title: Human HSC, EP, biological rep3

city: Bronx

first: Britta

last: Will

state: NEW YORK

address: 1300 Morris Park Ave

department: Department of Cell Biology

institute: Albert Einstein College of Medicine

description: Gene expression data from Human HSCs after 16-hours in vitro treatment with Eltrombopag

hyb_protocol: Following fragmentation, labeled cRNA of each individual sample was hybridized to Affymetrix GeneChip Human Gene ST 2.0 array, respectively, and stained according to the manufacturer's instructions.

scan_protocol: Hybridization signals were scanned and analyzed with GeneChip Scanner 3000 7G system (Affymetrix) according to standard protocols.

data_processing: For analysis of microarray data, intensity normalization was performed across samples with the CEL files using RMA algorithm of Oligo Bioconductor package. For analysis of differential gene expression, paired, linear modeling of Limma Bioconductor package was used to compare the treated samples versus the matched, non-treated controls. Differential expression was defined as fold change > 1.5 (both up and down in) and p-value < 0.05 as estimated by Limma.

label: Biotin

label_protocol: Approximately 10ng of extracted RNA was amplified and labeled using the GeneChip™ 3' IVT Pico Kit (Affymetrix, Santa Clara, CA), according to the manufacturer's instructions

growth_protocol: Human HSCs were sorted, and cultured in Myelocult H5100 medium (Stem Cell Technologies, Vancouver, Canada) supplemented with 100 ng/ml rhSCF (Gemini Bio-Products, CA), 10^-6 M hydrocortisone (Acros Organics), and 200 µg/ml Primocin (InvivoGen, San Diego, CA).

extract_protocol: RNA was extracted using the RNeasy Micro kit (Qiagen, Valencia, CA) according to the manufacturer’s instructions. Quantity and quality were assessed using Nanodrop 3300 Fluorospectrometer (Thermo Fisher Scientific, Waltham, MA) or Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Human HSCs were treated with Eltrombopag (10 µg/ml, Novartis), rhTPO (100 ng/ml, Gemini Bio-Products, CA), or vehicle control (sterile H2O) in the liquid culture for 16 hours. Thereafter, cells were collected and lysed with RLT plus buffer (Qiagen, Valencia, CA). Cell lysates were stored in -80 °C until use.

value: FACS-sorted HSC

tag: age


title: Human HSC, TPO, biological rep3

status: Public on Sep 17 2018

type: RNA

country: USA

description: Gene expression data from Human HSCs after 16-hours in vitro treatment with Thrombopoietin

molecule: total RNA

organism: Homo sapiens

tag: tissue


title: Skin LS Week 4 Drug RU-004

city: New York

first: Ana

last: Pavel

state: NY

address: One Gustave L. Levy Place

department: Dermatology

institute: Icahn School of Medicine at Mount Sinai

description: Gene expression data from skin biopsy

hyb_protocol: Affymetrix Human U133Plus 2.0 gene arrays were used. Hybridization conditions: 4.4um ssDNA, 45C, 18h, 55-60rpm.

scan_protocol: Hewlett-Packard GeneArray Scanner G2500A

data_processing: Quality control of Affymetrix chips was done using standard QC metrics and R packages. Microarray quality control images were scrutinized for spatial artifacts using Harshlight. Expression measures were obtained using GC Robust Multi-array Average (GCRMA) algorithm. Batch effects corresponding to the hybridization date and chip lot number were detected by principal component analyses and adjusted using ComBat algorithm from R’s sva package. Probe sets with expression >3 in at least 15 samples were used for further analyses. Gene expression changes were modeled using mixed-effect models, with treatment, time and tissue type as a fixed interaction term, and a random effect for each patient. Fold changes (FCHs) for the comparisons of interest were estimated, and hypothesis testing was conducted with contrasts under the general framework of linear models in the R limma package. P-values were adjusted for multiple hypotheses using the Benjamini-Hochberg procedure, which controls the false discovery rate (FDR).

label: biotin

source_name: Skin biopsy

label_protocol: Ovation WB Reagent (Nugen)

extract_protocol: Skin biopsies from lesional and non-lesional skin at baseline, week 4 and week 12 were stored in RNAlater® (Invitrogen) until further processing. RNA was extracted (Covance Genomics Lab).

tag: patient id

tag: lot

value: LS

tag: week

value: Wk 4

tag: treatment

value: Drug


title: Skin NL Week 12 Placebo RU-006

description: Gene expression data from skin biopsy

value: NL

value: Wk 12

value: Placebo


title: Skin LS Week 12 Drug RU-003

description: Gene expression data from skin biopsy


title: Skin LS Week 0 Drug RU-004

description: Gene expression data from skin biopsy

value: Wk 0


title: Human HSC, NT, biological rep3

description: Gene expression data from Human HSCs after 16-hours in vitro treatment with vehicle


title: Human HSC, TPO, biological rep2

source_name: Human HSCs after 16-hours in vitro treatment with Thrombopoietin


title: ade6-3049_mbs1D

type: genomic

city: San Francisco

first: Kyle

last: Fowler

state: California

address: 600 16th Street

institute: University of California San Francisco

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed.

scan_protocol: Slides were imaged on an Agilent G2565AA Microarray Scanner and quantified using Agilent Feature Extraction Software (v 10.1.1.1 or 10.5.1.1).

data_processing: Dark spot and control probes were removed.  For sample ade6-3057_mbs1+, using GPL16421, non-unique probes were also removed.  Output ratios were then normalized to the genome median.

molecule: genomic DNA

organism: Schizosaccharomyces pombe

source_name: DSBs (IP Rec12 covalently linked to DNA)

label_protocol: Immunoprecipitated material was PCR amplified to increase signal and incorporate Cy3/Cy5-labeled dUTPs.

growth_protocol: S. pombe cells were grown in minimal media without nitrogen for ~18 hours to synchronize cells; nitrogen was added and the temperature shifted to 34°C marking the start of meiosis.

extract_protocol: No exogenous crosslinking agent was used and cells were broken with a bead beater; chromatin was sonicated to ~500-1000 bp and Rec12-FLAG was immunoprecipitated.

tag: ade6 allele

tag: mbs1 allele

value: mbs1-20 (deletion)

source_name: Whole-cell input from meiotic culture


title: Skin LS Week 4 Drug RU-003

description: Gene expression data from skin biopsy


title: Skin LS Week 12 Placebo RU-002

description: Gene expression data from skin biopsy


title: Human HSC, EP, biological rep2

source_name: Human HSCs after 16-hours in vitro treatment with Eltrombopag


title: Skin NL Week 0 Placebo RU-002

description: Gene expression data from skin biopsy


title: Skin NL Week 0 Drug RU-001

description: Gene expression data from skin biopsy


title: Skin NL Week 0 Placebo MSSM-05

description: Gene expression data from skin biopsy


title: Skin LS Week 0 Drug RU-003

description: Gene expression data from skin biopsy


title: Skin NL Week 12 Placebo RU-002

description: Gene expression data from skin biopsy


title: Human HSC, NT, biological rep2

source_name: Human HSCs after 16-hours in vitro treatment with vehicle


title: Skin LS Week 4 Placebo RU-002

description: Gene expression data from skin biopsy


title: Human HSC, EP, biological rep1


title: Skin LS Week 4 Drug RU-001

description: Gene expression data from skin biopsy


title: Skin NL Week 12 Drug RU-001

description: Gene expression data from skin biopsy


title: Human HSC, NT, biological rep1


title: Skin NL Week 4 Placebo RU-002

description: Gene expression data from skin biopsy


title: Skin LS Week 12 Drug RU-001

description: Gene expression data from skin biopsy


title: Human HSC, TPO, biological rep1


title: Skin NL Week 4 Drug RU-001

description: Gene expression data from skin biopsy


title: Skin LS Week 0 Placebo RU-002

description: Gene expression data from skin biopsy


title: Skin LS Week 0 Drug MSSM-38

description: Gene expression data from skin biopsy


title: Skin LS Week 4 Placebo MSSM-40

description: Gene expression data from skin biopsy


title: Skin LS Week 12 Placebo MSSM-40

description: Gene expression data from skin biopsy


title: Skin LS Week 0 Placebo MSSM-40

description: Gene expression data from skin biopsy


title: Skin LS Week 0 Drug MSSM-37

description: Gene expression data from skin biopsy


title: Skin LS Week 0 Drug RU-001

description: Gene expression data from skin biopsy


title: Skin LS Week 4 Drug MSSM-37

description: Gene expression data from skin biopsy


title: P41

type: SRA

city: Rehovot

first: Keren

last: Bahar-Halpern

address: Herzl St 234

country: Israel

institute: Weizmann Institute

library_source: transcriptomic

data_processing:
Note: Paired-end, but the second read contained only cell and molecule barcodes. This information was appended to the fastq entry header
bcl2fastq/2.15.0.4
Sequences with RMT of low quality (defined as RMT with minimum Phred score of less than 27) were filtered out.
Pool-barcode and well-barcode-RMT were extracted from the first and second end of the read (respectively) and concatenated to the fastq header, delimited by a underscore i.e. POOL_BARCODE_WELL_BARCODE_RMT while "NNNNNN" was used as a place holders if plate barcode was not used.
Reads were separated by POOL_BARCODE_WELL_BARCODE header data, allowing 1 sequencing error. This process created a single fastq file for each source well.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include mRNA molecule count values for each Sample
Supplementary_files_format_and_content: NPCs_umitab.txt: single cell expression matrix
Supplementary_files_format_and_content: PairedCells_umitab.txt: expression matrix
Supplementary_files_format_and_content: experimental_design.txt: Meta data file associating each single cell with its amplification batch and index sorting readouts

molecule: polyA RNA

organism: Mus musculus

source_name: Liver cells

growth_protocol: C57bl6 male mice were housed under reverse phase cycle, and fasted for 2 hours starting at 7AM.

extract_protocol:
Mouse hepatocytes were isolated by a modification of the two-step collagenase perfusion method of Seglen. Digestion step was performed with Liberase Blendzyme 3 recombinant collagenase (Roche Diagnostics), or Collagenase D, according to the manufacturer’s instruction.
3' end mRNA libraries were prepared for sequencing using MARS-seq (Jaitin et al, Science 2014)
single cell RNA-seq for gene expression quantitation

treatment_protocol: Mice were anesthetized with an intraperitoneal injection of a ketamine (100 mg/kg) and xylazine (10 mg/kg) mixture.

tag: strain

value: postnatal seven weeks

value: Liver cells


title: P16


title: wt_2: wild-type lung

city: bad nauheim

first: Stefan

last: Günther

address: ludwigtr. 43

country: Germany

institute: MPI for heart and lung research

data_processing:
The resulting raw reads were assessed for quality, adapter content and duplication rates with FastQC (Andrews S. 2010, FastQC: a quality control tool for high throughput sequence data. Available online at: http://www.bioinformatics.babraham.ac.uk/projects/fastqc). Reaper version 15-065 was employed to trim reads after a quality drop below a mean of Q20 in a window of 20 nucleotides (Davis et al., Kraken: A set of tools for quality control and analysis of high-throughput sequence data). Only reads between 15 and 75 nucleotides were cleared for further analyses.
Trimmed and filtered reads were aligned versus the Ensembl mouse genome version mm10 (GRCm38) using STAR 2.4.0a with the parameter “--outFilterMismatchNoverLmax 0.1” to increase the maximum ratio of mismatches to mapped length to 10% (Dobin et al., STAR: ultrafast universal RNA-seq aligner).
The number of reads aligning to genes was counted with featureCounts 1.5.1 tool from the Subread package (Liao et al., featureCounts: an efficient general purpose program for assigning sequence reads to genomic features). Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded. Differentially expressed genes were identified using DESeq2 version 1.14.1 (Love et al., Moderated estimation of fold change and dispersion for RNA-Seq data with DESeq2).
Only genes with a minimum fold change of +- 2 (log2 +-1), a maximum Benjamini-Hochberg corrected p-value of 0.05, and a minimum combined mean of 5 reads were deemed to be significantly differentially expressed. The Ensembl annotation was enriched with UniProt data (release 24.03.2017) based on Ensembl gene identifiers (Activities at the Universal Protein Resource (UniProt)).
Genome_build: mm10
Supplementary_files_format_and_content: library sitze and batch effect normalized count tables

source_name: Embryonic day 17 lung (left lobe)

growth_protocol: mouse embryonic day 17 lungs

extract_protocol:
Total RNA was isolated from E17 lungs (left lobes) of two wild-type and two Myh10L458R/L458R mice using Trizol (Life Technologies) combined with on-column DNase digestion (TURBO DNAse, Ambion) to avoid contamination by genomic DNA.
3µg of total RNA was used as input for Truseq Stranded mRNA Library preparation following the low sample protocol (Illumina).

treatment_protocol: no treatment

tag: developmental stage

value: Embryonic day 17

value: lung (left lobe)

tag: genotype

value: wild type


title: wt_1: wild-type lung


title: mut_2: Myh10L458R/L458R lung


title: mut_1: Myh10L458R/L458R lung


title: P14


title: P13


title: Skin LS Week 0 Drug MSSM-01

description: Gene expression data from skin biopsy


title: Skin NL Week 0 Drug MSSM-37

description: Gene expression data from skin biopsy


title: Skin NL Week 4 Drug MSSM-36

description: Gene expression data from skin biopsy


title: Skin NL Week 12 Drug MSSM-04

description: Gene expression data from skin biopsy


title: Skin LS Week 12 Drug MSSM-36

description: Gene expression data from skin biopsy


title: Skin LS Week 0 Drug MSSM-36

description: Gene expression data from skin biopsy


title: P12


title: Skin NL Week 4 Drug MSSM-37

description: Gene expression data from skin biopsy


title: Skin LS Week 4 Drug MSSM-36

description: Gene expression data from skin biopsy


title: Skin NL Week 0 Drug MSSM-38

description: Gene expression data from skin biopsy


title: P10


title: P9


title: Skin NL Week 12 Drug MSSM-36

description: Gene expression data from skin biopsy


title: P15


title: Skin LS Week 12 Drug MSSM-37

description: Gene expression data from skin biopsy


title: P6


title: P8


title: P5


title: P7


title: P11


title: Skin NL Week 12 Drug MSSM-37

description: Gene expression data from skin biopsy


title: Skin NL Week 12 Placebo MSSM-35

description: Gene expression data from skin biopsy


title: Skin LS Week 12 Placebo MSSM-35

description: Gene expression data from skin biopsy


title: Skin NL Week 0 Placebo MSSM-35

description: Gene expression data from skin biopsy


title: Skin NL Week 4 Placebo MSSM-35

description: Gene expression data from skin biopsy


title: Skin LS Week 12 Drug MSSM-04

description: Gene expression data from skin biopsy


title: P4


title: Skin NL Week 0 Drug MSSM-36

description: Gene expression data from skin biopsy


title: P3


title: Skin LS Week 4 Placebo MSSM-35

description: Gene expression data from skin biopsy


title: P1

value: postnatal six weeks


title: AB2085

source_name: Liver non-parenchymal cells

value: postnatal four months

value: Liver non-parenchymal cells


title: P2


title: AB2084


title: AB2086


title: AB2082


title: AB2083


title: AB2081


title: Skin LS Week 0 Placebo MSSM-35

description: Gene expression data from skin biopsy


title: Skin LS Week 12 Drug MSSM-34

description: Gene expression data from skin biopsy


title: AB1694

value: postnatal three months


title: AB1693


title: AB1692


title: AB1691


title: AB1690


title: Skin NL Week 12 Drug MSSM-34

description: Gene expression data from skin biopsy


title: Skin LS Week 4 Drug MSSM-34

description: Gene expression data from skin biopsy

value: LS


title: Skin LS Week 4 Drug MSSM-33

description: Gene expression data from skin biopsy

value: Wk 4


title: Skin LS Week 4 Drug MSSM-04

description: Gene expression data from skin biopsy

value: Drug


title: Skin NL Week 12 Drug MSSM-33

description: Gene expression data from skin biopsy

value: NL


title: Skin NL Week 4 Drug MSSM-34

description: Gene expression data from skin biopsy


title: Skin NL Week 0 Drug MSSM-33

description: Gene expression data from skin biopsy


title: Skin NL Week 0 Drug MSSM-34

description: Gene expression data from skin biopsy


title: Skin LS Week 0 Drug MSSM-33

description: Gene expression data from skin biopsy


title: Skin LS Week 12 Drug MSSM-33

description: Gene expression data from skin biopsy

value: Wk 12


title: Skin LS Week 0 Drug MSSM-34

description: Gene expression data from skin biopsy


title: Skin NL Week 4 Drug MSSM-33

description: Gene expression data from skin biopsy


title: Skin LS Week 12 Drug MSSM-32

description: Gene expression data from skin biopsy


title: Skin NL Week 4 Drug MSSM-32

description: Gene expression data from skin biopsy


title: Skin LS Week 4 Drug MSSM-32

description: Gene expression data from skin biopsy


title: Skin LS Week 0 Placebo MSSM-05

description: Gene expression data from skin biopsy

value: Placebo


title: Skin NL Week 0 Drug MSSM-32

description: Gene expression data from skin biopsy

value: Wk 0


title: Skin LS Week 0 Drug MSSM-32

description: Gene expression data from skin biopsy


title: Skin LS Week 12 Drug MSSM-31

description: Gene expression data from skin biopsy


title: Skin LS Week 4 Drug MSSM-31

description: Gene expression data from skin biopsy


title: Skin NL Week 0 Drug MSSM-31

description: Gene expression data from skin biopsy


title: Skin NL Week 4 Drug MSSM-04

description: Gene expression data from skin biopsy


title: Skin LS Week 0 Drug MSSM-31

description: Gene expression data from skin biopsy


title: Skin NL Week 12 Drug MSSM-32

description: Gene expression data from skin biopsy


title: Skin LS Week 12 Drug MSSM-30

description: Gene expression data from skin biopsy


title: Skin LS Week 4 Drug MSSM-30

description: Gene expression data from skin biopsy


title: Skin NL Week 12 Drug MSSM-30

description: Gene expression data from skin biopsy


title: Skin LS Week 0 Drug MSSM-04

description: Gene expression data from skin biopsy


title: Skin NL Week 4 Drug MSSM-30

description: Gene expression data from skin biopsy


title: Skin NL Week 12 Drug MSSM-31

description: Gene expression data from skin biopsy


title: Skin LS Week 0 Placebo MSSM-29

description: Gene expression data from skin biopsy


title: Input for Yth1-ChIPseq

city: Goettingen

first: Michael

last: Lidschreiber

address: Am Fassberg 11

institute: Max-Planck-Institute for Multidisciplinary Scienes

library_source: genomic

data_processing:
Paired-end 50 bp reads were aligned to the S. cerevisiae genome (sacCer3, version 64.2.1) using the short read aligner Bowtie (version 2.2.3) (Langmead and Salzberg, 2012). SAMTools was used to quality filter SAM files (Li et al., 2009). Alignments with MAPQ smaller than 7 (-q 7) were skipped and only proper pairs (-f99, -f147, -f83, -f163) were selected. The BEDTools toolset (Quinlan and Hall, 2010) was used to obtain coverage tracks that were subsequently imported into R/Bioconductor where further processing of the data was carried out. Normalization between IP and Input was done using the signal extraction scaling (SES) factor obtained with the estimateScaleFactor function from deepTools (Ramirez et al., 2014) with options: -l 100 -n 100000 and the median fragment size (-f) estimated from the data (around 200 bp). ChIP enrichments were obtained by dividing SES-normalized IP intensities by the corresponding input intensities: log2(IP/Input).
Genome_build: sacCer3, version 64.2.1
Supplementary_files_format_and_content: For each ChIP-seq experiment SES normalized log2(IP/Input) signals (Ramirez et al., 2014) are provided as processed data tracks in .bw (bigwig) format. Signals from replicates were averaged.

organism: Saccharomyces cerevisiae

source_name: Yeast cell extract

growth_protocol: Yeast strains were grown in 600 mL YPD medium to mid-log phase (OD600, ~ 0.8).

extract_protocol:
Cells were collected by centrifugation, washed with TBS (20 mM Tris-HCL at pH 7.5, 150 mM NaCl) and twice with lysis buffer (50 mM HEPES-KOH at pH 7.5, 150 mM NaCl, 1 mM EDTA, 1% Triton X100, 0.1% Na deoxycholate, 0.1% SDS). Cell pellets were resuspended in 2 mL lysis buffer and lysed by bead beating and the lysate was sonicated in a Covaris S220 system. Chromatin was washed with FA lysis buffer and solubilized via sonication with a Covaris S220 instrument (COVARIS, INC.) to yield an average DNA fragment size of 200 bp as determined on an Agilent 2200 TapeStation instrument (see below). This was achieved by sonicating the sample for 18 minutes using the following parameters: Peak Incident Power (W): 140; Duty Factor: 5%; Cycles per Burst: 200. 30 µL and 50 µL of the washed and fragmented chromatin samples were saved as input materials and for control of the average chromatin fragment size, respectively. The remaining chromatin sample was immunoprecipitated with 100 µL antibody-coated and prewashed magnetic Dynabeads Protein G (life technologies) at 4C for 3 hr on a turning wheel. Immunoprecipitated chromatin was washed 5 times with ChIP wash buffer (100 mM Tris-HCl at pH 7.5, 500 mM LiCl, 1% NP-40, 1% Na deoxycholate) and one time with TE buffer (10 mM Tris-HCl at pH 7.5, 1 mM EDTA). Immunoprecipitated chromatin was eluted for 10 minutes at 70C in the presence of ChIP elution buffer (100 mM Sodium bicarbonate, 1% SDS). Eluted immunoprecipitated chromatin as well as input material and material for control of the average chromatin fragment size were incubated with 10 µL RNase A (10 mg/mL) at 37C for 30 minutes and subsequently subjected to Proteinase K (20 µL of 20 mg/mL Proteinase K, Bioline, BIO-37084) digestion at 37C for 2 hr and reversal of crosslinks (at 65C over night). DNA of the IP, mock IP, input, and fragment size control samples was purified with the QIAquick MinElute PCR Purification Kit (Qiagen) according to the manufacturers instructions. Samples used for determining the average chromatin fragment size were analyzed on an Agilent 2200 TapeStation instrument. DNA concentration of the IP and Input samples was determined with Qubit 1.0, dsDNA HS. Before preparing libraries for Illumina sequencing, IP and input samples were analysed via qRT-PCR on 4 housekeeping genes to access quality of sample DNA.
To prepare libraries of ChIP samples, 1-10 ng of IP or Input DNA were used for sequencing library preparation according to the manufacturer's recommendations using the ThruPLEX DNA-seq Kit. Libraries were qualified on an Agilent 2200 TapeStation instrument and quantified with Qubit 1.0. Libraries were pooled and sequenced on an Illumina HiSeq 2500 sequencer.

treatment_protocol: Cell cultures were treated with formaldehyde (1%, Sigma F1635) for 20 minutes at 20C. Crosslinking was quenched with 75 mL of 3 M glycine for 5 minutes at 20C.

tag: expressing

value: TAP-tagged protein

tag: chip reagent


title: Skin NL Week 0 Drug MSSM-30

description: Gene expression data from skin biopsy


title: Yth1-ChIPseq

value: IgG from rabbit serum (Sigma) directed against the Protein A content of the C-terminal TAP tag


title: Syc1-WT-Replicate2-RNAseq

description:
L_Syc1_WT_Rep2
S.cerevisiae.mRNA.snRNA.snoRNA.anno_Steinmetz_2013_rawHTSeq-counts.txt
S.cerevisiae.mRNA.snRNA.snoRNA.anno_Steinmetz_2013_DESeq2_results_table.txt

data_processing:
Acquisition of data obtained from 4tU-Seq experiments was performed as described (Schulz et al., 2013), with minor modifications. Briefly, paired-end 50 base reads with additional 6 base reads of barcodes were obtained for labeled RNA. Reads were demultiplexed and aligned to the S. cerevisiae genome (sacCer3, version 64.2.1) using STAR (version 2.3.0) (Dobin et al., 2013). SAMTools was used to quality filter SAM files (Li et al., 2009). Alignments with MAPQ smaller than 7 (-q 7) were skipped and only proper pairs (-f99, -f147, -f83, -f163) were selected. Further processing of the data was carried out using R/Bioconductor (Gentleman et al., 2004; Ihaka and Gentleman, 1996). Piled-up counts for every genomic position were summed up over replicates, using fragment coverage i.e. counting both sequenced bases covered by reads and unsequenced bases spanned between proper mate-pair reads.
Genome_build: sacCer3, version 64.2.1
Supplementary_files_format_and_content: Tabular containing raw read counts according to S.cerevisiae.mRNA.snRNA.snoRNA.anno_Steinmetz_2013.gtf and also DESeq2 results table including log2 fold changes and p-values.

growth_protocol: Inoculate strain from O/N culture at OD600 0.1, grow at 30C in YPD to OD600 0.8, label with 5mM 4thiouracil final conc. for 6 minutes, spin 1 min, discard supernatant, freeze in lN2

extract_protocol:
Extract total RNA with phenol/chloroform, purify labeled RNA
Using NUGen Ovation Universal RNA-Seq System starting with 100 ng RNA input

treatment_protocol: Label with 5mM 4thiouracil final conc. for 6 minutes

value: wild-type

tag: method

value: labeled with 4thiouracil


title: Syc1-WT-Replicate1-RNAseq

description:
L_Syc1_WT_Rep1
S.cerevisiae.mRNA.snRNA.snoRNA.anno_Steinmetz_2013_rawHTSeq-counts.txt
S.cerevisiae.mRNA.snRNA.snoRNA.anno_Steinmetz_2013_DESeq2_results_table.txt


title: Skin NL Week 12 Placebo MSSM-29

description: Gene expression data from skin biopsy


title: Skin LS Week 4 Placebo MSSM-29

description: Gene expression data from skin biopsy


title: Skin LS Week 12 Placebo MSSM-29

description: Gene expression data from skin biopsy


title: Skin NL Week 12 Drug MSSM-28

description: Gene expression data from skin biopsy


title: Input for Ref2-ChIPseq


title: Input for Syc1-ChIPseq


title: Skin LS Week 0 Drug MSSM-28

description: Gene expression data from skin biopsy


title: Skin LS Week 0 Drug MSSM-30

description: Gene expression data from skin biopsy


title: Skin NL Week 4 Placebo MSSM-29

description: Gene expression data from skin biopsy


title: Input for Cft2-ChIPseq


title: Skin LS Week 12 Drug MSSM-28

description: Gene expression data from skin biopsy


title: Skin LS Week 4 Drug MSSM-28

description: Gene expression data from skin biopsy


title: Skin NL Week 0 Drug MSSM-28

description: Gene expression data from skin biopsy


title: Skin LS Week 4 Placebo MSSM-27

description: Gene expression data from skin biopsy


title: Skin NL Week 0 Placebo MSSM-27

description: Gene expression data from skin biopsy


title: Skin LS Week 12 Placebo MSSM-27

description: Gene expression data from skin biopsy


title: Skin NL Week 12 Placebo MSSM-27

description: Gene expression data from skin biopsy


title: Skin NL Week 4 Drug MSSM-28

description: Gene expression data from skin biopsy


title: Skin NL Week 0 Placebo MSSM-29

description: Gene expression data from skin biopsy


title: Ref2-ChIPseq


title: Skin NL Week 4 Placebo MSSM-27

description: Gene expression data from skin biopsy


title: Skin LS Week 0 Placebo MSSM-27

description: Gene expression data from skin biopsy


title: Syc1-KO-Replicate1-RNAseq

description:
L_Syc1_KO_Rep1
S.cerevisiae.mRNA.snRNA.snoRNA.anno_Steinmetz_2013_rawHTSeq-counts.txt
S.cerevisiae.mRNA.snRNA.snoRNA.anno_Steinmetz_2013_DESeq2_results_table.txt


title: Syc1-ChIPseq


title: Skin LS Week 12 Drug MSSM-03

description: Gene expression data from skin biopsy


title: Cft2-ChIPseq


title: Swd2-PAR-CLIP

description: crosslinked RNA

data_processing:
Adapter sequences are first trimmed from the raw sequencing files. The quality filter then discards all reads containing unidentified nucleotides (N), Phreds scores below 30, reads shorter than 15 nucleotides (nt), or reads that are flagged by Illumina’s internal chastity filter. Quality-trimmed reads are aligned to the S. cerevisiae genome (sacCer3, version 64.2.1) using the short read aligner STAR (version 2.5.2b; options: --outFilterMultimapNmax 1, --outFilterMismatchNmax 1, --scoreDelOpen -10000, --scoreInsOpen -10000, --alignSJoverhangMin 10000, --alignSJstitchMismatchNmax 0 0 0 0). The resulting SAM files are then converted into BAM and PileUp files using SAMTools.
Genome_build: sacCer3, version 64.2.1
Supplementary_files_format_and_content: For each factor PAR-CLIP crosslinked sites (p-values < 0.005) are provided in tab delimited text files (CLsites_Rpb1normalized_occupancies.table). For each crosslinked site the following is specified: chromosome, position, observed number of T-to-C transitions (m), number of reads covering the position (r), p-value, strand, and Rpb1 normalized RNA-binding occupancies (occ). To obtain these normalized occupancies, (m) was divided by the number of Rpb1 PAR-CLIP reads (Baejen et al., 2017) at that position. Finally, we set the maximal occupancy to the 95% quantile of all occupancies.

growth_protocol: Cells expressing the TAP-tagged protein were grown at 30 °C and 160 rpm. PAR-CLIP experiments were carried out in CSM minimal medium (Formedium) supplemented with 10 mg/l uracil, 100 µM 4-thiouracil and 2 % glucose.

extract_protocol:
Cells were lysed by bead beating and the lysate was sonicated in a Covaris S220 system. Immunoprecipitation was performed at 4 °C with rabbit IgG-conjugated Protein G magnetic Dynabeads.
For 3′ adaptor ligation, beads were resuspended in 1× T4 RNA ligase buffer (NEB) containing 10 U/µL T4 RNA ligase 2 (KQ) (NEB, M0373), 3′ adaptor [5 μM] (5′ rApp-TGGAATTCTCGGGTGCCAAGG-3ddC 3′, IDT), 1 U/µL RNase OUT, and 15% (w/v) PEG 8000. The bead suspension was incubated for 18 hr at 16°C and 600 rpm. Beads were washed in PNK buffer to remove unligated adapters. For 5′ adaptor ligation, beads were resuspended in 1× T4 RNA ligase buffer (NEB) containing 2 U/µL T4 RNA ligase 1 (NEB), 10 μM 5′ adaptor (5′ 5InvddT-GUUCAGAGUUCUACAGUCCGACGAUCNNNNN-OH 3′, IDT), 1 mM ATP, 1 U/µL RNase OUT, 5% (v/v) DMSO, and 10% (w/v) PEG 8000. The suspension was incubated for 4 hr at 24 °C and 600 rpm. Beads were washed twice in PNK buffer, and twice in proteinase K buffer (50 mM Tris-HCl pH 7.5, 6.25 mM EDTA, 75 mM NaCl). Beads were boiled twice at 95 °C for 5 minutes in proteinase K buffer with 1% SDS and eluted RNA-protein complexes were treated with 1.5 mg/mL proteinase K (NEB) for 2 hr at 55 °C. RNA was recovered by acidic phenol/chloroform extraction followed by ethanol precipitation supported by addition of 0.5 µL GlycoBlue (Invitrogen) and 100 μM RT primer (5′ HO-CCTTGGCACCCGAGAATTCCA-OH 3′). Reverse transcription was performed for 1 hr at 44 °C using SuperScript III RTase. For PCR amplification, NEXTflex barcode primer and universal primer and phusion HF master mix (NEB) were added.

treatment_protocol: 900 µM 4-thiouracil were added and cells were grown further for 4 h before they were UV-irradiated with an energy dose of 12 J/cm2 at 365 nm.

tag: rip reagent


title: Syc1-KO-Replicate2-RNAseq

description:
L_Syc1_KO_Rep2
S.cerevisiae.mRNA.snRNA.snoRNA.anno_Steinmetz_2013_rawHTSeq-counts.txt
S.cerevisiae.mRNA.snRNA.snoRNA.anno_Steinmetz_2013_DESeq2_results_table.txt


title: Syc1-PAR-CLIP

description: crosslinked RNA

value: rabbit IgG-conjugated Protein G magnetic Dynabeads


title: Skin NL Week 12 Drug MSSM-26

description: Gene expression data from skin biopsy


title: Skin NL Week 4 Drug MSSM-26

description: Gene expression data from skin biopsy


title: control.4_transgenic.4

city: Urbana

first: Sang Yeol

last: Kim

state: IL

address: 1201 W Gregory st, ERML #197,Urbana, IL 61801

department: IGB

institute: University of Illinois Urbana-Champaign

description: array D

hyb_protocol: Samples were hybridized in an Agilent Hybridization Cassette according to standard protocols.

scan_protocol: Scanned on an Axon GenePix 4000B scanner; Images were quantified using Axon GenePix 6.1.

data_processing: Median foreground intensites (no background subtraction) were normalized in R (version 3.4.1) using the loess within-array method and the scale between-array method in limma (version 3.32.4) . Spots with -100 flags were weighted zero before normalization.

organism: Arabidopsis thaliana

source_name: two weeks old control plant leaves which were exposesd light for an hour

label_protocol: 200 ng of total RNA was labeled using the Agilent's Two-Color Low Input Quick Amp labeling kit according to the manufacturers protocol.

growth_protocol: Seeds were germinated on MS agar plates and grown in long day photoperiod growth chamber for 2 weeks. Seedlings were frozen at 1 hour after lights were on

extract_protocol: Total RNA was extracted using Qiagen kit

tag: ecotype

value: Columbia

tag: group

value: control

source_name: two weeks old transgenic plant leaves which were exposesd light for an hour

value: transgenic


title: Skin NL Week 0 Placebo MSSM-25

description: Gene expression data from skin biopsy


title: control.2_transgenic.2

description: array B


title: Skin LS Week 4 Placebo MSSM-25

description: Gene expression data from skin biopsy


title: transgenic.3_control.3

description: array C


title: Skin LS Week 0 Placebo MSSM-25

description: Gene expression data from skin biopsy


title: Skin LS Week 12 Placebo MSSM-24

description: Gene expression data from skin biopsy


title: Skin LS Week 12 Drug MSSM-26

description: Gene expression data from skin biopsy


title: Skin NL Week 12 Drug MSSM-03

description: Gene expression data from skin biopsy


title: Skin LS Week 0 Drug MSSM-26

description: Gene expression data from skin biopsy


title: Skin NL Week 0 Drug MSSM-23

description: Gene expression data from skin biopsy


title: Skin LS Week 0 Drug MSSM-23

description: Gene expression data from skin biopsy


title: Skin NL Week 0 Placebo MSSM-24

description: Gene expression data from skin biopsy


title: Skin LS Week 4 Placebo MSSM-22

description: Gene expression data from skin biopsy


title: Skin LS Week 0 Placebo MSSM-24

description: Gene expression data from skin biopsy


title: Skin LS Week 4 Drug MSSM-03

description: Gene expression data from skin biopsy


title: Skin NL Week 12 Placebo MSSM-24

description: Gene expression data from skin biopsy


title: Skin LS Week 4 Drug MSSM-26

description: Gene expression data from skin biopsy


title: Skin NL Week 4 Placebo MSSM-22

description: Gene expression data from skin biopsy


title: Skin NL Week 4 Placebo MSSM-25

description: Gene expression data from skin biopsy


title: Skin LS Week 12 Placebo MSSM-22

description: Gene expression data from skin biopsy


title: Skin LS Week 0 Placebo MSSM-22

description: Gene expression data from skin biopsy


title: Skin NL Week 4 Placebo MSSM-24

description: Gene expression data from skin biopsy


title: Skin NL Week 0 Placebo MSSM-22

description: Gene expression data from skin biopsy


title: MB-24h-AR_4

city: Halifax

first: Spencer

middle: Gordon

last: Jones

state: NS

address: 5850 College St

department: Biochemistry and Molecular Biology

country: Canada

institute: Dalhousie University

description: Mushroom body nuclei extracted from courtship conditioned males 24-hours after sexual rejection.

data_processing:
Raw sequence reads were trimmed using Prinseq (version 0.20.4) quality trimming to a minimum base quality score of 30
Trimmed reads were aligned to D. melangaster genome (dm6, Ensembl release 88) using STAR. Reads were also aligned to C. elegans unc-84 gene (NC_003284.9). Only uniquely aligned reads with a maximum of four mismatches were used downstream.
Gene counts were obtained using HTSeq-count (version 0.7.1) using union setting to generate genic regions.
Genome_build: dm6
Supplementary_files_format_and_content: tab-delimited text files include raw gene counts for genic regions obtained using HTSeq

molecule: nuclear RNA

organism: Drosophila melanogaster

source_name: MB-24h-AR, Mushroom body nuclei

extract_protocol:
Fly heads were obtained from samples of 50-60 flies through flash freezing with liquid nitrogen, followed by vortexing and separation through a series of a sieves. Fly heads were then suspended in homogenization buffer and nuclei released into solution through chemical and physical agitation of the cell membrane. A whole head fraction (WH) was then taken from this homogenate as a representation of the whole fly head, containing both MB-specific GFP nuclei untagged non-MB nuclei. Anti-GFP bound beads were then used to isolate GFP-positive nuclei from the whole head homogenate to represent the mushroom body-specific fraction (MB). RNA was then isolated from both WH and MB-fractions using a PicoPure RNA Isolation Kit (Invitrogen:KIT0204) according to the manufacturer instructions.
RNA libraries were generated using the Nugen Ovation Drosophila RNA-Seq System 1-16 (Nugen: NU035032) according to manufacturer instructions.

value: Mushroom body

tag: age

value: adult males four to six days old

value: X; unc84-GFP/+;R14H06Gal4/attP2

value: 24h, AR


title: transgenic.1_control.1

description: array A


title: Skin NL Week 12 Placebo MSSM-22

description: Gene expression data from skin biopsy

tag: tissue


title: Skin NL Week 12 Drug MSSM-21

description: Gene expression data from skin biopsy

tag: patient id

value: Drug


title: Skin NL Week 4 Drug MSSM-03

description: Gene expression data from skin biopsy

tag: lot

value: NL

value: Wk 4


title: Skin NL Week 12 Drug MSSM-20

description: Gene expression data from skin biopsy

tag: week

value: Wk 12


title: Skin LS Week 4 Drug MSSM-21

description: Gene expression data from skin biopsy

value: LS

tag: treatment


title: Skin LS Week 0 Drug MSSM-21

description: Gene expression data from skin biopsy

value: Wk 0


title: MB-24h-AR_2


title: Skin LS Week 12 Drug MSSM-20

description: Gene expression data from skin biopsy


title: Skin LS Week 4 Placebo MSSM-24

description: Gene expression data from skin biopsy

value: Placebo


title: Skin LS Week 4 Drug MSSM-20

description: Gene expression data from skin biopsy


title: MB-24h-AR_3


title: Skin LS Week 12 Drug MSSM-21

description: Gene expression data from skin biopsy


title: MB-1h-AR_3

description: Mushroom body nuclei extracted from courtship conditioned males 1-hour after sexual rejection.

source_name: MB-1h-AR, Mushroom body nuclei

value: 1h, AR


title: MB-1h-AR_4


title: MB-1h-AR_2


title: Patient_14T17450_EBV+

city: TOULOUSE

first: Pauline

last: Gravelle

address: 1 Avenue Irène Joliot Curie

department: Anatomy-Pathology

country: France

institute: IUCT-ONCOPOLE

description:
Gene expression data from patient n°14T17450, frozen PL biopsy
9 - 14T17450 EBV+

hyb_protocol: Labeled complementary RNA (cRNA) from these samples was then fragmented and hybridized to Affymetrix GeneChip® Human Gene 2.0 ST microarrays.

scan_protocol: The chips were then washed, scanned on the Affymetrix Fluidics Station 400, and controlled for quality, before analysis.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings, and then RMA normalized on Expression Console version 1.4.1 (Affymetrix).

source_name: Patient n°14T17450, frozen PL biopsy

label_protocol: RNAs were amplified, prepared and labelled from 500 pg total RNA, with the Ovation Pico WTA system (NUGEN, San Carlos, CA, USA).

growth_protocol: No culture was performed, frozen tissues were used for RNA extraction.

extract_protocol: Extraction of total RNA from frozen samples was performed according to the manufacturer's instructions. RNA quality was controlled on a Bioanalyzer (Agilent).

treatment_protocol: No treatment

value: PL biopsy (sternum)

tag: ebv status

value: EBV+


title: MB-1h-AR_1


title: Skin NL Week 12 Drug MSSM-19

description: Gene expression data from skin biopsy


title: Patient_14P11667_EBV+

description:
Gene expression data from patient n°14P11667, frozen PL biopsy
6 - 14P11667 EBV+

source_name: Patient n°14P11667, frozen PL biopsy

value: PL biopsy (nose)


title: Skin NL Week 0 Drug MSSM-21

description: Gene expression data from skin biopsy


title: MB-Naïve_4

description: Mushroom body nuclei extracted from socially isolated males, collected at the same time of day as 1h-AR and 24h-AR samples.

source_name: MB-Naïve, Mushroom body nuclei

value: Naïve


title: MB-Naïve_2


title: MB-Naïve_3


title: Skin LS Week 0 Drug MSSM-20

description: Gene expression data from skin biopsy

source_name: Skin biopsy


title: Skin NL Week 0 Drug MSSM-04

description: Gene expression data from skin biopsy


title: Skin NL Week 0 Drug MSSM-20

description: Gene expression data from skin biopsy


title: Skin LS Week 12 Drug MSSM-19

description: Gene expression data from skin biopsy


title: Skin NL Week 4 Drug MSSM-20

description: Gene expression data from skin biopsy


title: MB-Naïve_1


title: Patient_14P11148_EBV-

description:
Gene expression data from patient n°14P11148, frozen PL biopsy
7 - 14P11148 EBV-

source_name: Patient n°14P11148, frozen PL biopsy

value: PL biopsy (sphenoid bone)

value: EBV-


title: Patient_P11.417_reactionnel

description:
Gene expression data from patient n°P11.417, frozen lymph node
10 - Temoin P11.417

source_name: Patient n°P11.417, frozen lymph node

value: Reactive cervical lymph node


title: Patient_14P11149_EBV+

description:
Gene expression data from patient n°14P11149, frozen PL biopsy
3 - 14P11149 EBV+

source_name: Patient n°14P11149, frozen PL biopsy

value: PL biopsy (trachea)


title: Patient_12P12002_EBV+

description:
Gene expression data from patient n°12P12002, frozen PL biopsy
4 - 12P12002 EBV+

source_name: Patient n°12P12002, frozen PL biopsy

value: PL biopsy (kidney)


title: Patient_P14.290_EBV-

description:
Gene expression data from patient n°P14.290, frozen PL biopsy
5 - P14.290 EBV-

source_name: Patient n°P14.290, frozen PL biopsy

value: PL biopsy (sub mandibulary gland)


title: WH-24h-AR_4

description: Whole fly head nuclei extracted from courtship conditioned males 24-hours after sexual rejection.

source_name: WH-24h-AR, Whole fly head nuclei

value: Whole fly head

value: adult males four to six days old

value: X; unc84-GFP/+;R14H06Gal4/attP2

value: 24h, AR


title: WH-24h-AR_2


title: Skin NL Week 0 Drug MSSM-01

description: Gene expression data from skin biopsy

value: NL

value: Wk 0

value: Drug


title: Skin LS Week 4 Drug MSSM-19

description: Gene expression data from skin biopsy

value: LS

value: Wk 4


title: ade6-3057_mbs1+

source_name: DSBs (IP Rec12 covalently linked to DNA)

tag: ade6 allele

tag: mbs1 allele

value: mbs1+ (WT)

source_name: Whole-cell input from meiotic culture


title: WH-24h-AR_1


title: WH-1h-AR_3

description: Whole fly head nuclei extracted from courtship conditioned males 1-hour after sexual rejection.

source_name: WH-1h-AR, Whole fly head nuclei

value: 1h, AR


title: WH-1h-AR_1


title: WH-Naïve_5

description: Whole fly head nuclei extracted from socially isolated males, collected at the same time of day as 1h-AR and 24h-AR samples.

source_name: WH-Naïve, Whole fly head nuclei

value: Naïve


title: WH-1h-AR_2


title: WH-Naïve_4


title: WH-Naïve_3


title: WH-24h-AR_3


title: WH-Naïve_2


title: Patient_10P6274_EBV-

description:
Gene expression data from patient n°10P6274, frozen PL biopsy
1 - 10P6274 EBV-

source_name: Patient n°10P6274, frozen PL biopsy

value: PL biopsy (rhinopharynx)

value: EBV-


title: WH-Naïve_1


title: Patient_14P5581_EBV+

description:
Gene expression data from patient n°14P5581, frozen PL biopsy
2 - 14P5581 EBV+

source_name: Patient n°14P5581, frozen PL biopsy

value: PL biopsy (cervical lymph node)

value: EBV+


title: Rec27-GFP_rec8D_de-crosslinked

data_processing:
Base calling: Illumina Real Time Analysis software, v1.12.4 or v1.17.21.3
De-multiplexing: Illumina CASAVA software, v1.8.0 or 1.8.2
Read alignment: Burrows-Wheeler Aligner, v 0.7.9a
Terminal base (bp 50) removed from each read; only first 49 used for alignment.  One mismatch was permitted in the 49 bp.  Each paired-end read was mapped separately and only analyzed further if both ends successfully mapped to single chromosomal position.
Uniquely mapping paired-reads were compiled and analyzed in R
Genome_build: Sanger Center S. pombe genome, August 2010 version
Supplementary_files_format_and_content: Unique ligation list

source_name: Meiotic culture

growth_protocol: S. pombe cells were grown in minimal media without nitrogen for ~18 hours to synchronize the cells. Nitrogen was added and the temperature shifted to 34°C, marking the start of meiosis, and cells harvested at 3.5hr.

extract_protocol:
Formaldehyde was added to a final concentration of 1% in 500 mL of culture. Chromatin was prepared and sonicated as in Fowler et al. 2013 Mol. Cell 49:983-996.  DNA was sheared to ~1000 bp and the epitope tagged protein of interest was immunoprecipitated.  For conformation capture samples ("interacting"), the immunoprecipitate was ligated while immobilized on magnetic beads and subsequently eluted.  Crosslinks were removed with high temperature incubation and protein digested using proteinase K.  For "de-crosslinked" samples, immunoprecipitated chromatin was eluted, crosslinks removed, and protein digested prior to DNA ligation.  In both cases, the ligated DNA was finally ethanol precipitated and amplified using one of two different kits (Sequenase Version 2.0 DNA Sequencing Kit, Affymetrix; or REPLI-g Single Cell Kit, Qiagen).
DNA from all samples was amplified using either a Sequenase Version 2.0 DNA Sequencing Kit (for anti-GFP) or a Qiagen REPLI-g Single Cell Kit (for anti-FLAG).  DNA was quantified using a Bioanalyzer (Invitrogen).  Sequencing libraries were each prepared from 1 µg of DNA.  DNA was initially fragmented with a Covaris LE220 Focused-ultrasonicator (Covaris, Woburn, MA) using factory settings for an average size of 300 bp.  Library DNA was prepared using the KAPA DNA Library Preparation and HiFi PCR Kits (Kapa Biosystems, Wilmington, MA) on a PerkinElmer Sciclone NGSx Workstation (PerkinElmer, Waltham, MA) for Rec25-FLAG and Rec27-FLAG IPs, or the Epicentre Nextera DNA Sample Prep kit (Illumina, Inc., San Diego, CA) manually for Rec27-GFP IPs.

tag: epitope tag

tag: relevant genotype

value: pat1-114 rec8D

tag: material ligated

value: Purified IP (de-crosslinked) DNA


title: Mouse HSC, EP, biological rep4

description: Gene expression data from mouse HSCs after 16-hours in vitro treatment with Eltrombopag

hyb_protocol: Following fragmentation, labeled cRNA of each individual sample was hybridized to Affymetrix Mouse Clariom S microarrays (Affymetrix), and stained according to the manufacturer's instructions.

source_name: Mouse HSCs after 16-hours in vitro treatment with Eltrombopag

label_protocol: Around 10ng of extracted RNA was amplified and labeled using the GeneChip™ 3' IVT Pico Kit (Affymetrix, Santa Clara, CA), according to the manufacturer's instructions

growth_protocol: Mouse HSCs (Lineage−c-Kit+Sca-1+CD150+CD48−) were sorted, and cultured in Myelocult M5300 medium (Stem Cell Technologies) supplemented with 100 ng/ml rmSCF(Gemini Bio-Products, CA) and 200 µg/ml Primocin (InvivoGen, San Diego, CA).

treatment_protocol: Mouse HSCs were treated with either Eltrombopag (10 µg/ml, Novartis), or vehicle control (sterile H2O) in the liquid culture for 16 hours. Thereafter, cells were collected and lysed with RLT plus buffer (Qiagen, Valencia, CA). Cell lysates were stored in -80 °C until use.

value: FACS-sorted HSC

value: 6-10 weeks


title: Mouse HSC, EP, biological rep2


title: Mouse HSC, EP, biological rep3


title: Mouse HSC, EP, biological rep1


title: Mouse HSC, NT, biological rep4

description: Gene expression data from mouse HSCs after 16-hours in vitro treatment with vehicle

source_name: Mouse HSCs after 16-hours in vitro treatment with vehicle


title: Rec27-GFP_de-crosslinked

value: pat1-114 rec12D


title: Skin LS Week 0 Drug MSSM-03

description: Gene expression data from skin biopsy


title: Patient_14T8922_EBV+

description:
Gene expression data from patient n°14T8922, frozen PL biopsy
8 - 14T8922 EBV+

source_name: Patient n°14T8922, frozen PL biopsy

value: PL biopsy (testis)


title: Mouse HSC, NT, biological rep3


title: Mouse HSC, NT, biological rep1


title: Mouse HSC, NT, biological rep2


title: Rec27-GFP_rec8D_interacting

value: Crosslinked DNA complexes


title: Rec27-GFP_interacting


title: PAO1 versus PA3898 mutant rep3

status: Public on Sep 16 2018

city: Honolulu

first: Tung

last: Hoang

state: HI

address: 1800 East-West Road

department: Microbiology

institute: University of Hawaii at Manoa

description: Replicate 3 of 3

hyb_protocol: cDNA from PAO1 and PA3898 mutant strains were mixed and hybridized to microarray slides for 20 h at 42oC.

scan_protocol: Scanned on a GenePix 4000 microarray scanner.

data_processing: Individual TIFF images from each channel were processed with Spotfinder software 3.2.1 to generate mev data. Microarray data were then normalized by low intensity filtering, LOWESS normalization, standard deviation regularization, and in-slide replicate analysis using MIDAS software 2.21.  Finally, the mev files from MIDAS were used to generate the data table in MEV software 4.5.1. The fold-change data for all detected genes were then obtained by combining the triplicate samples.

organism: Pseudomonas aeruginosa

label_protocol: Extracted RNA was verified on an agarose gel and 10 ug used in subsequent reverse transcription reactions, cDNA was purified and labeled with amino-allyl-dUTP. PAO1 cDNA was labeled with Cy3 and PA3898 with Cy5.

growth_protocol: P. aeruginosa wildtype strain PAO1 and PA3898 mutant strain were grown overnight in LB medium. Bacteria were harvested from overnight cultures, washed twice with LB, and and diluted 200 times in fresh LB medium. Subcultured PAO1 and PA3898 muatnt strains were grown at 30°C for 48 h without shaking.

extract_protocol: Total RNA was extracted using Qiagen RNeasy columns, including the additional on-column DNaseI digestion.

tag: sample type

value: Static biofilm

source_name: PA3898 mutant


title: MB-24h-AR_1

description: Mushroom body nuclei extracted from courtship conditioned males 24-hours after sexual rejection.

source_name: MB-24h-AR, Mushroom body nuclei

value: Mushroom body

value: adult males four to six days old

tag: genotype

value: X; unc84-GFP/+;R14H06Gal4/attP2

value: 24h, AR


title: PAO1 versus PA3898 mutant rep2

description: Replicate 2 of 3


title: Knockout Day 6 Replicate  2

first: Marion

middle: Dejosez

last: Zwaka

address: 1425 Madison Ave

department: Black Family Stem Cell Institute

description: Gene expression data of cells treated with tamoxifen for 6 days to incude Ronin knockout.

hyb_protocol: Affymetrix Hybridization

scan_protocol: GeneChip Scanner 3000

data_processing: Data were processed (RMA) and normalized (quantile normalization) with the GenePattern online tool (https://genepattern. broadinstitute.org) and visualized with the Multiplot Studio software (GenePattern, Broad Institute of MIT and Harvard).

source_name: embryonic stem cell line

label_protocol: Affymetrix Labeling

growth_protocol: Roninflox/flox (control) or Ert2CRE; Roninflox/flox mouse ES cells were plated at a density of 100,000 cell per 10 cm2 and cultured in standard mouse ES cell medium.

extract_protocol: RNA was isolated with RNeasy Mini columns (Qiagen) following the manufacturer's recommendations.

treatment_protocol: Cells were treated with 0.25 µM tamoxifen for 1.5, 3 or 6 days. Cells were split on day 4 and plated at a density of 100,000 cell/ 10 cm2.

tag: cell type

value: embyronic stem cells

value: CreERT2; Roninflox/flox


title: PAO1 versus PA3898 mutant rep1

description: Replicate 1 of 3


title: Control Day 3 Replicate  1

description: Gene expression data of control cells treated with tamoxifen for 3 days to account for tamoxifen induced expression changes.

value: Roninflox/flox


title: CJ11168_serine_8hr_0mM

city: Tsukuba

first: ayako

last: watanabe

state: Ibaraki

address: 3-1-5 Kannondai

department: National Institute of Animal Health

country: Japan

institute: National Agriculture and Food Research Organization

description: Gene expression after 8hr in 0mM-serine Campylobacter jejuni

hyb_protocol: 0.6 ug of Cy3-labelled cRNA (specific activity >15 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent GE hybridization buffer HI-RPM was added to the fragmentation mixture and hybridized to SurePrint G3 Human Gene Expression v3 8x60K Microarray (Agilent, G4851C) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for one color scan setting for 4x44K array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 12.0.3.1 (Agilent) using default parameters (protocol GE1_1200_Jun14 and Grid 072363_D_F_20150612) to obtain background subtracted and spatially detrended Processed Signal intensities. The 75th percentile shift normalization and baseline transformation (baseline to median of all samples) were performed using Agilent GeneSpring GX.

organism: Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819

source_name: Bacterial cells, serine_0mM

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100 ng Total RNA using Low Input Quick Amp WT Labeling Kit (Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: C. jejuni NCTC 11168 was routinely grown in Muller-Hinton (MH) broth (Becton Dickinson and Company, USA) or on MH agar at 42°C in a microaerophilic incubator (10% O2, 5% CO2, 85% N2).

extract_protocol: Total RNA was extracted using the RNeasy mini kit (QIAGEN) with the on-column DNase digestion according to the manufacturer's recommendations.

treatment_protocol: C. jejuni cells grown in MEM with or without 20 mM serine (Wako Pure Chemical Industries, Ltd., Japan) at 42°C under microaerophilic condition for 8 h (exponential phase).

value: serine-untreated

tag: growth media

value: MEM


title: pTet-pLac-BC-linked

status: Public on Sep 15 2018

city: Paris

first: Harry

middle: E.

last: Kemble

address: UMR 1137 – UFR de Médecine Paris 7 Denis Diderot,  16 rue Henri Huchard

institute: IAME, INSERM

description:
processed data file: BC-promoter_dictionary
Amplicons amplified from initial mutant library after bringing mutagenised promoters physically adjacent to barcode region, used to uncover which barcodes were attached to which promoter genotypes

data_processing:
All base-calling and demultiplexing was performed by standard Illumina software
pTet-pLac-BC-linked reads were quality-filtered by size (>199 bases), number of uncalled bases (<3 Ns) and length of the longest homopolymer stretch (<9 bases), using Mothur (version 1.37.6) with default settings
Entire PLtetO-1 promoter sequences were then extracted from Read 1, and plasmid barcode sequences and entire PLlacO-1 promoter from Read 2, by Needleman alignment to reference sequences (default alignment parameters), using Mothur (version 1.37.6). Reads for which either the PLtetO-1, PLlacO-1 or barcode region contained insertions or did not generate a full alignment with the reference were discarded.
The Mothur (version 1.37.6) Precluster algorithm was then used to cluster barcode sequences differing by a Hamming distance of 1, with the aim of correcting for PCR and sequencing errors
Aligned, clustered sequences were then de-gapped and re-grouped using Mothur (version 1.37.6)
For each barcode cluster, the associated complete PLtetO-1-PLlacO-1 concatenate sequences were grouped and their abundaces analysed, using a custom Python script (version 3.5)
For all other samples (those from competition experiments), forward and reverse reads were joined into contigs using Mothur’s (version 1.37.6) make.contigs command with the default parameters.
Contigs were then quality-filtered by size (<131bp), number of uncalled bases (no Ns) and length of longest homopolymer stretch (<9 bases), using Mothur (version 1.37.6) with default settings
To remove the majority of PCR duplicates arising from the 2nd PCR (made possible by randomised hexamers introduced during the 1st PCR), if a particular full contig was present more than once, only one copy was kept
Precise barcode sequences were then extracted after aligning contigs to the reference sequence (Needleman global alignment, default settings in Mothur version 1.37.6). Reads containing insertions or not generating a full alignment with the reference were discarded
The Mothur (version 1.37.6) Precluster algorithm was then used to cluster barcode sequences differing by a Hamming distance of 1, with the aim of correcting for PCR and sequencing errors
Aligned, clustered sequences were then de-gapped and re-grouped using Mothur (version 1.37.6)
For each competition experiment, barcode abundances were tabulated across time-points, using  Mothur (version 1.37.6)
Genome_build: For pTet-pLac-BC-linked, CGTGTCCTTATAGAGTCGCAGAGCTCGTGCTCAGTATCTCTATCACTGATAGGGATGTCAATCTCTATCACTGATAGGGAGGCGC for read1 and GTCCGGCGTAGAGGATCTGAAGATNNNNNATNNNNNATNNNNNATNNNNNAAGTCGAGGTGCTCAGTATCTTGTTATCCGATCACAATGTCAATTGTTATCCGCTCACAATTATAGGAAC for read 2
Genome_build: For all other samples (those from competition experiments), GTGAACGCTCTCACTAGTGGCGCGCCGTCGACTTNNNNNATNNNNNATNNNNNATNNNNNATCTTCAGATCCTCTACGCCGGACGCATCGTGGCCGGATCTTG
Supplementary_files_format_and_content: BC-promoter_dictionary: Table showing plasmid barcode sequences, the concatenated double-promoter genotype most frequently associated with each barcode, the number of reads containing each barcode and the fraction of those reads containing the second-most frequently associated double-promoter genotype for each barcode
Supplementary_files_format_and_content: All other processed data files (names ending in "barcode_counts") are tables showing the read abundance of barcodes across time points, in the different experimental environments

molecule: other

organism: Escherichia coli

source_name: Engineered bacterial plasmid

extract_protocol:
Plasmid DNA was purified from bacteria using QIAprep Spin Miniprep Kit (Qiagen)
A standard Illumina two-step PCR protocol was used to amplify the regions of interest and add Illumina adaptors/indexes and randomised hexamers (to increase amplicon diversity).

value: Engineered bacterial plasmid

tag: amplicon structure

value: PLtetO-1-araA - PLlacO-1-araB - PlasmidBarcode

tag: experimental environment

value: Uncompeted library

tag: time-point


title: Knockout Day 6 Replicate  1


title: Knockout Day 1.5 Replicate  2

description: Gene expression data of cells treated with tamoxifen for 1.5 days to incude Ronin knockout.


title: Control Day 6 Replicate  2

description: Gene expression data of control cells treated with tamoxifen for 6 days to account for tamoxifen induced expression changes.


title: Knockout Day 3 Replicate  2

description: Gene expression data of cells treated with tamoxifen for 3 days to incude Ronin knockout.


title: Control Day 3 Replicate  2


title: Control Day 1.5 Replicate  2

description: Gene expression data of control cells treated with tamoxifen for 1.5 days to account for tamoxifen induced expression changes.


title: Knockout Day 3 Replicate  1


title: CJ11168_serine_8hr_20mM

description: Gene expression after 8hr in 20mM-serine Campylobacter jejuni

source_name: Bacterial cells, serine_20mM

value: serine-treated

value: MEM+20mM serine


title: Control Day 6 Replicate  1


title: Control Day 1.5 Replicate 1


title: Knockout Day 1.5 Replicate  1


title: Female offspring-21days-Control dam-PBMCs_replicate 05

city: Wageningen

first: Evert

middle: M.

last: van Schothorst

address: De Elst 1

country: Netherlands

institute: Wageningen University

description: Cy3 samples were pooled on a equimolar basis and served as reference pool, and individual Cy5-labelled samples were hybridized against the reference pool.

hyb_protocol: Individual Cy5-labelled samples were hybridized against the Cy3-labelled reference pool according to the manufacturers' procedure using 2x Hybridization buffer (Agilent). Samples were applied to 4x44K microarrays enclosed in Agilent SureHyb hybridization chambers and hybridized at 65C for 17 hours at 10rpm rotation. After hybridization, slides were washed sequential with GE Wash buffer 2 for 1 minute at 37C, followed by acetonitrile for 1 minute at room temperature, and finally with a stabilization and drying solution for 30 seconds at room temperature according to Agilents' recommendations.

scan_protocol: Scanned with an Agilent Scanarray scanner (G2505C US22502548) with 10 and 100% laser-power intensities.

data_processing: Images were quantified using Agilent Feature Extraction Software (10.5.1.1) to obtain raw median signal and background values for both Cy5 and Cy3. QC checks were done on raw data and all but one array passed. Spots with a mean signal higher than twice the background value over all arrays and both channels were considered to be expressed. Data was normalized according to Pellis et al. (Physiol Genomics 2003; 16:99-106) based on the Cy3-reference pool, including locally weighted linear regression (lowess) analysis before values  were log2 transformed.

organism: Rattus norvegicus

source_name: PBMCs

label_protocol: 40 ng of purified individual total RNA was used for cDNA synthesis, splitted in two equal fractions and used for subsequent cRNA labeling and synthesis using Cy5 and Cy3 dyes and the Agilent low RNA input fluorescent lineair amplification protocol, as described previously by van Schothorst et al. (Anal Biochem 2007;363:315-7). All Cy3-labeled samples  were used for the reference pool.

extract_protocol: Total RNA was isolated using EZNA TOTAL RNA kit (Omega Bio-Tek, Norcross, GA, USA) from PBMCs obtained from offspring at age 21 days, quantified using Nanodrop (Nanodrop technologieds, Ins., Wilmington, DE, USA) and qualified using Bioanalyzer 2100 (Agilent). All samples had a RIN-number above 8.0.

treatment_protocol: The study was conducted on male and female Wistar rats from 16 different litters. All animals were housed under standard conditions of controlled temperature (22 _C), the normal 12 h light and 12 h dark cycle, free access to tap water and a standard chow diet (3 kcal/g, with 8 % calories from fat; Panlab, Barcelona, Spain), unless specified otherwise. Briefly, 16 virgin female Wistar rats (body weight 225–260 g) were mated with male rats (Charles River Laboratories, Barcelona, Spain). After mating, each female was placed in an individual cage. On day 1 after delivery, excess pups in each litter were removed aiming for 10 pups per dam (five males and five females, when possible). Dams were assigned to either the control (n = 11 dams) or calorie-restricted (n = 5 dams) group. Control dams were fed ad libitum with standard chow diet, while calorie-restricted dams were fed daily with a 20 % calorie-restricted diet throughout lactation, starting on day 1 after delivery until weaning (day 21) as previously described (Palou et al. 2012). During the lactating period, body weight of male and female offspring of control and calorie-restricted dams (control and CR, respectively) was followed. At weaning at age 21 days, a set of animals made up of 24 pups from control (12 males and 12 females) and 24 from CR (12 males and 12 females) group were killed by decapitation under ad libitum feeding conditions. One half of pups (n = 6/group) were used to obtain trunk blood samples for peripheral blood mononuclear cells (PBMCs) isolation. Another set of animals, 28 control pups (12 males and 16 females) and 26 CR pups (14 males and 12 females), were kept alive. They were placed two per cage, paired with another animal of the same group and fed ad libitum with a normal-fat (NF) diet (3.8 kcal/g, 10 % calories from fat, Research Diets, Inc., NJ, USA) until the age of 6 months. Body weight and food intake of those animals were followed. Moreover, at the age of 6 months (prior to sacrifice), blood samples were collected at fed state and after 12 h fasting to obtain plasma. All the animals were decapitated under ad libitum feeding conditions at the age of 6 months, and samples of trunk blood for PBMCs isolation were collected. Body length (from the tip of the nose to the anus) and body composition (by EchoMRI-700TM, Echo Medical Systems, LLC, TX, USA) were measured in control and CR animals without anesthesia when animals were 21 days and 6 months old. PBMCs were collected using heparin in NaCl (0.9%) as anticoagulant and then diluted with equal volume of balanced salt solution, and separated using Ficoll density gradient.

tag: test

value: Wistar Female offspring-21days-Control dam-PBMCs

tag: reference

value: pooled on a equimolar basis


title: Male offspring-21days-CR dam-PBMCs_replicate 04

value: Wistar Male offspring-21days-CR dam-PBMCs


title: Female offspring-21days-Control dam-PBMCs_replicate 06


title: Male offspring-21days-Control dam-PBMCs_replicate 05

value: Wistar Male offspring-21days-Control dam-PBMCs


title: Male offspring-21days-Control dam-PBMCs_replicate 06


title: Female offspring-21days-Control dam-PBMCs_replicate 03


title: Female offspring-21days-Control dam-PBMCs_replicate 04


title: Female offspring-21days-CR dam-PBMCs_replicate 05

value: Wistar Female offspring-21days-CR dam-PBMCs


title: Male offspring-21days-CR dam-PBMCs_replicate 03


title: Male offspring-21days-Control dam-PBMCs_replicate 04


title: Female offspring-21days-CR dam-PBMCs_replicate 06


title: Male offspring-21days-CR dam-PBMCs_replicate 05


title: Female offspring-21days-CR dam-PBMCs_replicate 03


title: Female offspring-21days-CR dam-PBMCs_replicate 04


title: Male offspring-21days-CR dam-PBMCs_replicate 02


title: Female offspring-21days-CR dam-PBMCs_replicate 01


title: Male offspring-21days-Control dam-PBMCs_replicate 02


title: Female offspring-21days-Control dam-PBMCs_replicate 01


title: Male offspring-21days-Control dam-PBMCs_replicate 01


title: Male offspring-21days-CR dam-PBMCs_replicate 01


title: Female offspring-21days-Control dam-PBMCs_replicate 02


title: Female offspring-21days-CR dam-PBMCs_replicate 02


title: Male offspring-21days-Control dam-PBMCs_replicate 03


title: HOS-1: HOS cell cultured in Matrigel, biological rep1

city: Nanjing

last: Yao

address: Shizi Street, Hongshan Road

country: China

institute: Affiliated Hospital of Integrated Traditional Chinese and Western Medicine, Nanjing University of Chinese Medicine

description: Gene expression data from HOS cells cultured in Matrigel after 24 hours

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hour at 45℃ on GeneChip Human Transcriptome Array 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G3000 7G.

data_processing: The data were analyzed with RMA using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: HOS cell cultured in Matrigel after 24 hours

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

growth_protocol: Human osteosarcoma cells 143B and HOS (ATCC) were cultivated according to the recommendation of the supplier (Gibco Life Technologies) in a humidified incubator at 37°C with 5% CO2, and culture medium exchange was performed every 24 hours.

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

treatment_protocol: A 6-well plate was evenly coated with 1 mL/well cold Matrigel (BD Biosciences) and allowed to solidify at 37°C for 30 min. Then cell suspension was added onto the surface of the plate, incubated at 37°C for 24 hours and placed on ice in the Trizol solution (Invitrogen)

tag: cell line

value: HOS

tag: tissue

value: osteosarcama cell line

tag: tumor phenotype

value: non-vasculogenic mimicry


title: 143B-2: 143B cell cultured in Matrigel, biological rep2

description: Gene expression data from 143B cells cultured in Matrigel after 24 hours

source_name: 143B cell cultured in Matrigel after 24 hours

value: vasculogenic mimicry


title: African American primary proximal tubule cells (K10224_post)

city: Winston Salem

first: Lijun

last: Ma

state: NC

address: 1 Medical Center Blvd

department: Nephrology

institute: Wake Forest School of Medicine

hyb_protocol: Following fragmentation and labeling, 5.2 µg ss-cDNA was hybridized for 16 hr at 45 °C in hybridization oven, rotating at 60 rpm on GeneChip® Human Transcriptome Array 2.0. Cartridges were washed and stained using the GeneChip Fluidics Station according to standard Affymetrix operating procedures (Affymetrix®GeneChip® Fluidics Station 450 User's Guide AGCC (P/N 08-0295), the GeneChip® Expression Wash, Stain, and Scan User Manual for Cartridge Arrays (PN 702731)

scan_protocol: Cartridges were scanned using the GeneChip® Scanner 3000 7G according to the standard Affymetrix protocol (GeneChip® Expression Wash,Stain, and Scan User Manual for Cartridge Arrays (PN 702731) and the Affymetrix® GeneChip® Command Console® User Manual (P/N 702569)).

data_processing: Raw data were generated using TAC software and normalized by the RMA method. Log intensity distributions, pair-wise correlations and internal Affymerix controls were examined to evaluate hybridization quality.

source_name: APOL1 Genotype_G2G0 post-polyIC Stimulation

label_protocol: Approximately 250 ng of purified total RNA was processed to produce amplified and biotinylated sense-strand DNA targets.

extract_protocol: Total RNA was isolated from primary proximal tubule cells using the QIAGEN Rneasy Mini Kit (QIAGEN Cat # 74104).

tag: ethnicity

value: African American

value: APOL1 Genotype G2G0

tag: time

value: post-polyIC Stimulation

value: primary proximal tubule cells


title: HOS-3: HOS cell cultured in Matrigel, biological rep3


title: HOS-2: HOS cell cultured in Matrigel, biological rep2


title: 143B-1: 143B cell cultured in Matrigel, biological rep1


title: acute Cort (1) 3 h rep2

city: Sendai

first: Ikuko

middle: N

last: Motoike

state: Miyagi

address: 2-1 Seiryo-cho Aoba-ku

department: Tohoku Medical Meagabank Organizataion

institute: Tohoku Univertisy

data_processing:
Data was processed using RTA 1.12.4.3 and CASAVA 1.8.2.
Sequenced reads were mapped to rn6 whole genome using tophat v2.1.1 with parameters -g 1
Fragments per kilobase of exon per million reads mapped (FPKM) were calculated using cufflinks v2.2.1.
Genome_build: rn6
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for each Sample

source_name: hypothalams (PVH region)

extract_protocol:
Immediately after decapitation, hypothalamic tissue containing the PVH was dissected out on ice, frozen on dry ice, and RNA was harvested using TrizolTM followed by purification with RNeasy mini kit TM reagents and column DNase digestion. Illumina TruSeq RNA Sample Prep Kits, version 2, was used with 1 microgram of total RNA for the construction of sequencing libraries.
mRNA libraries were constructed from 1,000 ng high-quality total RNA using the Illumina TruSeq RNA Sample Prep Kits, version 2. The resulting cDNA was fragmented using a Covaris E210 (Covaris, Inc., Woburn, MA). Library amplification was performed using 10 cycles to minimize the risk of over-amplification.

tag: strain

value: Wistar

value: hypothalams (PVH region)

tag: age

value: post natal weeks 12

value: wild type


title: African American primary proximal tubule cells (K10222_post)

source_name: APOL1 Genotype_G0G0 post-polyIC Stimulation

value: APOL1 Genotype G0G0


title: African American primary proximal tubule cells (K10223_post)


title: 143B-3: 143B cell cultured in Matrigel, biological rep3


title: African American primary proximal tubule cells (K10221_post)

source_name: APOL1 Genotype_G1G0 post-polyIC Stimulation

value: APOL1 Genotype G1G0


title: African American primary proximal tubule cells (K10218_post)


title: MSC-Day3-Induction

city: Taipei

first: Yu-Chuan

last: Liu

address: 128 Academia Road, Section 2, Nankang

department: Genomic Research Center

country: Taiwan

institute: Academia Sinica

description: primary MSCs cultured in osteogenic induction medium for 3 day

hyb_protocol: After aRNA fragmentation, 12.5 ug of fragmented aRNA were hybridized for 16 hr at 45C on GeneChip® Human Genome U133 Plus 2.0 Array. Affymetrix Fluidics Station 450 was used for gene chips washing and staining.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings followed by analysis with Gene Spring Software 12 to normalize data (RMA mode).

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 250ng total RNA (GeneChip® 3’ IVT Express Kit, Affymetrix).

growth_protocol: Human mesenchymal stem cells were used to differentiated into osteoblasts. Mesenchymal stem cells were not used over ten passage. The cells were cultured in MesenPro RS media (Invitrogen, Carlsbad, CA, USA) and the osteogenic induction medium consisted of Dulbecco's modified Eagle's medium/LG (Invitrogen, Carlsbad, CA, USA) with 10% FBS, 0.1 uM dexamethasome (Sigma, St. Louis, MO, USA), 0.05mM L-ascorbic acid phosphate (Sigma, St. Louis, MO, USA), 10mM beta-glycerophosphate (Sigma, St. Louis, MO, USA)

extract_protocol: RNeasy micro kit extraction of total RNA was performed according to the manufacturer's instructions. (Qiagen, Dusseldorf, Germany)

treatment_protocol: Mesenchymal stem cells were treated with ApoA-I (200ng/ml) for 1, 3, 5 days during osteogenesis and then compared the transcriptomic profiles of different time-point treatment with day 0 control.

value: human bone marrow MSCs


title: African American primary proximal tubule cells (K10217_post)


title: MSC-Day1 Induction-ApoA1

description: primary MSCs cultured in osteogenic induction medium and ApoA-I  for 1 day

scan_protocol: GeneChip® Human Genome U133 Plus 2.0 Array

source_name: MSC-Day1 Induction-ApoA1


title: African American primary proximal tubule cells (K10220_post)


title: MSC-Day3-Induction-ApoA1

description: primary MSCs cultured in osteogenic induction medium and ApoA-I  for 3 day


title: African American primary proximal tubule cells (K10219_post)


title: MSC-Day5-Induction

description: primary MSCs cultured in osteogenic induction medium for 5 day


title: MSC-Day0

description: primary MSCs without osteogenic induction


title: African American primary proximal tubule cells (K10210_post)


title: MSC-Day1-Induction

description: primary MSCs cultured in osteogenic induction medium for 1 day


title: African American primary proximal tubule cells (K10205_post)


title: acute Cort (1) 1 h rep2


title: MSC-Day5-Induction-ApoA-1

description: primary MSCs cultured in osteogenic induction medium and ApoA-I  for 5 day


title: African American primary proximal tubule cells (K10203_post)

source_name: APOL1 Genotype_G1G1 post-polyIC Stimulation

value: APOL1 Genotype G1G1


title: acute Cort (1) 1 h rep1


title: ADX + Cort suppl rep2


title: African American primary proximal tubule cells (K10199_post)


title: African American primary proximal tubule cells (K10214_post)


title: African American primary proximal tubule cells (K10202_post)

source_name: APOL1 Genotype_G1G2 post-polyIC Stimulation

value: APOL1 Genotype G1G2


title: 7-day ADX rep2


title: 12-day high Cort rep2


title: 12-day high Cort rep1


title: ADX + Cort suppl rep1


title: acute Cort (1) 3 h rep1


title: sham-ADX rep1


title: starved_naive_5

city: Kansas City

first: Chris

middle: W

last: Seidel

state: MO

department: Genomics

institute: Stowers Institute

description:
rpkm.txt
starved_naive_5

data_processing:
Basecalls performed using CASAVA version 1.8.2
Reads were aligned to Drosophila genome dm6 with tophat v2.0.13 using -g 1 and gene models in gtf format from Ensembl 84
Reads were quantified on reduced transcripts from genes in Ensembl 84 using the countOverlap function in the Bioconductor package GenomicFeatures.
RPKM values were determined using Bioconductor package edgeR version edgeR_3.18.1 using the count of mapped reads on the reduced exonic intervals for each gene.
Genome_build: dm6
Supplementary_files_format_and_content: rpkm.txt text file of expression values per sample in RPKM format.

growth_protocol: Flies were maintained at 25 °C, with a 12:12 light:dark period.

extract_protocol:
After indicated behavioral treatment, individuals heads were collected on a dry-ice block and RNA was isolated with the Maxwell® 16 LEV simplyRNA Tissue Kit (Promega).
Non-stranded RNA-Seq libraries were constructed using TRUSEQ RNA SAMPLE PREP KIT v2 from Illumina.

treatment_protocol: training as indicated

tag: training

value: naive

tag: hours post-training

tag: precondition

value: starved

tag: sugar

value: fly head

tag: replicate


title: sham-ADX rep2

tag: genotype


title: African American primary proximal tubule cells (K10189_post)

tag: cell type


title: starved_naive_3

description:
rpkm.txt
starved_naive_3


title: African American primary proximal tubule cells (K10182_post)


title: starved_naive_4

description:
rpkm.txt
starved_naive_4


title: starved_naive_1

description:
rpkm.txt
starved_naive_1


title: African American primary proximal tubule cells (K10176_post)


title: African American primary proximal tubule cells (K10165_post)


title: African American primary proximal tubule cells (K10174_post)


title: African American primary proximal tubule cells (K10159_post)


title: African American primary proximal tubule cells (K10188_post)


title: African American primary proximal tubule cells (K10156_post)


title: African American primary proximal tubule cells (K10169_post)


title: starved_trained_4hr_5

description:
rpkm.txt
starved_trained_4hr_5

value: trained

value: sucrose


title: starved_trained_4hr_4

description:
rpkm.txt
starved_trained_4hr_4


title: starved_trained_4hr_3

description:
rpkm.txt
starved_trained_4hr_3


title: starved_naive_2

description:
rpkm.txt
starved_naive_2


title: starved_trained_4hr_6

description:
rpkm.txt
starved_trained_4hr_6


title: naive_6

description:
rpkm.txt
naive_6

source_name: naïve


title: naive_5

description:
rpkm.txt
naive_5


title: African American primary proximal tubule cells (K10148_post)

value: African American


title: African American primary proximal tubule cells (K10141_post)

value: APOL1 Genotype G2G0

value: post-polyIC Stimulation


title: African American primary proximal tubule cells (K10133_post)

value: primary proximal tubule cells


title: African American primary proximal tubule cells (K10150_post)


title: starved_trained_4hr_1

description:
rpkm.txt
starved_trained_4hr_1


title: African American primary proximal tubule cells (K10113_post)


title: African American primary proximal tubule cells (K10110_post)


title: naive_1

description:
rpkm.txt
naive_1


title: naive_2

description:
rpkm.txt
naive_2


title: starved_trained_1hr_6

description:
rpkm.txt
starved_trained_1hr_6


title: African American primary proximal tubule cells (K10144_post)


title: African American primary proximal tubule cells (K10109_post)


title: African American primary proximal tubule cells (K10111_post)


title: African American primary proximal tubule cells (K10160_post)


title: African American primary proximal tubule cells (K10106_post)


title: African American primary proximal tubule cells (K10107_post)


title: African American primary proximal tubule cells (K10102_post)


title: African American primary proximal tubule cells (K10101_post)


title: starved_trained_1hr_4

description:
rpkm.txt
starved_trained_1hr_4


title: starved_trained_1hr_3

description:
rpkm.txt
starved_trained_1hr_3


title: starved_trained_1hr_2

description:
rpkm.txt
starved_trained_1hr_2


title: naive_3

description:
rpkm.txt
naive_3


title: starved_trained_1hr_5

description:
rpkm.txt
starved_trained_1hr_5


title: starved_trained_1hr_1

description:
rpkm.txt
starved_trained_1hr_1


title: trained_Sucrose_6

description:
rpkm.txt
Sucrose_6

value: Sucrose


title: African American primary proximal tubule cells (K10097_post)


title: African American primary proximal tubule cells (K10095_post)


title: trained_Sucrose_3

description:
rpkm.txt
Sucrose_3


title: African American primary proximal tubule cells (K10073_post)


title: African American primary proximal tubule cells (K10056_post)


title: trained_Sucrose_2

description:
rpkm.txt
Sucrose_2


title: trained_Sucrose_5

description:
rpkm.txt
Sucrose_5


title: African American primary proximal tubule cells (K10075_post)


title: African American primary proximal tubule cells (K10047_post)


title: trained_Sorbose_6

description:
rpkm.txt
Sorbose_6

value: Sorbose


title: trained_Sorbose_5

description:
rpkm.txt
Sorbose_5


title: trained_Sorbose_4

description:
rpkm.txt
Sorbose_4


title: trained_Sorbose_3

description:
rpkm.txt
Sorbose_3


title: trained_Sorbose_2

description:
rpkm.txt
Sorbose_2


title: trained_Sucrose_4

description:
rpkm.txt
Sucrose_4


title: African American primary proximal tubule cells (K10032_post)


title: African American primary proximal tubule cells (K10041_post)


title: African American primary proximal tubule cells (K10223_pre)

source_name: APOL1 Genotype_G2G0 pre-polyIC Stimulation

value: pre-polyIC Stimulation


title: African American primary proximal tubule cells (K10024_post)


title: African American primary proximal tubule cells (K10221_pre)

source_name: APOL1 Genotype_G1G0 pre-polyIC Stimulation


title: African American primary proximal tubule cells (K10015_post)

value: APOL1 Genotype G0G0


title: African American primary proximal tubule cells (K10023_post)


title: naive_Odor_6

description:
rpkm.txt
Odor_6


title: African American primary proximal tubule cells (K10224_pre)


title: African American primary proximal tubule cells (K10222_pre)

source_name: APOL1 Genotype_G0G0 pre-polyIC Stimulation


title: naive_Odor_3

description:
rpkm.txt
Odor_3


title: naive_Odor_4

description:
rpkm.txt
Odor_4


title: trained_Sorbose_1

description:
rpkm.txt
Sorbose_1


title: African American primary proximal tubule cells (K10018_post)


title: naive_Odor_5

description:
rpkm.txt
Odor_5


title: African American primary proximal tubule cells (K10054_post)

value: APOL1 Genotype G1G0


title: African American primary proximal tubule cells (K10220_pre)


title: African American primary proximal tubule cells (K10219_pre)


title: naive_Odor_2

description:
rpkm.txt
Odor_2


title: African American primary proximal tubule cells (K10218_pre)


title: naive_Odor_1

description:
rpkm.txt
Odor_1


title: 7-day ADX rep1

value: Wistar

value: hypothalams (PVH region)

value: post natal weeks 12

value: wild type


title: African American primary proximal tubule cells (K10210_pre)


title: African American primary proximal tubule cells (K10214_pre)


title: African American primary proximal tubule cells (K10217_pre)


title: African American primary proximal tubule cells (K10203_pre)

source_name: APOL1 Genotype_G1G1 pre-polyIC Stimulation

value: APOL1 Genotype G1G1


title: African American primary proximal tubule cells (K10202_pre)

source_name: APOL1 Genotype_G1G2 pre-polyIC Stimulation

value: APOL1 Genotype G1G2


title: African American primary proximal tubule cells (K10205_pre)


title: African American primary proximal tubule cells (K10188_pre)


title: African American primary proximal tubule cells (K10174_pre)


title: African American primary proximal tubule cells (K10111_pre)


title: African American primary proximal tubule cells (K10150_pre)


title: African American primary proximal tubule cells (K10160_pre)


title: African American primary proximal tubule cells (K10107_pre)


title: African American primary proximal tubule cells (K10165_pre)


title: African American primary proximal tubule cells (K10156_pre)


title: African American primary proximal tubule cells (K10159_pre)


title: African American primary proximal tubule cells (K10199_pre)


title: African American primary proximal tubule cells (K10148_pre)


title: African American primary proximal tubule cells (K10189_pre)


title: African American primary proximal tubule cells (K10169_pre)


title: African American primary proximal tubule cells (K10144_pre)


title: African American primary proximal tubule cells (K10133_pre)


title: African American primary proximal tubule cells (K10110_pre)


title: African American primary proximal tubule cells (K10106_pre)


title: African American primary proximal tubule cells (K10109_pre)


title: African American primary proximal tubule cells (K10095_pre)


title: African American primary proximal tubule cells (K10102_pre)


title: African American primary proximal tubule cells (K10141_pre)


title: African American primary proximal tubule cells (K10101_pre)


title: African American primary proximal tubule cells (K10176_pre)


title: African American primary proximal tubule cells (K10113_pre)


title: African American primary proximal tubule cells (K10097_pre)


title: African American primary proximal tubule cells (K10182_pre)


title: African American primary proximal tubule cells (K10075_pre)


title: African American primary proximal tubule cells (K10054_pre)


title: African American primary proximal tubule cells (K10073_pre)


title: trained_Sucrose_1

description:
rpkm.txt
Sucrose_1

value: trained

value: fly head


title: African American primary proximal tubule cells (K10018_pre)

value: African American


title: African American primary proximal tubule cells (K10056_pre)


title: African American primary proximal tubule cells (K10032_pre)


title: African American primary proximal tubule cells (K10023_pre)


title: African American primary proximal tubule cells (K10047_pre)


title: African American primary proximal tubule cells (K10015_pre)


title: African American primary proximal tubule cells (K10024_pre)

value: APOL1 Genotype G2G0


title: ANXEXP041_b1

city: Munich

first: Angelika

last: Erhardt

address: Kraepelinstraße 2-10

department: Translational Research in Psychiatry

institute: Max Planck Institute of Psychiatry

hyb_protocol: Illumina Human-HT-12 v4 BeadChips.

scan_protocol: Illumina Bead Array Reader, Illumina GenomeStudio v2011.1 Gene Expression module.

data_processing: Variance stabilization normalization.

source_name: blood plasma

label_protocol: Illumina TotalPrep RNA Amplification Kit.

extract_protocol: Whole blood, PAXgene Blood RNA Kit.

treatment_protocol: Exposure session within the framework of cognitive behavioral therapy.

tag: disease

value: panic disorder

value: blood plasma

tag: Sex

value: not determined

tag: medication

tag: timepoint

tag: individual


title: ANXEXP041_p24_1

tag: tissue


title: African American primary proximal tubule cells (K10041_pre)

tag: ethnicity

value: primary proximal tubule cells


title: ANXEXP041_pe1


title: ANXEXP021_pe1

value: female


title: ANXEXP021_p24_1


title: ANXEXP038_p24_1


title: ANXEXP039_b1


title: ANXEXP021_b1


title: ANXEXP038_b1


title: ANXEXP031_pe1

value: male


title: ANXEXP033_p24_1


title: ANXEXP033_b1


title: ANXEXP038_pe1


title: ANXEXP034_b1


title: ANXEXP039_p24_1


title: ANXEXP039_pe1


title: ANXEXP034_pe1


title: ANXEXP034_p24_1


title: ANXEXP031_b1


title: ANXEXP029_p24_1


title: ANXEXP027_p24_1


title: ANXEXP027_b1


title: ANXEXP029_b1


title: ANXEXP027_pe1


title: ANXEXP031_p24_1


title: ANXEXP014_b1


title: ANXEXP014_p24_1


title: ANXEXP014_pe1


title: ANXEXP033_pe1


title: ANXEXP029_pe1


title: trained_3X_5

description:
rpkm.txt
T_3X_5

data_processing:
base calls were performed by bcl2fastq2 version 2.18
Reads were aligned to Drosophila genome dm6 with tophat v2.0.13 using -g 1 and gene models in gtf format from Ensembl 84
Reads were quantified on reduced transcripts from genes in Ensembl 84 using the countOverlap function in the Bioconductor package GenomicFeatures.
RPKM values were determined using Bioconductor package edgeR version edgeR_3.18.1 using the count of mapped reads on the reduced exonic intervals for each gene.
Genome_build: dm6
Supplementary_files_format_and_content: rpkm.txt text file of expression values per sample in RPKM format.

extract_protocol:
After indicated behavioral treatment, individuals heads were collected on a dry-ice block and RNA was isolated with the Maxwell® 16 LEV simplyRNA Tissue Kit (Promega).
Non-stranded RNA-Seq Libraries were constructed using Clontech SMART-Seq  v4 Ultra Low Input RNA for Sequencing on a Mantis robot using 1/4 size reactions.

tag: training cycles


title: trained_3X_4

description:
rpkm.txt
T_3X_4


title: trained_3X_6

description:
rpkm.txt
T_3X_6


title: Rubcn+/- sample (scRNA-seq)

city: Memphis

first: Doug

last: Green

state: Tn

address: 262 Danny Thomas Pl

department: Immunology

institute: St. Jude Children's Research Hospital

data_processing:
The bam files have cell barcodes in the CB tags and molecular barcodes in the UB tags.
Cellranger 1.3.1 was used to align the reads, collapse UMIs, and generate count matrices
All data analysis was performed in R using custom code
Genome_build: mm10
Supplementary_files_format_and_content: Processed data contain counts of transcripts for each gene in each cell after removal of read duplicates using UMIs

source_name: tumor-infiltrating myeloid cells

growth_protocol: LLC1 were cultivated in DMEM (Gibco) supplemented with 10% fetal bovine serum, 200 mM L-glutamine and 100 units ml-1 penicillin-streptomycin for a week after thawning before injection

extract_protocol: Libraries were prepared with Chromium Single Cell 3’ Library and gel Bead Kit v2, 10X Genomics (cat. #120267) according to manufacturer's instructions

treatment_protocol: 10^5 LLC1 cells were injected subcutaneously and tumors were harvested 14 days post-implantation

value: Rubcn+/-

tag: strain

tag: cell line

value: LLC1 (ATCC CRL-1642) tumor cell line


title: trained_3X_3

description:
rpkm.txt
T_3X_3

tag: training


title: Rubcn-/- sample (scRNA-seq)

value: Rubcn-/-


title: Env3_t6

description:
processed data file: Env3_barcode_counts
Plasmid barcode amplicons amplified from samples taken during pooled competition assay

source_name: Engineered bacterial plasmid

value: Engineered bacterial plasmid

tag: amplicon structure

value: plasmid barcode

tag: experimental environment

value: Env3 (200 ng/ml aTc and no IPTG) competition experiment

tag: time-point


title: ANXEXP020_p24_1


title: ANXEXP024_p24_1


title: ANXEXP024_b1


title: trained_3X_2

description:
rpkm.txt
T_3X_2

tag: replicate


title: ANXEXP019_p24_1


title: ANXEXP024_pe1


title: ANXEXP020_pe1


title: ANXEXP019_pe1


title: ANXEXP013_b1


title: trained_3X_1

description:
rpkm.txt
T_3X_1


title: ANXEXP013_pe1


title: Env3_t4


title: Env3_t1


title: ANXEXP013_p24_1


title: ANXEXP026_p24_1


title: ANXEXP026_pe1


title: ANXEXP026_b1


title: Env3_t2


title: trained_1X_6

description:
rpkm.txt
T_1X_6


title: trained_1X_5

description:
rpkm.txt
T_1X_5


title: Env2_t6

description:
processed data file: Env2_barcode_counts
Plasmid barcode amplicons amplified from samples taken during pooled competition assay

value: Env2 (5 ng/ml aTc and no IPTG) competition experiment


title: trained_1X_4

description:
rpkm.txt
T_1X_4

value: trained


title: trained_1X_3

description:
rpkm.txt
T_1X_3

value: fly head


title: ANXEXP018_b1


title: ANXEXP020_b1


title: trained_1X_2

description:
rpkm.txt
T_1X_2


title: ANXEXP019_b1


title: Env2_t1


title: ANXEXP018_p24_1


title: ANXEXP012_pe1


title: ANXEXP018_pe1


title: Env2_t2


title: ANXEXP015_b1


title: ANXEXP015_pe1


title: ANXEXP015_p24_1


title: ANXEXP012_b1


title: ANXEXP010_b1


title: ANXEXP010_pe1


title: ANXEXP006_pe1


title: trained_1X_1

description:
rpkm.txt
T_1X_1


title: mock_3X_6

description:
rpkm.txt
N_3X_6

value: mock


title: Env1_t6

description:
processed data file: Env1_barcode_counts
Plasmid barcode amplicons amplified from samples taken during pooled competition assay

value: Env1 (20 ng/ml aTc and 30µM IPTG) competition experiment


title: Env2_t4


title: Env1_t4


title: mock_3X_5

description:
rpkm.txt
N_3X_5


title: Env1_t2


title: mock_3X_4

description:
rpkm.txt
N_3X_4


title: Env1_t1


title: mock_3X_3

description:
rpkm.txt
N_3X_3


title: mock_3X_1

description:
rpkm.txt
N_3X_1


title: Env1Prelim_t6

description:
processed data file: Env1Prelim_barcode_counts
Plasmid barcode amplicons amplified from samples taken during pooled competition assay

value: Env1 (20 ng/ml aTc and 30µM IPTG) , preliminary competition experiment


title: Env1Prelim_t4


title: ANXEXP010_p24_1

value: panic disorder

value: blood plasma


title: 1213423_03C_AT_ONLY_3_S61 (bulk RNA-seq)

data_processing:
For bulk RNA-seq data, reads were aligned with STAR v2.5.3a using splice junctions inferred from Gencode M15 gene annotations. Unmapped reads were then re-aligned with BWA.
For aligned bulk RNA-seq data, gene counts were calculated using FeatureCounts v1.5.1.
Genome_build: mm10
Supplementary_files_format_and_content: For single-cell RNA-seeq data, processed data contain counts of transcripts for each gene in each cell after removal of read duplicates using UMIs. For bulk RNA-seq data, the processed data file includes counts for each gene per sample.

source_name: aopototic thymocytes

growth_protocol:
Thymocytes (AT) were harvested from 4-6 weeks old C57BL/6 mice an maintained in DMEM 10% FBS.
6 mice an maintained in DMEM 10% FBS.

extract_protocol: TruSeq Stranded RNA

treatment_protocol: 1 million BMDM were untreated (NS) or fed with apoptotic thymocytes (1 mM staurosporine for 3h, washed in phosphate-buffered saline) in DMEM 10% FBS for 16 hours

tag: genotype

tag: treatment

value: Non-stimulated

value: aopototic thymocytes


title: ANXEXP022_pe1

tag: disease

value: female


title: ANXEXP007_pe1

tag: Sex

value: male


title: 1213422_03B_AT_ONLY_2_S60 (bulk RNA-seq)

tag: cell type


title: mock_1X_6

description:
rpkm.txt
N_1X_6


title: ANXEXP006_p24_1

tag: medication

tag: timepoint


title: ANXEXP007_p24_1

tag: tissue

tag: individual


title: ANXEXP007_b1


title: Env1Prelim_t2


title: 1213420_02G_KO_AT_4_S58 (bulk RNA-seq)

source_name: bone marrow-derived macrophages

growth_protocol:
Bone marrow cells were harvested from the femur and differentiated for 6 days in DMEM (Gibco) supplemented with 10% fetal bovine serum (FBS), 20 ng/ml recombinant M-CSF (Biolegend cat #574806) 200 mM L-glutamine and 100 units/ml penicillin-streptomycin.
6 mice an maintained in DMEM 10% FBS.

treatment_protocol:
10^6 BMDM were fed with apoptotic thymocytes (1 mM staurosporine for 3h, washed in phosphate-buffered saline) in DMEM 10% FBS for 16 hours
1 million BMDM were untreated (NS) or fed with apoptotic thymocytes (1 mM staurosporine for 3h, washed in phosphate-buffered saline) in DMEM 10% FBS for 16 hours

value: Stimulated

value: bone marrow-derived macrophages


title: ANXEXP022_p24_1


title: ANXEXP006_b1


title: ANXEXP009_pe1


title: 1213419_02G_KO_AT_3_S57 (bulk RNA-seq)


title: ANXEXP022_b1


title: mock_3X_2

description:
rpkm.txt
N_3X_2

tag: training cycles


title: mock_1X_5

description:
rpkm.txt
N_1X_5


title: ANXEXP009_b1


title: ANXEXP012_p24_1


title: ANXEXP002_pe1


title: Env1Prelim_t8

value: Engineered bacterial plasmid


title: ANXEXP002_p24_1


title: ANXEXP002_b1


title: Env1Prelim_t1

value: plasmid barcode


title: Env1Prelim_t0


title: mock_1X_4

description:
rpkm.txt
N_1X_4


title: mock_1X_3

description:
rpkm.txt
N_1X_3


title: mock_1X_2

description:
rpkm.txt
N_1X_2


title: 1213421_03A_AT_ONLY_1_S59 (bulk RNA-seq)


title: ANXEXP009_p24_1


title: 1213415_02C_KO_NS_3_S53 (bulk RNA-seq)

treatment_protocol:
10^6 BMDM were left untreated in DMEM 10% FBS for 16 hours
1 million BMDM were untreated (NS) or fed with apoptotic thymocytes (1 mM staurosporine for 3h, washed in phosphate-buffered saline) in DMEM 10% FBS for 16 hours


title: 1213417_02E_KO_AT_1_S55 (bulk RNA-seq)


title: 1213412_01H_WT_AT_4_S50 (bulk RNA-seq)


title: mock_1X_1

description:
rpkm.txt
N_1X_1


title: 1213416_02D_KO_NS_4_S54 (bulk RNA-seq)


title: 1213413_02A_KO_NS_1_S51 (bulk RNA-seq)