title: Rat 7 Adipose Quantseq

description:
Quantseq
S2.xlsx
S1.xlsx


title: Rat 7 Liver Quantseq

status: Public on Sep 05 2020

type: SRA

city: Ames

first: Joe

last: Webb

state: IA

address: 2302 Osborn drive, 220 Mackay Hall

country: USA

institute: Iowa State University

description:
Quantseq
S2.xlsx
S1.xlsx

library_source: transcriptomic

data_processing:
Basecalls performed by the ISU DNA facility and data processing steps were followed according to the manufacturers guidelines here: https://www.lexogen.com/wp-content/uploads/2015/11/015UG009V0211_QuantSeq-Illumina.pdf
Briefly, fastq quality control tool FastQC was used to examine the quality of the sequencing run.
Next, adapters were trimmed using BBDUK and sequences were reanalyzed using FastQC
Reads were mapped to the RNO_6 genome using RNA STAR and read counts were simultaneously quantified using the --read-counts flag
Genome_build: RNO_6
Supplementary_files_format_and_content: mRNA DESEQ results.xlsx
Supplementary_files_format_and_content: mRNA Raw Reads.xlsx
Supplementary_files_format_and_content: microRNA DESEQ results.xlsx
Supplementary_files_format_and_content: microRNA Raw Reads.xlsx

molecule: total RNA

organism: Rattus norvegicus

source_name: Liver

extract_protocol:
Tissue samples were homogenized on ice and total RNA was extracted using a Lexogen SPLIT RNA Extraction kit following the manufacturers instructions.
Libraries were prepared according to Lexogens instructions accompanying the QuantSeq 3’ mRNA-Seq Library Prep Kit FWD for Illumina and small RNA sequencing kits. Briefly, the Quantseq kit uses total RNA as input, hence no prior poly(A) enrichment  or rRNA depletion is needed. Library generation starts with oligodT priming containing the  Illumina-specific Read 2 linker sequence.  After first strand synthesis the RNA is removed. Second strand synthesis is initiated by random priming and a DNA  polymerase. The random primer contains the Illumina-specific Read 1  linker sequence. At this step Unique Molecular Identifiers (UMIs)  can be introduced by exchanging the Second Strand Synthesis Mix 1  (SS1) from the standard QuantSeq FWD Kit with UMI Second Strand  Synthesis Mix (USS). No purification is required between first and second strand synthesis.  Second strand synthesis is followed by a magnetic bead-based  purification step rendering the protocol compatible with automation. During the library amplification step sequences required  for cluster generation are introduced. NGS reads are generated towards the poly(A) tail and directly  correspond to the mRNA sequence. To pinpoint the exact 3’ end,  Libraries were sequenced on the Illumina HiSeq 3000 following the manufacturer's protocols.
RNA-seq, miRNA-seq

treatment_protocol: Animals were fed their respective diets, either Whole Egg or Casein.

tag: animal number

tag: treatment

value: Whole Egg

tag: strain

value: ZDF


title: Rat 6 Adipose microRNA seq

description:
microRNA seq
S4.xlsx
S3.xlsx

source_name: Adipose


title: Rat 6 Kidney microRNA seq

description:
microRNA seq
S4.xlsx
S3.xlsx

source_name: Kidney


title: Rat 7 Brain Quantseq

description:
Quantseq
S2.xlsx
S1.xlsx

source_name: Brain


title: Rat 6 Liver microRNA seq

description:
microRNA seq
S4.xlsx
S3.xlsx


title: Rat 6 Brain microRNA seq

description:
microRNA seq
S4.xlsx
S3.xlsx


title: Rat 6 Kidney Quantseq

description:
Quantseq
S2.xlsx
S1.xlsx


title: Rat 6 Adipose Quantseq

description:
Quantseq
S2.xlsx
S1.xlsx


title: Rat 6 Liver Quantseq

description:
Quantseq
S2.xlsx
S1.xlsx


title: Rat 6 Brain Quantseq

description:
Quantseq
S2.xlsx
S1.xlsx


title: Rat 5 Kidney microRNA seq

description:
microRNA seq
S4.xlsx
S3.xlsx

value: Casein


title: Rat 5 Adipose microRNA seq

description:
microRNA seq
S4.xlsx
S3.xlsx


title: Rat 7 Kidney microRNA seq

description:
microRNA seq
S4.xlsx
S3.xlsx


title: Rat 5 Liver microRNA seq

description:
microRNA seq
S4.xlsx
S3.xlsx


title: Rat 7 Liver microRNA seq

description:
microRNA seq
S4.xlsx
S3.xlsx


title: Rat 5 Brain microRNA seq

description:
microRNA seq
S4.xlsx
S3.xlsx


title: Rat 5 Liver Quantseq

description:
Quantseq
S2.xlsx
S1.xlsx


title: Rat 5 Kidney Quantseq

description:
Quantseq
S2.xlsx
S1.xlsx


title: Rat 7 Brain microRNA seq

description:
microRNA seq
S4.xlsx
S3.xlsx


title: Rat 4 Adipose microRNA seq

description:
microRNA seq
S4.xlsx
S3.xlsx


title: Rat 4 Brain microRNA seq

description:
microRNA seq
S4.xlsx
S3.xlsx


title: Rat 4 Adipose Quantseq

description:
Quantseq
S2.xlsx
S1.xlsx


title: Rat 5 Brain Quantseq

description:
Quantseq
S2.xlsx
S1.xlsx


title: Rat 4 Brain Quantseq

description:
Quantseq
S2.xlsx
S1.xlsx


title: Rat 4 Kidney Quantseq

description:
Quantseq
S2.xlsx
S1.xlsx


title: Rat 4 Liver microRNA seq

description:
microRNA seq
S4.xlsx
S3.xlsx


title: Rat 4 Liver Quantseq

description:
Quantseq
S2.xlsx
S1.xlsx


title: Rat 3 Adipose microRNA seq

description:
microRNA seq
S4.xlsx
S3.xlsx


title: Rat 3 Liver microRNA seq

description:
microRNA seq
S4.xlsx
S3.xlsx


title: Rat 3 Kidney microRNA seq

description:
microRNA seq
S4.xlsx
S3.xlsx


title: Rat 3 Brain microRNA seq

description:
microRNA seq
S4.xlsx
S3.xlsx


title: Rat 3 Liver Quantseq

description:
Quantseq
S2.xlsx
S1.xlsx


title: Rat 3 Adipose Quantseq

description:
Quantseq
S2.xlsx
S1.xlsx


title: Rat 3 KIdney Quantseq

description:
Quantseq
S2.xlsx
S1.xlsx


title: Rat 5 Adipose Quantseq

description:
Quantseq
S2.xlsx
S1.xlsx


title: Rat 21 Liver Quantseq

description:
Quantseq
S2.xlsx
S1.xlsx

value: Lean


title: Rat 2 Kidney microRNA seq

description:
microRNA seq
S4.xlsx
S3.xlsx


title: Rat 2 Liver microRNA seq

description:
microRNA seq
S4.xlsx
S3.xlsx


title: Rat 3 Brain Quantseq

description:
Quantseq
S2.xlsx
S1.xlsx


title: Rat 2 Adipose Quantseq

description:
Quantseq
S2.xlsx
S1.xlsx


title: Rat 2 Adipose microRNA seq

description:
microRNA seq
S4.xlsx
S3.xlsx


title: Rat 4 Kidney microRNA seq

description:
microRNA seq
S4.xlsx
S3.xlsx


title: Rat 2 Brain microRNA seq

description:
microRNA seq
S4.xlsx
S3.xlsx


title: Rat 1 Adipose microRNA seq

description:
microRNA seq
S4.xlsx
S3.xlsx


title: Rat 2 Kidney Quantseq

description:
Quantseq
S2.xlsx
S1.xlsx


title: Rat 2 Liver Quantseq

description:
Quantseq
S2.xlsx
S1.xlsx


title: Rat 1 Kidney microRNA seq

description:
microRNA seq
S4.xlsx
S3.xlsx


title: Rat 2 Brain Quantseq

description:
Quantseq
S2.xlsx
S1.xlsx


title: Rat 1 Liver microRNA seq

description:
microRNA seq
S4.xlsx
S3.xlsx


title: Rat 1 Liver Quantseq

description:
Quantseq
S2.xlsx
S1.xlsx


title: Rat 1 Adipose Quantseq

description:
Quantseq
S2.xlsx
S1.xlsx


title: Rat 1 Brain Quantseq

description:
Quantseq
S2.xlsx
S1.xlsx


title: Liver-Crtc1 KO_1

city: Shenzhen

first: Zhihua

last: Wang

address: No. 12, Langshan Road, Xili Street, Nanshan District, Shenzhen

department: Shenzhen Key Laboratory of Cardiovascular Disease

country: China

institute: Fuwai Hospital Chinese Academy of Medical Sciences, Shenzhen

data_processing:
BGI used BGISEQ-500 platform for RNA-Seq
The raw data include low quality, contamination of joints, and high levels of unknown base n reads, which need to be removed before analysis to ensure the reliability of the results
The clean reads were align to the reference genome sequnence using HISAT
The clean reads were align to the reference genome sequnence using Bowtie2
Genome_build: NCBI, Mus_musculus, GCF_000001635.26_GRCm38.p6
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Mus musculus

growth_protocol: Mice were fed on a normal diet with 12 h of light ,12 h of darkness and adequate drinking water.

extract_protocol:
A piece of liver and eWAT were used to extracted RNA according to the manufacturer's instructions using Trizol reagent.
RNA libraries were prepared for sequencing according to manufacturer's instructions of Beijing Genomics Institution (BGI)

treatment_protocol: After fasting for 16 hours, the mice were sacrificed.

tag: tissue

value: Liver

tag: genotype

tag: age

value: 12 weeks


title: Liver-Crtc1 WT_1


title: eWAT-Crtc1 KO_1

source_name: epididymal white adipose tissue (eWAT)

value: epididymal white adipose tissue (eWAT)


title: eWAT-Crtc1 WT_1


title: eWAT-Crtc1 KO_2


title: eWAT-Crtc1 WT_2


title: Liver-Crtc1 KO_2


title: Rat 1 Brain microRNA seq

description:
microRNA seq
S4.xlsx
S3.xlsx


title: CEMBA180430_8B_3_CEMBA180430_8B_4_H8_ad008

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

library_source: genomic

data_processing:
Library strategy: snmC-seq2
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted mm10 reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column

molecule: genomic DNA

source_name: C57BL/6J Male P56 Mouse Brain

growth_protocol: All mice are C57BL/6J Male, brain dissected in P56

extract_protocol:
the brain of P56 male C57BL/6J mouse will be removed and cut into 600 microns thick coronal sections using a tissue matrix. Then each region will be microdissected from the coronal tissue sections based on identified landmarks and brain atlas coordinates, as defined in Allen brain atlas CCF3 (Avaliable at: http://atlas.brain-map.org). For each dissection region, the tissue from several littermate mice will be combined together into to separate replicate groups. The number of animals in a replicate depends on the size of the tissue. Nuclei preparation will be stained with the fluorescently labeled anti-NeuN body and nucleic acid stain Hoechst 33342.
Library prepared following protocol discribed in Luo, Chongyuan, Angeline Rivkin, Jingtian Zhou, Justin P. Sandoval, Laurie Kurihara, Jacinta Lucero, Rosa Castanon, et al. 2018. “Robust Single-Cell DNA Methylome Profiling with snmC-seq2.” Nature Communications 9 (1): 3824.

tag: brain region

value: SSp

tag: Sex

value: male


title: CEMBA180430_8B_3_CEMBA180430_8B_4_H8_ad002


title: CEMBA180430_8B_3_CEMBA180430_8B_4_H7_ad006


title: CEMBA180430_8B_3_CEMBA180430_8B_4_H7_ad001


title: CEMBA180430_8B_3_CEMBA180430_8B_4_H8_ad010


title: CEMBA180430_8B_3_CEMBA180430_8B_4_H9_ad006


title: CEMBA180430_8B_3_CEMBA180430_8B_4_H8_ad006


title: CEMBA180430_8B_3_CEMBA180430_8B_4_H9_ad008


title: Rat 1 Kidney Quantseq

description:
Quantseq
S2.xlsx
S1.xlsx


title: CEMBA180430_8B_3_CEMBA180430_8B_4_H8_ad001


title: CEMBA180430_8B_3_CEMBA180430_8B_4_H8_ad004


title: CEMBA180430_8B_3_CEMBA180430_8B_4_H9_ad004


title: CEMBA180430_8B_3_CEMBA180430_8B_4_H9_ad010


title: CEMBA180430_8B_3_CEMBA180430_8B_4_H7_ad002


title: CEMBA180430_8B_3_CEMBA180430_8B_4_H6_ad010


title: Liver-Crtc1 WT_2


title: CEMBA180430_8B_3_CEMBA180430_8B_4_H6_ad007


title: CEMBA180430_8B_3_CEMBA180430_8B_4_H6_ad006


title: CEMBA180430_8B_3_CEMBA180430_8B_4_H9_ad012


title: Rat 18 Liver Quantseq

description:
Quantseq
S2.xlsx
S1.xlsx


title: CEMBA180430_8B_3_CEMBA180430_8B_4_H7_ad004


title: CEMBA180430_8B_3_CEMBA180430_8B_4_H5_ad002


title: CEMBA180430_8B_3_CEMBA180430_8B_4_H7_ad007


title: CEMBA180430_8B_3_CEMBA180430_8B_4_H5_ad012


title: CEMBA180430_8B_3_CEMBA180430_8B_4_H5_ad001


title: CEMBA180430_8B_3_CEMBA180430_8B_4_H6_ad002


title: CEMBA180430_8B_3_CEMBA180430_8B_4_H6_ad012


title: CEMBA180430_8B_3_CEMBA180430_8B_4_H5_ad004


title: CEMBA180430_8B_3_CEMBA180430_8B_4_H4_ad008


title: CEMBA180430_8B_3_CEMBA180430_8B_4_H4_ad004


title: CEMBA180430_8B_3_CEMBA180430_8B_4_H4_ad002


title: CEMBA180430_8B_3_CEMBA180430_8B_4_H4_ad006


title: CEMBA180430_8B_3_CEMBA180430_8B_4_H3_ad001


title: CEMBA180430_8B_3_CEMBA180430_8B_4_H4_ad010


title: CEMBA180430_8B_3_CEMBA180430_8B_4_H3_ad007


title: CEMBA180430_8B_3_CEMBA180430_8B_4_H5_ad007


title: CEMBA180430_8B_3_CEMBA180430_8B_4_H3_ad004


title: CEMBA180430_8B_3_CEMBA180430_8B_4_H2_ad010


title: CEMBA180430_8B_3_CEMBA180430_8B_4_H3_ad002


title: CEMBA180430_8B_3_CEMBA180430_8B_4_H3_ad010


title: CEMBA180430_8B_3_CEMBA180430_8B_4_H4_ad012


title: CEMBA180430_8B_3_CEMBA180430_8B_4_H3_ad008


title: CEMBA180430_8B_3_CEMBA180430_8B_4_H2_ad001


title: CEMBA180430_8B_3_CEMBA180430_8B_4_H2_ad008


title: CEMBA180430_8B_3_CEMBA180430_8B_4_H12_ad012


title: CEMBA180430_8B_3_CEMBA180430_8B_4_H5_ad008


title: CEMBA180430_8B_3_CEMBA180430_8B_4_H12_ad010


title: CEMBA180430_8B_3_CEMBA180430_8B_4_H12_ad007


title: CEMBA180430_8B_3_CEMBA180430_8B_4_H12_ad008


title: CEMBA180430_8B_3_CEMBA180430_8B_4_H12_ad002


title: CEMBA180430_8B_3_CEMBA180430_8B_4_H2_ad006


title: CEMBA180430_8B_3_CEMBA180430_8B_4_H11_ad010


title: CEMBA180430_8B_3_CEMBA180430_8B_4_H11_ad012


title: CEMBA180430_8B_3_CEMBA180430_8B_4_H12_ad004


title: CEMBA180430_8B_3_CEMBA180430_8B_4_H2_ad004


title: CEMBA180430_8B_3_CEMBA180430_8B_4_H2_ad007


title: CEMBA180430_8B_3_CEMBA180430_8B_4_H12_ad006


title: CEMBA180430_8B_3_CEMBA180430_8B_4_H3_ad006


title: CEMBA180430_8B_3_CEMBA180430_8B_4_H11_ad008


title: CEMBA180430_8B_3_CEMBA180430_8B_4_H10_ad007


title: CEMBA180430_8B_3_CEMBA180430_8B_4_H10_ad001


title: CEMBA180430_8B_3_CEMBA180430_8B_4_H11_ad001


title: CEMBA180430_8B_3_CEMBA180430_8B_4_H10_ad004


title: CEMBA180430_8B_3_CEMBA180430_8B_4_H11_ad004


title: CEMBA180430_8B_3_CEMBA180430_8B_4_H11_ad002


title: CEMBA180430_8B_3_CEMBA180430_8B_4_H10_ad006


title: CEMBA180430_8B_3_CEMBA180430_8B_4_H11_ad007


title: CEMBA180430_8B_3_CEMBA180430_8B_4_H12_ad001


title: CEMBA180430_8B_3_CEMBA180430_8B_4_H10_ad002


title: CEMBA180430_8B_3_CEMBA180430_8B_4_H1_ad012


title: CEMBA180430_8B_3_CEMBA180430_8B_4_H1_ad010


title: CEMBA180430_8B_3_CEMBA180430_8B_4_H10_ad008


title: CEMBA180430_8B_3_CEMBA180430_8B_4_H1_ad004


title: CEMBA180430_8B_3_CEMBA180430_8B_4_H1_ad006


title: CEMBA180430_8B_3_CEMBA180430_8B_4_H1_ad002


title: CEMBA180430_8B_3_CEMBA180430_8B_4_H10_ad012


title: CEMBA180430_8B_3_CEMBA180430_8B_4_G9_ad001


title: CEMBA180430_8B_3_CEMBA180430_8B_4_H1_ad001


title: CEMBA180430_8B_3_CEMBA180430_8B_4_H1_ad008


title: CEMBA180430_8B_3_CEMBA180430_8B_4_G9_ad004


title: CEMBA180430_8B_3_CEMBA180430_8B_4_G9_ad002


title: CEMBA180430_8B_3_CEMBA180430_8B_4_G9_ad008


title: CEMBA180430_8B_3_CEMBA180430_8B_4_G8_ad012


title: CEMBA180430_8B_3_CEMBA180430_8B_4_G8_ad007


title: CEMBA180430_8B_3_CEMBA180430_8B_4_G7_ad012


title: CEMBA180430_8B_3_CEMBA180430_8B_4_G8_ad006


title: CEMBA180430_8B_3_CEMBA180430_8B_4_G8_ad004


title: CEMBA180430_8B_3_CEMBA180430_8B_4_G8_ad010


title: CEMBA180430_8B_3_CEMBA180430_8B_4_G8_ad002


title: CEMBA180430_8B_3_CEMBA180430_8B_4_G7_ad002


title: CEMBA180430_8B_3_CEMBA180430_8B_4_G7_ad004


title: CEMBA180430_8B_3_CEMBA180430_8B_4_G6_ad012


title: CEMBA180430_8B_3_CEMBA180430_8B_4_G6_ad006


title: CEMBA180430_8B_3_CEMBA180430_8B_4_G8_ad008


title: CEMBA180430_8B_3_CEMBA180430_8B_4_G7_ad007


title: CEMBA180430_8B_3_CEMBA180430_8B_4_G7_ad010


title: CEMBA180430_8B_3_CEMBA180430_8B_4_G7_ad006


title: CEMBA180430_8B_3_CEMBA180430_8B_4_G6_ad004


title: CEMBA180430_8B_3_CEMBA180430_8B_4_G6_ad010


title: CEMBA180430_8B_3_CEMBA180430_8B_4_G5_ad012


title: CEMBA180430_8B_3_CEMBA180430_8B_4_G5_ad007


title: CEMBA180430_8B_3_CEMBA180430_8B_4_G5_ad001


title: CEMBA180430_8B_3_CEMBA180430_8B_4_G5_ad010


title: CEMBA180430_8B_3_CEMBA180430_8B_4_G5_ad002


title: CEMBA180430_8B_3_CEMBA180430_8B_4_G5_ad004


title: CEMBA180430_8B_3_CEMBA180430_8B_4_G7_ad001


title: CEMBA180430_8B_3_CEMBA180430_8B_4_G5_ad008


title: CEMBA180430_8B_3_CEMBA180430_8B_4_G4_ad010


title: CEMBA180430_8B_3_CEMBA180430_8B_4_G7_ad008


title: CEMBA180430_8B_3_CEMBA180430_8B_4_G4_ad004


title: CEMBA180430_8B_3_CEMBA180430_8B_4_G4_ad008


title: CEMBA180430_8B_3_CEMBA180430_8B_4_G4_ad012


title: CEMBA180430_8B_3_CEMBA180430_8B_4_G3_ad001


title: CEMBA180430_8B_3_CEMBA180430_8B_4_G3_ad010


title: CEMBA180430_8B_3_CEMBA180430_8B_4_G4_ad002


title: CEMBA180430_8B_3_CEMBA180430_8B_4_G4_ad001


title: CEMBA180430_8B_3_CEMBA180430_8B_4_G3_ad004


title: CEMBA180430_8B_3_CEMBA180430_8B_4_G3_ad006


title: CEMBA180430_8B_3_CEMBA180430_8B_4_G3_ad008


title: CEMBA180430_8B_3_CEMBA180430_8B_4_G2_ad001


title: CEMBA180430_8B_3_CEMBA180430_8B_4_G3_ad007


title: CEMBA180430_8B_3_CEMBA180430_8B_4_G3_ad002


title: CEMBA180430_8B_3_CEMBA180430_8B_4_G2_ad010


title: CEMBA180430_8B_3_CEMBA180430_8B_4_G12_ad008


title: CEMBA180430_8B_3_CEMBA180430_8B_4_G12_ad007


title: CEMBA180430_8B_3_CEMBA180430_8B_4_G12_ad004


title: CEMBA180430_8B_3_CEMBA180430_8B_4_G2_ad004


title: CEMBA180430_8B_3_CEMBA180430_8B_4_G2_ad007


title: CEMBA180430_8B_3_CEMBA180430_8B_4_G2_ad012


title: CEMBA180430_8B_3_CEMBA180430_8B_4_G12_ad006


title: CEMBA180430_8B_3_CEMBA180430_8B_4_G12_ad002


title: CEMBA180430_8B_3_CEMBA180430_8B_4_G11_ad010


title: CEMBA180430_8B_3_CEMBA180430_8B_4_G11_ad008


title: CEMBA180430_8B_3_CEMBA180430_8B_4_G11_ad012


title: CEMBA180430_8B_3_CEMBA180430_8B_4_G11_ad006


title: CEMBA180430_8B_3_CEMBA180430_8B_4_G2_ad008


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title: CEMBA180430_8B_3_CEMBA180430_8B_4_D1_ad002


title: CEMBA180430_8B_3_CEMBA180430_8B_4_D1_ad004


title: CEMBA180430_8B_3_CEMBA180430_8B_4_D12_ad012


title: CEMBA180430_8B_3_CEMBA180430_8B_4_D1_ad007


title: CEMBA180430_8B_3_CEMBA180430_8B_4_D1_ad008


title: CEMBA180430_8B_3_CEMBA180430_8B_4_C9_ad012


title: CEMBA180430_8B_3_CEMBA180430_8B_4_C9_ad007


title: CEMBA180430_8B_3_CEMBA180430_8B_4_D11_ad007


title: CEMBA180430_8B_3_CEMBA180430_8B_4_C9_ad010


title: CEMBA180430_8B_3_CEMBA180430_8B_4_D1_ad006


title: CEMBA180430_8B_3_CEMBA180430_8B_4_C9_ad004


title: CEMBA180430_8B_3_CEMBA180430_8B_4_D11_ad004


title: CEMBA180430_8B_3_CEMBA180430_8B_4_D10_ad010


title: CEMBA180430_8B_3_CEMBA180430_8B_4_C9_ad008


title: CEMBA180430_8B_3_CEMBA180430_8B_4_C9_ad002


title: CEMBA180430_8B_3_CEMBA180430_8B_4_C8_ad012


title: CEMBA180430_8B_3_CEMBA180430_8B_4_C8_ad010


title: CEMBA180430_8B_3_CEMBA180430_8B_4_C8_ad004


title: CEMBA180430_8B_3_CEMBA180430_8B_4_C8_ad006


title: CEMBA180430_8B_3_CEMBA180430_8B_4_C8_ad007


title: BMDM_scATAC_VISTA.1_LPS

city: Lebanon

first: Evelien

last: Schaafsma

state: New Hampshire

address: One Medical Drive

institute: Dartmouth

description: BMDMs were stimulated with 10 ng/ml LPS and anti-VISTA for 15 hours, washed 5 times with 1× PBS, then allowed to rest for 2 hours in LPS-free complete medium.

data_processing:
RNA-seq and scATAC-seq: Illumina Casava1.7 software used for basecalling.
RNA-seq: The quality of the runs was confirmed using the FastQC software. Sequenced reads were trimmed for adaptor sequence, masked for low-complexity or low-quality sequence, and mapped to GRCm38 whole genome using STAR v2.6.1 with parameters  --quantMode. The count data were transformed to log2-transformed transcripts per million (TPM) for downstream analyses and heatmap displays.
scATAC-seq: The CellRanger ATAC v1.1.0 pipeline as used for initial processing. Raw base call (BCL) files were demultiplexed into FASTQ files using “mkfastq”. Reads were aligned to the mouse mm10 reference genome using “count”. Peak count matrices were aggregated into one file using the “aggr” function.
Genome_build: mm10 and hg19
Supplementary_files_format_and_content: Matrix tables with raw gene counts for every gene and every sample. Matrix tables with raw read counts for every peak and cell.

source_name: Bone Marrow-Derived Macrophages

growth_protocol:
Primary Bone marrow-derived macrophages (BMDMs) were generated by isolation and culture of mouse bone marrow in complete RPMI supplemented with 20 ng/ml recombinant murine M-CSF (Peprotech, 315-02) for up to 7 days.
See sample information

extract_protocol:
RNA-seq: RNA was extracted using the Kapa Hyperprep with RiboErase kit, according to the manufacturer’s instructions. scATAC-seq: Nuclei from BMDMs were isolated following the 10X Genomics protocol.
RNA-seq and scATAC-seq: RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: See sample information

tag: cell type

value: BMDM

value: anti-VISTA (803)+LPS


title: BMDM_scATAC_VISTA.2_LPS


title: BMDM_scATAC_VISTA.2

description: BMDMs were treated with anti-VISTA for 15 hours, washed 5 times with 1× PBS, then allowed to rest for 2 hours in LPS-free complete medium.

value: anti-VISTA (803)


title: BMDM_scATAC_VISTA.1


title: CEMBA180430_8B_3_CEMBA180430_8B_4_C8_ad002


title: BMDM_scATAC_IgG.2_LPS

description: BMDMs were stimulated with 10 ng/ml LPS and control Ig for 15 hours, washed 5 times with 1× PBS, then allowed to rest for 2 hours in LPS-free complete medium.

value: Control IgG+LPS


title: CEMBA180430_8B_3_CEMBA180430_8B_4_C9_ad006


title: BMDM_scATAC_IgG.1

description: BMDMs were treated with control Ig for 15 hours, washed 5 times with 1× PBS, then allowed to rest for 2 hours in LPS-free complete medium.

value: Control IgG


title: BMDM_scATAC_IgG.1_LPS


title: CEMBA180430_8B_3_CEMBA180430_8B_4_C8_ad008


title: BMDM_RNA_803.3_16hr

description: BMDMs treated with anti-VISTA (10 mg/ml) for 16 hours.


title: CEMBA180430_8B_3_CEMBA180430_8B_4_C7_ad007


title: BMDM_RNA_803.2_16hr


title: CEMBA180430_8B_3_CEMBA180430_8B_4_C7_ad006


title: CEMBA180430_8B_3_CEMBA180430_8B_4_C7_ad010


title: BMDM_scATAC_IgG.2


title: CEMBA180430_8B_3_CEMBA180430_8B_4_C7_ad004


title: CEMBA180430_8B_3_CEMBA180430_8B_4_C8_ad001


title: BMDM_RNA_803.1_16hr


title: CEMBA180430_8B_3_CEMBA180430_8B_4_C7_ad002


title: BMDM_RNA_803.1_8hr

description: BMDMs treated with anti-VISTA (10 mg/ml) for 8 hours.


title: BMDM_RNA_803.2_8hr


title: CEMBA180430_8B_3_CEMBA180430_8B_4_C7_ad008


title: BMDM_RNA_803.3_4hr

description: BMDMs treated with anti-VISTA (10 mg/ml) for 4 hours.


title: CEMBA180430_8B_3_CEMBA180430_8B_4_C7_ad001


title: BMDM_RNA_803.2_2hr

description: BMDMs treated with anti-VISTA (10 mg/ml) for 2 hours.


title: BMDM_RNA_803.1_4hr


title: CEMBA180430_8B_3_CEMBA180430_8B_4_C6_ad012


title: CEMBA180430_8B_3_CEMBA180430_8B_4_C6_ad001


title: BMDM_RNA_803.1_2hr


title: BMDM_RNA_803.2_4hr


title: CEMBA180430_8B_3_CEMBA180430_8B_4_C6_ad010


title: CEMBA180430_8B_3_CEMBA180430_8B_4_C6_ad006


title: BMDM_RNA_803.2_1hr

description: BMDMs treated with anti-VISTA (10 mg/ml) for 1 hour.


title: CEMBA180430_8B_3_CEMBA180430_8B_4_C6_ad007


title: BMDM_RNA_IgG2.1_16hr

description: BMDMs treated with IgG (10 mg/ml) for 16 hours.


title: BMDM_RNA_IgG2.3_16hr


title: BMDM_RNA_IgG2.2_16hr


title: CEMBA180430_8B_3_CEMBA180430_8B_4_C5_ad010


title: CEMBA180430_8B_3_CEMBA180430_8B_4_C6_ad008


title: CEMBA180430_8B_3_CEMBA180430_8B_4_C5_ad002


title: CEMBA180430_8B_3_CEMBA180430_8B_4_C6_ad004


title: CEMBA180430_8B_3_CEMBA180430_8B_4_C5_ad008


title: BMDM_RNA_IgG2.2_8hr

description: BMDMs treated with IgG (10 mg/ml) for 8 hours.


title: CEMBA180430_8B_3_CEMBA180430_8B_4_C5_ad007


title: CEMBA180430_8B_3_CEMBA180430_8B_4_C5_ad004


title: BMDM_RNA_IgG2.3_4hr

description: BMDMs treated with IgG (10 mg/ml) for 4 hours.


title: BMDM_RNA_IgG2.1_8hr


title: BMDM_RNA_IgG2.2_4hr


title: BMDM_RNA_IgG2.1_4hr


title: BMDM_RNA_IgG2.2_2hr

description: BMDMs treated with IgG (10 mg/ml) for 2 hours.


title: BMDM_RNA_803.1_1hr


title: CEMBA180430_8B_3_CEMBA180430_8B_4_C4_ad002


title: CEMBA180430_8B_3_CEMBA180430_8B_4_C4_ad008


title: CEMBA180430_8B_3_CEMBA180430_8B_4_C4_ad010


title: CEMBA180430_8B_3_CEMBA180430_8B_4_C5_ad012


title: CEMBA180430_8B_3_CEMBA180430_8B_4_D5_ad010


title: BMDM_RNA_IgG2.2_1hr

description: BMDMs treated with IgG (10 mg/ml) for 1 hour.


title: BMDM_RNA_IgG2.1_2hr


title: BMDM_RNA_IgG2.1_1hr


title: CEMBA180430_8B_3_CEMBA180430_8B_4_C6_ad002


title: CEMBA180430_8B_3_CEMBA180430_8B_4_C4_ad012


title: CEMBA180430_8B_3_CEMBA180430_8B_4_C3_ad012


title: BMDM_RNA_VISTA_803_Tol_2

description: BMDMs were stimulated with 10 ng/ml LPS and anti-VISTA for 15 hours, washed 5 times with 1× PBS, then allowed to rest for 2 hours in LPS-free complete medium. BMDMs were then stimulated with 1 μg/ml LPS for 4 h


title: CEMBA180430_8B_3_CEMBA180430_8B_4_C4_ad001


title: CEMBA180430_8B_3_CEMBA180430_8B_4_C3_ad001


title: BMDM_RNA_VISTA_803_Imm_3

description: BMDMs were stimulated with anti-VISTA for 15 hours, washed 5 times with 1× PBS, then allowed to rest for 2 hours in LPS-free complete medium. BMDMs were then stimulated with 1 μg/ml LPS for 4 h


title: CEMBA180430_8B_3_CEMBA180430_8B_4_C3_ad007


title: CEMBA180430_8B_3_CEMBA180430_8B_4_C4_ad007


title: BMDM_RNA_VISTA_803_Imm_2


title: BMDM_RNA_VISTA_803_Imm_1


title: BMDM_RNA_IgG2_Tol_3

description: BMDMs were stimulated with 10 ng/ml LPS and control Ig for 15 hours, washed 5 times with 1× PBS, then allowed to rest for 2 hours in LPS-free complete medium. BMDMs were then stimulated with 1 μg/ml LPS for 4 h


title: CEMBA180430_8B_3_CEMBA180430_8B_4_C3_ad010


title: BMDM_RNA_VISTA_803_Tol_1


title: BMDM_RNA_IgG2_Tol_2


title: CEMBA180430_8B_3_CEMBA180430_8B_4_C3_ad004


title: CEMBA180430_8B_3_CEMBA180430_8B_4_C3_ad002


title: BMDM_RNA_IgG2_Imm_2

description: BMDMs were stimulated with control Ig for 15 hours, washed 5 times with 1× PBS, then allowed to rest for 2 hours in LPS-free complete medium. BMDMs were then stimulated with 1 μg/ml LPS for 4 h


title: BMDM_RNA_VISTA_803_Tol_3


title: BMDM_RNA_IgG2_Imm_1


title: BMDM_RNA_IgG2_Tol_1


title: BMDM_RNA_IgG2_Imm_3


title: CEMBA180430_8B_3_CEMBA180430_8B_4_C2_ad006


title: CEMBA180430_8B_3_CEMBA180430_8B_4_C2_ad012


title: CEMBA180430_8B_3_CEMBA180430_8B_4_C2_ad002


title: CEMBA180430_8B_3_CEMBA180430_8B_4_C2_ad004


title: CEMBA180430_8B_3_CEMBA180430_8B_4_C3_ad006


title: CEMBA180430_8B_3_CEMBA180430_8B_4_C2_ad008


title: CEMBA180430_8B_3_CEMBA180430_8B_4_C12_ad010


title: CEMBA180430_8B_3_CEMBA180430_8B_4_C12_ad007


title: CEMBA180430_8B_3_CEMBA180430_8B_4_C11_ad012


title: CEMBA180430_8B_3_CEMBA180430_8B_4_C11_ad007


title: CEMBA180430_8B_3_CEMBA180430_8B_4_C12_ad008


title: CEMBA180430_8B_3_CEMBA180430_8B_4_C12_ad001


title: CEMBA180430_8B_3_CEMBA180430_8B_4_C11_ad002


title: CEMBA180430_8B_3_CEMBA180430_8B_4_C11_ad006


title: CEMBA180430_8B_3_CEMBA180430_8B_4_C12_ad012


title: CEMBA180430_8B_3_CEMBA180430_8B_4_C11_ad008


title: CEMBA180430_8B_3_CEMBA180430_8B_4_C11_ad010


title: CEMBA180430_8B_3_CEMBA180430_8B_4_C11_ad001


title: CEMBA180430_8B_3_CEMBA180430_8B_4_C10_ad012


title: CEMBA180430_8B_3_CEMBA180430_8B_4_C3_ad008


title: CEMBA180430_8B_3_CEMBA180430_8B_4_C11_ad004


title: CEMBA180430_8B_3_CEMBA180430_8B_4_C10_ad008


title: CEMBA180430_8B_3_CEMBA180430_8B_4_C10_ad007


title: CEMBA180430_8B_3_CEMBA180430_8B_4_C4_ad006


title: CEMBA180430_8B_3_CEMBA180430_8B_4_C10_ad006


title: CEMBA180430_8B_3_CEMBA180430_8B_4_C10_ad001


title: CEMBA180430_8B_3_CEMBA180430_8B_4_C10_ad004


title: CEMBA180430_8B_3_CEMBA180430_8B_4_C1_ad012


title: CEMBA180430_8B_3_CEMBA180430_8B_4_C1_ad007


title: CEMBA180430_8B_3_CEMBA180430_8B_4_C12_ad004


title: CEMBA180430_8B_3_CEMBA180430_8B_4_C10_ad010


title: CEMBA180430_8B_3_CEMBA180430_8B_4_C1_ad010


title: CEMBA180430_8B_3_CEMBA180430_8B_4_C1_ad006


title: CEMBA180430_8B_3_CEMBA180430_8B_4_C1_ad004


title: CEMBA180430_8B_3_CEMBA180430_8B_4_B9_ad001


title: CEMBA180430_8B_3_CEMBA180430_8B_4_B9_ad004


title: CEMBA180430_8B_3_CEMBA180430_8B_4_B9_ad007


title: CEMBA180430_8B_3_CEMBA180430_8B_4_B9_ad012


title: CEMBA180430_8B_3_CEMBA180430_8B_4_B9_ad010


title: CEMBA180430_8B_3_CEMBA180430_8B_4_B8_ad012


title: CEMBA180430_8B_3_CEMBA180430_8B_4_B9_ad006


title: CEMBA180430_8B_3_CEMBA180430_8B_4_B9_ad002


title: CEMBA180430_8B_3_CEMBA180430_8B_4_C1_ad002


title: CEMBA180430_8B_3_CEMBA180430_8B_4_B9_ad008


title: CEMBA180430_8B_3_CEMBA180430_8B_4_B8_ad010


title: CEMBA180430_8B_3_CEMBA180430_8B_4_B8_ad006


title: CEMBA180430_8B_3_CEMBA180430_8B_4_C1_ad001


title: CEMBA180430_8B_3_CEMBA180430_8B_4_B8_ad004


title: CEMBA180430_8B_3_CEMBA180430_8B_4_B8_ad008


title: CEMBA180430_8B_3_CEMBA180430_8B_4_B7_ad012


title: CEMBA180430_8B_3_CEMBA180430_8B_4_B7_ad001


title: CEMBA180430_8B_3_CEMBA180430_8B_4_B7_ad010


title: CEMBA180430_8B_3_CEMBA180430_8B_4_B7_ad006


title: CEMBA180430_8B_3_CEMBA180430_8B_4_B7_ad002


title: CEMBA180430_8B_3_CEMBA180430_8B_4_B7_ad004


title: CEMBA180430_8B_3_CEMBA180430_8B_4_B6_ad001


title: CEMBA180430_8B_3_CEMBA180430_8B_4_B6_ad012


title: CEMBA180430_8B_3_CEMBA180430_8B_4_B8_ad007


title: CEMBA180430_8B_3_CEMBA180430_8B_4_C1_ad008


title: CEMBA180430_8B_3_CEMBA180430_8B_4_B6_ad007


title: CEMBA180430_8B_3_CEMBA180430_8B_4_B7_ad007


title: CEMBA180430_8B_3_CEMBA180430_8B_4_B6_ad006


title: CEMBA180430_8B_3_CEMBA180430_8B_4_B6_ad002


title: CEMBA180430_8B_3_CEMBA180430_8B_4_B5_ad001


title: CEMBA180430_8B_3_CEMBA180430_8B_4_B5_ad008


title: CEMBA180430_8B_3_CEMBA180430_8B_4_B7_ad008


title: CEMBA180430_8B_3_CEMBA180430_8B_4_B6_ad004


title: CEMBA180430_8B_3_CEMBA180430_8B_4_B5_ad004


title: CEMBA180430_8B_3_CEMBA180430_8B_4_B5_ad006


title: CEMBA180430_8B_3_CEMBA180430_8B_4_B8_ad002


title: CEMBA180430_8B_3_CEMBA180430_8B_4_B5_ad012


title: CEMBA180430_8B_3_CEMBA180430_8B_4_B4_ad001


title: CEMBA180430_8B_3_CEMBA180430_8B_4_B5_ad002


title: CEMBA180430_8B_3_CEMBA180430_8B_4_B4_ad007


title: CEMBA180430_8B_3_CEMBA180430_8B_4_B4_ad010


title: CEMBA180430_8B_3_CEMBA180430_8B_4_B4_ad006


title: CEMBA180430_8B_3_CEMBA180430_8B_4_B4_ad004


title: CEMBA180430_8B_3_CEMBA180430_8B_4_B4_ad008


title: CEMBA180430_8B_3_CEMBA180430_8B_4_B3_ad001


title: CEMBA180430_8B_3_CEMBA180430_8B_4_B3_ad007


title: CEMBA180430_8B_3_CEMBA180430_8B_4_B6_ad008


title: CEMBA180430_8B_3_CEMBA180430_8B_4_B3_ad004


title: CEMBA180430_8B_3_CEMBA180430_8B_4_B3_ad006


title: CEMBA180430_8B_3_CEMBA180430_8B_4_B3_ad002


title: CEMBA180430_8B_3_CEMBA180430_8B_4_B12_ad010


title: CEMBA180430_8B_3_CEMBA180430_8B_4_B12_ad002


title: CEMBA180430_8B_3_CEMBA180430_8B_4_B12_ad004


title: CEMBA180430_8B_3_CEMBA180430_8B_4_B11_ad004


title: CEMBA180430_8B_3_CEMBA180430_8B_4_B11_ad010


title: CEMBA180430_8B_3_CEMBA180430_8B_4_B11_ad002


title: CEMBA180430_8B_3_CEMBA180430_8B_4_B11_ad008


title: CEMBA180430_8B_3_CEMBA180430_8B_4_B6_ad010


title: CEMBA180430_8B_3_CEMBA180430_8B_4_B11_ad007


title: CEMBA180430_8B_3_CEMBA180430_8B_4_B12_ad001


title: CEMBA180430_8B_3_CEMBA180430_8B_4_B11_ad001


title: CEMBA180430_8B_3_CEMBA180430_8B_4_B10_ad007


title: CEMBA180430_8B_3_CEMBA180430_8B_4_B10_ad008


title: CEMBA180430_8B_3_CEMBA180430_8B_4_B10_ad006


title: CEMBA180430_8B_3_CEMBA180430_8B_4_B10_ad012


title: CEMBA180430_8B_3_CEMBA180430_8B_4_B4_ad002


title: CEMBA180430_8B_3_CEMBA180430_8B_4_B10_ad001


title: CEMBA180430_8B_3_CEMBA180430_8B_4_B3_ad010


title: CEMBA180430_8B_3_CEMBA180430_8B_4_B10_ad004


title: CEMBA180430_8B_3_CEMBA180430_8B_4_B5_ad010


title: CEMBA180430_8B_3_CEMBA180430_8B_4_B10_ad002


title: CEMBA180430_8B_3_CEMBA180430_8B_4_B1_ad001


title: CEMBA180430_8B_3_CEMBA180430_8B_4_B1_ad007


title: CEMBA180430_8B_3_CEMBA180430_8B_4_B1_ad006


title: CEMBA180430_8B_3_CEMBA180430_8B_4_B1_ad002


title: CEMBA180430_8B_3_CEMBA180430_8B_4_B1_ad008


title: CEMBA180430_8B_3_CEMBA180430_8B_4_B12_ad012


title: CEMBA180430_8B_3_CEMBA180430_8B_4_A9_ad012


title: CEMBA180430_8B_3_CEMBA180430_8B_4_A9_ad004


title: CEMBA180430_8B_3_CEMBA180430_8B_4_A9_ad006


title: CEMBA180430_8B_3_CEMBA180430_8B_4_A8_ad012


title: CEMBA180430_8B_3_CEMBA180430_8B_4_A9_ad008


title: CEMBA180430_8B_3_CEMBA180430_8B_4_A9_ad007


title: CEMBA180430_8B_3_CEMBA180430_8B_4_A7_ad001


title: CEMBA180430_8B_3_CEMBA180430_8B_4_A8_ad010


title: CEMBA180430_8B_3_CEMBA180430_8B_4_A8_ad004


title: CEMBA180430_8B_3_CEMBA180430_8B_4_A8_ad007


title: CEMBA180430_8B_3_CEMBA180430_8B_4_A7_ad012


title: CEMBA180430_8B_3_CEMBA180430_8B_4_A8_ad002


title: CEMBA180430_8B_3_CEMBA180430_8B_4_A7_ad010


title: CEMBA180430_8B_3_CEMBA180430_8B_4_A7_ad007


title: CEMBA180430_8B_3_CEMBA180430_8B_4_A8_ad008


title: CEMBA180430_8B_3_CEMBA180430_8B_4_A7_ad006


title: CEMBA180430_8B_3_CEMBA180430_8B_4_B1_ad012


title: CEMBA180430_8B_3_CEMBA180430_8B_4_A7_ad002


title: CEMBA180430_8B_3_CEMBA180430_8B_4_A6_ad012


title: CEMBA180430_8B_3_CEMBA180430_8B_4_A6_ad001


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title: CEMBA180430_8B_1_CEMBA180430_8B_2_F4_ad010


title: CEMBA180430_8B_1_CEMBA180430_8B_2_F4_ad007


title: CEMBA180430_8B_1_CEMBA180430_8B_2_F4_ad012


title: CEMBA180430_8B_1_CEMBA180430_8B_2_F5_ad008


title: CEMBA180430_8B_1_CEMBA180430_8B_2_F4_ad001


title: CEMBA180430_8B_1_CEMBA180430_8B_2_F3_ad001


title: CEMBA180430_8B_1_CEMBA180430_8B_2_F4_ad006


title: CEMBA180430_8B_1_CEMBA180430_8B_2_F3_ad010


title: CEMBA180430_8B_1_CEMBA180430_8B_2_F4_ad002


title: CEMBA180430_8B_1_CEMBA180430_8B_2_F4_ad008


title: CEMBA180430_8B_1_CEMBA180430_8B_2_F3_ad004


title: CEMBA180430_8B_1_CEMBA180430_8B_2_F4_ad004


title: CEMBA180430_8B_1_CEMBA180430_8B_2_F3_ad007


title: CEMBA180430_8B_1_CEMBA180430_8B_2_F3_ad002


title: CEMBA180430_8B_1_CEMBA180430_8B_2_F6_ad008


title: CEMBA180430_8B_1_CEMBA180430_8B_2_F2_ad001


title: CEMBA180430_8B_1_CEMBA180430_8B_2_F2_ad007


title: CEMBA180430_8B_1_CEMBA180430_8B_2_F2_ad012


title: CEMBA180430_8B_1_CEMBA180430_8B_2_F3_ad012


title: CEMBA180430_8B_1_CEMBA180430_8B_2_F2_ad002


title: CEMBA180430_8B_1_CEMBA180430_8B_2_F5_ad004


title: CEMBA180430_8B_1_CEMBA180430_8B_2_F2_ad010


title: CEMBA180430_8B_1_CEMBA180430_8B_2_F12_ad007


title: CEMBA180430_8B_1_CEMBA180430_8B_2_F12_ad008


title: CEMBA180430_8B_1_CEMBA180430_8B_2_F2_ad004


title: CEMBA180430_8B_1_CEMBA180430_8B_2_F12_ad006


title: CEMBA180430_8B_1_CEMBA180430_8B_2_F12_ad002


title: CEMBA180430_8B_1_CEMBA180430_8B_2_F2_ad008


title: CEMBA180430_8B_1_CEMBA180430_8B_2_F12_ad004


title: CEMBA180430_8B_1_CEMBA180430_8B_2_F11_ad012


title: CEMBA180430_8B_1_CEMBA180430_8B_2_F11_ad010


title: CEMBA180430_8B_1_CEMBA180430_8B_2_F12_ad001


title: CEMBA180430_8B_1_CEMBA180430_8B_2_F11_ad006


title: CEMBA180430_8B_1_CEMBA180430_8B_2_F11_ad008


title: CEMBA180430_8B_1_CEMBA180430_8B_2_F11_ad004


title: CEMBA180430_8B_1_CEMBA180430_8B_2_F11_ad001


title: CEMBA180430_8B_1_CEMBA180430_8B_2_F11_ad002


title: CEMBA180430_8B_1_CEMBA180430_8B_2_F10_ad008


title: CEMBA180430_8B_1_CEMBA180430_8B_2_F10_ad007


title: CEMBA180430_8B_1_CEMBA180430_8B_2_F10_ad002


title: CEMBA180430_8B_1_CEMBA180430_8B_2_F10_ad004


title: CEMBA180430_8B_1_CEMBA180430_8B_2_F10_ad006


title: CEMBA180430_8B_1_CEMBA180430_8B_2_F1_ad007


title: CEMBA180430_8B_1_CEMBA180430_8B_2_F1_ad010


title: CEMBA180430_8B_1_CEMBA180430_8B_2_F1_ad001


title: CEMBA180430_8B_1_CEMBA180430_8B_2_F1_ad012


title: CEMBA180430_8B_1_CEMBA180430_8B_2_F1_ad006


title: CEMBA180430_8B_1_CEMBA180430_8B_2_F10_ad001


title: CEMBA180430_8B_1_CEMBA180430_8B_2_F1_ad002


title: CEMBA180430_8B_1_CEMBA180430_8B_2_F1_ad004


title: CEMBA180430_8B_1_CEMBA180430_8B_2_E9_ad007


title: CEMBA180430_8B_1_CEMBA180430_8B_2_E9_ad010


title: CEMBA180430_8B_1_CEMBA180430_8B_2_E9_ad006


title: CEMBA180430_8B_1_CEMBA180430_8B_2_E9_ad004


title: CEMBA180430_8B_1_CEMBA180430_8B_2_E9_ad002


title: CEMBA180430_8B_1_CEMBA180430_8B_2_E8_ad012


title: CEMBA180430_8B_1_CEMBA180430_8B_2_E8_ad010


title: CEMBA180430_8B_1_CEMBA180430_8B_2_E9_ad008


title: CEMBA180430_8B_1_CEMBA180430_8B_2_E8_ad007


title: CEMBA180430_8B_1_CEMBA180430_8B_2_E8_ad001


title: CEMBA180430_8B_1_CEMBA180430_8B_2_E8_ad002


title: CEMBA180430_8B_1_CEMBA180430_8B_2_E8_ad006


title: CEMBA180430_8B_1_CEMBA180430_8B_2_E7_ad007


title: CEMBA180430_8B_1_CEMBA180430_8B_2_E7_ad012


title: CEMBA180430_8B_1_CEMBA180430_8B_2_E7_ad010


title: CEMBA180430_8B_1_CEMBA180430_8B_2_E7_ad001


title: CEMBA180430_8B_1_CEMBA180430_8B_2_E8_ad008


title: CEMBA180430_8B_1_CEMBA180430_8B_2_E7_ad006


title: CEMBA180430_8B_1_CEMBA180430_8B_2_E7_ad004


title: CEMBA180430_8B_1_CEMBA180430_8B_2_E9_ad012


title: CEMBA180430_8B_1_CEMBA180430_8B_2_E6_ad012


title: CEMBA180430_8B_1_CEMBA180430_8B_2_E7_ad002


title: CEMBA180430_8B_1_CEMBA180430_8B_2_E7_ad008


title: CEMBA180430_8B_1_CEMBA180430_8B_2_E9_ad001


title: CEMBA180430_8B_1_CEMBA180430_8B_2_E6_ad001


title: CEMBA180430_8B_1_CEMBA180430_8B_2_E6_ad010


title: CEMBA180430_8B_1_CEMBA180430_8B_2_E6_ad006


title: CEMBA180430_8B_1_CEMBA180430_8B_2_E5_ad002


title: CEMBA180430_8B_1_CEMBA180430_8B_2_E5_ad008


title: CEMBA180430_8B_1_CEMBA180430_8B_2_E6_ad004


title: CEMBA180430_8B_1_CEMBA180430_8B_2_E5_ad010


title: CEMBA180430_8B_1_CEMBA180430_8B_2_E6_ad008


title: CEMBA180430_8B_1_CEMBA180430_8B_2_E5_ad001


title: CEMBA180430_8B_1_CEMBA180430_8B_2_E5_ad012


title: CEMBA180430_8B_1_CEMBA180430_8B_2_E4_ad012


title: CEMBA180430_8B_1_CEMBA180430_8B_2_E4_ad001


title: CEMBA180430_8B_1_CEMBA180430_8B_2_E4_ad006


title: CEMBA180430_8B_1_CEMBA180430_8B_2_E4_ad010


title: CEMBA180430_8B_1_CEMBA180430_8B_2_E4_ad008


title: CEMBA180430_8B_1_CEMBA180430_8B_2_E4_ad002


title: CEMBA180430_8B_1_CEMBA180430_8B_2_E3_ad012


title: CEMBA180430_8B_1_CEMBA180430_8B_2_E3_ad001


title: CEMBA180430_8B_1_CEMBA180430_8B_2_E3_ad010


title: CEMBA180430_8B_1_CEMBA180430_8B_2_E3_ad007


title: CEMBA180430_8B_1_CEMBA180430_8B_2_E6_ad007


title: CEMBA180430_8B_1_CEMBA180430_8B_2_E3_ad006


title: CEMBA180430_8B_1_CEMBA180430_8B_2_E3_ad004


title: CEMBA180430_8B_1_CEMBA180430_8B_2_E3_ad002


title: CEMBA180430_8B_1_CEMBA180430_8B_2_E2_ad001


title: CEMBA180430_8B_1_CEMBA180430_8B_2_E2_ad012


title: CEMBA180430_8B_1_CEMBA180430_8B_2_E5_ad006


title: CEMBA180430_8B_1_CEMBA180430_8B_2_E2_ad010


title: CEMBA180430_8B_1_CEMBA180430_8B_2_E2_ad008


title: CEMBA180430_8B_1_CEMBA180430_8B_2_E12_ad012


title: CEMBA180430_8B_1_CEMBA180430_8B_2_E2_ad004


title: CEMBA180430_8B_1_CEMBA180430_8B_2_E2_ad002


title: CEMBA180430_8B_1_CEMBA180430_8B_2_E2_ad006


title: CEMBA180430_8B_1_CEMBA180430_8B_2_E4_ad007


title: CEMBA180430_8B_1_CEMBA180430_8B_2_E12_ad007


title: CEMBA180430_8B_1_CEMBA180430_8B_2_E12_ad010


title: CEMBA180430_8B_1_CEMBA180430_8B_2_E4_ad004


title: CEMBA180430_8B_1_CEMBA180430_8B_2_E12_ad002


title: CEMBA180430_8B_1_CEMBA180430_8B_2_E11_ad010


title: CEMBA180430_8B_1_CEMBA180430_8B_2_E11_ad012


title: CEMBA180430_8B_1_CEMBA180430_8B_2_E11_ad008


title: CEMBA180430_8B_1_CEMBA180430_8B_2_E11_ad007


title: CEMBA180430_8B_1_CEMBA180430_8B_2_E11_ad002


title: CEMBA180430_8B_1_CEMBA180430_8B_2_E3_ad008


title: CEMBA180430_8B_1_CEMBA180430_8B_2_E11_ad001


title: CEMBA180430_8B_1_CEMBA180430_8B_2_E11_ad006


title: CEMBA180430_8B_1_CEMBA180430_8B_2_E2_ad007


title: CEMBA180430_8B_1_CEMBA180430_8B_2_E10_ad007


title: CEMBA180430_8B_1_CEMBA180430_8B_2_E10_ad010


title: CEMBA180430_8B_1_CEMBA180430_8B_2_E10_ad006


title: CEMBA180430_8B_1_CEMBA180430_8B_2_E10_ad001


title: CEMBA180430_8B_1_CEMBA180430_8B_2_E1_ad001


title: CEMBA180430_8B_1_CEMBA180430_8B_2_E10_ad002


title: CEMBA180430_8B_1_CEMBA180430_8B_2_E1_ad012


title: CEMBA180430_8B_1_CEMBA180430_8B_2_E1_ad007


title: CEMBA180430_8B_1_CEMBA180430_8B_2_E12_ad008


title: CEMBA180430_8B_1_CEMBA180430_8B_2_E1_ad002


title: CEMBA180430_8B_1_CEMBA180430_8B_2_D9_ad002


title: CEMBA180430_8B_1_CEMBA180430_8B_2_D9_ad008


title: CEMBA180430_8B_1_CEMBA180430_8B_2_E12_ad006


title: CEMBA180430_8B_1_CEMBA180430_8B_2_E1_ad008


title: CEMBA180430_8B_1_CEMBA180430_8B_2_E1_ad004


title: CEMBA180430_8B_1_CEMBA180430_8B_2_D8_ad001


title: CEMBA180430_8B_1_CEMBA180430_8B_2_D8_ad012


title: CEMBA180430_8B_1_CEMBA180430_8B_2_D8_ad010


title: CEMBA180430_8B_1_CEMBA180430_8B_2_D8_ad006


title: CEMBA180430_8B_1_CEMBA180430_8B_2_D8_ad008


title: CEMBA180430_8B_1_CEMBA180430_8B_2_D8_ad007


title: CEMBA180430_8B_1_CEMBA180430_8B_2_D7_ad001


title: CEMBA180430_8B_1_CEMBA180430_8B_2_E10_ad004


title: CEMBA180430_8B_1_CEMBA180430_8B_2_D8_ad004


title: CEMBA180430_8B_1_CEMBA180430_8B_2_D7_ad006


title: CEMBA180430_8B_1_CEMBA180430_8B_2_D7_ad012


title: CEMBA180430_8B_1_CEMBA180430_8B_2_D6_ad012


title: CEMBA180430_8B_1_CEMBA180430_8B_2_D6_ad001


title: CEMBA180430_8B_1_CEMBA180430_8B_2_D7_ad004


title: CEMBA180430_8B_1_CEMBA180430_8B_2_E1_ad010


title: CEMBA180430_8B_1_CEMBA180430_8B_2_D9_ad006


title: CEMBA180430_8B_1_CEMBA180430_8B_2_D6_ad007


title: CEMBA180430_8B_1_CEMBA180430_8B_2_D6_ad006


title: CEMBA180430_8B_1_CEMBA180430_8B_2_D5_ad007


title: CEMBA180430_8B_1_CEMBA180430_8B_2_D6_ad008


title: CEMBA180430_8B_1_CEMBA180430_8B_2_D5_ad010


title: CEMBA180430_8B_1_CEMBA180430_8B_2_D5_ad006


title: CEMBA180430_8B_1_CEMBA180430_8B_2_D6_ad004


title: CEMBA180430_8B_1_CEMBA180430_8B_2_D4_ad010


title: CEMBA180430_8B_1_CEMBA180430_8B_2_D4_ad008


title: CEMBA180430_8B_1_CEMBA180430_8B_2_D5_ad008


title: CEMBA180430_8B_1_CEMBA180430_8B_2_D7_ad008


title: CEMBA180430_8B_1_CEMBA180430_8B_2_D5_ad002


title: CEMBA180430_8B_1_CEMBA180430_8B_2_D4_ad001


title: CEMBA180430_8B_1_CEMBA180430_8B_2_D4_ad012


title: CEMBA180430_8B_1_CEMBA180430_8B_2_D5_ad001


title: CEMBA180430_8B_1_CEMBA180430_8B_2_F2_ad006


title: CEMBA180430_8B_1_CEMBA180430_8B_2_D3_ad010


title: CEMBA180430_8B_1_CEMBA180430_8B_2_D10_ad012


title: CEMBA180430_8B_1_CEMBA180430_8B_2_D12_ad001


title: CEMBA180430_8B_1_CEMBA180430_8B_2_D12_ad002


title: CEMBA180430_8B_1_CEMBA180430_8B_2_D11_ad004


title: CEMBA180430_8B_1_CEMBA180430_8B_2_D11_ad012


title: CEMBA180430_8B_1_CEMBA180430_8B_2_D11_ad008


title: CEMBA180430_8B_1_CEMBA180430_8B_2_D11_ad007


title: CEMBA180430_8B_1_CEMBA180430_8B_2_D3_ad008


title: CEMBA180430_8B_1_CEMBA180430_8B_2_D11_ad001


title: CEMBA180430_8B_1_CEMBA180430_8B_2_D12_ad008


title: CEMBA180430_8B_1_CEMBA180430_8B_2_D11_ad006


title: CEMBA180430_8B_1_CEMBA180430_8B_2_D11_ad010


title: CEMBA180430_8B_1_CEMBA180430_8B_2_D12_ad010


title: 20nM EFV evolution experiment 2 [D16 CF Chip2 001]

city: Durban

first: Alex

last: Sigal

state: KwaZulu-Natal

address: 719 Umbilo Road, K-RITH Tower building, Level 5

country: South Africa

institute: Africa Health Research Institute

description: D16 CF Chip2 001

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence and then mapped to HIV NL4-3 using Geneious v 11.1.5
For SNP detection in cell population experiments: minimum variant frequency of 0.01 and maximum variant p-value 0.0001
Genome_build: pNL43-annotated.xdna.fasta
Supplementary_files_format_and_content: csv files of known drug resistance mutations as well as detected SNPs

organism: Homo sapiens

source_name: 20nM EFV evolution experiment 2

growth_protocol: Cell culture and experiments were performed in complete RPMI 1640 medium supplemented with L-Glutamine, sodium pyruvate, HEPES, non-essential amino acids (Lonza), and 10\% heat-inactivated FBS (Hyclone).

extract_protocol:
For infected single cells, the cells were lysed and DNA was kept suspended in the lysis buffer. For infected cell populations, genomic DNA was extracted using the QIAamp DNA mini kit (Qiagen)
Phusion hot start II DNA polymerase (New England Biolabs) PCR reaction mix (10$ul 5 x Phusion HF buffer, 1ul dNTPs, 2.5ul of the forward primer, 2.5ul of the reverse primer, 0.5ul Phusion hot start II DNA polymerase, 2.5ul of DMSO and molecular biology grade water to 50ul reaction volume) was added to the lysed single cells or extracted genomic DNA of cell populations. Two rounds of PCR were performed. The first-round reaction amplified a region of the RT gene in the proviral DNA using the forward primer 5’ tcgtcggcagcgtcagatgtgtataagagacagTTAATAAGAGAACTCAAGATTTC 3’ and reverse primer 5’ gtctcgtgggctcggagatgtgtataagagacagCCCCACCTCAACAGATGTTGTC 3’. Non-capitalized portion of the primers represent the Nextera XT Index Kit adaptors. Cycling program was 98C for 30 seconds, then 35 cycles of 98C for 10 seconds, 50C for 30 seconds and 72C for 15 seconds with a final extension of 72C for 5 minutes. 1$\mu l$ of the first round product was then transferred into a PCR mix as above, with second round Nextera XT Index Kit adaptor primers (forward 5’ tcgtcggcagcgtcagatgtgtataagagacag 3’, reverse 5’ gtctcgtgggctcggagatgtgtataagagacag 3’). The second round PCR amplified a 400bp product which was then visualized on a 1% agarose gel. The PCR amplicon was gel extracted using the QIAquick gel extraction kit (Qiagen). Illumina indices were attached to the amplicon with the Nextera XT Index Kit and deep sequenced using the Illumina Miseq. Fast-q files were analysed in Geneious.
Amplicon sequencing using illumina MiSeq with adaptors from Nextera kit or Ion Torrent PGM

treatment_protocol: The first round of infection in the absence of drug was initiated by cell-free infection of 2.5x10^6 RevCEM-E7 with 5x10^8 viral copies of HIV NL4-3 and incubated for 48 hours. In the second round of infection, cells infected in the first round were added to 3x10^6 uninfected RevCEM-E7 cells to a final concentration of 0.5% infected cells and incubated for 48 hours. The infection was then separated into infected cells and cell-free virus by centrifugation at 300 g for 5 minutes followed by filtration of the supernatant through a 0.45 micron filter. 1.2x10^6 infected cells or supernatant from  1.2x10^6 infected cells were added to new uninfected target cells such that the final number of cells in the culture was 6x10^6 at a concentration of 1x10^6 cells/ml. EFV at the concentration of 20nM or 40nM was was then added to the cultures. Thereafter, cultures were maintained every 48 hours by the addition of new uninfected target cells at a $1:3$ ratio of infected to fresh cells. In the experiments where FTC was added, FTC at the concentration of 770nM in addition to the the EFV was added 4 days after addition of 20nM EFV alone. Thereafter, cultures were maintained at a maximum of 1% infected cells by adding fresh cells every 48 hours.

tag: cell type/genotype

value: RevCEM E7 cells infection with Nl4-3

value: Experiment carried out at 20nM EFV

tag: molecule subtype

value: Reverse transcriptase region of HIV provirus


title: 20nM EFV evolution experiment 2 [D18 C2C Chip 2 005]

description: D18 C2C Chip 2 005


title: 20nM EFV evolution experiment 2 [D18 CF Chip 2 004]

description: D18 CF Chip 2 004


title: 20nM EFV evolution experiment 2 [D16 C2C 20% Chip 2 003]

description: D16 C2C 20% Chip 2 003


title: CEMBA180430_8B_1_CEMBA180430_8B_2_D10_ad008


title: CEMBA180430_8B_1_CEMBA180430_8B_2_D11_ad002


title: CEMBA180430_8B_1_CEMBA180430_8B_2_D2_ad004


title: CEMBA180430_8B_1_CEMBA180430_8B_2_D2_ad002


title: CEMBA180430_8B_1_CEMBA180430_8B_2_D2_ad008


title: CEMBA180430_8B_1_CEMBA180430_8B_2_D12_ad012


title: CEMBA180430_8B_1_CEMBA180430_8B_2_D2_ad006


title: CEMBA180430_8B_1_CEMBA180430_8B_2_D2_ad010


title: CEMBA180430_8B_1_CEMBA180430_8B_2_D2_ad012


title: CEMBA180430_8B_1_CEMBA180430_8B_2_D2_ad007


title: CEMBA180430_8B_1_CEMBA180430_8B_2_D2_ad001


title: CEMBA180430_8B_1_CEMBA180430_8B_2_D10_ad007


title: CEMBA180430_8B_1_CEMBA180430_8B_2_D10_ad006


title: 20nM EFV evolution experiment 2 [D12 C2C 20% Chip 1 013]

description: D12 C2C 20% Chip 1 013


title: 20nM EFV evolution experiment 2 [D8 CF Chip 1 005]

description: D8 CF Chip 1 005


title: 20nM EFV evolution experiment 2 [D10 CF Chip 1 008]

description: D10 CF Chip 1 008


title: CEMBA180430_8B_1_CEMBA180430_8B_2_D10_ad004


title: CEMBA180430_8B_1_CEMBA180430_8B_2_D10_ad002


title: 20nM EFV evolution experiment 2 [D14 CF Chip 1 014]

description: D14 CF Chip 1 014


title: 59

city: Belmont

first: Nikolaos

last: Daskalakis

state: MA

address: Oaks Building 328, Mailstop 212, 115 Mill Street

department: Department of Psychiatry

institute: McLean Hospital/ Harvard Medical School

data_processing:
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36.
The reads were then mapped to the Mus musculus GRCm38 reference genome available on ENSEMBL using the STAR aligner.
There resulting BAM files were sorted using the samtools sort function and used for gene counting.
Count files were processed with edgeR.
8204 gene symbols with cpm>4 in all samples were retained.
Samples were retained according to the full capturing of their behavioral data and based on outlier determination, according to a consensus of hierarchical clustering, PCA and MDS. 44 samples were retained.
Log transformed data were then voom normalized
Genome_build: Mus musculus GRCm38 reference genome
Supplementary_files_format_and_content: The normalized matrix has genes as rows and individual mice as columns.

molecule: polyA RNA

source_name: CRH TRAPSeq

extract_protocol:
Tissue was homogenized and mRNA’s isolated from GFP-tagged ribosomes (TRAP). RNA quantity and quality were assessed using Bioanalyzer Pico Chip (Agilent).
Libraries were prepared using SMARTer HV kit (Clontech) and NexteraXT DNAkit.
Microelectrophoresis was used to validate libraries followed by quantification, pooling and clustering on the Illumina TruSeq v3 flowcell. Clustered flowcell was sequenced using an Illumina HiSeq 1000 in 50bp- paired end mode. Twenty-five million reads per sample was were targeted.

treatment_protocol: For all FC and EXT experiments involving gene analyses, mice were habituated to the chamber (Med Associates) for 10 minutes for the two days preceding FC. On the  day of training mice were exposed to five tone-shock pairings (Pre-CS period: 180s, CS:30s 6000Hz, 65-70 db, co-terminating shock (US): .5s, .65 mA, ITI between CS’s: 90s). For TA control group shocks were omitted by turning shock generator off. The EXT group was returned to the animal care facility while FC and TA groups were left in holding room until sacrifice. The next day EXT group was tested in a novel context. Alternative context was provided in different set of apparatuses in a different room and had different olfactory cue, lighting conditions and flooring. Mice were exposed to 30CSs in the absence of any US reinforcer (Pre-CS period: 180s, CS:30s 6000Hz, 65-70 db, ITI between CS’s: 60s). Following EXT, mice were returned to the holding room until sacrifice. TRAP was performed in accordance with methods published by Heiman et al.. Adult Crh-TRAP mice were quickly anesthetized with isofluorane, decapitated, brains removed and snap-frozen. Punches centered over the amygdala were taken bilaterally using a 1mm punch.

value: Crh-TRAP

value: Central Amygdala

tag: group

value: EXT

tag: batch

value: M


title: CEMBA180430_8B_1_CEMBA180430_8B_2_D1_ad007


title: 55


title: 20nM EFV evolution experiment 2 [D4 Chip 1 001  ]

description: D4 Chip 1 001


title: CEMBA180430_8B_1_CEMBA180430_8B_2_D1_ad004


title: 60


title: 20nM EFV evolution experiment 2 [D6 CF Chip 1 002]

description: D6 CF Chip 1 002


title: 20nM EFV evolution experiment 2 [D8 C2C 20% Chip 1 007]

description: D8 C2C 20% Chip 1 007


title: 58


title: 20nM EFV evolution experiment 2 [D12 CF Chip 1 011]

description: D12 CF Chip 1 011


title: 53

value: F


title: 20nM EFV evolution experiment 2 [D10 C2C 20% Chip 1 010]

description: D10 C2C 20% Chip 1 010


title: 57


title: 51


title: CEMBA180430_8B_1_CEMBA180430_8B_2_D1_ad006


title: 20nM EFV evolution experiment 2 [D14 C2C 20% Chip 1 016]

description: D14 C2C 20% Chip 1 016


title: CEMBA180430_8B_1_CEMBA180430_8B_2_D10_ad001


title: CEMBA180430_8B_1_CEMBA180430_8B_2_D1_ad010


title: CEMBA180430_8B_1_CEMBA180430_8B_2_D1_ad012


title: CEMBA180430_8B_1_CEMBA180430_8B_2_D1_ad001


title: 52


title: 20nM EFV evolution experiment 2 [D6 C2C 20% Chip 1 004]

description: D6 C2C 20% Chip 1 004


title: 20nM EFV evolution experiment 1 [Day18CF]

source_name: 20nM EFV evolution experiment 1


title: CEMBA180430_8B_1_CEMBA180430_8B_2_D1_ad002


title: 49

value: FC


title: 20nM EFV evolution experiment 1 [Day18CC]


title: 48


title: 47


title: 20nM EFV evolution experiment 1 [Day16CF]


title: 44


title: 20nM EFV evolution experiment 1 [Day14CF]


title: CEMBA180430_8B_1_CEMBA180430_8B_2_C9_ad012


title: 45


title: 20nM EFV evolution experiment 1 [Day16CC]


title: CEMBA180430_8B_1_CEMBA180430_8B_2_C9_ad007


title: CEMBA180430_8B_1_CEMBA180430_8B_2_C9_ad001


title: 20nM EFV evolution experiment 1 [Day14CC]


title: 20nM EFV evolution experiment 1 [Day10CC]


title: CEMBA180430_8B_1_CEMBA180430_8B_2_C9_ad002


title: 20nM EFV evolution experiment 1 [Day8CF]


title: CEMBA180430_8B_1_CEMBA180430_8B_2_C9_ad008


title: 42


title: 43


title: CEMBA180430_8B_1_CEMBA180430_8B_2_C9_ad004


title: 40

value: TA


title: 20nM EFV evolution experiment 1 [Day6CF]


title: 39


title: 38


title: 37


title: CEMBA180430_8B_1_CEMBA180430_8B_2_C9_ad010

value: SSp


title: CEMBA180430_8B_1_CEMBA180430_8B_2_C8_ad001

value: male


title: 36


title: CEMBA180430_8B_1_CEMBA180430_8B_2_C8_ad012


title: CEMBA180430_8B_1_CEMBA180430_8B_2_C8_ad006


title: Drug step evoltion experiment 3 [D26-CF-3_S45]

source_name: Drug step evoltion experiment 3

value: Experiment carried out at 20nM EFV for the first 3 viral cycles and thereafter in a combination of 20nM EFV and 770 FTC


title: 35


title: 20nM EFV evolution experiment 1 [Day8CC]


title: CEMBA180430_8B_1_CEMBA180430_8B_2_C8_ad002


title: Drug step evoltion experiment 3 [D24-CF-3_S43]


title: 32


title: 34


title: Drug step evoltion experiment 3 [D26-CC-3_S46]


title: CEMBA180430_8B_1_CEMBA180430_8B_2_C8_ad008


title: Drug step evoltion experiment 3 [D24-CC-3_S44]


title: Drug step evoltion experiment 3 [D22-CF-3_S41]


title: CEMBA180430_8B_1_CEMBA180430_8B_2_C8_ad007


title: 33


title: CEMBA180430_8B_1_CEMBA180430_8B_2_C8_ad004


title: 31


title: Drug step evoltion experiment 3 [D22-CC-3_S42]


title: 28


title: CEMBA180430_8B_1_CEMBA180430_8B_2_C7_ad001


title: CEMBA180430_8B_1_CEMBA180430_8B_2_C7_ad012


title: 26


title: 20nM EFV evolution experiment 1 [Day4]


title: CEMBA180430_8B_1_CEMBA180430_8B_2_C7_ad010


title: CEMBA180430_8B_1_CEMBA180430_8B_2_C7_ad006


title: 25


title: Drug step evoltion experiment 3 [D20-CF-3_S39]


title: Drug step evoltion experiment 3 [D20-CC-3_S40]


title: Drug step evoltion experiment 3 [D18-CF-3_S37]


title: CEMBA180430_8B_1_CEMBA180430_8B_2_C7_ad008


title: 21


title: 22


title: Drug step evoltion experiment 3 [D16-CF-3_S35]


title: 23


title: 18


title: 19


title: CEMBA180430_8B_1_CEMBA180430_8B_2_C6_ad012


title: Drug step evoltion experiment 3 [D14-CF-3_S33]


title: CEMBA180430_8B_1_CEMBA180430_8B_2_C6_ad007


title: 16


title: Drug step evoltion experiment 3 [D12-CF-3_S31]


title: CEMBA180430_8B_1_CEMBA180430_8B_2_C6_ad006


title: 24


title: CEMBA180430_8B_1_CEMBA180430_8B_2_C7_ad004


title: CEMBA180430_8B_1_CEMBA180430_8B_2_C6_ad004


title: 13


title: Drug step evoltion experiment 3 [D18-CC-3_S38]


title: CEMBA180430_8B_1_CEMBA180430_8B_2_C6_ad002


title: 17


title: CEMBA180430_8B_1_CEMBA180430_8B_2_C6_ad001


title: CEMBA180430_8B_1_CEMBA180430_8B_2_C7_ad002


title: 12


title: Drug step evoltion experiment 3 [D10-CC-3_S30]


title: Drug step evoltion experiment 3 [D14-CC-3_S34]


title: CEMBA180430_8B_1_CEMBA180430_8B_2_C6_ad010


title: CEMBA180430_8B_1_CEMBA180430_8B_2_C5_ad004


title: Drug step evoltion experiment 3 [D12-CC-3_S32]


title: Drug step evoltion experiment 3 [D8-CF-3_S27]


title: Drug step evoltion experiment 3 [D10-CF-3_S29]


title: CEMBA180430_8B_1_CEMBA180430_8B_2_C6_ad008


title: Drug step evoltion experiment 3 [D16-CC-3_S36]


title: 10


title: Drug step evoltion experiment 3 [D8-CC-3_S28]


title: 9


title: 8


title: 5


title: Drug step evoltion experiment 3 [D6-CF-3_S25]


title: CEMBA180430_8B_1_CEMBA180430_8B_2_C5_ad007


title: 4


title: 1


title: CEMBA180430_8B_1_CEMBA180430_8B_2_C5_ad006


title: Drug step evoltion experiment 3 [D6-CC-3_S26]


title: CEMBA180430_8B_1_CEMBA180430_8B_2_C5_ad002


title: Drug step evoltion experiment 2 [D26-CC-2_S23]

source_name: Drug step evoltion experiment 2


title: Drug step evoltion experiment 3 [D4-3_S24]


title: Drug step evoltion experiment 2 [D26-CF-2_S22]


title: CEMBA180430_8B_1_CEMBA180430_8B_2_C5_ad008


title: CEMBA180430_8B_1_CEMBA180430_8B_2_C5_ad012


title: CEMBA180430_8B_1_CEMBA180430_8B_2_C4_ad008


title: Drug step evoltion experiment 2 [D24-CC-2_S21]


title: CEMBA180430_8B_1_CEMBA180430_8B_2_C4_ad002


title: Drug step evoltion experiment 2 [D24-CF-2_S20]


title: CEMBA180430_8B_1_CEMBA180430_8B_2_C4_ad007


title: Drug step evoltion experiment 2 [D22-CF-2_S18]


title: Drug step evoltion experiment 2 [D22-CC-2_S19]


title: CEMBA180430_8B_1_CEMBA180430_8B_2_C4_ad006


title: Drug step evoltion experiment 2 [D20-CF-2_S16]


title: CEMBA180430_8B_1_CEMBA180430_8B_2_C4_ad001


title: Sample_PAG141 Malaria Symptomatic stage mRNA Year2

city: Abu dhabi

first: Youssef

last: Idaghdour

state: Abu dhabi

address: Saadiyat Marina District

department: Biology

country: United Arab Emirates

institute: NYUAD

data_processing:
raw reads were processed using Trimmomatic v0.36 to remove adapter sequences and low-quality bases (Phred quality score < 20).
 Filtered reads were then mapped to the human reference genome (Ensembl GRCh38 release-84) using STAR v2.5.0c.
Transcripts abundances were estimated as transcripts per million
Only genes with a minimum of 1 TPM in 10 samples per experimental condition were retained for downstream analyses
Genome_build: hg38

source_name: Blood

extract_protocol:
globin-mRNA depletion using the GlobinClear kit (Thermo Fisher)
KAPA Stranded RNA-Seq kit with RiboErase (Kapa Biosystems) and 100 bp paired-end sequencing using the TruSeq SBS Kit v3 - HS (Illumina)

tag: visit

value: Malaria Symptomatic stage


title: Sample_PAG178 Malaria Symptomatic stage mRNA Year2


title: CEMBA180430_8B_1_CEMBA180430_8B_2_C4_ad012


title: 20nM EFV evolution experiment 1 [Day10CF]


title: Drug step evoltion experiment 2 [D20-CC-2_S17]


title: CEMBA180430_8B_1_CEMBA180430_8B_2_C3_ad012


title: Drug step evoltion experiment 2 [D18-CF-2_S14]


title: Sample_PAG163 Malaria Symptomatic stage mRNA Year2


title: Drug step evoltion experiment 2 [D16-CF-2_S12]


title: Sample_PAG155 Malaria Symptomatic stage mRNA Year2


title: Drug step evoltion experiment 2 [D16-CC-2_S13]


title: CEMBA180430_8B_1_CEMBA180430_8B_2_C3_ad001


title: Sample_PAG153 Malaria Symptomatic stage mRNA Year2


title: CEMBA180430_8B_1_CEMBA180430_8B_2_C3_ad006


title: CEMBA180430_8B_1_CEMBA180430_8B_2_C3_ad007


title: CEMBA180430_8B_1_CEMBA180430_8B_2_C3_ad004


title: Sample_PAG158 Malaria Symptomatic stage mRNA Year2


title: Sample_PAG151 Malaria Symptomatic stage mRNA Year2


title: Drug step evoltion experiment 2 [D14-CF-2_S10]


title: Drug step evoltion experiment 2 [D14-CC-2_S11]


title: CEMBA180430_8B_1_CEMBA180430_8B_2_C3_ad002


title: Drug step evoltion experiment 2 [D18-CC-2_S15]


title: Sample_PAG146 Malaria Symptomatic stage mRNA Year2


title: CEMBA180430_8B_1_CEMBA180430_8B_2_C2_ad012


title: Drug step evoltion experiment 2 [D12-CF-2_S8]


title: CEMBA180430_8B_1_CEMBA180430_8B_2_C2_ad001


title: Sample_PAG145 Malaria Symptomatic stage mRNA Year2


title: Drug step evoltion experiment 2 [D12-CC-2_S9]


title: Sample_PAG144 Malaria Symptomatic stage mRNA Year2


title: Sample_PAG174 Malaria Symptomatic stage mRNA Year2


title: CEMBA180430_8B_1_CEMBA180430_8B_2_C2_ad007


title: Sample_PAG143 Malaria Symptomatic stage mRNA Year2


title: Drug step evoltion experiment 2 [D10-CF-2_S6]


title: CEMBA180430_8B_1_CEMBA180430_8B_2_C2_ad004


title: Drug step evoltion experiment 2 [D10-CC-2_S7]


title: CEMBA180430_8B_1_CEMBA180430_8B_2_C2_ad010


title: Sample_PAG137 Malaria Symptomatic stage mRNA Year2


title: Drug step evoltion experiment 2 [D8-CF-2_S4]


title: Sample_PAG136 Malaria Symptomatic stage mRNA Year2


title: CEMBA180430_8B_1_CEMBA180430_8B_2_C2_ad008


title: Drug step evoltion experiment 2 [D6-CF-2_S2]


title: Sample_PAG132 Malaria Symptomatic stage mRNA Year2


title: Sample_PAG124 Malaria Symptomatic stage mRNA Year2


title: CEMBA180430_8B_1_CEMBA180430_8B_2_C2_ad002


title: Sample_PAG121 Malaria Symptomatic stage mRNA Year2


title: Drug step evoltion experiment 2 [D8-CC-2_S5]


title: Sample_PAG120 Malaria Symptomatic stage mRNA Year2


title: CEMBA180430_8B_1_CEMBA180430_8B_2_C12_ad007


title: Drug step evoltion experiment 2 [D6-CC-2_S3]


title: CEMBA180430_8B_1_CEMBA180430_8B_2_C12_ad008


title: Sample_PAG117 Malaria Symptomatic stage mRNA Year2


title: CEMBA180430_8B_1_CEMBA180430_8B_2_C12_ad006


title: Drug step evoltion experiment 1 [D24-CF_S20]

source_name: Drug step evoltion experiment 1


title: Drug step evoltion experiment 2 [D4-2_S1]


title: Sample_PAG115 Malaria Symptomatic stage mRNA Year2


title: Drug step evoltion experiment 1 [D22-CF_S18]


title: Drug step evoltion experiment 1 [D24-CC_S21]


title: CEMBA180430_8B_1_CEMBA180430_8B_2_C12_ad004


title: Sample_PAG111 Malaria Symptomatic stage mRNA Year2


title: Drug step evoltion experiment 1 [D20-CF_S16]


title: CEMBA180430_8B_1_CEMBA180430_8B_2_C12_ad001


title: Sample_PAG102 Malaria Symptomatic stage mRNA Year2


title: Sample_PAG100 Malaria Symptomatic stage mRNA Year2


title: Drug step evoltion experiment 1 [D22-CC_S19]


title: CEMBA180430_8B_1_CEMBA180430_8B_2_C11_ad012


title: CEMBA180430_8B_1_CEMBA180430_8B_2_C12_ad012


title: Drug step evoltion experiment 1 [D18-CF_S14]


title: Drug step evoltion experiment 1 [D20-CC_S17]


title: CEMBA180430_8B_1_CEMBA180430_8B_2_C11_ad010


title: Sample_PAG094 Malaria Symptomatic stage mRNA Year2


title: CEMBA180430_8B_1_CEMBA180430_8B_2_C11_ad008


title: Sample_PAG083 Malaria Symptomatic stage mRNA Year2


title: CEMBA180430_8B_1_CEMBA180430_8B_2_C11_ad007


title: Sample_PAG099 Malaria Symptomatic stage mRNA Year2


title: Drug step evoltion experiment 1 [D18-CC_S15]


title: Sample_PAG080 Malaria Symptomatic stage mRNA Year2


title: Drug step evoltion experiment 1 [D16-CF_S12]


title: Sample_PAG076 Malaria Symptomatic stage mRNA Year2


title: CEMBA180430_8B_1_CEMBA180430_8B_2_C11_ad004


title: Drug step evoltion experiment 1 [D14-CF_S10]


title: CEMBA180430_8B_1_CEMBA180430_8B_2_C12_ad002


title: Sample_PAG072 Malaria Symptomatic stage mRNA Year2


title: CEMBA180430_8B_1_CEMBA180430_8B_2_C11_ad002


title: CEMBA180430_8B_1_CEMBA180430_8B_2_C10_ad012


title: Drug step evoltion experiment 1 [D14-CC_S11]


title: Sample_PAG064 Malaria Symptomatic stage mRNA Year2


title: Sample_PAG069 Malaria Symptomatic stage mRNA Year2


title: Drug step evoltion experiment 1 [D12-CC_S9]


title: Drug step evoltion experiment 1 [D10-CF_S6]


title: Sample_PAG053 Malaria Symptomatic stage mRNA Year2


title: CEMBA180430_8B_1_CEMBA180430_8B_2_C11_ad006


title: Sample_PAG061 Malaria Symptomatic stage mRNA Year2


title: CEMBA180430_8B_1_CEMBA180430_8B_2_C10_ad010


title: Drug step evoltion experiment 1 [D16-CC_S13]


title: Sample_PAG050 Malaria Symptomatic stage mRNA Year2


title: CEMBA180430_8B_1_CEMBA180430_8B_2_C10_ad006


title: CEMBA180430_8B_1_CEMBA180430_8B_2_C10_ad004


title: Drug step evoltion experiment 1 [D8-CF_S4]


title: Drug step evoltion experiment 1 [D10-CC_S7]


title: Sample_PAG044 Malaria Symptomatic stage mRNA Year2


title: Drug step evoltion experiment 1 [D8-CC_S5]


title: CEMBA180430_8B_1_CEMBA180430_8B_2_C10_ad002


title: CEMBA180430_8B_1_CEMBA180430_8B_2_C10_ad001


title: Drug step evoltion experiment 1 [D6-CF_S2]


title: Sample_PAG037 Malaria Symptomatic stage mRNA Year2


title: Drug step evoltion experiment 1 [D12-CF_S8]


title: Drug step evoltion experiment 1 [D6-CC_S3]


title: Sample_PAG034 Malaria Symptomatic stage mRNA Year2


title: Drug step evoltion experiment 1 [D4_S1]


title: Sample_PAG031 Malaria Symptomatic stage mRNA Year2


title: CEMBA180430_8B_1_CEMBA180430_8B_2_C10_ad008


title: Sample_PAG030 Malaria Symptomatic stage mRNA Year2


title: CEMBA180430_8B_1_CEMBA180430_8B_2_C1_ad008


title: CEMBA180430_8B_1_CEMBA180430_8B_2_C1_ad007


title: 40nM EFV evolution experiment 3 [D16CF3_S23]

source_name: 40nM EFV evolution experiment 3

value: Experiment carried out at 40nM EFV


title: CEMBA180430_8B_1_CEMBA180430_8B_2_C10_ad007


title: 40nM EFV evolution experiment 3 [D16CC3_S24]


title: Sample_PAG049 Malaria Symptomatic stage mRNA Year2


title: Sample_PAG029 Malaria Symptomatic stage mRNA Year2


title: 40nM EFV evolution experiment 3 [D14CF3_S21]


title: CEMBA180430_8B_1_CEMBA180430_8B_2_C1_ad002


title: CEMBA180430_8B_1_CEMBA180430_8B_2_C1_ad006


title: CEMBA180430_8B_1_CEMBA180430_8B_2_C1_ad012


title: 40nM EFV evolution experiment 3 [D14CC3_S22]


title: 40nM EFV evolution experiment 3 [D12CC3_S20]


title: CEMBA180430_8B_1_CEMBA180430_8B_2_B9_ad001


title: 40nM EFV evolution experiment 3 [D10CF3_S17]


title: CEMBA180430_8B_1_CEMBA180430_8B_2_C1_ad010


title: CEMBA180430_8B_1_CEMBA180430_8B_2_B9_ad007


title: 40nM EFV evolution experiment 3 [D10CC3_S18]


title: Sample_PAG016 Malaria Symptomatic stage mRNA Year2


title: CEMBA180430_8B_1_CEMBA180430_8B_2_B9_ad010


title: Sample_PAG019 Malaria Symptomatic stage mRNA Year2


title: Sample_PAG018 Malaria Symptomatic stage mRNA Year2


title: Sample_PAG008 Malaria Symptomatic stage mRNA Year2


title: Sample_PAG025 Malaria Symptomatic stage mRNA Year2


title: 40nM EFV evolution experiment 3 [D8CC3_S16]


title: CEMBA180430_8B_1_CEMBA180430_8B_2_B9_ad002


title: Sample_PAG002 Malaria Symptomatic stage mRNA Year2


title: Sample_PAG006 Malaria Symptomatic stage mRNA Year2


title: Sample_PAG020 Malaria Symptomatic stage mRNA Year2


title: Sample_PAG021 Malaria Symptomatic stage mRNA Year2


title: 40nM EFV evolution experiment 3 [D6CC3_S14]


title: CEMBA180430_8B_1_CEMBA180430_8B_2_B9_ad008


title: 40nM EFV evolution experiment 3 [D12CF3_S19]


title: CEMBA180430_8B_1_CEMBA180430_8B_2_B9_ad012


title: CEMBA180430_8B_1_CEMBA180430_8B_2_B8_ad012


title: 40nM EFV evolution experiment 2 [D16CF2_S12]

source_name: 40nM EFV evolution experiment 2


title: 40nM EFV evolution experiment 2 [D16CC2_S13]


title: 40nM EFV evolution experiment 2 [D14CF2_S10]


title: 40nM EFV evolution experiment 2 [D14CC2_S11]


title: 40nM EFV evolution experiment 3 [D8CF3_S15]


title: CEMBA180430_8B_1_CEMBA180430_8B_2_B8_ad004


title: PAG_150 Malaria Symptomatic stage miRNA Year1 Sample

data_processing:
Poor quality reads/bases or technical sequences such as adapters are removed from the paired end reads using Trimmomatic v0.32
Trimmed reads were further processed with the FASTX Toolkit v0.0.14 to filter out reads with tail quality < 15 nucleotides and retain reads of 16-25 nucleotides length for downstream analyses.
High-quality reads were subject to small RNAs annotation and quantification using the online tool OASIS and miRbase v21
miRNAs expressed at a minimum count of 10 reads in at least 50% of the samples per experimental condition were retained
Genome_build: hg38

extract_protocol:
Tempus Spin RNA Isolation Kit
Truseq small rna library prep kit (Illumina) and KAPA Stranded RNA-Seq kit with RiboErase (Kapa Biosystems), respectively. Small RNA


title: 40nM EFV evolution experiment 2 [D12CF2_S8]


title: CEMBA180430_8B_1_CEMBA180430_8B_2_B8_ad006


title: PAG_150 Post treatment miRNA Year1 Sample

value: Post treatment


title: CEMBA180430_8B_1_CEMBA180430_8B_2_B8_ad002


title: CEMBA180430_8B_1_CEMBA180430_8B_2_B9_ad004


title: PAG_149 Malaria Symptomatic stage miRNA Year1 Sample


title: 40nM EFV evolution experiment 2 [D12CC2_S9]


title: PAG_149 Malaria non-symptomatic stage miRNA Year1 Sample

value: Malaria non-symptomatic stage


title: CEMBA180430_8B_1_CEMBA180430_8B_2_B8_ad008


title: Sample_PAG001 Malaria Symptomatic stage mRNA Year2


title: 40nM EFV evolution experiment 2 [D10CF2_S6]

value: RevCEM E7 cells infection with Nl4-3


title: PAG_144 Malaria Symptomatic stage miRNA Year1 Sample


title: CEMBA180430_8B_1_CEMBA180430_8B_2_B8_ad007


title: 40nM EFV evolution experiment 2 [D8CF2_S4]


title: PAG_141 Post treatment miRNA Year1 Sample


title: PAG_144 Noninfective stage miRNA Year1 Sample

value: Noninfective stage


title: CEMBA180430_8B_1_CEMBA180430_8B_2_B7_ad004


title: PAG_149 Noninfective stage miRNA Year1 Sample


title: 40nM EFV evolution experiment 2 [D10CC2_S7]

value: Reverse transcriptase region of HIV provirus


title: CEMBA180430_8B_1_CEMBA180430_8B_2_B7_ad006


title: CEMBA180430_8B_1_CEMBA180430_8B_2_B7_ad002


title: PAG_141 Malaria Symptomatic stage miRNA Year1 Sample


title: 40nM EFV evolution experiment 2 [D8CC2_S5]


title: 40nM EFV evolution experiment 2 [D6CF2_S2]


title: CEMBA180430_8B_1_CEMBA180430_8B_2_B7_ad012


title: PAG_141 Noninfective stage miRNA Year1 Sample


title: 40nM EFV evolution experiment 2 [D6CC2_S3]


title: 40nM EFV evolution experiment 1 [D16-CF-40_S20]

source_name: 40nM EFV evolution experiment 1


title: CEMBA180430_8B_1_CEMBA180430_8B_2_B6_ad012


title: PAG_137 Malaria non-symptomatic stage miRNA Year1 Sample


title: 40nM EFV evolution experiment 1 [D16-CC-40_S26]


title: CEMBA180430_8B_1_CEMBA180430_8B_2_B6_ad006


title: CEMBA180430_8B_1_CEMBA180430_8B_2_B6_ad002


title: PAG_129 Malaria Symptomatic stage miRNA Year1 Sample


title: CEMBA180430_8B_1_CEMBA180430_8B_2_B7_ad010


title: CEMBA180430_8B_1_CEMBA180430_8B_2_B6_ad007


title: 40nM EFV evolution experiment 1 [D12-CF-40_S18]


title: 40nM EFV evolution experiment 1 [D14-CF-40_S19]


title: PAG_123 Malaria non-symptomatic stage miRNA Year1 Sample


title: 40nM EFV evolution experiment 1 [D14-CC-40_S25]


title: PAG_123 Post treatment miRNA Year1 Sample


title: 40nM EFV evolution experiment 1 [D12-CC-40_S24]


title: CEMBA180430_8B_1_CEMBA180430_8B_2_B6_ad001


title: PAG_129 Noninfective stage miRNA Year1 Sample


title: PAG_129 Post treatment miRNA Year1 Sample


title: PAG_117 Post treatment miRNA Year1 Sample


title: CEMBA180430_8B_1_CEMBA180430_8B_2_B6_ad008


title: CEMBA180430_8B_1_CEMBA180430_8B_2_B5_ad007


title: CEMBA180430_8B_1_CEMBA180430_8B_2_B5_ad012


title: CEMBA180430_8B_1_CEMBA180430_8B_2_B5_ad001


title: 40nM EFV evolution experiment 1 [D10-CF-40_S17]


title: 40nM EFV evolution experiment 1 [D8-CF-40_S16]


title: 40nM EFV evolution experiment 1 [D10-CC-40_S23]


title: PAG_123 Noninfective stage miRNA Year1 Sample


title: 40nM EFV evolution experiment 1 [D8-CC-40_S22]


title: PAG_117 Noninfective stage miRNA Year1 Sample


title: PAG_150 Noninfective stage miRNA Year1 Sample


title: CEMBA180430_8B_1_CEMBA180430_8B_2_B5_ad010


title: PAG_117 Malaria non-symptomatic stage miRNA Year1 Sample


title: PAG_116 Post treatment miRNA Year1 Sample


title: 40nM EFV evolution experiment 1 [D6-CC-40_S21]


title: 40nM EFV evolution experiment 1 [D6-CF-40_S15]


title: 40nM EFV evolution experiment 1 [D4-40_S14]


title: CEMBA180430_8B_1_CEMBA180430_8B_2_B4_ad001


title: CEMBA180430_8B_1_CEMBA180430_8B_2_B4_ad007


title: CEMBA180430_8B_1_CEMBA180430_8B_2_B5_ad008


title: CEMBA180430_8B_1_CEMBA180430_8B_2_B4_ad010


title: CEMBA180430_8B_1_CEMBA180430_8B_2_B4_ad006


title: CEMBA180430_8B_1_CEMBA180430_8B_2_B5_ad004


title: 20nM EFV evolution experiment 3  [D16-CF-20_S7]

source_name: 20nM EFV evolution experiment 3

value: Experiment carried out at 20nM EFV


title: 20nM EFV evolution experiment 3  [D14-CF-20_S6]


title: 20nM EFV evolution experiment 3  [D16-CC-20_S13]


title: CEMBA180430_8B_1_CEMBA180430_8B_2_B5_ad006


title: PAG_116 Noninfective stage miRNA Year1 Sample


title: CEMBA180430_8B_1_CEMBA180430_8B_2_B4_ad004


title: PAG_116 Malaria non-symptomatic stage miRNA Year1 Sample


title: 20nM EFV evolution experiment 3  [D12-CC-20_S11]


title: PAG_116 Malaria Symptomatic stage miRNA Year1 Sample


title: 20nM EFV evolution experiment 3  [D12-CF-20_S5]


title: PAG_115 Malaria non-symptomatic stage miRNA Year1 Sample


title: PAG_115 Malaria Symptomatic stage miRNA Year1 Sample


title: PAG_115 Post treatment miRNA Year1 Sample


title: CEMBA180430_8B_1_CEMBA180430_8B_2_B4_ad002


title: CEMBA180430_8B_1_CEMBA180430_8B_2_B4_ad008


title: 20nM EFV evolution experiment 3  [D10-CF-20_S4]


title: PAG_114 Post treatment miRNA Year1 Sample


title: PAG_114 Malaria Symptomatic stage miRNA Year1 Sample


title: CEMBA180430_8B_1_CEMBA180430_8B_2_B3_ad001


title: PAG_114 Noninfective stage miRNA Year1 Sample


title: 20nM EFV evolution experiment 3  [D10-CC-20_S10]


title: CEMBA180430_8B_1_CEMBA180430_8B_2_B3_ad010


title: 20nM EFV evolution experiment 3  [D14-CC-20_S12]


title: PAG_112 Post treatment miRNA Year1 Sample


title: CEMBA180430_8B_1_CEMBA180430_8B_2_B3_ad008


title: CEMBA180430_8B_1_CEMBA180430_8B_2_B3_ad006


title: 20nM EFV evolution experiment 3  [D8-CC-20_S9]


title: PAG_112 Malaria Symptomatic stage miRNA Year1 Sample


title: 20nM EFV evolution experiment 3  [D8-CF-20_S3]


title: 20nM EFV evolution experiment 3  [D6-CF-20_S2]


title: PAG_115 Noninfective stage miRNA Year1 Sample


title: PAG_111 Malaria non-symptomatic stage miRNA Year1 Sample


title: CEMBA180430_8B_1_CEMBA180430_8B_2_B3_ad004


title: 20nM EFV evolution experiment 3  [D6-CC-20_S8]


title: 20nM EFV evolution experiment 3  [D4-20_S1]


title: PAG_109 Malaria Symptomatic stage miRNA Year1 Sample


title: CEMBA180430_8B_1_CEMBA180430_8B_2_B12_ad008


title: PAG_104 Post treatment miRNA Year1 Sample


title: PAG_112 Noninfective stage miRNA Year1 Sample


title: CEMBA180430_8B_1_CEMBA180430_8B_2_B2_ad012