title: Ctrl_s10b

status: Public on Apr 30 2018

type: SRA

city: St. Louis

first: Makedonka

last: Mitreva

state: Missouri

address: 4444 Forest Park Ave

country: USA

institute: McDonnell Genome Institute

library_source: transcriptomic

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were adapter trimmed using Flexbar (v2.4) --max-uncalled 150 –min-read-length 25 adapter-trim-end LEFT adpater-min-overlap 7 adapter-threshold 3 adapter-match 1 adapter-mismatch -1 adapter-gap -7
Trimmed reads were mapped the the GRCh37.75 human reference using TopHat2 (v2.0.8) (default parameters except for -r 250)
FPKM values per sample per gene were generated using cufflinks (v1.2.1)
Genome_build: GRCh37.75
Supplementary_files_format_and_content: FPKM per gene per sample

molecule: total RNA

organism: Homo sapiens

source_name: peripheral blood mononuclear cell (PBMC)

extract_protocol:
ABI PRISM 6100 Nucleic Acid PrepStation
RNA libraries were prepared for sequencing using the NuGen Kit v2

tag: individual

tag: infection

value: uninfected control

tag: time

value: follow-up (no treatment)

tag: cell type

value: PBMC


title: Sh_s9b

value: S.haemotobium infected

value: follow-up (post-treatment)


title: Sh_s10a

value: baseline (pre-treatment)


title: Sh_s9a


title: Ctrl_s8a

value: baseline (no treatment)


title: Sh_s10b


title: Ctrl_s6b


title: Ctrl_s10a


title: Ctrl_s7a


title: Ctrl_s8b


title: Ctrl_s9b


title: Ctrl_s7b


title: Ctrl_s9a


title: Ctrl_s6a


title: Sh_s7b


title: Sh_s8a


title: Sh_s7a


title: Sh_s8b


title: Ctrl_s5a


title: Ctrl_s5b


title: Ctrl_s4b


title: Ctrl_s4a


title: Sh_s6b


title: Sh_s6a


title: Sh_s5b


title: Sh_s5a


title: PFNF54-Pfs16-GFP-LUC parasites 7 days after induction to produce gametocytes

type: RNA

city: Pretoria

first: LynMarie

last: Birkholtz

state: Gauteng

address: c/o Lunnon Road and Heroldt Street, Hatifeld

department: Biochemistry

country: South Africa

institute: University of Pretoria

description: Day 7.txt

hyb_protocol: Painter, H. J., Altenhofen, L. M., Kafsack, B. F. C. & Llinás, M. Whole-genome analysis of Plasmodium spp. Utilizing a new agilent technologies DNA microarray platform. Methods Mol. Biol. 923, 213–219 (2013).

scan_protocol: Agilent G2600D Microarray Scanner. Images were quantified using Agilent Feature Extraction Software (version 11.5.1.1).

data_processing: Agilent Feature Extraction Software (v 11.5.1.1) was used for background subtraction.

organism: Plasmodium falciparum

source_name: PFNF54-Pfs16-GFP-LUC Day 7 RNA

growth_protocol: P. falciparum NF54-Pfs16-GFP-LUC were induced by culturing in glucose-deficient media to produce gametocytes, before removing asexual parasites from the population by daily 5% D-sorbitol treatments from day 1-4 and thereafter culturing the parasites in glucose positive media and grown under stationary conditions for the entire time course.

extract_protocol: Samples were harvested from culture by 0.01%(w/v) saponin addition on days -2 to 7 and via density centrifugation using Nycoprep 1.077 cushions on days 8-13 and stored at -80˚C until RNA isolation using TRIZOL reagent along with on-column extraction using the Qiagen RNeasy kit (Qiagen, Germany).

tag: strain

tag: days after induction

source_name: 3D7 Mixed Stage asexual + NF54-Pfs16-GFP-LUC Mixed Stage gametocyte Reference Pool

value: 3D7 + NF54-Pfs16-GFP-LUC

tag: sample type

value: Reference Pool


title: PFNF54-Pfs16-GFP-LUC parasites 8 days after induction to produce gametocytes

description: Day 8.txt

source_name: PFNF54-Pfs16-GFP-LUC Day 8 RNA

label_protocol: Painter, H. J., Altenhofen, L. M., Kafsack, B. F. C. & Llinás, M. Whole-genome analysis of Plasmodium spp. Utilizing a new agilent technologies DNA microarray platform. Methods Mol. Biol. 923, 213–219 (2013).


title: PFNF54-Pfs16-GFP-LUC parasites 11 days after induction to produce gametocytes

description: Day 11.txt

source_name: PFNF54-Pfs16-GFP-LUC Day 11 RNA


title: PFNF54-Pfs16-GFP-LUC parasites 12 days after induction to produce gametocytes

description: Day 12.txt

source_name: PFNF54-Pfs16-GFP-LUC Day 12 RNA


title: PFNF54-Pfs16-GFP-LUC parasites 10 days after induction to produce gametocytes

description: Day 10.txt

source_name: PFNF54-Pfs16-GFP-LUC Day 10 RNA


title: PFNF54-Pfs16-GFP-LUC parasites 3 days after induction to produce gametocytes

description: Day 3.txt

source_name: PFNF54-Pfs16-GFP-LUC Day 3 RNA


title: PFNF54-Pfs16-GFP-LUC parasites 13 days after induction to produce gametocytes

description: Day 13.txt

source_name: PFNF54-Pfs16-GFP-LUC Day 13 RNA


title: PFNF54-Pfs16-GFP-LUC parasites 2 days after induction to produce gametocytes

description: Day 2.txt

source_name: PFNF54-Pfs16-GFP-LUC Day 2 RNA


title: PFNF54-Pfs16-GFP-LUC parasites 9 days after induction to produce gametocytes

description: Day 9.txt

source_name: PFNF54-Pfs16-GFP-LUC Day 9 RNA


title: PFNF54-Pfs16-GFP-LUC parasites 4 days after induction to produce gametocytes

description: Day 4.txt

source_name: PFNF54-Pfs16-GFP-LUC Day 4 RNA


title: PFNF54-Pfs16-GFP-LUC parasites 1 day after induction to produce gametocytes

description: Day 1.txt

source_name: PFNF54-Pfs16-GFP-LUC Day 1 RNA


title: PFNF54-Pfs16-GFP-LUC parasites 5 days after induction to produce gametocytes

description: Day 5.txt

source_name: PFNF54-Pfs16-GFP-LUC Day 5 RNA


title: PFNF54-Pfs16-GFP-LUC parasites 6 days after induction to produce gametocytes

description: Day 6.txt

source_name: PFNF54-Pfs16-GFP-LUC Day 6 RNA


title: Zeamays_bsd2_BScells_218_A

city: Ithaca

first: Thomas

middle: P.

last: Brutnell

state: NY

address: Cornell University

institute: Boyce Thompson Institute for Plant Research

description:
The mutant bundle sheath defective2 (bsd2) lacks the accumulation of Rubisco small and large subunits (Roth et al 1996; Brutnell et al 1999) and cannot perform the Calvin Cycle (Smith et al 1998). The loss of Rubisco may lead to changes in the spatial regulation of typically BS- and M-enriched genes. To detect such changes, gene expression profiles of bsd2 BS cells and wild-type BS cells from sibling plants were compared using the Maize Oligonucleotide Array. Tissue and RNA isolations for this experiment were performed as previously described (Covshoff et al 2008). Six biological replicates were conducted in a dye swap arrangement using the Array 900MPX Expression Array Detection Kit and company protocol (Genisphere).
References:
Brutnell TP, Sawers RJ, Mant A, and Langdale JA (1999). BUNDLE SHEATH DEFECTIVE2, a novel protein required for post-translational regulation of the rbcL gene of maize. Plant Cell 11, 849-864.
Covshoff S, Majeran W, Liu P, Kolkman JM, van Wijk KJ, Brutnell TP (2008) Deregulation of maize C4 photosynthetic development in a mesophyll cell-defective mutant. Plant Physiol 146: 1469-1481.
Roth R, Hall LN, Brutnell TP, and Langdale JA (1996). bundle sheath defective2, a mutation that disrupts the coordinated development of bundle sheath and mesophyll cells in the maize leaf. Plant Cell 8, 915-927.
Smith LH, Langdale JA, and Chollet R (1998). A functional Calvin cycle
is not indispensable for the light activation of C4 phosphoenolpyruvate carboxylase kinase and its target enzyme in the maize mutant bundle sheath defective2-mutable1. Plant Physiol 118, 191-197.

hyb_protocol: Followed Genisphere Array 900MPX instructions using buffer 6. cDNA hybridization overnight at 55°C. Washed slides in 2X SSC, 0.5%SDS; 0.5X SSC; 0.05X SSC for 5 min each. First wash buffer was used at 55°C.

scan_protocol: See: Sawers, R.J., Liu, P., Anufrikova, K., Hwang, J.T., and Brutnell, T.P. (2007). A multi-treatment experimental system to examine photosynthetic differentiation in the maize leaf. BMC Genomics 8, 12.

data_processing:
Feature intensity values were log-transformed, corrected for local background, and filtered to include only those that were at least 2x background. The data was then LOWESS normalized (Sawers et al 2007) and corrected for dye-effect (Smyth 2004). Differentially expressed genes were identified by moderated-t test and the false discovery rate (q) was calculated as previously described (Storey and Tibshirani 2003).
References:
Sawers, R.J., Liu, P., Anufrikova, K., Hwang, J.T., and Brutnell, T.P. (2007). A multi-treatment experimental system to examine photosynthetic differentiation in the maize leaf. BMC
Genomics 8, 12.
Smyth, G.K. (2004). Linear models and empirical bayes methods for assessing differential expression in microarray experiments. Stat Appl Genetic Mol Biol 3, Article3.
Storey, J.D., and Tibshirani, R. (2003). Statistical significance for genomewide studies. Proc Natl Acad Sci U S A 100, 9440-9445.
.

organism: Zea mays

source_name: wild-type sibling of bsd2 mutant, bundle sheath cells, replicate 1

growth_protocol: Grown for 11 days in growth chamber (16h/8h light/darkness, 50% humidity, 28°C, approx 40 µmol/s-1/m-2) in soil. BS cells collected from second leaves of 3rd leaf emerging stage seedlings.

extract_protocol:
BS strands were isolated as previously described with slight modification; only second leaf blades were used. For full protocol see Markelz, N.H., Costich, D.E., and Brutnell, T.P. (2003). Photomorphogenic responses in maize seedling development. Plant Physiol 133, 1578-1591.
RNA was isolated as in Sheehan, M.J., Farmer, P.R., and Brutnell, T.P. (2004). Structure and expression of maize phytochrome family homeologs. Genetics 167, 1395-1405.

tag: W22 cultivar, bsd2 segregating line, harvested at 3rd leaf emerging stage


title: Zeamays_bsd2_BScells_022_A

data_processing:
Feature intensity values were log-transformed, corrected for local background, and filtered to include only those that were at least 2x background. The data was then LOWESS normalized (Sawers et al 2007) and corrected for dye-effect (Smyth 2004). Differentially expressed genes were identified by moderated-t test and the false discovery rate (q) was calculated as previously described (Storey and Tibshirani 2003).
References:
Sawers, R.J., Liu, P., Anufrikova, K., Hwang, J.T., and Brutnell, T.P. (2007). A multi-treatment experimental system to examine photosynthetic differentiation in the maize leaf. BMC
Genomics 8, 12.
Smyth, G.K. (2004). Linear models and empirical bayes methods for assessing differential expression in microarray experiments. Stat Appl Genetic Mol Biol 3, Article3.
Storey, J.D., and Tibshirani, R. (2003). Statistical significance for genomewide studies. Proc Natl Acad Sci U S A 100, 9440-9445.

source_name: wild-type sibling of bsd2 mutant, bundle sheath cells, replicate 3

label_protocol: Followed Genisphere Array 900MPX instructions using buffer 6. cDNA hybridization overnight at 55°C. Washed slides in 2X SSC, 0.5%SDS; 0.5X SSC; 0.05X SSC for 5 min each. First wash buffer was used at 55°C.


title: Zeamays_bsd2_Mcells_036_A

description:
The mutant bundle sheath defective2 (bsd2) lacks the accumulation of Rubisco small and large subunits (Roth et al 1996; Brutnell et al 1999) and cannot perform the Calvin Cycle (Smith et al 1998). The loss of Rubisco may lead to changes in the spatial regulation of typically BS- and M-enriched genes. To detect such changes, gene expression profiles of bsd2 M cells and wild-type M cells from sibling plants were compared using the Maize Oligonucleotide Array (University of Arizona). Tissue and RNA isolations for this experiment were performed as previously described (Covshoff et al 2008). Six biological replicates were conducted in a dye swap arrangement using the Array 900MPX Expression Array Detection Kit and company protocol (Genisphere).
References:
Brutnell TP, Sawers RJ, Mant A, and Langdale JA (1999). BUNDLE SHEATH DEFECTIVE2, a novel protein required for post-translational regulation of the rbcL gene of maize. Plant Cell 11, 849-864.
Covshoff S, Majeran W, Liu P, Kolkman JM, van Wijk KJ, Brutnell TP (2008) Deregulation of maize C4 photosynthetic development in a mesophyll cell-defective mutant. Plant Physiol 146: 1469-1481.
Roth R, Hall LN, Brutnell TP, and Langdale JA (1996). bundle sheath defective2, a mutation that disrupts the coordinated development of bundle sheath and mesophyll cells in the maize leaf. Plant Cell 8, 915-927.
Smith LH, Langdale JA, and Chollet R (1998). A functional Calvin cycle
is not indispensable for the light activation of C4 phosphoenolpyruvate carboxylase kinase and its target enzyme in the maize mutant bundle sheath defective2-mutable1. Plant Physiol 118, 191-197.

source_name: wild-type sibling of bsd2 mutant, mesophyll cells, replicate 3

growth_protocol: Grown for 11 days in growth chamber (16h/8h light/darkness, 50% humidity, 28°C, approx 40 µmol/s-1/m-2) in soil. M cells collected from second leaves of 3rd leaf emerging stage seedlings.

extract_protocol:
M protoplasts were isolated as previously described with slight modification; only second leaf blades were used. For full protocol see Markelz, N.H., Costich, D.E., and Brutnell, T.P. (2003). Photomorphogenic responses in maize seedling development. Plant Physiol 133, 1578-1591.
RNA was isolated as in Sheehan, M.J., Farmer, P.R., and Brutnell, T.P. (2004). Structure and expression of maize phytochrome family homeologs. Genetics 167, 1395-1405.


title: Zeamays_bsd2_BScells_217_A

source_name: wild-type sibling of bsd2 mutant, bundle sheath cells, replicate 5


title: Zeamays_bsd2_Mcells_081_A

source_name: wild-type sibling of bsd2 mutant, mesophyll cells, replicate 6


title: 1-B cells and C2

city: West Lafayette

first: Chang

last: Kim

state: IN

address: 725 Harrison St

department: Comparative Pathobiology

institute: Purdue

description: Gene expression data from B cell culture

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized with a GeneChip Hybridization Oven 640 for 16 hr at 45C on GeneChip Mouse 430 2.0 Arrays. GeneChips were washed and stained in the Affymetrix GeneChip Fluidics Station 400 with fludics protocol EukGE_WS2v5 and user prepared solutions, as per protocols provided by Affymetrix in the GeneChip Expression Analysis Technical Manual, 2004. This included Enzo Life Sciences' BioArray Eukaryotic Hybridization Controls.

scan_protocol: GeneChips were scanned using GeneChip Scanner 3000 7G enabled forHigh-Resolution Scanning. The instruments were controlled using GCOS version1.4 software.

data_processing: The data were condensed with MAS 5.0 using the GeneChip Operation Software.

label: biotin

organism: Mus musculus

source_name: cultured spleen B cells, sodium acetate

label_protocol: Biotinylated cRNA were prepared from 2 ug total RNA according to the Single Round RNA Amplification and Biotin Labeling System (Enzo Life Sciences Intl. Plymouth Meeting, PA).

growth_protocol: Spleen CD19+ B cells were activated with anti-IgM in the presence of mature BM-DCs at 2:1 ratio in the presence or absence of sodium acetate for 5 days in RPMI medium (10% FBS).

extract_protocol: Trizol and Qiagen Total RNA isolation kit

treatment_protocol: The cells were cultured in the presence or absence of sodium acetate (10 mM) for 5 days.

value: spleen B cells


title: PFNF54-Pfs16-GFP-LUC parasites on day of induction to produce gametocytes

description: Day 0.txt

source_name: PFNF54-Pfs16-GFP-LUC Day 0 RNA

source_name: 3D7 Mixed Stage asexual + NF54-Pfs16-GFP-LUC Mixed Stage gametocyte Reference Pool


title: Zeamays_bsd2_Mcells_041_A

source_name: wild-type sibling of bsd2 mutant, mesophyll cells, replicate 4


title: 2-B cells and C2


title: PFNF54-Pfs16-GFP-LUC parasites 1 day before induction to produce gametocytes

description: Day -1.txt

source_name: PFNF54-Pfs16-GFP-LUC Day -1 RNA


title: AK-T.3

city: Adelaide

first: Susan

last: Woods

state: Select State

address: Level 5 South, SAHMRI building, North Terrace

department: School of Medicine

country: Australia

institute: The University of Adelaide

data_processing:
bcl2fastq2 2.20 was used for base calling
Sequenced reads were trimmed for adaptor sequence and low-quality sequence, then mapped to UCSC mouse genome mm10 using STAR aligner 2.4.2a modified with parameters --outFilterMismatchNmax 2 --outFilterMultimapNmax 1 --chimSegmentMin 20 --twopassMode None --outSAMtype BAM SortedByCoordinate --quantMode GeneCounts
Raw counts calculated by STAR aligner with parameter --quantamode were merged to create count matrix. Counts on the second column of each file were used. Downstream differential expression analyses were performed in in R with Bioconductor edgeR Package version 3.16.5. Differentially expressed genes were defined as FDR < 0.05, and absolute value of logFC > 2
Transcript counts generated from STAR aligner were sub-grouped into files with pairwise comparison groups of tumour to normal colon. The PreprocessReadCounts (V1 Beta) module of GenePattern was used to normalise and transform counts. Briefly, lowly expressed genes were removed from the analysis if they had <1 read/million in four of the samples, as four is the smallest group of biological replicates . The remaining data was then normalised using Trimmed Mean of M-values. Meanvariance transformation to approximate a normal distribution was performed subsequently using voom. Gene set enrichment analyses were performed using online module GSEA (v18).
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files include raw counts for each sample
column 1: gene ID
column 2: counts for unstranded RNA-seq
column 3: counts for the 1st read strand aligned with RNA (htseq-count option -s yes)
column 4: counts for the 2nd read strand aligned with RNA (htseq-count option -s reverse)
Only the column 2 values are used to feed into edgeR for downstream analyses.

source_name: Tumour

extract_protocol:
Total RNA and gDNA was extracted from organoids, tumours and normal control colon tissue using AllPrep DNA/RNA Mini or RNeasy Mini Kit (QIAGEN) or UltraClean® Tissue & Cells DNA Isolation Kit (Mo Bio Laboratories).
For RNAseq analysis, 1ug of total RNA was used for sequencing library preparation using a BIOO stranded Poly-A kit (PerkinElmer) according to the manufacturer’s instructions and sequenced on Illumina HiSeq to generate 1 x 100bp single-end reads.

value: NSG

tag: tissue

value: Tumour

tag: genotype


title: AK-T.2


title: AK-T.1


title: AK-T.4


title: N.4

source_name: Normal colon

value: Normal colon

value: wild type


title: 1-B cells

source_name: cultured spleen B cells


title: Zeamays_bsd2_BScells_221_A

source_name: wild-type sibling of bsd2 mutant, bundle sheath cells, replicate 2


title: PFNF54-Pfs16-GFP-LUC parasites 2 days before induction to produce gametocytes

description: Day -2.txt

source_name: PFNF54-Pfs16-GFP-LUC Day-2 RNA


title: Zeamays_bsd2_BScells_216_A

source_name: wild-type sibling of bsd2 mutant, bundle sheath cells, replicate 4


title: Zeamays_bsd2_Mcells_042_A

source_name: bsd2 mutant, mesophyll cells, replicate 3


title: Zeamays_bsd2_Mcells_222_A

description:
The mutant bundle sheath defective2 (bsd2) lacks the accumulation of Rubisco small and large subunits (Roth et al 1996; Brutnell et al 1999) and cannot perform the Calvin Cycle (Smith et al 1998). The loss of Rubisco may lead to changes in the spatial regulation of typically BS- and M-enriched genes. To detect such changes, gene expression profiles of bsd2 M cells and wild-type M cells from sibling plants were compared using the Maize Oligonucleotide Array (University of Arizona). Tissue and RNA isolations for this experiment were performed as previously described (Covshoff et al 2008). Six biological replicates were conducted in a dye swap arrangement using the Array 900MPX Expression Array Detection Kit and company protocol (Genisphere).
References:
Brutnell TP, Sawers RJ, Mant A, and Langdale JA (1999). BUNDLE SHEATH DEFECTIVE2, a novel protein required for post-translational regulation of the rbcL gene of maize. Plant Cell 11, 849-864.
Covshoff S, Majeran W, Liu P, Kolkman JM, van Wijk KJ, Brutnell TP (2008) Deregulation of maize C4 photosynthetic development in a mesophyll cell-defective mutant. Plant Physiol 146: 1469-1481.
Roth R, Hall LN, Brutnell TP, and Langdale JA (1996). bundle sheath
defective2, a mutation that disrupts the coordinated development of bundle sheath and mesophyll cells in the maize leaf. Plant Cell 8, 915-927.
Smith LH, Langdale JA, and Chollet R (1998). A functional Calvin cycle
is not indispensable for the light activation of C4 phosphoenolpyruvate carboxylase kinase and its target enzyme in the maize mutant bundle sheath defective2-mutable1. Plant Physiol 118, 191-197.

source_name: wild-type sibling of bsd2 mutant, mesophyll cells, replicate 5


title: 2-B cells


title: Zeamays_bsd2_BScells_019_A

source_name: wild-type sibling of bsd2 mutant, bundle sheath cells, replicate 6


title: BTPRZM-T.3


title: BTPRZM-T.4


title: Zeamays_bsd2_Mcells_223_A

source_name: wild-type sibling of bsd2 mutant, mesophyll cells, replicate 1


title: BTPRZM-T.2


title: BTPRZ-T.4


title: BTPRZM-T.1


title: BTPRZ-T.2


title: N.2


title: BTPRZ-T.3


title: BTPRZ-T.1


title: N.1


title: BT-T.2


title: BT-T.3


title: BT-T.1


title: BT-T.4


title: Apoe-KO rep2

city: Seoul

first: Heeju

last: Ryu

address: 1 Gwanak-ro

country: South Korea

institute: Seoul National University

data_processing:
Basecalls performed using CASAVA version 1.8.2
RNA-seq reads were aligned to the mm10 genome assembly using Tophat version 2.0.13
The aligned results were added to Cuffdiff version 2.2.0 to report differentially expressed genes.
For ontology analysis, genes after 2 fold change were picked (for mouse samples, genes with 2fold&pvalue<0.05&FDR<0.1 were selected for ontology analysis) and applied to DAVID version 6.8 as an input to get a comprehensive set of functional annotation.
Genome_build: mm10
Supplementary_files_format_and_content: fpkm values were assigned for each samples.

source_name: mouse lymphocytes

extract_protocol:
Lymph nodes and spleens were harvested, prepared as single cells, and RNA was collected using Invitrogen mirVana miRNA Isolation Kit (Cat#AM1561). RNA purity was determined by assaying 1 µl of total RNA extract on a NanoDrop8000 spectrophotometer. Total RNA integrity was checked using an Agilent Technologies 2100 Bioanalyzer with an RNA Integrity Number (RIN) value.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: lymph nodes and spleens

tag: age

value: Apoe-/-

value: follicular T helper cells


title: Apoe-KO rep1


title: WT rep1


title: WT rep2


title: N.3


title: RUES-1 hESC OGT-E339G

city: Athens

first: Lance

last: Wells

state: GA

address: 315 Riverbend Rd

institute: Complex Carbohydrate Research Center, University of Georgia

data_processing:
Post-processing of the sequencing reads from RNA-seq experiments for each sample was performed using HudsonAlpha’s unique in-house RNA-seq data analysis pipeline. Briefly, quality control checks on raw sequence data for each sample were performed using FastQC (Babraham Bioinformatics, Cambridge, UK). Raw reads were mapped to the reference hg19 using TopHat v2.0. The alignment metrics of the mapped reads were estimated using SAMtools. Aligned reads were imported to the commercial data analysis platform AvadisNGS (Strand Scientifics, CA, USA). After quality inspection, the aligned reads were filtered on the basis of read quality metrics; reads with a base quality score of less than 30, alignment score of less than 95, and mapping quality of less than 40 were removed. Remaining reads were then filtered on the basis of their read statistics; missing mates, translocated, unaligned, and flipped reads were removed. The reads list was then filtered to remove duplicates. Samples were grouped and transcript abundance was quantified for this final read list using Trimmed Means of M-values (TMM) as the normalization method. Output data utilized for all subsequent comparisons were summarized as normalized signal values generated by AvadisNGS. Differential expression of genes was calculated on the basis of fold changes (using the default cut-off ≥ ±2.0) observed in comparisons between defined conditions,
Genome_build: hg19
Supplementary_files_format_and_content: Excel files include expression values for each Sample

source_name: RUES-1 human ES cells edited with Crispr/Cas9 to encode OGT-E339G

growth_protocol: RUES-1 male human ES cells were obtained from the Laboratory of Molecular Embryology at the Rockefeller University. XLID OGT-TPR point mutations in these cells were introduced using Crispr/Cas9 as a pay-for-service by Applied StemCell. Cells were maintained in TeSRTM E8TM media (STEMCELL Technologies) in 5% CO2. Media was changed every day and at appropriate confluency, cells were split 1:3 or 1:5 using an enzyme-free dissociation buffer (1X DPBS – Ca2+ and Mg2+ free (Thermo) supplemented with sterile-filtered 0.5 mM EDTA and 150 mM NaCl).

extract_protocol:
Total RNA was isolated from cells harvested from confluent 60 mm dishes using the RNeasy Plus Mini Kit (Qiagen) according to the manufacturer's instructions.
The concentration and integrity of the extracted total RNA were estimated using the Qubit® 2.0 Fluorometer (Invitrogen) and Agilent 2100 Bioanalyzer (Applied Biosystems, Carlsbad, CA, USA), respectively. Five hundred nanograms of total RNA was required for downstream RNA-seq applications. Polyadenylated RNAs were isolated using NEBNext Magnetic Oligo d(T)25 Beads. Next, first strand synthesis was performed using NEBNext RNA first strand synthesis module (New England BioLabs Inc., Ipswich, MA, USA). Immediately, directional second strand synthesis was performed using NEBNExt Ultra Directional second strand synthesis kit. The NEBNext® DNA Library Prep Master Mix Set for Illumina® was then used to prepare individually bar-coded next-generation sequencing expression libraries as per manufacturer's recommended protocol. Library quality was assessed using the Qubit 2.0 Fluorometer, and the library concentration was estimated by utilizing a DNA 1000 Chip on an Agilent 2100 Bioanalyzer. Accurate quantification for sequencing applications was determined using the qPCR-based KAPA Biosystems Library Quantification Kit (Kapa Biosystems, Inc., Woburn, MA, USA). Paired-end sequencing (50 bp) was performed on an Illumina HiSeq2500 sequencer to obtain approximately 50 million reads per sample. Raw reads were de-multiplexed using bcl2fastq Conversion Software (Illumina, Inc.) with default settings.

treatment_protocol: All cell lines are maintained in the same way

value: embryo/blastocyst-derived cell line

value: XY - male, OGT c.1016 A>G


title: RUES-1 hESC OGT-A259T

source_name: RUES-1 human ES cells edited with Crispr/Cas9 to encode OGT-LA259T

value: XY - male, OGT c.775 G>A


title: RUES-1 hESC OGT-L254F

source_name: RUES-1 human ES cells edited with Crispr/Cas9 to encode OGT-L254F

value: XY - male, OGT c.762 G>T


title: male young rep1

city: Box

first: Stuart

last: Shankland

state: WA

address: 1959 NE Pacific Avenue

department: Nephrology

institute: University of Washington, Seattle

data_processing:
RNA-seq were aligned to mm9/NCBIM37 using Tophat (version 2.0.13)
Gene-level read counts were quantified using featureCounts using Ensembl NCBIM37 gene annotations.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited file of read counts for all samples in one single file

source_name: Cells of Renin Lineage (CoRL), kidney

growth_protocol: Ren1cCre|ZsGreen mice as previously described were bred and maintained in house and allowed to age for either 2 months (n = 5, 3M, 2F) or 27 months (n = 5, 3M, 2F) prior to sacrifice. These mice are the product of breeding the Ren1cCre mouse with the ZsGreen mouse, and results in the constitutive and permanent labeling of all cells that have expressed renin.  Mice were housed, provided ad lib chow and water, in the animal care facility of the University of Washington, under specific pathogen-free conditions. Studies were reviewed and approved by the University of Washington Institutional Animal Care and Use Committee (2968-04). At the ages stated above, animals were sacrificed, the kidneys were removed and dissected free of fat and the kidney capsule. Kidney cortex was digested in 0.2mg/ml Liberase™ TL (Sigma-Aldrich, St. Louis, MO), 100 U/ml DNAse I (Sigma-Aldrich, St. Louis, MO) in RPMI 1640 medium, without L-glutamine or phenol red (GE Healthcare Bio-Sciences, Pittsburgh, PA) by shaking in a 37oC water bath for 30 minutes. The digest was passed through a 22G needle (Becton Dickenson, Franklin Lakes, NJ) 10 times to further dissociate the tissue, then inactivated by combining with 5ml of in media consisting of RPMI 1640 medium, without L-glutamine or phenol red (GE Healthcare Bio-Sciences, Pittsburgh, PA) supplemented with 1mM sodium pyruvate (ThermoFisher Scientific, Waltham, MA), 9% Nu-Serum™ IV Growth Medium Supplement (Corning Incorporated - Life Sciences, Durham, NC) and 100U/ml Penicillin-Streptomycin (ThermoFisher Scientific, Waltham, MA). The suspension was passed through a 100µm, then a 40 µm cell strainer (BD Biosciences, San Jose, CA), to clear multicellular debris, then pelleted by centrifugation at 200G at 4oC for 5 minutes. The cells were re-suspended in the media described above, counted and isolated using multicolor fluorescence-activated cell sorting (FACS) on a BD FACS Aria II (BD Biosciences, San Jose, CA) housed within a BSL1/2 approved biosafety cabinet. Sorted cells were pelleted by centrifugation and snap frozen in liquid nitrogen until isolation of RNA. The entire procedure took 6-7h per animal. Samples were then shipped on dry ice to Roswell Park Cancer Institute for further processing.

extract_protocol:
The purification of total and RNA was performed using the miRNeasy micro kit (Qiagen, Germantown, MD).  Flow sorted cells were homogenized with the addition of 700 ul of QIAzol Lysis Reagent. After addition of chloroform, the homogenate was separated into aqueous and organic phases by centrifugation.  The upper,aqueous phase was extracted.  On-column DNAse digestion was also performed to remove any residual genomic DNA contamination followed by additional washes.  High quality RNA was then eluted in 14 ul of RNase-free water.  Quantitative assessment of the purified total RNA was accomplished by using a Qubit Broad Range RNA kit (Thermo Fisher, Waltham, MA).  The RNA was further evaluated qualitatively by a 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).
Amplified cDNA was generated using the SMART-Seq v4 Ultra Low Input RNA kit (Clontech, Mountain View, CA).  Total RNA (10 ng) was used to synthesize first-strand cDNA utilizing proprietary template switching oligos.  Amplified double stranded cDNA is created by LD PCR using blocked PCR primers and unique sample barcodes were incorporated.  The result-ing cDNA was purified using AmpureXP beads (Beckman Coulter, Brea, CA).  Abundant Ribosomal cDNA was then depleted using R probes and 12 cycles of PCR with universal PCR primers completed the library.  The final libraries were purified using AmpureXP beads, and validated for appropriate size on a 4200 TapeStation D1000 Screentape (Agilent Technologies,, Santa Clara, CA).  The DNA libraries were quantitated using KAPA Biosystems qPCR kit and pooled together in an equimolar fashion.  Each pool was denatured and diluted to 16pM for On-Board Cluster Generation and sequencing on a HiSeq2500 sequencer for 100 paired-end sequencing following the manufac-turer’s recommended protocol (Illumina Inc., San Diego, CA).

tag: Sex

value: Male

value: 2 months


title: female aged rep2

value: Female

value: 27 months


title: female young rep2


title: RUES-1 hESC OGT-R284P

source_name: RUES-1 human ES cells edited with Crispr/Cas9 to encode OGT-R284P

value: XY - male, OGT c.851 G>C


title: male aged rep1


title: male young rep3


title: female aged rep1


title: female young rep1


title: male young rep2


title: male aged rep3


title: male aged rep2


title: RUES-1 hESC OGT-WT

source_name: RUES-1 human embryonic stem (ES) cells

value: RUES-1 human ES cell

value: XY - male


title: haploid_hESC_library_Day23_rep2_run2

city: Jerusalem

first: Mordecai

last: Peretz

address: The Edmond J. Safra Campus

country: Israel

institute: Hebrew University of Jerusalem

description: gRNA sequences+surrounding bases

library_source: genomic

data_processing:
Library strategy: DNA-Seq
Align the fastq files against the library’s sgRNAs sequences list using Bowtie2
Genome_build: The sgRNAs sequences as appear in Table S1 of Wang, T. et al. Identification and characterization of essential genes in the human genome. Science 350, 1096–1101 (2015).
Supplementary_files_format_and_content: rawCounts

molecule: genomic DNA

source_name: embryonic stem cells

growth_protocol: Haploid hESCs were cultured at 37 0C and 5% CO2 on feeder layer growth-arrested mouse embryonic fibroblasts (MEFs) in standard hESC growth medium, composed of Knockout Dulbecco’s Modified Eagle’s Medium (DMEM) supplemented with 15% Knockout Serum Replacement (KSR, Thermo Fisher Scientific), 2 mM L-Glutamine, 0.1 mM nonessential amino acids, 50 units ml-1 penicillin, 50 µg ml-1 streptomycin, 0.1 mM β-mercaptoethanol and 8 ng ml-1 basic fibroblast growth factor (bFGF). Cells were passaged by a quick trypsinization using Trypsin-EDTA (Biological Industries) and plated in the presence of 10 µM ROCK inhibitor Y-27632 (Stemgent) for 1 day after splitting.

extract_protocol:
Genomic DNA was extracted with Blood & Cell Culture DNA Midi Kit (QIAGEN) according to manufacturer’s instructions.
The region containing the sgRNA integration was amplified with the following primers that also contain overhang sequences compatible for Nextera DNA library preparations (Illumina):  5’-TCGTCGGCAGCGTCAGATGTGTATAAGAGACAGGGCTTTATATATCTTGTGGAAAGGACG-3’ (forward)  and 5’-GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAGACGGACTAGCCTTATTTTAACTTGC-3’ (reverse).   Total genomic DNA for each time point was divided into 50 µl PCR reactions with 4 µg DNA input. PCR settings were described previously51. After the purification of the 160 base pair product, a second PCR reaction was performed using Nextera adapter primers in order to generate Nextera DNA library according to manufacturer’s instructions (Illumina). DNA libraries containing sgRNA constructs from two replicate experiments were sequenced using NextSeq 500 (Illumina) with 75 bp single-end reads.

treatment_protocol: For transduction, haploid hESCs were trypsinized with Trypsin-EDTA, centrifuged and resuspended in hESC growth medium supplemented with 10 µM ROCK inhibitor Y-27632 and 8 µg ml-1 polybrene (Sigma). The viruses were then added to the cell suspension. Transduced haploid hESCs were densely plated on feeder layer MEFs for overnight (3 million cells in 1.5 ml hESC medium for one well of a 6-well plate). 24 hours after transduction, cells were passaged on feeder layer of DR3 MEFs at a ratio of 1:3 in the presence of 5 µM ROCK inhibitor Y-27632. During this passaging, 35 million cells were harvested for DNA extraction and sgRNA analysis for ‘Day 1’ time point after infection. 12 hours after this passaging, the medium of the cells was replaced with puromycin-containing medium (0.3 mg/ml, Sigma). Cells were kept under puromycin selection for 7 days and then passaged again. 9 days after initial transduction, 55 million cells (300-fold of the size of sgRNA library) were harvested and mixed for DNA extraction and sgRNA analysis for ‘Day 9’ time point after infection. Transduced haploid hESCs were passaged every 4-5 days while maintaining at least 400-fold representation of the sgRNA library. 55 million cells were harvested for each time points ‘Day 23’ and ‘Day 30’ after infection, as well.

value: embryonic stem cells

value: pooled mutant cells

tag: source cell line

tag: time point


title: haploid_hESC_library_Day1_rep1_run1

description: gRNA sequences+surrounding bases


title: haploid_hESC_library_Day1_rep2_run2

description: gRNA sequences+surrounding bases


title: haploid_hESC_library_Day30_rep1_run1

description: gRNA sequences+surrounding bases


title: haploid_hESC_library_Day23_rep2_run1

description: gRNA sequences+surrounding bases


title: haploid_hESC_library_Day23_rep1_run1

description: gRNA sequences+surrounding bases


title: haploid_hESC_library_Day1_rep2_run1

description: gRNA sequences+surrounding bases


title: haploid_hESC_library_Day30_rep1_run2

description: gRNA sequences+surrounding bases


title: haploid_hESC_library_Day9_rep1_run1

description: gRNA sequences+surrounding bases


title: Fibroblasts_4days_rapamycin_rep2

data_processing:
Reads were mapped to the reference genome using STAR 2.5.3 software.
Reads were annotated using HTSeq software.
Genome_build: GRCh38 reference genome
Supplementary_files_format_and_content: comma separated values (csv) file contains transcript counts for each sample.

source_name: fibroblasts

growth_protocol: hESCs were cultured at 37 0C and 5% CO2 in feeder-free conditions on Matrigel-coated 6-well plates (Corning) in mTeSR1 (STEMCELL Technologies). Fibroblasts were cultured at 37 0C and 5% CO2 on uncoated 6-well plates (Corning).

extract_protocol:
Treated cells were harvested two or four days after rapamycin treatment. Total RNA was isolated from three independent biological replicates with RNeasy Mini Kit (QIAGEN).
mRNA fraction of total RNA was enriched by pulldown of poly(A)-RNA (1ug per sample). RNA sequencing libraries were generated using the Illumina TruSeq RNA prep kit v2 according to manufacturer’s protocol and sequenced using Illumina NextSeq 500 with 84 bp single-end reads.

treatment_protocol: Briefly, hESCs and fibroblasts were treated with 50nM rapamycin in the regular growth medium of each cell type. The medium was replaced every day with fresh rapamycin for both cell types. The cells were grown two or four days in the presence of rapamycin and then harvested.

tag: agent

value: rapamycin

value: fibroblasts

value: wild type

value: BJ


title: Fibroblasts_4days_rapamycin_rep3


title: Fibroblasts_2days_rapamycin_rep2


title: Fibroblasts_2days_rapamycin_rep1


title: Fibroblasts_2days_rapamycin_rep3


title: Fibroblasts_4days_rapamycin_rep1


title: Fibroblasts_control_rep3

value: none, control


title: hESCs_4days_rapamycin_rep2


title: hESCs_4days_rapamycin_rep3


title: Fibroblasts_control_rep2


title: hESCs_4days_rapamycin_rep1


title: Fibroblasts_control_rep1


title: hESCs_control_rep3


title: hESCs_2days_rapamycin_rep3


title: hESCs_2days_rapamycin_rep1


title: hESCs_control_rep2


title: hESCs_2days_rapamycin_rep2


title: hESCs_control_rep1


title: L100209-a_HEP

city: Sophia Antipolis

first: CORINNE

last: MENIGOT

address: 2400 route des colles

country: France

institute: GALDERMA R & D

description: Human skin

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

scan_protocol: GeneChips were scanned using Affymetrix Gene Chip Scanner 3000.

data_processing: The data were analyzed with Expression Console (Affymetrix) with RMA normalization.

source_name: epidermis without sebaceous glands

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 300 ng total RNA).

extract_protocol: RNeasy Micro Kit_Qiagen RNA extraction was performed according to the manufacturer's instructions.

value: epidermis without sebaceous glands

tag: subject id


title: L100415-a_HGS

description: Human skin

source_name: Sebaceous glands

value: Sebaceous glands


title: L100415-a_HEP

description: Human skin


title: L100121-a_HEP

description: Human skin


title: L100209-a_HGS

description: Human skin


title: 9035_PS10_L-NI

source_name: Scar-prone non-lesional skin

value: Whole skin


title: 9024_PS04_L-NI


title: L100408-b_HGS

description: Human skin


title: 9034_PS09_L-NI


title: 9033_PS08_L-NI


title: 9027_PS05_L-NI


title: L100121-a_HGS

description: Human skin


title: L100408-b_HEP

description: Human skin


title: L100531-a_HEP

description: Human skin


title: L100531-a_HGS

description: Human skin


title: 9029_PS06_L-NI


title: 9018_PS01_L-NI


title: 9022_PS02_L-NI


title: 9029_PS06_L3

source_name: Scar-prone papule at 21 days


title: 9023_PS03_L3


title: 9033_PS08_L3


title: 9035_PS10_L3


title: 9035_PS10_L1

source_name: Scar-prone papule less than 48 H old


title: 9023_PS03_L-NI


title: 9024_PS04_L3


title: 9034_PS09_L3


title: 9022_PS02_L3


title: 9027_PS05_L3


title: 9018_PS01_L3


title: 9034_PS09_L1


title: 9033_PS08_L1


title: 9027_PS05_L1


title: 9023_PS03_L1


title: 9022_PS02_L1


title: 9020_NPS04_L-NI

source_name: Non-scar-prone non-lesional skin


title: 9018_PS01_L1


title: 9032_NPS09_L-NI


title: 9017_NPS01_L-NI


title: 9028_NPS08_L-NI


title: 9019_NPS03_L-NI


title: 9025_NPS06_L-NI


title: 9029_PS06_L1


title: 9016_NPS02_L-NI


title: 9021_NPS05_L-NI


title: 9026_NPS07_L-NI


title: 9024_PS04_L1


title: 9028_NPS08_L3

source_name: Non-scar-prone papule at 21 days


title: 9019_NPS03_L3


title: 9028_NPS08_L1

source_name: Non-scar-prone papule less than 48 H old


title: 9016_NPS02_L3


title: 9021_NPS05_L3


title: 9021_NPS05_L1


title: 9025_NPS06_L3


title: 9032_NPS09_L1


title: 9026_NPS07_L3


title: 9032_NPS09_L3


title: WT_BiolRep2

city: Iowa City

first: John

middle: F

last: Engelhardt

state: Iowa

address: 1-111L BSB 51 Newton Rd.

department: Anatomy and Cell Biology

institute: University of Iowa

data_processing:
The number of transcripts per million was calculated for each RNAseq sample using RSEM and Log2 TPM+1 transformed.
Genes with a mean expression value greater than three times the standard deviation of that gene within MECWT or  MECLef-1KI sample groups were selected from the dataset as stably expressed genes.
Genome_build: mm10
txt files were generated in R by filtering compiled datasets.
Supplementary_files_format_and_content: log TPM

source_name: Primary tracheal gland cells were pooled from three to five mice.

growth_protocol: Primary tracheal gland cells were pooled from three to five ACTA2 -CreERT2:Lef-1KI or ACTA2-CreERT2:ROSA-TG mice. Primary cells were cultured in modified SAGM with the addition of 10 µM Y-27632, 1 µM DMH-1, 1 µM A83-01, and 1 µM CHIR 99021 (Tocris) on tissue culture plastic pre-treated with filter-sterilized laminin-enriched 804G-conditioned media as previously described (Mou et al., 2016; PMID: 27320041).

extract_protocol:
P1 cells were analyzed and sorted on a FACS Aria II (BD Biosciences) collecting lineage-tagged MECs—GFP+ cells (MECWT) were isolated from ACTA2-CreERT2:ROSA-TG cultures, and GFP– cells (MECLef-1KI) were isolated from ACTA2-CreERT2:Lef-1KI+/+ cultures. Cells were sorted directly into RNA lysis buffer and RNA was extracted using an RNeasy Plus Mini Kit (Qiagen). Samples were treated with DNase and RNA Integrity Numbers (RIN) were assessed using an Agilent BioAnalyzer 2100. All samples had RIN values >10.
Indexed cDNA libraries were constructed using a TruSeq mRNA stranded preparation.

treatment_protocol: Mice were administered tamoxifen daily for five days prior to airway cell harvest.

value: Myoepithelial cell

tag: mouse strain

tag: lineage tag

value: GFP+


title: 9026_NPS07_L1


title: 9020_NPS04_L3


title: 9025_NPS06_L1


title: WT_BiolRep4


title: WT_BiolRep3


title: WT_BiolRep1


title: 9019_NPS03_L1


title: Lef1KI_BiolRep5

value: ACTA2 -CreERT2:Lef-1KI+/+

value: GFP-


title: Lef1KI_BiolRep4


title: Lef1KI_BiolRep3


title: Lef1KI_BiolRep1


title: Lef1KI_BiolRep2


title: leiomyosarcoma, OncoScan

type: genomic

city: Rostock

first: Carsten

last: Holzmann

address: Ernst-Heydemann-Str. 8

department: Institute of Medical Genetics

country: Germany

institute: University Rostock Medical Center

description:
genomic copynumber+SNP array data of a  derivative leiomyosarcoma
12814-15

hyb_protocol: Prior to hybridization samples were denatured at 95°C. The hybridization was carried out at 49°C (OncoScan) or 45°C (Clariom D) in the GeneChipR Hybridization Oven 645 (Affymetrix) over night. Staining and washing was done using a GeneChip Fluidics Station 450 (Affymetrix) following the manufacturer’s instructions.

scan_protocol: Arrays were scanned using the GeneChipR Scanner 3000.

data_processing: OncoScan arrays were analyzed through the Nexus Copy Number 9 Software (BioDiscovery, El Segundo, CA, USA).

source_name: cystic adnexal mass of the same patient, removed by laparotomy 28 months after LASH

label_protocol: For OncoScan FFPE assay, labelling of 80 ng dsDNA was done following the manufacturer’s instructions (Affymetrix P/N 703175). For Clariom D assay, 45 ng whole RNA was used for  first strand cDNA synthesis is introducing by N6-‐ and Oligo-‐dT priming a T7 promoter sequence 5extended with an universal PCR primer site. To perform a preamplification (Pre-‐IVT Amplification) the primer site at the 5`ends of the first cDNA strand is countered by a second strand synthesis random primed (N6) with an adaptor attaching the reverse primer site to each end of the second strand fragments produced by Klenow polymerase. These templates were amplified exponentially for 6 cycles followed by a linear amplification step using the T7 promoter in an over night reaction (IVT, 14 h). Using 20 mg of each aRNA sample after purification as template in a reverse 3 transcription reaction a strand-‐identical single strand DNA was produced by adding random primers and dNTP`s. To enable an endpoint fragmentation reaction a certain fraction of dTTP is replaced by dUTP. After complete RNA removal (RNaseH) the enzymatic fragmentation is performed by uracil deglycosidase for removing uracil in combination with apurinic apyrimidinic endonuclease 1, which is breaking the free endonucleolytic phosphodiester bonds. Desoxynucleotidyl--‐transferase is adding Biotin--‐ 11--‐dXTP to the 3ends.

extract_protocol: Simultaneous extraction and purification of DNA and RNA from FFPE tissue samples using Covaris adaptive focused acoutics (AFATM) and truXTRACTM FFPE DNA and RNA kits: The emulsification of the paraffin was done applying 5 minutes focused acoustic waves of 75 watts to a 10 mm FFPE section using a Covaris M220 device (Woburn, Massachusetts, USA). A Proteinase K digestions was performed at 56° C for 15 minutes. The paraffin including the genomic DNA was sedimented at 16.000 g. For RNA isolation the supernatant was heated to 80° C to reverse the formaldehyde crosslink followed by a DNaseI digestion step and a spincolumn cleanup procedure. Accordingly the pellet was subjected to spincolumn cleanup of the genomic DNA after an additional Proteinase K digestion. Fluorometric quantification was performed with the QubitTM 2.0 fluorometer using the QubitTM dsDNA HS-‐ and RNA HS Assay Kit (Thermo Fisher Scientific).

treatment_protocol: Laparoscopic supracervical hysterectomy (LASH) due to multiple uterine fibroids. Further tumors were removed by laparotomy. For histologic examination tissues were fixed in paraformaldehyde (4% in PBS), and processed for paraffin embedding using standard techniques.

value: uterus

tag: histology

value: leiomyosarcoma

tag: gender

value: female


title: leiomyoma D, OncoScan

description:
genomic copynumber+SNP array data of a  morcellated leiomyoma specimen
7065-13D

source_name: 50 year old woman, morcellated specimen of uterine fibroids after LASH

value: leiomyoma


title: 9020_NPS04_L1


title: 9017_NPS01_L1


title: 9016_NPS02_L1


title: Peripheral blood, multiple myeloma, sample 908_187

city: Salamanca

first: Maria

middle: Eugenia

last: Alonso

state: Salamanca

address: Paseo San Vicente, 88-182

department: Hematology

country: Spain

institute: Complejo Asistencial Universitario de Salamanca

hyb_protocol: Hybridization protocol was performed according to manufacturer´s recomendations (Axiom exome array, Affymetrix)

scan_protocol: After ligation, the arrays are stained and imaged on the GeneTitan MC Instrument (Affymetrix, Santa Clara, CA, USA)

data_processing:
Using rawdata (cel files) as input, data analysis was conducted by Affymetrix Genotyping Console. Genotype calls as well as CHP files were obtained running the birdseed-v2 algorithm.
primary data description: SNP Log ratios and Call codes

source_name: Peripheral blood

label_protocol: Affymetrix protocol

growth_protocol: Not applicable

extract_protocol: DNA was extracted from fresh peripheral blood samples using Maxwell® 16 System for Genomic DNA Extraction (Promega, (Mannheim, Germany) and quantified using NanoDrop® Spectrophotometer (NanoDrop Products, Wilmington, DE). DNA integrity was confirmed by running a 1% agarose gel.

treatment_protocol: Induction treatment was given according to the GEM2005MAS65, which compared bortezomib/melphalan/prednisone (VMP) with bortezomib/thalidomide/prednisone (VTP).

value: Peripheral blood

tag: disease state

value: multiple myeloma

tag: treatment

value: VMP

tag: response

value: IF+CR

tag: peripheral neuropathy

value: Unaffected


title: leiomyoma B, OncoScan

description:
genomic copynumber+SNP array data of a  morcellated leiomyoma specimen
7065-13B


title: Peripheral blood, multiple myeloma, sample 912_238

value: SD


title: leiomyoma A, OncoScan

description:
genomic copynumber+SNP array data of a  morcellated leiomyoma specimen
7065-13 A2


title: Peripheral blood, multiple myeloma, sample 912_186

value: VTP


title: leiomyoma C, OncoScan

description:
genomic copynumber+SNP array data of a  morcellated leiomyoma specimen
7065-13C


title: Peripheral blood, multiple myeloma, sample F07_pl1

value: PR

value: Affected


title: Peripheral blood, multiple myeloma, sample 904_244


title: Peripheral blood, multiple myeloma, sample 906_258


title: Peripheral blood, multiple myeloma, sample 904_74


title: Peripheral blood, multiple myeloma, sample 904_092

value: IF-CR


title: Peripheral blood, multiple myeloma, sample 904_241


title: batch 2 CD44 low

city: Memphis

first: Xiang

last: Chen

state: TN

address: 262 Danny Thomas Place

institute: St. Jude Children's Research Hospital

description:
bulk Sample C4
SJRHB046412_C4

data_processing:
The Cell Ranger 2.0.1 Single-Cell Software Suite (10x Genomics) was implemented to process the raw sequencing data from the Illumina HiSeq run. This pipeline performed de-multiplexing, alignment (GRCh38/STAR), and barcode processing to generate gene-cell matrices used for downstream analysis. For bulk RNA-seq, HTSeq was used to produce the count data.
Genome_build: GRCh38
Supplementary_files_format_and_content: cell ranger count matrix for single cells in each sample

growth_protocol: The human alveolar rhabdomyosarcoma cell line, Rh41, was cultured in a 5% CO2 incubator in 75cm2 vented flask containing DMEM media supplemented with 10% FBS, and 2X glutamine until the cells reached 75% confluence at approximately 3.6X106 cells.

extract_protocol:
The cells were detached from the flask with 7 mls of 1X citrate saline to which 7mls of DPBS was added followed by centrifugation at 300xG for 7 minutes. The cells pellet was resuspended in 300 ul of blocking buffer (Rat IgG/PBS) and incubated on ice for 30 minutes. 50ul of the cells in blocking buffer were transferred to a separate tube for the isotype control. The cells were washed with1ml of staining buffer (5% BSA/PBS) and centrifuged at 300XG for 5 minutes. The pellet containing approximately 3X106 cells was incubated with Rat IgG2B anti-CD44-Alexa 488 antibody (R&D systems) in staining buffer (15ul antibody + 135 ul of staining buffer) for 30 minutes on ice. For the isotype control ~600,000 cells were incubated with 5ul of Rat IgG2B-Alexa488 (R&D systems) + 45ul of staining buffer for 30 minutes on ices. After the incubation both sets of cells were pelleted and washed with 1ml of staining buffer as described above and resuspended in staining buffer, followed by flow cytometric analysis to identify the fraction of CD44 positive and negative populations.
For the single cell experiment Rh41 cells were cultured and harvested and washed in DPBS as described above, and resuspended in PBS/0.2%BSA at a concentration of 1X106 cells per ml. The 10x Genomics single-cell platform performs 3’ gene expression profiling by poly-A selection of mRNA within a single cell, which utilizes a cell barcode and UMIs (unique molecular identifiers) for each transcript. Single-cell suspensions were loaded onto the Chromium Controller according to their respective cell counts to generate approximately 6000 partitioned single-cell GEMs (Gel Bead-In-EMulsions). The library was prepared using the Chromium Single Cell 3’ v2 Library and Gel Bead Kit (10x Genomics) according to the manufacturers protocol. The cDNA content of each sample after cDNA amplification of 12 cycles was quantified and quality checked by High-Sensitivity DNA chip on a 2100 Bioanalyzer (Agilent Technologies) at a dilution of 1:6. This quantification was used to determine final library amplification cycles in the protocol, which calculated out to 12 cycles. After library quantification and quality check by DNA 1000 chip (Agilent Technologies), samples were diluted to 3.5nM for loading onto the HiSeq 4000 (Illumina) with a 2 x 75 Paired-end kit using the following read length: 26 bp Read1 (10x cell barcode and UMI), 8 bp i7 Index (sample index), and 98 bp Read2 (insert). An average of 400,000,000 reads per sample was obtained, which translated to roughly 80,000 mean reads per cell, per sample.
For bulk RNA-seq, RNA was isolated from the sorted subpopulations using Trizol (Thermo Fisher Scientific) following the manufacture recommendations. RNA libraries were prepared using the Kapa RNA HyperPrep with Riboerase RNA kit (Roche) using the recommended conditions. Briefly, 200ng of total RNA was used as input for fragmentation, reverse transcription, and second strand synthesis.  After clean up, end repair, and A tailing, Nextflex adapters (Bioo Scientific) were ligated to the fragments followed by 12 cycles of PCR amplification on a C1000 (bio-rad).  Paired end sequencing was performed (151 bases per read) on a HiSeq 4000 (Illumina).

tag: cell line

tag: cell type

tag: cell subpopulation

tag: batch

value: batch 2


title: batch 3 CD44 low

description:
bulk Sample C5
SJRHB046412_C5

value: human alveolar rhabdomyosarcoma cell line

value: batch 3


title: batch 2 CD44 high

description:
bulk Sample C6
SJRHB046412_C6


title: Peripheral blood, multiple myeloma, sample 804_66

tag: tissue

value: MR


title: batch 3 CD44 high

description:
bulk Sample C7
SJRHB046412_C7


title: batch 3 Rh41 unsorted

description:
bulk Sample C9
SJRHB046412_C9


title: Peripheral blood, multiple myeloma, sample 202_09


title: Peripheral blood, multiple myeloma, sample 201_237


title: Peripheral blood, multiple myeloma, sample 202_07


title: Peripheral blood, multiple myeloma, sample 2002_022


title: Peripheral blood, multiple myeloma, sample 804_70


title: Peripheral blood, multiple myeloma, sample 809_73


title: batch 2 Rh41 unsorted

description:
bulk Sample C8
SJRHB046412_C8


title: Peripheral blood, multiple myeloma, sample 1614_219


title: Peripheral blood, multiple myeloma, sample 1614_218


title: Peripheral blood, multiple myeloma, sample 1614_114


title: Peripheral blood, multiple myeloma, sample 804_214


title: Peripheral blood, multiple myeloma, sample 804_077


title: Peripheral blood, multiple myeloma, sample 904_142


title: Rh41 scRNA-seq

description:
single cell Sample 1
possorted_genome_bam

source_name: Rh41 single cell


title: 9017_NPS01_L3

value: Whole skin


title: Peripheral blood, multiple myeloma, sample 1605_269


title: Peripheral blood, multiple myeloma, sample 1609_156


title: Peripheral blood, multiple myeloma, sample 1608_183


title: Peripheral blood, multiple myeloma, sample 1609_207


title: batch 1 Rh41 unsorted

description:
bulk Sample C1
SJRHB046412_C1

value: batch 1


title: batch 1 CD44 low

description:
bulk Sample C3
SJRHB046412_C3


title: Peripheral blood, multiple myeloma, sample 1609_157


title: Peripheral blood, multiple myeloma, sample 1605_112


title: Peripheral blood, multiple myeloma, sample 1503_272


title: Peripheral blood, multiple myeloma, sample 1605_179


title: Peripheral blood, multiple myeloma, sample 1605_185


title: Peripheral blood, multiple myeloma, sample 1605_134


title: Peripheral blood, multiple myeloma, sample 1605_090


title: Peripheral blood, multiple myeloma, sample 1503_275


title: Peripheral blood, multiple myeloma, sample 1604_163


title: Peripheral blood, multiple myeloma, sample 1605_133


title: Peripheral blood, multiple myeloma, sample 1301_251


title: Peripheral blood, multiple myeloma, sample 1301_119


title: Peripheral blood, multiple myeloma, sample 1605_221


title: Peripheral blood, multiple myeloma, sample 1602_45


title: Peripheral blood, multiple myeloma, sample 1503_278


title: Peripheral blood, multiple myeloma, sample 1503_089


title: Peripheral blood, multiple myeloma, sample 1301_085


title: Peripheral blood, multiple myeloma, sample 1105_235

value: PD


title: Peripheral blood, multiple myeloma, sample 1301_023

value: Peripheral blood


title: Peripheral blood, multiple myeloma, sample 1303_054

value: multiple myeloma


title: Peripheral blood, multiple myeloma, sample 1301_261

value: VMP


title: Peripheral blood, multiple myeloma, sample 1503_177


title: Peripheral blood, multiple myeloma, sample 1503_096


title: Peripheral blood, multiple myeloma, sample 1503_161


title: Peripheral blood, multiple myeloma, sample 1104_239


title: batch 1 CD44 high

description:
bulk Sample C2
SJRHB046412_C2


title: Peripheral blood, multiple myeloma, sample 1104_136


title: Peripheral blood, multiple myeloma, sample 1104_132


title: Peripheral blood, multiple myeloma, sample 1503_116


title: Peripheral blood, multiple myeloma, sample 1503_111


title: Peripheral blood, multiple myeloma, sample 1503_63


title: Peripheral blood, multiple myeloma, sample 1103_273


title: Peripheral blood, multiple myeloma, sample 1103_255


title: Peripheral blood, multiple myeloma, sample 1003_129


title: Peripheral blood, multiple myeloma, sample 1103_109


title: Peripheral blood, multiple myeloma, sample 1503_50


title: Peripheral blood, multiple myeloma, sample 094_212


title: Peripheral blood, multiple myeloma, sample 0910_268


title: Peripheral blood, multiple myeloma, sample 1003_162


title: Peripheral blood, multiple myeloma, sample 0908_095


title: Peripheral blood, multiple myeloma, sample 0906_287


title: Peripheral blood, multiple myeloma, sample 0912_285


title: Peripheral blood, multiple myeloma, sample 0907_205


title: Peripheral blood, multiple myeloma, sample 0908_226


title: Peripheral blood, multiple myeloma, sample 0906_246


title: Peripheral blood, multiple myeloma, sample 0906_191


title: Peripheral blood, multiple myeloma, sample 0908_82


title: Peripheral blood, multiple myeloma, sample 0906_108

value: IF+CR


title: Peripheral blood, multiple myeloma, sample 0906_276

value: Unaffected


title: Peripheral blood, multiple myeloma, sample 0906_053


title: Peripheral blood, multiple myeloma, sample 0906_044


title: Peripheral blood, multiple myeloma, sample 0905_155


title: Peripheral blood, multiple myeloma, sample 0905_113


title: Peripheral blood, multiple myeloma, sample 0904_35


title: Peripheral blood, multiple myeloma, sample 0904_34


title: Peripheral blood, multiple myeloma, sample 0905_181


title: Peripheral blood, multiple myeloma, sample 0905_055

value: SD


title: Peripheral blood, multiple myeloma, sample 0905_091

value: VTP


title: Peripheral blood, multiple myeloma, sample 0904_48

value: PR


title: Peripheral blood, multiple myeloma, sample 0904_51

value: Affected


title: Peripheral blood, multiple myeloma, sample 0904_31


title: Peripheral blood, multiple myeloma, sample 0904_193

value: IF-CR


title: Peripheral blood, multiple myeloma, sample 0904_236


title: Peripheral blood, multiple myeloma, sample 0904_277


title: Peripheral blood, multiple myeloma, sample 0904_131


title: Peripheral blood, multiple myeloma, sample 1103_242


title: Peripheral blood, multiple myeloma, sample 0904_016


title: Peripheral blood, multiple myeloma, sample 0904_140


title: Peripheral blood, multiple myeloma, sample 0902_15


title: Peripheral blood, multiple myeloma, sample 0904_047


title: Peripheral blood, multiple myeloma, sample 0809_081


title: Peripheral blood, multiple myeloma, sample 0809_175


title: Peripheral blood, multiple myeloma, sample 0809_229


title: Peripheral blood, multiple myeloma, sample 0904_27


title: Peripheral blood, multiple myeloma, sample 0805_195


title: Peripheral blood, multiple myeloma, sample 0809_069


title: Peripheral blood, multiple myeloma, sample 0904_019


title: Peripheral blood, multiple myeloma, sample 0904_281


title: Peripheral blood, multiple myeloma, sample 0809_137


title: Peripheral blood, multiple myeloma, sample 0906_147


title: Peripheral blood, multiple myeloma, sample 0809_192


title: Peripheral blood, multiple myeloma, sample 0804_138


title: Peripheral blood, multiple myeloma, sample 0804_194


title: Peripheral blood, multiple myeloma, sample 0804_118


title: Peripheral blood, multiple myeloma, sample 0804_160


title: Peripheral blood, multiple myeloma, sample 0805_105


title: Peripheral blood, multiple myeloma, sample 0804_148


title: Peripheral blood, multiple myeloma, sample 0201_64


title: Peripheral blood, multiple myeloma, sample 0805_079


title: Peripheral blood, multiple myeloma, sample 0804_33


title: Peripheral blood, multiple myeloma, sample 0804_110


title: Peripheral blood, multiple myeloma, sample 0804_099


title: Peripheral blood, multiple myeloma, sample 0204_143


title: Peripheral blood, multiple myeloma, sample 0201_61


title: Peripheral blood, multiple myeloma, sample 0201_038


title: Peripheral blood, multiple myeloma, sample 0804_37


title: Peripheral blood, multiple myeloma, sample 0201_30


title: Peripheral blood, multiple myeloma, sample 0201_225


title: Peripheral blood, multiple myeloma, sample 82948


title: Peripheral blood, multiple myeloma, sample 0804_017


title: Peripheral blood, multiple myeloma, sample 84057


title: Peripheral blood, multiple myeloma, sample 84270


title: Peripheral blood, multiple myeloma, sample 82702


title: Peripheral blood, multiple myeloma, sample 83350


title: Peripheral blood, multiple myeloma, sample 82542


title: Peripheral blood, multiple myeloma, sample 81499


title: Peripheral blood, multiple myeloma, sample 83305


title: Peripheral blood, multiple myeloma, sample 0804_013


title: Peripheral blood, multiple myeloma, sample 81184


title: Peripheral blood, multiple myeloma, sample 80767


title: Peripheral blood, multiple myeloma, sample 81351


title: Peripheral blood, multiple myeloma, sample 81653


title: Peripheral blood, multiple myeloma, sample 74280


title: Peripheral blood, multiple myeloma, sample 80353


title: Peripheral blood, multiple myeloma, sample 80765


title: Peripheral blood, multiple myeloma, sample 85802


title: Peripheral blood, multiple myeloma, sample 74326


title: Peripheral blood, multiple myeloma, sample 80289


title: Peripheral blood, multiple myeloma, sample 81142


title: Peripheral blood, multiple myeloma, sample 84148


title: Peripheral blood, multiple myeloma, sample 74230


title: Peripheral blood, multiple myeloma, sample 83848


title: Peripheral blood, multiple myeloma, sample 74200


title: Peripheral blood, multiple myeloma, sample 72621


title: Peripheral blood, multiple myeloma, sample 73952


title: Peripheral blood, multiple myeloma, sample 80506


title: Peripheral blood, multiple myeloma, sample 71955


title: Case 470455

city: Guangzhou

first: Xiao-Peng

last: Tian

address: 651 Dong Feng RD East

department: Department of Medical Oncology

country: China

institute: Sun Yat-sen University Cancer Center

hyb_protocol: The labeled RNAs were hybridized to the array with a 1×hybridization solution (5× Denhart’s solution, 0.5% SDS, 5× SSC) in a Hybridization Chamber (Corning Inc, Corning, NY, USA) at 46°C for 12 to 16 hours.

scan_protocol: Scanned in a InnoScan 710 Microarray Scanner (Innopsys,Carbonne, France).The microarray scanning images were digitized with GenPix Pro 6.0 program.

data_processing:
The raw signal data were extracted, computed the average and subtracted background.Then we normalized (Quantile normalization) using GPR analysis software (edited in-house).
The "400" values were calculated by our automatic software.  If the original normalized data is less than 400, it is deemed as no signal, and  assigned 400 value (the maximum background value), in order to eliminate nonspecific signal.

source_name: T-cell lymphoblastic lymphoma

label_protocol: 2.5 μg of total RNA of tissue was employed with 100 nmol/L of pCp-DY647 (Dharmacon, Lafayette, CO, USA) and 15 Units of T4 RNA ligase (Life Technologies, Carlsbad, CA, USA) in a total reaction volume of 20 µL at 16°C overnight

extract_protocol: Total RNA was extracted using an acid phenol/chloroform extraction method followed by ethanol precipitation.

tag: age

value: 64 years

tag: Sex

value: female

value: T-cell lymphoblastic lymphoma


title: Case 329300

value: 21 years

value: male


title: Case 509543

value: 27 years


title: Case 585446

value: 37 years


title: Peripheral blood, multiple myeloma, sample 71552

value: Peripheral blood


title: Case 477944

value: 52 years


title: Peripheral blood, multiple myeloma, sample 71263

value: multiple myeloma

value: MR


title: Peripheral blood, multiple myeloma, sample 72535

value: VMP

value: Unaffected


title: Peripheral blood, multiple myeloma, sample 71757


title: Peripheral blood, multiple myeloma, sample 73850

value: VTP


title: Case 596326


title: Peripheral blood, multiple myeloma, sample 71603

value: PR


title: Case 366478

value: 58 years


title: Peripheral blood, multiple myeloma, sample 73842


title: Peripheral blood, multiple myeloma, sample 73949

value: IF+CR


title: Case 337506

value: 20 years


title: Case 491613

value: 33 years


title: Case 531689

value: 19 years

value: female

value: T-cell lymphoblastic lymphoma


title: Peripheral blood, multiple myeloma, sample 71036


title: Case 597102

value: 31 years

value: male


title: Peripheral blood, multiple myeloma, sample 73719

value: Peripheral blood


title: Case 395256

value: 18 years


title: Case 371810

value: 62 years


title: Peripheral blood, multiple myeloma, sample 70975

value: multiple myeloma


title: Peripheral blood, multiple myeloma, sample 70676

value: VMP


title: Peripheral blood, multiple myeloma, sample 72599

value: Unaffected


title: Case 469390

value: 64 years


title: Case 554593

value: 23 years


title: Peripheral blood, multiple myeloma, sample 63827

value: PR


title: Peripheral blood, multiple myeloma, sample 61802


title: Peripheral blood, multiple myeloma, sample 61179

value: VTP


title: Peripheral blood, multiple myeloma, sample 62276

value: IF-CR

value: Affected


title: Peripheral blood, multiple myeloma, sample 61382


title: Peripheral blood, multiple myeloma, sample 70209


title: Peripheral blood, multiple myeloma, sample 71166

value: MR


title: Case 400490

value: 30 years


title: Case 637868

value: 49 years

value: T-cell lymphoblastic lymphoma


title: Case 379940A

value: 39 years

value: male


title: Case 461192

value: 21 years


title: Case 422642

value: 36 years


title: Case 349042


title: Case 344877

value: female


title: Case 629300

value: 45 years


title: Case 344257

value: 19 years


title: Case 522187

value: 22 years


title: Case 395446


title: Case 379217

value: 32 years


title: Case 407854

value: 46 years


title: Case 368357

value: 53 years


title: Case 623374

value: 52 years


title: Case 474398

value: 24 years


title: Case 636951

value: 48 years


title: Case 498815


title: Case 388875


title: Case 321503


title: Case 473646

value: 27 years


title: Case 453650

value: 40 years


title: Case 545540

value: 44 years

value: T-cell lymphoblastic lymphoma


title: Case 487653


title: Case 522280

value: male


title: Case 382837

value: 42 years


title: Case 455048


title: Case 617810

value: 39 years


title: Case 510689

value: 37 years


title: Case 621628

value: 25 years


title: Case 345948

value: 47 years


title: Case 442157

value: 22 years


title: Case 550982

value: 30 years


title: ciliated, biological rep1

description: gene expression data from ciliated cells

hyb_protocol: Affymetrix protocol

scan_protocol: Affymetrix protocol

data_processing: Raw array CEL files were pre-processed using the mogene10stprobeset.db function within the biocLite package in R and normalized using the Robust Multi-array Average (RMA) algorithm.

source_name: primary cells

growth_protocol: Primary cells were isolated from C57BL/6 mice.

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

treatment_protocol: For fractionating SAE into basal, club, and ciliated populations, cells were stained with EpCAM-PECy7 (eBiosciences), GSIβ4-FITC (Sigma), SSEA1-Alexa Fluor® 647 (BioLegend), and CD24-PE (BD Pharmingen) for 30 minutes on ice as previously described (Zhao et al., 2014), prior to FACS. Basal cells were considered EpCAM+ and GSIβ4+. Secretory cells were considered EpCAM+ and SSEA1+. Ciliated cells were considered EpCAM+, GSIβ4- and CD24+.

value: surface airway epithelial ciliated cells

tag: strain


title: club, biological rep1

description: gene expression data from club cells

value: surface airway epithelial club cells


title: basal, biological rep2

description: gene expression data from basal cells

value: surface airway epithelial basal cells


title: ciliated, biological rep2


title: Case 513643

value: female


title: club, biological rep2

description: gene expression data from club cells


title: A2.L.F.PRE_D5

city: St Louis

first: Joseph

middle: D

last: Dougherty

address: 4566 Scott Ave, box 8232

department: Genetics and Psychiatry

institute: Washington University

hyb_protocol: Hybridization performed using Illumina Mouse WG6 microarrays per manufacturer's instructions.

scan_protocol: Scanned per manufacturer's instructions

data_processing: Data were analyzed using Bioconductor/R. Examination of distribution of expression levels led to the exclusion of one Slc6a4 TRAP sample and one hindbrain sample due to poor hybridization and/or RNA quality.  Remaining TRAP and hindbrain samples were separately normalized using the lumi package. Data underwent variance stabilizing transformation (vst) with lumiT followed by rank invariant normalization (rsn) with lumiN. Appropriate clustering of replicates was confirmed with correlation and hierarchical clustering.  Hindbrain mRNAs were again compared to TRAP samples and confirmed enrichment of markers of each respective cell type. Only genes with TRAP/hindbrain expression >.85, and absolute expression >200 fluorescent units were included for downstream comparing sex or LPS/PBS.  For each mouse line, probes were defined as differentially expressed if p<.05 on a paired T-test (pairing by experimental batch and covariate) and Log2 change was +/- .585 (1.5 fold) across 3 of 4 paired comparisons. For balance purposes, the remaining replicate was used twice to replace the low quality excluded Slc6a4 TRAP sample, which could inflate false positive rates for these cells.  However, very few changes were detected in these cells in either sex or LPS comparisons.

label: Biotin

source_name: Pre-IP RNA, Slc6a2, female, LPS treatment, WTA batch 1

label_protocol: 3-7 ngs total RNA per sample was amplified with Nugen Ovation PicoSL. After amplification with the Ovation PicoSL WTA system, (3310-48, Nugen), labeling used the Encore BiotinIL Module (4210-48, Nugen).

extract_protocol: Hindbrains were dissected and processed for TRAP as described (see PMID: 24810037).  Controls/comparisons were total RNA extracted from hindbrain in parallel either from an aliquot of lysate prior to TRAP (Pre-IP) or after TRAP (Unbound).  As Pre-IPs were largely indistinguishable from Unbounds in clustering, these were pooled for subsequent analyses.

treatment_protocol: Mice were surgically implanted with peritoneal G2 E-Mitter Transponders (Phillips Respironics), then single housed for 48 hours to allow continuous telemetric monitoring of temperature and activity using the Vital View software and ER-4000 Energizer Receivers. Housing was maintained at 30 C (thermoneutral for a mouse), to permit induction of fever.  On the day of experiment, mice were injected at 07:30 intraperitoneally with 100 ug/kg of LPS (Sigma 0111:B4) or vehicle (sterile PBS) and monitored for lethargy and induction of fever with telemetery. Experimental mice were euthanized at 14:00-14:30, at which point mean fever induction was 2.175C +/- 1.18 SD above preceding minimal body temperature, with substantial lethargy.

value: hindbrain

tag: rna type

value: Pre-IP

value: adult (6-12 weeks)

tag: line

tag: trap driver gene

value: LPS

tag: wta batch


title: Case 402024

value: T-cell lymphoblastic lymphoma


title: basal, biological rep1

description: gene expression data from basal cells


title: A4.L.M.UB_F2

source_name: Unbound RNA, Slc6a4, male, LPS treatment, WTA batch 2

value: Unbound

value: male


title: A4.L.F.PRE_E6

source_name: Pre-IP RNA, Slc6a4, female, LPS treatment, WTA batch 1


title: A2.P.M.UB_D3

source_name: Unbound RNA, Slc6a2, male, PBS treatment, WTA batch 2

value: PBS


title: A4.P.F.IP_C4

source_name: TRAP'd RNA, Slc6a4, female, PBS treatment, WTA batch 1

value: TRAP


title: A4.P.M.UB_E3

source_name: Unbound RNA, Slc6a4, male, PBS treatment, WTA batch 2


title: A2.L.M.UB_F1

source_name: Unbound RNA, Slc6a2, male, LPS treatment, WTA batch 2


title: A2.P.F.IP_C3

source_name: TRAP'd RNA, Slc6a2, female, PBS treatment, WTA batch 1


title: A2.P.M.PRE_D4

source_name: Pre-IP RNA, Slc6a2, male, PBS treatment, WTA batch 1


title: A4.P.F.UB_E1

source_name: Unbound RNA, Slc6a4, female, PBS treatment, WTA batch 2


title: A4.P.M.PRE_E5

source_name: Pre-IP RNA, Slc6a4, male, PBS treatment, WTA batch 1


title: A4.P.F.PRE_F3

source_name: Pre-IP RNA, Slc6a4, female, PBS treatment, WTA batch 1


title: A4.L.F.UB_E2

source_name: Unbound RNA, Slc6a4, female, LPS treatment, WTA batch 2


title: A2.P.F.PRE_D6

source_name: Pre-IP RNA, Slc6a2, female, PBS treatment, WTA batch 1


title: Case 572450

value: 28 years


title: A4.L.M.PRE_E4

source_name: Pre-IP RNA, Slc6a4, male, LPS treatment, WTA batch 1


title: A4.L.M.IP_C2

source_name: TRAP'd RNA, Slc6a4, male, LPS treatment, WTA batch 2


title: A2.L.F.UB_D2

source_name: Unbound RNA, Slc6a2, female, LPS treatment, WTA batch 2


title: Case 465734

source_name: T-cell lymphoblastic lymphoma

value: 51 years


title: A2.P.F.UB_D1

source_name: Unbound RNA, Slc6a2, female, PBS treatment, WTA batch 2


title: Case 371753

value: 64 years


title: Case 473795

value: 27 years


title: Case 435936

value: 18 years


title: Case 412160

value: 26 years


title: Case 432378

value: 34 years


title: A4.L.M.IP_B4

source_name: TRAP'd RNA, Slc6a4, male, LPS treatment, WTA batch 1


title: Case 504721

value: 19 years

value: female


title: Case 547196

value: 21 years


title: A2.L.M.IP_C1

source_name: TRAP'd RNA, Slc6a2, male, LPS treatment, WTA batch 2

value: hindbrain

value: adult (6-12 weeks)


title: A4.L.F.IP_B6

source_name: TRAP'd RNA, Slc6a4, female, LPS treatment, WTA batch 1

value: LPS


title: Case 453291

value: 60 years

value: T-cell lymphoblastic lymphoma


title: A4.L.F.IP_B2

source_name: TRAP'd RNA, Slc6a4, female, LPS treatment, WTA batch 2


title: A2.L.F.IP_A6

source_name: TRAP'd RNA, Slc6a2, female, LPS treatment, WTA batch 1


title: A2.L.M.IP_A4

source_name: TRAP'd RNA, Slc6a2, male, LPS treatment, WTA batch 1

value: male


title: A2.P.M.IP_A5

source_name: TRAP'd RNA, Slc6a2, male, PBS treatment, WTA batch 1

value: TRAP

value: PBS


title: A4.P.M.IP_B3

source_name: TRAP'd RNA, Slc6a4, male, PBS treatment, WTA batch 2


title: A2.P.M.IP_A3

source_name: TRAP'd RNA, Slc6a2, male, PBS treatment, WTA batch 2


title: Case 562723

value: 30 years


title: Tumor microenvironment at Day 14 [D14-2]

city: Farmington

first: Djamel

last: Nehar-Belaid

state: CONNECTICUT

address: 10 discovery drive

institute: THE JACKSON LABORATORY

description: replicate 2

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing:
Raw data were log2 transformed and filtered for probes with bad detection p-values in all samples within a comparison. A given probe is kept if detected in 67% of samples within at least one experimental group, resulting in 7,016 normalized data rows.
The data were normalised using quantile normalization with IlluminaGUI in R

source_name: Tumor microenvironment at Day 14

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

extract_protocol: Tissues were lysed using Tissue Lyser (Qiagen). RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

value: BALB/C

value: 8 weeks

tag: time point

value: at Day 14 after tumor inoculation

value: tumor microenvironment tissues


title: Tumor microenvironment at Day 14 [D14-5]

description: replicate 5


title: Case 479837

value: 18 years


title: A4.P.F.IP_B1

source_name: TRAP'd RNA, Slc6a4, female, PBS treatment, WTA batch 2


title: Tumor microenvironment at Day 4 [D4-5]

description: replicate 5

source_name: Tumor microenvironment at Day 4

value: at Day 4 after tumor inoculation


title: Tumor microenvironment at Day 4 [D4-4]

description: replicate 4


title: Tumor microenvironment at Day 4 [D4-3]

description: replicate 3


title: Tumor microenvironment at Day 14 [D14-3]

description: replicate 3


title: A2.P.F.IP_A1

source_name: TRAP'd RNA, Slc6a2, female, PBS treatment, WTA batch 2

value: female


title: Tumor microenvironment at Day 14 [D14-4]

description: replicate 4


title: Case 411929

value: 33 years


title: Case 577816

value: 37 years


title: Case 352973

value: 47 years


title: Case 463991

value: 34 years


title: Case 314519

value: 31 years


title: Tumor microenvironment at Day 4 [D4-6]

description: replicate 6


title: A2.L.F.IP_A2

source_name: TRAP'd RNA, Slc6a2, female, LPS treatment, WTA batch 2

value: hindbrain

value: adult (6-12 weeks)

value: LPS


title: Tumor microenvironment at Day 14 [D14-1]

description: replicate 1


title: Tumor microenvironment at Day 4 [D4-2]

description: replicate 2


title: Control Tissue  [CTRL 3]

description: replicate 3

source_name: Control Tissue

value: control tissue


title: Control Tissue  [CTRL 2]

description: replicate 2


title: Tumor microenvironment at Day 4 [D4-1]

description: replicate 1


title: Case 542777

source_name: T-cell lymphoblastic lymphoma

value: male

value: T-cell lymphoblastic lymphoma


title: Case 617078

value: 32 years


title: Case 394891A

value: 27 years


title: Case 473425

value: 43 years


title: Case 444563

value: 36 years


title: Case 584047

value: 59 years


title: Case 609733

value: 24 years


title: Control Tissue  [CTRL 1]

description: replicate 1

value: BALB/C

value: 8 weeks


title: Case 502001

value: 53 years


title: T47D.mimic.miR.489.3

city: Columbia

first: Hexin

state: SC

address: 715 Sumter Street,PSC621

department: Biological sciences

institute: University of South Carolina

description:
Replicate 3
Cultured cells of T47D breast epithelial cell line

data_processing: The data were normalized using the default quantile normalisation with R/bioconductor package lumi version 3.2.2

source_name: T47D cells trasfected with Mimic

growth_protocol: T47D cells were cultured in RPMI 1640 media with 10% Fetal Bovine serum supplement

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

treatment_protocol: T47D cells were transfected with miR-489 mimic or control scramble siRNA for 72 hours.

tag: tissue type

value: Breast cancer


title: T47D.Scr.3

source_name: T47D cells trasfected with Scr


title: T47D.mimic.miR.489.2

description:
Replicate 2
Cultured cells of T47D breast epithelial cell line


title: Zeamays_bsd2_Mcells_043_B

data_processing:
Feature intensity values were log-transformed, corrected for local background, and filtered to include only those that were at least 2x background. The data was then LOWESS normalized (Sawers et al 2007) and corrected for dye-effect (Smyth 2004). Differentially expressed genes were identified by moderated-t test and the false discovery rate (q) was calculated as previously described (Storey and Tibshirani 2003).
References:
Sawers, R.J., Liu, P., Anufrikova, K., Hwang, J.T., and Brutnell, T.P. (2007). A multi-treatment experimental system to examine photosynthetic differentiation in the maize leaf. BMC
Genomics 8, 12.
Smyth, G.K. (2004). Linear models and empirical bayes methods for assessing differential expression in microarray experiments. Stat Appl Genetic Mol Biol 3, Article3.
Storey, J.D., and Tibshirani, R. (2003). Statistical significance for genomewide studies. Proc Natl Acad Sci U S A 100, 9440-9445.

source_name: wild-type sibling of bsd2 mutant, mesophyll cells, replicate 4

extract_protocol:
M protoplasts were isolated as previously described with slight modification; only second leaf blades were used. For full protocol see Markelz, N.H., Costich, D.E., and Brutnell, T.P. (2003). Photomorphogenic responses in maize seedling development. Plant Physiol 133, 1578-1591.
RNA was isolated as in Sheehan, M.J., Farmer, P.R., and Brutnell, T.P. (2004). Structure and expression of maize phytochrome family homeologs. Genetics 167, 1395-1405.

tag: W22 cultivar, bsd2 segregating line, harvested at 3rd leaf emerging stage


title: Case A1687-2 (fetal)

source_name: fetal thymus

value: <1 years

value: female

value: fetal thymus


title: Case 9844-12A (fetal)


title: Case 9838 (fetal)


title: Case 9841-3 (fetal)


title: Zeamays_bsd2_Mcells_247_B

source_name: wild-type sibling of bsd2 mutant, mesophyll cells, replicate 1


title: Zeamays_bsd2_BScells_248_B

source_name: wild-type sibling of bsd2 mutant, bundle sheath cells, replicate 2

extract_protocol:
BS strands were isolated as previously described with slight modification; only second leaf blades were used. For full protocol see Markelz, N.H., Costich, D.E., and Brutnell, T.P. (2003). Photomorphogenic responses in maize seedling development. Plant Physiol 133, 1578-1591.
RNA was isolated as in Sheehan, M.J., Farmer, P.R., and Brutnell, T.P. (2004). Structure and expression of maize phytochrome family homeologs. Genetics 167, 1395-1405.


title: Zeamays_bsd2_Mcells_121_B

source_name: wild-type sibling of bsd2 mutant, mesophyll cells, replicate 2


title: Zeamays_bsd2_Mcells_249_B

description:
The mutant bundle sheath defective2 (bsd2) lacks the accumulation of Rubisco small and large subunits (Roth et al 1996; Brutnell et al 1999) and cannot perform the Calvin Cycle (Smith et al 1998). The loss of Rubisco may lead to changes in the spatial regulation of typically BS- and M-enriched genes. To detect such changes, gene expression profiles of bsd2 M cells and wild-type M cells from sibling plants were compared using the Maize Oligonucleotide Array (University of Arizona). Tissue and RNA isolations for this experiment were performed as previously described (Covshoff et al 2008). Six biological replicates were conducted in a dye swap arrangement using the Array 900MPX Expression Array Detection Kit and company protocol (Genisphere). References:
Brutnell TP, Sawers RJ, Mant A, and Langdale JA (1999). BUNDLE SHEATH DEFECTIVE2, a novel protein required for post-translational regulation of the rbcL gene of maize. Plant Cell 11, 849-864.
Covshoff S, Majeran W, Liu P, Kolkman JM, van Wijk KJ, Brutnell TP (2008) Deregulation of maize C4 photosynthetic development in a mesophyll cell-defective mutant. Plant Physiol 146: 1469-1481.
Roth R, Hall LN, Brutnell TP, and Langdale JA (1996). bundle sheath defective2, a mutation that disrupts the coordinated development of bundle sheath and mesophyll cells in the maize leaf. Plant Cell 8, 915-927.
Smith LH, Langdale JA, and Chollet R (1998). A functional Calvin cycle
is not indispensable for the light activation of C4 phosphoenolpyruvate carboxylase kinase and its target enzyme in the maize mutant bundle sheath defective2-mutable1. Plant Physiol 118, 191-197.

source_name: wild-type sibling of bsd2 mutant, mesophyll cells, replicate 5


title: T47D.Scr.2


title: T47D.mimic.miR.489.1

description:
Replicate 1
Cultured cells of T47D breast epithelial cell line


title: Zeamays_bsd2_BScells_246_B

source_name: wild-type sibling of bsd2 mutant, bundle sheath cells, replicate 5


title: T47D.Scr.1


title: Case 9839-15 (fetal)


title: Case A1725-2 (fetal)


title: Zeamays_bsd2_BScells_243_B

source_name: wild-type sibling of bsd2 mutant, bundle sheath cells, replicate 4


title: Case 9842-3 (fetal)


title: Zeamays_bsd2_Mcells_081_B

data_processing:
Feature intensity values were log-transformed, corrected for local background, and filtered to include only those that were at least 2x background. The data was then LOWESS normalized (Sawers et al 2007) and corrected for dye-effect (Smyth 2004). Differentially expressed genes were identified by moderated-t test and the false discovery rate (q) was calculated as previously described (Storey and Tibshirani 2003).

References:
Sawers, R.J., Liu, P., Anufrikova, K., Hwang, J.T., and Brutnell, T.P. (2007). A multi-treatment experimental system to examine photosynthetic differentiation in the maize leaf. BMC
Genomics 8, 12.
Smyth, G.K. (2004). Linear models and empirical bayes methods for assessing differential expression in microarray experiments. Stat Appl Genetic Mol Biol 3, Article3.
Storey, J.D., and Tibshirani, R. (2003). Statistical significance for genomewide studies. Proc Natl Acad Sci U S A 100, 9440-9445.

source_name: wild-type sibling of bsd2 mutant, mesophyll cells, replicate 6


title: Case A1685-2 (fetal)


title: Case A1728-2 (fetal)


title: Case A1718-2 (fetal)


title: Case A1726-2 (fetal)


title: Case A1719-2 (fetal)


title: Zeamays_bsd2_Mcells_042_B

source_name: bsd2 mutant, mesophyll cells, replicate 2


title: AG03512 (Control)

city: A Coruña

first: María

middle: C

last: Arufe

state: A Coruña

address: As Xubias

department: Fisioterapia, Medicina y Ciencias Biomédicas

institute: UDC

data_processing:
sequencing data was generated on Hiseq 1500 on a rapid mode flow cell from Illumina
The raw RNA-Seq reads for each sample were aligned to the reference human genome browser (GRCh38.p12 assembly) using Bowtie2 and Tophat2.
An average of 23 million paired-end 100-bp reads was obtained per sample. After alignment, raw sequence read depths were converted to estimate transcript abundance measured as fragments per kilobase of exons per million (FPKM), and the cuffinks of differentially expressed genes and transcripts were calculate with Cuffdidd.
Genome_build: GRCh38.p12 assembly
Supplementary_files_format_and_content: Differentially expressed genes and transcripts were calculated with Cuffdiff.The fold-change thresholds had to be greater than 1.2 and lower than 0.8.

source_name: Fibroblast

extract_protocol:
RNA was harvested using Trizol reagent. Illumina SureSelect Strand Specific RNA library Prep was used. 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Skin Fibroblast

tag: passes

tag: genotype

value: wild type


title: AG03257 (Control)


title: AG03199 (HGPS)

value: Hutchinson-Gilford Progeria Syndrome


title: Case A1727-2 (fetal)

value: male


title: Zeamays_bsd2_BScells_017_B

city: Ithaca

first: Thomas

address: Cornell University

institute: Boyce Thompson Institute for Plant Research

source_name: wild-type sibling of bsd2 mutant, bundle sheath cells, replicate 3


title: Case A1683-2 (fetal)


title: Case A1692-2 (fetal)


title: Case A1695-2 (fetal)


title: Case A1686-2 (fetal)


title: AG03513 (HGPS)


title: Case A1682-2 (fetal)


title: Zeamays_bsd2_BScells_239_B

source_name: wild-type sibling of bsd2 mutant, bundle sheath cells, replicate 1


title: Urines_Sham_rep2

city: Genoa

first: Alberto

last: Izzotti

address: Via A. Pastore 1

country: Italy

institute: University of Genoa

description:
DISSALMouse3Kv2.0_051
For evaluating the expression of miRNAs, we used the 7th generation miRCURY LNATM microRNA Array (Exiqon), which contains 3100 capture probes covering human, mouse, and rat miRNAs.  In particular, this microarray

hyb_protocol: The hybridization was performed in GlassArray Hybridization Cassettes (Invitrogen Ltd, Paisley, UK) in a water bath at 37°C for 16 h and then a wash sequence was performed.

scan_protocol: The array was dried by centrifugation and scanned by a laser scanner (ScanArray, PerkinElmer, Waltham, MA) to record fluorescent signals produced by each spotted probe effectively hybridized with the corresponding miRNA.

data_processing:
The microarray data were processed by GeneSpring software and their overall variability, as related to treatments, was examined by box-plot analysis, scatter-plot analysis (SPA), hierarchical cluster analysis (HCA),and principal component analysis (PCA). Due to the huge number of datasets to be analyzed, pooled analysis of microarray data was performed without taking into account intergender differences, a goal that was out of the scope of the present study and that had been evaluated in previous studies  (Izzotti et al., Oncotarget 2016).
Differences in body weight gain between MCS-exposed and sham-exposed mice was evaluated for statistical significance by ANOVA followed by Student’s t test for unpaired data.  miRNA microarray data, after local background subtraction, log transformation, and normalization were analyzed by GeneSpring software (Agilent, Santa Clara, CA).

source_name: Urines,Sham

label_protocol: The total RNA from each sample is labeled with Label IT® miRNA Labeling Kits, Version 2 (Mirus Bio, WI) following the standard protocol

growth_protocol: Immediately after sacrifice, the BAL was performed by intubating the trachea and lavaging with 5 ml of PBS per mouse. The blood was collected by heart puncture and used for preparing serum.  The urines were collected for 8 h and pooled from the mice belonging to each experimental group by using metabolic cages during the day preceding euthanasia of mice.

extract_protocol: RNA was extracted individually from the 10 organs of mice belonging to all experimental groups, whereas the body fluids were pooled within each group, irrespective of gender due to the low amounts of samples available.  RNA was extracted from mouse organs (miRNeasy, Qiagen, Hilden, Germany) and body fluids (Exiqon’s miRCURY™ RNA Isolation Kit – Biofluids (Exiqon, Vedbaek, Denmark)

treatment_protocol: Ten organs, including lungs, liver, heart, kidney, spleen, urinary bladder, skeletal muscle (left gastrocnemius), colon, stomach, and brain, were collected.  Immediately after collection, each organ or fluid was immersed in RNAlater and kept at -80°C. The urines were centrifuged in order to remove the sediment.

tag: gender

value: Female

tag: treatment

value: Sham

tag: organs

value: Urines


title: Urines_MCS_rep2

description:
DISSALMouse3Kv2.0_053
For evaluating the expression of miRNAs, we used the 7th generation miRCURY LNATM microRNA Array (Exiqon), which contains 3100 capture probes covering human, mouse, and rat miRNAs.  In particular, this microarray

source_name: Urines,MCS

value: MCS


title: Urines_Sham_rep1

description:
DISSALMouse3Kv2.0_050
For evaluating the expression of miRNAs, we used the 7th generation miRCURY LNATM microRNA Array (Exiqon), which contains 3100 capture probes covering human, mouse, and rat miRNAs.  In particular, this microarray

value: Male


title: Zeamays_bsd2_BScells_041_B

last: Brutnell

description:
The mutant bundle sheath defective2 (bsd2) lacks the accumulation of Rubisco small and large subunits (Roth et al 1996; Brutnell et al 1999) and cannot perform the Calvin Cycle (Smith et al 1998). The loss of Rubisco may lead to changes in the spatial regulation of typically BS- and M-enriched genes. To detect such changes, gene expression profiles of bsd2 BS cells and wild-type BS cells from sibling plants were compared using the Maize Oligonucleotide Array. Tissue and RNA isolations for this experiment were performed as previously described (Covshoff et al 2008). Six biological replicates were conducted in a dye swap arrangement using the Array 900MPX Expression Array Detection Kit and company protocol (Genisphere).
References:
Brutnell TP, Sawers RJ, Mant A, and Langdale JA (1999). BUNDLE SHEATH DEFECTIVE2, a novel protein required for post-translational regulation of the rbcL gene of maize. Plant Cell 11, 849-864.
Covshoff S, Majeran W, Liu P, Kolkman JM, van Wijk KJ, Brutnell TP (2008) Deregulation of maize C4 photosynthetic development in a mesophyll cell-defective mutant. Plant Physiol 146: 1469-1481.
Roth R, Hall LN, Brutnell TP, and Langdale JA (1996). bundle sheath defective2, a mutation that disrupts the coordinated development of bundle sheath and mesophyll cells in the maize leaf. Plant Cell 8, 915-927.
Smith LH, Langdale JA, and Chollet R (1998). A functional Calvin cycle
is not indispensable for the light activation of C4 phosphoenolpyruvate carboxylase kinase and its target enzyme in the maize mutant bundle sheath defective2-mutable1. Plant Physiol 118, 191-197.

source_name: wild-type sibling of bsd2 mutant, bundle sheath cells, replicate 6


title: Serum _MCS_rep1

description:
DISSALMouse3Kv2.0_048
For evaluating the expression of miRNAs, we used the 7th generation miRCURY LNATM microRNA Array (Exiqon), which contains 3100 capture probes covering human, mouse, and rat miRNAs.  In particular, this microarray

source_name: Serum, MCS

value: Serum


title: Serum _MCS_rep2

description:
DISSALMouse3Kv2.0_049
For evaluating the expression of miRNAs, we used the 7th generation miRCURY LNATM microRNA Array (Exiqon), which contains 3100 capture probes covering human, mouse, and rat miRNAs.  In particular, this microarray


title: Case A1677-2 (fetal)


title: Serum _Sham_rep2

description:
DISSALMouse3Kv2.0_047
For evaluating the expression of miRNAs, we used the 7th generation miRCURY LNATM microRNA Array (Exiqon), which contains 3100 capture probes covering human, mouse, and rat miRNAs.  In particular, this microarray

source_name: Serum,Sham


title: Serum _Sham_rep1

description:
DISSALMouse3Kv2.0_046
For evaluating the expression of miRNAs, we used the 7th generation miRCURY LNATM microRNA Array (Exiqon), which contains 3100 capture probes covering human, mouse, and rat miRNAs.  In particular, this microarray


title: Balf_MCS_rep2

description:
DISSALMouse3Kv2.0_045
For evaluating the expression of miRNAs, we used the 7th generation miRCURY LNATM microRNA Array (Exiqon), which contains 3100 capture probes covering human, mouse, and rat miRNAs.  In particular, this microarray

source_name: Balf,MCS

value: Balf


title: Balf_MCS_rep1

description:
DISSALMouse3Kv2.0_044
For evaluating the expression of miRNAs, we used the 7th generation miRCURY LNATM microRNA Array (Exiqon), which contains 3100 capture probes covering human, mouse, and rat miRNAs.  In particular, this microarray


title: Balf_Sham_rep2

description:
DISSALMouse3Kv2.0_043
For evaluating the expression of miRNAs, we used the 7th generation miRCURY LNATM microRNA Array (Exiqon), which contains 3100 capture probes covering human, mouse, and rat miRNAs.  In particular, this microarray

source_name: Balf,Sham


title: Balf_Sham_rep1

description:
DISSALMouse3Kv2.0_042
For evaluating the expression of miRNAs, we used the 7th generation miRCURY LNATM microRNA Array (Exiqon), which contains 3100 capture probes covering human, mouse, and rat miRNAs.  In particular, this microarray


title: Spleen_MCS_rep1

description:
DISSALMouse3Kv2.0_040
For evaluating the expression of miRNAs, we used the 7th generation miRCURY LNATM microRNA Array (Exiqon), which contains 3100 capture probes covering human, mouse, and rat miRNAs.  In particular, this microarray

source_name: Spleen,MCS

value: Spleen


title: Spleen_MCS_rep2

description:
DISSALMouse3Kv2.0_041
For evaluating the expression of miRNAs, we used the 7th generation miRCURY LNATM microRNA Array (Exiqon), which contains 3100 capture probes covering human, mouse, and rat miRNAs.  In particular, this microarray


title: Urines_MCS_rep1

description:
DISSALMouse3Kv2.0_052
For evaluating the expression of miRNAs, we used the 7th generation miRCURY LNATM microRNA Array (Exiqon), which contains 3100 capture probes covering human, mouse, and rat miRNAs.  In particular, this microarray


title: Spleen_Sham_rep1

description:
DISSALMouse3Kv2.0_038
For evaluating the expression of miRNAs, we used the 7th generation miRCURY LNATM microRNA Array (Exiqon), which contains 3100 capture probes covering human, mouse, and rat miRNAs.  In particular, this microarray

source_name: Spleen,Sham


title: Stomach_Sham_rep2

description:
DISSALMouse3Kv2.0_036
For evaluating the expression of miRNAs, we used the 7th generation miRCURY LNATM microRNA Array (Exiqon), which contains 3100 capture probes covering human, mouse, and rat miRNAs.  In particular, this microarray analyzes the expression of 1135 mouse miRNAs. The total RNA from each sample is labeled with Label IT® miRNA Labeling Kits, Version 2 (Mirus Bio, WI) following the standard protocol.  Total RNA (500 ng) was mixed with 10 µl 10x labeling buffer, 4 µl Label IT reagent (containing Cy 3 or Cy 5 fluorescent tracers), and water to 86 µl

source_name: Stomach,Sham

value: Stomach


title: Stomach_MCS_rep1

description:
DISSALMouse3Kv2.0_037
For evaluating the expression of miRNAs, we used the 7th generation miRCURY LNATM microRNA Array (Exiqon), which contains 3100 capture probes covering human, mouse, and rat miRNAs.  In particular, this microarray

source_name: Stomach,MCS