title: Armillaria sporocarp biological rep 3, technical rep 2

city: Lincoln

first: Rachel

middle: Anne

last: Koch

state: NE

address: 1875 N 38th Street

department: Plant Pathology

institute: University of Nebraska

description:
"pure" tissue containing Armillaria mellea
Armillaria.counts.genes.q30.matrix.txt
Arm.TMM.q30.csv
Arm4_2

data_processing:
Sequencer: Illumina HiSeq 2500; Basecalling pipeline: HiSeq Control Software 2.2.38
Sequenced reads were trimmed for adaptors and sequencing contaminants were removed using bbduk (https://jgi.doe.gov/data-and-tools/bbtools/)
Reads were then mapped to the de novo E. abortivum or Armillaria assembled transcriptome using RSEM and Bowtie v 2, and only reads with a mapq score of q = or greater than 30 retained
The count data from RSEM was then normalized using TMM, implemented in edgeR
Genome_build: de novo transcriptome assembly of both E. abortivum and Armillaria mellea (will be submitted to the transcriptome assembly database on Genbank)
Supplementary_files_format_and_content: Entoloma.counts.genes.q30.matrix.txt: E. abortivum matrix table with raw gene counts for every gene and every sample for E. abortivum sporocarps and carpophoroids
Supplementary_files_format_and_content: Armillaria.counts.genes.q30.matrix.txt: Armillaria mellea matrix table with raw gene counts for every gene and every sample for Armillaria mellea sporocarps and carpophoroids
Supplementary_files_format_and_content: Ent.TMM.q30.csv: E. abortivum .csv file including TMM (normalized) values for each sample and gene for E. abortivum sporocarps and the carpophoroids
Supplementary_files_format_and_content: Arm.TMM.q30.csv: Armillaria mellea .csv file including TMM (normalized) values for each sample and gene for Armillaria mellea sporocarps and the carpophoroids

organism: Armillaria mellea

source_name: Armillaria sporocarp

extract_protocol:
Total RNA was extracted from the ground tissue using the Qiagen RNeasy kit (Qiagen Inc., Hilden, Germany) according to manufacturer’s protocol
Libraries were constructed with the TruSeq Standard Total RNA Library Preparation Kit with Ribo-Zero ribosomal reduction following the protocol developed by Schuierer et al (2017)

value: sporocarp


title: Armillaria sporocarp biological rep 3, technical rep 1

status: Public on Sep 23 2021

type: SRA

country: USA

description:
"pure" tissue containing Armillaria mellea
Armillaria.counts.genes.q30.matrix.txt
Arm.TMM.q30.csv
Arm4_1

library_source: transcriptomic

molecule: total RNA

tag: tissue


title: Armillaria sporocarp biological rep 3, technical rep 3

description:
"pure" tissue containing Armillaria mellea
Armillaria.counts.genes.q30.matrix.txt
Arm.TMM.q30.csv
Arm4_3


title: Armillaria sporocarp biological rep 1, technical rep 3

description:
"pure" tissue containing Armillaria mellea
Armillaria.counts.genes.q30.matrix.txt
Arm.TMM.q30.csv
Arm1_3


title: Bcell_37-V7

city: Chicago

first: Slim

last: Fourati

state: Illinois

address: 300 E Superior St

department: Medicine

institute: Northwestern University

data_processing:
Raw reads were trimmed for low quality reads and miscalled nucleotides using Trimmomatic v. 0.33.
Reads that passed the trimming step were aligned to human genome (Ensembl GRCh38 release 80) using the STAR aligner (version 2.4.2a).
Aligned reads were counted using HTSeq (version 0.6.1).
Supplementary_files_format_and_content: tab-delimited text files include raw counts for each sample.

molecule: polyA RNA

organism: Homo sapiens

source_name: Blood B cells

extract_protocol:
RNA was extracted from sorted cells from PBMC of HVTN 505 vaccinees using RNAzolRT (MRC Inc.) as per recommendations from the manufacturer.
Polyadenylated transcripts were purified on oligo-dT magnetic beads, fragmented, reverse transcribed using random hexamers and incorporated into barcoded cDNA libraries based on the Illumina TruSeq platform. Next, libraries were validated by electrophoresis, quantified, pooled and clustered on Illumina TruSeq v2 flow cells. Clustered flow cells were sequenced on an Illumina HiSeq (2000/4000) using 2 x 75 base paired-end runs.

tag: cell type

value: Blood B cells

tag: participant id

tag: visit id

tag: timepoint

value: month 7

tag: treatment

value: Vaccine

tag: hiv-1 acquisition

value: No


title: Bcell_27-V2

value: pre-vaccination


title: A375-BRAFV600E/NRASQ61K_2

type: RNA

city: Tucson

first: Georg

middle: Thomas

last: Wondrak

state: Arizona

address: UA Cancer Center, 1515 N Campbell Ave, Room 3971

department: Pharm/Tox

institute: University of Arizona

description: Total RNA analyzed for gene expression of 770 transcripts by nCounter PanCancer Progression panel

hyb_protocol: All samples were run targeting 100 ng of total RNA (19 h at 65°C) prior to being processed on the nCouner FLEX Analysis System.

scan_protocol: Samples were run on the nCounter Prep Station with high sensitivity settings followed by imaging on the Digital Analyzer with FOV (Field of View) data resolution set to 555.

data_processing:
Raw data files were uploaded (RCC files) to the NanoString nSolver Analysis 4.0 software. According to nSolver Advanced Analysis Module (version 2.0.115) specifications, the geNorm algorithm (pairwise variation statistics) was used to choose an ideal set of housekeeping genes (from a total set of 30) with minimal pairwise variation for normalization. Based on NanoString cancer pathway score analysis [indicating expression changes relevant to EMT (epithelial to mesenchymal transition)], a select number of genes (23 in total) displaying statistically significant expression changes was included in our manuscript, substantiating the specific role of NRAS-driven EMT changes in malignant melanoma.
The nCounterTM Advanced Analysis software (version 2.0.115) within a NanoString nSolver analysis 4.0 software was used for p-value adjustment (Benjamini-Yekutieli false discovery rate). Data with p-values lower than 0.05 were deemed statistically significant. Genes relevant to melanoma EMT were included in the tabular summary of expression changes as displayed in our manuscript.

label: reporter probe: fluorescent barcode; capture probe: biotin

label_protocol: NanoString nCounter gene expression assay protocol was followed (https://www.nanostring.com/wp-content/uploads/2021/03/MAN-10056-05-Gene-Expression-Hybridization-Protocol.pdf).

growth_protocol: Both isogenic malignant melanoma cell lines were grown in DMEM media supplemented with 10% FBS at 37°C, 5%CO2 (analysis occurred no later than 5 population doublings after thawing).

extract_protocol: Total RNA was extracted from cell lysates using Qiagen RNeasy Mini kit according to manufacturer instructions.

treatment_protocol: No special treatment was performed; two isogenic malignant melanoma cell lines differing in NRAS status [NRAS wildtype and NRAS mutant (NRAS Q61K)] were compared.

tag: cell line

value: ATCC  CRL-1619IG-2-LUC2

value: malignant melanoma cell line


title: A375-BRAFV600E/NRASQ61K_3


title: Bcell_36-V7


title: Bcell_39-V7


title: Armillaria sporocarp biological rep 1, technical rep 2

description:
"pure" tissue containing Armillaria mellea
Armillaria.counts.genes.q30.matrix.txt
Arm.TMM.q30.csv
Arm1_2


title: Bcell_26-V7


title: Armillaria sporocarp biological rep 2, technical rep 1

description:
"pure" tissue containing Armillaria mellea
Armillaria.counts.genes.q30.matrix.txt
Arm.TMM.q30.csv
Arm3_1


title: Bcell_40-V2

value: Yes


title: Bcell_26-V2


title: Bcell_25-V2


title: E. abortivum/Armillaria carpophoroid biological rep 3, technical rep 2

description:
"mixed" tissue containing E. abortivum and Armillaria
Entoloma.counts.genes.q30.matrix.txt
Ent.TMM.q30.csv
Armillaria.counts.genes.q30.matrix.txt
Arm.TMM.q30.csv
Abor5_2

organism:
Armillaria mellea
Entoloma abortivum

source_name: carpophoroid

value: carpophoroid


title: Armillaria sporocarp biological rep 2, technical rep 3

description:
"pure" tissue containing Armillaria mellea
Armillaria.counts.genes.q30.matrix.txt
Arm.TMM.q30.csv
Arm3_3


title: Bcell_25-V7


title: Bcell_21-V7


title: E. abortivum/Armillaria carpophoroid biological rep 2, technical rep 3

description:
"mixed" tissue containing E. abortivum and Armillaria
Entoloma.counts.genes.q30.matrix.txt
Ent.TMM.q30.csv
Armillaria.counts.genes.q30.matrix.txt
Arm.TMM.q30.csv
Abor4_3


title: Bcell_37-V2


title: E. abortivum/Armillaria carpophoroid biological rep 1, technical rep 2

description:
"mixed" tissue containing E. abortivum and Armillaria
Entoloma.counts.genes.q30.matrix.txt
Ent.TMM.q30.csv
Armillaria.counts.genes.q30.matrix.txt
Arm.TMM.q30.csv
Abor2_2


title: Bcell_28-V7


title: Armillaria sporocarp biological rep 1, technical rep 1

description:
"pure" tissue containing Armillaria mellea
Armillaria.counts.genes.q30.matrix.txt
Arm.TMM.q30.csv
Arm1_1


title: Bcell_21-V9

value: month 12


title: Armillaria sporocarp biological rep 2, technical rep 2

description:
"pure" tissue containing Armillaria mellea
Armillaria.counts.genes.q30.matrix.txt
Arm.TMM.q30.csv
Arm3_2


title: E. abortivum/Armillaria carpophoroid biological rep 1, technical rep 1

description:
"mixed" tissue containing E. abortivum and Armillaria
Entoloma.counts.genes.q30.matrix.txt
Ent.TMM.q30.csv
Armillaria.counts.genes.q30.matrix.txt
Arm.TMM.q30.csv
Abor2_1


title: E. abortivum/Armillaria carpophoroid biological rep 3, technical rep 3

description:
"mixed" tissue containing E. abortivum and Armillaria
Entoloma.counts.genes.q30.matrix.txt
Ent.TMM.q30.csv
Armillaria.counts.genes.q30.matrix.txt
Arm.TMM.q30.csv
Abor5_3


title: E. abortivum/Armillaria carpophoroid biological rep 3, technical rep 1

description:
"mixed" tissue containing E. abortivum and Armillaria
Entoloma.counts.genes.q30.matrix.txt
Ent.TMM.q30.csv
Armillaria.counts.genes.q30.matrix.txt
Arm.TMM.q30.csv
Abor5_1


title: E. abortivum/Armillaria carpophoroid biological rep 2, technical rep 2

description:
"mixed" tissue containing E. abortivum and Armillaria
Entoloma.counts.genes.q30.matrix.txt
Ent.TMM.q30.csv
Armillaria.counts.genes.q30.matrix.txt
Arm.TMM.q30.csv
Abor4_2


title: Bcell_18-V7


title: E. abortivum/Armillaria carpophoroid biological rep 1, technical rep 3

description:
"mixed" tissue containing E. abortivum and Armillaria
Entoloma.counts.genes.q30.matrix.txt
Ent.TMM.q30.csv
Armillaria.counts.genes.q30.matrix.txt
Arm.TMM.q30.csv
Abor2_3


title: Bcell_21-V2


title: E. abortivum/Armillaria carpophoroid biological rep 2, technical rep 1

description:
"mixed" tissue containing E. abortivum and Armillaria
Entoloma.counts.genes.q30.matrix.txt
Ent.TMM.q30.csv
Armillaria.counts.genes.q30.matrix.txt
Arm.TMM.q30.csv
Abor4_1


title: Bcell_19-V2


title: Bcell_19-V9


title: Bcell_25-V9


title: Bcell_17-V2


title: Bcell_17-V9


title: Bcell_26-V9


title: Bcell_19-V7


title: Bcell_17-V7


title: Bcell_16-V7


title: Bcell_15-V9


title: Bcell_18-V2


title: Bcell_15-V2


title: Bcell_11-V7


title: Bcell_15-V7


title: Bcell_11-V2


title: Bcell_07-V9


title: Bcell_08-V7


title: Bcell_07-V7


title: Bcell_05-V7


title: Bcell_05-V2


title: Bcell_07-V2


title: kidney, 37

status: Public on Sep 24 2021

city: Warsaw

first: Michal

last: Mikula

address: Roentgena 5

department: Experimental Oncology

country: Poland

data_processing:
Raw sequences were trimmed according to quality using Trimmomatic (version 0.39) using default parameters, except MINLEN, which was set to 36
Trimmed sequences were mapped to Mus musculus, version mm10, reference genome provided by Ensembl, using Hisat2 with default parameters.
Optical duplicates were removed using MarkDuplicates tool from GATK package (version 4.1.2.0) with default parameters except the Optical Duplicate Pixel Distance parameter set to 12000
Mapped reads were associated with transcripts defined in Ensembl database (GRCm38, version 95) using HTSeq-count (version 0.9.1) with default parameters except –stranded set to “reverse”.
Genome_build: mm10
Supplementary_files_format_and_content: COUNTS (Ensembl ID; Gene name; read counts)

organism: Mus musculus

source_name: kidney

growth_protocol: 50000 RAW 264.7 cells were seeded in a presence of 10% Fetal Bovine Serum (FBS) on a 6-well plate a day before the treatment. Next day, cells were pretreated with 500 nM SCH772984 for 1h and then challenged with 10µg/ml LPS for 1h, 4h and 24hrs in 500 nM SCH772984 presence. Cells were collected at indicated time points and pellets were frozen at -80oC.

extract_protocol:
Total RNA was isolated from RAW 264.7 cells and tissues using TRIzol reagents (Sigma; T9424)
TruSeq Stranded Total RNA with RiboZero Gold H/M/R; 100bp PE (library preparation and sequencing at CeGaT GmbH)

treatment_protocol: C57BL/6W (own breeding) mice males, 16-20 wk of age, were maintained under the specific pathogen–free animal facility at Maria Skłodowska-Curie National Research Institute of Oncology according to the institutional guidelines, with the experimental protocols approved by The 2nd Local Ethical Committee for Animal Research in Warsaw, Poland (WAW2/47/2017 granted on 17th May 2017). 2 hours following the cececal ligation and puncture (CLP) procedure mice were injected i.p. with 10 mg/kg SCH772984 or formulation (3% DMSO + 10% Polyethylene Glycol) and every 6hr with another dose of SCH772984 or vehicle. At indicated time points (6h and 12h) anesthesia was induced again with isoflurane and blood collected via cardiac puncture. Sham-operated animals were used as control. The chest was opened and the heart and lungs collected rapidly into cryovials which were immediately snap-frozen in liquid nitrogen. Kidney and liver were collected in a similar fashion immediately thereafter. Lung, kidney, liver and heart tissues collected from four animals in CLP, CLP+ SCH772984 and sham group at 6h and 12h time points post-CLP were subjected to RNA-Seq. Sets of organs are matching same animals in a given group.

tag: strain

value: kidney

tag: passage

tag: drugs

value: vehicle

tag: rin values


title: Bcell_04-V2


title: Bcell_04-V9


title: PDAC-81

city: New York

first: Masataka

last: Amisaki

state: NY

address: 1275 York Ave

department: Human oncology & pathogenesis program(HOPP)

institute: Memorial Sloan Kettering Cancer Center

description: Gene expression data from human primary PDAC

hyb_protocol: Following fragmentation, upto 100 ng of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner 3000.

data_processing: The data were analyzed with probe set expression summarization files that can be loaded into Affymetrix® Expression Console Software and AffymetrixTranscriptome Analysis Console (TAC) Softwareusing Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

label: biotin

source_name: Primary PDAC

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from upto 100ng total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

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

tag: disease state

value: Pancreatic ductal adecnocarcinoma


title: PDAC-79


title: Bcell_04-V7


title: PDAC-80


title: PDAC-78


title: PDAC-75


title: PDAC-66


title: PDAC-76


title: Bcell_01-V7


title: Bcell_02-V7


title: Bcell_02-V2


title: PDAC-77


title: PDAC-73


title: PDAC-70


title: PDAC-72


title: PDAC-74


title: PDAC-64


title: PDAC-68


title: Bcell_03-V2


title: PDAC-69


title: BM_Therapy

city: Vienna

first: Sebastian

last: Eder

address: Zimmermannplatz 10

country: Austria

institute: Children's Cancer Research Institute

data_processing:
Single-cell RNA-seq was performed using the 10x-Genomics Chromium Single Cell Controller with the Chromium Single Cell 3′ v3 Kit. The raw sequencing data were processed with Cell Ranger v3.0.2 software (10x-Genomics) for demultiplexing and alignment to the GRCh38 human reference transcriptome.
Genome_build: GRCh38
Supplementary_files_format_and_content: Cell ranger output

source_name: BMMC

extract_protocol: Peripheral blood and bone marrow cells were isolated by density gradient centrifugation and subsets were purified by fluorescence-activating cell sorting using a FACScan flow cytometer (BD FACSAria).

value: bone marrow

value: vemurafenib

tag: patient diagnosis

value: Langerhans cell histiocytosis (LCH)


title: PDAC-71


title: PB_Therapy

source_name: PBMC

value: peripheral blood


title: PDAC-67


title: PDAC-65


title: PDAC-62


title: BM_Diagnosis


title: PDAC-63


title: Human_tissue_Rabbit_IgG_control

city: Los Angeles

first: Meng

last: Qu

state: California

address: 1002 West Childs Way

department: Keck Medical School

institute: University of Southern California

library_source: genomic

data_processing:
Illumina HiSeq 150 bp reads produced by ChIP-Seqs were mapped to the mm10 or hg38 genome using Bowtie2.
Peak calling was performed with MACS2.
Genome_build: mm10, hg38
Supplementary_files_format_and_content: bigWig files were merged replicates and generated using DeepTools with RPGC normalization. Peak files were generated by MACS2.

molecule: genomic DNA

source_name: U2OS cells

extract_protocol:
~ 50 mg of blood perfused liver tissue were dissected and snap frozen in liquid nitrogen. Frozen liver tissues were minced with razor blades and homogenized by pushing through 18G needle followed by 21G needle to release nuclei. Nuclei were immediately crosslinked with 1% formaldehyde for 10 min at room temperature and then quenched with glycine. After two washes, the nuclei were lysed in nuclear lysis buffer (50 mM Tris-HCl pH 8.0, 1% SDS, 10 mM EDTA) containing 1x EDTA-free protease inhibitor cocktail (Roche) and kept on ice for 5 min. Immediately, the lysates were sonicated 17 times for 30 sec by using Bioruptor (Diagenode). After centrifugation at 17,000 rpm for 15 minutes at 4°C, fragmented chromatin was diluted 10-fold with IP dilution buffer (20 mM Tris-HCl pH 8.0, 150 mM NaCl, 1% Triton X-100, 1 mM EDTA) supplemented with 1x EDTA-free protease inhibitor cocktail, and incubated with antibody overnight at 4°C. Dynabeads Protein G (Invitrogen cat. #10004D) was added to the chromatin and incubated for another 3 h. Afterwards, the beads were washed once with low salt wash buffer (20 mM Tris-HCl pH 8.0, 150 mM NaCl, 1% Triton X-100, 0.1% SDS, 2 mM EDTA) and once with high salt wash buffer (20 mM Tris-HCl pH 8.0, 500 mM NaCl, 1% Triton X-100, 0.1% SDS, 2 mM EDTA). IP elution buffer (1% SDS, 100 mM NaHCO3) was applied to the bead pellet and incubated at 30°C for 15 min. The eluate was added with NaCl to final conc. of 200 mM and reverse-crosslinked at 65°C overnight. To remove RNA and protein, RNase A and proteinase K were subsequently applied by incubating at 45°C for 1 h. Finally, DNA was purified with QIAquick PCR Purification columns.   ChIP-seq experiments with human cell lines were similar. The differences are the cells were crosslinked in culture dishes with 1% formaldehyde, and then scraped off for cell lysis and chromatin fragmentation.
2 ng of each sample was prepared using the NEB Ultra DNA Library Prep Kit for Illumina following manufacturer’s instructions. Each library was dual size selected with 0.55X and 0.14X Ampure beads followed by PCR amplification with Kappa HiFi 2x PCR mix (15 cycles). PCR product was then quantitated using the Qubit (Thermo Fisher) and BioAnalyzer (Agilent BioAnalyzer 2100) to determine library quantity. Libraries were then gel purified on a 2% agarose gel to remove secondary PCR amplification artifacts, quantitated on the Qubit and loaded onto HiSeq to generate more than 20M reads per sample.

tag: genotype

value: wild type

value: U2OS cells

tag: chip antibody


title: PB_Diagnosis


title: HepG2_HNF4A_ChIPseq_3

description:
HNF4A_ChIP-seq
HepG2_HNF4A_merged.bw

source_name: HepG2 cells

value: HepG2 cells


title: HepG2_HNF4A_ChIPseq_2

description:
HNF4A_ChIP-seq
HepG2_HNF4A_merged.bw


title: PDAC-59


title: PDAC-60


title: PDAC-61


title: Hep3B_HNF4A_ChIPseq_2

description:
HNF4A_ChIP-seq
Hep3B_HNF4A_merged.bw

source_name: Hep3B cells

value: Hep3B cells


title: Human_tissue_Mouse_IgG_control


title: Hep3B_BMAL1_ChIPseq_2

description:
BMAL1_ChIP-seq
Hep3B_BMAL1_merged.bw


title: PDAC-58


title: HepG2_HNF4A_ChIPseq_1

description:
HNF4A_ChIP-seq
HepG2_HNF4A_merged.bw


title: Hep3B_HNF4A_ChIPseq_1

description:
HNF4A_ChIP-seq
Hep3B_HNF4A_merged.bw


title: PDAC-56


title: PDAC-57


title: Hep3B_HNF4A_ChIPseq_3

description:
HNF4A_ChIP-seq
Hep3B_HNF4A_merged.bw


title: Hep3B_BMAL1_ChIPseq_3

description:
BMAL1_ChIP-seq
Hep3B_BMAL1_merged.bw


title: PDAC-50


title: PDAC-54


title: PDAC-53


title: PDAC-55


title: PDAC-44


title: PDAC-46


title: PDAC-48


title: Hep3B_BMAL1_ChIPseq_1

description:
BMAL1_ChIP-seq
Hep3B_BMAL1_merged.bw


title: U2OS_GFP_H3K27ac_ChIPseq_1

description:
H3K27ac_ChIP-seq
U2OS_GFP_H3K27ac_merged.bw
U2OS_GFP_H3K27ac_merged.bed

value: GFP overexpressed


title: PDAC-52


title: PDAC-49


title: U2OS_HNF4A_H3K27ac_ChIPseq_1

description:
H3K27ac_ChIP-seq
U2OS_HNF4A_H3K27ac_merged.bw
U2OS_HNF4A_H3K27ac_merged.bed

value: HNF4A overexpressed


title: PDAC-47


title: PDAC-51


title: U2OS_HNF4A_H3K27ac_ChIPseq_2


title: U2OS_GFP_H3K27ac_ChIPseq_2


title: U2OS_HNF4A_H3K4me1_ChIPseq_1

description:
H3K4me1_ChIP-seq
U2OS_HNF4A_H3K4me1_merged.bw
U2OS_HNF4A_H3K4me1_merged.bed


title: U2OS_GFP_H3K4me1_ChIPseq_2

description:
H3K4me1_ChIP-seq
U2OS_GFP_H3K4me1_merged.bw
U2OS_GFP_H3K4me1_merged.bed


title: U2OS_HNF4A_BMAL1_ChIPseq_3

description:
BMAL1_ChIP-seq
U2OS_HNF4A_BMAL1_merged.bw
U2OS_HNF4A_BMAL1_merged.bed


title: U2OS_HNF4A_H3K4me1_ChIPseq_2


title: PDAC-41


title: U2OS_GFP_H3K4me1_ChIPseq_1


title: U2OS_HNF4A_BMAL1_ChIPseq_2


title: PDAC-45


title: U2OS_GFP_BMAL1_ChIPseq_3

description:
BMAL1_ChIP-seq
U2OS_GFP_BMAL1_merged.bw
U2OS_GFP_BMAL1_merged.bed


title: U2OS_GFP_BMAL1_ChIPseq_2


title: PDAC-42


title: PDAC-38


title: U2OS_GFP_BMAL1_ChIPseq_1


title: PDAC-39


title: PDAC-40


title: PDAC-43


title: U2OS_HNF4A_BMAL1_ChIPseq_1


title: PDAC-35


title: PDAC-36


title: PDAC-37


title: PDAC-34


title: PDAC-30


title: PDAC-24


title: PDAC-32


title: PDAC-29


title: PDAC-27


title: PDAC-25


title: PDAC-26


title: PDAC-19


title: PDAC-23


title: PDAC-16


title: PDAC-31


title: PDAC-20


title: PDAC-22


title: PDAC-21


title: PDAC-17


title: PDAC-28


title: PDAC-11


title: PDAC-8


title: PDAC-12


title: PDAC-13


title: PDAC-18


title: PDAC-7


title: PDAC-9


title: 12M WTAB

first: Caghan

last: Kizil

institute: Columbia University Irving Medical Center

description: 10X Chromium, single-cell sequencing

data_processing:
The fastq files were aligned to zebrafish transcript (Ensembl Version 95)by using STAR. The BAM files were as input for Cell Ranger (10X genmoics) to generate processed data files that include gene names (row names) and cell names (column names) and counts. Further analysis done by using Seurat package in R.
Genome_build: danRer11
Supplementary_files_format_and_content: tab-delimited file, with gene names in rows and cell names and counts in columns.

organism: Danio rerio

source_name: telencephalon

growth_protocol: Fish were kept at 28 °C water system with 14/10 hours light/dark cycles

extract_protocol: Cells from telencephalon were dissociated and cell tracking dye positve cells were sorted.  The library preparation was performed by 10X Genomics as per manufactur protocol

treatment_protocol: Zebfrafish brains were injected with neutral cell tracking dye and 5-6 min post-injection fish were sacrificed.

tag: age

value: 12 months


title: PDAC-15


title: PDAC-14


title: PDAC-6


title: PDAC-33


title: PDAC-10


title: R4-proscoop12+SCOOP12_ZME

city: BEAUCOUZE

first: Sandra

last: Pelletier

address: 42, rue Georges Morel - BP 60057

country: France

institute: INRA

data_processing:
Reads obtained (ranging from 26.3 to 49.6 million of read pairs according to the samples) have been mapped on reference transcriptional units from Araport11 with the Salmon software (Patro et al., 2017).
Mapping rates obtained range from 88 to 93%.
Analyses for the identification of differentially expressed genes (DEGs) were performed with DESeq2 (Love et al., 2014).
Genome_build: TAIR  Araport11_cds_20210622_representative_gene_model
Supplementary_files_format_and_content: Count files : tab-delimited text file with respectively : sequence name, sequence length, number of  reads aligned, number of reads unaligned.

organism: Arabidopsis thaliana

source_name: RNA extracted from roots

growth_protocol: in growth chamber in short-day conditions (photoperiod of 8 h light at 22 °C/16 h dark at 21 °C, with 70% relative humidity)

extract_protocol:
Total RNAs were independently extracted from each sample using the Nucleospin® RNA Plus Kit (Macherey-Nagel, Düren, Germany).
Libraries were obtained thanks to the Illumina mRNA Stranded protocol and sequenced with the Illumina NovaSeq 6000 S4 PE100 reads technology (Génome Québec, Canada).

tag: tissus

tag: genetic background

value: Ws

value: proscoop12-(Ws) mutant

tag: phenotype

value: longer root compared to wild-type

value: SCOOP12 [100nM]

value: 11 days


title: R4-proscoop12_ZD

value: control - H20


title: R4-Ws+SCOOP12_ZME

value: Wild-type Ws


title: R4-proscoop12+SCOOP12_ZD


title: Neurons-WT-n3

city: Corbeil-Essonnes

first: Hélène

last: Polvèche

address: 28, Rue Henri Desbruères

institute: I-Stem

description: Replicate 3

data_processing:
Samples were loaded on an Ion PI v3 Chip and sequenced on the Ion Proton System using Ion PI  Hi-Q sequencing  200 kit chemistry (200 bp read length; Thermofisher Scientific)
To determine genes that are differentially expressed between groups mapped reads were quantified using Partek E/M algorithm normalised by the Total count/sample (the resulting counts represent the gene expression levels on reads/millions for over 20,800 different genes present in the AmpliSeq Human Gene Expression panel)
Differentially expressed gene were identified using Partek Gene Specific Analysis (GSA) algorithm
Genome_build: hg19
Supplementary_files_format_and_content: Differentially expressed gene files (xlsx)

source_name: Neurons

growth_protocol: After thawing, NSCs were seeded on poly-L-ornithin/laminin (PO/LAM) coated support, in N2B27 medium consisting of DMEM/F12, neurobasal, N2 and B27 supplements, 0.1% β-mercaptoethanol and 0.1% penicillin / streptomycin (all from ThermoFisher Scientific) supplemented with 10 ng/mL of FGF2 and EGF (Peprotech) and 10 µM of Y-27632 (Stemcell Technologies) medium was change the next day without Y-27632 and then changed every two days. NSCs were passaged twice a week using Trypsine-EDTA 0.05 % (ThermoFisher Scientific) and seeded on PO/LAM-coated support at a density of 50,000 cells/cm² for amplification.  Neuronal differentiation was induced by plating the NSCs at low density (50,000 cells/cm2) in PO/LAM-coated culture plates in N2B27 medium without FGF2 and EGF. At day 4, 10 µM DAPT (R&D Systems) was added to the medium to stop cell proliferation. The medium was changed every 4 days and neurons were obtained after 18-21 days of in vitro (DIV) differentiation.

extract_protocol:
50 ng of total RNA was reverse transcribed using the Ion AmpliSeq Transcriptome Human Gene Expression kit following the protocol of the manufacturer (Thermofisher Scientific)
The cDNA libraries were amplified and barcoded using Ion AmpliSeq Transcriptome Human Gene Expression core panel and Ion Xpress Barcode Adapter (Thermofisher Scientific). The amplicons were quantified using Agilent High Sensitivity DNA kit  before the samples were pooled in sets of eight. Emulsion PCR and  Enrichment was performed on the Ion OT2 system Instrument using the Ion PI Hi-Q OT2 200 kit (Thermofisher Scientific)
OTHER (Ampli-Seq)

tag: extract

value: Total cells


title: R4-Ws+SCOOP12_ZD


title: R4-proscoop12_ZME


title: Neurons-WFS-n3

description: Replicate 3

value: Wolfram syndrom


title: Neurons-WT-n2

description: Replicate 2


title: R4-Ws_ZD


title: PDAC-5

value: Pancreatic ductal adecnocarcinoma


title: R3-proscoop12_ZD


title: R3-proscoop12+SCOOP12_ZD


title: Neurons-WFS-n2

description: Replicate 2


title: R4-Ws_ZME


title: Neurons-WT-n1

description: Replicate 1


title: Neurons-WFS-n1

description: Replicate 1


title: R3-proscoop12+SCOOP12_ZME


title: NSC-WFS-n3

description: Replicate 3

source_name: Neural Stem Cells (NSC)


title: NSC-WFS-n1

description: Replicate 1


title: NSC-WT-n4

description: Replicate 4


title: PDAC-82


title: R3-proscoop12_ZME


title: NSC-WFS-n2

description: Replicate 2


title: PDAC-2


title: PDAC-4


title: PDAC-1


title: NSC-WT-n3

description: Replicate 3


title: R3-Ws+SCOOP12_ZD


title: R3-Ws+SCOOP12_ZME


title: PDAC-3


title: NSC-WT-n1

description: Replicate 1


title: R3-Ws_ZD


title: R3-Ws_ZME


title: R1-proscoop12+SCOOP12_ZD


title: R1-proscoop12_ZME


title: R1-proscoop12+SCOOP12_ZME


title: wild-type cerebellum [CBLM447]

city: Chapel Hill

first: Robert

middle: G

last: Mealer

state: NC

address: 120 Mason Farm Road, 5023F

institute: University of North Carolina at Chapel Hill

data_processing:
Transcriptome mapping was performed with STAR (PMID:23104886) using the Ensembl annotation of mm9 reference genome. Read counts for individual genes were produced using HTSeq (PMID:25260700).
Read counts for individual genes were produced using HTSeq (PMID:25260700). Differential expression analysis was performed using the EdgeR package (PMID:19910308) after normalizing read counts and including only those genes with CPM > 1 for at least one out of all samples.
Genome_build: mm9
Supplementary_files_format_and_content: htseq_output

source_name: wild-type cerebellum

extract_protocol:
RNA from snap frozen cortex and cerebellum was purified using the RNeasy Lipid Tissue Mini Kit (QIAGEN, 74804) per manufacturer’s protocol.
RNA-seq libraries were prepared from total RNA using polyA selection followed by the NEBNext Ultra II Directional RNA Library Prep Kit protocol (New England Biolabs, E7760S).

value: wild type

tag: tissue

value: Cerebellum


title: wild-type cerebellum [CBLM480]


title: A391T cerebellum [CBLM462]

source_name: A391T cerebellum

value: Slc39a8 A391T (A393T) mutant


title: R1-Ws_ZME

tag: treatment


title: wild-type cerebellum [CBLM448]


title: wild-type cerebellum [CBLM479]


title: R1-proscoop12_ZD


title: A391T cerebellum [CBLM461]


title: A391T cerebellum [CBLM446]


title: SAM3

city: Manchester

first: Jean-Michel

last: Fustin

state: England

address: Faculty of Biology, Medicine and Health, , Oxford road

department: Centre for Biological Timing

country: United Kingdom

institute: University of Manchester

data_processing:
Trimmomatic
Hisat2
Stringtie
edgeR, CPM filter >1 in all samples
Genome_build: GRCm39, vM27.annotations
Supplementary_files_format_and_content: EdgeR output, tabular file containing normalised counts for all genes.

source_name: Embryonic fibroblasts

growth_protocol: PER2::LUC MEFs were cultivated in standard DMEM/F12 with 10% FBS and antibiotic/antimycotic.

extract_protocol:
24h after drug treatment, medium was removed and cells were lysed in the dish with 2ml Trizol, harvested with a cell scraper and transferred to two 1.5ml microtubes. Total RNA was extracted following manufacturers's protocol (Invitrogen), the RNA pellets were resuspended in 100 microl, then pooled. 10 microg total RNA from each sample were then submitted for cDNA library generation.
Quality and integrity of the RNA samples were assessed using a 4200 TapeStation (Agilent Technologies) and then libraries generated using the Illumina® Stranded mRNA Prep. Ligation kit (Illumina, Inc.) according to the manufacturer’s protocol. Briefly, total RNA (typically 0.025-1g) was used as input material from which polyadenylated mRNA was purified using poly-T, oligo-attached, magnetic beads. Next, the mRNA was fragmented under elevated temperature and then reverse transcribed into first strand cDNA using random hexamer primers and in the presence of Actinomycin D (thus improving strand specificity whilst mitigating spurious DNA-dependent synthesis). Following removal of the template RNA, second strand cDNA was then synthesized to yield blunt-ended, double-stranded cDNA fragments. Strand specificity was maintained by the incorporation of deoxyuridine triphosphate (dUTP) in place of dTTP to quench the second strand during subsequent amplification. Following a single adenine (A) base addition, adapters with a corresponding, complementary thymine (T) overhang were ligated to the cDNA fragments. Pre-index anchors were then ligated to the ends of the double-stranded cDNA fragments to prepare them for dual indexing. A subsequent PCR amplification step was then used to add the index adapter sequences to create the final cDNA library. The adapter indices enabled the multiplexing of the libraries, which were pooled prior to cluster generation using a cBot instrument. The loaded flow-cell was then paired-end sequenced (76 + 76 cycles, plus indices) on an Illumina HiSeq4000 instrument. Finally, the output data was demultiplexed and BCL-to-Fastq conversion performed using Illumina’s bcl2fastq software, version 2.20.0.422.

treatment_protocol: Cells were allowed to grow until confluence before replacing the culture medium with new medium containing the appropriate drugs.

value: C57 PER2::LUC

tag: cell type

value: Embryonic fibroblasts

value: SAM


title: A391T cerebellum [CBLM445]


title: wild-type cortex [CTX479]

source_name: wild-type cortex

value: Cortex (brain)


title: wild-type cortex [CTX480]


title: single-cell RNA-seq

city: New Haven

first: Rolando

last: Garcia-Milian

state: CT

address: 333 Cedar St

department: CWML

institute: Yale University

data_processing:
scRNA sequencing data was processed with Cell Ranger v 3.1.0. 62.7% of reads were confidently aligned to a modified version of the mouse transcriptome mm10 that includes the sequence for the gene ZsGreen1. The top cell barcodes selected by Cell Ranger were then utilized for downstream analysis.
Cell Barcode Clustering  and Annotation: All analyses were performed in R version 3.6.1. Graph embedding and clustering were performed using the R package Seurat v.3.1.0. UMI counts were scaled to 10,000 UMIs per cell, then natural log transformed with a pseudo-count of one (log((TPM/100) + 1)). Feature selection, principal component analysis, neighbor embedding and Louvain modularity clustering were recursively performed on the data for the purpose of identifying clusters of discretely identifiable cell populations. Clusters were then annotated as either a multiplet population or known cell type by expert curation of transcriptional marker genes. Multiplets were identified as cell populations whose transcriptomic profile resembled a combination of 2 or more cell populations found in the data. Following cell annotation, immune cells and multiplets were discarded; the remaining clusters of epithelial, endothelial and mesenchymal cells were then used to generate a Uniform Manifold Approximation and Projection (UMAP) embedding to visualize ZsGreen1 and Pdgfrb expression.
Genome_build: mm10

source_name: Lung PDGFR-β+ cells

growth_protocol: Pdgfrb-CreER, Zs/+ mice were given tamoxifen (see TM administration section in methods) rested for 5 days, and harvested lungs were digested in an enzymatic cocktail [Enzyme A and D) in the Miltenyi Lung-Tissue Dissociation Kit using a gentleMACS Dissociator (Miltenyi Inc.) following manufacturer’s protocol. After enzymatic digestion for 30 min in 37°C, the digestion mixture was filtered through a 70-μm sterile filter (Fischer). Single-cell suspension was centrifuged and washed twice in DMEM with 0.1% BSA and resuspended in the same buffer with 1:2000 DAPI (nuclear marker for the dead cells). Both Zs+ DAPI- and Zs- DAPI- cells were sorted in equal numbers in separate tubes using fluorescence-activated cell sorting at the Yale university facility.

extract_protocol: Single cells were barcoded using the 10× chromium single-cell platform, and complementary DNA (cDNA) libraries were prepared according to the manufacturer’s protocol (Single Cell 3′ Reagent Kits v2, 10× Genomics, USA). Cell suspensions, reverse transcription master mix, and partitioning oil were loaded on a single-cell “A” chip with a targeted cell output of 10,000 cells per library, assuming 100% viability, and then run on the Chromium Controller. Reverse transcription was performed within the droplets at 53°C for 45 min. cDNA was amplified for 12 cycles total on a Bio-Rad C1000 Touch thermocycler. cDNA size selection was performed using SPRIselect beads (Beckman Coulter, USA) and a ratio of SPRIselect reagent volume to a sample volume of 0.6. cDNA was analyzed on an Agilent Bioanalyzer High Sensitivity DNA chip for qualitative control purposes. cDNA was fragmented using the proprietary fragmentation enzyme blend for 5 min at 32°C, followed by end-repair and A-tailing at 65°C for 30 min. cDNA were double-sided size selected using SPRIselect beads. Sequencing adaptors were ligated to the cDNA at 20°C for 15 min. cDNA was amplified using a sample-specific index oligo as a primer, followed by another round of double-sided size selection using SPRIselect beads. Final libraries were analyzed on an Agilent Bioanalyzer High Sensitivity DNA chip for qualitative control purposes. cDNA libraries were sequenced on a HiSeq 4000 Illumina platform aiming for 150 million reads per library and a sequencing configuration of 26 base pair (bp) on read1 and 98 bp on read2.

value: Lung

value: 12-weeks old

value: WT

value: lung cells


title: wild-type cortex [CTX447]


title: A391T cortex [CTX462]

source_name: A391T cortex


title: wild-type cortex [CTX448]


title: A391T cortex [CTX461]


title: R1-Ws+SCOOP12_ZD

value: Ws

value: SCOOP12 [100nM]

value: 11 days


title: Adenine3

value: Adenine


title: SAM1


title: DZ1

value: DZ


title: DZ2


title: A391T cortex [CTX446]


title: SAM2


title: Adenine1


title: DZ3


title: Adenine2


title: lower small intestinal epithelial cells

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

country: Japan

institute: Osaka univ.

data_processing:
Sequencing was performed on an Illumina HiSeq 2500 platform in a 75-base single-end mode.
Illumina Casava1.8.2 software was used for base calling.
The sequenced reads were mapped to the mouse reference genome sequences (mm10) using TopHat version 2.0.13 in combination with Bowtie2 version 2.2.3 and SAMtools version 0.1.19.
The fragments per kilobase of exon per million mapped fragments (FPKMs) were calculated using Cufflinks version 2.2.1.
Genome_build: mm10
Supplementary_files_format_and_content: FPKM processed value in csv file

extract_protocol:
Total RNAs were extracted using RNeasy Mini kit (Qiagen) according to the  manufacturer’s instructions.
Library preparation was performed using a TruSeq stranded mRNA sample prep kit (Illumina, San Diego, CA) according to the manufacturer’s instructions.

treatment_protocol: To isolate large and small intestinal epithelial cells, intestines were opened longitudinally and washed in PBS to remove feces. Intestines were placed in HBSS with 5 mM EDTA and incubated at 37 °C for 20 min in a shaking water bath. After removing the intestines, epithelia cells in HBSS with 5 mM EDTA were centrifuged at 780 × g for 5 minutes at 4 °C and washed with PBS.

value: lower small intestinal epithelial cells


title: CTL2

value: CTL


title: A391T cortex [CTX445]


title: CTL3


title: upper small intestinal epithelial cells

tag: strain background

value: CRC mouse model MC38, in which derived tumors show increased infiltration of immunosuppressive cells, such as MDSCs, and excluding T cells (Mariathasan et al., 2018, Mosely et al., 2017)

value: upper small intestinal epithelial cells


title: CTL1

tag: strain

value: C57 PER2::LUC


title: large intestinal epithelial cells

value: large intestinal epithelial cells


title: Mouse_tissue_Mouse_IgG_control

source_name: liver

tag: sampling time

value: wild type

value: liver

value: 10-week old


title: Mouse_tissue_Rabbit_IgG_control


title: WT_ZT16_ATACseq_1

description:
ATAC-seq_ZT16
WT_ZT16_ATACseq_merged.bw
WT_ZT16_ATACseq_merged.broadPeak


title: WT_ZT16_ATACseq_2


title: Input

city: Napoli

first: Ilaria

last: Granata

address: Via Pietro Catellino, 111

department: Institute for high performance computing and networking (ICAR)

country: Italy

institute: National Research Council of Italy (CNR)

data_processing:
Reads were aligned to the human genome (hg38) using the BWA algorithm (default settings)
Duplicate reads were removed and only uniquely mapped reads (mapping quality >25) were used for further analysis.
Alignments were extended in silico at their 3’-ends to a length of 200 bp, which is the average genomic fragment length in the size-selected library, and assigned to 32-nt bins along the genome. The resulting histograms (genomic “signal maps”) were stored in bigWig files.
Peak locations were determined using the MACS algorithm (v2.1.0) (Zhang et al., 2008) with a cutoff of p-value = 1e-7. Peaks that were on the ENCODE blacklist of known false ChIP-Seq peaks were removed. Signal maps and peak locations were used as input data to Active Motifs proprietary analysis program, which creates Excel tables containing detailed information on sample comparison, peak metrics, peak locations and gene annotations.
Motif analysis was carried out using the Homer software (Heinz et al., 2010).  Regions of 200 bp surrounding the summit of the top 2,500 peaks (based on MACS2 p-values) were analysed.
Genome_build: hg38
Supplementary_files_format_and_content: peak lists in UCSC Genome Browser BED format

source_name: NMP-like axial progenitors

growth_protocol: hESCs were cultured routinely in feeder-free conditions in either Essential 8 (Thermo Fisher or made in-house) or mTeSR1 (Stem Cell Technologies) medium on laminin 521 (Biolamina) or Geltrex LDEV-Free reduced growth factor basement membrane matrix (Thermo Fisher).

extract_protocol:
Approximately 10 million cells/sample (three pooled replicates per sample), fixed with 1% formaldehyde solution (11% formaldehyde, 0.1M NaCl, 1mM EDTA (pH 8.0), 50mM HEPES (pH 7.9)) for 15 minutes at room temperature on a shaking apparatus. Fixation was quenched with 125mM of glycine (1/20 volume of 2.5M stock) for 5 minutes and then adherent cells were scraped thoroughly from the culture surface. Cells were washed, centrifuged at 800 x g for 10 minutes at 4oC and pellets were resuspended in 10ml chilled PBS-Igepal (1X PBS (pH 7.4), 0.5% Igepal CA-630). This pellet wash was repeated and cells were resuspended in 10 ml chilled PBS-Igepal and 1mM PMSF. Samples were centrifuged at 800 x g for 10 minutes at 4oC for a third time, after which the supernatant was removed and pellets were snap-frozen on dry ice and stored at -80oC. . Chromatin was isolated by adding lysis buffer, followed by disruption with a Dounce homogenizer. Lysates were sonicated and the DNA sheared to an average length of 300-500 bp with Active Motif’s EpiShear probe sonicator (cat# 53051). Genomic DNA (Input) was prepared by treating aliquots of chromatin with RNase, proteinase K and heat for de-crosslinking, followed by SPRI beads clean up (Beckman Coulter) and quantitation by Clariostar (BMG Labtech). Extrapolation to the original chromatin volume allowed determination of the total chromatin yield. An aliquot of chromatin (50 µg) was precleared with protein G agarose beads (Invitrogen) and genomic DNA regions of interest were isolated using 4 µg of antibody against Brachyury (R&D Systems, cat# AF2085, lot# KQP0719121). Complexes were washed, eluted from the beads with SDS buffer, and subjected to RNase and proteinase K treatment. Crosslinks were reversed by incubation overnight at 65oC, and ChIP DNA was purified by phenol-chloroform extraction and ethanol precipitation.
Illumina sequencing libraries were prepared from the ChIP and Input DNAs by the standard consecutive enzymatic steps of end-polishing, dA-addition, and adaptor ligation. Steps were performed on an automated system (Apollo 342, Wafergen Biosystems/Takara).

treatment_protocol: hESCs were dissociated using Accutase solution (Merck Life Science) and plated at a density of approximately 50,000 cells/cm2 on vitronectin (Thermo Fisher)-coated culture plates in N2B27 basal medium containing 50:50 DMEM F12 (Merck Life Science / Neurobasal medium (Gibco) and 1x N2 supplement (Gibco), 1x B27 (Gibco), 1x GlutaMAX (Gibco), 1x MEM NEAA (Gibco), 2-Mercaptoethanol (50 μM, Gibco). N2B27 medium was supplemented with CHIR99021 (3 μM, Tocris), FGF2 (20 ng/ml, R&D Systems) and Rho-Associated Coil Kinase (ROCK) inhibitor Y-27632 2HCl (10 μM, Adooq Biosciences) with the latter being withdrawn from the differentiation medium after the first day of NMP induction.

value: hESCs


title: TBXT-POS


title: RNA-Seq hPSC_3

data_processing:
The quality of raw reads in fastq format was analyzed by FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc).
Adapter contamination in the reads were removed using Trim Galore v. 0.4.0
Paired-end reads were aligned to the human reference genome using STAR v2.4.2a in two pass mode
Expected gene counts were extracted using RSEM v1.3.0
Genome_build: hg38 assembly (Ensembl Build 79)

source_name: Undifferentiated hESCs

extract_protocol:
Total RNA was isolated using using the Norgen Biotek kit-QC before library construction was carried out via: (1) Nanodrop: for RNA purity (OD260/OD280).  (2) Agarose gel electrophoresis: for RNA integrity and potential contamination.  (3) Agilent 2100
Double stranded cDNA synthesis, end repair, poly A/Adaptor addition, fragment selection, PCR

treatment_protocol: hESCs were dissociated using Accutase solution (Merck Life Science) and plated at a density of approximately 50,000 cells/cm2 on vitronectin (Thermo Fisher)-coated culture plates in N2B27 basal medium containing 50:50 DMEM F12 (Merck Life Science / Neurobasal medium (Gibco) and 1x N2 supplement (Gibco), 1x B27 (Gibco), 1x GlutaMAX (Gibco), 1x MEM NEAA (Gibco), 2-Mercaptoethanol (50 μM, Gibco). N2B27 medium was supplemented with CHIR99021 (3 μM, Tocris), FGF2 (20 ng/ml, R&D Systems) and Rho-Associated Coil Kinase (ROCK) inhibitor Y-27632 2HCl (10 μM, Adooq Biosciences) with the latter being withdrawn from the differentiation medium after the first day of NMP induction. For TBXT inducible knockdown, NMP medium was supplemented with 1μg/ml tetracycline hydrochloride and replenished every other day.

value: hESC


title: WT_ZT6_ATACseq_2

description:
ATAC-seq_ZT6
WT_ZT6_ATACseq_merged.bw
WT_ZT6_ATACseq_merged.broadPeak


title: WT_ZT6_ATACseq_1


title: JetLag_4w_ZT16_ChIPseq_3

description:
HNF4A_ChIP-seq
JL_HNF4A_ZT16_ChIP_merged.bw
JL_HNF4A_ZT16_ChIP_merged.narrowPeak


title: RNA-Seq D3_TN_3

source_name: NMP-like axial progenitors (-Tet)


title: JetLag_4w_ZT16_ChIPseq_1


title: RNA-Seq D3_TP_3

source_name: NMP-like axial progenitors (+Tet)


title: RNA-Seq D3_TP_2


title: RNA-Seq D3_TN_2


title: RNA-Seq D3_TN_1


title: JetLag_4w_ZT4_ChIPseq_3

description:
HNF4A_ChIP-seq
JL_HNF4A_ZT4_ChIP_merged.bw
JL_HNF4A_ZT4_ChIP_merged.narrowPeak


title: TBXT-NEG


title: RNA-Seq D3_TP_1


title: BKO_FOXA2_ZT16_ChIPseq_3

description:
FOXA2_ChIP-seq
BKO_FOXA2_ZT16_ChIP_merged.bw
BKO_FOXA2_ZT16_ChIP_merged.narrowPeak

value: Bmal1 knockout


title: JetLag_4w_ZT4_ChIPseq_1


title: JetLag_4w_ZT4_ChIPseq_2


title: BKO_FOXA2_ZT16_ChIPseq_2


title: BWT_FOXA2_ZT16_ChIPseq_3

description:
FOXA2_ChIP-seq
BWT_FOXA2_ZT16_ChIP_merged.bw
BWT_FOXA2_ZT16_ChIP_merged.narrowPeak


title: BKO_FOXA2_ZT16_ChIPseq_1


title: HSPC from elderly healthy donor 2

city: Dublin

first: Marina

last: Ainciburu

state: Dublin

address: Foster Avenue

department: Bioinformatics

country: Ireland

institute: NIBRT

data_processing:
Demultiplexing, alignment to the hg38 genome and quantification was carried out with Cellranger (v2.1 and v3.1)
Posterior analysis (quality control, clustering, integration and differential expression) was performed with Seurat v3
Genome_build: hg38
Supplementary_files_format_and_content: HDF5 Feature Barcode matrices

source_name: HSPC

extract_protocol:
Cells were sorted from bone marrow aspirates.
Single cell 3' RNA sequencing libraries were prepared using the chromiun controller from 10X Genomics. NEXTGEM Single Cell 3' Reagent Kits v2 and v3.1  were used.

value: Bone marrow

tag: condition

value: Elderly healthy donor

tag: facs gating

tag: reagent kit version

tag: cellranger version


title: HSPC from young healthy donor 5

value: Young healthy donor


title: BWT_FOXA2_ZT16_ChIPseq_2

tag: genotype


title: HSPC from elderly healthy donor 3


title: RNA-Seq hPSC_2


title: HSPC from young healthy donor 4


title: HSPC from young healthy donor 3


title: RNA-Seq hPSC_1


title: BKO_H3K27ac_ZT16_ChIPseq_3

description:
H3K27ac_ChIP-seq
BKO_H3K27ac_ZT16_ChIP_merged.bw
BKO_H3K27ac_ZT16_ChIP_merged.narrowPeak

tag: chip antibody


title: JetLag_4w_ZT16_ChIPseq_2

tag: age


title: HSPC from young healthy donor 2


title: BKO_H3K27ac_ZT16_ChIPseq_2


title: BKO_H3K27ac_ZT16_ChIPseq_1


title: BWT_H3K27ac_ZT16_ChIPseq_3

description:
H3K27ac_ChIP-seq
BWT_H3K27ac_ZT16_ChIP_merged.bw
BWT_H3K27ac_ZT16_ChIP_merged.narrowPeak


title: BWT_H3K27ac_ZT16_ChIPseq_2


title: BKO_H3K4me1_ZT16_ChIPseq_3

description:
H3K4me1_ChIP-seq
BKO_H3K4me1_ZT16_ChIP_merged.bw
BKO_H3K4me1_ZT16_ChIP_merged.narrowPeak


title: BKO_H3K4me1_ZT16_ChIPseq_2


title: HSPC from elderly healthy donor 1


title: BWT_FOXA2_ZT16_ChIPseq_1


title: BKO_H3K4me1_ZT16_ChIPseq_1


title: BWT_H3K4me1_ZT16_ChIPseq_3

description:
H3K4me1_ChIP-seq
BWT_H3K4me1_ZT16_ChIP_merged.bw
BWT_H3K4me1_ZT16_ChIP_merged.narrowPeak


title: BKO_HNF4A_ZT16_ChIPseq_3

description:
HNF4A_ChIP-seq
BKO_HNF4A_ZT16_ChIP_merged.bw
BKO_HNF4A_ZT16_ChIP_merged.narrowPeak


title: BWT_H3K4me1_ZT16_ChIPseq_1


title: BKO_HNF4A_ZT16_ChIPseq_2


title: BWT_HNF4A_ZT16_ChIPseq_3

description:
HNF4A_ChIP-seq
BWT_HNF4A_ZT16_ChIP_merged.bw
BWT_HNF4A_ZT16_ChIP_merged.narrowPeak


title: HSPC from young healthy donor 1


title: BWT_HNF4A_ZT16_ChIPseq_2


title: BWT_HNF4A_ZT16_ChIPseq_1


title: BWT_H3K27ac_ZT16_ChIPseq_1


title: HKO_H3K27ac_ChIPseq_3

description:
H3K27ac_ChIP-seq
HKO_H3K27ac_ZT6_ChIP_merged.bw
HKO_H3K27ac_ZT6_ChIP_merged.narrowPeak

value: Hnf4a knockout


title: HKO_H3K27ac_ChIPseq_2


title: BWT_H3K4me1_ZT16_ChIPseq_2


title: HWT_H3K27ac_ChIPseq_3

description:
H3K27ac_ChIP-seq
HWT_H3K27ac_ZT6_ChIP_merged.bw
HWT_H3K27ac_ZT6_ChIP_merged.narrowPeak


title: HKO_H3K27ac_ChIPseq_1


title: HWT_H3K27ac_ChIPseq_2


title: 3DRG36H

city: Nantong

first: Lili

last: Zhao

address: 19 Qixiu

country: China

institute: Nantong university

hyb_protocol: The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000. 1 μg of each labeled cRNA was fragmented by adding 11 μl 10 × Blocking Agent and 2.2 μl of 25 × Fragmentation Buffer, then heated the mixture at 60 °C for 30 min, finally 55 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 100 μl of hybridization solution was dispensed into the gasket slide and assembled to the gene expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven. The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2505C).

scan_protocol: Then the slides were scanned immediately with the Agilent DNA Microarray Scanner (part number 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 v11.5.1 software package (Agilent Technologies)
Quantile normalization was performed with using the GeneSpring GX v11.5.1 software package (Agilent Technologies)

organism: Rattus norvegicus

source_name: gene expression at 36h in cultured DRG neurons

label_protocol: Sample labeling and array hybridization were performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology). Briefly, total RNA from each sample was linearly amplified and labeled with Cy3-UTP.

growth_protocol: DRG neurons were obtained from the adult male Sprague-Dawley rats (180–220 g). After isolated from spinal cord, DRGs were rinsed twice in CMF-HBSS and then primary digesting with 0.1% collagenase type I and 0.25% trypsin. The single-cell suspension was spun for 5 min at 900 rpm with 15% BSA after triturated 3 times with 1 ml pipette tip. After discarding the supernatant, the cells were resuspended and planted with DMEM/F12 (Invitrogen) medium.

extract_protocol: Total RNA was isolated using TRIzol (Invitrogen) and miRNeasy mini kit (QIAGEN) according to manufacturer’s instructions, which efficiently recovered all RNA species, including miRNAs. RNA quality and quantity was measured by using nanodrop spectrophotometer (ND-1000, Nanodrop Technologies) and RNA Integrity was determined by gel electrophoresis.

treatment_protocol: At 0h, 1.5h, 3h, 6h, 12h, 18h, 24h, 30h, 36h after neurons planted, the total RNA was isolated from these cells

value: Sprague-Dawley

tag: gender

value: male

value: Cultured DRG neurons

tag: timepoint


title: 3DRG12H

source_name: gene expression at 12h in cultured DRG neurons


title: HWT_H3K27ac_ChIPseq_1


title: 3DRG24H

source_name: gene expression at 24h in cultured DRG neurons


title: 3DRG1.5H

source_name: gene expression at 1.5h in cultured DRG neurons


title: HKO_H3K4me1_ChIPseq_3

description:
H3K4me1_ChIP-seq
HKO_H3K4me1_ZT6_ChIP_merged.bw
HKO_H3K4me1_ZT6_ChIP_merged.narrowPeak


title: BKO_HNF4A_ZT16_ChIPseq_1


title: HKO_H3K4me1_ChIPseq_2


title: 3DRG18H

source_name: gene expression at 18h in cultured DRG neurons


title: 3DRG0H

source_name: gene expression at 0h in cultured DRG neurons


title: 2DRG36H


title: 3DRG30H

source_name: gene expression at 30h in cultured DRG neurons


title: 3DRG6H

source_name: gene expression at 6h in cultured DRG neurons


title: HKO_H3K4me1_ChIPseq_1


title: HWT_H3K4me1_ChIPseq_3

description:
H3K4me1_ChIP-seq
HWT_H3K4me1_ZT6_ChIP_merged.bw
HWT_H3K4me1_ZT6_ChIP_merged.narrowPeak


title: 3DRG3H

source_name: gene expression at 3h in cultured DRG neurons


title: HWT_H3K4me1_ChIPseq_2


title: 2DRG24H


title: 2DRG30H


title: HWT_H3K4me1_ChIPseq_1


title: 2DRG18H


title: HKO_BMAL1_ChIPseq_3

description:
BMAL1_ChIP-seq
HKO_BMAL1_ZT6_ChIP_merged.bw
HKO_BMAL1_ZT6_ChIP_merged.narrowPeak


title: 2DRG12H


title: 1DRG36H


title: HKO_BMAL1_ChIPseq_1


title: HKO_BMAL1_ChIPseq_2


title: 2DRG0H


title: 2DRG3H


title: 2DRG1.5H


title: HWT_BMAL1_ChIPseq_3

description:
BMAL1_ChIP-seq
HWT_BMAL1_ZT6_ChIP_merged.bw
HWT_BMAL1_ZT6_ChIP_merged.narrowPeak


title: HWT_BMAL1_ChIPseq_2


title: Monocyte_82-V7

data_processing:
Raw reads were trimmed for low quality reads and miscalled nucleotides using Trimmomatic v. 0.33.
Reads that passed the trimming step were aligned to human genome (Ensembl GRCh38 release 80) using the STAR aligner (version 2.4.2a).
Aligned reads were counted using HTSeq (version 0.6.1).
Supplementary_files_format_and_content: tab-delimited text files include raw counts for each sample.

source_name: Blood Monocytes

extract_protocol:
RNA was extracted from sorted cells from PBMC of HVTN 505 vaccinees using RNAzolRT (MRC Inc.) as per recommendations from the manufacturer.
Polyadenylated transcripts were purified on oligo-dT magnetic beads, fragmented, reverse transcribed using random hexamers and incorporated into barcoded cDNA libraries based on the Illumina TruSeq platform. Next, libraries were validated by electrophoresis, quantified, pooled and clustered on Illumina TruSeq v2 flow cells. Clustered flow cells were sequenced on an Illumina HiSeq (2000/4000) using 2 x 75 base paired-end runs.

value: Blood Monocytes

tag: participant id

tag: visit id

value: month 7

value: Vaccine

tag: hiv-1 acquisition

value: No


title: Monocyte_82-V9

value: month 12

tag: treatment


title: 2DRG6H

tag: tissue


title: non-infected - 3

city: Lille

first: Mathieu

last: Gissot

address: 1, rue du Pr. calmette

institute: CNRS

data_processing:
Clusters were generated on a flow cell within a cBot using the Cluster Generation Kit (Illumina), and libraries were sequenced as 50-bp reads on a HiSeq 2000 using a Sequence By Synthesis (SBS) technique (Illumina).
Image analysis and base calling were performed using the HiSeq Control Software and Real-Time Analysis component. Demultiplexing was performed using Illumina’s conversion software (bcl2fastq 2.17). The quality of the data was assessed using FastQC from the Babraham Institute and the Illumina software Sequence Analysis Viewer (SAV). Potential contaminants were investigated with the FastQ Screen software from the Babraham Institute.
Datasets were aligned with HiSAT2 v2.1.0  against the T. gondii ME49 genome from (ToxoDB-39)  and to the rat genome (Rattus norvegicus Rn6 (UCSC)). Final read alignments having more than three mismatches were discarded. Gene counting was performed using HTSeq-count 0.6.1p1 (union mode). Because the data come from a strand-specific assay, the read must be mapped to the opposite strand of the gene. Before statistical analysis, genes with less than 15 reads (combining all the analyzed samples) were filtered out. Differentially expressed genes were identified using the Bioconductor package edgeR 3.6.7. The data were normalized using the Relative Log Expression (RLE) normalization factors. Genes with adjusted p-values less than 5% (according to the FDR method from Benjamini-Hochberg) were declared differentially expressed.

source_name: Brain cell primary culture

growth_protocol: Intracellular parasite were grown for 1, 2, 4, 7 and 14 days

extract_protocol:
Total RNA was extrated using TRIzol reagent according to manufacturer’s protocol.
Library preparation was performed using the TruSeq Stranded mRNA Sample Preparation kit (Illumina) according to the manufacturer’s instructions. Libraries were validated using a Fragment Analyzer and quantified by qPCR (ROCHE LightCycler 480).

value: Brain cell primary culture


title: Monocyte_82-V2

first: Slim

last: Fourati

tag: cell type

value: pre-vaccination


title: 1DRG30H

tag: strain


title: 1DRG18H


title: DMSO - m6A_rep3

city: Beijing

first: Min

last: Zhu

state: China

address: 49 North Garden Rd.,Haidian District

institute: Peking University Third Hospital

data_processing:
Basecalls performed using RTA2 software
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Rnor6 whole genome using bowtie HISAT2 v2.1.0
Each sample peaks and differentially enriched peaks were analyzed by exomePeak (v2.13.2)
Genome_build: Rnor6

source_name: neonatal rat cardiac myocytes

growth_protocol: NRCMs were isolated from newborn SD rats aged 1–2 days. These isolated NRCMs were grown in Dulbecco's modified Eagle's medium (DMEM) supplemented with 10% fetal bovine serum (FBS) and 100 U/ml penicillin/streptomycin, and maintained at 37°C in 5% CO2.

extract_protocol:
The whole RNA of NRCMs treated with CYP or DMSO was harvested using Trizol reagent.Total RNA of the sample was subjected to test the RNA integrity using agarose gel electrophoresis, then quantified and examined by NanoDrop ND-1000.1-2 ug of total RNA was selected for each sample for sequencing library construction. After polyA mRNA was enriched by oligo dT method, mRNA was interrupted into 100-300nt fragment, and using m6A antibody for enriching methylated RNAs
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample(KitKAPA Stranded mRNA-seq Kit). Including cDNA synthesis, add A in 3’end, 3‘adaptor ligation, PCR amplication, purify cDNA library.

treatment_protocol: NRCMs were treated with CYP or DMSO for 48 hours.

value: neonatal rat cardiac myocytes

value: treated with DMSO for 48 hours

tag: rip-antibody

value: m6A antibody (Synaptic Systems, 202003, lot 2-108)


title: Monocyte_81-V7

city: Chicago

address: 300 E Superior St

institute: Northwestern University

value: Yes


title: DMSO_input


title: DMSO - m6A_rep2


title: non-infected - 2


title: HWT_BMAL1_ChIPseq_1

source_name: liver

tag: sampling time

value: wild type

value: liver

value: 10-week old


title: 1DRG24H

value: Sprague-Dawley


title: 1DRG1.5H

value: male


title: 1DRG3H

value: Cultured DRG neurons


title: 1DRG6H


title: Monocyte_81-V9

value: Blood Monocytes


title: 3DRG36H [miRNA]

hyb_protocol: After stopping the labeling procedure, the Hy3TM-labeled samples were hybridized on the miRCURYTM LNA Array (v.18.0) (Exiqon) according to array manual. The total 25 μL mixture from Hy3TM-labeled samples with 25 μL hybridization buffer were first denatured for 2 min at 95°C, incubated on ice for 2 min and then hybridized to the microarray for 16–20 h at 56°C in a 12-Bay Hybridization Systems (Hybridization System - Nimblegen Systems, Inc., Madison, WI, USA). Following hybridization, the slides were achieved, washed several times using Wash buffer kit (Exiqon), and finally dried by centrifugation for 5 min at 400 rpm.

scan_protocol: Then the slides were scanned immediately using the Axon GenePix 4000B microarray scanner (Axon Instruments, Foster City, CA).

data_processing:
Scanned images were then imported into GenePix Pro 6.0 software (Axon) for grid alignment and data extraction.
Expressed data were normalized using the Median normalization. After normalization, significant differentially expressed miRNAs between two groups were identified through Volcano Plot filtering. Hierarchical clustering was performed using MEV software (v4.6, TIGR).

source_name: miRNA expression at 36h in cultured DRG neurons

label_protocol: After RNA isolation from the samples, the miRCURY™ Hy3™/Hy5™ Power labeling kit (Exiqon, Vedbaek, Denmark) was used according to the manufacturer’s guideline for miRNA labelling. One microgram of each sample was 3'-end-labeled with Hy3TM fluorescent label, using T4 RNA ligase.


title: non-infected - 1


title: 3DRG24H [miRNA]

source_name: miRNA expression at 24h in cultured DRG neurons


title: 1DRG12H


title: DMSO - m6A_rep1


title: CYP - m6A_rep3

value: treated with CYP for 48 hours


title: Monocyte_80-V9

value: Vaccine


title: 3DRG6H [miRNA]

source_name: miRNA expression at 6h in cultured DRG neurons


title: 3DRG12H [miRNA]

source_name: miRNA expression at 12h in cultured DRG neurons


title: 3DRG3H [miRNA]

source_name: miRNA expression at 3h in cultured DRG neurons


title: 3DRG1.5H [miRNA]

source_name: miRNA expression at 1.5h in cultured DRG neurons


title: CYP_input


title: Monocyte_80-V7

value: month 7


title: CYP - m6A_rep2


title: Monocyte_81-V2


title: 3DRG18H [miRNA]

source_name: miRNA expression at 18h in cultured DRG neurons


title: 2DRG36H [miRNA]


title: 3DRG0H [miRNA]

source_name: miRNA expression at 0h in cultured DRG neurons


title: 1DRG0H


title: 2DRG30H [miRNA]

source_name: miRNA expression at 30h in cultured DRG neurons


title: Monocyte_80-V2


title: 2DRG24H [miRNA]


title: 2DRG18H [miRNA]


title: Monocyte_79-V7

value: No


title: 2DRG6H [miRNA]


title: Monocyte_79-V2


title: 2DRG12H [miRNA]


title: 2DRG3H [miRNA]


title: Monocyte_79-V9

value: month 12


title: Monocyte_75-V7


title: 2DRG1.5H [miRNA]


title: 1DRG30H [miRNA]


title: 1DRG36H [miRNA]


title: 1DRG24H [miRNA]


title: Monocyte_74-V7


title: 1DRG18H [miRNA]


title: NHP_4_Hoti_Day28

city: Frederick

first: Catherine

middle: E

last: Arnold

state: MD

address: 1425 Porter St

department: Diagnostic Systems Division

institute: US Army Medical Research Institute of Infectious Diseases

description:
50 ng extracted total RNA was hybridized to probes and read using the NanoString SPRINT
20200130_30102369120321-01_Sample10_10

hyb_protocol: Seventy microliters of hybridization buffer was added to the reporter code set to make a master mixture. Eight microliters of this master mixture was then incubated in separate tubes containing 50 ng of extracted host RNA and 2 ul of the capture code set. This hybridization mixture was incubated at 65°C for 17 hours followed by 4°C until the samples were placed on NanoString Sprint Profiler analysis system.

data_processing: Raw counts were normalized to geometric mean counts of the synthetic positive controls included on the codeset. nCAAM and the geNorm algorithm was used to normalize each dataset by taking the five most stable housekeeping genes across samples and using it on all datasets.

organism: Macaca fascicularis

source_name: whole blood

extract_protocol: All whole blood samples were initially diluted 1:1 with purified molecular grade water prior to being vigorously mixed with a 3:1 ratio of TRIzol LS (ThermoFisher Scientific). All TRIzol LS mixtures and residual matrices were then frozen at -80°C until subsequent extraction and/or analysis. RNA for NanoString analysis was manually extracted using the miRNeasy kit (Qiagen) following manufacturer’s instructions with the modification that the initial TRIzol-LS/water/whole blood mixture was placed in a Phasemaker phase separation tube (ThermoFisher Scientific) prior to being centrifuged at 12,000 x g for 15 min at room temperature. The top aqueous layer was then transferred into a miRNeasy kit column.

treatment_protocol: Cynomolgus macaques were intravenously challenged with a target dose of 6 log10 plaque forming units of virus (either Kosava Hoti or Afghan09-2990).  Whole blood was collected on days 0, 1-7, 9, 12, 14, 21, and 28.

tag: virus

value: Kosava Hoti

tag: nhp no.

tag: tb status

tag: day post challenge

value: whole blood


title: Monocyte_75-V2

value: pre-vaccination


title: NHP_7_Afghan_Day2

description:
50 ng extracted total RNA was hybridized to probes and read using the NanoString SPRINT
20200130_30102369120321-01_Sample07_07


title: NHP_10_Afghan_Day6

description:
50 ng extracted total RNA was hybridized to probes and read using the NanoString SPRINT
20200130_30102369120321-01_Sample01_01


title: NHP_7_Afghan_Day5

description:
50 ng extracted total RNA was hybridized to probes and read using the NanoString SPRINT
20200130_30102369120321-01_Sample04_04


title: CYP - m6A_rep1

value: neonatal rat cardiac myocytes

value: m6A antibody (Synaptic Systems, 202003, lot 2-108)


title: 1DRG12H [miRNA]


title: NHP_11_Afghan_Day7

description:
50 ng extracted total RNA was hybridized to probes and read using the NanoString SPRINT
20200122_30102365730321-01_Sample02_02

value: Yes


title: NHP_8_Afghan_Day21

description:
50 ng extracted total RNA was hybridized to probes and read using the NanoString SPRINT
20200122_30102365730321-01_Sample03_03


title: 1DRG1.5H [miRNA]


title: Monocyte_71-V7


title: Monocyte_71-V2


title: 2DRG0H [miRNA]


title: 1DRG3H [miRNA]


title: Monocyte_74-V2


title: NHP_5_Hoti_Day2

description:
50 ng extracted total RNA was hybridized to probes and read using the NanoString SPRINT
20200122_30102365730321-01_Sample04_04


title: NHP_1_Hoti_Day4

description:
50 ng extracted total RNA was hybridized to probes and read using the NanoString SPRINT
20200114_30102420230621-01_Sample11_11


title: 1DRG6H [miRNA]


title: 1DRG0H [miRNA]


title: NHP_9_Afghan_Day9

description:
50 ng extracted total RNA was hybridized to probes and read using the NanoString SPRINT
20200114_30102420230621-01_Sample12_12


title: NHP_4_Hoti_Day7

description:
50 ng extracted total RNA was hybridized to probes and read using the NanoString SPRINT
20200122_30102365730321-01_Sample01_01


title: Monocyte_70-V7


title: NHP_10_Afghan_Day12

description:
50 ng extracted total RNA was hybridized to probes and read using the NanoString SPRINT
20200114_30102420230621-01_Sample10_10


title: Monocyte_70-V2


title: Monocyte_68-V2


title: Monocyte_69-V2


title: Monocyte_69-V9


title: NHP_11_Afghan_Day1

description:
50 ng extracted total RNA was hybridized to probes and read using the NanoString SPRINT
20200114_30102420230621-01_Sample07_07


title: NHP_2_Hoti_Day6

description:
50 ng extracted total RNA was hybridized to probes and read using the NanoString SPRINT
20200114_30102420230621-01_Sample09_09


title: Monocyte_74-V9


title: Monocyte_69-V7


title: NHP_8_Afghan_Day4

description:
50 ng extracted total RNA was hybridized to probes and read using the NanoString SPRINT
20200114_30102420230621-01_Sample03_03


title: NHP_11_Afghan_Day9

description:
50 ng extracted total RNA was hybridized to probes and read using the NanoString SPRINT
20200114_30102420230621-01_Sample05_05


title: NHP_12_Afghan_Day6

description:
50 ng extracted total RNA was hybridized to probes and read using the NanoString SPRINT
20200114_30102420230621-01_Sample08_08


title: Monocyte_68-V9


title: Monocyte_63-V9


title: 3DRG30H [miRNA]


title: Monocyte_63-V7


title: NHP_1_Hoti_Day3

description:
50 ng extracted total RNA was hybridized to probes and read using the NanoString SPRINT
20200114_30102420230621-01_Sample04_04


title: NHP_12_Afghan_Day21

description:
50 ng extracted total RNA was hybridized to probes and read using the NanoString SPRINT
20200114_30102365880321-01_Sample12_12


title: Monocyte_64-V7


title: Monocyte_64-V9


title: Monocyte_68-V7


title: NHP_9_Afghan_Day3

description:
50 ng extracted total RNA was hybridized to probes and read using the NanoString SPRINT
20200114_30102420230621-01_Sample02_02


title: Monocyte_63-V2


title: NHP_9_Afghan_Day5

description:
50 ng extracted total RNA was hybridized to probes and read using the NanoString SPRINT
20200114_30102420230621-01_Sample01_01


title: NHP_9_Afghan_Day7

description:
50 ng extracted total RNA was hybridized to probes and read using the NanoString SPRINT
20200114_30102365880321-01_Sample11_11


title: Monocyte_62-V7


title: Lung airway SMC siRNA rep3

description:
tpm-values-all-samples_SMC.txt
KD3_SMC

data_processing:
HISAT2 was used for alignment to the reference genome mm10
GENCODE annotations for mouse
ballgown/stringTie was used to generate the gene counts and transcript abundance estimates from the alignments.
DESeq2 was used for differential expression analysis using R
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Tracheal Smooth Muscle Cells

growth_protocol: Lungs were finely minced and incubated in 2 mg/ml collagenase  in PBS at 37oC for 20 min. The digestion mixture was passed through a 14-gauge pipetting needle (Cadence Science), incubated at 37oC for an additional 20 min and then filtered through a cell strainer (Falcon). This single cell suspension filtrate was centrifuged at 1200 rpm for 5 min, and the pellet was resuspended in cold PBS with 1% fetal bovine serum (FBS; Invitrogen). The resuspended cells were incubated with either PE-conjugated anti-PDGFR-b antibody (1:200, Miltenyi Biotec) for 20 min in the case of Pdgfrb-CreERT2, Klf4(flox/flox) mice or DAPI (1:1000) to label dead cells for 10 min in the case of Pdgfrb-CreERT2, ROSA26R(Zs/+) mice. The sample was then washed in cold PBS with 1% FBS and centrifuged at 1200 rpm for 5 min. The resulting pellet was resuspended in PBS containing 1% FBS and 0.02% EDTA. DAPI (1:2000) was added to the cells that had undergone incubation with anti-PDGFR- antibody. Finally, PDGFR-+DAPI- or Zs+DAPI- cells were sorted on a BD FACSAria II cell sorter. Cells stained with DAPI alone were used as a control for anti-PDGFR- antibody specificity. Lungs from C57BL/6 mice were processed similarly to those of Pdgfrb-CreERT2, ROSA26R(Zs/+) mice, and isolated cells were used as a control for auto-fluorescence in the Zs channel.

extract_protocol: RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Tracheal Smooth Muscle Cells were obtained from CellBiologics C57-6082 and maintained following cell culture indications

value: Trachea

value: cell line:CellBiologics C57-6082

tag: genotype

value: Klf4 KD

value: Klf4 siRNA


title: Lung airway SMC siRNA rep2

description:
tpm-values-all-samples_SMC.txt
KD2_SMC

tag: age


title: NHP_2_Hoti_Day1

description:
50 ng extracted total RNA was hybridized to probes and read using the NanoString SPRINT
20200114_30102365880321-01_Sample10_10


title: NHP_9_Afghan_Day0

description:
50 ng extracted total RNA was hybridized to probes and read using the NanoString SPRINT
20200114_30102365880321-01_Sample07_07


title: Monocyte_62-V2


title: Monocyte_62-V9


title: Monocyte_61-V7


title: Lung airway SMC siRNA rep1

description:
tpm-values-all-samples_SMC.txt
KD1_SMC


title: NHP_1_Hoti_Day9

description:
50 ng extracted total RNA was hybridized to probes and read using the NanoString SPRINT
20200114_30102365880321-01_Sample08_08


title: Lung airway SMC  scrRNA rep2

description:
tpm-values-all-samples_SMC.txt
C2_SMC

value: WT

value: Klf4 scr RNA


title: NHP_8_Afghan_Day6

description:
50 ng extracted total RNA was hybridized to probes and read using the NanoString SPRINT
20200114_30102365880321-01_Sample06_06


title: NHP_1_Hoti_Day0

description:
50 ng extracted total RNA was hybridized to probes and read using the NanoString SPRINT
20200114_30102365880321-01_Sample05_05


title: NHP_4_Hoti_Day2

description:
50 ng extracted total RNA was hybridized to probes and read using the NanoString SPRINT
20200114_30102365880321-01_Sample09_09


title: Monocyte_61-V2

value: Blood Monocytes


title: NHP_1_Hoti_Day28

description:
50 ng extracted total RNA was hybridized to probes and read using the NanoString SPRINT
20200114_30102365880321-01_Sample04_04


title: Lung PDGFR-β+ cells siRNA rep3

description:
tpm-values-all-samples_PDGFR.txt
KD3

source_name: Lung PDGFR-β+ cells

value: Lung

value: PDGFR-Beta+ cells

value: 12-weeks old


title: Lung PDGFR-β+ cells scrRNA rep3

description:
tpm-values-all-samples_PDGFR.txt
C3


title: Monocyte_59-V7

value: month 7

value: Vaccine

value: No


title: Lung PDGFR-β+ cells siRNA rep1

description:
tpm-values-all-samples_PDGFR.txt
KD1


title: Lung airway SMC  scrRNA rep3

description:
tpm-values-all-samples_SMC.txt
C3_SMC


title: Monocyte_57-V9

value: month 12


title: Lung airway SMC  scrRNA rep1

description:
tpm-values-all-samples_SMC.txt
C1_SMC


title: NHP_2_Hoti_Day2

description:
50 ng extracted total RNA was hybridized to probes and read using the NanoString SPRINT
20200114_30102365880321-01_Sample01_01

value: Kosava Hoti

value: whole blood


title: Monocyte_57-V7

value: Yes


title: NHP_4_Hoti_Day12

description:
50 ng extracted total RNA was hybridized to probes and read using the NanoString SPRINT
20200114_30102365880321-01_Sample02_02


title: K14-CreER Tet2L/L epidermis, tamoxifen treated KO_11

city: Boston

first: Matthew

last: Ramsey

state: MA

address: 77 Ave Louis Pasteur, HIM 668

department: Dermatology

institute: Brigham and Women's Hospital

description:
K14-CreER Tet2L/L epidermis, tamoxifen treated
Transcriptome expression levels from the epidermis of  K14-CreER Tet2L/L mice treated with tamoxifen

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36, then mapped to the Mus musculus GRCm38 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b
Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2. Only unique reads that fell within exon regions were counted
Using DESeq2, a comparison of gene expression between the customer-defined groups of samples was performed. The Wald test was used to generate p-values and log2 fold changes
Genome_build: GRCm38
Supplementary_files_format_and_content: Row names consist of Gene IDs and column names are the samples.

source_name: epidermis

growth_protocol: K14-CreER Tet2L/L mice were aged for forty weeks

extract_protocol:
RNeasy mini kit was used for RNA extraction
RNA libraries were prepared for sequencing using standard Illumina protocols
poly-A selection

treatment_protocol: 100mg/kg tamoxifen or vehicle control was delivered daily by IP injection for 5 consecutive days.  Samples were collected 14 days after first injection

tag: atf-3 status

value: Isolated epidermal keratinocyes


title: K14-CreER Tet2L/L epidermis, tamoxifen treated KO_16


title: K14-CreER Tet2L/L epidermis, vehicle treated WT_13

description:
K14-CreER Tet2L/L epidermis, vehicle treated
Transcriptome expression levels from the epidermis of  K14-CreER Tet2L/L mice treated with vehicle


title: K14-CreER Tet2L/L epidermis, vehicle treated WT_14


title: K14-CreER Tet2L/L epidermis, tamoxifen treated KO_15


title: Lung PDGFR-β+ cells siRNA rep2

description:
tpm-values-all-samples_PDGFR.txt
KD2


title: Monocyte_55-V2

source_name: Blood Monocytes

tag: timepoint

value: pre-vaccination


title: C3H10T1/2, H3.1G34W replicate2 (RNA-seq)

city: Madison

first: Peter

middle: W

last: Lewis

state: Wisconsin

address: 330 N Orchard Street

department: Department of Biomolecular Chemistry

institute: University of Wisconsin-Madison

data_processing:
rsem v1.2.4 was used to align reads to mm9 transcriptome and generate expression values
Differentially expressed genes between cells expressing H3.3WT or H3.3G34W were identified using EBSeq v1.20.0 (PPDE >= 0.95, Fold-change >=2)
Data was normalized using median normalization.
Genome_build: mm9
Supplementary_files_format_and_content: median normalized expression values

growth_protocol: Cells were grown in Dulbecco's modified Eagle's medium with 10% FBS

extract_protocol:
RNA was isolated using Trizol reagent (IBI)
mRNA was enriched using NEB E7490L and libraries were prepared using E7530L

treatment_protocol: Lentivurses for stable expression of transgenes were transduced in the cells for 2 days. Cells were selected with 1.5 µg/ml of Puromycin for 4 days.

tag: cell line

value: cells overexpressing H3.1G34W


title: C3H10T1/2, H3.3K27R replicate1 (RNA-seq)

value: cells overexpressing H3.3K27R


title: Monocyte_54-V9

tag: participant id

tag: visit id


title: NHP_11_Afghan_Day2

description:
50 ng extracted total RNA was hybridized to probes and read using the NanoString SPRINT
20200110_30102420220621-01_Sample10_10


title: NHP_1_Hoti_Day1

description:
50 ng extracted total RNA was hybridized to probes and read using the NanoString SPRINT
20200110_30102420220621-01_Sample11_11


title: Lung PDGFR-β+ cells scrRNA rep1

description:
tpm-values-all-samples_PDGFR.txt
C1

value: WT

tag: treatment


title: Monocyte_55-V7

tag: hiv-1 acquisition


title: NHP_10_Afghan_Day0

description:
50 ng extracted total RNA was hybridized to probes and read using the NanoString SPRINT
20200110_30102420220621-01_Sample09_09

tag: tissue


title: NHP_6_Hoti_Day12

description:
50 ng extracted total RNA was hybridized to probes and read using the NanoString SPRINT
20200110_30102420220621-01_Sample08_08


title: C3H10T1/2, H3.3K27R replicate2 (RNA-seq)


title: Monocyte_55-V9

tag: cell type


title: Lung PDGFR-β+ cells scrRNA rep2

description:
tpm-values-all-samples_PDGFR.txt
C2

tag: strain

value: Klf4 scr RNA


title: Monocyte_54-V7

value: Blood Monocytes


title: C3H10T1/2, H3.1WT replicate2 (RNA-seq)

value: cells overexpressing H3.1WT


title: NHP_2_Hoti_Day5

description:
50 ng extracted total RNA was hybridized to probes and read using the NanoString SPRINT
20200114_30102365880321-01_Sample03_03


title: C3H10T1/2, H3.1G34W replicate1 (RNA-seq)


title: C3H10T1/2, H3.3G34R replicate2 (RNA-seq)

value: cells overexpressing H3.3G34R


title: NHP_10_Afghan_Day5

description:
50 ng extracted total RNA was hybridized to probes and read using the NanoString SPRINT
20200110_30102420220621-01_Sample07_07


title: C3H10T1/2, H3.3G34W_K27R replicate2 (RNA-seq)

value: cells overexpressing H3.3G34W;K27R


title: C3H10T1/2, H3.3G34W_K36R replicate2 (RNA-seq)

value: cells overexpressing H3.3G34W;K36R


title: K14-CreER Tet2L/L epidermis, vehicle treated WT_12


title: C3H10T1/2, H3.3G34W_K36R replicate1 (RNA-seq)


title: C3H10T1/2, H3.3G34R replicate1 (RNA-seq)


title: Monocyte_48-V9

value: Vaccine


title: C3H10T1/2, H3.3G34W replicate2 (RNA-seq)

value: cells overexpressing H3.3G34W


title: C3H10T1/2, H3.3WT replicate2 (RNA-seq)

value: cells overexpressing H3.3WT


title: NHP_5_Hoti_Day28

description:
50 ng extracted total RNA was hybridized to probes and read using the NanoString SPRINT
20200110_30102420220621-01_Sample06_06

value: Kosava Hoti

value: No


title: C3H10T1/2, H3.3WT replicate1 (RNA-seq)


title: C3H10T1/2, H3.1WT replicate1 (RNA-seq)


title: C3H10T1/2, H3.3G34W_K27R replicate1 (RNA-seq)


title: C3H10T1/2, H3.3G34W replicate1 (RNA-seq)


title: Monocyte_51-V2

value: Yes


title: Monocyte_54-V2


title: Monocyte_51-V7

value: month 7


title: Monocyte_48-V2

value: pre-vaccination


title: Monocyte_48-V7


title: donor E

city: Newton

first: Margaret

middle: H

last: Chang

address: 300 Longwood Ave, Fegan 6

institute: Boston Children's Hospital

data_processing:
scRNA-seq reads were processed with Cell Ranger v3.1, which demultiplexed cells from different samples and quantified transcript counts per putative cell. Quantification was performed using the STAR aligner against the GRCh38 version of the genome. scRNA-seq data was normalized using Cell Ranger
Genome_build: GRCh38
Supplementary_files_format_and_content: barcodes.tsv.gz, tab delimited text file containing cell barcodes for all cells analyzed, corresponds to column in the matrix file
Supplementary_files_format_and_content: features.tsv.gz, tab delimited text file containing gene names of all genes expressed, corresponds to rows in the matrix file
Supplementary_files_format_and_content: matrix.mtx.gz, matrix of gene expression (genes - rows, cells - columns) compressed in a sparse matrix format

source_name: synovial tissue

extract_protocol:
Fresh synovial tissues were obtained immediately after surgeries. Bone and adipose tissues were removed with scissors and the remaining synovium was cut into small pieces then subjected to enzymatic digestion and mechanical dissociation. Tissue fragments were homogenized with gentleMACS (Miltenyi) and digested in RPMI with Liberase TL 0.1mg/mL (Roche) and DNase I 0.1mg/mL (Sigma-Aldrich) for 30 minutes at 37°C before filtering through a 70µm cell strainer. Cells were stained with antibodies, memory T cells (CD3+CD45RO+) were isolated by FACS sorting.
cDNA and library generation per 10X Genomics manufacturer protocol (Chromium Next GEM Single Cell 5’ Library & Gel Bead Kit v1.1, 10X Genomics).

tag: disease

value: rheumatoid arthritis

tag: Sex

value: F

tag: location

value: elbow

tag: rf or ccp positive

value: neg

tag: procedure

value: total elbow arthroplasty

tag: medication

value: methotrexate


title: NHP_3_Hoti_Day7

description:
50 ng extracted total RNA was hybridized to probes and read using the NanoString SPRINT
20200110_30102420220621-01_Sample02_02

tag: virus

tag: nhp no.

tag: tb status

tag: day post challenge

value: whole blood


title: NHP_4_Hoti_Day6

description:
50 ng extracted total RNA was hybridized to probes and read using the NanoString SPRINT
20200110_30102420220621-01_Sample01_01


title: NHP_6_Hoti_Day3

description:
50 ng extracted total RNA was hybridized to probes and read using the NanoString SPRINT
20200110_30102420220621-01_Sample05_05


title: Monocyte_46-V9

value: Blood Monocytes

tag: participant id

tag: timepoint

value: month 12


title: In labor myometrium rep14

city: Guangzhou

first: Kaiyuan

last: Ji

address: No.9 Jinsui Road, Guangzhou, China

department: Guangzhou Women and Children’s Medical Center

institute: Guangzhou Medical University

data_processing:
fastq files were trimmed with trimmomatic
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using hisat2.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.

source_name: Myometrium

extract_protocol:
Myometrium were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols. NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) was used  for the construction of sequencing libraries.

tag: ga at delivery   (weeks+days)

tag: labor durations  (hours)

tag: cervical dilatation（cm）

tag: maternal age (years)

tag: fetal weight（g）


title: In labor myometrium rep15


title: NHP_1_Hoti_Day21

description:
50 ng extracted total RNA was hybridized to probes and read using the NanoString SPRINT
20200109_30102420210621-01_Sample11_11

tag: tissue


title: donor D

tag: disease

tag: Sex

tag: age

value: knee

value: total knee arthroplasty


title: donor C

tag: location

tag: rf or ccp positive

value: RF+

tag: procedure

value: methotrexate, prednisone


title: In labor myometrium rep13


title: Monocyte_46-V7

tag: cell type

tag: visit id

tag: treatment

value: Vaccine

tag: hiv-1 acquisition


title: NHP_12_Afghan_Day14

description:
50 ng extracted total RNA was hybridized to probes and read using the NanoString SPRINT
20200110_30102420220621-01_Sample04_04

tag: virus

tag: nhp no.

tag: tb status

value: No

tag: day post challenge


title: NHP_2_Hoti_Day7

description:
50 ng extracted total RNA was hybridized to probes and read using the NanoString SPRINT
20200109_30102420210621-01_Sample10_10

value: Kosava Hoti

value: Yes


title: In labor myometrium rep12

tag: ga at delivery   (weeks+days)

tag: labor durations  (hours)

tag: cervical dilatation（cm）

tag: maternal age (years)


title: NHP_7_Afghan_Day1

description:
50 ng extracted total RNA was hybridized to probes and read using the NanoString SPRINT
20200109_30102420210621-01_Sample12_12

tag: tissue


title: donor B

tag: disease

value: rheumatoid arthritis

tag: Sex

value: M

tag: age

tag: medication

value: sulfasalazine, prednisone


title: Monocyte_44-V7

tag: cell type

tag: participant id

tag: timepoint

value: month 7


title: In labor myometrium rep11

tag: fetal weight（g）


title: donor A

value: F

tag: location

value: wrist

tag: rf or ccp positive

tag: procedure

value: arthrodesis

value: prednisone


title: Monocyte_44-V2

value: Blood Monocytes

tag: visit id

value: pre-vaccination

tag: treatment

tag: hiv-1 acquisition


title: NHP_5_Hoti_Day7

description:
50 ng extracted total RNA was hybridized to probes and read using the NanoString SPRINT
20200109_30102420210621-01_Sample09_09

tag: virus

tag: nhp no.

tag: tb status

tag: day post challenge

value: whole blood


title: In labor myometrium rep10

tag: ga at delivery   (weeks+days)

tag: labor durations  (hours)

tag: cervical dilatation（cm）

tag: maternal age (years)


title: blood sample from donor 2134 2 weeks post vaccination [VIC008890]

city: Silver Spring

first: Rasmi

last: Thomas

address: 503 Robert Grant Avenue

department: MHRP

institute: Walter Reed Army Institute of Research

description: processed data file: RV306_V6_norm_expr.txt

data_processing:
Libraries were sequenced and bases called with Illumina NovaSeq control software v1.4.0 and RTA v3.3.3
FASTQ files were generated from BCL files with Illumina bcl2fastq v2.20.0.422
fastp v0.19.7 was used to trim low-quality bases from both ends of each read with parameters --cut_front --cut_right --cut_mean_quality 20 --cut_window_size 15 --length_required 50
Trimmed reads were aligned to the human genome (GRCh38 build 92) using HISAT2 v2.1.0
Gene counts were generated from alignments using HTSeq (v0.9.1) with parameters -s yes -a 2 -t exon
Counts were filtered for protein coding genes and edgeR v3.28.0 was used to remove low-expressed genes and normalize counts with Trimmed mean of M-values (TMM) normalization method
Genome_build: GRCh38
Supplementary_files_format_and_content: normalized counts

source_name: whole blood_2 weeks after 4th immunization

extract_protocol:
Total RNA was extracted from whole blood collected in PAXgene Blood RNA tubes (cat# 762165) using Qiagen PAXgene Blood RNA kits (cat# 762164) and subjected to the ThermoFisher GlobinClear kit (cat# AM1980). cDNA was generated from 10 ng of RNA using the Takara Bio SMART-Seq v4 UltraLow Input RNA Prep kit (cat# 634891) per manufacturer’s suggestions, with control RNA spiked-in (Life Technologies ERCC Mix 1 cat# 4456740).
Sequencing libraries were generated using the Illumina Nextera XT DNA Sample Prep kit (cat# FC-131-1096) according to manufacturer's instructions and sequenced on Illumina NovaSeq 6000 with S2 Reagent Kit, 300 cycles (cat# 20012860)

tag: pid

value: high

value: 2 weeks after 4th immunization

tag: visit

tag: tissue


title: Monocyte_43-V9

tag: cell type

tag: participant id

tag: timepoint

value: month 12

value: Vaccine


title: In labor myometrium rep9

tag: fetal weight（g）


title: blood sample from donor 2109 2 weeks post vaccination [VIC008884]


title: NHP_9_Afghan_Day21

description:
50 ng extracted total RNA was hybridized to probes and read using the NanoString SPRINT
20200109_30102420210621-01_Sample08_08


title: In labor myometrium rep8


title: Monocyte_43-V2

tag: visit id

tag: treatment


title: NHP_12_Afghan_Day9

description:
50 ng extracted total RNA was hybridized to probes and read using the NanoString SPRINT
20200109_30102420210621-01_Sample07_07

tag: virus

value: No


title: In labor myometrium rep7


title: blood sample from donor 2106 2 weeks post vaccination [VIC008883]


title: Monocyte_43-V7

tag: hiv-1 acquisition

value: Yes


title: NHP_2_Hoti_Day3

description:
50 ng extracted total RNA was hybridized to probes and read using the NanoString SPRINT
20200109_30102420210621-01_Sample06_06

value: Kosava Hoti

tag: nhp no.

tag: tb status


title: Monocyte_42-V9


title: blood sample from donor 2099 2 weeks post vaccination [VIC008878]


title: blood sample from donor 2100 2 weeks post vaccination [VIC008879]


title: In labor myometrium rep6

tag: ga at delivery   (weeks+days)


title: NHP_5_Hoti_Day9

description:
50 ng extracted total RNA was hybridized to probes and read using the NanoString SPRINT
20200109_30102420210621-01_Sample05_05

tag: day post challenge


title: NHP_6_Hoti_Day28

description:
50 ng extracted total RNA was hybridized to probes and read using the NanoString SPRINT
20200109_30102420210621-01_Sample04_04


title: NHP_7_Afghan_Day6

description:
50 ng extracted total RNA was hybridized to probes and read using the NanoString SPRINT
20200109_30102420210621-01_Sample03_03


title: blood sample from donor 2098 2 weeks post vaccination [VIC008877]

value: low


title: blood sample from donor 2074 2 weeks post vaccination [VIC008872]


title: In labor myometrium rep5

tag: labor durations  (hours)

tag: cervical dilatation（cm）


title: Monocyte_42-V2


title: In labor myometrium rep4

tag: maternal age (years)


title: NHP_6_Hoti_Day4

description:
50 ng extracted total RNA was hybridized to probes and read using the NanoString SPRINT
20200109_30102420210621-01_Sample02_02


title: Monocyte_40-V2


title: blood sample from donor 2055 2 weeks post vaccination [VIC008868]

tag: pid

tag: visit


title: In labor myometrium rep3


title: NHP_9_Afghan_Day4

description:
50 ng extracted total RNA was hybridized to probes and read using the NanoString SPRINT
20200109_30102420210621-01_Sample01_01

tag: tissue


title: Monocyte_40-V7

tag: cell type

tag: participant id


title: Monocyte_39-V2

tag: timepoint


title: blood sample from donor 2036 2 weeks post vaccination [VIC008861]


title: blood sample from donor 2015 2 weeks post vaccination [VIC008853]


title: Monocyte_39-V7

tag: visit id


title: In labor myometrium rep1

tag: fetal weight（g）


title: Non-labor myometrium rep10


title: Monocyte_42-V7

tag: treatment


title: NHP_5_Hoti_Day0

description:
50 ng extracted total RNA was hybridized to probes and read using the NanoString SPRINT
20200109_30102365920321-01_Sample10_10

tag: virus


title: In labor myometrium rep2


title: Non-labor myometrium rep9


title: Monocyte_37-V7

tag: hiv-1 acquisition


title: NHP_2_Hoti_Day9

description:
50 ng extracted total RNA was hybridized to probes and read using the NanoString SPRINT
20200109_30102365920321-01_Sample11_11

tag: nhp no.

tag: tb status


title: NHP_8_Afghan_Day7

description:
50 ng extracted total RNA was hybridized to probes and read using the NanoString SPRINT
20200109_30102365920321-01_Sample08_08

tag: day post challenge


title: Non-labor myometrium rep8

tag: ga at delivery   (weeks+days)

tag: labor durations  (hours)


title: NHP_3_Hoti_Day2

description:
50 ng extracted total RNA was hybridized to probes and read using the NanoString SPRINT
20200109_30102365920321-01_Sample12_12


title: NHP_5_Hoti_Day21

description:
50 ng extracted total RNA was hybridized to probes and read using the NanoString SPRINT
20200109_30102365920321-01_Sample06_06


title: Monocyte_36-V7


title: blood sample from donor 1132 2 weeks post vaccination [VIC008846]


title: Non-labor myometrium rep7

tag: cervical dilatation（cm）

tag: maternal age (years)


title: blood sample from donor 1110 2 weeks post vaccination [VIC008840]

tag: pid

tag: visit


title: blood sample from donor 1125 2 weeks post vaccination [VIC008845]

tag: tissue


title: blood sample from donor 1123 2 weeks post vaccination [VIC008844]


title: Monocyte_28-V2

tag: cell type

tag: participant id


title: blood sample from donor 1076 2 weeks post vaccination [VIC008833]

tag: timepoint


title: NHP_1_Hoti_Day6

description:
50 ng extracted total RNA was hybridized to probes and read using the NanoString SPRINT
20200109_30102365920321-01_Sample03_03


title: Non-labor myometrium rep3

tag: fetal weight（g）


title: Monocyte_34-V7

tag: visit id

tag: treatment


title: NHP_3_Hoti_Day4

description:
50 ng extracted total RNA was hybridized to probes and read using the NanoString SPRINT
20200109_30102365920321-01_Sample07_07

tag: virus


title: blood sample from donor 1117 2 weeks post vaccination [VIC008843]


title: blood sample from donor 1109 2 weeks post vaccination [VIC008839]


title: Non-labor myometrium rep6


title: Non-labor myometrium rep5


title: NHP_4_Hoti_Day14

description:
50 ng extracted total RNA was hybridized to probes and read using the NanoString SPRINT
20200109_30102365920321-01_Sample05_05

tag: nhp no.


title: Non-labor myometrium rep4


title: Monocyte_37-V2

tag: hiv-1 acquisition


title: NHP_11_Afghan_Day4

description:
50 ng extracted total RNA was hybridized to probes and read using the NanoString SPRINT
20200109_30102365920321-01_Sample02_02

tag: tb status

tag: day post challenge


title: blood sample from donor 1073 2 weeks post vaccination [VIC008831]

description: processed data file: RV306_V6_norm_expr.txt


title: Monocyte_28-V7


title: NHP_7_Afghan_Day28

description:
50 ng extracted total RNA was hybridized to probes and read using the NanoString SPRINT
20200109_30102365920321-01_Sample04_04


title: Monocyte_27-V9


title: NHP_9_Afghan_Day6

description:
50 ng extracted total RNA was hybridized to probes and read using the NanoString SPRINT
20200109_30102365920321-01_Sample01_01


title: Non-labor myometrium rep1

tag: ga at delivery   (weeks+days)

tag: labor durations  (hours)


title: Monocyte_26-V9


title: blood sample from donor 1049 2 weeks post vaccination [VIC008827]


title: blood sample from donor 1069 2 weeks post vaccination [VIC008830]


title: Tachyzoite - 3

organism: Toxoplasma gondii

source_name: Purified T. gondii 76K tachyzoites grown in HFF cells

value: Tachyzoite


title: Monocyte_26-V7

value: month 7


title: Tachyzoite - 2


title: Monocyte_27-V7


title: Monocyte_25-V9


title: blood sample from donor 1003 2 weeks post vaccination [VIC008820]


title: Monocyte_27-V2


title: Non-labor myometrium rep2

tag: cervical dilatation（cm）

tag: maternal age (years)


title: NHP_2_Hoti_Day4

description:
50 ng extracted total RNA was hybridized to probes and read using the NanoString SPRINT
20200108_30102420200621-01_Sample12_12


title: Monocyte_26-V2


title: blood sample from donor 1028 2 weeks post vaccination [VIC008822]

tag: pid

tag: visit