title: L11_ROI01_Tumor [ICP20th-L11-ICPKilo-ROI01-Tumor-A02]

tag: roi

value: PanCK

tag: rawreads

tag: trimmedreads

tag: stitchedreads


title: 70% HEK293T [ZZ203-PP04-G05]

status: Public on Jun 10 2021

type: SRA

city: Seattle

first: Patrick

last: Danaher

state: WA

address: 530 Fairview Ave N

country: USA

institute: NanoString Technologies, Inc.

description:
photocleaved oligonucleotide barcodes
Samples were pooled during library preparation and split across lanes. Individual FASTQ files were generated for each lane, forward & reverse primers. The Fastq files contain the same identifier as the sample name for aggregation

library_source: transcriptomic

data_processing:
Library strategy: GeoMx-Seq
Adapter trimming with trim galore,  trimGaloreOpts = " --hardtrim5 26 --dont_gzip"
If paired-end, merge overlapping R1 and R2 with flash2, flash2Opts = " -m 26 -e 26 -f 26 -s 1 -r 27"
Extract UMIs in bowtie2, umiExtractOpts = " --bc-pattern=NNNNNNNNNNNNNN"
Align RTS_IDs (probe barcodes) using bowtie2, bowtie2Opts = " --end-to-end -L 4 --trim5 0 --trim3 0 --norc"
Deduplication using UMI-tools, umiDedupOpts = " --edit-distance-threshold=1"
Genome_build: N/A, sequencing of synthetic tags and alignment to whitelist of RTS_IDs (probe barcodes) found in the config.ini output from the GeoMx DSP platform
Supplementary_files_format_and_content: Digital Count Conversion (DCC) file format outputted from GeoMx NGS Pipeline, contains software versions, scan attributes, GeoMx NGS pipeline parameters and output metrics, Q30 scores, and list of deduplicated counts per RTS_ID (probe barcode)
Supplementary_files_format_and_content: Values represented in the collapsed target counts tab are the geometric mean of the probes for a given, removing any targets flagged as outliers. Analyzed counts represent the upper quartile normalized collapsed counts across the study after removing QC flagged segments.

molecule: total RNA

organism: Homo sapiens

source_name: HEK293T/CCRM-CEM mixture

extract_protocol:
Samples were incubated with DNA-oligo barcoded RNA-ISH probes which were conjugated with a UV-photocleavable linker following standard ISH protocols, along with flourescently labeled antibodies for visualization of morphological structures. Regions of interest within the tissue were illuminated with UV light and oligo barcodes were physically aspirated from the tissue and collected into microtiter plates by the GeoMx® Digital Spatial Profiler (DSP) platform. For more information about DSP protocols please see Merritt et al. Nature Biotech 2020 (doi: 10.1038/s41598-020-63539-x)
Each collection of oligo tags from one well (representing an AOI from the tissue section) was indexed with i7xi5 unique dual indexes using GeoMx SeqCode primers with 18 cycles of PCR.  After PCR, indexed AOIs were pooled and purified in two rounds of AMPure XP PCR purification using 1.2x bead:sample ratio.

tag: x

tag: panel

value: broad

tag: construct

value: directPCR

value: NEXTSEQ

value: CGCTACAC

value: GCCGGAAC

value: Giang CPA

value: solid

value: mixed cell line

tag: notes

value: CCRF-CEM

tag: mixprop

tag: hkfactor

tag: bgmean


title: 0% HEK293T [ZZ203-PP04-G08]

value: GTGCCTAC

value: ACCATTCG


title: 95% HEK293T [ZZ203-PP04-G04]

value: GTGCAGCT

value: CGATATTA


title: 100% HEK293T [ZZ203-PP04-G03]

value: CAGAGCCG

value: ACGCGCGT


title: 0% HEK293T [ZZ203-PP04-G02]

value: TACGAGTC

value: GCAAGAAT


title: 30% HEK293T [ZZ203-PP04-F12]

value: broad

value: AAGCGGCG

value: GTCCGAGG


title: L11_ROI05_Tumor [ICP20th-L11-ICPKilo-ROI05-Tumor-A10]

source_name: NSCLC tumor

tag: tissue

value: ICPKilo

value: Tumor

value: PanCK

value: grid/seg

tag: alignedreads

tag: deduplicatedreads

tag: sequencingsaturation

tag: uid

tag: normfactorhk

tag: roi x position

tag: roi y position

tag: nuclei


title: 100% HEK293T [ZZ203-PP04-F09]

value: directPCR

value: NEXTSEQ

value: CTCGACTC

value: ATAATCTC

value: Giang CPA

value: solid

value: mixed cell line


title: 95% HEK293T [ZZ203-PP04-F10]

value: CAATTGCG

value: TCCGGTCT

value: CCRF-CEM


title: 70% HEK293T [ZZ203-PP04-F11]

value: broad

value: GTGAGATT

value: ATTGCAAG


title: 0% HEK293T [ZZ203-PP04-B04]

value: TCTACCAA

value: AACCTACA

value: 293T CPA


title: 5% HEK293T [ZZ203-PP04-B02]

value: AAGCGTAA

value: TCCGCTTA


title: 99% HEK293T [ZZ203-PP04-A10]

value: directPCR

value: NEXTSEQ

value: TTGGTGTT

value: ATTGGACA


title: 95% HEK293T [ZZ203-PP04-A11]

value: AATGCACA

value: AAGTTGGT

value: solid


title: 70% HEK293T [ZZ203-PP04-A12]

value: CTCAACAA

value: TGTCTCTT

value: mixed cell line


title: 50% HEK293T [ZZ203-PP04-B01]

value: broad

value: GTTCGCGG

value: TATCGTGC

value: CCRF-CEM


title: 100% HEK293T [ZZ203-PP04-A09]

value: ACTGTCCT

value: ACAGACGT

value: 293T CPA


title: L11_ROI02_Tumor [ICP20th-L11-ICPKilo-ROI02-Tumor-A04]

value: ICPKilo

tag: roi

value: Tumor

value: PanCK

value: grid/seg

tag: rawreads

tag: trimmedreads

tag: stitchedreads


title: 1% HEK293T [ZZ203-PP04-A07]

tag: x

tag: panel

tag: construct

value: directPCR

value: NEXTSEQ

value: AGATTGAA

value: ACAAGGTT

tag: notes


title: 30% HEK293T [ZZ203-PP04-G06]

value: TCCGGTAA

value: AATAACGG

value: Giang CPA

value: solid

tag: mixprop

tag: hkfactor

tag: bgmean


title: 50% HEK293T [ZZ203-PP04-A05]

value: broad

value: TGCCGTGT

value: CAGCAGCG

value: mixed cell line


title: 5% HEK293T [ZZ203-PP04-A06]

value: AGGACCGG

value: CACTAATA

value: 293T CPA

value: CCRF-CEM


title: 0% HEK293T [ZZ203-PP04-A08]

value: TATCCTTA

value: GTTAACCT


title: 70% HEK293T [ZZ203-PP04-A04]

value: directPCR

value: NEXTSEQ

value: AGTTAATT

value: AGGCCAAC


title: 95% HEK293T [ZZ203-PP04-A03]

value: GAACGCGC

value: GAGATCAT


title: 99% HEK293T [ZZ203-PP04-A02]

value: CTCTGGAA

value: TATATTAC

value: solid


title: 0% HEK293T [ZZ203-PP02-G09]

value: broad

value: TCCGCCTC

value: CTCATCGG

value: Giang CPA


title: 30% HEK293T [ZZ203-PP02-G07]

value: ACGGCATC

value: GAGAGAGC

value: mixed cell line


title: 100% HEK293T [ZZ203-PP04-A01]

value: ATGCTGCA

value: CCAGAGTG

value: 293T CPA

value: CCRF-CEM


title: 5% HEK293T [ZZ203-PP04-G01]

value: directPCR

value: NEXTSEQ

value: AGTGGAAT

value: TATTCGGC


title: 70% HEK293T [ZZ203-PP02-G06]

value: TGCGCGCT

value: TAGCGCAG


title: 95% HEK293T [ZZ203-PP02-G05]

value: broad

value: GCGAGTAG

value: CGAACCGG

value: solid


title: 100% HEK293T [ZZ203-PP02-G04]

value: TTGTGAGA

value: GTTCAACA

value: Giang CPA


title: 1% HEK293T [ZZ203-PP04-B03]

value: GCAGATGA

value: AGCTATCT

value: mixed cell line


title: 0% HEK293T [ZZ203-PP02-G03]

value: CAATTATA

value: GCTAGTCG

value: CCRF-CEM


title: 95% HEK293T [ZZ203-PP02-F11]

value: directPCR

value: NEXTSEQ

value: CTTGGTTC

value: AATATGTA


title: 0% HEK293T [ZZ203-PP02-B04]

value: broad

value: CCGCGTTC

value: CCACCGAG

value: 293T CPA


title: 70% HEK293T [ZZ203-PP02-F12]

value: CTAGTTAG

value: TGCGACCG

value: solid


title: 5% HEK293T [ZZ203-PP02-B02]

value: TTCTATAC

value: ACCTTAAC


title: 70% HEK293T [ZZ203-PP02-A12]

value: TATTCAAG

value: ACGCTGCT

value: mixed cell line


title: 95% HEK293T [ZZ203-PP02-A11]

value: AGCCTCCT

value: CGTGCTGA

value: CCRF-CEM


title: 50% HEK293T [ZZ203-PP02-B01]

value: directPCR

value: NEXTSEQ

value: ACTCCATA

value: CTCATGTC


title: 100% HEK293T [ZZ203-PP02-A09]

value: broad

value: CACATTCA

value: GCAGCGTC


title: 99% HEK293T [ZZ203-PP02-A10]

value: GAGGACGG

value: TACTTATT

value: 293T CPA


title: 1% HEK293T [ZZ203-PP02-B03]

value: GTGCATGG

value: GAGCGACA

value: solid


title: 70% HEK293T [ZZ203-PP02-A04]

value: AGTTGGTC

value: GTATAAGG

value: mixed cell line


title: 5% HEK293T [ZZ203-PP02-A06]

value: GAGTGCGA

value: AGAATTCT

value: CCRF-CEM


title: 95% HEK293T [ZZ203-PP02-A03]

value: directPCR

value: NEXTSEQ

value: GACCTTAC

value: AACCGAAT


title: 1% HEK293T [ZZ203-PP02-A07]

value: broad

value: ACCACAGG

value: ACGTCACA


title: L13_ROI24_TME

tag: tissue

value: TME


title: 50% HEK293T [ZZ203-PP02-A05]

value: ATTGGTAA

value: GTCTGTCG

value: 293T CPA


title: 0% HEK293T [ZZ203-PP02-A08]

value: GACGATCG

value: AGTTGTTC

value: solid


title: 5% HEK293T [ZZ203-PP02-G08]

value: CTAGAGGA

value: CCGGCTGT

value: Giang CPA

value: mixed cell line


title: 99% HEK293T [ZZ203-PP02-A02]

value: directPCR

value: NEXTSEQ

value: ATTCTCTA

value: CTTATGGA

value: CCRF-CEM


title: 100% HEK293T [ZZ203-PP02-A01]

value: broad

value: GCTGCCGT

value: CCACAACA


title: 5% HEK293T [ZZ203-PP02-G02]

value: CTTCCAGG

value: TCCTTCTC


title: L13_ROI23_TME

value: TME


title: L13_ROI22_TME


title: 30% HEK293T [ZZ203-PP02-G01]

value: TCACAGCA

value: CCTCGCGA


title: L13_ROI23_Tumor

value: Tumor


title: L13_ROI22_Tumor


title: L13_ROI21_TME


title: 100% HEK293T [ZZ203-PP02-F10]

value: TCGTACTC

value: GTTCGCGC

value: solid


title: L13_ROI21_Tumor


title: L13_ROI20_TME


title: L13_ROI18_TME


title: L13_ROI20_Tumor


title: L13_ROI19_TME


title: L13_ROI17_TME


title: L13_ROI16_Tumor


title: L13_ROI18_Tumor


title: L13_ROI16_TME


title: L13_ROI14_TME


title: L13_ROI14_Tumor


title: L13_ROI15_Tumor


title: DDX6_FLAGplus rep2

city: Nakhon Pathom

first: Opas

last: Choksupmanee

address: 25/25 Phuttamonthon 4 Rd., Salaya, Phuttamonthon

country: Thailand

institute: Institute of Molecular Biosciences, Mahidol University

data_processing:
Illumina GA Pipeline v1.5 software used for basecalling.
The sequencing reads which containing low-quality, adaptor-polluted and high content of unknown base (N) reads, were filtered before downstream analyses. (Software information: SOAPnuke v1.5.2, parameters: -n 0.001 -l 20 -q 0.4 -A 0.25 -Q 2 -G)
HISAT2 (Hierarchical Indexing for Spliced Alignment of Transcripts) was used for mapping step onto reference genome(hg38_UCSC_20180118) (Software information: HISAT2 v2.0.4, Parameters: --phred33 --sensitive --no-discordant --no-mixed -I 1 -X 1000)
Data sets with 44 set as nucleotide bin size were then normalized and compared using bamCompare
Genome_build: GRCh38
Supplementary_files_format_and_content: Comma-delimited text files include raw gene counts, gene length and FPKM for each sample

source_name: DENV-2 infected HuH-7

growth_protocol: HuH-7 cells  in the presence/absence of exogeneous DDX6 expression were grown in completed DMEM (DMEM suplemented with 10%FBS and penicillin-streptomycin) (6 wells-plate)

extract_protocol:
Cell pellets were delivered to BGI for a service
Library construction was performed by BGI company based on DNA nanoballs (DNBs) technology

treatment_protocol: 80% confluency of HuH-7 cells were infected with dengue virus serotype 2 (16681) (MOI5) for 48 h

tag: cell line

tag: genotype

value: exogeneous DDX6 expression

tag: agent


title: DDX6_FLAG rep1


title: pcDNAplus rep2

value: pcDNA


title: pcDNAplus rep1


title: L13_ROI13_TME


title: L13_ROI15_TME


title: pcDNA rep1


title: DDX6_FLAG rep2


title: pcDNA rep2


title: L13_ROI13_Tumor


title: DDX6_FLAGplus rep1


title: 2016

type: RNA

city: Houston

first: Cintia

middle: S.

last: de Paiva

state: TX

address: 6565 Fannin Street NC505G

department: Ophthalmology

institute: Baylor College of Medicine

description: Immunology panel consisting of 594 genes; 15 housekeeping genes

hyb_protocol: One hundred nanograms of total RNA were hybridized with the NanoString Technologies nCounter Gene Expression GE-Human-Immunology v2 Panel Codeset containing 594 unique pairs of 35-50bp reporter probes and biotin-labeled capture probes, including internal reference controls. Overnight hybridization occurred for 20 hours at 65°C. Removal of excess probes with magnetic bead purification was performed on the nCounter Prep Station (software v4.0.11.2) on the High Sensitivity assay. Briefly, the probe-mRNA structure was affinity purified by its 3’ end to remove excess reporter probes, then by its 5’ end to remove excess capture probes. Once unbound probes were washed away, the tripartite structure was bound to the streptavidin-coated cartridge by the biotin capture probe, aligned by an electric current (negative to positive), and immobilized. Photobleaching and fluorophore degradation was prevented with the addition of SlowFade.

scan_protocol: The cartridge containing immobilized samples was transferred to the nCounter Digital Analyzer (software v3.0.1.4) and scanned at 555 field of view (FOV). An epi-fluorescent microscope and CCD camera identified sets of fluorescent spots, which were tabulated for data output. Quality control metrics were recorded using the nSolver Analysis Software v4.0.6.2.

data_processing: Data processing was analyzed with nCounter and Rosalind software.

extract_protocol: RNA was extracted using the Qiagen mini plus columns according to the manufacturer's protocol.

tag: Sex

value: female

value: conjunctiva

tag: diagnosis

value: Control

tag: age


title: 2018

value: SS KCS


title: 2015


title: 2014


title: 2017


title: 2009


title: L13_ROI12_Tumor

tag: roi


title: 1914


title: 1915


title: 1913


title: 2003


title: L13_ROI06_TME


title: L13_ROI07_Tumor


title: Rice Near Isogenic Line GRH

city: Miryang

first: ROLLY

middle: NKULU

last: KABANGE

state: Gyeongsangnamdo

address: Jompiljaero 20, Naei-dong

department: Department of Southern Area Crop Science

country: South Korea

institute: Rural Development Administration

description:
NO_1
Oryza sativa L.

data_processing:
Illumina HCS 3.3.52 software used for basecalling.
The total number of bases, reads, GC (%), Q20 (%), Q30 (%) were calculated for 4 samples. Trimmomatic program (Bolger et al., 2014) was used to remove adapter sequences and bases with base quality lower than three from the ends. Also using sliding window method, bases of reads that does not qualify for window size 4, and mean quality 15 are trimmed. Afterwards, reads with length shorter than 36bp are dropped to produce trimmed data.
For assembled genes, longest contigs of the assembled contigs were filtered and clustered into the non-redundant transcripts using CD-HIT-EST (Li et al., 2006; Li et al., 2001) . We defined these transcripts as ‘unigenes’ which are used for predicting the ORFs (Open Reading Frames), annotating against several known sequence databases, and analyzing differentially expressed genes (DEGs). ORF prediction for unigenes was performed using TransDecoder program to identify candidate coding regions within transcript sequence. After extracting ORFs that are at least 100 amino acids long, TransDecoder predicted the likely coding regions.
Fragments Per Kilobase of transcript per Million mapped reads (FPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
For functional annotation of the unigenes, the Gene Ontology (GO) database was applied to classify the annotated unigenes using BLASTX of DIAMOND with an E-value cut-off of 1.0E-5. Classification of GO terms was subsequently performed using in-house script. The GO terms belonging to biological process (BP), cellular component (CC) and molecular function (MF) were listed (Figure S2). The Oryza sativa japonica (Japanese rice) (RAPDB) was used for alignment.
To identify the proteins distributed in eukaryotic orthologous groups (KOG), clusters of orthologous groups (COGs), and non-supervised orthologous groups (NOGs), we carried out BLASTX of DIAMOND with an E-value cut-off of 1.0E-5 on EggNOG (Evolutionary genealogy of genes) database. The annotated unigenes were mapped to the annotation of the corresponding orthologous groups in EggNOG database.
For functional annotation of the unigenes, we carried out BLASTX of DIAMOND with an E-value cut-off of 1.0E-5 on Kyoto Encyclopedia of Genes and Genomes (KEGG) database. Bi-directional best hit (BBH), which is a widely used method to infer orthology was used to search against the KEGG database to obtain the KO (reference pathway) number of the KEGG annotation. The KO number of the transcriptome was also obtained according to KEGG annotation. For functional annotation of the unigenes, we carried out BLASTX of DIAMOND with an E-value cut-off of 1.0E-5 on UniProt (Universal Protein Resource) database. In addition to capturing the core data mandatory for each UniProtKB entry (mainly, the amino acid sequence, protein name or description, taxonomic data and citation information), as much annotation information as possible were added. For functional annotation of the unigenes, we carried out BLASTX of DIAMOND with an E-value cut-off of 1.0E-5 on Pfam database. The Pfam database is a large collection of protein families, each represented by multiple sequence alignments and hidden Markov models (HMMs). Proteins are generally composed of one or more functional regions, commonly termed domains. The identification of domains that occur within proteins can therefore provide insights into their function.
Genome_build: Oryza sativa japonica (Japanese rice) (RAPDB)
Supplementary_files_format_and_content: *.gene_abund.anno.tab: Tab-delimited text files include FPKM and TPM values for each Sample.
Supplementary_files_format_and_content: *.gtf
Supplementary_files_format_and_content: Expression_Profile.IRGSP-1.0_transcript_exon_2018-11-26.gene.txt
Supplementary_files_format_and_content: Expression_Profile.IRGSP-1.0_transcript_exon_2018-11-26.transcript.txt
Supplementary_files_format_and_content: MapMan_NIL.xls
Supplementary_files_format_and_content: MapMan_Ilpum.xls

organism: Oryza sativa

source_name: Leaf

growth_protocol: Two rice lines, Ilpum (the GRH susceptible cultivar) and a near isogenic line (NIL) carrying the Grh1 (a gene conferring resistance towards GRH) derived from a cross between Shingwang (indica, P1) and Ilpum (japonica, P2) (Park et al., 2013) were use as genetic materials to perform the experiments. Prior to germination, rice seeds were surfaced sterilized using nitric acid (HNO3, 0.7%) (CAS: 7697-37-2, Junsei Chemical Co. Ltd, Tokyo, Japan) overnight to break the dormancy (Kabange et al., 2021), followed by incubation for 48 h at 27 °C to induced germination. Then, germinated rice seeds were grown in 50-well trays containing an enriched soil (company name) until 3 leaf-stage.

extract_protocol:
Total RNA was isolated from leaf samples, and DNA contamination were eliminated using DNase. mRNA purification kit was used to prepare the library. RNA fragments were randomly purified for short read sequencing, followed by reverse transcription of fragmented RNA into cDNA. The adapters were ligated onto both ends of the cDNA fragments. After amplifying fragments using PCR, fragments with insert sizes between 200–400 bp were selected, and both ends of the cDNA were sequenced by the read length (paired-end sequencing).
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Seedlings with a uniform height were placed in test tubes after washing the loose soil from the roots. Seedlings were infested with second instar nymphs green rice leafhoppers for 48 h at room temperature as described earlier (Park et al., 2013). Leaf samples for RNA-Seq analysis were collected and sent for sequencing (Macrogen, Daejeon, Korea).

tag: line

value: Introgression

value: Near Isogenic line

value: Leaf

value: 21 days after germination

tag: treatment

value: Green rice leafhopper (GRH)


title: 1910


title: 2013


title: 2012


title: Rice Near Isogenic Line control

description:
NX_1
Oryza sativa L.


title: L13_ROI11_TME

value: TME


title: 2011


title: 2008


title: 2007


title: L13_ROI11_Tumor


title: L13_ROI10_TME


title: L13_ROI12_TME


title: 2005


title: 2002


title: L13_ROI09_TME


title: U87MG-rep3

city: Okayama

first: Masato

last: Maruyama

address: 1-1-1, Tsushima-naka, Kita-ku

country: Japan

institute: Okayama University

description: Gene expression in U87MG cells

hyb_protocol: 600 ng of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 μl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction,  25 μl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to SurePrint G3 Human GE 8x60K Microarray Ver2.0 (Agilent) for 17 hours at 65°C in a rotating hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute at 37°C with GE Wash buffer 2 (Agilent), then dried.

scan_protocol: Slides were scanned by Agilent Technologies Microarray Scanner (Scan Resolution 3 μm, TIFF file dynamic range 20 bit).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent).  Extracted data were 75% tile-normalized and baseline transformation was performed to the median of all samples by Genespring GX software (Agilent Technologies).  After removal of control spots, entities where at least 100% of the samples in any 1 out of 2 conditions have values within range were used in the analysis.

source_name: adherent

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 50 ng RNA using the Low Input Quick Amp Labeling kit (Agilent) according to the manufacturer's instructions, followed by RNeasy mini spin column purification (QIAGEN, Valencia, CA).  cRNA yield and quality were checked with the NanoDrop ND-1000 Spectrophotometer and Agilent 2100 Bioanalyzer series II.

growth_protocol: U87MG cells were maintained in Minimum Essential Medium (MEM; Sigma, St. Louis, MO) supplemented with 10% FBS, 1% non-essential amino acid (Gibco; Thermo Fisher Scientific, Waltham, MA), 1 mM sodium pyruvate (Nacalai Tesque, Kyoto, Japan), and 100 U/ml penicillin, 100 μg/ml streptomycin (Invitrogen; Thermo Fisher Scientific) in humidified air atmosphere containing 5% CO2 at 37 °C.  P4E8 cells were cultured as floating sphere in neurosphere medium (DMEM/F12 supplemented with 1% N2 Max Media Supplement (R&D Systems, Minneapolis, MN), 2% B27 Supplement Minus Vitamin A (Thermo Fisher Scientific, Waltham, MA), 3 mM sodium bicarbonate, 100 U/ml penicillin, 100 μg/ml streptomycin, 20 ng/ml bFGF and EGF)  in humidified air atmosphere containing 5% CO2 at 37 °C.

extract_protocol: Total RNA was extracted from U87MG and P4E8 cells with TRIzol reagent (Ambion, Thermo Fisher Scientific) and purified using the PureLink RNA Mini Kit (Ambion, Thermo Fisher Scientific).  RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer series II (Agilent Technologies, Santa Clara, CA).


title: 1917


title: 2001


title: 2010


title: L13_ROI09_Tumor


title: L13_ROI10_Tumor


title: KO 10

city: Beijing

first: Ting

last: Li

address: Taiping Road 27

country: China

institute: NCBA

data_processing:
High-throughput sequencing was performed using the Illumina NovaSeq 6000.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Mus musculus

growth_protocol: primary MEF cells (P3) were cultured in Dulbecco’s modified Eagle’s medium (DMEM) containing 10% fetal bovine serum (FBS).

extract_protocol:
A total amount of 2 μg RNA harvested by Trizol reagentper sample for each group was used as input material for the RNA sample preparations.
Libraries were prepared according to Illumina's standard protocol.

treatment_protocol: tamoxifen (1 μM, 48h)

tag: strain

value: tamoxifen (1 μM, 48h)

tag: cell type

value: primary MEF cells


title: KO 3


title: ZIKV+hNPC 24hr

city: SINGAPORE

first: Yu

last: Zhang

address: 60 Biopolis Street, Genome, #07,

country: Singapore

institute: GIS, A*STAR

data_processing:
the reads were mapped to hg19 transcriptome
FPKM was calculated by custom script
Genome_build: the transcriptome from hg19
Supplementary_files_format_and_content: csv, the expression matrix

molecule: polyA RNA

source_name: neuronal precursor cells

growth_protocol: Human neuronal precursor cells was infected with Zika ILM at MOI=1 and harvested 24hrs post-infection

extract_protocol:
The RNA was extracted using TRIzol, according to the manufacturer's instructions.
Library preparation was contructed using the NEBNExt Ultra directional RNA library preparation kit for Illumina (E7420L),  accordingly to the manufacturer's instructions

treatment_protocol: No treatment was done

value: Human neuronal precursor cells

tag: cell status

value: Differentiated from hESC into hNPC

tag: treatment group

value: ZIKV infected 24hr


title: L13_ROI08_TME


title: WT 5


title: 1905


title: 1904


title: 1903


title: 1902


title: 1901


title: L13_ROI02_Tumor

value: Tumor


title: L13_ROI06_Tumor


title: LH_12_2_2_bis

city: Santander

first: Lucio

last: Di Filippo

state: Cantabria

address: PCTCAN - Cl. Albert Einstein, 22

country: Spain

institute: IBBTEC

data_processing:
Illumina novaSeq base call (BCL) files are converted in fastq file through bcl2fastq (version v2.20.0.422)
Sequence reads were trimmed using bbduk software (bbmap suite 37.31)
Alignment was performed with STAR 2.6.0a
The expression levels of genes were determined with htseq-count 0.9.1
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include raw counts for each Sample

source_name: mouse fibroblasts

growth_protocol:
This study used fibroblasts extracted from a knockin mouse Per2::LUC.
cells were expanded in DMEM, 4.5 g/L glucose content, 10% FBS at 37 °C and with humidified 5% CO2.

extract_protocol:
Total RNA was extracted used RNeasy Plus Micro kit, according to manufacturer protocol
3'DGE mRNA-seq research sequencing service (Next Generation Diagnostics srl)

treatment_protocol: 3 cycles of 24h each alternating every 12h High (H) and Low (L) glucose-insulin content media. The treatment protocols implemented are : HL (12hH-12hL for 3 cycles), LH (12hL-12hH for 3 cycles), and HH (12hH-12hH for 3 cycles)

tag: expansion passages

value: PER2::LUC sv

tag: metabolic treatment

value: LH

tag: time


title: L13_ROI01_TME

tag: tissue


title: LH_12_2_1_bis


title: L13_ROI05_TME


title: L13_ROI05_Tumor


title: hNPC 16hr

value: non-infected 16hr


title: L13_ROI04_TME


title: L13_ROI04_Tumor


title: KO 7


title: P4E8-rep2

description: Gene expression in P4E8 cells

source_name: tumorsphere

tag: cell line


title: U87MG-rep2

description: Gene expression in U87MG cells


title: hNPC 24hr

value: non-infected 24hr


title: hNPC 2hr

value: non-infected 2hr


title: L12_ROI24_Tumor


title: hNPC 0hr

value: non-infected 0hr


title: U87MG-rep1

description: Gene expression in U87MG cells


title: WT 8

tag: genotype


title: L12_ROI23_TME


title: P4E8-rep1

description: Gene expression in P4E8 cells


title: L13_ROI03_TME


title: L12_ROI23_Tumor


title: RB2

city: seoul

first: Sara

last: Kim

address: 서울 성북구 안암동5가 1-2 고려대학교 안암캠퍼스 하나과학관 505호

department: Life sciences and biotechnology

institute: Korea university

data_processing:
The quantification of transcript expression was performed using Salmon
Differential expression analysis was performed using DESeq2
Genome_build: Araport11

organism: Arabidopsis thaliana

source_name: RiD-BRI1/BAK1_100 nM of brassinolide

growth_protocol: Seedlings were grown on medium containing 2 μM PPZ with 100 nM brassinolide or 100 nM rapamycin in the dark for 5 days

extract_protocol:
Total RNA was extracted from seedlings using the TaKaRa MiniBEST Plant RNA Extraction Kit (Takara) according to the manufacturer’s instructions
The isolated total RNA was processed for preparing mRNA sequencing library using the Illumina TruSeq Stranded mRNA Sample preparation kit (Illumina) accoding to the manufacturer’s protocol.

tag: genotype/variation

value: 5-day-old whole seedlings

value: 100 nM of brassinolide


title: RNA0288_APC73_Plate_1_14

city: Singapore

first: Florent

last: Ginhoux

address: 8A Biomedical Grove, Immunos Building, Level 3

institute: Singapore Immunology Network (SIgN), A*STAR

description: Human Skin RNA-seq

data_processing:
Raw reads were aligned to the human reference genome GRCh38 from GENCODE using RSEM program version 1.3.0 with default parameters. Gene expression values in transcripts per million (TPM) were calculated using the same RSEM program and the human GENCODE annotation version 25.
Genome_build: GRCh38.p7
Supplementary_files_format_and_content: Tab-delimited text files include TPM values for each Sample

source_name: Human Skin

extract_protocol:
We index-sorted cutaneous DC and monocyte-macrophages using flow cytometry based on expression of characteristic patterns of surface markers/proteins into 96 well plates containing Lysis buffer.
Single-cell cDNA libraries were prepared using the Smart-seq v2 protocol with the following modifications: (i) 1 mg/mL BSA Lysis buffer (Ambion Thermo Fisher Scientific, Waltham, MA, USA); and (ii) 200 pg cDNA with 1/5 reaction of Illumina Nextera XT kit. The length distribution of the cDNA libraries was monitored using a DNA High Sensitivity Reagent Kit on the Perkin Elmer Labchip. All samples were subjected to an indexed paired-end sequencing run of 2x151 cycles on an Illumina HiSeq 4000 system for about 1 million reads per sample.

value: Skin

tag: donor

tag: condition

value: AD


title: RB1

address: 서울 성북구 안암동5가 1-2 고려대학교 안암캠퍼스 하나과학관 505호


title: P4E8-rep3

description: Gene expression in P4E8 cells


title: HL_16_6_1_bis

value: HL


title: L13_ROI03_Tumor


title: L12_ROI21_TME

value: TME


title: ZIKV+hNPC 16hr

value: ZIKV infected 16hr


title: RR2

address: 서울 성북구 안암동5가 1-2 고려대학교 안암캠퍼스 하나과학관 505호

source_name: RiD-BRI1/BAK1_100 nM of rapamycin

value: 100 nM of rapamycin


title: ZIKV+hNPC 2hr

value: Human neuronal precursor cells

value: Differentiated from hESC into hNPC

value: ZIKV infected 2hr


title: WT 4

value: tamoxifen (1 μM, 48h)

value: primary MEF cells


title: LH_12_2_4_bis

value: PER2::LUC sv

value: LH


title: L13_ROI02_TME


title: HL_12_5_1_bis


title: ZIKV+hNPC 0hr

value: ZIKV infected 0hr


title: L13_ROI01_Tumor

value: Tumor


title: HL_08_4_4_bis


title: L12_ROI20_TME


title: RM2

address: 서울 성북구 안암동5가 1-2 고려대학교 안암캠퍼스 하나과학관 505호

value: 5-day-old whole seedlings

value: mock


title: LH_20_1_4_bis


title: RM1

address: 서울 성북구 안암동5가 1-2 고려대학교 안암캠퍼스 하나과학관 505호


title: L12_ROI24_TME


title: LH_20_1_3_bis


title: LH_20_1_2_bis


title: HL_16_6_4_bis


title: HL_08_4_2_bis


title: 375_Wang_input_BWX3370

city: Bloomington

first: Xindan

last: Wang

state: IN

address: 1001 E 3rd St

department: Biology

institute: Indiana University at Bloomington

description: parS∆9 no a.b., -1˚ parS (in parB)

library_source: genomic

data_processing:
Reads from each end of a DNA fragment were represented in each of the two FASTQ files generated by Illumina paired-end sequencing.
For Hi-C, we mapped reads in each FASTQ file back to the genome of Bacillus subtilis PY79 (NCBI Reference Sequence: NC_022898.1) independently by Bowtie version 2.1.0 to preserve the order of reads. All the processing steps afterwards were performed using an in-house Perl scripts.  For ChIP-seq, we mapped reads in each FASTQ file back to the genome of Bacillus subtilis PY79 (NCBI Reference Sequence: NC_022898.1) using CLC genomics workbench 8.0, and exported .csv file.
For Hi-C, the two resulting SAM files were then merged together. Unaligned reads were discarded.
For Hi-C, the Bacillus subtilis (PY79) genome was divided into HindIII restriction fragments. Each aligned read was sorted into its corresponding restriction fragment. We inferred that a DNA fragment resulted from non-ligation or self-ligation if reads from both ends were from the same restriction fragment; these reads were discarded. Only DNA fragments for which the reads came from different restriction fragments were retained and used for construction of a Hi-C contact map.
For Hi-C, the genomes of Bacillus subtilis (PY79) was then divided into bins 10 kb and the remaining reads were allocated to their corresponding bin. We then counted the number of fragments having reads with in different bins. A raw Hi-C contact map is the matrix of read counts in which each entry, mij, indicates the number of fragments with ends mapping to bins i and j. The raw Hi-C contact map/matrix is biased due to the uneven distribution of restriction enzyme sites and, to a lesser extent, differences in GC content and the mappability of individual reads. We normalized raw contact maps using an iterative normalization procedure (Imakaev et al., 2012 PMID: 22941365). Essentially, we converted the number of interactions, or read counts, into Hi-C scores by applying the following equation and iteratively repeating it for the resulting contact map after each cycle:  mij =mij * (total reads) / (total reads in bin i * total reads in bin j). The iterative procedure was repeated until the maximum relative error of the total number of Hi-C scores in a bin was less than 10-5. Resulting matrices were normalized so that Hi-C scores for each row and column sum to 1. Subsequent analysis and visualization was done using R scripts.
Genome_build: NC_022898.1
Supplementary_files_format_and_content: Files ending with .matrix.txt: tab-delimited text files of the iteratively-corrected Hi-C contact maps/matrices. Files ending with .csv: comma-separated values files of ChIP-seq results.

molecule: genomic DNA

organism: Bacillus subtilis PY79

source_name: Bacillus subtilis PY79

growth_protocol: Bacillus subtilis strains were derived from the prototrophic strain PY79 (Youngman et al 1983, PMID: 6300908). Cells were grown in defined rich medium (CH) (Harwood and Cutting 1990, Molecular Biological Methods for Bacillus) at specified temperature.

extract_protocol:
Hi-C experiments were performed using HindIII according to previous publications (Le et al, 2013, PMID: 24158908; Wang et al 2015, PMID: 26253537). ChIP-seq experiments were performed using anti-SMC antibodies according to previous publication (Graham et al 2014, PMID: 24829297).
Standard library construction protocol was used for Illumina Nextseq550 sequencing platforms. Illumina Truseq indexes were used.

treatment_protocol:
Cells were growing in CH medium at 37˚C, fixed by 3% formaldehyde for 30min at room temperature
None

tag: developmental stage

value: CH, 37degreeC

value: parSdelta9 no a.b., -1degree parS (in parB)

tag: restriction enzyme

tag: antibody

value: input sample (no antibodies)


title: HL_08_4_1_bis

value: HL


title: L12_ROI19_Tumor

tag: roi


title: 374_Wang_ChIPSMC_BWX3370

description: parS∆9 no a.b., -1˚ parS (in parB)

value: anti-SMC antibodies


title: L11_ROI130_TME [ICP20th-L11-ICPKilo-ROI130-TME-F11]

value: ICPKilo

value: TME

value: grid/seg

tag: rawreads

tag: trimmedreads

tag: stitchedreads

tag: alignedreads

tag: deduplicatedreads

tag: sequencingsaturation

tag: uid

tag: normfactorhk

tag: roi x position

tag: roi y position

tag: nuclei


title: L12_ROI18_TME

tag: tissue


title: L12_ROI22_TME


title: L12_ROI22_Tumor


title: HL_16_6_3_bis

tag: expansion passages

tag: genotype

tag: metabolic treatment

tag: time


title: HL_12_5_2_bis


title: L12_ROI21_Tumor

tag: roi


title: HL_12_5_4_bis


title: HL_04_3_2_bis


title: L12_ROI19_TME


title: RR1

address: 서울 성북구 안암동5가 1-2 고려대학교 안암캠퍼스 하나과학관 505호

tag: genotype/variation

tag: treatment

value: 100 nM of rapamycin


title: HL_12_2_3_bis


title: L12_ROI16_Tumor


title: HL_08_4_3_bis


title: L12_ROI15_TME


title: CR2

address: 서울 성북구 안암동5가 1-2 고려대학교 안암캠퍼스 하나과학관 505호

source_name: Col-0_100 nM of rapamycin


title: IRF8 KO pDC 3

city: St. Louis

first: David

middle: Alexander

last: Anderson III

state: Missouri

address: 660. S Euclid Ave., Campus Box 8118

department: Pathology and Immunology

institute: Washington University School of Medicine

description: B220+ SiglecH+

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: standard Affymetrix protocol

label: biotin

source_name: splenic pdc

label_protocol: standard Affymetrix protocol

extract_protocol: Total RNA was isolated from spelnic pDCs from mice of the indicated genotype. mRNA was reverse transcribed and amplified by NuGen PICO SL.

value: KO


title: HL_12_2_1_bis


title: L12_ROI20_Tumor


title: HL_04_3_1_bis


title: IRF8 KO pDC 2

description: B220+ SiglecH+


title: L12_ROI15_Tumor


title: CR1

address: 서울 성북구 안암동5가 1-2 고려대학교 안암캠퍼스 하나과학관 505호


title: LH_16_6_4_bis


title: HL_04_3_4_bis


title: IRF8 WT pDC 1

description: B220+ SiglecH+

value: WT


title: L12_ROI18_Tumor


title: CM1

address: 서울 성북구 안암동5가 1-2 고려대학교 안암캠퍼스 하나과학관 505호


title: L12_ROI17_TME


title: L12_ROI13_TME


title: L12_ROI17_Tumor


title: HL_12_2_4_bis

value: PER2::LUC sv


title: L12_ROI16_TME


title: L12_ROI12_Tumor


title: LH_12_5_3_bis

value: LH


title: CM2

address: 서울 성북구 안암동5가 1-2 고려대학교 안암캠퍼스 하나과학관 505호


title: L12_ROI11_TME


title: HL_12_2_2_bis


title: LH_12_5_1_bis


title: L12_ROI13_Tumor


title: LH_12_5_4_bis


title: L12_ROI11_Tumor


title: L12_ROI14_TME


title: LH_16_6_2_bis


title: LH_20_4_2_bis


title: IRF8 WT pDC 2

description: B220+ SiglecH+


title: IRF8 KO pDC 1

description: B220+ SiglecH+


title: IRF8 WT pDC 3

description: B220+ SiglecH+


title: memCD4_none_48_E_TC9_rep1

city: London

first: Reiner

last: Schulz

address: 8th floor Guy's Tower

department: Medical & Molecular Genetics

country: United Kingdom

institute: King's College London

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Raw signals, detection p-values, bead numbers, and bead-level standard errors were exported for regular and control probes from GenomeStudio. Data were imported into R using the Bioconductor beadarray and illuminaHumanv4.db packages. Data were background-corrected, quantile-normalised and log2-transformed using the limma implementation of the neqc method (Shi et al. Nucl Acids Res 2010).

source_name: memory CD4 T cells from donor E, mock-infected as part of experiment TC9, 48h post infection, intra-experimental technical replicate 1, hybridised Mar-13 (from sample well position A7)

label_protocol: Illumina® TotalPrep™ RNA Amplification Kit (Ambion); protocol according to manufacturer instructions (from 100-500 ng RNA).

growth_protocol: Primary CD4+ T cells and memory CD4+ T cells were isolated from PBMCs of healthy donors using the total CD4 T cell isolation kit II and the memory CD4+ T cell isolation kit by Miltenyi Biotec, respectively.

extract_protocol: 2E5 to 2E6 primary CD4+ T cells were harvested at the indicated time post-infection. RNA was isolated using the miRNeasy kit with on-column DNase treatment (Qiagen).

treatment_protocol: Infections were initiated by spin infection of the cells with HIV-1 particles (0,5 to 1 g/mL p24Gag) for 2 h at 2000 g and at 30 degrees Celsius. The cells were then incubated at 37 degrees for 1 h prior to extensive washes in PBS1X. Fresh and pre-warmed media (containing anti-CD3 and -CD28 antibodies) was added and the cells placed back at 37 degrees for the indicated incubation times, prior to RNA extraction.

tag: celltype

tag: virus

tag: vprsuppl

value: no

tag: timepoint

tag: donor

value: E

tag: age

tag: Sex

value: M

tag: arraybatch

tag: plateposition

tag: experiment

tag: replicate


title: LH_16_6_3_bis

tag: expansion passages

tag: genotype


title: LH_16_6_1_bis

tag: metabolic treatment

tag: time


title: memCD4_CH077.t_48_E_TC9_rep1

source_name: memory CD4 T cells from donor E, infected with HIV-1 strain CH077.t as part of experiment TC9, 48h post infection, intra-experimental technical replicate 1, hybridised Mar-13 (from sample well position A10)


title: L12_ROI14_Tumor

tag: tissue

value: Tumor

tag: roi


title: L12_ROI12_TME


title: memCD4_Ba-L_48_E_TC9_rep1

source_name: memory CD4 T cells from donor E, infected with HIV-1 strain Ba-L as part of experiment TC9, 48h post infection, intra-experimental technical replicate 1, hybridised Mar-13 (from sample well position A9)

tag: celltype

value: Ba-L


title: LH_12_5_2_bis


title: L12_ROI08_TME


title: LH_20_4_4_bis


title: LH_16_3_3_bis


title: L12_ROI10_TME


title: LH_20_4_3_bis


title: memCD4_REJO.c_48_E_TC9_rep1

source_name: memory CD4 T cells from donor E, infected with HIV-1 strain REJO.c as part of experiment TC9, 48h post infection, intra-experimental technical replicate 1, hybridised Mar-13 (from sample well position A12)

tag: virus


title: LH_16_3_1_bis


title: L12_ROI10_Tumor

source_name: NSCLC tumor


title: L12_ROI09_TME


title: LH_20_4_1_bis


title: L12_ROI09_Tumor


title: L12_ROI07_Tumor


title: L12_ROI06_TME


title: LH_16_3_4_bis


title: L12_ROI08_Tumor


title: HL_20_1_3_bis


title: memCD4_CH106.c_48_E_TC9_rep1

source_name: memory CD4 T cells from donor E, infected with HIV-1 strain CH106.c as part of experiment TC9, 48h post infection, intra-experimental technical replicate 1, hybridised Mar-13 (from sample well position A11)

tag: vprsuppl


title: LH_16_3_2_bis


title: HL_20_1_2_bis


title: L12_ROI07_TME


title: memCD4_CH106.c_12_E_TC9_rep1

source_name: memory CD4 T cells from donor E, infected with HIV-1 strain CH106.c as part of experiment TC9, 12h post infection, intra-experimental technical replicate 1, hybridised Mar-13 (from sample well position A5)

tag: timepoint


title: HH_16_6_4_bis

value: HH


title: Proband

type: genomic

first: Christopher

last: Grochowski

state: Texas

address: 1 Baylor Plaza

department: Molecular and Human Genetics

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

scan_protocol: Scanned on an Agilent G2505C  scanner. Images were quantified using Agilent Feature Extraction Software (version 12.0)

data_processing: Agilent Feature Extraction Software (version 12.0) was used for background subtraction and normalization.

source_name: Whole Blood

label_protocol: 1.2 ug of genomic patient and reference DNA were digested with AluI (5 U) and RsaI (5 U) (Promega, R6281 and R6371) for 2 hr at 37°C. Labeling reactions were performed according to the manufacturer’s instructions (BioPrime Array CGH Genomic Labeling Module,Invitrogen Corporation, #18095-012; Perkin-Elmer Las Inc. Cyanine Smart Pack dCTP,

extract_protocol: DNA was isolated from peripheral blood with a Puregene kit (Gentra Systems), following the manufacturer’s protocol

tag: gender

value: Male

source_name: Reference Sample BAB5319

tag: sample type

value: Reference Sample


title: Father


title: HH_16_6_2_bis

source_name: mouse fibroblasts


title: L12_ROI06_Tumor


title: memCD4_IIIB_12_E_TC9_rep1

source_name: memory CD4 T cells from donor E, infected with HIV-1 strain IIIB as part of experiment TC9, 12h post infection, intra-experimental technical replicate 1, hybridised Mar-13 (from sample well position A2)

value: IIIB

tag: donor

tag: age

tag: Sex


title: HH_16_6_1_bis


title: Unaffected Sibling 2

value: Female

source_name: Reference Sample BAB3778


title: L12_ROI05_TME

value: TME


title: L12_ROI04_TME


title: L12_ROI05_Tumor


title: HH_12_5_3_bis


title: L12_ROI03_TME


title: Mother


title: CD4_none_48_A_TC43_rep1

source_name: bulk CD4 T cells from donor A, mock-infected as part of experiment TC43, 48h post infection, intra-experimental technical replicate 1, hybridised Mar-13 (from sample well position G11)

value: A

value: F

tag: arraybatch

tag: plateposition

tag: experiment


title: memCD4_CH077.t_12_E_TC9_rep1

source_name: memory CD4 T cells from donor E, infected with HIV-1 strain CH077.t as part of experiment TC9, 12h post infection, intra-experimental technical replicate 1, hybridised Mar-13 (from sample well position A4)

tag: replicate


title: CD4_none_48_F_TC43_rep1

source_name: bulk CD4 T cells from donor F, mock-infected as part of experiment TC43, 48h post infection, intra-experimental technical replicate 1, hybridised Mar-13 (from sample well position G4)


title: CD4_CH077.t_48_F_TC43_rep1

source_name: bulk CD4 T cells from donor F, infected with HIV-1 strain CH077.t as part of experiment TC43, 48h post infection, intra-experimental technical replicate 1, hybridised Mar-13 (from sample well position G5)


title: HH_16_6_3_bis

tag: expansion passages

tag: genotype

tag: metabolic treatment


title: HL_20_1_4_bis

value: HL

tag: time


title: HH_08_4_4_bis


title: L12_ROI02_Tumor

tag: tissue

tag: roi


title: Unaffected Sibling 3


title: Unaffected Sibling 1


title: L12_ROI04_Tumor


title: HH_04_3_3_bis


title: HH_04_3_4_bis


title: memCD4_none_12_E_TC9_rep1

source_name: memory CD4 T cells from donor E, mock-infected as part of experiment TC9, 12h post infection, intra-experimental technical replicate 1, hybridised Mar-13 (from sample well position A1)

tag: celltype

tag: virus

tag: vprsuppl


title: L11_ROI24_TME


title: L12_ROI02_TME


title: CD4_IIIB.DVpr_Vpr_48_F_TC43_rep2

source_name: bulk CD4 T cells from donor F, infected with HIV-1 strain IIIB.DVpr as part of experiment TC43, Vpr supplemented, 48h post infection, intra-experimental technical replicate 2, hybridised Mar-13 (from sample well position G8)

value: yes

tag: timepoint


title: CD4_IIIB.DVpr_48_F_TC43_rep1

source_name: bulk CD4 T cells from donor F, infected with HIV-1 strain IIIB.DVpr as part of experiment TC43, 48h post infection, intra-experimental technical replicate 1, hybridised Mar-13 (from sample well position G6)

tag: donor


title: L12_ROI03_Tumor


title: HH_12_2_3_bis

value: PER2::LUC sv


title: HH_12_5_2_bis


title: CD4_IIIB_48_F_TC43_rep1

source_name: bulk CD4 T cells from donor F, infected with HIV-1 strain IIIB as part of experiment TC43, 48h post infection, intra-experimental technical replicate 1, hybridised Mar-13 (from sample well position H4)

tag: age


title: HH_20_1_3_bis


title: L12_ROI01_TME


title: HH_20_1_4_bis


title: L11_ROI22_TME


title: CD4_CH077.t_48_A_TC43_rep1

source_name: bulk CD4 T cells from donor A, infected with HIV-1 strain CH077.t as part of experiment TC43, 48h post infection, intra-experimental technical replicate 1, hybridised Mar-13 (from sample well position G12)

tag: Sex


title: HH_04_3_1_bis


title: L11_ROI24_Tumor

source_name: NSCLC tumor


title: L11_ROI22_Tumor


title: HH_20_1_2_bis


title: L11_ROI23_TME


title: CD4_IIIB.DVpr_Vpr_48_F_TC43_rep1

source_name: bulk CD4 T cells from donor F, infected with HIV-1 strain IIIB.DVpr as part of experiment TC43, Vpr supplemented, 48h post infection, intra-experimental technical replicate 1, hybridised Mar-13 (from sample well position G7)

tag: arraybatch


title: HH_12_2_1_bis


title: CD4_none_12_A_TC43_rep1

source_name: bulk CD4 T cells from donor A, mock-infected as part of experiment TC43, 12h post infection, intra-experimental technical replicate 1, hybridised Mar-13 (from sample well position G9)

tag: plateposition


title: L11_ROI23_Tumor


title: memCD4_Ba-L_12_E_TC9_rep1

source_name: memory CD4 T cells from donor E, infected with HIV-1 strain Ba-L as part of experiment TC9, 12h post infection, intra-experimental technical replicate 1, hybridised Mar-13 (from sample well position A3)

tag: experiment


title: L11_ROI21_Tumor


title: CD4_none_12_F_TC43_rep1

source_name: bulk CD4 T cells from donor F, mock-infected as part of experiment TC43, 12h post infection, intra-experimental technical replicate 1, hybridised Mar-13 (from sample well position F11)

tag: replicate


title: CD4_IIIB.DVpr_12_F_TC43_rep1

source_name: bulk CD4 T cells from donor F, infected with HIV-1 strain IIIB.DVpr as part of experiment TC43, 12h post infection, intra-experimental technical replicate 1, hybridised Mar-13 (from sample well position G1)


title: CD4_IIIB_12_F_TC43_rep1

source_name: bulk CD4 T cells from donor F, infected with HIV-1 strain IIIB as part of experiment TC43, 12h post infection, intra-experimental technical replicate 1, hybridised Mar-13 (from sample well position H2)


title: L11_ROI21_TME


title: CD4_CH077.t_12_A_TC43_rep1

source_name: bulk CD4 T cells from donor A, infected with HIV-1 strain CH077.t as part of experiment TC43, 12h post infection, intra-experimental technical replicate 1, hybridised Mar-13 (from sample well position G10)


title: L11_ROI20_TME


title: L11_ROI20_Tumor


title: LH_12_2_2

source_name: mouse fibroblasts

tag: expansion passages

value: LH


title: HH_20_1_1_bis

tag: genotype


title: LH_12_2_1

tag: metabolic treatment


title: LH_20_1_4

tag: time


title: CD4_IIIB.DVpr_Vpr_12_F_TC43_rep1

source_name: bulk CD4 T cells from donor F, infected with HIV-1 strain IIIB.DVpr as part of experiment TC43, Vpr supplemented, 12h post infection, intra-experimental technical replicate 1, hybridised Mar-13 (from sample well position G2)

value: no


title: L11_ROI19_TME

tag: tissue


title: CD4_IIIB.DVpr_Vpr_12_F_TC43_rep2

source_name: bulk CD4 T cells from donor F, infected with HIV-1 strain IIIB.DVpr as part of experiment TC43, Vpr supplemented, 12h post infection, intra-experimental technical replicate 2, hybridised Mar-13 (from sample well position G3)


title: L11_ROI19_Tumor

tag: roi


title: LH_20_1_3


title: LH_12_2_4


title: L11_ROI18_TME


title: LH_20_1_2


title: L11_ROI18_Tumor


title: CD4_none_48_C_TC42_rep1

source_name: bulk CD4 T cells from donor C, mock-infected as part of experiment TC42, 48h post infection, intra-experimental technical replicate 1, hybridised Mar-13 (from sample well position F9)

tag: celltype

value: C


title: HL_16_6_4


title: L11_ROI17_TME


title: HL_16_6_3


title: CD4_CH077.t_12_C_TC42_rep1

source_name: bulk CD4 T cells from donor C, infected with HIV-1 strain CH077.t as part of experiment TC42, 12h post infection, intra-experimental technical replicate 1, hybridised Mar-13 (from sample well position F8)

tag: virus


title: HL_16_6_2


title: CD4_none_12_H_TC40_rep1

source_name: bulk CD4 T cells from donor H, mock-infected as part of experiment TC40, 12h post infection, intra-experimental technical replicate 1, hybridised Mar-13 (from sample well position H1)

tag: vprsuppl

value: H

value: M


title: CD4_CH077.t_48_C_TC42_rep1

source_name: bulk CD4 T cells from donor C, infected with HIV-1 strain CH077.t as part of experiment TC42, 48h post infection, intra-experimental technical replicate 1, hybridised Mar-13 (from sample well position F10)

tag: timepoint


title: CD4_none_12_C_TC42_rep1

source_name: bulk CD4 T cells from donor C, mock-infected as part of experiment TC42, 12h post infection, intra-experimental technical replicate 1, hybridised Mar-13 (from sample well position F7)

tag: donor


title: HL_16_6_1


title: L11_ROI16_TME


title: L11_ROI16_Tumor

value: Tumor


title: CD4_none_48_I_TC18_rep1

source_name: bulk CD4 T cells from donor I, mock-infected as part of experiment TC18, 48h post infection, intra-experimental technical replicate 1, hybridised Mar-13 (from sample well position F2)

value: I

tag: age


title: CD4_IIIB_MMHAR2_48_I_TC18_rep1

source_name: bulk CD4 T cells from donor I, infected with HIV-1 strain IIIB as part of experiment TC18, IFNa/b R2 MAb added, 48h post infection, intra-experimental technical replicate 1, hybridised Mar-13 (from sample well position F4)

tag: Sex


title: CD4_none_48_H_TC40_rep1

source_name: bulk CD4 T cells from donor H, mock-infected as part of experiment TC40, 48h post infection, intra-experimental technical replicate 1, hybridised Mar-13 (from sample well position H3)

tag: arraybatch


title: L11_ROI15_TME

source_name: NSCLC tumor


title: HL_12_5_4


title: CD4_IIIB_48_I_TC18_rep1

source_name: bulk CD4 T cells from donor I, infected with HIV-1 strain IIIB as part of experiment TC18, 48h post infection, intra-experimental technical replicate 1, hybridised Mar-13 (from sample well position F3)

tag: plateposition


title: HL_12_5_2


title: CD4_IIIB.DVpr_MMHAR2_48_I_TC18_rep1

source_name: bulk CD4 T cells from donor I, infected with HIV-1 strain IIIB.DVpr as part of experiment TC18, IFNa/b R2 MAb added, 48h post infection, intra-experimental technical replicate 1, hybridised Mar-13 (from sample well position F6)

tag: experiment


title: L11_ROI15_Tumor


title: L11_ROI14_TME


title: CD4_none_12_I_TC18_rep1

source_name: bulk CD4 T cells from donor I, mock-infected as part of experiment TC18, 12h post infection, intra-experimental technical replicate 1, hybridised Mar-13 (from sample well position E9)

tag: replicate


title: L11_ROI17_Tumor


title: L11_ROI14_Tumor


title: L11_ROI13_TME


title: HL_08_4_3

tag: expansion passages


title: HL_08_4_2

tag: genotype


title: HL_08_4_4

tag: metabolic treatment


title: CD4_IIIB_12_I_TC18_rep1

source_name: bulk CD4 T cells from donor I, infected with HIV-1 strain IIIB as part of experiment TC18, 12h post infection, intra-experimental technical replicate 1, hybridised Mar-13 (from sample well position E10)


title: memCD4_REJO.c_12_E_TC9_rep1

source_name: memory CD4 T cells from donor E, infected with HIV-1 strain REJO.c as part of experiment TC9, 12h post infection, intra-experimental technical replicate 1, hybridised Mar-13 (from sample well position A6)

value: E


title: L11_ROI13_Tumor


title: HH_08_4_1_bis

source_name: mouse fibroblasts

value: HH

tag: time


title: L11_ROI12_TME

tag: tissue


title: HL_08_4_1


title: HL_04_3_4


title: HL_12_5_1


title: CD4_IIIB.DVpr_48_I_TC18_rep1

source_name: bulk CD4 T cells from donor I, infected with HIV-1 strain IIIB.DVpr as part of experiment TC18, 48h post infection, intra-experimental technical replicate 1, hybridised Mar-13 (from sample well position F5)


title: L11_ROI12_Tumor

tag: roi


title: HL_04_3_2


title: L11_ROI11_TME


title: HL_12_2_4


title: L11_ROI11_Tumor


title: HL_04_3_1


title: HL_12_2_3


title: L11_ROI10_TME


title: L12_ROI01_Tumor


title: L11_ROI10_Tumor


title: CD4_IIIB.DVpr_12_I_TC18_rep1

source_name: bulk CD4 T cells from donor I, infected with HIV-1 strain IIIB.DVpr as part of experiment TC18, 12h post infection, intra-experimental technical replicate 1, hybridised Mar-13 (from sample well position E12)

tag: celltype


title: L11_ROI09_TME


title: L11_ROI09_Tumor


title: HL_12_2_1


title: CD4_IIIB_MMHAR2_12_I_TC18_rep1

source_name: bulk CD4 T cells from donor I, infected with HIV-1 strain IIIB as part of experiment TC18, IFNa/b R2 MAb added, 12h post infection, intra-experimental technical replicate 1, hybridised Mar-13 (from sample well position E11)

tag: virus

value: IIIB


title: CD4_none_48_H_TC17_rep1

source_name: bulk CD4 T cells from donor H, mock-infected as part of experiment TC17, 48h post infection, intra-experimental technical replicate 1, hybridised Mar-13 (from sample well position E4)

tag: vprsuppl


title: CD4_IIIB.DVpr_MMHAR2_12_I_TC18_rep1

source_name: bulk CD4 T cells from donor I, infected with HIV-1 strain IIIB.DVpr as part of experiment TC18, IFNa/b R2 MAb added, 12h post infection, intra-experimental technical replicate 1, hybridised Mar-13 (from sample well position F1)

tag: timepoint


title: CD4_IIIB_MMHAR2_48_H_TC17_rep1

source_name: bulk CD4 T cells from donor H, infected with HIV-1 strain IIIB as part of experiment TC17, IFNa/b R2 MAb added, 48h post infection, intra-experimental technical replicate 1, hybridised Mar-13 (from sample well position E6)

tag: donor


title: CD4_IIIB.DVpr_MMHAR2_48_H_TC17_rep1

source_name: bulk CD4 T cells from donor H, infected with HIV-1 strain IIIB.DVpr as part of experiment TC17, IFNa/b R2 MAb added, 48h post infection, intra-experimental technical replicate 1, hybridised Mar-13 (from sample well position E8)

tag: age


title: CD4_IIIB_MMHAR2_12_H_TC17_rep1

source_name: bulk CD4 T cells from donor H, infected with HIV-1 strain IIIB as part of experiment TC17, IFNa/b R2 MAb added, 12h post infection, intra-experimental technical replicate 1, hybridised Mar-13 (from sample well position E1)

tag: Sex


title: LH_16_6_4


title: CD4_IIIB.DVpr_48_H_TC17_rep1

source_name: bulk CD4 T cells from donor H, infected with HIV-1 strain IIIB.DVpr as part of experiment TC17, 48h post infection, intra-experimental technical replicate 1, hybridised Mar-13 (from sample well position E7)

tag: arraybatch


title: CD4_IIIB_12_H_TC17_rep1

source_name: bulk CD4 T cells from donor H, infected with HIV-1 strain IIIB as part of experiment TC17, 12h post infection, intra-experimental technical replicate 1, hybridised Mar-13 (from sample well position D12)

tag: plateposition


title: CD4_IIIB_48_H_TC17_rep1

source_name: bulk CD4 T cells from donor H, infected with HIV-1 strain IIIB as part of experiment TC17, 48h post infection, intra-experimental technical replicate 1, hybridised Mar-13 (from sample well position E5)

tag: experiment


title: L11_ROI08_Tumor

source_name: NSCLC tumor


title: LH_16_6_3


title: CD4_none_12_H_TC17_rep1

source_name: bulk CD4 T cells from donor H, mock-infected as part of experiment TC17, 12h post infection, intra-experimental technical replicate 1, hybridised Mar-13 (from sample well position D11)

tag: replicate


title: HL_12_2_2

tag: expansion passages


title: L11_ROI07_Tumor


title: L11_ROI07_TME


title: LH_16_6_2

tag: genotype


title: LH_12_5_4

tag: metabolic treatment


title: L11_ROI06_TME


title: LH_16_6_1

tag: time


title: CD4_none_48_G_TC16_rep1

source_name: bulk CD4 T cells from donor G, mock-infected as part of experiment TC16, 48h post infection, intra-experimental technical replicate 1, hybridised Mar-13 (from sample well position D6)

value: G


title: CD4_IIIB.DVpr_12_H_TC17_rep1

source_name: bulk CD4 T cells from donor H, infected with HIV-1 strain IIIB.DVpr as part of experiment TC17, 12h post infection, intra-experimental technical replicate 1, hybridised Mar-13 (from sample well position E2)


title: LH_20_4_4


title: L11_ROI06_Tumor

tag: tissue


title: LH_12_5_2


title: LH_12_5_3


title: L11_ROI05_TME

value: TME

tag: roi


title: CD4_IIIB_MMHAR2_48_G_TC16_rep1

source_name: bulk CD4 T cells from donor G, infected with HIV-1 strain IIIB as part of experiment TC16, IFNa/b R2 MAb added, 48h post infection, intra-experimental technical replicate 1, hybridised Mar-13 (from sample well position D8)

tag: celltype


title: CD4_IIIB.DVpr_MMHAR2_12_H_TC17_rep1

source_name: bulk CD4 T cells from donor H, infected with HIV-1 strain IIIB.DVpr as part of experiment TC17, IFNa/b R2 MAb added, 12h post infection, intra-experimental technical replicate 1, hybridised Mar-13 (from sample well position E3)

tag: virus


title: L11_ROI05_Tumor


title: L11_ROI03_TME


title: CD4_IIIB_48_G_TC16_rep1

source_name: bulk CD4 T cells from donor G, infected with HIV-1 strain IIIB as part of experiment TC16, 48h post infection, intra-experimental technical replicate 1, hybridised Mar-13 (from sample well position D7)

tag: vprsuppl


title: L11_ROI02_TME


title: CD4_IIIB.DVpr_48_G_TC16_rep1

source_name: bulk CD4 T cells from donor G, infected with HIV-1 strain IIIB.DVpr as part of experiment TC16, 48h post infection, intra-experimental technical replicate 1, hybridised Mar-13 (from sample well position D9)

tag: timepoint


title: L11_ROI04_Tumor


title: LH_12_5_1

source_name: mouse fibroblasts


title: CD4_none_12_G_TC16_rep1

source_name: bulk CD4 T cells from donor G, mock-infected as part of experiment TC16, 12h post infection, intra-experimental technical replicate 1, hybridised Mar-13 (from sample well position D1)

tag: donor


title: CD4_IIIB_MMHAR2_12_G_TC16_rep1

source_name: bulk CD4 T cells from donor G, infected with HIV-1 strain IIIB as part of experiment TC16, IFNa/b R2 MAb added, 12h post infection, intra-experimental technical replicate 1, hybridised Mar-13 (from sample well position D3)

tag: age


title: CD4_IIIB_12_G_TC16_rep1

source_name: bulk CD4 T cells from donor G, infected with HIV-1 strain IIIB as part of experiment TC16, 12h post infection, intra-experimental technical replicate 1, hybridised Mar-13 (from sample well position D2)

tag: Sex


title: LH_20_4_3


title: CD4_IIIB.DVpr_MMHAR2_48_G_TC16_rep1

source_name: bulk CD4 T cells from donor G, infected with HIV-1 strain IIIB.DVpr as part of experiment TC16, IFNa/b R2 MAb added, 48h post infection, intra-experimental technical replicate 1, hybridised Mar-13 (from sample well position D10)

tag: arraybatch


title: CD4_CH077.t_12_F_TC43_rep1

source_name: bulk CD4 T cells from donor F, infected with HIV-1 strain CH077.t as part of experiment TC43, 12h post infection, intra-experimental technical replicate 1, hybridised Mar-13 (from sample well position F12)

tag: plateposition


title: memCD4_none_48_I_TC13_rep1

source_name: memory CD4 T cells from donor I, mock-infected as part of experiment TC13, 48h post infection, intra-experimental technical replicate 1, hybridised Mar-13 (from sample well position C7)

tag: experiment


title: CD4_IIIB.DVpr_MMHAR2_12_G_TC16_rep1

source_name: bulk CD4 T cells from donor G, infected with HIV-1 strain IIIB.DVpr as part of experiment TC16, IFNa/b R2 MAb added, 12h post infection, intra-experimental technical replicate 1, hybridised Mar-13 (from sample well position D5)

tag: replicate


title: LH_20_4_2

tag: expansion passages


title: L11_ROI01_Tumor


title: L11_ROI03_Tumor


title: L11_ROI02_Tumor


title: memCD4_IIIB_48_I_TC13_rep1

source_name: memory CD4 T cells from donor I, infected with HIV-1 strain IIIB as part of experiment TC13, 48h post infection, intra-experimental technical replicate 1, hybridised Mar-13 (from sample well position C8)


title: L10_ROI23_TME

source_name: NSCLC tumor


title: LH_20_4_1

tag: genotype


title: LH_16_3_1

tag: metabolic treatment


title: L10_ROI24_Tumor


title: LH_16_3_4

tag: time


title: L10_ROI23_Tumor

tag: tissue


title: L11_ROI01_TME

tag: roi


title: HL_20_1_2


title: memCD4_REJO.c_48_I_TC13_rep1

source_name: memory CD4 T cells from donor I, infected with HIV-1 strain REJO.c as part of experiment TC13, 48h post infection, intra-experimental technical replicate 1, hybridised Mar-13 (from sample well position C12)

tag: celltype


title: LH_16_3_3


title: L10_ROI24_TME


title: memCD4_Ba-L_48_I_TC13_rep1

source_name: memory CD4 T cells from donor I, infected with HIV-1 strain Ba-L as part of experiment TC13, 48h post infection, intra-experimental technical replicate 1, hybridised Mar-13 (from sample well position C9)

tag: virus

value: Ba-L


title: CD4_IIIB.DVpr_12_G_TC16_rep1

source_name: bulk CD4 T cells from donor G, infected with HIV-1 strain IIIB.DVpr as part of experiment TC16, 12h post infection, intra-experimental technical replicate 1, hybridised Mar-13 (from sample well position D4)

tag: vprsuppl

value: F


title: memCD4_CH106.c_48_I_TC13_rep1

source_name: memory CD4 T cells from donor I, infected with HIV-1 strain CH106.c as part of experiment TC13, 48h post infection, intra-experimental technical replicate 1, hybridised Mar-13 (from sample well position C11)

tag: timepoint


title: HL_20_1_4

value: HL


title: HL_20_1_3


title: HH_16_6_2


title: L10_ROI21_Tumor


title: L10_ROI20_TME


title: L10_ROI21_TME


title: memCD4_CH077.t_48_I_TC13_rep1

source_name: memory CD4 T cells from donor I, infected with HIV-1 strain CH077.t as part of experiment TC13, 48h post infection, intra-experimental technical replicate 1, hybridised Mar-13 (from sample well position C10)

tag: donor


title: LH_16_3_2


title: memCD4_REJO.c_12_I_TC13_rep1

source_name: memory CD4 T cells from donor I, infected with HIV-1 strain REJO.c as part of experiment TC13, 12h post infection, intra-experimental technical replicate 1, hybridised Mar-13 (from sample well position C6)

tag: age


title: HH_12_5_3


title: HH_16_6_4


title: L10_ROI20_Tumor


title: HH_16_6_1


title: HH_16_6_3


title: L10_ROI22_Tumor


title: L10_ROI22_TME


title: L10_ROI19_Tumor


title: HH_12_5_1


title: HH_08_4_4


title: L10_ROI18_TME


title: memCD4_Ba-L_12_I_TC13_rep1

source_name: memory CD4 T cells from donor I, infected with HIV-1 strain Ba-L as part of experiment TC13, 12h post infection, intra-experimental technical replicate 1, hybridised Mar-13 (from sample well position C3)

tag: Sex


title: HH_08_4_1

source_name: mouse fibroblasts


title: HH_12_5_2


title: memCD4_CH106.c_12_I_TC13_rep1

source_name: memory CD4 T cells from donor I, infected with HIV-1 strain CH106.c as part of experiment TC13, 12h post infection, intra-experimental technical replicate 1, hybridised Mar-13 (from sample well position C5)

tag: arraybatch


title: memCD4_none_12_I_TC13_rep1

source_name: memory CD4 T cells from donor I, mock-infected as part of experiment TC13, 12h post infection, intra-experimental technical replicate 1, hybridised Mar-13 (from sample well position C1)

tag: plateposition


title: L10_ROI18_Tumor


title: HH_04_3_4


title: memCD4_IIIB_12_I_TC13_rep1

source_name: memory CD4 T cells from donor I, infected with HIV-1 strain IIIB as part of experiment TC13, 12h post infection, intra-experimental technical replicate 1, hybridised Mar-13 (from sample well position C2)

tag: experiment


title: L10_ROI19_TME


title: HH_04_3_3


title: memCD4_IIIB_48_C_TC12_rep1

source_name: memory CD4 T cells from donor C, infected with HIV-1 strain IIIB as part of experiment TC12, 48h post infection, intra-experimental technical replicate 1, hybridised Mar-13 (from sample well position B8)

tag: replicate


title: memCD4_CH077.t_12_I_TC13_rep1

source_name: memory CD4 T cells from donor I, infected with HIV-1 strain CH077.t as part of experiment TC13, 12h post infection, intra-experimental technical replicate 1, hybridised Mar-13 (from sample well position C4)


title: L10_ROI17_TME


title: memCD4_REJO.c_48_C_TC12_rep1

source_name: memory CD4 T cells from donor C, infected with HIV-1 strain REJO.c as part of experiment TC12, 48h post infection, intra-experimental technical replicate 1, hybridised Mar-13 (from sample well position B12)


title: HH_04_3_1

tag: expansion passages


title: L10_ROI16_TME


title: memCD4_CH106.c_48_C_TC12_rep1

source_name: memory CD4 T cells from donor C, infected with HIV-1 strain CH106.c as part of experiment TC12, 48h post infection, intra-experimental technical replicate 1, hybridised Mar-13 (from sample well position B11)


title: memCD4_none_48_C_TC12_rep1

source_name: memory CD4 T cells from donor C, mock-infected as part of experiment TC12, 48h post infection, intra-experimental technical replicate 1, hybridised Mar-13 (from sample well position B7)


title: memCD4_CH077.t_48_C_TC12_rep1

source_name: memory CD4 T cells from donor C, infected with HIV-1 strain CH077.t as part of experiment TC12, 48h post infection, intra-experimental technical replicate 1, hybridised Mar-13 (from sample well position B10)


title: memCD4_Ba-L_48_C_TC12_rep1

source_name: memory CD4 T cells from donor C, infected with HIV-1 strain Ba-L as part of experiment TC12, 48h post infection, intra-experimental technical replicate 1, hybridised Mar-13 (from sample well position B9)


title: HH_12_2_4

tag: genotype


title: L10_ROI15_TME

source_name: NSCLC tumor


title: HH_12_2_3

tag: metabolic treatment


title: memCD4_REJO.c_12_C_TC12_rep1

source_name: memory CD4 T cells from donor C, infected with HIV-1 strain REJO.c as part of experiment TC12, 12h post infection, intra-experimental technical replicate 1, hybridised Mar-13 (from sample well position B6)


title: L10_ROI14_TME


title: L10_ROI17_Tumor


title: memCD4_IIIB_12_C_TC12_rep1

source_name: memory CD4 T cells from donor C, infected with HIV-1 strain IIIB as part of experiment TC12, 12h post infection, intra-experimental technical replicate 1, hybridised Mar-13 (from sample well position B2)


title: HH_12_2_1

tag: time


title: L10_ROI13_TME

tag: tissue


title: L10_ROI14_Tumor

tag: roi


title: memCD4_none_12_C_TC12_rep1

source_name: memory CD4 T cells from donor C, mock-infected as part of experiment TC12, 12h post infection, intra-experimental technical replicate 1, hybridised Mar-13 (from sample well position B1)

tag: celltype


title: HH_20_1_4


title: HH_20_1_3


title: memCD4_CH077.t_12_C_TC12_rep1

source_name: memory CD4 T cells from donor C, infected with HIV-1 strain CH077.t as part of experiment TC12, 12h post infection, intra-experimental technical replicate 1, hybridised Mar-13 (from sample well position B4)

tag: virus


title: memCD4_CH106.c_12_C_TC12_rep1

source_name: memory CD4 T cells from donor C, infected with HIV-1 strain CH106.c as part of experiment TC12, 12h post infection, intra-experimental technical replicate 1, hybridised Mar-13 (from sample well position B5)

tag: vprsuppl


title: L10_ROI13_Tumor


title: HH_20_1_2

source_name: mouse fibroblasts


title: L10_ROI12_Tumor


title: L10_ROI12_TME


title: HH_20_1_1


title: iWAT, KO_HFD_20

city: Edinburgh

first: Shaun

middle: Michael

last: Webb

address: 2.21 Swann Building, Kings Buildings

department: Wellcome Trust Centre for Cell Biology

institute: University of Edinburgh

data_processing:
Align to Mouse mm9 assembly with STAR v2.5.3.a
Filter for properly paired, unique alignments
Remove reads in blacklisted regions
Convert to bigWig
Pseudo-align reads with Salmon 0.13.1 and Ensembl 67 transcripts
Genome_build: mm9
Supplementary_files_format_and_content: bigWig coverage files per strand, TPM gene expresion file

source_name: iWAT

growth_protocol: 6 months old, group caged, female mice fed with high fat vs low fat diet for 15 weeks. Ad libitum access to water. 12h dark and 12h light cyckles in air conditioned facility. Research Diets Inc. low fat diet(10.5% fat) - D12328; high fat diet(58% fat) - D12331

extract_protocol:
total RNA was isolated by Rneasy Lipid Tissue Kit (Qiagen) - cat. No. 74804
Illumina TruSeq Stranded Total RNA Gold kit

treatment_protocol: wild type vs knockout mice fed with high fat diet vs low fat diet

tag: strain

value: female

value: subcutaneous inguinal white adipose tissue

tag: diet

value: high fat diet

value: knock out


title: iWAT, KO_HFD_21


title: memCD4_Ba-L_12_C_TC12_rep1

source_name: memory CD4 T cells from donor C, infected with HIV-1 strain Ba-L as part of experiment TC12, 12h post infection, intra-experimental technical replicate 1, hybridised Mar-13 (from sample well position B3)

value: no

tag: timepoint

tag: donor

value: C

tag: age


title: L10_ROI11_Tumor


title: L10_ROI11_TME


title: L10_ROI10_TME


title: iWAT, KO_HFD_18

tag: Sex


title: L10_ROI09_TME


title: iWAT, KO_HFD_19


title: L10_ROI10_Tumor


title: H3Ac_sant1234_rep1

first: xinjian

last: He

address: No. 7, zhongguancun life science park road, changping district

institute: National Institute of Biological Sciences

data_processing:
Basecalls performed using bcl2fastq version 2.16.
For data analysis, after removing the adapter and filtering low-quality reads, the clean reads were aligned to Arabidopsis genome (TAIR10) using Bowtie2(v2.4.2) allowing one mismatch.
The SICER2 was used to identify differentially enriched peaks between wild type and mutant with fold change <0.8 or fold change >1.2, FDR<0.05.
Genome_build: TAIR10
Supplementary_files_format_and_content: bigWig files were generated using bamCoverage.

source_name: Arabidopsis seedlings

growth_protocol: Arabidopsis seedlings were grown on MS (Murashige and Skoog) medium plates with a long-day (LD) photoperiod (23℃, 16 h light/ 22℃, 8 h darkness).

extract_protocol:
Chromatin isolated from 14-day-old seedlings in LD  were subjected to sonication and immunoprecipitation with the anti-H3Ac antibody.
Libraries were built for ChIP-seq (Illumina HiSeq X Ten; 150-bp pair-end sequencing)

tag: growth conditions

value: long day (16 h light, 8 h dark)

tag: chip antibody

value: Millipore, 06-599


title: iWAT, WT_HFD_15

value: wild type


title: CD4_IIIB_48_F_TC41_rep1

source_name: bulk CD4 T cells from donor F, infected with HIV-1 strain IIIB as part of experiment TC41, 48h post infection, intra-experimental technical replicate 1, hybridised Nov-12 (from sample well position H11)

value: M

tag: arraybatch

tag: plateposition

tag: experiment

tag: replicate


title: CD4_none_48_F_TC41_rep1

source_name: bulk CD4 T cells from donor F, mock-infected as part of experiment TC41, 48h post infection, intra-experimental technical replicate 1, hybridised Nov-12 (from sample well position H10)


title: CD4_IIIB.DVpr_48_F_TC41_rep1

source_name: bulk CD4 T cells from donor F, infected with HIV-1 strain IIIB.DVpr as part of experiment TC41, 48h post infection, intra-experimental technical replicate 1, hybridised Nov-12 (from sample well position H12)


title: CD4_none_12_F_TC41_rep1

source_name: bulk CD4 T cells from donor F, mock-infected as part of experiment TC41, 12h post infection, intra-experimental technical replicate 1, hybridised Nov-12 (from sample well position H7)


title: L10_ROI08_TME

tag: tissue


title: H3Ac_sant1234_rep2

tag: genotype


title: CD4_IIIB_12_F_TC41_rep1

source_name: bulk CD4 T cells from donor F, infected with HIV-1 strain IIIB as part of experiment TC41, 12h post infection, intra-experimental technical replicate 1, hybridised Nov-12 (from sample well position H8)

tag: celltype


title: iWAT, KO_HFD_17


title: CD4_none_48_D_TC37_rep1

source_name: bulk CD4 T cells from donor D, mock-infected as part of experiment TC37, 48h post infection, intra-experimental technical replicate 1, hybridised Nov-12 (from sample well position H4)

tag: virus

value: D


title: iWAT, WT_HFD_14


title: CD4_IIIB.DVpr_12_F_TC41_rep1

source_name: bulk CD4 T cells from donor F, infected with HIV-1 strain IIIB.DVpr as part of experiment TC41, 12h post infection, intra-experimental technical replicate 1, hybridised Nov-12 (from sample well position H9)

tag: vprsuppl


title: CD4_IIIB_12_D_TC37_rep1

source_name: bulk CD4 T cells from donor D, infected with HIV-1 strain IIIB as part of experiment TC37, 12h post infection, intra-experimental technical replicate 1, hybridised Nov-12 (from sample well position H2)

value: IIIB


title: H3Ac_rxt3_rep1


title: L10_ROI08_Tumor

source_name: NSCLC tumor

value: Tumor

tag: roi


title: iWAT, WT_HFD_13

tag: strain

tag: diet


title: H3Ac_mbd124_rep2


title: iWAT, WT_HFD_12


title: L10_ROI07_TME

value: TME


title: L10_ROI09_Tumor


title: H3Ac_mbd124_rep1


title: H3Ac_rxt3_rep2


title: L10_ROI07_Tumor


title: H3Ac_harb1_rep2


title: iWAT, WT_HFD_11


title: CD4_none_12_D_TC37_rep1

source_name: bulk CD4 T cells from donor D, mock-infected as part of experiment TC37, 12h post infection, intra-experimental technical replicate 1, hybridised Nov-12 (from sample well position H1)

tag: timepoint

tag: donor


title: CD4_IIIB.DVpr_12_D_TC37_rep1

source_name: bulk CD4 T cells from donor D, infected with HIV-1 strain IIIB.DVpr as part of experiment TC37, 12h post infection, intra-experimental technical replicate 1, hybridised Nov-12 (from sample well position H3)

tag: age

tag: Sex


title: CD4_IIIB_48_D_TC37_rep1

source_name: bulk CD4 T cells from donor D, infected with HIV-1 strain IIIB as part of experiment TC37, 48h post infection, intra-experimental technical replicate 1, hybridised Nov-12 (from sample well position H5)


title: L10_ROI06_TME


title: H3Ac_harb1_rep1

tag: growth conditions

tag: chip antibody


title: iWAT, KO_LFD_10

value: low fat diet


title: H3Ac_hda6_rep2


title: H3Ac_hda6_rep1


title: iWAT, KO_LFD_7


title: iWAT, KO_LFD_8


title: iWAT, KO_LFD_9


title: L10_ROI05_TME


title: L10_ROI06_Tumor


title: L10_ROI05_Tumor


title: H3Ac_hda19_rep2


title: iWAT, KO_LFD_6


title: L10_ROI04_TME


title: H3Ac_hda19_rep1


title: H3Ac_esant12_rep2


title: iWAT, WT_LFD_4


title: L10_ROI03_TME


title: L10_ROI04_Tumor


title: CD4_none_48_B_TC36_rep1

source_name: bulk CD4 T cells from donor B, mock-infected as part of experiment TC36, 48h post infection, intra-experimental technical replicate 1, hybridised Nov-12 (from sample well position F12)

value: B

tag: arraybatch

tag: plateposition


title: H3Ac_esant12_rep1


title: iWAT, WT_LFD_3


title: CD4_IIIB_48_B_TC36_rep1

source_name: bulk CD4 T cells from donor B, infected with HIV-1 strain IIIB as part of experiment TC36, 48h post infection, intra-experimental technical replicate 1, hybridised Nov-12 (from sample well position G6)

tag: experiment

tag: replicate


title: CD4_IIIB.DEnv_48_B_TC36_rep1

source_name: bulk CD4 T cells from donor B, infected with HIV-1 strain IIIB.DEnv as part of experiment TC36, 48h post infection, intra-experimental technical replicate 1, hybridised Nov-12 (from sample well position G12)


title: H3Ac_Col-0_rep5

tag: genotype


title: H3Ac_Col-0_rep4


title: L10_ROI02_TME

tag: tissue


title: iWAT, WT_LFD_1

source_name: iWAT


title: L10_ROI03_Tumor


title: L10_ROI02_Tumor


title: H3Ac_Col-0_rep3

source_name: Arabidopsis seedlings


title: iWAT, WT_LFD_5


title: L10_ROI01_TME


title: CD4_IIIB.DEnv_48_E_TC36_rep1

source_name: bulk CD4 T cells from donor E, infected with HIV-1 strain IIIB.DEnv as part of experiment TC36, 48h post infection, intra-experimental technical replicate 1, hybridised Nov-12 (from sample well position F4)

tag: celltype

tag: virus

value: E


title: H3Ac_Col-0_rep2


title: BMI1-KO MM-MΦs-3

city: Chengdu

first: Jingcao

last: Huang

state: Sichuan

address: No.88, South Keyuan Road

department: Department of Hematology

institute: West China Hospital, Sichuan University

data_processing:
Illumina Bcl2fastq (v2.17.1.14) software used for base-calling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence by Cutadapt (V1.9.1), then aligned to mm10 whole genome via software Hisat2 (v2.0.1).
FPKM (Fragments Per Kilo bases per Million reads) to estimate gene expression levels was performed by HTSeq (v0.6.1) according to Mortazavi et al. (2008).
Differential expression analysis used the DESeq2 Bioconductor package.
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: bone marrow derived macrophage

growth_protocol: BMI1fl/fl mice (Stock No: 028572) were purchased from Jackson lab (USA). An inducible BMI1 knockout mouse line was generated by crossing the BMI1fl/fl mice with Mx1-Cre C57BL/6 transgenic mice. To induce BMI1 knockout in adult mice (6 to 8-week-old), BMI1fl/fl and BMI1fl/fl Mx1-Cre mice were intraperitoneally injected every other day with 5 doses (15mg/kg) of poly-I:C (Sigma, Cat No. P1530, USA). 4 weeks after the final poly-I:C injection, bone marrow was isolated for in vitro macrophage culture. BMI1fl/fl mice receiving poly I:C were considered the wild type (wt) control group, while BMI1fl/fl Mx1-Cre mice receiving poly I:C formed the BMI1 knockout (BMI1-KO) group.

extract_protocol:
Total RNA was extracted using TRI reagent (MRC, Cat No. TR118, OH, USA) from flow sorted CD11b+ F4/80+ cells from murine BM-derived MΦs and MM-MΦs.
Libraries were prepared using the VAHTSTM total RNA-seq library prep Kit for IIumina (Vazyme, Cat No. NR603, Nanjing, China).

treatment_protocol: To generate murine BM-derived MΦs, BM cells were collected by crushing the hind leg bones in a mortar in FBS-free RPMI-1640. BM cells were collected by passing the suspension through a cell strainer. Red blood cells were lysed, and cells incubated in FBS-free RPMI-1640 for 2 hours. Adherent cells were then cultured in RPMI-1640 supplemented with 10% FBS and 5ng/mL murine M-CSF (R&D Systems, Cat No. 416-ML, USA) for 7 days into MΦs. The MΦs were then cocultured with 5TGM1 cells for another 48 hours to generate MM-MΦs.


title: BMI1-KO MM-MΦs-2


title: CD4_IIIB.DVpr_48_D_TC37_rep1

source_name: bulk CD4 T cells from donor D, infected with HIV-1 strain IIIB.DVpr as part of experiment TC37, 48h post infection, intra-experimental technical replicate 1, hybridised Nov-12 (from sample well position H6)

tag: vprsuppl

value: F


title: CD4_IIIB.DEnv_24_E_TC36_rep1

source_name: bulk CD4 T cells from donor E, infected with HIV-1 strain IIIB.DEnv as part of experiment TC36, 24h post infection, intra-experimental technical replicate 1, hybridised Nov-12 (from sample well position F3)


title: L10_ROI01_Tumor

first: Patrick

last: Danaher

data_processing:
Library strategy: GeoMx-Seq
Adapter trimming with trim galore,  trimGaloreOpts = " --hardtrim5 26 --dont_gzip"
If paired-end, merge overlapping R1 and R2 with flash2, flash2Opts = " -m 26 -e 26 -f 26 -s 1 -r 27"
Extract UMIs in bowtie2, umiExtractOpts = " --bc-pattern=NNNNNNNNNNNNNN"
Align RTS_IDs (probe barcodes) using bowtie2, bowtie2Opts = " --end-to-end -L 4 --trim5 0 --trim3 0 --norc"
Deduplication using UMI-tools, umiDedupOpts = " --edit-distance-threshold=1"
Genome_build: N/A, sequencing of synthetic tags and alignment to whitelist of RTS_IDs (probe barcodes) found in the config.ini output from the GeoMx DSP platform
Supplementary_files_format_and_content: Digital Count Conversion (DCC) file format outputted from GeoMx NGS Pipeline, contains software versions, scan attributes, GeoMx NGS pipeline parameters and output metrics, Q30 scores, and list of deduplicated counts per RTS_ID (probe barcode)
Supplementary_files_format_and_content: Values represented in the collapsed target counts tab are the geometric mean of the probes for a given, removing any targets flagged as outliers. Analyzed counts represent the upper quartile normalized collapsed counts across the study after removing QC flagged segments.

extract_protocol:
Samples were incubated with DNA-oligo barcoded RNA-ISH probes which were conjugated with a UV-photocleavable linker following standard ISH protocols, along with flourescently labeled antibodies for visualization of morphological structures. Regions of interest within the tissue were illuminated with UV light and oligo barcodes were physically aspirated from the tissue and collected into microtiter plates by the GeoMx® Digital Spatial Profiler (DSP) platform. For more information about DSP protocols please see Merritt et al. Nature Biotech 2020 (doi: 10.1038/s41598-020-63539-x)
Each collection of oligo tags from one well (representing an AOI from the tissue section) was indexed with i7xi5 unique dual indexes using GeoMx SeqCode primers with 18 cycles of PCR.  After PCR, indexed AOIs were pooled and purified in two rounds of AMPure XP PCR purification using 1.2x bead:sample ratio.

tag: roi


title: CD4_IIIB_24_E_TC36_rep1

source_name: bulk CD4 T cells from donor E, infected with HIV-1 strain IIIB as part of experiment TC36, 24h post infection, intra-experimental technical replicate 1, hybridised Nov-12 (from sample well position E9)


title: iWAT, WT_LFD_2

tag: strain

value: female

value: subcutaneous inguinal white adipose tissue

tag: diet


title: CD4_none_48_E_TC36_rep1

source_name: bulk CD4 T cells from donor E, mock-infected as part of experiment TC36, 48h post infection, intra-experimental technical replicate 1, hybridised Nov-12 (from sample well position E4)

tag: timepoint

tag: donor


title: CD4_IIIB.DEnv_24_B_TC36_rep1

source_name: bulk CD4 T cells from donor B, infected with HIV-1 strain IIIB.DEnv as part of experiment TC36, 24h post infection, intra-experimental technical replicate 1, hybridised Nov-12 (from sample well position G11)

tag: age

tag: Sex


title: CD4_none_24_E_TC36_rep1

source_name: bulk CD4 T cells from donor E, mock-infected as part of experiment TC36, 24h post infection, intra-experimental technical replicate 1, hybridised Nov-12 (from sample well position E3)


title: CD4_none_12_E_TC36_rep1

source_name: bulk CD4 T cells from donor E, mock-infected as part of experiment TC36, 12h post infection, intra-experimental technical replicate 1, hybridised Nov-12 (from sample well position E2)


title: CD4_BK132_48_E_TC36_rep1

source_name: bulk CD4 T cells from donor E, infected with HIV-1 strain BK132 as part of experiment TC36, 48h post infection, intra-experimental technical replicate 1, hybridised Nov-12 (from sample well position F6)


title: L09_Geome_MixedROI32

source_name: NSCLC tumor

value: Mixed

value: Geome


title: CD4_none_24_B_TC36_rep1

source_name: bulk CD4 T cells from donor B, mock-infected as part of experiment TC36, 24h post infection, intra-experimental technical replicate 1, hybridised Nov-12 (from sample well position F11)

value: no


title: H3Ac_Col-0_rep1

tag: growth conditions

value: long day (16 h light, 8 h dark)

tag: chip antibody


title: BMI1-KO MΦs-3


title: CD4_IIIB_24_B_TC36_rep1

source_name: bulk CD4 T cells from donor B, infected with HIV-1 strain IIIB as part of experiment TC36, 24h post infection, intra-experimental technical replicate 1, hybridised Nov-12 (from sample well position G5)

tag: arraybatch

tag: plateposition


title: CD4_IIIB_48_E_TC36_rep1

source_name: bulk CD4 T cells from donor E, infected with HIV-1 strain IIIB as part of experiment TC36, 48h post infection, intra-experimental technical replicate 1, hybridised Nov-12 (from sample well position E10)

tag: experiment

tag: replicate


title: BMI1-KO MM-MΦs-1

tag: genotype


title: BMI1-KO MΦs-2


title: H3Ac_arid14_rep1

value: Millipore, 06-599


title: H3Ac_arid14_rep2


title: L09_Geome_MixedROI30

tag: tissue


title: L09_Geome_MixedROI29


title: HNE-1 cells, NCsh

city: Chongqing

first: Chuntao

last: Tao

state: State...

address: China

institute: Chongqing Medical University

data_processing:
Bowtie2 was used to align raw data
The bam files was quantify by RSEM
Genome_build: mm9
Supplementary_files_format_and_content: genes_fpkm_expression.xlsx

source_name: KIF2C negative control cell

growth_protocol: HNE-1 cells were cultured in RPMI 1640 medium containing 50 units/mL penicillin, 50 mg/mL streptomycin, and 10% (v/v) FBS

extract_protocol:
The KIF2C knockdown cells and its corresponding negative control cells were collected, total RNA was extracted, and cDNA libraries were then constructed and subjected to RNA-seq analysis
RNA libraries were prepared for sequencing using standard MGI-G400/MGI-2000 protocols

treatment_protocol: HNE-1  cells were infected with the NCsh and KIF2Csh lentivirus particles with 5μg/mL polybrene for forty-eight hours

tag: cell line

value: KIF2C negative control cell


title: WT MM-MΦs-3

value: wild type


title: HNE-1 cells, KIF2Csh

source_name: KIF2C knockdown HNE-1 cell

value: KIF2C knockdown HNE-1 cell


title: L09_Geome_MixedROI28

address: 530 Fairview Ave N

institute: NanoString Technologies, Inc.


title: BMI1-KO MΦs-1


title: L09_Geome_MixedROI27


title: WT MM-MΦs-2


title: L09_Geome_MixedROI26


title: sant1234_rep2

data_processing:
Zebracall software used for basecalling.
More than 21 M of clean reads of each sample were mapped to the Arabidopsis genome (TAIR10) with the sensitive alignment program HISAT2 (2.1.0) with the default parameters.
The reads mapped on the exon were counted using featureCounts.
The significant (|log2 (fold change) |> 1 and P-value < 0.01) differentially expressed genes (DEGs) and TEs were identified by the edgeR.
Genome_build: TAIR10
Supplementary_files_format_and_content: Tab-delimited text file include normalized reads for each sample.

source_name: Arabidopsis seedlings

extract_protocol:
Total RNA was isolated from 14-day-old seedlings in LD using Trizol reagent.
Sequencing libraries were built for RNA-seq (the single-end 50-bp strategy).


title: sant1234_rep1


title: CD4_IIIB.DEnv_12_E_TC36_rep1

source_name: bulk CD4 T cells from donor E, infected with HIV-1 strain IIIB.DEnv as part of experiment TC36, 12h post infection, intra-experimental technical replicate 1, hybridised Nov-12 (from sample well position F2)

tag: celltype

tag: virus

tag: vprsuppl

value: M


title: rxt3_rep2


title: WT MM-MΦs-1

source_name: bone marrow derived macrophage

tag: strain


title: L09_Geome_MixedROI24

tag: roi


title: rxt3_rep1


title: L09_Geome_MixedROI23


title: L09_Geome_MixedROI25


title: WT MΦs-2


title: WT MΦs-1


title: L09_Geome_MixedROI22


title: CD4_IIIB_12_E_TC36_rep1

source_name: bulk CD4 T cells from donor E, infected with HIV-1 strain IIIB as part of experiment TC36, 12h post infection, intra-experimental technical replicate 1, hybridised Nov-12 (from sample well position E8)

value: IIIB

tag: timepoint

tag: donor


title: mbd124_rep2


title: mbd124_rep1


title: CD4_IIIB_12_B_TC36_rep1

source_name: bulk CD4 T cells from donor B, infected with HIV-1 strain IIIB as part of experiment TC36, 12h post infection, intra-experimental technical replicate 1, hybridised Nov-12 (from sample well position G4)

tag: age

tag: Sex


title: L09_Geome_MixedROI21


title: WT MΦs-3


title: CD4_IIIB.DEnv_12_B_TC36_rep1

source_name: bulk CD4 T cells from donor B, infected with HIV-1 strain IIIB.DEnv as part of experiment TC36, 12h post infection, intra-experimental technical replicate 1, hybridised Nov-12 (from sample well position G10)


title: CD4_none_12_B_TC36_rep1

source_name: bulk CD4 T cells from donor B, mock-infected as part of experiment TC36, 12h post infection, intra-experimental technical replicate 1, hybridised Nov-12 (from sample well position F10)


title: mnase seq +clamp rep 3 [Mnase CLAMP]

city: Munich

first: Nikolas

last: Eggers

address: Grosshaderner Strasse 9

department: Molecular Biology

country: Germany

institute: LMU Munich

description:
Mnase CLAMP
normalized.sum_clamp.bw

data_processing:
RTA software von Illumina, version ist 1.18.66.3
sequenced reads were demultiplexed and trimmed using JE Demultiplexer
Demultiplexed reads were aligned to the dm6 genome using bowtie 2 version 2.2.9. with settings: -p 24 --end-to-end --very-sensitive --no-unal --no-mixed --no-discordant -I 10 -X 220
filtering and sorting was done using samtools 1.9 with -q 10.
genomic tracks were made by Homer 4.9 and normalized to the negative control or the input.
replicates were summarized by subsampling them to the same read counts and adding them und samtools 1.9
peaks were called using findPeaks form Homer 4.9  with settings: -style factor -size 150 -F 8 -L 2
Genome_build: dm6
Supplementary_files_format_and_content: .bw files

organism: Drosophila melanogaster

source_name: BG-3 cells

growth_protocol: purified genomic DNA from bg-3 cells was assembled to chromatin for 5h.

extract_protocol:
DNA was purified using Phenol-Chloroform Extraction.
libraries were made using the NEB library Kit for Illumina

treatment_protocol: Respective Proteins were added to the chromatin and bound for 30 min. samples were crosslinked and partially digested by Mnase.

tag: ip target

value: Mnase

tag: factors added

value: 50nM CLAMP


title: CD4_none_8_E_TC36_rep1

source_name: bulk CD4 T cells from donor E, mock-infected as part of experiment TC36, 8h post infection, intra-experimental technical replicate 1, hybridised Nov-12 (from sample well position D12)

tag: arraybatch

tag: plateposition


title: hda6_rep2

tag: growth conditions


title: mnase seq +clamp rep 2 [Mnase CLAMP]

description:
Mnase CLAMP
normalized.sum_clamp.bw


title: CD4_BK132_12_E_TC36_rep1

source_name: bulk CD4 T cells from donor E, infected with HIV-1 strain BK132 as part of experiment TC36, 12h post infection, intra-experimental technical replicate 1, hybridised Nov-12 (from sample well position F5)

tag: experiment

tag: replicate


title: L09_Geome_MixedROI20

city: Seattle

tag: tissue


title: CD4_IIIB.DEnv_8_E_TC36_rep1

source_name: bulk CD4 T cells from donor E, infected with HIV-1 strain IIIB.DEnv as part of experiment TC36, 8h post infection, intra-experimental technical replicate 1, hybridised Nov-12 (from sample well position E12)

tag: celltype


title: hda6_rep1

tag: genotype


title: CD4_IIIB.DEnv_8_B_TC36_rep1

source_name: bulk CD4 T cells from donor B, infected with HIV-1 strain IIIB.DEnv as part of experiment TC36, 8h post infection, intra-experimental technical replicate 1, hybridised Nov-12 (from sample well position G8)

tag: virus

tag: vprsuppl

value: B


title: CD4_IIIB_8_E_TC36_rep1

source_name: bulk CD4 T cells from donor E, infected with HIV-1 strain IIIB as part of experiment TC36, 8h post infection, intra-experimental technical replicate 1, hybridised Nov-12 (from sample well position E6)

value: E


title: mnase seq +clamp rep 1 [Mnase CLAMP]

description:
Mnase CLAMP
normalized.sum_clamp.bw


title: L09_Geome_MixedROI19

source_name: NSCLC tumor

tag: roi


title: CD4_none_8_B_TC36_rep1

source_name: bulk CD4 T cells from donor B, mock-infected as part of experiment TC36, 8h post infection, intra-experimental technical replicate 1, hybridised Nov-12 (from sample well position F8)

tag: timepoint


title: hda19_rep2


title: mnase seq cntrl rep 3 [Mnase CLAMP]

description:
Mnase CLAMP
normalized.sum_neg.bw


title: L09_Geome_MixedROI18


title: L09_Geome_MixedROI17


title: hda19_rep1


title: mnase seq cntrl rep 2 [Mnase CLAMP]

description:
Mnase CLAMP
normalized.sum_neg.bw


title: mnase seq +100nM H1 rep 2 [Mnase H1]

description:
Mnase H1
normalized.sum_100nmh1.bw


title: L09_ROI16_TME

value: TME


title: Col-0_rep2 (wt control)


title: L09_ROI15_TME


title: esant12_rep1


title: L09_ROI16_Tumor

value: Tumor


title: Col-0_rep1 (wt control)


title: mnase seq H1 cntrl rep 2 [Mnase H1]

description:
Mnase H1
normalized.sum_0h1.bw


title: Mnase seq cntrl rep 1 [Mnase CLAMP]

description:
Mnase CLAMP
normalized.sum_neg.bw


title: Mnase seq H1 cntrl rep 1 [Mnase H1]

description:
Mnase H1
normalized.sum_0h1.bw


title: L09_ROI15_Tumor


title: mnase seq +100nM H1 rep 1 [Mnase H1]

description:
Mnase H1
normalized.sum_100nmh1.bw


title: L09_ROI14_Tumor


title: gaf Chip +GCM3 rep 2 [GAF IP]

description:
GAF IP
GAF_CHIP_GCM3_all.bw

value: GAF

value: CLAMP and MSL2 and 75nM GAF


title: arid14_rep2


title: L09_ROI13_TME


title: gaf Chip +GCM3 rep1 [GAF IP]

description:
GAF IP
GAF_CHIP_GCM3_all.bw


title: arid14_rep1


title: L09_ROI13_Tumor


title: srt1x2 Night time replicate2

city: Cambridge

first: Hugo

middle: P.

last: Bastos

address: Jeffrey Cheah Biomedical Centre, Puddicombe Way

department: Haematology

institute: Wellcome - MRC Cambridge Stem Cell Institute

data_processing:
The original image data is transformed into raw sequence data via base calling.
Sequenced reads were demultiplexed, pre-filtered and with the adaptor sequences trimmed off and then aligned against Arabidopis thaliana TAIR10 transcriptome models using bowtie2 with the “-very-sensitive” preset.
Transcript quantification was performed by the eXpress software v1.5.1 using default parameters.
Genome_build: TAIR10
Supplementary_files_format_and_content: Tab-delimited files include quantification metrics for each sample

source_name: seedlings

growth_protocol: Surface sterilised Arabidopsis thaliana seeds were sown directly onto half strength Murashige and Skoog (MS) (Duchefa Biochemie, Netherlands) 0.8 % bactoagar (BD, USA). Stratification at 4° C in the dark was for two days, before transfer to Sanyo (UK) growth cabinets (19 – 22° C, 100 µmol m-2 s-2; 12 hours light/12 hours dark).   40 mg fresh weight of two-week-old seedlings were collected for RNA extraction.

extract_protocol:
RNA was extracted from 40 mg fresh weight of two-week-old seedlings using a Qiagen (Manchester, UK) RNeasy plant mini kit with on-column DNase treatment as per manufacturer’s instructions.
RNA libraries were prepared using the Illumina TruSeq RNA Prep Kit v2

treatment_protocol: Arabidopsis two-week-old seedlings were collected at ZT6 and ZT18 representing the day and night samples.

value: srt2-1 x heterozygous srt1-4


title: srt1x2 Night time replicate3


title: gaf Chip +GCM2 rep 2 [GAF IP]

description:
GAF IP
GAF_CHIP_GCM2_all.bw

value: CLAMP and MSL2 and 25nM GAF


title: srt1x2 Night time replicate1


title: gaf Chip +GCM2 rep1 [GAF IP]

description:
GAF IP
GAF_CHIP_GCM2_all.bw


title: srt2-1  Night time replicate3


title: L09_ROI10_Tumor


title: gaf Chip +GCM1 rep1 [GAF IP]

description:
GAF IP
GAF_CHIP_GCM1_all.bw

value: CLAMP and MSL2 and 8nM GAF


title: srt2-1  Night time replicate2


title: L09_ROI11_Tumor


title: L09_ROI08_TME


title: L09_ROI09_Tumor


title: srt2-1  Night time replicate1


title: srt1-4   Night time replicate3

value: srt1-4 (At5g55760, SAIL_552_E02; heterozygous)


title: gaf Chip +GCM1 rep 2 [GAF IP]

description:
GAF IP
GAF_CHIP_GCM1_all.bw


title: gaf chip + G rep1 [GAF IP]

description:
GAF IP
GAF_CHIP_G_all.bw

value: 25nM GAF


title: L09_ROI08_Tumor


title: gaf chip + G rep 2 [GAF IP]

description:
GAF IP
GAF_CHIP_G_all.bw


title: srt1-4   Night time replicate2


title: CD4_none_4.5_E_TC36_rep1

source_name: bulk CD4 T cells from donor E, mock-infected as part of experiment TC36, 4.5h post infection, intra-experimental technical replicate 1, hybridised Nov-12 (from sample well position D11)

value: no

tag: donor


title: gaf chip neg rep 2 [GAF IP]

description: GAF IP


title: srt1-4   Night time replicate1


title: L09_ROI06_Tumor


title: CD4_IIIB_4.5_B_TC36_rep1

source_name: bulk CD4 T cells from donor B, infected with HIV-1 strain IIIB as part of experiment TC36, 4.5h post infection, intra-experimental technical replicate 1, hybridised Nov-12 (from sample well position G1)

tag: age


title: L09_ROI07_Tumor


title: CD4_IIIB_4.5_E_TC36_rep1

source_name: bulk CD4 T cells from donor E, infected with HIV-1 strain IIIB as part of experiment TC36, 4.5h post infection, intra-experimental technical replicate 1, hybridised Nov-12 (from sample well position E5)

tag: Sex


title: CD4_IIIB.DEnv_4.5_E_TC36_rep1

source_name: bulk CD4 T cells from donor E, infected with HIV-1 strain IIIB.DEnv as part of experiment TC36, 4.5h post infection, intra-experimental technical replicate 1, hybridised Nov-12 (from sample well position E11)


title: CD4_IIIB_12_F_TC35_rep1

source_name: bulk CD4 T cells from donor F, infected with HIV-1 strain IIIB as part of experiment TC35, 12h post infection, intra-experimental technical replicate 1, hybridised Nov-12 (from sample well position C12)

value: F


title: nurf chip +C rep 2 [NURF IP]

description:
NURF IP
merged.nurf_chip_cm.bw

tag: ip target

value: NURF

value: 25nM CLAMP


title: p1x2x3  Night time replicate3

value: parp1-2 x parp2-1 x parp3


title: CD4_IIIB.DEnv_4.5_B_TC36_rep1

source_name: bulk CD4 T cells from donor B, infected with HIV-1 strain IIIB.DEnv as part of experiment TC36, 4.5h post infection, intra-experimental technical replicate 1, hybridised Nov-12 (from sample well position G7)

value: M