single cell

value: Day 206


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_ATGCGCAG-TCGCATAA

description: Single cell

value: plate 4

value: Day 205


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_ATGCGCAG-TATGCAGT

description: Single cell

value: plate 5

value: Day 204


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_ATGCGCAG-TACTCCTT

description: Single cell

value: Day 203


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_ATGCGCAG-TAAGGCTC

description: Single cell

value: Day 202


title: airway basal cells from human healthy donor_4

value: airway basal cells


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_ATGCGCAG-CTTAATAG

description: Single cell

value: Day 201


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_ATGCGCAG-CTCCTTAC

description: Single cell

value: Day 200


title: d18_mock_4

value: mock


title: d18_H3N2_10


title: 60 mins with laminar shear stress conditions

city: Taipei

first: Tzu-Hao

last: Chang

address: 250 Wu-Xin Street

department: Graduate Institute of Biomedical Informatics

country: Taiwan

institute: Taipei Medical University

description: SAMPLE 5

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in R

source_name: orbital fat-derived stem cells

label_protocol: Standard Illumina label protocol

extract_protocol: Standard Illumina extract protocol

value: orbital fat-derived stem cells

tag: duration of stress

value: 60 min


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_ATGCGCAG-CTAGTCGA

description: Single cell

value: Day 199


title: d18_mock_3

value: hippocampus

value: female


title: 30 mins with laminar shear stress conditions

description: SAMPLE 3

value: 30 min


title: 4 hours with laminar shear stress conditions

description: SAMPLE 6

value: 4 hours


title: d18_mock_2


title: 0 min with laminar shear stress conditions

description: SAMPLE 1

value: 0 min


title: d18_mock_1


title: 45 mins with laminar shear stress conditions

description: SAMPLE 4

value: 45 min


title: 15 mins with laminar shear stress conditions

description: SAMPLE 2

value: 15 min


title: d30_H7N7_37


title: d30_H7N7_36


title: Naltrindole 2 uM

city: Taipei city

first: Shiang-Jong

last: Tzeng

address: 11F, No.1, Sec.1, Ren-ai Rd

department: Department and Graduate Institute of Pharmacology, College of Medicine

institute: National Taiwan University

description: total RNA

hyb_protocol: A total of 1.5 ug cRNA was subsequently hybridized to Illumina Human HT-12 v4.0 beadchip at 58°C at the Illumina Bead Station. After hybridization for 14-20 h, the BeadChip was stained by Cy3 and washed.

scan_protocol: Standard Illumina scanning protocol.

data_processing: The data were normalised using quantile normalisation with 'limma' package in R.

source_name: BJAB B cell line

label_protocol: A total of 500 ng RNAs per sample were converted to double-stranded cDNA, followed by an amplification step with in vitro transcription to generate biotin-labeled cRNA.

growth_protocol: Cells were grown in RPMI 1640 supplemented with 10% FCS and penicillin/streptomycin/amphotericin B.

extract_protocol: Total RNAs of each sample were extracted with Trizol following manufacturer's protocol. Total RNA samples with A260/A280 = 1.8-2.0 were assessed for RNA integrity. Samples with RIN > 9 were processed for gene expression profiling. The RNA concentration of samples was adjusted to the 50 ng/μl with DEPC-treated H2O.

treatment_protocol: Cells (2×10^6/ml) were treated with 2 uM or 10 uM of BNTX, naloxone or naltrindole for 9 hours.

value: BJAB

value: B cell lymphoma

tag: treatment

value: Naltrindole 2 uM


title: d30_H7N7_35


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_ATGCGCAG-CGGAGAGA

description: Single cell

value: plate 4

tag: age

value: Day 198


title: Naloxone 10 uM

description: total RNA

tag: cell line

value: Naloxone 10 uM


title: BNTX 2 uM

description: total RNA

value: BNTX 2 uM


title: DMSO

description: total RNA

value: DMSO


title: BNTX 10 uM

description: total RNA

value: BNTX 10 uM


title: Naltrindole 10 uM

description: total RNA

value: Naltrindole 10 uM


title: Naloxone 2 uM

description: total RNA

value: Naloxone 2 uM


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_ATGCGCAG-ATTAGACG

description: Single cell

value: plate 5

value: Day 197


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_ATGCGCAG-ATAGAGAG

description: Single cell

value: Day 195


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_ATGCGCAG-ATAGCCTT

description: Single cell

value: Day 196


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_ATGCGCAG-AGGCTTAG

description: Single cell

value: Day 194


title: d30_H7N7_34

value: hippocampus

tag: strain

value: female


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_ATGCGCAG-AGAGGATA

description: Single cell

value: Day 192


title: d30_H3N2_31

tag: gender


title: d30_H3N2_30


title: Control_5

city: Milan

first: Fabio

last: Martelli

address: via morandi 30

country: Italy

institute: IRCCS-Policlinico San Donato

description: SAMPLE 5

hyb_protocol: The obtained cRNAs were hybridized on a HumanHT-12 v4 Expression BeadChip according to the Standard Illumina hybridization protocol.

scan_protocol: Scanned and the background subtracted intensities were generated by GenomeStudio Software, according to the standard Illumina scanning protocol.

data_processing:
Between arrays normalization (quantile) and differential expression analysis were performed by limma package (Bioconductor, RStudio v 0.98.501).
The intensities were log2 transformed and quantile normalized. Subsequently, genes were filtered for expression, by applying a threshold of Detection Pval < 0.01 for each of the samples.

source_name: HAOEC, Control

label_protocol: Biotinylated cRNA was prepared using the Ambion Illumina RNA amplification kit.

growth_protocol: HAOEC were grown in EGM-2 (Lonza) containing 2% FBS.

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

treatment_protocol: HAOEC were transfected with 50 nM of antisense LNA™ GapmeRs customer-designed for BACE1-AS or Negative control A (Exiqon).

value: HAOEC

tag: experiment type

value: Negative Control

tag: experiment id


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_ATGCGCAG-ACTCTAGG

description: Single cell

value: plate 4

value: Day 191


title: BACE1AS block_4

description: SAMPLE 4

source_name: HAOEC, BACE1AS block

value: BACE1AS GAPmer


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_ATGCGCAG-AGCTAGAA

description: Single cell

value: Day 193


title: Control_3

description: SAMPLE 3


title: Control_6

description: SAMPLE 6


title: BACE1AS block_2

description: SAMPLE 2


title: d30_H3N2_32


title: d30_H3N2_29


title: d30_mock_20

value: mock


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_ATCTCAGG-TCTTACGC

description: Single cell

value: Day 190


title: d30_mock_21


title: d30_mock_23


title: Control_1

description: SAMPLE 1


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_ATCTCAGG-TCGCATAA

description: Single cell

value: plate 3

value: Day 189


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_ATCTCAGG-TATGCAGT

description: Single cell

value: Day 188


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_ATCTCAGG-TACTCCTT

description: Single cell

value: Day 187


title: PPs_CTR_BB9

city: Uppsala

first: Haoyu

last: Liu

address: Husargatan 3

department: Medicinsk Cellbiologi, Avdelningen för Fysiologi

country: Sweden

institute: Uppsala Universuity

description: Gene expression of BB from control

hyb_protocol: Clariom™ D mouse arrays (previous name: GeneChip™ Mouse Transcriptome Array 1.0) were hybridized for 16 hours in a 45°C incubator, rotated at 60 rpm. According to the GeneChip™ Expression Wash, Stain and Scan Manual (P/N 702731, ThermoFisher Scientific Inc., Life Technologies, Carlsbad, CA 92008 USA) the arrays were then washed and stained using the GeneChip™ Fluidics Station 450

scan_protocol: Scanning was performed using the GeneChip™ Scanner 3000 7G

data_processing: The raw data was normalized to gene level in Expression Console, provided by Affymetrix (http://www.affymetrix.com), using the SST-RMA version of the robust multi-array average (RMA) method

source_name: Peyer's patches

label_protocol: 2 nanograms of total RNA from each sample were used to generate amplified and biotinylated sense-strand cDNA from the entire expressed genome according to the GeneChip™ WT Pico Reagent Kit Manual (P/N 703262 ThermoFisher Scientific Inc., Life Technologies, Carlsbad, CA 92008 USA)

growth_protocol: Mice were gavaged by freshly prepared bacteria daily for 7 days, or gavaged by sterile PBS. And weighed daily.

extract_protocol:
B cells were enriched by negative selection using MACS columns with a Cocktail of biotin-conjugated monoclonal antibodies against CD3ε, CD4, CD8a, CD49b, Gr-1, and Ter119. The sample was further stained with anti-CD19 and anti-B220 antibodies to confirm 95% purity and subjected to FACS-AriaIII and sorted by FSC-A
Total RNA was isolated using RNeasy® Micro kit (Qiagen)

treatment_protocol: Peyer's patcehs were dissected from mouse small intestine and pooled as one individual to prepare single cell suspension. The sample was then stained by a combination of antibody surface marker and sorted by  FACS-AriaIII

tag: Sex

value: male

value: 8-14 weeks old mice

value: BB

tag: agent


title: PPs_CTRl_SB9

description: Gene expression of SB from control

value: SB


title: PPs_TRT_BB16

description: Gene expression of BB from treated mice

value: bacteria


title: E13.5 Soma_rep3

city: Sendai

first: Yohei

last: Hayashi

state: Miyagi

address: 4-1 Seiryo-machi, Aobaku

department: Institute of Development, Aging and Cancer

country: Japan

institute: Tohoku University

description:
Gene expression of Somas from mouse E13.5 male embryo genital ridges.
Replicate3

hyb_protocol: 1.65ug of Cy3-labelled cRNAs from each sample were fragmented and hybridized to microarrays according to the manufacturer's instructions using the Gene Expression Hybridization kit (Agilent 5188-5242) and Agilent hybridization oven. After hybridization, microarrays were washed using the Gene Expression Wash Pack (Agilent 5188-5327).

scan_protocol: The microarrays were scanned using the Agilent DNA microarray scanner (Agilent G2505C). The spot signals were quantified using Feature Extraction software.

data_processing: Data was normalized using 75th percentile shift and analyzed by GeneSpring GX (Agilent).

source_name: gonadal somatic cell

label_protocol: Cy3-labeled cRNA samples were prepared using the Agilent Low Input Quick Amp Labeling Kit (one-color) (5190-2305) and RNA Spike-In Kit (one-color) (5188-5282) according to the manufacturer's instructions. Input was 100 ng of total RNA from each sample.

extract_protocol: Total RNA was purified using the RNeasy micro kit according to the manufacturer's instructions.

tag: strain/background

value: MCH x C57BL6/J (Oct5<delta>PE-GFP Tg)

tag: developmental stage

value: gonadal somatic cell


title: VR15 ESC_rep3

description:
Gene expression of mouse male ESCs (Vasa::RFP Tg).
Replicate3

source_name: embryonic stem cell

value: Embryonic stem cell (Vasa::RFP Tg)

tag: cell type

value: embryonic stem cell


title: VR15 ESC_rep2

description:
Gene expression of mouse male ESCs (Vasa::RFP Tg).
Replicate2


title: PPs_TRT_SB16

description: Gene expression of SB from treated mice


title: E13.5 Soma_rep2

description:
Gene expression of Somas from mouse E13.5 male embryo genital ridges.
Replicate2


title: PPs_TRT_SB14

description: Gene expression of SB from treated mice


title: PPs_TRT_BB15

description: Gene expression of BB from treated mice


title: PPs_TRT_BB14

description: Gene expression of BB from treated mice


title: E13.5 Soma_rep1

description:
Gene expression of Somas from mouse E13.5 male embryo genital ridges.
Replicate1


title: NCI-H716_Genome-wide_400K_CGH

type: genomic

city: Harbin

first: Xueyuan

last: Jia

address: 157 Baojian Road, Nangang District

country: China

institute: Harbin Medical University

hyb_protocol: After sample denaturation and pre-annealing with 5µl of Human Cot-1 DNA (Invitrogen, Carlsbad, CA), hybridization was performed at 65°C with shaking for 24 hours.

scan_protocol: Scanned on an Agilent scanner. Images were quantified using Agilent Feature Extraction Software (version 9.1).

data_processing: The data was processed on Cytogenomics 2.9.1.3 using the Default Analysis Method (The z-score algorithm at threshold 4) - CGH v2 proposed by Agilent.

molecule: genomic DNA

source_name: Human colorectal cancer cell line NCI-H716

label_protocol: Tumor and control DNA were labeled by random priming with Cy5- and Cy3-dUTP dyes, respectively using the Agilent Genomic DNA Enzymatic Labeling Kit.

growth_protocol: The cells were cultured in RPMI1640 medium (Gibco, Carlsbad, CA, US) supplemented with 10% fetal bovine serum (Gibco, Carlsbad, CA, US) in a humidified atmosphere of 5% CO2 at 37°C. Cells were authenticated by short tandem repeat profiling analysis (Beijing Microread Genetics, Beijing, China).

extract_protocol: Genomic DNA from cultured cells were isolated with an AllPrep DNA/RNA mini kit (Qiagen, Hilden, Germany) following the manufacturer's protocol.

value: colorectal adenocarcinoma

value: cancer cell line

source_name: Commercial Male DNA reference from Agilent

value: peripheral blood


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_ATCTCAGG-CTTAATAG

description: Single cell

source_name: human oligodendrocyte spheroids

tag: plate id

value: Day 185

tag: line


title: PPs_TRT_SB13

description: Gene expression of SB from treated mice


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_ATCTCAGG-CTCCTTAC

description: Single cell

value: plate 3

value: Day 184


title: PPs_TRT_BB13

description: Gene expression of BB from treated mice


title: VR15 ESC_rep1

description:
Gene expression of mouse male ESCs (Vasa::RFP Tg).
Replicate1


title: PPs_CTR_BB12

description: Gene expression of BB from control


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_ATCTCAGG-CTAGTCGA

description: Single cell

value: Day 183


title: PPs_CTR_SB12

description: Gene expression of SB from control


title: PPs_CTR_SB11

description: Gene expression of SB from control


title: anti-Thy1 model killed at day 4 (4d-10H-2)

city: Beijing

first: Yang

last: Lu

address: 8th fuxing road

institute: PLA general hospital

description: Gene expression of glomerulus in anti-Thy1 model killed at day 4

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Rat 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 (Cat.# G2565CA) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel: Green, Scan resolution=5μm, PMT 100%, 10%, 16bit).

data_processing: The scanned images were analyzed with GeneSpring Software 12.6.1 (Agilent technologies, Santa Clara, CA, US) to perform quantile normalization

organism: Rattus

source_name: anti-Thy1 model killed at day 4

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 1.65μg RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was prepared using the TRIzol following the manufacturer's recommendations.

treatment_protocol: Thirty rats were injected with an anti-Thy1 antibody and six were injected with saline (controls).

value: SD

value: anti-Thy1 antibody

tag: weight

tag: time

value: day 4

tag: tissue

value: glomerulus


title: Chicken PR3 sample 18

city: Dummerstorf

first: Klaus

last: Wimmers

address: Wilhelm-Stahl-Allee 2

department: Genome Biology

institute: FBN Dummerstorf

description: Gene level expression of bursal tissues in chicken.

hyb_protocol: Labelled DNA was hybridized for 16 hr at 42°C on ChiGene-1_0-st Arrays. Chips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: Scanning using the GeneChip scanner 3000 was performed according to Affymetrix protocols.

data_processing: Data were analysed with Affymetrix GCOS 1.1.1 software using global scaling to a target signal of 500 and BioConductor.

organism: Gallus gallus

source_name: Bursa of Fabricius

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 500 ng total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Animals were kept at the Experimental Poultry farm of the University of Chiang Mai, Thailand; animals were fed ad libitum.

extract_protocol: Total RNA was isolated using TRIZOL according to the manufacturer’s protocol. After DNaseI treatment, the RNA was cleaned up using the RNeasy Kit (Qiagen, Hilden, Germany).

treatment_protocol: Samples were obtained at 80 days of age.

tag: breed

value: CheeFah

value: Bursa of Fabricius

value: Male


title: BS_HJ149

city: Davis

first: Hong

last: Ji

address: County Rd 98 & Hutchison Drive

institute: University of California Davis

description: Bronchial epithelial cell line obtained from UT Southwestern Medical Center

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium MethylationEPIC Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: RnBeads

label: Cy5 and Cy3

label_protocol: Standard Illumina Protocol

growth_protocol: Human bronchial epithelial cells (HBECs) (a cell line obtained from Dr. John Minna’s lab at UT Southwestern Medical Center) were grown to ~70% confluence in Keratinocyte-SFM serum-free medium (10724-011, Life Technologies, Grand Island, NY) supplemented with human recombinant Epidermal Growth Factor (10450-013, Life Technologies, Grand Island, NY)  and Bovine Pituitary Extract (13028-014, Life Technologies, Grand Island, NY)

extract_protocol: Genomic DNA was extracted using Qiagen Allprep micro kit according to manufacturer’s  instructions.

treatment_protocol: Human bronchial epithelial cells were treated with PBS, diesel exhaust particles (5ug/cm2), and house dust mite (25ug/ml) for 24 hours.

tag: treatment

value: HDM

tag: replicate


title: PPs_CTR_BB10

description: Gene expression of BB from control

tag: strain

value: male

tag: age

value: 8-14 weeks old mice

value: BB


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_ATCTCAGG-ATTAGACG

description: Single cell

extract_protocol:
Single cells were sorted into lysis buffer according to a published Smartseq2  protocol (Picelli, S. et al. 2014). ERCC RNA Spike-In Mix was added at 1: 2.4X10^7  dilution in the buffer.
Sorted cells in 96-well plates were used for library preparation following the  Smartseq2 protocol (Picelli, S. et al. 2014) with modifications. Briefly, plates were  incubated at 72˚C, 3 min for annealing with Oligo-dT 30 VN. Reverse transcription  mixture was added 6ul per well, and RT was performed at 42˚C for 90 min, followed  by 70˚C, 5 min. To amplify the whole transcriptome, 15ul of DNA amplification  mixture was added and cDNA was amplified for 21 cycles. Amplified cDNA was then  purified using PCRClean DX beads. cDNA quality and quantity were assessed using a  Fragment Analyzer (AATI, High Sensitivity NGS Fragment Analysis Kit:1 bp - 6000  bp), and samples with concentrations below 0.08ng/ul or abnormal peak patterns  were filtered out. A total of 295 cDNA samples (retaining 88.9% of initially sorted)  were diluted down to 0.15ng/ul (only if above it) and consolidated into a 384-well  plate using a Mosquito X1 (TTP Labtech). Library preparation was performed using  Nextera XT DNA Sample Prep Kit (Illumina, Cat: FC-131-1096) and Nextera XT 384  dual index primers, with the help of a Mosquito HTS machine for liquid transfer.  Tagmentation was performed in 1.2ul at 55˚C for 10 min and amplification was  performed in 4ul system, 10 cycles. In the end, all samples were pooled (0.5ul each)  together into a 1.5ml Eppendorf tube, and the mixed libraries were purified twice  with PCRClean DX beads. The final sample was reconstituted in 50ul EB buffer, and  the concentration and peaks were measured by Qubit and Bioanalyzer before  Illumina sequencing (Hiseq).
Single cell RNA-seq

value: Day 181


title: oxBS_HJ149


title: BS_HJ147

value: DEP


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_ATCTCAGG-TAAGGCTC

description: Single cell

value: Day 186


title: PPs_CTR_SB10

description: Gene expression of SB from control

value: SB


title: anti-Thy1 model killed at day 4 (4d-10H-1)


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_ATCTCAGG-ATAGCCTT

description: Single cell

value: plate 3

value: Day 180


title: anti-Thy1 model killed at day 2 (2d-10H-4)

description: Gene expression of glomerulus in anti-Thy1 model killed at day 2

source_name: anti-Thy1 model killed at day 2

value: SD

value: day 2


title: BS_HJ145


title: oxBS_HJ145


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_ATCTCAGG-CGGAGAGA

description: Single cell

value: Day 182


title: oxBS_HJ146

value: control


title: oxBS_HJ148


title: anti-Thy1 model killed at day 4 (4d-10H-3)

value: anti-Thy1 antibody

value: day 4

value: glomerulus


title: BS_HJ148

value: HDM


title: Chicken RR3 sample 15

value: FhaLuang

value: Bursa of Fabricius

value: Male


title: BS_HJ144


title: PPs_CTR_BB11

description: Gene expression of BB from control

value: male

value: 8-14 weeks old mice

value: BB


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_ATCTCAGG-ATAGAGAG

description: Single cell

value: Day 179


title: Chicken RR2 sample 14


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_ATCTCAGG-AGGCTTAG

description: Single cell

value: plate 3

value: Day 178


title: anti-Thy1 model killed at day 2 (2d-10H-3)

value: SD


title: BS_HJ146


title: oxBS_HJ147

value: DEP


title: Chicken PR1 sample 16

value: CheeFah


title: oxBS_HJ144

value: control


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_ATCTCAGG-ACTCTAGG

description: Single cell

value: Day 175


title: Chicken PR2 sample 17


title: Chicken CF3 sample 12

value: Pradhuhangdum x Rhode Island Red


title: Chicken CF2 sample 11


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_AGGCAGAA-TCGCATAA

description: Single cell

value: plate 1

value: Day 173


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_ATCTCAGG-AGCTAGAA

description: Single cell

value: Day 177


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_AGGCAGAA-TCTTACGC

description: Single cell

value: Day 174


title: PPs_TRT_SB15

description: Gene expression of SB from treated mice

value: SB

value: bacteria


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_ATCTCAGG-AGAGGATA

description: Single cell

value: Day 176


title: Chicken RR1 sample 13

value: FhaLuang

value: Bursa of Fabricius

value: Male


title: Chicken CF1 sample 10


title: Chicken FL3 sample 6

value: Rhode Island Red


title: Chicken MS3 sample 9

value: Mae Hong Son


title: anti-Thy1 model killed at day 2 (2d-10H-2)

value: SD

value: anti-Thy1 antibody

value: day 2

value: glomerulus


title: Chicken MS1 sample 7


title: Chicken FL2 sample 5


title: Chicken FL1 sample 4


title: anti-Thy1 model killed at day 5 (5d-10H-5)

description: Gene expression of glomerulus in anti-Thy1 model killed at day 5

source_name: anti-Thy1 model killed at day 5

value: day 5


title: anti-Thy1 model killed at day 5 (5d-10H-4)


title: Chicken PD2 sample 2

value: Pradhuhangdum


title: Chicken PD3 sample 3


title: Chicken PD1 sample 1


title: Chicken MS2 sample 8


title: anti-Thy1 model killed at day 5 (5d-10H-2)


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_AGGCAGAA-TATGCAGT

description: Single cell

value: plate 1

value: Day 172


title: anti-Thy1 model killed at day 3 (3d-10H-4)

description: Gene expression of glomerulus in anti-Thy1 model killed at day 3

source_name: anti-Thy1 model killed at day 3

value: day 3


title: anti-Thy1 model killed at day 3 (3d-10H-3)


title: anti-Thy1 model killed at day 3 (3d-10H-2)


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_AGGCAGAA-TACTCCTT

description: Single cell

value: Day 171


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_AGGCAGAA-TAAGGCTC

description: Single cell

value: Day 170


title: anti-Thy1 model killed at day 1 (1d-10H-5)

description: Gene expression of glomerulus in anti-Thy1 model killed at day 1

source_name: anti-Thy1 model killed at day 1

value: day 1


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_AGGCAGAA-CTCCTTAC

description: Single cell

value: Day 168


title: WM2664-LGX818-24ha

city: Emeryville

first: Guoying

middle: Karen

last: Yu

address: 4560 Horton St, MS 4.1

department: bioinformatics

institute: Novartis - NIBR

description: LGX818 treatment 24hr

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

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000.

data_processing: The data were analyzed with Bioconductor affy package (http://bioconductor.org) with RMA method and HGU133Plus2_Hs_ENTREZG custom CDF v16 for target gene definition (Dai et al., 2005)

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

growth_protocol: WM266-4 cells or WM266-6 carrying inducible shRNAs were seeded on 6-well plates at 300,000 cells per well, 24hr before treatment

extract_protocol: Total RNA was extracted with RNAeasy Plus kit (Qiagen) according to the manufacturer's instructions.

treatment_protocol: WM266-4 cells were treated with 0.05uM LGX818, 0.003uM trametinib, 0.3uM MEK162,  0.2uM ERK1/2 inhibitor or DMSO for 3hr or 24hr in triplicates. WM266-4 cells carrying inducible shRNAs were treated with 100ng/ml doxycycline for 3 or 7 days in triplicates.

tag: cell line

tag: genotype

value: BRAF V600D

tag: time point


title: WM2664-trametinib-24hc

description: trametinib treatment 24hr

value: trametinib 0.003 uM


title: WM2664-trametinib-24hb

description: trametinib treatment 24hr


title: WM2664-trametinib-24ha

description: trametinib treatment 24hr


title: WM2664-LGX818-24hc

description: LGX818 treatment 24hr


title: anti-Thy1 model killed at day 1 (1d-10H-4)

tag: agent


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_AGGCAGAA-CGGAGAGA

description: Single cell

data_processing:
Read alignment: reads were aligned to the hg38 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ).
Per-gene read assignement: aligned reads were converted to counts for every gene using FeatureCounts (-p -t exon -g gene_id -a ).
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample

value: Day 166


title: WM2664-LGX818-24hb

description: LGX818 treatment 24hr


title: WM2664-ERK1/2-inhibitor-24hc

description: ERK1/2 inhibitor treatment 24hr

value: ERK1/2-inhibitor 0.2 uM


title: anti-Thy1 model killed at day 1 (1d-10H-1)

value: SD


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_AGGCAGAA-ATTAGACG

description: Single cell

value: Day 165


title: WM2664-MER162-24hc

description: MEK162 treatment 24hr


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_AGGCAGAA-CTTAATAG

description: Single cell

value: Day 169


title: WM2664-MER162-24hb

description: MEK162 treatment 24hr


title: WM2664-ERK1/2-inhibitor-24hb

description: ERK1/2 inhibitor treatment 24hr


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_AGGCAGAA-CTAGTCGA

description: Single cell

value: Day 167


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_AGGCAGAA-ATAGCCTT

description: Single cell

value: Day 164


title: Normal control (0d-10H-4)

description: Gene expression of glomerulus in Normal control

source_name: Normal control

value: control

value: day 0

value: glomerulus


title: WM2664-DMSO-24hc

description: DMSO treatment  24hr

value: DMSO


title: WM2664-MEK162-24ha

description: MEK162 treatment 24hr


title: Normal control (0d-10H-5)


title: Normal control (0d-10H-2)


title: WM2664-ERK1/2-inhibitor-24ha

description: ERK1/2 inhibitor treatment 24hr


title: WM2664-DMSO-24ha

description: DMSO treatment  24hr


title: WM2664-LGX818-3hb

description: LGX818 treatment 3hr


title: WM2664-LGX818-3ha

description: LGX818 treatment 3hr


title: WM2664-LGX818-3hc

description: LGX818 treatment 3hr


title: WM2664-trametinib-3hc

description: trametinib treatment 3hr


title: WM2664-MER162-3hc

description: MEK162 treatment 3hr


title: WM2664-trametinib-3hb

description: trametinib treatment 3hr


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_AGGCAGAA-ACTCTAGG

description: Single cell

value: plate 1

value: Day 159


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_AGGCAGAA-AGGCTTAG

description: Single cell

value: Day 162


title: WM2664-trametinib-3ha

description: trametinib treatment 3hr


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_AGGCAGAA-AGAGGATA

description: Single cell

value: Day 160


title: WM2664-MER162-3hb

description: MEK162 treatment 3hr

value: BRAF V600D


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_AGGCAGAA-AGCTAGAA

description: Single cell

value: Day 161


title: WM2664-DMSO-3hb

description: DMSO treatment  3hr


title: WM2664-DMSO-3ha

description: DMSO treatment  3hr


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_AGGCAGAA-ATAGAGAG

description: Single cell

value: Day 163


title: WM2664-ERK1/2-inhibitor-3ha

description: ERK1/2 inhibitor treatment 3hr

value: ERK1/2-inhibitor 0.2 uM


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_ACTCGCTA-TCTTACGC

description: Single cell

value: Day 158


title: WM2664-ERK1/2-inhibitor-3hb

description: ERK1/2 inhibitor treatment 3hr


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_ACTCGCTA-TCGCATAA

description: Single cell

value: plate 3

value: Day 157


title: WM2664-DMSO-3hc

description: DMSO treatment  3hr


title: WM2664-NT-D7b

description: non-targeting shRNA treatment  day 7

value: Doxycycline-NT


title: WM2664-NT-D7a

description: non-targeting shRNA treatment  day 7


title: WM2664-NT-D7c

description: non-targeting shRNA treatment  day 7


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_ACTCGCTA-TATGCAGT

description: Single cell

value: Day 156


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_ACTCGCTA-TACTCCTT

description: Single cell

value: Day 155


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_ACTCGCTA-TAAGGCTC

description: Single cell

value: Day 154


title: WM2664-ERK1/2-inhibitor-3hc

description: ERK1/2 inhibitor treatment 3hr


title: WM2664-shERK2-D7c

description: shERK2 treatment  day 7


title: WM2664-shERK1-D7b

description: shERK1 treatment  day 7


title: WM2664-shERK2-D7a

description: shERK2 treatment  day 7


title: WM2664-shERK2-D7b

description: shERK2 treatment  day 7


title: WM2664-shERK1-D7a

description: shERK1 treatment  day 7


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_ACTCGCTA-CTTAATAG

description: Single cell

value: Day 153


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_ACTCGCTA-CTCCTTAC

description: Single cell

value: Day 152


title: WM2664-shERK1-D7c

description: shERK1 treatment  day 7


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_ACTCGCTA-CTAGTCGA

description: Single cell

value: Day 151


title: WM2664-D7c

description: untreated parental  day 7

value: Doxycycline


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_ACTCGCTA-ATTAGACG

description: Single cell

value: Day 149


title: WM2664-D7a

description: untreated parental  day 7


title: WM2664-NT-D3b

description: non-targeting shRNA treatment  day 3


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_ACTCGCTA-CGGAGAGA

description: Single cell

value: Day 150


title: WM2664-shERK2-D3c

description: shERK2 treatment  day 3

value: BRAF V600D


title: WM2664-shERK2-D3b

description: shERK2 treatment  day 3


title: WM2664-shERK1-D3c

description: shERK1 treatment  day 3


title: WM2664-shERK2-D3a

description: shERK2 treatment  day 3


title: WM2664-NT-D3a

description: non-targeting shRNA treatment  day 3


title: WM2664-D3c

description: untreated parental  day 3


title: WM2664-NT-D3c

description: non-targeting shRNA treatment  day 3


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_ACTCGCTA-ATAGAGAG

description: Single cell

value: Day 147


title: WM2664-shERK1-D3a

description: shERK1 treatment  day 3


title: WM2664-shERK1-D3b

description: shERK1 treatment  day 3


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_ACTCGCTA-AGCTAGAA

description: Single cell

value: Day 145


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_ACTCGCTA-AGAGGATA

description: Single cell

value: Day 144


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_ACTCGCTA-AGGCTTAG

description: Single cell

value: Day 146


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_ACTCGCTA-ATAGCCTT

description: Single cell

value: plate 3

value: Day 148


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_AAGAGGCA-TCGCATAA

description: Single cell

value: plate 2

value: Day 141


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_AAGAGGCA-TCTTACGC

description: Single cell

value: Day 142


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_ACTCGCTA-ACTCTAGG

description: Single cell

value: Day 143


title: WM2664-D7b

description: untreated parental  day 7


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_AAGAGGCA-TATGCAGT

description: Single cell

value: Day 140


title: WM2664-D3a

description: untreated parental  day 3


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_AAGAGGCA-TACTCCTT

description: Single cell

value: Day 139


title: WM2664-D3b

description: untreated parental  day 3


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_AAGAGGCA-TAAGGCTC

description: Single cell

value: Day 138


title: WT_Na_BAPN_1

city: Kurume

first: Hiroki

last: Aoki

state: Fukuoka

address: 67 Asahimachi

department: Cardiovascular Research Institute

institute: Kurume University

hyb_protocol: cRNA was hybridized to a 60K 60-mer oligomicroarray (SurePrint G3 Mouse Gene Expression Microarray 8x60K ; Agilent Technologies) according to the manufacturer's instructions.

scan_protocol: The hybridized microarray slides were scanned using an Agilent scanner. The relative hybridization intensities and background hybridization values were calculated using Feature Extraction Software version 9.5.1.1 (Agilent Technologies).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. The raw signal intensities and flags for each probe were calculated from the hybridization intensities and spot information according to the procedures recommended by Agilent Technologies using the Flag criteria in the GeneSpring Software. The raw signal intensities of all samples were  normalized by the quantile algorithm with the Bioconductor.

source_name: Wild type, NaCl + BAPN, repliate1

label_protocol: cRNA was amplified and labelled using a Low input Quick Amp Labelling Kit (Agilent Technologies).

growth_protocol: Wild type C57BL/6 mice or IL-17-deicient mice were kept on normal chow throughout the experimental period.

extract_protocol: The total RNA was isolated from cells using TRIzol Reagent (nitrogen) and purified using SV Total RNA Isolation System (Promega) according to the manufacturer's instructions.

treatment_protocol: Wild type C57BL/6 mice or IL-17-deicient mice were with or without high salt challenge by 1% NaCl as drinking water prior to and during 3 days of continuous infusion of BAPN and angiotensin II or vehicle.

tag: genotype/variation

value: Wild type

value: NaCl + BAPN

tag: cell

value: aorta


title: WT_Na_BAPN_2

source_name: Wild type, NaCl + BAPN, repliate2


title: WT_BAPN_3

source_name: Wild type, BAPN, repliate3

value: BAPN


title: WT_Na_BAPN_3

source_name: Wild type, NaCl + BAPN, repliate3


title: WT_Na_4

source_name: Wild type, NaCl, repliate3

value: NaCl


title: WT_Na_2

source_name: Wild type, NaCl, repliate1


title: WT_BAPN_2

source_name: Wild type, BAPN, repliate2


title: WT_BAPN_1

source_name: Wild type, BAPN, repliate1


title: WT_Cont_3

source_name: Wild type, Control, repliate3

value: vehicle


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_AAGAGGCA-CTCCTTAC

city: Atlanta

first: Steven

last: Sloan

address: 615 Michael Street, Whitehead Building Room 375

institute: Emory University

description: Single cell

source_name: human oligodendrocyte spheroids

value: Day 136


title: WT_Na_3

source_name: Wild type, NaCl, repliate2


title: ZNF341 Th17

city: Darlinghurst

first: Stuart

last: Tangye

state: NSW

address: 384 Victoria St

department: Immunology

country: Australia

institute: Garvan Institute of Medical Research

hyb_protocol: 3 µg fragemented biotin labelled ss cDNA was hybridised to Affymetrix Human Gene Array version 2.1ST. Samples were hybridised to arrays for 16 houts at 45C in the Affymetrix GeneTitan Instrument

scan_protocol: not provided

data_processing: Expression Console, Transcription Analysis Console software packages used. Genome vesion: hg19

source_name: Memory CD4+ T cells

label_protocol: 1 ng of total RNA was used as input for the amplification and labelling of samples using Affymetrix WT Pico Kit

growth_protocol: Human memory CD4+ T cells were cultured in vitro for 4 days

extract_protocol: RNA was isolated from cultured populations of activated memory CD4+ T cells using QIAGEN RNA isolation kits

treatment_protocol: Cells were treated under either Th0 (anti-CD2/CD3/CD28 mAbs) or Th17 conditions (anti-CD2/CD3/CD28 mAbs + TGFb/IL-1b/IL-6/IL-21/IL-23)

value: Memory CD4+ T cells

tag: diagnosis

value: ZNF341 mutation


title: ZNF341 Th0


title: Healthy Control 2 Th17

value: healthy


title: Healthy Control 4 Th0


title: WT_Cont_1

source_name: Wild type, Control, repliate1


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_AAGAGGCA-CTAGTCGA

description: Single cell

tag: plate id

value: plate 2

value: Day 135


title: WT_Cont_2

source_name: Wild type, Control, repliate2


title: Healthy Control 3 Th0


title: Healthy Control 1 Th0


title: Healthy Control 1 Th17


title: Healthy Control 2 Th0


title: ADJ6h_3

city: Tokyo

first: Hidehiro

last: Kondo

address: 4-5-7 Konan, Minato

institute: Tokyo University of Marine Science and Technology

hyb_protocol: After hybridization cocktails preparation, the Agilent 8x15 k custom oligo DNA microarray was hybridized with the fragmented labelled cRNA for 15 h at 65 °C as described in the Agilent QuickAmp Labeling kit one-color protocol.

scan_protocol: The microarray was scanned with a Agilent G2565CA scanner. Scanner setting was a 5μm resolution using a PMT setting of 600 and a laser power of 100 percents.

data_processing: The scanned images were analyzed with Feature Extraction Software v9.5.3.1 (Agilent, USA) using default parameters (protocol GE1-v5_95 and Grid: 016320_D_F_20070321) to obtain background subtracted and spatially detrended Processed Signal intensities (raw values). Limma calculated normalized values that the log summarized values from the baseline transformed by control samples after corrected the average of a 50th percentile values of the arrays in the experiments.

organism: Paralichthys olivaceus

source_name: Spleen isolated from fish at 6h after intraperitoneally injected with FKC + FCA

label_protocol: The RNA was reverse-transcribed into cDNA with a T7-(dT) oligomer to prime the double-strand synthesis. double-strand cDNA was converted and labeled into cRNA with Cy3. Cy3-labeld cRNA was purified using the RNeasy mini kit. Following cleanup, fragmentation of the cRNA for target preparation was done according to the Agilent QuickAmp Labeling kit one-color protocol.

extract_protocol: Total RNA was extracted from fish spleen using the RNeasy Mini Kit.

treatment_protocol: Fish were treated with Edwardsiella tarda formallin-killed cells (FKC) or FKC with Freund's complete adjuvant

value: Edwardsiella tarda formallin-killed cells (FKC) with Freund's complete adjuvant

value: 6 hours

value: spleen