title: sequencing of TCG-1-1 gene in HeLa-iCas9-ArgTCG sgRNA cells, before iCas9 induction, repeat1

city: Rehovot

first: Roni

last: Rak

institute: Agriculture Research Organization

description:
ArgTCGsgRNA_d0_TCG-1-1_HeLa_rep1
processed data file: genomictRNAseq_CRISPResso_tRNAtargetedHeLa_Rep1.csv

growth_protocol: HeLa- iCas9 with single sgRNAs  cells (targeteing 4 different human tRNA families) were grown in DMEM + NEAA (Life Technologies; 10938-025) - Dulbecco’s Modified Eagle medium with 4.5mg/ml D-Glucose and Non-Essential amino acids. Supplemented with 10% FBS, 1% penicillin/ streptomycin (P/S), 1% L-Glutamine and 1% Sodium Pyruvate. The medium was supplemented with 200µg/ml Hygromycin (for iCas9 selection, Thermo Fisher; 10687010), 2µg/ml Puromycin (for sgRNA selection, Sigma-Aldrich; 58-58-2) and 1µg/ml Doxycycline (for iCas9 induction, Sigma-Aldrich; 10592-13-9).   WI38 fast iCas9 with single sgRNAs cells (targeteing 2 different human tRNA families) were grown in in MEM-EAGLE + NEAA– Earle’s salts base with Non-Essential amino acids (Biological Industries; 01-025-1A), supplemented with 10% FBS, 1% penicillin/ streptomycin (P/S) and 1% L-Glutamine. The medium was supplemented with 200µg/ml Hygromycin (for iCas9 selection, Thermo Fisher; 10687010), 10 µg/ml Blasticidin (for sgRNA selection, InvivoGen; BLL-38-02A)  and 1µg/ml Doxycycline (for iCas9 induction, Sigma-Aldrich; 10592-13-9).   Upon iCas9 induction, each cell population was samples every 4 days, and fresh medium containing all  antibiotics was replaced every two days for 12 days.

value: HeLa


title: E3 B4 d7 BAL

status: Public on Dec 22 2020

type: RNA

city: Berlin

first: Hans-Joachim

last: Mollenkopf

address: Charitéplatz 1

country: Germany

institute: Max-Planck-Institute for Infection Biology

description: d7 M.tuberculosis BAL sample

hyb_protocol: Whole mouse genome 8x60K microarray hybridizations and washing were done according to the supplier’s protocol (Agilent Technologies).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting and 20bit image depth with 3 x 3 micron  pixel resolution.

data_processing: The scanned images were analyzed with Feature Extraction Software 11.5.1.1. (Agilent) using default parameters (protocol GE1_1105_Oct12) to obtain background subtracted and spatially detrended Processed Signal intensities. Background correction ( normexp) and normalization between arrays  (quantile). Control probe removed.

molecule: total RNA

organism: Mus musculus

source_name: BAL

label_protocol: RNA labeling was performed with the low input Quick Amp Labeling Kit (Agilent Technologies) according supplier's instructions.

growth_protocol: For BAL collection, mice were lethally anesthetized.

extract_protocol: Total RNA was isolated by the Trizol (Invitrogen) method following the manufacturer´s protocol using Glycogen as carrier.

treatment_protocol: The bronchoalveolar space was flushed with 1ml of PBS containing protease inhibitor cocktail (Roche). Cells were pelleted and the supernatant sterilized by filtration (0.22 µm) and frozen at -20°C for protein analyses. Subsequently, the alveolar space was flushed 3 additional times with 1ml PBS containing 5 mM EDTA and collected on ice. Cells were pelleted and supernatant discarded. Cells from all washes were combined and kept on ice until further use.

tag: experiment

value: exp 3

tag: treatment

value: day 7

tag: strain


title: Skin_WT_T_cells-Exp1-845_IGO

type: SRA

city: New York

first: Akanksha

last: Verma

state: New York

address: 1300, York Avenue

department: Department of Physiology and Biophysics

country: USA

institute: Weill Cornell Medical College

library_source: transcriptomic

data_processing:
Illumina Casava1.8 software used for basecalling.
RNAseq: Sequence reads were aligned to mm10 STAR with default parameters
RNAseq: FPKM were obtained using CuffLinks
Genome_build: mm10
Supplementary_files_format_and_content: RNAseq: tab-delimited FPKM values for each Refseq gene.

molecule: polyA RNA

source_name: Skin

growth_protocol: 1X10^5 WT CD8+ OT-1 T cells were mixed with 1x10^5 PD-1 -/- CD8+ OT-1 T cells and were co-adoptively transferred to WT recipients one day before infection

extract_protocol: Total RNA was extracted from samples using the RNeasy Mini kit (Life Technologies). Samples were then subject to poly(A) selection using oligo-dT beads (Life Technologies) using Clonetech SMART-Seq v4 Ultra Low Input RNA Kit.

treatment_protocol: Recipient mice were vaccinated by VACV-OVAss on each ear with 1x10^6 and on the base of the tail with 2x10^6 viral p.f.u.  At day 14, WT or PD-1-/- donor CD8+ T cells were isolated from ear skin and sorted into trizol medium. Naïve CD8+ OT-1 T cells were isolated from lymph node and spleen of naive mice by negative selection on MACS beads and stored in trizol medium before RNA extraction.

tag: cell type

value: CD8+ T cells

tag: genotype/variation

value: Wild type OT-1

value: 1X10^5 WT CD8+ OT-1 T cells were mixed with 1x10^5 PD-1 -/- CD8+ OT-1 T cells and were co-adoptively transferred to WT recipients one day before VACV-OVA skin scarification. At day 14, WT donor CD8+ T cells were isolated from ear skin and sorted into trizol medium.


title: wk6_rep1

city: Des Moines

first: Chunfa

last: Jie

state: IA

address: 3200 Grand Ave

institute: Des Moines University

hyb_protocol: The Cy3-labeled cDNA were hybridized overnight (17 hours, 65°C) to an Agilent Whole Mouse Genome Oligo Microarrays 4x44K using Agilent's recommended hybridation chamber and oven. Then the microarrays were washed once with the Agilent Gene Expression Wash Buffer 1 for 1 min at room temperature followed by a second wash with preheated Agilent Gene Expression Wash Buffer 2 (37°C) for 1 min. The last washing step was performed with acetonitrile.

scan_protocol: Fluorescence signals of the hybridized Agilent Microarrays were detected using Agilent’s Microarray Scanner System (Agilent Technologies).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain raw median signal in green channel.  Quality assessment was first performed on the microarray data.  Spatial images of the foreground and background signals were made for each microarray sample to check any potential image artifacts, using the R/bioconductor package mArray vserion 1.66.0.  The distribution of the data was checked with density and box plots.  The raw microarray signal data were normalized with the quantile normalization method (Bolstad, 2003) to reduce the obscuring variation between microarrays, which might be introduced during the processes of sample preparation, manufacture, fluorescence labeling, hybridization and/or scanning.  Signals were averaged for a small subset of intra-microarray replicate probes.  Between-treatment and between-replicate variations were examined with the pair-wise MvA plots, in which the base 2 log ratios (M) between two samples are plotted against their averaged base 2 log signals (A).  Principal Component analysis (PCA) was also performed to assess sample variability.  The probes of incomplete functional annotation including “unknown”, “predicted gene”, “hypothetical protein” and “RIKEN cDNA” were filtered out in the downstream analysis.

organism: Musculus

source_name: gene expression of CD4 cells of lymph nodes and spleens of female DO11.10 mouse, week 6, replicate 1

label_protocol: 250 ng of each of the cDNAs were used as template for Cy3 labeling which was performed according to Miltenyi Biotec’s undisclosed protocol.

extract_protocol: RNA was prepared using SuperAmp Preparation kit (Miltenyi Biotec, Auburn, CA)following the manufacturer's recommendations. The protocol includes lysis of sorted lymphocytes with Proteinase K, and on-column magnetic isolation of mRNA with small superparamagnetic MACS SuperAmp Microbeads. cDNA was synthesized and amplifiled by a global PCR reaction (Roche). The cDNA was quantified using a NanoDrop-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE) and quality was mornitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Splenocytes of female DO11.10 mice were transferred into age-matched BALB/c recipients i.v. followed by Vaccinia-OVA virus injection i.p. 24h later. Draining lymph nodes and spleens were extracted at times 0 and 9 days, 5 weeks, 6- and 10.5 months later. Cells were stained and cells positive for CD4, CD44, and KJ1.26 Ab were sorted on a high-performance MoFlo sorter. Cells from sex and age-matched old naïve DO11.10 mice served as naive controls.

value: CD4+ cells

tag: gender

value: Female


title: day9_rep3

source_name: gene expression of CD4 cells of lymph nodes and spleens of female DO11.10 mouse, day 9, replicate 3


title: E3 B5 d7 BAL

description: d7 M.tuberculosis BAL sample


title: Infection_2_ATAC_seq_salivary_glands

city: Granada

first: Jose

middle: Luis

last: Ruiz Rodriguez

state: Granada

address: Avda. del Conocimiento 17. P. T. Ciencias de la Salud

country: Spain

institute: IPBLN-CSIC

description:
Infection_2_ATACseq_sgs
Sequencing approach: paired-end
processed data file: Table_S3_ATAC_seq_THSs.xlsx

library_source: genomic

data_processing:
First, raw ATAC-seq reads were trimmed 20 bases from the 3′ end of each read (-3 20), and aligned to the An. gambiae PEST genome (AgamP4) with Bowtie2 (v2.4.1) using default parameters, except for –no-unal –no-mixed -X 2000.
We applied a MAPQ score threshold (10) and sorted and deduplicated the reads using SAMtools (v1.10).
To adjust the known bias and ensure the mapping of Tn5 cutting sites, we shifted aligned reads +4 bp for + strands and −5 bp for – strands with ATACSeqQC (v1.10).
We removed not properly-paired reads and extracted nucleosome-free fragments with a size threshold of 130 bp (SAMtools).
We performed peak-calling on nucleosome-free reads with MACS2 (v.2.1.2) callpeak module and the following parameters: -f BAMPE -g 273109044 -q 0.01 -B --keep-dup all --nomodel --nolambda
To identify THSs unique or common across samples, we used BEDTools intersect requiring a minimum overlap of 51% (-f/-F 0.51).
We annotated THSs to genomic features combining HOMER (v4.11) and ChIPseeker (v1.22). We used the AgamP4.12 gene set and considered the first coordinate of the 5’ UTRs as the TSSs. For genes without an annotated 5’ UTR we took the translation start site (ATG codon) as the reference point. In either case, the 1 Kb upstream window was considered as the putative promoter region.
To quantify the ATAC-seq nucleosome-free signal enrichment at genomic regions of interest, we used BEDTools intersect -c. The read counts were normalized (RPKM) and we added a pseudocount (0.1) when required to get finite values.
We trimmed adapters from the RNA-seq raw reads using BBDuk (v38.79) with -tbo -tpe -minlength=35 parameters and removed rRNA contamination using SortMeRNA (v4.2) with default parameters. Apart from the default rRNA databases, we used additional large and small subunit An. gambiae and P. falciparum rRNA sequences from the SILVA database (LSU r132/SSU r138).
Cleaned directional RNA-seq reads were mapped against the AgamP4 v2.00 reference genome using STAR (v2.7.3a). Two different sets of reads were available, 2x150 bp and 1x75bp, which were processed in parallel until we combined the raw counts. We took unique mapping reads using SAMtools.
Raw counts at the gene level were obtained using CoCo (v.0.2.2) and then provided to DESeq2 (v1.26) for normalization.
Genome_build: AgamP4.12 (VectorBase)
Supplementary_files_format_and_content: *bw: Tracks of the aligned ATAC-seq and RNA-seq signal (bigWig, bw, files obtained using bamCompare).
Supplementary_files_format_and_content: Table_S3_ATAC_seq_THSs.xlsx: Excel table with full results of MACS2 peak-calling process.

molecule: genomic DNA

organism: Anopheles gambiae

source_name: salivary glands

growth_protocol: Five-day-old female An. gambiae Kisumu mosquitoes from a genetically outbred laboratory colony in the University of Glasgow were used for experimental infections. Mosquitoes were maintained under standard insectary conditions (27 ± 2 °C, 80 ± 5% relative humidity, 12:12 LD).

extract_protocol:
We performed dissection of midguts on adults at 7 days post-infection and of salivary glands at 14 days post-blood meal.
We performed the ATAC-seq protocol using fresh tissues from ~20 individual mosquitoes. Mosquito tissues were resuspended in lysis buffer to permeabilize membranes. The nuclei pellet was resuspended in the transposition reaction mix (25 μl of 2× TD Buffer, 1.25 μl of Tn5 Transposase and 23.75 μl of nuclease free water), and incubated for 30 min at 37°C. All samples were purified using the Qiagen MiniElute Kit. Library amplification was carried out with 2X KAPA HiFi mix and 1.25 μM of Nextera primers. The optimal cycle number was determined by qPCR. ATAC-seq libraries were sequenced at BGI (China) with an Illumina HiSeq4000 sequencer to obtain 25-37 M of 50 bp paired-end reads.

treatment_protocol: Females were fed through membrane feeders on blood containing gametocytes of P. falciparum clone 3D7, prepared according to standard protocols. Thereafter the mosquitoes were given access to a solution of 5% glucose/ 0.05% 4-aminobenzoic acid ad libitum. Three independent experimental infections (Infections 1, 2 and 3) were carried out.

value: Kisumu

tag: Sex

tag: tissue

value: Salivary glands

tag: infection status

value: Infected with P. falciparum

tag: time point

value: 14 days

tag: replicate


title: E3 B3 d7 BAL

description: d7 M.tuberculosis BAL sample


title: Infection_1_ATAC_seq_salivary_glands

description:
Infection_1_ATACseq_sgs
Sequencing approach: paired-end
processed data file: Table_S3_ATAC_seq_THSs.xlsx


title: Skin_PD1KO_T_cells-Exp3-835_set2

value: PD-1 KO OT-1

value: 1X10^5 WT CD8+ OT-1 T cells were mixed with 1x10^5 PD-1 -/- CD8+ OT-1 T cells and were co-adoptively transferred to WT recipients one day before VACV-OVA skin scarification. At day 14, PD-1-/- donor CD8+ T cells were isolated from ear skin and sorted into trizol medium.


title: E3 B1 d7 BAL

description: d7 M.tuberculosis BAL sample


title: E3 B2 d7 BAL

description: d7 M.tuberculosis BAL sample


title: Naive_T_cells-WT_set_B

source_name: Spleen + Lymph node

value: Naïve CD8+ OT-1 T cells were isolated from lymph node and spleen of naive mice by negative selection on MACS beads and stored in trizol medium before RNA extraction.


title: Skin_PD1KO_T_cells-Exp1-831_set2


title: ON_rep2

source_name: gene expression of CD4 cells of lymph nodes and spleens of female DO11.10 mouse, Naive, replicate 2


title: Infection_1_ATAC_seq_midguts

description:
Infection_1_ATACseq_mgs
Sequencing approach: paired-end
processed data file: Table_S3_ATAC_seq_THSs.xlsx

source_name: midguts

value: Midguts

value: 7 days


title: Infection_2_ATAC_seq_midguts

description:
Infection_2_ATACseq_mgs
Sequencing approach: paired-end
processed data file: Table_S3_ATAC_seq_THSs.xlsx


title: ON_rep1

source_name: gene expression of CD4 cells of lymph nodes and spleens of female DO11.10 mouse, Naive, replicate 1


title: day9_rep2

source_name: gene expression of CD4 cells of lymph nodes and spleens of female DO11.10 mouse, day 9, replicate 2


title: day9_rep1

source_name: gene expression of CD4 cells of lymph nodes and spleens of female DO11.10 mouse, day 9, replicate 1


title: Naive_T_cells-WT_set_A


title: ON_rep3

source_name: gene expression of CD4 cells of lymph nodes and spleens of female DO11.10 mouse, Naive, replicate 3


title: E3 A3 d7 BAL

description: d7 M.tuberculosis BAL sample


title: time0_rep3

source_name: gene expression of CD4 cells of lymph nodes and spleens of female DO11.10 mouse, time 0, replicate 3


title: time0_rep2

source_name: gene expression of CD4 cells of lymph nodes and spleens of female DO11.10 mouse, time 0, replicate 2


title: time0_rep1

source_name: gene expression of CD4 cells of lymph nodes and spleens of female DO11.10 mouse, time 0, replicate 1


title: EZH2 KO_RNAseq_rep2

city: Shanghai

first: Huairui

last: Yuan

address: 320 Yueyang Road

department: Shanghai Institutes for Biological Sciences

country: China

institute: Chinese Academy of Sciences

data_processing:
For RNA-Seq, transcriptome reads from Hiseq RNA-Seq experiments were mapped to the reference genome (mm10) by using Bowtie tool. Gene expression levels were quantified by a software package called RSEM. The list of significance was operated by setting fold changes threshold at level of 1.5 and p value < 0.05.
For ChIP-Seq, the 75-nt sequence reads generated by Illumina sequencing (using NextSeq 500) are mapped to the genome using the BWA algorithm with default settings. Only reads that pass Illumina’s purity filter, align with no more than 2 mismatches, and map uniquely to the genome are used in the subsequent analysis.tags are extended in silico (using Active Motif software) at their 3´-ends to a length of 150-250 bp, depending on the average fragment length in the size selected library (normally 200 bp).To identify the density of fragments (extended tags) along the genome, the genome is divided into 32-nt bins and the number of fragments in each bin is determined.The two main peak callers used at Active Motif are MACS (Zhang et al., Genome Biology 2008, 9:R137) and SICER (Zang et al., Bioinformatics 25, 1952-1958, 2009).
Genome_build: mm10
Supplementary_files_format_and_content: bigWig for ChIP-Seq and count/rpkm for RNA-seq

source_name: organoid cells

growth_protocol: The mouse prostatic organoid cells generation and organoids formation assay were according to previously reported protocol (Drost et al., 2016).

extract_protocol:
For RNA-seq, total RNA was extracted from the prostatic organoid cells derived from 3-month-old PtenPC+/- and PtenPC+/-; Setd2PC-/- mice with or without Ezh2 deletion, and then subjected to PE150 Hiseq. The chromatin was prepared and followed by ChIP-Seq analysis by Active Motif, Inc. using the antibody against H3K27me3 ( Active Motif 39155).
Libraries were prepared according to standard Illumina protocols.

value: Prostate epithelial cells


title: E3 A1 d7 BAL

description: d7 M.tuberculosis BAL sample

value: exp 3


title: E3 A2 d7 BAL

description: d7 M.tuberculosis BAL sample

value: day 7


title: E3 A4 d7 BAL

description: d7 M.tuberculosis BAL sample


title: E3 A5 d7 BAL

description: d7 M.tuberculosis BAL sample


title: E1 B5 24h BAL

description: 24h M.tuberculosis BAL sample

value: exp 1

value: 24 hours


title: CSA_1_CSB_1_NR_REPLICATE3 [CSAB1_NR_3]

city: Baltimore

first: Supriyo

last: De

state: Maryland

address: 251 Bayview Blvd

department: Laboratory of Genetics and Genomics

institute: NIA-IRP, NIH

hyb_protocol: A total of 600 ng Cy3-labeled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 microL containing 0.5x Agilent fragmentation buffer and 2x Agilent gene expression blocking agent following the manufacturers instructions.  On completion of the fragmentation reaction, 25 microL of 2× Hi-RPM Hybridization Buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint GE3 Mouse 8x60k v2 gene expression microarrays 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), and dried by slowly removing from Wash buffer 2.

scan_protocol: Following posthybridization rinses, arrays were scanned using an Agilent SureScan microarray Scanner at 5 micron, and hybridization intensity data extracted from the scanned images using Agilent’s Feature Extraction Software 9.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.

data_processing:
Raw microarray hybridization intensity data were filtered to remove undetected and array control probes, before computing log z-score for each sample to identify and exclude possible outlying samples via clustering, scatter plots, and principal components analysis. After removal of the outlying samples, a sample-specific quantile normalization of the filtered raw average signal was employed to yield quantile normalized log scale z-scores. These quantile z-scores were used to ensure a standard normal distribution in further statistical analysis, including ANOVA, t- and z-testing. Z-ratio values of ± 1.5 were used as cut-off values and calculated using a combination of thresholds, including p<value 0.05, 30% false discovery rate (FDR), and average signal intensity of comparison >0. The gene expression change z-ratio values were then used as input to perform Parametric Analysis of Gene Set Enrichment (PAGE) testing. For each gene set change, an aggregate z-score, and p-value with false discovery change was calculated and reported for statistical significance.
Quantile normalized z-score of the signal intensity (Z transformation of the natural log (base 10) of the quantile normalized intensity values).

organism: Caenorhabditis elegans

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 200 ng total RNA using the Low-Input Quick Amp Labeling Kit (Agilent, Santa Clara, CA) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were evaluated with the NanoDrop ND-1000 Spectrophotometer (Wilmington, DE).

growth_protocol: All C. elegans strains were maintained and grown on standard nematode growth medium (NGM). Bristol strain N2 (wildtype) were obtained from the Caenorhabditis Genetics Center (CGC). Worm populations were synchronized via egg lay and all experiments were conducted at 25oC unless otherwise noted. csa-1 (tm4539) and csb-1 (ok2335) were provided by Dr. Bjorn Schumacher (University of Cologne, Cologne, Germany).

extract_protocol: RNA was purified using a Qiagen RNeasy mini kiton a QIAcube following the manufacturer’s protocol (Qiagen, Germantown, MD).

treatment_protocol: N2, csa-1, csb-1, csa-1;csb-1 worms were exposed to 500 µM  of the NAD+ precursor NR from the L4 stage and whole body tissue was collected at adult day 7. Water was used as a vehicle control.

tag: strain background

value: Bristol strain N2

tag: age

value: NR

tag: treatment duration

value: whole body


title: USA100 N315 Planktonic 24 hour

city: Tampa

first: Lindsey

middle: N

last: Shaw

state: FL

address: 4202 E Fowler Avenue

department: CMMB

institute: University of South Florida

data_processing:
Raw data files (.fastq) were exported from the Illumina BaseSpace Server
Raw data files (.fastq) were imported into Qiagen CLC Genomics Workbench (version 20) as paired-end reads for analysis and adapter indices trimmed.
Reads corresponding to ribosomal RNA were filtered out and removed
Gene expression values were calculated using the Expression Browser tool
Differential expression between biofilm and planktonic samples were generated for each strain and timepoint individually using the Differential Expression in Two Groups tool
Fold change comparisons were exported in excel format
Genome_build: The accession number for the Genbank genome files used as reference are: USA100 (NC_002745), USA200 (NC_002952), USA300 (NC_007793), USA400 (NC_003923), and USA500 (NC_007793).
Supplementary_files_format_and_content: Differential expression in biofilm populations relative to their planktonic counterpart are presented as fold-change values in excel format.

organism: Staphylococcus aureus

source_name: bacterial cells

growth_protocol: Overnight S. aureus cultures were used to inoculate fresh tryptic soy broth at an optical density (OD600) of 0.5 in 96-well microtiter plates, in biological triplicate. Test cultures were grown for 5 h, 10 h and 24 h at 37°C in a static incubator prior to collection. To collect planktonic samples, 75 μL of supernatant was removed from the top of each well, and those for like strains were pooled. Samples were immediately combined with 5 mL of ice-cold PBS, and pelleted by refrigerated centrifugation for subsequent RNA isolation. For biofilm samples, the remaining supernatant was removed and biofilm containing wells were washed three times with 200 μL of ice-cold PBS. Ice-cold PBS was added a final time, pipetted vigorously to disrupt biofilm cells, and like strains were pooled. Samples were then immediately combined with an additional 5 mL of ice-cold PBS and pelleted by refrigerated centrifugation for subsequent RNA isolation.

extract_protocol:
Total bacterial RNA was isolated utilizing an RNeasy Kit (Qiagen) and contaminating DNA was removed by treatment with TURBO DNA-free kit (Ambion). Samples with a RIN of >9.7 measured by Agilent 2100 Bioanalyzer system and corresponding RNA 6000 Nano kit (Agilent) were used in this study. Ribosomal RNA was removed using a Ribo-Zero Kit for Gram-positive Bacteria (Illumina) and MICROBExpress Bacterial mRNA enrichment kit (Agilent).
Library construction was performed using the TruSeq Stranded mRNA Kit from Illumina omitting mRNA enrichment steps.

treatment_protocol: Samples were stored at -80°C prior to RNA extraction.

tag: genotype

value: Wildtype

tag: growth medium

value: TSB

tag: growth conditions

value: Static planktonic, 24 h, 37°C


title: USA300 LAC Planktonic 24 hour

value: LAC


title: E2 B1 d14 BAL

description: d14 M.tuberculosis BAL sample

source_name: BAL

tag: experiment

value: exp 2

value: day 14


title: USA500 NRS385 Biofilm 24 hour

value: Static biofilm, 24 h, 37°C


title: USA500 NRS385 Planktonic 24 hour


title: USA400 MW2 Planktonic 24 hour


title: CSA_1_CSB_1_NR_REPLICATE2 [CSAB1_NR_2]

tag: treatment


title: USA200 MRSA252 Planktonic 24 hour

tag: strain


title: USA400 MW2 Biofilm 24 hour


title: USA300 LAC Biofilm 24 hour


title: CSA_1_CSB_1_NR_REPLICATE1 [CSAB1_NR_1]


title: CSA_1_CSB_1_VEH_REPLICATE4 [CSAB1_VEH_4]

value: CTR


title: E1 B2 24h BAL

description: 24h M.tuberculosis BAL sample


title: CSA_1_CSB_1_VEH_REPLICATE2 [CSAB1_VEH_2]

value: 7 days


title: USA200 MRSA252 Biofilm 24 hour


title: E1 B3 24h BAL

description: 24h M.tuberculosis BAL sample


title: CSA_1_CSB_1_VEH_REPLICATE3 [CSAB1_VEH_3]


title: USA100 N315 Biofilm 24 hour


title: E1 B1 24h BAL

description: 24h M.tuberculosis BAL sample


title: E1 A5 24h BAL

description: 24h M.tuberculosis BAL sample


title: E1 A4 24h BAL

description: 24h M.tuberculosis BAL sample


title: CSB_1_NR_REPLICATE4 [CSB1_NR_4]


title: USA500 NRS385 Planktonic 10 hour

value: Static planktonic, 10 h, 37°C


title: CSA_1_CSB_1_NR_REPLICATE4 [CSAB1_NR_4]


title: CSA_1_CSB_1_VEH_REPLICATE1 [CSAB1_VEH_1]


title: E1 A1 24h BAL

description: 24h M.tuberculosis BAL sample


title: E1 A2 24h BAL

description: 24h M.tuberculosis BAL sample


title: CSB_1_NR_REPLICATE2 [CSB1_NR_2]


title: E1 B3 naive BAL

description: naive BAL sample

value: naive


title: E1 B4 naive BAL

description: naive BAL sample


title: USA400 MW2 Planktonic 10 hour


title: USA300 LAC Planktonic 10 hour


title: E1 B2 naive BAL

description: naive BAL sample


title: CSB_1_NR_REPLICATE1 [CSB1_NR_1]


title: CSB_1_NR_REPLICATE3 [CSB1_NR_3]


title: USA200 MRSA252 Planktonic 10 hour


title: CSB_1_VEH_REPLICATE4 [CSB1_CTR_4]


title: CSB_1_VEH_REPLICATE3 [CSB1_CTR_3]


title: E1 B1 naive BAL

description: naive BAL sample


title: E1 A4 naive BAL

description: naive BAL sample


title: E1 A3 naive BAL

description: naive BAL sample


title: CSB_1_VEH_REPLICATE1 [CSB1_CTR_1]


title: CSB_1_VEH_REPLICATE2 [CSB1_CTR_2]


title: USA500 NRS385 Biofilm 10 hour

value: Static biofilm, 10 h, 37°C


title: USA400 MW2 Biofilm 10 hour


title: USA300 LAC Biofilm 10 hour


title: E1 A2 naive BAL

description: naive BAL sample

value: exp 1


title: USA100 N315 Planktonic 10 hour


title: CSA_1_NR_REPLICATE4 [CSA1_NR_4]


title: PDep6 BAL B4

description: depleted M.tuberculosis BAL sample

value: Depletion


title: USA200 MRSA252 Biofilm 10 hour


title: E1 A1 naive BAL

description: naive BAL sample


title: CSA_1_NR_REPLICATE3 [CSA1_NR_3]

value: Bristol strain N2


title: USA100 N315 Biofilm 10 hour


title: MSC_OM05

type: genomic

city: Houston

first: Katayoun

last: Rezvani

state: Texas

address: 1515 Holcombe Blvd

department: Department of Stem Cell Transplantation and Cellular Therapy

institute: The University of Texas MD Anderson Cancer Center

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation850k Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader (Illumina HiSeq2000) using standard recommended Illumina scanner setting

data_processing: Raw IDAT files were processed using R package SeSAMe with noob background correction, non-linear dye bias correction, and non-detection masking. Methylation beta values were called as quantitative percentage of methylated signals over both unmethylated and methylated signals ranging from 0 to 1, with “0” indicating full lack of methylation and “1” full methylation. We excluded measurements from sub-optimally designed probes due to overlap with SNPs and repeat elements, as suggested by previous studies and implemented in SeSAMe.

label: Cy5 and Cy3

organism: Homo sapiens

source_name: MSCs derived from normal omentum from patient with a stage II clear cell endometrial cancer

label_protocol: Standard Illumina Protocol

extract_protocol: DNA was quantified by Qubit fluorimetry (Life Technologies) and 500ng of DNA from each sample was bisulfite converted using the Zymo EZ DNA Methylation Kit (Zymo Research, Irvine, CA USA) following the manufacturer’s protocol using the specified modifications for the Illumina Infinium Methylation Assay.  After conversion, all bisulfite reactions were cleaned using the Zymo-Spin binding columns, and eluted in 12 uL of Tris buffer. Following elution, BS converted DNA was processed through the EPIC array protocol. To perform the assay, 7uL of converted DNA was denatured with 1ul 0.4N sodium hydroxide.  DNA was then amplified, hybridized to the EPIC bead chip, and an extension reaction was performed using flurophore labeled nucleotides per the manufacturer’s protocol.  Array beadchips were scanned on the Illumina iScan platform.  DNA methylome was captured by HumanMethylationEPIC (EPIC) BeadChip (Illumina, CA, USA) using the manufacturer’s standard protocol.

treatment_protocol: No treatment

tag: ethnicity


title: PDep6 BAL B3

description: depleted M.tuberculosis BAL sample


title: USA500 NRS385 Planktonic 5 hour

value: Static planktonic, 5 h, 37°C


title: CSA_1_NR_REPLICATE1 [CSA1_NR_1]

tag: genotype/variation

value: NR

value: whole body


title: CSA_1_NR_REPLICATE2 [CSA1_NR_2]


title: MSC_OM01b

description: DNA was quantified by Qubit fluorimetry (Life Technologies) and 500ng of DNA from each sample was bisulfite converted using the Zymo EZ DNA Methylation Kit (Zymo Research, Irvine, CA USA) following the manufacturer’s protocol using the specified modifications for the Illumina Infinium Methylation Assay.  After conversion, all bisulfite reactions were cleaned using the Zymo-Spin binding columns, and eluted in 12 uL of Tris buffer. Following elution, BS converted DNA was processed through the EPIC array protocol. To perform the assay, 7uL of converted DNA was denatured with 1ul 0.4N sodium hydroxide.  DNA was then amplified, hybridized to the EPIC bead chip, and an extension reaction was performed using flurophore labeled nucleotides per the manufacturer’s protocol.

source_name: MSCs derived from normal omental tissue undergoing surgery for benign indications


title: USA400 MW2 Planktonic 5 hour

value: Wildtype

value: TSB


title: MSC_OM01a


title: MSC_FT07

source_name: MSCs derived from normal fallopian tube


title: MSC_AD02

source_name: MSCs derived from adipose purchased through ATCC


title: CSA_1_VEH_REPLICATE4 [CSA1_CTR_4]


title: MSC_OM01c


title: PDep6 BAL B2

description: depleted M.tuberculosis BAL sample


title: MSC-FT-BrcaL

source_name: MSCs derived from left fallopian tube with BRCA2 mutation


title: USA300 LAC Planktonic 5 hour

value: LAC


title: PDep6 BAL B1

description: depleted M.tuberculosis BAL sample

value: exp 2


title: MSC_AD01


title: MSC_OM01d


title: CSA_1_VEH_REPLICATE2 [CSA1_CTR_2]


title: PDep6 BAL A3

description: control M.tuberculosis BAL sample

value: Control


title: USA200 MRSA252 Planktonic 5 hour


title: USA100 N315 Planktonic 5 hour


title: MSC_OM07

source_name: MSCs derived from normal omentum


title: PDep6 BAL A2

description: control M.tuberculosis BAL sample


title: CSA_1_VEH_REPLICATE1 [CSA1_CTR_1]


title: MSC-FT-BrcaR

source_name: MSCs derived from right fallopian tube with BRCA2 mutation


title: MSC_FT02


title: USA500 NRS385 Biofilm 5 hour

value: Static biofilm, 5 h, 37°C


title: WT_NR_REPLICATE4 [N2_NR_4]

value: WT


title: MSC_FT04


title: USA400 MW2 Biofilm 5 hour


title: PDep10 BAL B4

description: depleted M.tuberculosis BAL sample


title: CSA_1_VEH_REPLICATE3 [CSA1_CTR_3]

value: 7 days

value: CTR


title: WT_NR_REPLICATE3 [N2_NR_3]


title: MSC_FT03

source_name: MSCs derived from normal fallopian tube but with hydrosalpinx


title: USA300 LAC Biofilm 5 hour


title: WT_NR_REPLICATE2 [N2_NR_2]


title: WT_NR_REPLICATE1 [N2_NR_1]


title: PDep10 BAL B2

description: depleted M.tuberculosis BAL sample


title: MSC_FT01


title: PDep6 BAL A4

description: control M.tuberculosis BAL sample


title: WT_VEH_REPLICATE4 [N2_CTR_4]


title: USA100 N315 Biofilm 5 hour


title: MSC_OMneo04

source_name: MSCs derived from omentum that was never involved with cancer (stage II ovarian cancer) but patient had neoadjuvant chemotherapy


title: MSC_OMneo02

source_name: MSCs derived from omentum that was initially involved with high grade serous ovarian cancer but had a complete pathologic response to neoadjuvant chemotherapy


title: USA200 MRSA252 Biofilm 5 hour


title: PDep10 BAL B1

description: depleted M.tuberculosis BAL sample


title: PDep6 BAL A1

description: control M.tuberculosis BAL sample


title: Lab_WT_PMB_0120594

city: Seoul

first: Jaeeun

last: Park

address: 145, Anam-ro, Seongbuk-gu, Seoul, Republic of Korea

country: South Korea

institute: Korea university

data_processing:
RNA sequencing was performed on an Illumina HiSeq 2500 platform using single end 50-bp sequencing
The reference genome sequence was retrieved from the NCBI database.
Quality-filtered reads were aligned to the reference genome sequence using Bowtie2.
The relative abundance of transcripts is presented as RPKM, defined as the total exon reads/(mapped reads in millions × exon length in kilobases.
The mean of RPKM values are 372, 395, 378 and 314, respectively, in order of file name.

organism: Acinetobacter baumannii ATCC 17978

source_name: Acinetobacter bauammnnii ATCC 17978 Lab-WT treated 0.5 MIC of PMB in LB media

growth_protocol: Exponential phase on PMB supplemented LB media

extract_protocol:
Using an RNeasy Kit (Qiagen, Hilden, Germany) according to the manufacturer’s instructions
Illumina sequencing library was constructed by the TruSeq Stranded mRNA Library Prep Lit (Illumina, San Diego, CA, USA) following the manufacturer's protocol

tag: cell type

value: Exponential phase


title: Lab_WT_0120592

source_name: Acinetobacter bauammnnii ATCC 17978 Lab-WT in LB media


title: WT_VEH_REPLICATE3 [N2_CTR_3]


title: PDep10 BAL A4

description: control M.tuberculosis BAL sample


title: MSC_OMneo03


title: I16R043h07: TG_12m_5

status: Public on Dec 21 2020

city: Saarbrücken

first: Julia

middle: Maria

last: Schulze-Hentrich

address: Campus, Building A2.4

department: Genetics and Epigenetics

institute: Saarland University

data_processing:
Paired-end fastq files were aligned with STAR (v2.6.0a) allowing gapped alignments to account for splicing, otherwise default parameters.
Read counts for all genes were determined using Rsubread (v2.0.0).
Genome_build: Ensembl v93 R.norvegicus
Supplementary_files_format_and_content: CVS file with raw read counts per gene identified by Ensembl gene ID

organism: Rattus norvegicus

source_name: frontal cortex

extract_protocol:
Total RNA was extracted using AllPrep DNA/RNA/miRNA Universal Kit (Qiagen, Cat No.: 80224)
Using the TruSeq RNA Sample Prep Kit (Illumina) and 100 ng of total RNA for each sequencing library, poly-A selected paired-end sequencing libraries (125 bp read length) were generated according to the manufacturer’s instructions.
Libraries were sequenced on an Illumina HiSeq 2500 platform at a depth of 20-35 mio reads each.

treatment_protocol: Frontal cortex tissue was incubated in RNAlater (Qiagen, Cat No.: 76104) before storage at -80°C

value: Sprague-Dawley

value: 12 months

value: transgene overexpressing human SNCA


title: MSC_OMneo01


title: I16R043h06: TG_12m_4


title: I16R043h03: TG_12m_2


title: I16R043h05: TG_12m_3


title: PDep10 BAL A2

description: control M.tuberculosis BAL sample

value: exp 1


title: I16R043g05: WT_12m_3

value: wildtype


title: I16R043g01: WT_12m_1


title: WT_VEH_REPLICATE1 [N2_CTR_1]

value: Bristol strain N2


title: I16R043g07: WT_12m_5


title: I16R043g06: WT_12m_4


title: I16R043g04: WT_12m_2


title: I16R020d06: TG_5m_5

value: 5 months


title: PDep10 BAL B3

description: depleted M.tuberculosis BAL sample

value: Depletion


title: PDep10 BAL A1

description: control M.tuberculosis BAL sample


title: I16R020d04: TG_5m_4


title: CAMSC_OV02

source_name: CAMSCSs derived from ovary involved with high grade serous ovarian cancer


title: CAMSC_OV03

source_name: CAMSCSs derived from ovary involved with ovarian cancer


title: I16R020d03: TG_5m_3


title: CAMSC_OV01


title: I16R020c06: WT_5m_5


title: I16R020c01: WT_5m_1


title: I16R020d01: TG_5m_1


title: I16R020c04: WT_5m_3


title: wm6: wmASTRs sample 6

city: Groningen

first: Marissa

last: Dubbelaar

address: Antonius Deusinglaan 1

department: Biomedical Sciences of Cells & Systems

country: Netherlands

institute: University Medical Center Groningen

data_processing:
Sequenced reads were trimmed for adaptor and low-quality sequences then mapped to the rattus norvegicus genome (38.82) using hisat v0.1.5, allowing two mismatches
Aligned data was sorted using SAMtools v1.2 and gene level quantification was performed using HTSeq v0.6.1p1 with parameters --stranded=no and --mode=union
High and low expressed genes were distinguished using the Data-adaptive flag method for RNA-sequencing (DAFS), a protocol from George and Chang, BMC bioinformatics, 2014.
Genome_build: Rattus norvegicus (GRCm38.82)
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Brain

growth_protocol: Adult ASTRs were isolated from young adult female Wistar rats brains. To obtain gmASTRs, the cerebral cortices were dissected and meninges removed. Of the residual tissue, the amygdala was discarded and the remaining parts non-cortical parts (WM tracts including corpus callosum, mixed GM and WM tracts, including hippocampus and thalamus, and deep GM parts, including basal ganglia) were kept in HBSS and used to obtain non-cortical, mainly wmASTRs. Of note, adult gmASTRs and wmASTRs were always generated at the same time from the same animal via a non-shake off procedure and cultured at similar conditions. The cells were cultured for 20 days at 37°C in poly-L-lysine-coated tissue flasks. Medium exchange occurred once every 3-4 days. The cells were passaged at least once using trypsin.

extract_protocol:
Cells were scraped in RNA protect (Qiagen) and mRNA was isolated using the RNeasy Plus Micro Kit (Qiagen) according to manufacturer’s instructions. The quality of the mRNA was assessed using a BioRad Experion Highsense RNA kit according to manufacturer’s instructions. All RIN-values were higher than 7.9.
Library preparation was performed with the Lexogen QuantSeq 3'mRNA-Seq Library Prep kit for Illumina (Lexogen GmbH) according to manufacture's instructions. All samples were pooled and sequenced on the Illumina NextSeq500.
RNA-Seq,  SR run with 73 + 7 bp (with 12 dark cycles)

value: Wistar

value: Non-cortex

value: Astrocyte


title: wm5: wmASTRs sample 5


title: I16R020c05: WT_5m_4


title: wm2: wmASTRs sample 2


title: I16R020c03: WT_5m_2


title: I16R043h02: TG_12m_1


title: wm4: wmASTRs sample 4


title: gm6: gmASTRs sample 6

value: Cortex


title: gm5: gmASTRs sample 5


title: wm1: wmASTRs sample 1


title: gm4: gmASTRs sample 4


title: CAMSC_OM08

source_name: CA-MSCs derived from the omental metastasis of patients with ovarian carcinosarcoma


title: WT_VEH_REPLICATE2 [N2_CTR_2]

value: whole body


title: gm3: gmASTRs sample 3


title: I16R020d02: TG_5m_2


title: gm2: gmASTRs sample 2


title: PDep10 BAL A3

description: control M.tuberculosis BAL sample

source_name: BAL

value: Control


title: gm1: gmASTRs sample 1


title: CAMSC_OM06a

source_name: CA-MSCs derived from the omental metastasis of patients with high grade serous ovarian cancer


title: Pnmt41_TAP_Mmi1 Pnmt1_3xFLAG_Mei2_2_WCE

city: JOUY-EN-JOSAS

first: Alicia

last: Nevers

address: Domaine de Vilvert

department: Micalis

country: France

institute: Institut national de la recherche agronomique (Inrae)

description: WCE

data_processing:
Demultiplexing using bcl2fastq2-2.18.12
Adaptors trimming with Cutadapt 1.15
Read alignment to reference genome with Bowtie2 in Galaxy. Write unaligned reads (in fastq format) to separate file(s): False; Write aligned reads (in fastq format) to separate file(s): False; Do you want to set paired-end options?: no  Will you select a reference genome from your history or use a built-in index?: indexed; Select reference genome: Schizosaccharomyces_pombe_1.1; Set read groups information?: do_not_set; Select analysis mode: simple; Do you want to use presets?: Very fast end-to-end (--very-fast); Save the bowtie2 mapping statistics to the history: True
Read counting with MulticovBed in Galaxy. Calculation based on strandedness?: Only overlaps occurring on the **same** strand.; minimum overlap required as a fraction of A: 1e-09; Require that the fraction of overlap be reciprocal for A and B: False; Treat split/spliced BAM or BED12 entries as distinct BED intervals when computing coverage: False; Minimum mapping quality (MAPQ) allowed:0; Include duplicate reads: True; Include failed-QC reads: False; Only count proper pairs: False
Genome_build: Schizosaccharomyces_pombe_1.1 (Galaxy)
Supplementary_files_format_and_content: raw count txt files

organism: Schizosaccharomyces pombe

source_name: liquid culture in minimal medium

growth_protocol: Schizosaccharomyces pombe cells were cultured in minimal medium (EMM) for 2 days at 30°C . Samples were collected during exponential phase (OD = 1).

extract_protocol:
Phenol Chlorofom extraction of total (WCE) and immunoprecipitated (IP) RNAs
After Ribosomal RNA depletion on WCE RNA samples, NextSeq 500/550 Mid Output Kit v2 was used to construct library
Paired-end 75 sequencing performed on a NextSeq instrument

treatment_protocol: Sample crosslink with 0.2% formaldehyde, cell lysis in liquid nitrogen, lysates clarification, first immunoprecipitation against the TAP-tag (IgG) with TEV protease elution, second immunoprecipitation against 3X FLAG (anti-FLAG)

tag: protein tags

value: TAP-Mmi1 and 3x-FLAG-Mei2

tag: developmental stage


title: CAMSC_FT01

source_name: CAMSCs derived from fallopian tube invovled with high grade serous ovarian cancer


title: Pnmt41_GFP_Mmi1 Pnmt1_3xFLAG_Mei2_2_WCE

description: WCE

value: GFP-Mmi1 and 3x-FLAG-Mei2


title: Pnmt41_TAP_Mmi1 Pnmt1_3xFLAG_Mei2_1_IP

description: Immunoprecipitated RNA

value: Exponential phase


title: Pnmt41_TAP_Mmi1 Pnmt1_3xFLAG_Mei2_1_WCE

description: WCE


title: Pnmt41_GFP_Mmi1 Pnmt1_3xFLAG_Mei2_2_IP

description: Immunoprecipitated RNA


title: Pnmt41_GFP_Mmi1 Pnmt1_3xFLAG_Mei2_1_IP

description: Immunoprecipitated RNA


title: CAMSC_OM09


title: CAMSC_OM06b


title: LAD tissues with lymph node metastasis lncRNAs 2

city: Weifang

first: chonggao

last: Yin

state: Shan dong

address: No.7166,Baotongxi Street

institute: Weifang medical university

description: lncRNA expression  Lung adenocarcinoma (LAD) tissue with lymph node metastasis2

hyb_protocol: The labeled cRNAs were hybridized onto the Arraystar Human lncRNA Arrays, and incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: After washing, slides were scanned with the Agilent DNA Microarray Scanner G2505C.

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v12.1 software package (Agilent Technologies). After quantile normalization of the raw data, LncRNAs and mRNAs that at least 3 out of 9 samples have flags in Present or Marginal (“All Targets Value”) were chosen for further data analysis. Differentially expressed LncRNAs and mRNAs with statistical significance between the two groups were identified through P-value/FDR filtering. Differentially expressed LncRNAs and mRNAs between the two samples were identified through Fold Change filtering. Hierarchical Clustering and combined analysis were performed using homemade scripts.

source_name: LAD tissues with lymph node metastasis

label_protocol: Total RNA from each sample was amplified and transcribed into fluorescent cRNA utilizing ramdom primer according to Arraystar Super RNA Labeling protocol (Arraystar, Inc.)

growth_protocol: LAD tissues with or without lymph node metastasis and matched non-tumor lung tissues

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

treatment_protocol: Tissues from LAD surgury and promptly frozen in liquid nitrogen.

tag: tissue

value: lung

tag: disease state

value: Lung adenocarcinoma with lymph node metastasis

tag: gender

value: male


title: CAMSC_OM03b


title: Brain endothelial cell 977

city: Uppsala

first: L.

last: He

address: Dag Hammarskjölds Väg 20

country: Sweden

institute: Uppsala University

description: Brain endothelial cell 977

data_processing:
The sequencing reads were first aligned to the mouse reference genome GRCm38 (mm10) with tophat (version 2.1.1). The duplicated reads were removed using samtools software (version 0.1.18). The raw read counts for each gene were then calculated using featureCounts function from the Subread package (version 1.4.6-p5)
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text files include raw counts values for each sample

extract_protocol:
Pdgfb ret mice were crossed with Cldn5-GFP; Cspg4-DsRed mice for endothelial cell (positive for GFP, negative for dsRed) isolation based on fluorescence-activated cell sorting (FACS),  followed by the SmartSeq2 methodology for the generation and sequencing of full length polyadenylated cDNAs
Libraries for RNA-seq were prepared by using SMART-seq2 methodology

value: brain

value: adult mice

value: Pdgfb ret/ret

value: endothelial cell


title: Brain endothelial cell 979

description: Brain endothelial cell 979


title: Brain endothelial cell 980

description: Brain endothelial cell 980


title: Brain endothelial cell 981

description: Brain endothelial cell 981


title: Brain endothelial cell 974

description: Brain endothelial cell 974


title: Pnmt41_GFP_Mmi1 Pnmt1_3xFLAG_Mei2_1_WCE

description: WCE


title: Brain endothelial cell 982

description: Brain endothelial cell 982


title: Brain endothelial cell 978

description: Brain endothelial cell 978


title: Brain endothelial cell 976

description: Brain endothelial cell 976


title: LAD tissues with lymph node metastasis lncRNAs 4

description: lncRNA expression  Lung adenocarcinoma (LAD) tissue with lymph node metastasis4

value: female


title: normal lung tissue lncRNAs 2

description: lncRNA expression data from Homo sapiens lung 2

source_name: normal lung tissue

value: normal


title: Pnmt41_TAP_Mmi1 Pnmt1_3xFLAG_Mei2_2_IP

description: Immunoprecipitated RNA


title: Brain endothelial cell 972

description: Brain endothelial cell 972


title: Brain endothelial cell 975

description: Brain endothelial cell 975


title: wm3: wmASTRs sample 3

value: Wistar

value: Non-cortex


title: LAD tissues without lymph node metastasis lncRNAs 2

description: lncRNA expression  Lung adenocarcinoma (LAD) tissue without lymph node metastasis 2

value: Lung adenocarcinoma without lymph node metastasis


title: CAMSC_OM01


title: CAMSC_OM02


title: LAD tissues without lymph node metastasis lncRNAs 1

description: lncRNA expression  Lung adenocarcinoma (LAD) tissue without lymph node metastasis 1


title: normal lung tissue lncRNAs 3

description: lncRNA expression data from Homo sapiens lung 3


title: Brain endothelial cell 973

description: Brain endothelial cell 973


title: LAD tissues with lymph node metastasis lncRNAs 3

description: lncRNA expression  Lung adenocarcinoma (LAD) tissue with lymph node metastasis3


title: Brain endothelial cell 971

description: Brain endothelial cell 971


title: Brain endothelial cell 970

description: Brain endothelial cell 970


title: Brain endothelial cell 968

description: Brain endothelial cell 968


title: Brain endothelial cell 969

description: Brain endothelial cell 969


title: Brain endothelial cell 963

description: Brain endothelial cell 963


title: Brain endothelial cell 967

description: Brain endothelial cell 967


title: Brain endothelial cell 966

description: Brain endothelial cell 966


title: Brain endothelial cell 964

description: Brain endothelial cell 964


title: CAMSC_OM05


title: Brain endothelial cell 965

description: Brain endothelial cell 965


title: Brain endothelial cell 983

description: Brain endothelial cell 983


title: Brain endothelial cell 959

description: Brain endothelial cell 959


title: Brain endothelial cell 958

description: Brain endothelial cell 958


title: Brain endothelial cell 960

description: Brain endothelial cell 960


title: Brain endothelial cell 962

description: Brain endothelial cell 962


title: Brain endothelial cell 957

description: Brain endothelial cell 957


title: Brain endothelial cell 944

description: Brain endothelial cell 944


title: Brain endothelial cell 950

description: Brain endothelial cell 950


title: Brain endothelial cell 954

description: Brain endothelial cell 954


title: Brain endothelial cell 948

description: Brain endothelial cell 948


title: Brain endothelial cell 949

description: Brain endothelial cell 949


title: Brain endothelial cell 955

description: Brain endothelial cell 955


title: Brain endothelial cell 961

description: Brain endothelial cell 961


title: Brain endothelial cell 956

description: Brain endothelial cell 956


title: Brain endothelial cell 938

description: Brain endothelial cell 938


title: Brain endothelial cell 945

description: Brain endothelial cell 945


title: Brain endothelial cell 941

description: Brain endothelial cell 941


title: Brain endothelial cell 939

description: Brain endothelial cell 939


title: Brain endothelial cell 946

description: Brain endothelial cell 946


title: Brain endothelial cell 952

description: Brain endothelial cell 952


title: Brain endothelial cell 951

description: Brain endothelial cell 951


title: Brain endothelial cell 942

description: Brain endothelial cell 942


title: Brain endothelial cell 947

description: Brain endothelial cell 947


title: Brain endothelial cell 953

description: Brain endothelial cell 953


title: Brain endothelial cell 937

description: Brain endothelial cell 937


title: Brain endothelial cell 943

description: Brain endothelial cell 943


title: Brain endothelial cell 940

description: Brain endothelial cell 940


title: Brain endothelial cell 936

description: Brain endothelial cell 936


title: Brain endothelial cell 931

description: Brain endothelial cell 931


title: Brain endothelial cell 932

description: Brain endothelial cell 932


title: Brain endothelial cell 933

description: Brain endothelial cell 933


title: Brain endothelial cell 934

description: Brain endothelial cell 934


title: Brain endothelial cell 935

description: Brain endothelial cell 935


title: Brain endothelial cell 924

description: Brain endothelial cell 924


title: LAD tissues without lymph node metastasis lncRNAs 3

description: lncRNA expression  Lung adenocarcinoma (LAD) tissue without lymph node metastasis 3


title: Brain endothelial cell 919

description: Brain endothelial cell 919


title: Brain endothelial cell 918

description: Brain endothelial cell 918


title: Brain endothelial cell 922

description: Brain endothelial cell 922


title: Brain endothelial cell 921

description: Brain endothelial cell 921


title: Brain endothelial cell 920

description: Brain endothelial cell 920


title: Brain endothelial cell 914

description: Brain endothelial cell 914


title: Brain endothelial cell 917

description: Brain endothelial cell 917


title: Brain endothelial cell 928

description: Brain endothelial cell 928


title: Brain endothelial cell 923

description: Brain endothelial cell 923


title: Brain endothelial cell 912

description: Brain endothelial cell 912


title: Brain endothelial cell 926

description: Brain endothelial cell 926


title: Brain endothelial cell 913

description: Brain endothelial cell 913


title: normal lung tissue lncRNAs 1

description: lncRNA expression data from Homo sapiens lung 1


title: Brain endothelial cell 927

description: Brain endothelial cell 927


title: Brain endothelial cell 910

description: Brain endothelial cell 910


title: Brain endothelial cell 911

description: Brain endothelial cell 911


title: Brain endothelial cell 930

description: Brain endothelial cell 930


title: Brain endothelial cell 908

description: Brain endothelial cell 908


title: Brain endothelial cell 916

description: Brain endothelial cell 916


title: Brain endothelial cell 906

description: Brain endothelial cell 906


title: Brain endothelial cell 905

description: Brain endothelial cell 905


title: Brain endothelial cell 907

description: Brain endothelial cell 907


title: Brain endothelial cell 904

description: Brain endothelial cell 904


title: Brain endothelial cell 901

description: Brain endothelial cell 901


title: Brain endothelial cell 902

description: Brain endothelial cell 902


title: Brain endothelial cell 892

description: Brain endothelial cell 892


title: Brain endothelial cell 894

description: Brain endothelial cell 894


title: Brain endothelial cell 896

description: Brain endothelial cell 896


title: Brain endothelial cell 898

description: Brain endothelial cell 898


title: Brain endothelial cell 897

description: Brain endothelial cell 897


title: Brain endothelial cell 895

description: Brain endothelial cell 895


title: Brain endothelial cell 899

description: Brain endothelial cell 899


title: Brain endothelial cell 903

description: Brain endothelial cell 903


title: Brain endothelial cell 891

description: Brain endothelial cell 891


title: Brain endothelial cell 890

description: Brain endothelial cell 890


title: Brain endothelial cell 886

description: Brain endothelial cell 886


title: Brain endothelial cell 887

description: Brain endothelial cell 887


title: Brain endothelial cell 888

description: Brain endothelial cell 888


title: Brain endothelial cell 915

description: Brain endothelial cell 915


title: Brain endothelial cell 909

description: Brain endothelial cell 909


title: Brain endothelial cell 885

description: Brain endothelial cell 885


title: Brain endothelial cell 900

description: Brain endothelial cell 900


title: Brain endothelial cell 884

description: Brain endothelial cell 884


title: Brain endothelial cell 883

description: Brain endothelial cell 883


title: Brain endothelial cell 893

description: Brain endothelial cell 893


title: CAMSC_OM03a


title: Brain endothelial cell 881

description: Brain endothelial cell 881


title: Brain endothelial cell 882

description: Brain endothelial cell 882


title: Brain endothelial cell 879

description: Brain endothelial cell 879


title: Brain endothelial cell 877

description: Brain endothelial cell 877


title: Brain endothelial cell 876

description: Brain endothelial cell 876


title: Brain endothelial cell 869

description: Brain endothelial cell 869


title: Brain endothelial cell 874

description: Brain endothelial cell 874


title: Brain endothelial cell 871

description: Brain endothelial cell 871


title: Brain endothelial cell 872

description: Brain endothelial cell 872


title: Brain endothelial cell 868

description: Brain endothelial cell 868


title: Brain endothelial cell 866

description: Brain endothelial cell 866


title: Brain endothelial cell 875

description: Brain endothelial cell 875


title: Brain endothelial cell 867

description: Brain endothelial cell 867


title: Brain endothelial cell 862

description: Brain endothelial cell 862


title: Brain endothelial cell 865

description: Brain endothelial cell 865


title: Brain endothelial cell 864

description: Brain endothelial cell 864


title: Brain endothelial cell 863

description: Brain endothelial cell 863


title: Brain endothelial cell 873

description: Brain endothelial cell 873


title: Brain endothelial cell 878

description: Brain endothelial cell 878


title: Brain endothelial cell 856

description: Brain endothelial cell 856


title: Brain endothelial cell 858

description: Brain endothelial cell 858


title: Brain endothelial cell 859

description: Brain endothelial cell 859


title: Brain endothelial cell 857

description: Brain endothelial cell 857


title: Brain endothelial cell 880

description: Brain endothelial cell 880


title: Brain endothelial cell 855

description: Brain endothelial cell 855


title: Brain endothelial cell 852

description: Brain endothelial cell 852


title: Brain endothelial cell 851

description: Brain endothelial cell 851


title: Brain endothelial cell 847

description: Brain endothelial cell 847


title: Brain endothelial cell 844

description: Brain endothelial cell 844


title: Brain endothelial cell 845

description: Brain endothelial cell 845


title: Brain endothelial cell 846

description: Brain endothelial cell 846


title: Brain endothelial cell 843

description: Brain endothelial cell 843


title: Brain endothelial cell 850

description: Brain endothelial cell 850


title: Brain endothelial cell 861

description: Brain endothelial cell 861


title: Brain endothelial cell 841

description: Brain endothelial cell 841


title: Brain endothelial cell 842

description: Brain endothelial cell 842


title: Brain endothelial cell 840

description: Brain endothelial cell 840


title: Brain endothelial cell 839

description: Brain endothelial cell 839


title: Brain endothelial cell 854

description: Brain endothelial cell 854


title: Brain endothelial cell 836

description: Brain endothelial cell 836


title: Brain endothelial cell 838

description: Brain endothelial cell 838


title: Brain endothelial cell 853

description: Brain endothelial cell 853


title: Brain endothelial cell 860

description: Brain endothelial cell 860


title: Brain endothelial cell 833

description: Brain endothelial cell 833


title: Brain endothelial cell 834

description: Brain endothelial cell 834


title: Brain endothelial cell 837

description: Brain endothelial cell 837


title: Brain endothelial cell 835

description: Brain endothelial cell 835


title: Brain endothelial cell 832

description: Brain endothelial cell 832


title: Brain endothelial cell 831

description: Brain endothelial cell 831


title: Brain endothelial cell 830

description: Brain endothelial cell 830


title: Brain endothelial cell 870

description: Brain endothelial cell 870


title: Brain endothelial cell 849

description: Brain endothelial cell 849


title: Brain endothelial cell 829

description: Brain endothelial cell 829


title: Brain endothelial cell 848

description: Brain endothelial cell 848


title: Brain endothelial cell 828

description: Brain endothelial cell 828


title: Brain endothelial cell 825

description: Brain endothelial cell 825


title: Brain endothelial cell 827

description: Brain endothelial cell 827


title: Brain endothelial cell 826

description: Brain endothelial cell 826


title: Brain endothelial cell 818

description: Brain endothelial cell 818


title: Brain endothelial cell 821

description: Brain endothelial cell 821


title: Brain endothelial cell 820

description: Brain endothelial cell 820


title: Brain endothelial cell 819

description: Brain endothelial cell 819


title: Brain endothelial cell 823

description: Brain endothelial cell 823


title: Brain endothelial cell 822

description: Brain endothelial cell 822


title: Brain endothelial cell 815

description: Brain endothelial cell 815


title: Brain endothelial cell 817

description: Brain endothelial cell 817


title: Brain endothelial cell 810

description: Brain endothelial cell 810


title: Brain endothelial cell 816

description: Brain endothelial cell 816


title: Brain endothelial cell 814

description: Brain endothelial cell 814


title: Brain endothelial cell 812

description: Brain endothelial cell 812


title: Brain endothelial cell 809

description: Brain endothelial cell 809


title: Brain endothelial cell 813

description: Brain endothelial cell 813


title: Brain endothelial cell 808

description: Brain endothelial cell 808


title: Brain endothelial cell 805

description: Brain endothelial cell 805


title: Brain endothelial cell 803

description: Brain endothelial cell 803


title: Brain endothelial cell 811

description: Brain endothelial cell 811


title: Brain endothelial cell 801

description: Brain endothelial cell 801


title: Brain endothelial cell 802

description: Brain endothelial cell 802


title: Brain endothelial cell 824

description: Brain endothelial cell 824


title: Brain endothelial cell 804

description: Brain endothelial cell 804


title: Brain endothelial cell 798

description: Brain endothelial cell 798


title: Brain endothelial cell 797

description: Brain endothelial cell 797


title: Brain endothelial cell 807

description: Brain endothelial cell 807


title: Brain endothelial cell 806

description: Brain endothelial cell 806


title: Brain endothelial cell 794

description: Brain endothelial cell 794


title: Brain endothelial cell 796

description: Brain endothelial cell 796


title: Brain endothelial cell 790

description: Brain endothelial cell 790


title: Brain endothelial cell 788

description: Brain endothelial cell 788


title: Brain endothelial cell 786

description: Brain endothelial cell 786


title: Brain endothelial cell 783

description: Brain endothelial cell 783


title: Brain endothelial cell 785

description: Brain endothelial cell 785


title: Brain endothelial cell 792

description: Brain endothelial cell 792


title: Brain endothelial cell 784

description: Brain endothelial cell 784


title: Brain endothelial cell 780

description: Brain endothelial cell 780


title: Brain endothelial cell 781

description: Brain endothelial cell 781


title: Brain endothelial cell 800

description: Brain endothelial cell 800


title: Brain endothelial cell 782

description: Brain endothelial cell 782


title: Brain endothelial cell 776

description: Brain endothelial cell 776


title: Brain endothelial cell 799

description: Brain endothelial cell 799


title: Brain endothelial cell 789

description: Brain endothelial cell 789


title: Brain endothelial cell 779

description: Brain endothelial cell 779


title: Brain endothelial cell 778

description: Brain endothelial cell 778


title: Brain endothelial cell 777

description: Brain endothelial cell 777


title: Brain endothelial cell 925

description: Brain endothelial cell 925


title: Brain endothelial cell 795

description: Brain endothelial cell 795


title: Brain endothelial cell 793

description: Brain endothelial cell 793


title: Brain endothelial cell 775

description: Brain endothelial cell 775


title: Brain endothelial cell 774

description: Brain endothelial cell 774


title: Brain endothelial cell 772

description: Brain endothelial cell 772


title: Brain endothelial cell 773

description: Brain endothelial cell 773


title: Brain endothelial cell 929

description: Brain endothelial cell 929


title: Brain endothelial cell 791

description: Brain endothelial cell 791


title: Brain endothelial cell 769

description: Brain endothelial cell 769


title: Brain endothelial cell 770

description: Brain endothelial cell 770


title: Brain endothelial cell 767

description: Brain endothelial cell 767


title: Brain endothelial cell 766

description: Brain endothelial cell 766


title: Brain endothelial cell 768

description: Brain endothelial cell 768


title: Brain endothelial cell 764

description: Brain endothelial cell 764


title: Brain endothelial cell 765

description: Brain endothelial cell 765


title: Brain endothelial cell 758

description: Brain endothelial cell 758


title: Brain endothelial cell 761

description: Brain endothelial cell 761


title: Brain endothelial cell 759

description: Brain endothelial cell 759


title: Brain endothelial cell 760

description: Brain endothelial cell 760


title: Brain endothelial cell 753

description: Brain endothelial cell 753


title: Brain endothelial cell 762

description: Brain endothelial cell 762


title: Brain endothelial cell 763

description: Brain endothelial cell 763


title: Brain endothelial cell 756

description: Brain endothelial cell 756


title: Brain endothelial cell 757

description: Brain endothelial cell 757


title: Brain endothelial cell 787

description: Brain endothelial cell 787


title: Brain endothelial cell 754

description: Brain endothelial cell 754


title: Brain endothelial cell 752

description: Brain endothelial cell 752


title: Brain endothelial cell 771

description: Brain endothelial cell 771


title: Brain endothelial cell 751

description: Brain endothelial cell 751


title: Brain endothelial cell 749

description: Brain endothelial cell 749


title: Brain endothelial cell 748

description: Brain endothelial cell 748


title: Brain endothelial cell 755

description: Brain endothelial cell 755


title: Brain endothelial cell 745

description: Brain endothelial cell 745


title: Brain endothelial cell 747

description: Brain endothelial cell 747


title: Brain endothelial cell 746

description: Brain endothelial cell 746


title: Brain endothelial cell 750

description: Brain endothelial cell 750


title: Brain endothelial cell 744

description: Brain endothelial cell 744


title: Brain endothelial cell 889

description: Brain endothelial cell 889


title: Brain endothelial cell 742

description: Brain endothelial cell 742


title: Brain endothelial cell 743

description: Brain endothelial cell 743


title: Brain endothelial cell 740

description: Brain endothelial cell 740


title: Brain endothelial cell 739

description: Brain endothelial cell 739


title: Brain endothelial cell 738

description: Brain endothelial cell 738


title: Brain endothelial cell 736

description: Brain endothelial cell 736


title: Brain endothelial cell 734

description: Brain endothelial cell 734


title: Brain endothelial cell 737

description: Brain endothelial cell 737


title: Brain endothelial cell 741

description: Brain endothelial cell 741


title: Brain endothelial cell 735

description: Brain endothelial cell 735


title: Brain endothelial cell 730

description: Brain endothelial cell 730


title: Brain endothelial cell 731

description: Brain endothelial cell 731


title: Brain endothelial cell 727

description: Brain endothelial cell 727


title: Brain endothelial cell 728

description: Brain endothelial cell 728


title: Brain endothelial cell 726

description: Brain endothelial cell 726


title: Brain endothelial cell 729

description: Brain endothelial cell 729


title: Brain endothelial cell 732

description: Brain endothelial cell 732


title: Brain endothelial cell 725

description: Brain endothelial cell 725


title: Brain endothelial cell 723

description: Brain endothelial cell 723


title: Brain endothelial cell 721

description: Brain endothelial cell 721


title: Brain endothelial cell 724

description: Brain endothelial cell 724


title: Brain endothelial cell 718

description: Brain endothelial cell 718


title: Brain endothelial cell 716

description: Brain endothelial cell 716


title: Brain endothelial cell 722

description: Brain endothelial cell 722


title: Brain endothelial cell 717

description: Brain endothelial cell 717


title: Brain endothelial cell 733

description: Brain endothelial cell 733


title: Brain endothelial cell 715

description: Brain endothelial cell 715


title: Brain endothelial cell 714

description: Brain endothelial cell 714


title: Brain endothelial cell 713

description: Brain endothelial cell 713


title: Brain endothelial cell 711

description: Brain endothelial cell 711


title: Brain endothelial cell 712

description: Brain endothelial cell 712


title: Brain endothelial cell 708

description: Brain endothelial cell 708


title: Brain endothelial cell 709

description: Brain endothelial cell 709


title: Brain endothelial cell 707

description: Brain endothelial cell 707


title: Brain endothelial cell 706

description: Brain endothelial cell 706


title: Brain endothelial cell 720

description: Brain endothelial cell 720


title: Brain endothelial cell 699

description: Brain endothelial cell 699


title: Brain endothelial cell 697

description: Brain endothelial cell 697


title: Brain endothelial cell 700

description: Brain endothelial cell 700


title: Brain endothelial cell 698

description: Brain endothelial cell 698


title: Brain endothelial cell 701

description: Brain endothelial cell 701


title: Brain endothelial cell 703

description: Brain endothelial cell 703


title: Brain endothelial cell 710

description: Brain endothelial cell 710


title: Brain endothelial cell 694

description: Brain endothelial cell 694


title: Brain endothelial cell 696

description: Brain endothelial cell 696


title: Brain endothelial cell 695

description: Brain endothelial cell 695


title: Brain endothelial cell 705

description: Brain endothelial cell 705


title: Brain endothelial cell 719

description: Brain endothelial cell 719


title: Brain endothelial cell 693

description: Brain endothelial cell 693


title: Brain endothelial cell 692

description: Brain endothelial cell 692


title: Brain endothelial cell 691

description: Brain endothelial cell 691


title: Brain endothelial cell 690

description: Brain endothelial cell 690


title: Brain endothelial cell 688

description: Brain endothelial cell 688


title: Brain endothelial cell 687

description: Brain endothelial cell 687


title: Brain endothelial cell 689

description: Brain endothelial cell 689


title: Brain endothelial cell 685

description: Brain endothelial cell 685


title: Brain endothelial cell 684

description: Brain endothelial cell 684


title: Brain endothelial cell 683

description: Brain endothelial cell 683


title: Brain endothelial cell 704

description: Brain endothelial cell 704


title: Brain endothelial cell 702

description: Brain endothelial cell 702


title: Brain endothelial cell 681

description: Brain endothelial cell 681


title: Brain endothelial cell 680

description: Brain endothelial cell 680


title: Brain endothelial cell 679

description: Brain endothelial cell 679


title: Brain endothelial cell 676

description: Brain endothelial cell 676


title: Brain endothelial cell 674

description: Brain endothelial cell 674


title: Brain endothelial cell 673

description: Brain endothelial cell 673


title: Brain endothelial cell 671

description: Brain endothelial cell 671


title: Brain endothelial cell 682

description: Brain endothelial cell 682


title: Brain endothelial cell 668

description: Brain endothelial cell 668


title: Brain endothelial cell 669

description: Brain endothelial cell 669


title: Brain endothelial cell 678

description: Brain endothelial cell 678


title: Brain endothelial cell 670

description: Brain endothelial cell 670


title: Brain endothelial cell 667

description: Brain endothelial cell 667


title: Brain endothelial cell 665

description: Brain endothelial cell 665


title: Brain endothelial cell 666

description: Brain endothelial cell 666


title: Brain endothelial cell 686

description: Brain endothelial cell 686


title: Brain endothelial cell 664

description: Brain endothelial cell 664


title: Brain endothelial cell 677

description: Brain endothelial cell 677


title: Brain endothelial cell 675

description: Brain endothelial cell 675


title: Brain endothelial cell 661

description: Brain endothelial cell 661


title: Brain endothelial cell 660

description: Brain endothelial cell 660


title: Brain endothelial cell 659

description: Brain endothelial cell 659


title: Brain endothelial cell 657

description: Brain endothelial cell 657


title: Brain endothelial cell 663

description: Brain endothelial cell 663


title: Brain endothelial cell 656

description: Brain endothelial cell 656


title: Brain endothelial cell 655

description: Brain endothelial cell 655


title: Brain endothelial cell 672

description: Brain endothelial cell 672


title: Brain endothelial cell 654

description: Brain endothelial cell 654


title: Brain endothelial cell 652

description: Brain endothelial cell 652


title: Brain endothelial cell 653

description: Brain endothelial cell 653


title: Brain endothelial cell 651

description: Brain endothelial cell 651


title: Brain endothelial cell 649

description: Brain endothelial cell 649


title: Brain endothelial cell 650

description: Brain endothelial cell 650


title: Brain endothelial cell 648

description: Brain endothelial cell 648


title: Brain endothelial cell 646

description: Brain endothelial cell 646


title: Brain endothelial cell 662

description: Brain endothelial cell 662


title: Brain endothelial cell 645

description: Brain endothelial cell 645


title: Brain endothelial cell 644

description: Brain endothelial cell 644


title: Brain endothelial cell 641

description: Brain endothelial cell 641


title: Brain endothelial cell 642

description: Brain endothelial cell 642


title: Brain endothelial cell 639

description: Brain endothelial cell 639


title: Brain endothelial cell 643

description: Brain endothelial cell 643


title: Brain endothelial cell 640

description: Brain endothelial cell 640


title: Brain endothelial cell 658

description: Brain endothelial cell 658


title: Brain endothelial cell 638

description: Brain endothelial cell 638


title: Brain endothelial cell 636

description: Brain endothelial cell 636


title: Brain endothelial cell 634

description: Brain endothelial cell 634


title: Brain endothelial cell 633

description: Brain endothelial cell 633


title: Brain endothelial cell 635

description: Brain endothelial cell 635


title: Brain endothelial cell 631

description: Brain endothelial cell 631


title: Brain endothelial cell 632

description: Brain endothelial cell 632


title: Brain endothelial cell 630

description: Brain endothelial cell 630


title: Brain endothelial cell 628

description: Brain endothelial cell 628


title: Brain endothelial cell 637

description: Brain endothelial cell 637


title: Brain endothelial cell 627

description: Brain endothelial cell 627


title: Brain endothelial cell 626

description: Brain endothelial cell 626


title: Brain endothelial cell 625

description: Brain endothelial cell 625


title: Brain endothelial cell 624

description: Brain endothelial cell 624


title: Brain endothelial cell 621

description: Brain endothelial cell 621


title: Brain endothelial cell 622

description: Brain endothelial cell 622


title: Brain endothelial cell 647

description: Brain endothelial cell 647


title: Brain endothelial cell 619

description: Brain endothelial cell 619


title: Brain endothelial cell 620

description: Brain endothelial cell 620


title: Brain endothelial cell 618

description: Brain endothelial cell 618


title: Brain endothelial cell 616

description: Brain endothelial cell 616


title: Brain endothelial cell 611

description: Brain endothelial cell 611


title: Brain endothelial cell 617

description: Brain endothelial cell 617


title: Brain endothelial cell 612

description: Brain endothelial cell 612


title: Brain endothelial cell 610

description: Brain endothelial cell 610


title: Brain endothelial cell 609

description: Brain endothelial cell 609


title: Brain endothelial cell 608

description: Brain endothelial cell 608


title: Brain endothelial cell 613

description: Brain endothelial cell 613


title: Brain endothelial cell 607

description: Brain endothelial cell 607


title: Brain endothelial cell 605

description: Brain endothelial cell 605


title: Brain endothelial cell 604

description: Brain endothelial cell 604


title: Brain endothelial cell 603

description: Brain endothelial cell 603


title: Brain endothelial cell 606

description: Brain endothelial cell 606


title: Brain endothelial cell 602

description: Brain endothelial cell 602


title: Brain endothelial cell 601

description: Brain endothelial cell 601


title: Brain endothelial cell 600

description: Brain endothelial cell 600


title: Brain endothelial cell 599

description: Brain endothelial cell 599


title: Brain endothelial cell 598

description: Brain endothelial cell 598


title: Brain endothelial cell 623

description: Brain endothelial cell 623


title: Brain endothelial cell 597

description: Brain endothelial cell 597


title: Brain endothelial cell 614

description: Brain endothelial cell 614


title: Brain endothelial cell 594

description: Brain endothelial cell 594


title: Brain endothelial cell 595

description: Brain endothelial cell 595


title: Brain endothelial cell 629

description: Brain endothelial cell 629


title: Brain endothelial cell 593

description: Brain endothelial cell 593


title: Brain endothelial cell 592

description: Brain endothelial cell 592


title: Brain endothelial cell 589

description: Brain endothelial cell 589

value: Pdgfb ret/+


title: Brain endothelial cell 590

description: Brain endothelial cell 590


title: Brain endothelial cell 587

description: Brain endothelial cell 587


title: Brain endothelial cell 588

description: Brain endothelial cell 588


title: Brain endothelial cell 586

description: Brain endothelial cell 586


title: Brain endothelial cell 584

description: Brain endothelial cell 584


title: Brain endothelial cell 582

description: Brain endothelial cell 582


title: Brain endothelial cell 585

description: Brain endothelial cell 585


title: Brain endothelial cell 581

description: Brain endothelial cell 581


title: Brain endothelial cell 576

description: Brain endothelial cell 576


title: Brain endothelial cell 577

description: Brain endothelial cell 577


title: Brain endothelial cell 575

description: Brain endothelial cell 575


title: Brain endothelial cell 580

description: Brain endothelial cell 580


title: Brain endothelial cell 574

description: Brain endothelial cell 574


title: Brain endothelial cell 596

description: Brain endothelial cell 596


title: Brain endothelial cell 578

description: Brain endothelial cell 578


title: Brain endothelial cell 570

description: Brain endothelial cell 570


title: Brain endothelial cell 571

description: Brain endothelial cell 571


title: Brain endothelial cell 572

description: Brain endothelial cell 572


title: Brain endothelial cell 591

description: Brain endothelial cell 591


title: Brain endothelial cell 573

description: Brain endothelial cell 573


title: Brain endothelial cell 566

description: Brain endothelial cell 566


title: Brain endothelial cell 567

description: Brain endothelial cell 567


title: Brain endothelial cell 569

description: Brain endothelial cell 569


title: Brain endothelial cell 565

description: Brain endothelial cell 565


title: Brain endothelial cell 564

description: Brain endothelial cell 564


title: Brain endothelial cell 615

description: Brain endothelial cell 615


title: Brain endothelial cell 563

description: Brain endothelial cell 563


title: Brain endothelial cell 562

description: Brain endothelial cell 562


title: Brain endothelial cell 579

description: Brain endothelial cell 579


title: Brain endothelial cell 559

description: Brain endothelial cell 559


title: Brain endothelial cell 560

description: Brain endothelial cell 560


title: Brain endothelial cell 558

description: Brain endothelial cell 558


title: Brain endothelial cell 561

description: Brain endothelial cell 561


title: Brain endothelial cell 556

description: Brain endothelial cell 556


title: Brain endothelial cell 557

description: Brain endothelial cell 557


title: Brain endothelial cell 568

description: Brain endothelial cell 568


title: Brain endothelial cell 551

description: Brain endothelial cell 551


title: Brain endothelial cell 549

description: Brain endothelial cell 549


title: Brain endothelial cell 550

description: Brain endothelial cell 550


title: Brain endothelial cell 555

description: Brain endothelial cell 555


title: Brain endothelial cell 554

description: Brain endothelial cell 554


title: Brain endothelial cell 548

description: Brain endothelial cell 548


title: Brain endothelial cell 552

description: Brain endothelial cell 552


title: Brain endothelial cell 553

description: Brain endothelial cell 553


title: Brain endothelial cell 543

description: Brain endothelial cell 543


title: Brain endothelial cell 544

description: Brain endothelial cell 544


title: Brain endothelial cell 545

description: Brain endothelial cell 545


title: Brain endothelial cell 542

description: Brain endothelial cell 542


title: Brain endothelial cell 541

description: Brain endothelial cell 541


title: Brain endothelial cell 540

description: Brain endothelial cell 540


title: Brain endothelial cell 535

description: Brain endothelial cell 535


title: Brain endothelial cell 539

description: Brain endothelial cell 539


title: Brain endothelial cell 532

description: Brain endothelial cell 532


title: Brain endothelial cell 533

description: Brain endothelial cell 533


title: Brain endothelial cell 534

description: Brain endothelial cell 534


title: Brain endothelial cell 530

description: Brain endothelial cell 530


title: Brain endothelial cell 529

description: Brain endothelial cell 529


title: Brain endothelial cell 531

description: Brain endothelial cell 531


title: Brain endothelial cell 528

description: Brain endothelial cell 528


title: Brain endothelial cell 547

description: Brain endothelial cell 547


title: Brain endothelial cell 527

description: Brain endothelial cell 527


title: Brain endothelial cell 525

description: Brain endothelial cell 525


title: Brain endothelial cell 524

description: Brain endothelial cell 524


title: Brain endothelial cell 520

description: Brain endothelial cell 520


title: Brain endothelial cell 521

description: Brain endothelial cell 521


title: Brain endothelial cell 519

description: Brain endothelial cell 519


title: Brain endothelial cell 522

description: Brain endothelial cell 522


title: Brain endothelial cell 518

description: Brain endothelial cell 518


title: Brain endothelial cell 523

description: Brain endothelial cell 523


title: Brain endothelial cell 526

description: Brain endothelial cell 526


title: Brain endothelial cell 516

description: Brain endothelial cell 516


title: Brain endothelial cell 537

description: Brain endothelial cell 537


title: Brain endothelial cell 538

description: Brain endothelial cell 538


title: Brain endothelial cell 546

description: Brain endothelial cell 546


title: Brain endothelial cell 536

description: Brain endothelial cell 536


title: Brain endothelial cell 513

description: Brain endothelial cell 513


title: Brain endothelial cell 512

description: Brain endothelial cell 512


title: Brain endothelial cell 517

description: Brain endothelial cell 517


title: Brain endothelial cell 511

description: Brain endothelial cell 511


title: Brain endothelial cell 583

description: Brain endothelial cell 583


title: NESTED_S3

city: Little Rock

first: Stephanie

middle: D

last: Byrum

state: Arkansas

address: 501 Jack Stephens Dr, Jackson T. Stephens Bldg 4th floor

institute: University of Arkansas for Medical Sciences

description: We processed data using short_read_TA_counts from bioinformatics pipeline on (github).

data_processing:
Reads were trimmed using fastp v0.19.5
Alignment to reference using bwa v0.7.17-r1188
Filtering for reads at TA sites and counting using bedtools v2.25.0
for ONT samples: Basecalling using Guppy v3.4.5; alignment using minimap2 v2.17-r941
Genome_build: (chromosome: CP055225; cryptic plasmid: CP055226)
Supplementary_files_format_and_content: All processed data files are in the BedGraph format. They detail the location of detected transposon insertions and number of reads mapped to each inserton.

source_name: Bacteria

growth_protocol: TnSeq libraries were grown in rich media (Tryptic Soy broth) to either exponential or stationary phase with constant aeration and agitation at 37C

extract_protocol:
1 µg of sheared gDNA was subjected to the NEBNext® UltraTM II DNA Library Prep Kit for Illumina® (New England Biolabs, Ipswich, MA) protocol with key modifications to the PCR amplification step. Specifically, in the PCR15 and PCR25 samples the olj511 forward primer specific to the transposon inverted repeat (IR) (PMID: 29554137) and the NEBNext Indexed reverse primers obtained from NEBNext® Multiplex Oligos for Illumina® were used to amplify the transposon-genomic junctions and add the p5 and p7 illumina adaptors as well as a unique barcode to each sample by implementing either 15 or 25 PCR cycles respectively. The cycling conditions for this PCR were 98°C for 30 sec, 98°C for 10 sec followed by 65°C for 75 sec for 15 or 25 cycles, and 65°C for 5 min. In the NESTED method, the junctions were amplified via a nested PCR consisting of two reactions, similarly to previous reports (PMID: 29554137). Here, the olj510 forward primer (PMID: 29554137) specific to the transposon but upstream to the inverted repeat region and the NEBNext Indexed reverse primers obtained from NEBNext® Multiplex Oligos for Illumina® were used in the first PCR reaction. The cycling conditions for this PCR were 98°C for 30 sec, 98°C for 10 sec followed by 65°C for 75 sec for 25 cycles, and 65°C for 5 min. In the second PCR reaction, the forward olj511 inverted region-specific primer and the same reverse primers used in the previous reaction were used to enhance the specificity towards the transposon and add the p7 illumina adaptor via 15 PCR cycles. The cycling conditions for this reaction were 98°C for 30 sec, 98°C for 10 sec followed by 65°C for 75 sec for 15 cycles, and 65°C for 5 min. The quality of the libraries was then assessed via Agilent TapeStation (Santa Clara, CA) and quantitative real-time PCR (qRT-PCR) using the olj512 primer (PMID: 29554137) specific to the transposon terminal inverted repeat. The validated libraries were then sequenced with the custom sequencing primer olj512 (PMID: 29554137) using an Illumina HiSeq 2500, Single-End 100, at the TUFTS University Core Facility. Each flow cell was loaded with six total multiplexed libraries. Thus, six samples prepared by each of the PCR methods (PCR15, PCR25 and NESTED) were loaded onto a separate flow cell.
genomic DNA was extracted using the NucleoBond HMW DNA kit
Detailed in 'SAMPLES'

tag: growth phase

value: stationary

tag: number of pcr cycles

tag: sequencing platform

value: Illumina HiSeq


title: NESTED_S1


title: NESTED_E2

value: exponential


title: NESTED_S2


title: Brain endothelial cell 510

description: Brain endothelial cell 510

tag: age

tag: genotype


title: NESTED_E3


title: Brain endothelial cell 508

description: Brain endothelial cell 508


title: Brain endothelial cell 515

description: Brain endothelial cell 515


title: Brain endothelial cell 514

description: Brain endothelial cell 514


title: NESTED_E1


title: Brain endothelial cell 503

description: Brain endothelial cell 503


title: Brain endothelial cell 505

description: Brain endothelial cell 505


title: Brain endothelial cell 502

description: Brain endothelial cell 502


title: Brain endothelial cell 504

description: Brain endothelial cell 504


title: Brain endothelial cell 501

description: Brain endothelial cell 501


title: PCR25_E2


title: PCR25_S1


title: PCR25_E1


title: Brain endothelial cell 506

description: Brain endothelial cell 506


title: PCR15_S2


title: Brain endothelial cell 507

description: Brain endothelial cell 507


title: PCR15_S3


title: Brain endothelial cell 500

description: Brain endothelial cell 500


title: PCR25_E3


title: Brain endothelial cell 497

description: Brain endothelial cell 497


title: Brain endothelial cell 509

description: Brain endothelial cell 509


title: Brain endothelial cell 496

description: Brain endothelial cell 496


title: PCR15_S1


title: PCR15_E3


title: PCR15_E2


title: Brain endothelial cell 495

description: Brain endothelial cell 495


title: Brain endothelial cell 498

description: Brain endothelial cell 498


title: PCR25_S3


title: Brain endothelial cell 494

description: Brain endothelial cell 494


title: PCR25_S2


title: Brain endothelial cell 493

description: Brain endothelial cell 493


title: Brain endothelial cell 499

description: Brain endothelial cell 499


title: Brain endothelial cell 491

description: Brain endothelial cell 491


title: Brain endothelial cell 489

description: Brain endothelial cell 489


title: A3 blood NKG2a/chighCD16+

city: Paris

first: Rachel

last: Legendre

address: 28, rue du docteur Roux

department: Research and Resource Center for Scientific Informatics

institute: Institut Pasteur

description:
African green monkeys (Caribbean Chlorocebus sabaeus, AGM)
PB-2-101

data_processing:
Reads were cleaned of adapter sequences and low-quality sequences using cutadapt version 1.11.Only sequences at least 25 nt in length were considered for further analysis.
STAR version 2.5.0a, with default parameters, was used for alignment on the reference genome
Genes were counted using featureCounts version 1.4.6-p3  from Subreads package (parameters: -t gene -g ID -s 1).
Count data were analyzed using R version 3.4.3  and the Bioconductor package DESeq2 version 1.18.1. The normalization and dispersion estimation were performed with DESeq2 using the default parameters and statistical tests for differential expression were performed applying the independent filtering algorithm. A generalized linear model including the monkey identifier as blocking factor was set in order to test for the differential expression between the biological conditions (à completer/modifier en function des résultats exploités). For each pairwise comparison, raw p-values were adjusted for multiple testing according to the Benjamini and Hochberg (BH) procedure and genes with an adjusted p-value lower than 0.05 were considered differentially expressed.
Genome_build: chlorocebus sabaeus, from Ensembl release 90
Supplementary_files_format_and_content: Matrix from DESseq2

organism: Chlorocebus sabaeus

source_name: blood node NK cell subset from  SIV chronically infected AGM (SV101)

extract_protocol:
Cells were directly collected in a lysis buffer (RLT plus) containing TCEP. RNA was isolated using the RNeasy Plus® Micro Kit (74034, Qiagen). RNA integrity was verified with the Agilent Bioanalyzer. RNA from the different NK subsets were treated for library preparation using the Truseq Stranded mRNA sample preparation kit (Illumina, San Diego, California) according to manufacturer’s instructions.
Directional libraries were prepared using the Smarter Stranded Total RNA-Seq kit- Pico Input Mammalian following the manufacturer’s instructions (Clontech 635005). The quality of all libraries was checked with the DNA-1000 kit (Agilent) on a 2100 Bioanalyzer and quantification was performed with Quant-It assays on a Qubit 3.0 fluorometer (Invitrogen).  Clusters were generated for the resulting libraries, with Illumina HiSeq SR Cluster Kit v4 reagents. Sequencing was performed with the Illumina HiSeq 2500 system and HiSeq SBS kit v4 reagents. Runs were carried out over 100 cycles, including seven indexing cycles, to obtain 100-bp single-end reads. Sequencing data were processed with Illumina Pipeline software (Casava version 1.9).

treatment_protocol: A 8-color panels was used to phenotype, surface stain, and sort NK cells from blood and pLN from 3 chronically infected AGM. Cells were first thawed in 20% fetal bovine serum-containing media supplemented with Benzonase nuclease, and counts and viabilities were performed (life Technologies). Cells were washed and stained with Aqua Live/Dead stain (Molecular Probes). Cells were washed and blocked using normal mouse IgG (Caltag). For the NKG2a/cHIGH/low CD16+/- and CXCR5+ phenotyping panel, PBMC and pLN were surface-stained for CD3 (SP34.2, dilution 1/10, BD), CD8 (BW135/80, dilution 1/20, Miltenyi), CD16 (3G8, dilution 1/20, Beckman Coulter, Inc.), NKG2a/c (Z199, dilution 1/20, Beckman Coulter, Inc.), CD20 (2H7, dilution 1/20, Biolegend), CD14 (M5E2,dilution 1/25, BD) and CXCR5(MU5BEE, dilution 1:20, eBioscience™). Post surface staining cells were washed, filtered, and CXCR5+, NKG2a/clowCD16-, NKG2a/cHIGHCD16-, NKG2a/clowCD16+ and NKG2a/cHIGHCD16+ NK cells sorted on a FACS ARIA II (BD Biosciences).

tag: time post infection

value: Blood

value: NK cells

tag: subset

value: NKG2a/c HIGH CD16 pos


title: A2 blood NKG2a/clowCD16+

description:
African green monkeys (Caribbean Chlorocebus sabaeus, AGM)
PB-3-093

source_name: blood  NK cell subset from  SIV chronically infected AGM (SV093)

value: NKG2a/c LOW CD16pos


title: Brain endothelial cell 490

description: Brain endothelial cell 490

value: brain


title: A3 blood NKG2a/cHighCD16-

description:
African green monkeys (Caribbean Chlorocebus sabaeus, AGM)
PB-1-101

value: NKG2a/c HIGH CD16 neg


title: A2 blood NKG2a/cHighCD16-

description:
African green monkeys (Caribbean Chlorocebus sabaeus, AGM)
PB-1-093


title: A1 blood NKG2a/cHighCD16-

description:
African green monkeys (Caribbean Chlorocebus sabaeus, AGM)
PB-1-083

source_name: blood NK cell subset from  SIV chronically infected AGM (SV083)


title: Brain endothelial cell 484

description: Brain endothelial cell 484

value: adult mice


title: Brain endothelial cell 487

description: Brain endothelial cell 487

value: endothelial cell


title: A3 blood NKG2a/clowCD16+

description:
African green monkeys (Caribbean Chlorocebus sabaeus, AGM)
PB-3-101


title: Brain endothelial cell 488

description: Brain endothelial cell 488


title: Brain endothelial cell 483

description: Brain endothelial cell 483


title: A2 blood NKG2a/chighCD16+

description:
African green monkeys (Caribbean Chlorocebus sabaeus, AGM)
PB-2-093


title: A3 pLN X5+

description:
African green monkeys (Caribbean Chlorocebus sabaeus, AGM)
LN-C-101

source_name: lymph node NK cell subset from  SIV chronically infected AGM (SV101)

value: axillary lymph node

value: CXCR5 pos


title: A3 blood NKG2a/clowCD16-

description:
African green monkeys (Caribbean Chlorocebus sabaeus, AGM)
PB-0-101

value: NKG2a/c LOW CD16 neg


title: A1 blood NKG2a/clowCD16-

description:
African green monkeys (Caribbean Chlorocebus sabaeus, AGM)
PB-0-083


title: Brain endothelial cell 485

description: Brain endothelial cell 485


title: PCR15_E1


title: Brain endothelial cell 492

description: Brain endothelial cell 492


title: Brain endothelial cell 481

description: Brain endothelial cell 481


title: A2 pLN X5+

description:
African green monkeys (Caribbean Chlorocebus sabaeus, AGM)
LN-C-093

source_name: lymph node NK cell subset from  SIV chronically infected AGM (SV093)


title: A1 pLN X5+

description:
African green monkeys (Caribbean Chlorocebus sabaeus, AGM)
LN-C-083

source_name: lymph node NK cell subset from  SIV chronically infected AGM (SV083)


title: A1 blood NKG2a/clowCD16+

description:
African green monkeys (Caribbean Chlorocebus sabaeus, AGM)
PB-3-083


title: A1 blood NKG2a/chighCD16+

description:
African green monkeys (Caribbean Chlorocebus sabaeus, AGM)
PB-2-083


title: Brain endothelial cell 486

description: Brain endothelial cell 486


title: Brain endothelial cell 480

description: Brain endothelial cell 480


title: Brain endothelial cell 482

description: Brain endothelial cell 482


title: A2 blood NKG2a/clowCD16-

description:
African green monkeys (Caribbean Chlorocebus sabaeus, AGM)
PB-0-093


title: Brain endothelial cell 478

description: Brain endothelial cell 478


title: Brain endothelial cell 479

description: Brain endothelial cell 479


title: A3 pLN NKG2a/clowCD16+

description:
African green monkeys (Caribbean Chlorocebus sabaeus, AGM)
LN-23-101


title: Brain endothelial cell 477

description: Brain endothelial cell 477


title: A1 pLN NKG2a/clowCD16+

description:
African green monkeys (Caribbean Chlorocebus sabaeus, AGM)
LN-23-083


title: Brain endothelial cell 476

description: Brain endothelial cell 476


title: A2 pLN NKG2a/clowCD16+

description:
African green monkeys (Caribbean Chlorocebus sabaeus, AGM)
LN-23-093


title: A3 pLN NKG2a/cHighCD16-

description:
African green monkeys (Caribbean Chlorocebus sabaeus, AGM)
LN-1-101


title: A2 pLN NKG2a/cHighCD16-

description:
African green monkeys (Caribbean Chlorocebus sabaeus, AGM)
LN-1-093


title: Brain endothelial cell 475

description: Brain endothelial cell 475


title: A2 pLN NKG2a/clowCD16-

description:
African green monkeys (Caribbean Chlorocebus sabaeus, AGM)
LN-0-093


title: A1 pLN NKG2a/clowCD16-

description:
African green monkeys (Caribbean Chlorocebus sabaeus, AGM)
LN-0-083


title: Brain endothelial cell 470

description: Brain endothelial cell 470


title: A1 pLN NKG2a/cHighCD16-

description:
African green monkeys (Caribbean Chlorocebus sabaeus, AGM)
LN-1-083


title: Brain endothelial cell 471

description: Brain endothelial cell 471


title: A3 pLN NKG2a/clowCD16-

description:
African green monkeys (Caribbean Chlorocebus sabaeus, AGM)
LN-0-101


title: Brain endothelial cell 473

description: Brain endothelial cell 473


title: Brain endothelial cell 472

description: Brain endothelial cell 472