title: YJF1484 T19

city: Rochester

first: Justin

last: Fay

state: NY

address: 319 Hutchison Hall, University of Rochester

department: Biology

institute: University of Rochester

description: Cultures of each strain were taken at each time-point (hours) after inoculation.

data_processing:
Reads were mapped to combined reference genomes using Bowtie2 v2.1.0 using the local alignment setting (--local) and a maximum of one mismatch in the seed alignment (-N 1).
Duplicate reads were marked using PicardTools
Htseq-count was used to quantify allele-specific expression by counting reads that mapped to each allele in the combined reference genomes. Htseq-count was run to remove reads mapping to overlapping features (-mode union) and removal of reads with a mapping quality less than 10 (default).
Genome_build: Reference genomes were generated using the S288c (R64.1.1) genome as a template and GATK’s FastaAlternateReferenceMaker command to incorporate variants present in each strain. Genome annotations were generated using liftOver (PMC4383971) to transfer S288c annotations to each of the three other genomes. For mapping interspecific hybrid reads we used reference genomes and annotations (Scannell et al. 2011) for S. cerevisiae (S288c), S. paradoxus (N17) and S. uvarum (CBS7001).
Supplementary_files_format_and_content: Matrix table with read counts for each strain, gene, allele and time-point

organism: Saccharomyces cerevisiae x Saccharomyces uvarum

source_name: yeast culture

growth_protocol: Each hybrid strain was cultured in 125 mL YPD at 250 rpm at 30°C with an initial density of ~3x106 cells/mL

extract_protocol:
Approximately ~3x108 cells were taken at each time-point, centrifuged, supernatant removed and flash frozen in liquid nitrogen. RNA was extracted with phenol-chloroform and mRNA purified by oligo-dT (Dynabeads mRNA Direct kit, Invitrogen).
cDNA libraries were made by reverse transcription, fragmentation and adaptor ligation

treatment_protocol: A total of 19 samples were collected during the switch from fermentation to respiration

tag: strain

tag: time-point

tag: medium

value: Rich medium (YPD)


title: 3.IP

status: Public on Jan 27 2021

type: SRA

city: Shanghai

first: Xiaolin

last: Qu

address: No.415, Fengyang Road

department: Department of neurosurgery

country: China

institute: Changzheng Hospital affliated to Naval Medical University

library_source: transcriptomic

data_processing:
library strategy: meRIP-seq
m6A: Paired-end reads were harvested from Illumina HiSeq 4000 sequencer, and were quality controlled by Q30. After 3’ adaptor-trimming and low quality reads removing by cutadapt software (v1.9.3). First, clean reads of all libraries were aligned to the reference genome (UCSC RN5)  by Hisat2 software (v2.0.4).
m6A: Methylated sites on RNAs (peaks) were identified by MACS software. Differentially methylated sites were identified by diffReps. These peaks identified by both softwares overlapping with exons of mRNA were figured out and chosen by home-made scripts. GO and Pathway enrichment analysis were performed by the differentially methylated protein coding genes.
input: Paired-end reads were harvested from Illumina HiSeq 4000 sequencer, and were quality controlled by Q30. After 3’ adaptor-trimming and low quality reads removing by cutadapt software (v1.9.3), the high quality clean reads were aligned to the reference genome(UCSC RN5) with hisat2 software (v2.0.4).
input: Then, guided by the Ensembl gtf gene annotation file, cuffdiff software (part of cufflinks) was used to get the gene level FPKM as the expression profiles of mRNA, and fold change and p-value were calculated based on FPKM, differentially expressed mRNA were identified. GO and Pathway enrichment analysis were performed based on the differentially expressed mRNAs.
Genome_build: UCSC  RN5
Supplementary_files_format_and_content: excel format

molecule: total RNA

organism: Rattus norvegicus

source_name: retina from control rats

growth_protocol: The protocols for animal studies were approved by the Animal Ethics Committee of the Naval Medical University (Shanghai, China), Ethic Certificate No:81371382. All experiments were performed under the guidance of the National Institute of Health Guide for the Care and Use of Laboratory Animals. Male Sprague-Dawley (SD) rats (220-250 g, 7–8 weeks of age) were housed for at least 7 days in a temperature-regulated (22-25℃) and humidity-controlled (50% relative humidity) animal faculty with a 12-hour light/dark circle. During the experiments, all rats had free access to water and food, except that food was withheld overnight before surgery.

extract_protocol:
Total RNA was isolated using trizol.Total RNA (1 μg) was used for removing the rRNAs using NEBNext rRNA Depletion Kit (New England Biolabs, Inc., Massachusetts, USA)  following the manufacturer's instructions
m6A RNA immunoprecipitation was performed with the GenSeqTM m6A RNA IP Kit (GenSeq Inc., China) by following the manufacturer’s instructions. Both the input sample without immunoprecipitation and the m6A IP samples were used for RNA-seq library generation with NEBNext® Ultra II Directional RNA Library  Prep Kit (New England Biolabs, Inc., USA).
m6A: The library quality was evaluated with BioAnalyzer 2100 system (Agilent Technologies, Inc., USA). Library sequencing was performed on an illumina Hiseq instrument with 150bp paired-end reads.
input: RNA libraries were constructed by using rRNA-depleted RNAs with TruSeq Stranded Total RNA Library Prep Kit (Illumina, San Diego, CA,  USA) according to the manufacturer’s instructions. Libraries were controlled for quality and quantified using  the BioAnalyzer 2100 system (Agilent Technologies, Inc., USA).
input: 10 pM libraries were denatured as single-stranded DNA molecules, captured on Illumina flow cells, amplified in situ as clusters and finally sequenced for 150 cycles on Illumina HiSeq Sequencer according to the manufacturer’s instructions.

treatment_protocol: In this study, the TON model was established by clamping the optic nerve of rats, as previously described (Jiang et al., 2013; Ibrahim et al., 2018; Oku et al., 2019). Briefly, adult male SD rats were intraperitoneally anesthetized with pentobarbital sodium (1%, 35 mg/kg body mass) and placed on an electric heating blanket to ensure the stabilization of body temperature at 37℃ (Zhou et al., 2019). After anesthesia, microsurgical instruments were used to cut the upper eyelid skin vertically under a microscope. The optic nerve was then exposed by cutting the bulbar conjunctiva and conducting the blunt separation of retrobulbar adipose tissue. To cause the injury, the optic nerve was directly clamped at 2 mm behind the eyeball for 10 s by forceps with a 40 g constant holding force. After injury, the surgical incision was sutured, chlortetracycline eye ointment was used for anti-infection. In the sham-operated group, rats received identical surgical procedure, but without clamping applied to the optic nerve. A total of 40 rats were assigned to TON model group and 36 to sham group.

tag: strain background

value: Sprague-Dawley (SD)

tag: age

value: 7-8 weeks

tag: group

value: control

tag: tissue

value: extracted retinal tissue


title: C9: CD8_LN_CD69neg_rep3

city: Stockholm

first: Marcus

last: Buggert

state: PA

address: C2:94; Karolinska Universitetssjukhuset Huddinge

department: Microbiology

country: Sweden

institute: Karolinska Institutet

data_processing:
Raw FASTQ files from RNAseq paired-end sequencing were aligned to the  hg38 reference genome using STAR2.5.2a
Counts were corrected/normalized using PORT(github.com/itmat/normalization)
Genes with differential  expression across samples (DEGs) were assessed using the R package DeSeq2
Differential genes were calculated using a FDR cutoff of 0.05 and Log2 fold change of 1 otherwise indicated
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text file with counts

organism: Homo sapiens

source_name: Lymph Node(LN)

extract_protocol:
mRNA was extracted using RNeasy Plus Micro kit  (Qiagen) following manufacturer’s protocol and eluted in 14μl of RNAse free water.  mRNA quality was assessed on a 2200 TapeStation (Agilent Technologies) using  High Sensitivity RNA ScreenTape (Agilent Technologies).mRNA from each  biological replicate (5ng/sample) was converted into cDNA and amplified (9 cycles)  using the SMART-Seq V4 Ultra Low Input RNA Kit (Takara Bio).
10ng of cDNA  was used to prepare DNA libraries using Nextera XT DNA Library Prep Kit  (Illumina). Barcoded samples were pooled, diluted at 1.8pM, loaded onto a TG  NextSeq 500/550 High Output Kit v2 (150 cycles, 400M reads, Illumina) and  paired-end sequencing was performed on a NextSeq 550 (Illumina)

treatment_protocol: Sorted cells were centrifuged, resuspended in 350μl of RLT buffer (RNeasy Plus  Micro kit, Qiagen) in DNA LoBind tubes (Eppendorf), vortexed for 30s, flash-frozen  on dry ice and stored at -80oC

value: Lymph Node(LN)

tag: cell type

value: CD69neg CD8+ T cell


title: YJF1453 T19

country: USA

organism: Saccharomyces cerevisiae x Saccharomyces paradoxus


title: B9: CD8_LN_CD69neg_rep2


title: Rothamsted 1 (ROTH)

city: Newcastle upon Tyne

first: Robert

last: Edwards

address: Agriculture Building, Newcastle University, King's Rd

department: School of  Natural and Environmental Sciences

country: United Kingdom

institute: Newcastle University

description:
salmon_counts-Rothamsted.txt
AlopecurusROTH1

data_processing:
A de novo transcriptome assembly was carried out with Trinity v2.8.5. using default parameters
Trimmomatic option
coding regions of the assembled transcripts were identified by TransDecoder v5.5.0 with the default parameters and the -single_best_only option to limit to a single ORF per transcript.
Differentially expressed genes (³1-fold and £5% false discovery rate) were identified by linear modeling and Bayesian statistics using the Limma package
Transcript quantification was performed using salmon with the autodetect strandedness and validation mappings parameters.
Tximport was used to transform the salmon expression count data into the DESeq data set. Genes with a single count or not counts across all the samples were removed. Counts were transformed and normalized using the DESeq2 package in R Studio
Weight co-expression network analysis performed in WGCNA R package with normalized reads (log+1)
Genome_build: de novo assembly (Alopecurus_Trinity.fasta, Alopecurus_Trinity.fasta_mapping.gene_trans_map)
Supplementary_files_format_and_content: counts

organism: Alopecurus myosuroides

source_name: 7-days old seedlings of Rothamsted population (isolated in Rothamsted, UK)

growth_protocol: Black-grass seeds were pre-germinated in petri-dishes on 4 layers of filter paper (Whatman No. 1, Sigma Aldrich, Gillingham, UK) wetted with 7 mL of sterile deionized water. Petri-dishes were maintained at 4°C in the dark for 7 days prior to transfer to a growth cabinet with a 16h/8h (light/dark) and 18°C/16°C temperature cycle. For each population, five seedlings were sown into 10 cm plastic pots (n=5), containing John Innes No.2 compost (Marshalls, Huntingdon, UK) mixed with osmocote fertilizer (Osmocote, Suffolk, UK) and propagated in the growth cabinet (Sanyo, MLR-351 SANYO Electric Co., Ltd., Osaka, Japan)

extract_protocol:
The aerial tissue from five 1-2 tiller black grass plants were used for RNA extraction. Total RNA was extracted from frozen tissues (n=5), using NucleoSpin RNA plant kits (Macherey-Nagel, Dueren, Germany) according to the manufacturer’s instructions
Libraries were prepared using the NEBNext Ultra™ RNA Library Prep Kit for Illumina  according to the manufacturer’s instructions. 1ug of the poly (A) mRNA was purified from the total RNA using Oligo d(T)25 paramagnetics beads and the mRNA Magnetic Isolation Module (NEB). Barcodes were incorporated by using NEBNext Multiplex Oligos for Illumina® (96 Unique Dual Index Primer Pairs, NEB)
RNA-seq. Run in NovaSeq 6000 (Illumina) along with NovaSeq 6000 SP cluster cartridge

treatment_protocol: Plants were not treated

tag: population

value: Rothamsted

tag: phenotype

value: Sensitive to all herbicides

tag: genotype

value: wild-type

value: 7-days old seedlings

tag: treatment

value: untreated


title: K17/3551

city: Gent

first: Mattias

last: Hofmans

address: C. Heymanslaan 10

department: Department of pediatrics

country: Belgium

institute: Ghent University Hospital

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 reference genome using STAR v2.4.2 using a 2-pass strategy for identification of novel transcripts
Known gene quantification was performed on gencode v25 during the first pass.
Differential expression analysis of known genes was performed in R with DESeq2 v1.14.1
Genome_build: hg38
Supplementary_files_format_and_content: normalizedCounts_Deseq2.txt

extract_protocol:
Mononuclear cell preparations were isolated from bone marrow or peripheral blood using Ficoll density gradient (Axis-shield). Next, Total RNA was extracted using the miRNeasy Mini Kit (Qiagen) in combination with on-column DNase I digestion (RNase-Free DNase set, Qiagen) according to manufacturer’s instructions. The quality of the extracted RNA was assessed using the RNA 6000 Nano and RNA 6000 PICO assays on an 2100 Bioanalyzer (Agilent).
Sequencing libraries were prepared using a TruSeq Stranded Total RNA Kit adapted for long fragments (+/- 550 bp) with the Ribo-Zero Gold rRNA Removal Kit (Illumina), according to the manufacturer’s instructions. Prepared libraries were run on a HiSeq3000 high-throughput sequencing system (Illumina) and paired end reads were generated (average of 52 million  reads per sample)

tag: disease state

value: JMML

tag: hemoglobin (%)

tag: karyotype

tag: mutation

tag: platelets (x 10^9/l)

tag: Cause of death

tag: survival from diagnosis (os) (years)

value: No event

tag: survival from hsct (efs) (years)


title: YJF1484 T18

tag: strain

tag: time-point

tag: medium


title: YJF1453 T18


title: K17/3874

value: NRAS

value: no SCT


title: K17/3873

value: Disease progression and respiratory failure

value: Relapse


title: K17/3545


title: YJF1484 T17

value: Rich medium (YPD)


title: YJF1453 T17


title: YJF1484 T16


title: A_LV_S136: TDL_TEMRA_rep3

library_source: genomic

data_processing:
Paired-end reads were mapped to the hg19 reference genome using Bowtie2
Only concordantly mapped pairs were kept for further analysis
Peak calling was performed using MACS v2 to identify areas of sequence tag enrichment
BedTools was used to find common intersection between identified peaks (1bp minimum overlap) and to create a merged peak list
ATAC-seq tag enrichment, DNA motif analysis across the merged peak list,and GO term assessment were computed using HOMER (homer.salk.edu)
Genome_build: hg19
Supplementary_files_format_and_content: bed files generated by peak calling

molecule: genomic DNA

source_name: CD8 T cells

extract_protocol:
Mononuclear cells from mesenteric LN, TDL were thawed, rested overnight, and sorted in cell numbers of 5-25,000 into complete RPMI with 50% FBS. Nuclei from cell pellets (5,000-25,000 cells) were isolated using a lysis buffer and pelleted in low-bind 1.5mL tubes (Eppendorf).
Nuclei were resuspended in 25ml TD buffer with Tn transposase (Illumina). The transposition reaction was continued for 45 minutes at 37°C. The resulting DNA fragments were purified using the MinElute PCR purification Kit (Qiagen). Libraries were prepared using Nextera (Illumina) and sequenced by the Children’s Hospital of Philadelphia partnership with the Bejing Genomics Institute on two lanes of a Hiseq 4000 paired-end sequencing (100 bp read length).

tag: tissue

value: Tumor Draining Lymph Node(TDL)

value: CD8 T cells


title: YJF1484 T15


title: Rothamsted 4 (ROTH)

description:
salmon_counts-Rothamsted.txt
AlopecurusROTH4


title: K17/3550


title: K17/3548

value: KRAS


title: YJF1484 T14


title: YJF1453 T16


title: A_LV_S135: TDL_EM_rep3

tag: cell type


title: A_LV_S132: TDL_TEMRA_rep2


title: YJF1453 T15


title: K17/3547

value: No data


title: YJF1453 T14


title: YJF1484 T13


title: A_LV_S131: TDL_EM_rep2


title: A9: CD8_LN_CD69neg_rep1

value: Lymph Node(LN)

value: CD69neg CD8+ T cell


title: YJF1484 T12


title: K17/3546


title: YJF1453 T12


title: K17/3549

source_name: no_information_available (either Bone_Marrow_MNCs or Peripheral_Blood_MNCs)

value: Progress, no SCT


title: YJF1484 T11


title: YJF1453 T13


title: A_LV_S128: TDL_TEMRA_rep1


title: YJF1453 T11


title: K17/3872

value: TRM


title: A_LV_S127: TDL_EM_rep1


title: YJF1484 T09


title: A_LV_S126: TDL_CD8_naive_rep1


title: YJF1453 T10


title: YJF1484 T08


title: YJF1484 T10


title: A_LV_S109: LN_EM_rep3


title: K17/3541


title: YJF1453 T09


title: K17/3539


title: YJF1484 T07


title: YJF1453 T08


title: A_LV_S106: LN_EM_rep2


title: YJF1453 T07


title: A_LV_S101: LN_CD8_naive_rep1


title: SETDB1-ChIP(Ythdc1-cKO -4OHT)

city: GuangZhou

first: Jiangping

last: He

address: Kai yuan avenue 190

institute: Guangzhou Institutes of Biomedicine and Health (GIBH), CAS

data_processing:
bcl2fastq conversion software v2.17 used for basecalling.
Reads were aligned to the genome(mm10) with bowtie2
ChIP-seq reads were aligned to the mouse mm10 genome using bowtie247 with the options ‘-p 20– very-sensitive–end-to-end–no-unal–no-mixed -X 2000’. The multimapped reads were kept for TE analysis, but only the best alignment is reported for those reads, if more than one equivalent best alignment was found, then one random alignment was reported. Whereas the reads mapping to mitochondrial DNA or unassigned sequences were discarded
Genome_build: mm10

organism: Mus musculus

source_name: embryonic stem cells

growth_protocol: Male mouse embryonic stem cells (mESCs) were derived from 3.5 d.p.c inner cell mass (ICM) from female 129 mice (Stock No.: 217, Beijing Vital River Laboratory Animal Technology Co., Ltd.). Animal care and experimental protocols were approved by the animal ethics committee of the Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences. ESCs with genetic engineering, including Ythdc1-conditional knockout (cKO), MERVL::tdTomato reporter, and Halo- Ythdc1 knockin (KI) , and TurboID overexpression (OE) were constructed and cultured in feeder- free condition, using serum/LIF medium containing high-glucose Dulbecco’s modified Eagle’s medium (DMEM, HyClone, #SH30022.01), 15% fetal bovine serum (FBS, Front Biomedical, # OPT500), 1× GlutaMAX, 1× nonessential amino acids (NEAA, Gibco, #11140076), 1× Penicillin- Streptomycin (Hyclone, #SV30010), 1× Sodium Pyruvate (Gibco, #11360070), 1 mM 2- Mercaptoethanol (Gibco, # 21985023), and 1000 U/ml LIF. HEK293T (ATCC, # CRL-1126) and NIH3T3 (ATCC, #CRL-1658) cells were maintained in high-glucose DMEM supplemented with 10% FBS (Natocor, #SFBE), 1× GlutaMAX (Gibco, #35050079), and 1× NEAA. All the cell lines were cultivated at 37°C in a humidified atmosphere containing 5% CO2.

extract_protocol:
genomic DNA
Native ChIP-seq was performed as described44. In brief, 1 × 107 cells were harvested and resuspended in 500 μl Buffer 1 (0.32 M sucrose, 15 mM Tris-HCl pH 7.5, 60 mM KCl, 15 mM NaCl, 5 mM MgCl2, 0.5 mM DTT, 0.1 mM EGTA, 0.1 mM PMSF, 1:1000 EDTA-free protease inhibitor cocktail [Roche, #4693132001]) supplemented with 0.1% IGEPAL CA-630 (Sigma, # I8896) on ice for 10 min. The lysates was carefully layered on the top of 1 ml Buffer 3 (1.2 M sucrose, 15 mM Tris-HCl pH 7.5, 60 mM KCl, 15 mM NaCl, 5 mM MgCl2, 0.5 mM DTT, 0.1 mM EGTA, 0.1 mM PMSF, 1:1000 PIC). After centrifugation (10,000 ×g for 20 min at 4°C), the nuclei were resuspended in 500 μl Buffer A (0.34 M sucrose, 60 mM KCl, 15 mM HEPES pH7.4, 15 mM NaCl, 4 mM MgCl2, 1 mM DTT, 0.1 mM PMSF, 1:1000 PIC) supplemented with 3 mM CaCl2 and 2 U/μl MNase (NEB, # M0247S) and digested for 15 min at 37°C. Then 5 mM EGTA was added to stop the reaction. After centrifuged at 13,500 ×g for 10 min at 4°C, chromatin was resuspended in 10 mM EDTA (pH 8.0) supplemented with 1 mM PMSF and 1:1000 PIC, followed by rotation at 4 °C for 2-4 h. The mixture was adjusted to 500 mM NaCl and rotated for additional 45 min. After centrifugation, the supernatant containing chromatin was diluted to 100 ng/μl with buffer B (20 mM Tris-HCl pH8.0, 5 mM EDTA, 500 mM NaCl, 0.2% Tween 20) and the fragmentation of chromatin was detected by agarose electrophoresis. A total of 2.5 μg fragmented chromatin was kept as the input. For immunoprecipitation, the reaction mixture, including 20 μg fragmented chromatin, 2 μg anti-H3K9me3 antibody (Abcam, #ab8898), and 50 μl protein A/G dynabeads (GE Healthcare) was incubated overnight with gentle rotation at 4°C. The beads were washed three times with Buffer B, and once with Buffer B without Tween 20 at 4°C for 5 min. The DNA was eluted with 300 μl elution buffer (20 mM Tris-HCl pH8.0, 20 mM EDTA, 0.5% SDS), digested with PK enzyme (NEB, #P8107S), and purified using a MinElute kit (Qiagen, #28006). The ChIP DNA library was constructed by a KAPA HTP/LTP Library Preparation Kit according to the manufacturer’s instructions.

value: embryonic stem cells


title: K17/3535


title: YJF1484 T05


title: SETDB1-ChIP(Ythdc1-cKO +4OHT)


title: scTCRseq of TDL HIV-specific CD8+ T-cells from HIVPosSmpl2

data_processing:
Library strategy: single-cell TCR-seq
basecalling and demultiplexing with cellranger/v4.0.0 mkfastq with bcl2fastq2/v2.20.0.422
generating barcode/feature matrices with cellranger/v4.0.0 count
generating clonotype data with cellranger/v4.0.0 vdj
Genome_build: hg38
Supplementary_files_format_and_content: cellranger vdj output

source_name: lymphocytes

extract_protocol: Chromium Single-cell VDJ v1.1 kit (10X Genomics)

value: TDL

value: HIVpos

value: HIV-specific memory CD8+ T-cells

tag: antigen-specificity

value: HIV


title: YJF1484 T04


title: YJF1453 T06


title: YJF1453 T05


title: IVO-3

city: nanjing

first: Zhang

last: haolin

address: xiaolingwei street

institute: Zhang haolin

data_processing:
filtering of clean reads
alignment with Ribosome RNA(rRNA)
alignment with reference genome
quantification of Gene Abundance
differentially expressed genes(DEGs)
Genome_build: mm9
Supplementary_files_format_and_content: Matrix table with raw gene FPKM for every gene and every sample

source_name: oocyte

extract_protocol:
1. Take 100μl cell suspension and place it in a 1.5 mL centrifuge tube, then remove the supernatant.2.Operate on ice, add 350μl lysate and 3.5μl β-mercaptoethanol to the precipitate, mix well and let stand for 3-5 minutes.3. Add ethanol, mix and transfer all the solution to the centrifugal tube with filter membrane.4. centrifugal force 9000×g for 30s, discard the waste liquid.5.Add 350μL eluent, centrifugal force 9000×g, centrifuge for 30s, discard the waste liquid.6.Add DNASEI mixture 80μl to a centrifuge tube and let stand for 15min.6.Add 350μL eluent, centrifuge at 9000×g for 30s, then discard the waste liquid.7.Add 500μL eluent, centrifuge at 9000×g for 30s, then discard the waste liquid.8.Add 500μL eluent, centrifuge at 9000×g for 30s, then discard the waste liquid.  9, Add 500μL eluent and centrifuge with centrifugal force at 9000×g for 3min, then discard the waste liquid.  10. The centrifuge tube is emptied again for 1min.  11. Place the casing in a new 1.5 mL centrifuge tube with a centrifugal force of 9000×g for 1min, discard the casing, in the centrifuge, discard the casing, and RNA solution is in the centrifuge tube.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: oocyte

tag: Stage

value: Metaphase II

tag: culture environment

value: in vivo


title: scTCRseq of Blood HIV-specific CD8+ T-cells (with B-cell spike in) from HIVPosSmpl2

value: Blood

value: HIV-specific memory CD8+ T-cells + B cells spike in


title: YJF1484 T03

value: Rich medium (YPD)


title: scTCRseq of TDL CMV-specific CD8+ T-cells (with B-cell spike in) from HIVPosSmpl2

value: CMV-specific memory CD8+ T-cells + B cells spike in

value: CMV


title: IVO-1


title: IVO-2


title: YJF1453 T04


title: scTCRseq of Blood CMV-specific CD8+ T-cells from HIVPosSmpl2

value: CMV-specific memory CD8+ T-cells


title: IVM-3

value: in vitro maturation


title: YJF1484 T02


title: YJF1484 T01


title: YJF1484 T06


title: A_LV_S102: LN_EM_rep1

value: Lymph Node(LN)

value: CD8 T cells


title: scTCRseq of TDL HIV-specific CD8+ T-cells (with B-cell spike in) from HIVPosSmpl1


title: YJF1453 T01


title: YJF1453 T02


title: scTCRseq of Blood HIV-specific CD8+ T-cells (with B-cell spike in) from HIVPosSmpl1


title: IVM-1


title: scTCRseq of TDL memory CD8+ T-cells from HUP222

value: HIVneg

value: Memory CD8+ T-cells


title: WGBS_KO3

city: Grand Rapids

first: Gerd

middle: P

last: Pfeifer

state: MI

address: 333 Bostwick Ave NE

department: Center for Epigenetics

institute: Van Andel Research Institute

data_processing:
Sequencing was performed with an Illumina HiSeqX with 150-bp paired-end-read runs.
Paired-end whole genome bisulfite reads were trimmed using TrimGalore with the following parameters to remove the library preparation artifacts and low quality bases: --length 50; --clip_R1 10; --clip_R2 18; --three_prime_clip_R1 10 --three_prime_clip_R2 10.
Trimmed reads were aligned to the mm9 primary chromosomes using Bismark and Bowtie2  with the following parameters: -X 1000; --nucleotide_coverage; --bowtie2. Duplicates were marked and removed using the deduplicate_bismark script provided with Bismark. CpG methylation values were extracted using the bismark_methylation_extractor script provided with Bismark and the following parameters: --no_overlap; --comprehensive; --merge_non_CpG; --cytosine_report.
We used DMRseq to identify differentially methylated regions (DMRs). Briefly, CpG loci with fewer than 5 reads were not considered for DMR calling and a single CpG coefficient cutoff of 0.05 was used for candidate regions.
Genome_build: mm9
Supplementary_files_format_and_content: Text file containing cytosine coverage that is an output from the Bismark analysis workflow.

source_name: Embryonic stem cells

growth_protocol: All ES cells were cultured cultured under feeder-free conditions on 0.1% gelatin-coated tissue culture plates in knockout DMEM supplemented with 15% fetal bovine serum, 1,000 U/ml LIF, 1x non-essential amino acids, 100 µM β-mercaptoethanol   and 2 mM L-glutamine.

extract_protocol:
The DNA was extracted with the Zymo's Quick-DNA Mini Prep Kit accoding to manufacturer’s instructions.
we used Swift, Accel-NGS Methyl-Seq DNA Library Kit and Zymo’s EZ DNA Methylation-Lightning kit, according to the manufacturer’s instructions.

value: Embryonic stem cells


title: YJF1453 T03


title: Pendimethalin 5 (PEN)

description:
salmon_counts-Pendimethalin.txt
AlopecurusPEND5

source_name: 7-days old seedlings of Pendimethalin population

tag: population

value: Pendimethalin

tag: phenotype

value: Resistant to ACCases and pendimethalin herbicides, derived from Rothamsted after repeated field-rate applications of pendimethalin during 8 years

tag: genotype

value: still remain unknown. derived from wild-type

value: 7-days old seedlings

tag: treatment

value: untreated


title: WGBS_KO2


title: scTCRseq of TDL memory CD8+ T-cells from HUP217

value: TDL

tag: disease state


title: WGBS_KO1


title: Pendimethalin 4 (PEN)

description:
salmon_counts-Pendimethalin.txt
AlopecurusPEND4


title: IVM-2

value: oocyte

value: Metaphase II


title: Pendimethalin 3 (PEN)

description:
salmon_counts-Pendimethalin.txt
AlopecurusPEND3


title: Pendimethalin 2 (PEN)

description:
salmon_counts-Pendimethalin.txt
AlopecurusPEND2


title: Pendimethalin 1 (PEN)

description:
salmon_counts-Pendimethalin.txt
AlopecurusPEND1


title: scTCRseq of TDL memory CD8+ T-cells from HUP213


title: scTCRseq of Blood memory CD8+ T-cells from HUP217

value: Blood


title: Cabbage Rep 2 RNA-seq

city: East Lansing

first: Chad

middle: E.

last: Niederhuth

state: M

address: 612 Wilson Road

department: Plant Biology

institute: Michigan State University

description: Replicate 2 of 24-day old developing Cabbage leaves and meristems RNA-seq

data_processing:
Reads were trimmed using Cutadapt version 2.4 with the arguments: "--trim-n -m 30 -g" and supplied with the following adaptor/primer sequences: Clontech_SMART_CDS_Primer_II_A: "TAAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTT" and Illumina_Paired_End_PCR_Primer_2: "TAGCAGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTAT"
Read quality was determined before and after trimming using FastQC.
A STAR index was first created, supplied with B. oleracea annotations using the arguments "--genomeFastaFiles TO1000.fa --sjdbGTFfile annotations/TO1000.gtf --sjdbOverhang 96". The TO1000 B. oleracea genome was downloaded from EnsemblPlants from the ftp link: "ftp://ftp.ensemblgenomes.org/pub/plants/release-44/fasta/brassica_oleracea/dna/Brassica_oleracea.BOL.dna.toplevel.fa.gz". Annotations were downloaded from the ftp link: "ftp://ftp.ensemblgenomes.org/pub/plants/release-44/gff3/brassica_oleracea/Brassica_oleracea.BOL.44.gff3.gz"
Reads were aligned to the B. oleracea genome using two passes of STAR.  In the first pass of mapping, each sample was individually mapped with STAR to discover novel splice-junctions using the arguments "--readFilesCommand zcat --outSAMtype BAM SortedByCoordinate --outSAMstrandField intronMotif --outFilterType BySJout --outFilterMultimapNmax 10 --alignSJoverhangMin 5 --alignSJDBoverhangMin 3 --alignIntronMin 20 --alignIntronMax 0 --outFilterScoreMinOverLread 0.33 --outFilterMatchNminOverLread 0.33 --outFilterMismatchNmax 10 --outFilterMismatchNoverReadLmax 0.1". Each sample was then realigned in the second pass using STAR  supplied with a combined list of novel junctions discovered during the first pass of mapping using the arguments: "--sjdbFileChrStartEnd <list_of_paths_to_novel_junctions> --readFilesCommand zcat --outSAMtype BAM SortedByCoordinate --outSAMstrandField intronMotif --outFilterType BySJout --outFilterMultimapNmax 10 --alignSJoverhangMin 5 --alignSJDBoverhangMin 3 --alignIntronMin 20 --alignIntronMax 0 --outFilterScoreMinOverLread 0.33 --outFilterMatchNminOverLread 0.33 --outFilterMismatchNmax 10 --outFilterMismatchNoverReadLmax 0.1 --quantMode GeneCounts".  Read counts for each gene were quantified in the second-pass and used for differential gene expression anlaysis using DESeq2.
Genome_build: TO1000 v2
Supplementary_files_format_and_content: Read counts files are tab-delimited files with column 1 being the gene name and column two the count of reads mapping to that gene.

organism: Brassica oleracea

source_name: Young leaf, stem, and meristem

growth_protocol: Single accessions of Cabbage (B. oleracea var. sabadua), Kale (B. oleracea var. viridis) and TO1000 (B. oleracea var. alboglabra) were grown in an environmental chamber under uniform conditions:  10hr day (light 7AM to 5PM, Dark 5:01PM to 6:59AM daily) and watered every other day. Morphotypes were planted in a completely randomized block design. Initially, two seeds per pot were planted, then only one was picked (32 plants per morphotype total). A random number generator was used to move plants and flats around every other day. Tissues were collected 24 days after seeds were planted. The upper portion of the stems, including immature leaves, and apical and lateral meristems were flash frozen in liquid nitrogen. The assumption was made that genes involved in developing different morphologies should be expressed in younger leaves, shoots, and meristems. Three biological replicates per morphotype were collected, each replicate consisting of pooled tissue from eight plants.

extract_protocol:
Lysis and homogenization of fresh soft tissue were performed before RNA extraction; PureLink Micro-to-Midi Total RNA Purification System (Invitrogen, Cat. No 12183-018, Carlsbad, California, USA) was used. A total of eight plants were pooled per replicate in a single tube for a total of eight plants per replicate. RNA extraction was done using the Purelink RNA Mini Kit (Ambion, Cat. No12183-018A, Carlsbad, California, USA). DNase was not used before proceeding with cDNA synthesis as recommended in the protocol. For cDNA synthesis MINT (Evrogen, Cat. No SK001, Moscow, Russia) was used, this kit is used to synthesize full-length-enriched double stranded cDNA from a total polyA+ RNA. The cDNA was then amplified by 16 -- 21 cycles of polymerase chain reaction and purified using a PCR Purification Kit (Invitrogen K3100-01 Carlsbad, California, USA).
Protocols previously published by Steele et al. (2012) were used. End repair was performed on 400ul with 3ug of normalized ds-cDNA prior to ligating barcoding adapters for multiplexing, using NEB Prep kit E600L (New England Biolabs, Ipswich, Massachusetts, USA). Shearing was done using a Bioruptor® sonication device (Diagenode, Denville New Jersey), at 4°C, continuously, for 15min. total (7mix) on high. The three replicates per morphotype were tagged with different adaptors and sequenced on a single lane. Oligonucleotides used as adapters were: Cabbage (1: ACGT, 2: GCTT, 3: TGCT), Kale (1: TACT, 2:ATGT, 3:GTAT), TO1000 (1:CTGT, 2:AGCT, 3:TCAT). To prepare the adapters, equal volumes were combined of each adapter at 100 μmol/L floating them in a beaker of boiling water for 30min. and snap cooling them on ice. Ligation products were run on a 2% low-melt agarose gel and size-selected for ~300 bp using an x-tracta Disposable Gel Extraction Tool (USA Scientific, Ocala Florida). Fragments were enriched using PCR in 50 μL volumes containing 3 μL of ligation product, 20 μL of ddH2O, 25 μL master mix (from NEB kit), and 1 μL each of a 25 μmol/L solution of each forward and reverse primer (forward 5′-AAT GAT ACG GCG ACC ACC GAG ATC TAC ACT CTT TCC CTA CAC GAC GCT CTT CCG ATC* T-3′; reverse 5′-CAA GCA GAA GAC GGC ATA CGA GAT CGG TCT CGG CAT TCC TGC TGA ACC GCT CTT CCG ATC*-3′; both HPLC purified). Thermal cycle routine was as follows: 98°C for 30 s, followed by 15 cycles of 98°C for 10 s, 65°C for 30 s, and 72°C for 30 s, with a final extension step of 72°C for 5 min. Products were run on a 2% low-melt agarose gel and the target product was excised and purified with the tools described above. DNA was purified at each step during the end repair, adapter ligation, size selection and fragment enrichment with either a Gel Extraction kit (Qiagen, Germantown Maryland) or a DNA QIAquick PCR Purification kit (Qiagen, Germantown Maryland).

tag: accession

value: B. oleracea var. sabadua

tag: age

value: 24-days post sowing


title: Kale Rep 3 RNA-seq

description: Replicate 3 of 24-day old developing Kale leaves and meristems RNA-seq

value: B. oleracea var. viridis


title: Kale Rep 1 RNA-seq

description: Replicate 1 of 24-day old developing Kale leaves and meristems RNA-seq


title: TO1000 Rep 3 RNA-seq

description: Replicate 3 of 24-day old developing TO1000 leaves and meristems RNA-seq

value: B. oleracea var. alboglabra


title: TO1000 Rep 2 RNA-seq

description: Replicate 2 of 24-day old developing TO1000 leaves and meristems RNA-seq


title: scTCRseq of Blood memory CD8+ T-cells from HUP213


title: Kale Rep 2 RNA-seq

description: Replicate 2 of 24-day old developing Kale leaves and meristems RNA-seq


title: TO1000 Rep 1 RNA-seq

description: Replicate 1 of 24-day old developing TO1000 leaves and meristems RNA-seq


title: Cabbage Rep 1 RNA-seq

description: Replicate 1 of 24-day old developing Cabbage leaves and meristems RNA-seq


title: WGBS_WT1


title: scTCRseq of Blood memory CD8+ T-cells from HUP222


title: WGBS_WT3


title: Aatoe2_IL_shoot apex_rep2

status: Public on Jan 26 2021

city: Köln

first: Maria

last: Albani

address: Carl-von-Linné-Weg 10

department: Botanical institute

country: Germany

institute: University of Cologne

description:
Table S3 DEGs in Aatoe2_IL vs wild-type in shoot apex and V3 buds.xlsx
Raw_counts_for_DEseq.csv

data_processing:
Reads derived from the Illumina library were aligned to the reference genome (A. alpina_V5) using STAR
Raw read counts per gene were quantified with HTSeq v0.5.4p1
Differential expression between samples was determined using DESeq
The differentially expressed genes with more than 2-fold change and an adjusted p-value below 0.05 were obtained using DESeq2 and selected for further analysis.
Genome_build: Arabis alpina V5 genome
Supplementary_files_format_and_content: Files include average count and log2foldchange for each Sample

molecule: polyA RNA

organism: Arabis alpina

source_name: 8-week-old plants being vernalized 8 weeks

growth_protocol: Plants are grown for 8 weeks at long day and then vernalized in short day for 8 weeks

extract_protocol:
RNA was isolated using RNeasy Plant RNA isolation kit (Qiagen) according to manufacturer's instructions
polyA enrichment was conducted with 1 µg total RNA using NEBNext Poly(A) mRNA Magnetics Isolation Module (New England Biolabs), followed by library preparation with NEBNext Ultra Directional RNA Library Prep Kit for Illumina (New England Biolabs). Quality and quantity were assessed at all steps via capillary electrophoresis (TapeStation, Agilent Technologies) and fluorometry (Qubit, Thermo Fisher Scientific). Sequencing was performed on HiSeq2500 (Illumina) with 1 x 100 bp single reads.

value: dissected shoot apices

value: Pajares


title: WT_V3 buds_rep2

value: dissected V3 buds

value: wild-type


title: Aatoe2_IL_V3 buds_rep3


title: Aatoe2_IL_shoot apex_rep1


title: WT_V3 buds_rep3


title: Aatoe2_IL_V3 buds_rep2


title: Aatoe2_IL_shoot apex_rep3


title: WGBS_WT2

value: Embryonic stem cells


title: WT_V3 buds_rep1


title: WT_shoot apex_rep3


title: WT_shoot apex_rep1


title: Aatoe2_IL_V3 buds_rep1


title: WT_shoot apex_rep2


title: Ratio of Riplet KO effector CD8 T cells to WT effector CD8 T cells

type: RNA

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: 10-1 tebiro 6-chome

country: Japan

institute: Toray Industries,Inc.

description: Gene expression of Riplet KO effector CD8 T cells normalized to that of WT effector CD8 T cells

hyb_protocol: Hybridized for 16 h at 37 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc..

scan_protocol: 3D-Gene Scanner ((Toray Industries Inc., Tokyo, Japan) was used for scanning. Images were quantified using Extraction(Toray Industries Inc., Tokyo, Japan).

data_processing: F635 Median column as Red signal and F532 Median column as Green signal. Global normalized, background subtracted data obtained from log2 of processed Green signal/processed Red signal.

source_name: KO 4h CD8

label_protocol: cDNA and Amino Allyl aRNA was synthesis by Amino Allyl MessageAmp II aRNA Amplification Kit (Ambion#1753). CyeDye Coupling and fragmentation were performed as the protocol supplied by TORAY Industries, Inc..

growth_protocol: Naïve CD8 T cells from WT and Riplet KO mice were stimulated with anti-CD3 and anti-CD28 Abs for 3 days and rested for 1 day.

extract_protocol: RNA samples were extracted from effector T cells using TRI Reagent (Molecular Research Center Inc) and RNeasy mini kit (Qiagen).

treatment_protocol: After resting culture, WT and Riplet KO effector CD8 T cells were restimulated with anti-CD3 Ab for 4 hours.

value: CD8 T cells

value: Riplet KO

source_name: WT 4h CD8

value: WT


title: AML_validation_B41

city: Prague

first: Sarka

last: Sestakova

address: U Nemocnice 2094/1

department: Genomics

country: Czech Republic

institute: Institute of Hematology and Blood Transfusion

data_processing:
Quality check using FasQC and MultiQC
Trimming and filtering of fastq files with Cutadapt 2.4
Mapping with software Segemehl to human genome (assembly hg19) with added sequence of Enterobacteria phage lambda NC_001416.1
Sorting and indexing of BAM files with Samtools
Selection of methylated positions with Haarz tool (included in Segemehl software) with enabled "callmethyl" option
In R 4.0.0, positions corresponding to lambda phage sequence were removed (used for the computation of bisulfite conversion ratio) and from the remaining data only CpG sites were selected
Genome_build: hg19
Supplementary_files_format_and_content: table of CpG sites and their methylation values (percentage of methylated reads)

source_name: whole blood

extract_protocol:
Diagnostic DNA of AML patients was either isolated from whole peripheral blood with MagCore system (RBSBioscience) or from peripheral blood leukocytes lysed in RLT buffer using AllPrep DNA/RNA Mini Kit (Qiagen). Healthy donors’ DNA was isolated with MagCore system from CD34+ cells harvested from buffy coats using MicroBeads kit (Miltenyi Biotec).
Each sequencing library consisted of 16-18 samples and libraries were prepared according to SeqCap Epi protocol (Roche) with KAPA HyperPrep Kit (Roche). First, Bisulfite-conversion Control (unmethylated DNA from Enterobacteria phage lambda, a component of SeqCap Epi Accessory kit (Roche)) was added to 800–1,200 ng of patients/donors’ DNA. This DNA mixture was subsequently fragmented either via Bioruptor Pico instrument (Diagenode) or E220 Focused ultrasonicator (Covaris) to get ~ 200 bp DNA fragments. The size of fragments was checked in two random samples from each library on 4200 TapeStation System (Agilent Technologies) using Agilent D1000 ScreenTape (Agilent Technologies). EZ DNA Methylation Lightning Kit (Zymo Research) was used for the bisulfite conversion, as recommended in the SeqCap Epi workflow. Each library was hybridized for ~ 68 hours with probes from our custom DNA methylation sequencing panel (made by Roche). KAPA Library Quantification Kit (Roche) was utilized to assess the final concentration of sequencing libraries. Average size of the libraries’ fragments was measured on 4200 TapeStation System with Agilent D1000 ScreenTape (Agilent Technologies). Sequencing was performed using MiSeq Reagent Kit v2 (300-cycles) (Illumina) on MiSeq instrument (Illumina).
targeted bisulfite sequencing using custom probes

value: acute myeloid leukemia

value: whole blood

tag: gender

value: female

tag: fab classification


title: AML_validation_B36

value: male


title: AML_validation_B44


title: AML_validation_B38


title: AML_validation_B39


title: AML_validation_B47


title: AML_validation_B50


title: AML_validation_B46


title: AML_validation_B37


title: AML_validation_B42


title: AML_validation_B49


title: AML_validation_B40


title: AML_validation_B48


title: AML_validation_B45


title: AML_validation_B43


title: AML_validation_B35


title: AML_validation_B34


title: AML_validation_B33


title: AML_validation_B30


title: AML_validation_B31


title: AML_validation_B32


title: AML_validation_B27


title: AML_validation_B28


title: AML_validation_B26


title: AML_validation_B29


title: AML_validation_B25


title: AML_validation_B24


title: AML_validation_B23


title: AML_validation_B22


title: AML_validation_B21


title: AML_validation_B20


title: AML_validation_B16


title: AML_validation_B19


title: AML_validation_B18


title: AML_validation_B2


title: AML_validation_B1


title: AML_validation_B4


title: AML_validation_B12


title: AML_validation_B3


title: AML_validation_B6


title: AML_validation_B10


title: AML_test_A126


title: AML_test_A124


title: AML_validation_B15


title: AML_validation_B9


title: AML_validation_B13


title: AML_validation_B7


title: AML_test_A127


title: AML_validation_B11


title: AML_test_A123


title: AML_test_A122


title: AML_test_A128


title: AML_validation_B5


title: AML_test_A120


title: AML_validation_B8


title: AML_validation_B17


title: AML_test_A121


title: AML_validation_B14


title: AML_test_A125


title: AML_test_A118


title: AML_test_A116


title: AML_test_A109


title: AML_test_A104


title: AML_test_A107


title: AML_test_A105


title: AML_test_A117


title: AML_test_A106


title: AML_test_A103


title: AML_test_A115


title: AML_test_A100


title: AML_test_A102


title: AML_test_A112


title: AML_test_A108


title: AML_test_A111


title: AML_test_A114


title: AML_test_A96


title: AML_test_A113


title: AML_test_A98


title: AML_test_A97


title: AML_test_A110


title: AML_test_A99


title: AML_test_A101


title: AML_test_A119


title: AML_test_A93


title: AML_test_A94


title: AML_test_A90


title: AML_test_A92


title: AML_test_A95


title: AML_test_A91


title: AML_test_A87


title: AML_test_A88


title: AML_test_A85


title: AML_test_A86


title: AML_test_A84


title: AML_test_A83


title: CTRL Infected 14 DPI small RNA Rep 3

city: University Park

first: Cory

last: Henderson

address: Room W127, Millennium Science Complex

department: molecular cellular and integrative biosciences

institute: Pennsylvania State University

description:
small RNA
smallGLM.xlsx
miRNACounts.csv

data_processing:
Adapter trimming and low quality bases removed with Trimmomatic using base settings
miRDeep2 pipeline to identify novel and known miRNAs and read counts mapping to them in each sample
miRNAs with a miRDeep score of less than 3, a minimum free energy value of less than – 20, or a Randfold p-value < 0.05 were considered false IDs
Differential expression of miRNAs was conducted using a negative binomial GLM with the EdgeR package in R
Genome_build: ASM30077v2 and ASM154264v1
Supplementary_files_format_and_content: Contains either read counts mapping to each mirBase miRNA ID considered in the analysis (.csv) or differential expression results for each miRNA in all considered contrasts in the GLM (.xlsx).

organism: Anopheles stephensi

source_name: Whole mosquito

growth_protocol: Mosquito colonies were reared and maintained at at 27˚C ± 1˚C, 12 hour light 12 hour dark diurnal cycle at 80% relative humidity in 30×30×30-cm cages. Ground fish flakes were used to feed larvae, and upon emergence adult mosquitoes were maintained with a 10% sucrose solution.

extract_protocol:
Mosquitoes were anesthesized with triethylamine and RNA was extracted from each individual mosquito using mirVana RNA extraction kit (Life Technologies) applying the protocol for extraction of total RNA.
The NEBNext Ultra II RNA library kit (New England Biolabs) was used for RNA-Seq library construction for total RNA. Small RNA libraries were created using the New England Biolabs small RNA library protocol.

treatment_protocol: Mosquitoes were allowed to feed on either human blood spiked with Mayaro virus at 1*10^7 FFU/mL or a control bloodmeal with no virus via a glass feeder jacketed with 37˚C distilled for 1 hour.

value: Uninfected control

tag: days post infection


title: AML_test_A79


title: AML_test_A80


title: CTRL Infected 14 DPI small RNA Rep 2

description:
small RNA
smallGLM.xlsx
miRNACounts.csv


title: AML_test_A75


title: AML_test_A78


title: CTRL Infected 14 DPI small RNA Rep 1

description:
small RNA
smallGLM.xlsx
miRNACounts.csv


title: AML_test_A81


title: AML_test_A77


title: AML_test_A76


title: CTRL Infected 2 DPI small RNA Rep 2

description:
small RNA
smallGLM.xlsx
miRNACounts.csv


title: CTRL Infected 7 DPI small RNA Rep 2

description:
small RNA
smallGLM.xlsx
miRNACounts.csv


title: CTRL Infected 2 DPI small RNA Rep 3

description:
small RNA
smallGLM.xlsx
miRNACounts.csv


title: AML_test_A74


title: AML_test_A89


title: AML_test_A73


title: MAYV Infected 14 DPI small RNA Rep 2

description:
small RNA
smallGLM.xlsx
miRNACounts.csv

value: MAYV infected


title: AML_test_A72


title: CTRL Infected 2 DPI small RNA Rep 1

description:
small RNA
smallGLM.xlsx
miRNACounts.csv


title: MAYV Infected 14 DPI small RNA Rep 3

description:
small RNA
smallGLM.xlsx
miRNACounts.csv


title: AML_test_A71


title: AML_test_A82


title: AML_test_A70


title: MAYV Infected 7 DPI small RNA Rep 3

description:
small RNA
smallGLM.xlsx
miRNACounts.csv


title: CTRL Infected 7 DPI small RNA Rep 3

description:
small RNA
smallGLM.xlsx
miRNACounts.csv


title: MAYV Infected 14 DPI small RNA Rep 1

description:
small RNA
smallGLM.xlsx
miRNACounts.csv


title: AML_test_A68


title: CTRL Infected 7 DPI small RNA Rep 1

description:
small RNA
smallGLM.xlsx
miRNACounts.csv


title: MAYV Infected 7 DPI small RNA Rep 2

description:
small RNA
smallGLM.xlsx
miRNACounts.csv


title: MAYV Infected 7 DPI small RNA Rep 1

description:
small RNA
smallGLM.xlsx
miRNACounts.csv


title: MAYV Infected 2 DPI small RNA Rep 3

description:
small RNA
smallGLM.xlsx
miRNACounts.csv


title: AML_test_A66


title: MAYV Infected 2 DPI small RNA Rep 1

description:
small RNA
smallGLM.xlsx
miRNACounts.csv


title: AML_test_A69


title: CTRL Infected 14 DPI mRNA Rep 3

description:
C_D14_Rep_3
GLM.xlsx
readCounts.csv

data_processing:
Adapter trimming and low quality bases removed with Trimmomatic using base settings
Align reads to genome using STAR RNA sequencing aligner
Filter reads less than 75 bp and mapping quality less than 20 from further analysis
Read counts calculated using rSubread package in R
Differential expression was conducted using a negative binomial GLM with the EdgeR package in R
Genome_build: ASM30077v2
Supplementary_files_format_and_content: Contains either read counts mapping to each gene ID in the ASM30077v2 (.csv) or differential expression results for each gene ID in all considered contrasts in the GLM (.xlsx).


title: AML_test_A67


title: AML_test_A65


title: AML_test_A61


title: CTRL Infected 7 DPI mRNA Rep 3

description:
C_D7_Rep_3
GLM.xlsx
readCounts.csv


title: AML_test_A60


title: AML_test_A59


title: CTRL Infected 7 DPI mRNA Rep 2

description:
C_D7_Rep_2
GLM.xlsx
readCounts.csv


title: AML_test_A62


title: CTRL Infected 14 DPI mRNA Rep 2

description:
C_D14_Rep_2
GLM.xlsx
readCounts.csv


title: CTRL Infected 14 DPI mRNA Rep 1

description:
C_D14_Rep_1
GLM.xlsx
readCounts.csv


title: AML_test_A58


title: CTRL Infected 7 DPI mRNA Rep 1

description:
C_D7_Rep_1
GLM.xlsx
readCounts.csv


title: CTRL Infected 2 DPI mRNA Rep 3

description:
C_D2_Rep_3
GLM.xlsx
readCounts.csv


title: AML_test_A57


title: CTRL Infected 2 DPI mRNA Rep 2

description:
C_D2_Rep_2
GLM.xlsx
readCounts.csv


title: CTRL Infected 2 DPI mRNA Rep 1

description:
C_D2_Rep_1
GLM.xlsx
readCounts.csv


title: AML_test_A55


title: AML_test_A56


title: AML_test_A54


title: MAYV Infected 2 DPI small RNA Rep 2

description:
small RNA
smallGLM.xlsx
miRNACounts.csv


title: AML_test_A53


title: AML_test_A63


title: MAYV Infected 14 DPI mRNA Rep 1

description:
V_D14_Rep_1
GLM.xlsx
readCounts.csv


title: AML_test_A51


title: AML_test_A50


title: AML_test_A52


title: MAYV Infected 7 DPI mRNA Rep 1

description:
V_D7_Rep_1
GLM.xlsx
readCounts.csv


title: MAYV Infected 7 DPI mRNA Rep 3

description:
V_D7_Rep_3
GLM.xlsx
readCounts.csv


title: AML_test_A49


title: AML_test_A47


title: MAYV Infected 2 DPI mRNA Rep 3

description:
V_D2_Rep_3
GLM.xlsx
readCounts.csv


title: MAYV Infected 2 DPI mRNA Rep 1

description:
V_D2_Rep_1
GLM.xlsx
readCounts.csv


title: MR-1 high cdgmp strain rep5

city: Oxford

first: Chun Kiat

last: Ng

address: Parks Road

department: Engineering Science

institute: University of Oxford

data_processing:
Quality of the RNA samples was determined using the Quant-iT™ RiboGreen® RNA Assay Kit (Invitrogen) and Quant-iT™ PicoGreen® dsDNA Assay Kit (Invitrogen) on a Bioanalyzer RNA 6000 Nano Chip (Agilent).
The mRNA purification step was omitted and instead, 200 ng of total RNA was directly added to the elute-fragment-prime step.
The PCR amplification step, which selectively enriches for library fragments that have adapters ligated on both ends, was performed according to the manufacturer's recommendation but the number of amplification cycles was reduced to 12.
Library concentration was normalized to 2 nM and the concentration was validated by qPCR on a ViiA-7 real-time thermocycler (Applied Biosystems), using qPCR primers recommended in Illumina's qPCR protocol and Illumina's PhiX control library as a standard.
Supplementary_files_format_and_content: The Illumina reads were functionally assigned by mapping against the published genome of S. oneidensis MR-1 (Heidelberg, et al., 2002) using the CLC Genomics Workbench (CLC bio, Aarhus, Denmark) (Mortazavi, et al., 2008). RPKM.

organism: Shewanella oneidensis

source_name: bacteria

growth_protocol: S. oneidensis MR-1 WT and pYedQ2 cultures were grown in LB medium aerobically for 8 h at 30 °C with shaking at 200 rpm

extract_protocol:
This was followed by RNA isolation using the RNeasy mini Kit (Qiagen, Germany), with the DNA being depleted using RNase-free DNase set (Qiagen, Germany) according to the manufacturer’s instructions. The concentration of RNA in each samples was determined using Nanodrop 2000 spectrophotometer (Thermo Scientific, USA) and further confirmed using Qubit 2.0 Fluorometer (Life Technologies, Germany).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

value: high level of c-di-GMP


title: AML_test_A45


title: AML_test_A43


title: AML_test_A44


title: MAYV Infected 14 DPI mRNA Rep 2

description:
V_D14_Rep_2
GLM.xlsx
readCounts.csv


title: MR-1 high cdgmp strain rep4


title: MAYV Infected 14 DPI mRNA Rep 3

description:
V_D14_Rep_3
GLM.xlsx
readCounts.csv


title: AML_test_A42


title: AML_test_A41


title: MR-1 high cdgmp strain rep3


title: MR-1 high cdgmp strain rep2


title: MR-1 high cdgmp strain rep1


title: MAYV Infected 2 DPI mRNA Rep 2

description:
V_D2_Rep_2
GLM.xlsx
readCounts.csv


title: AML_test_A40


title: MR-1 wt rep6

value: normal level of c-di-GMP

value: wild type


title: AML_test_A48


title: AML_test_A46


title: MAYV Infected 7 DPI mRNA Rep 2

description:
V_D7_Rep_2
GLM.xlsx
readCounts.csv


title: AML_test_A38


title: MR-1 wt rep4


title: MR-1 wt rep3


title: MR-1 high cdgmp strain rep6


title: AML_test_A36


title: MR-1 wt rep2


title: AML_test_A35


title: MR-1 wt rep1


title: AML_test_A34


title: KO-rep3

city: Xiamen

first: Zhenkui

last: Li

state: Fujian

address: Xiangan south road

institute: Xiamen University

description: All gene expression.txt

data_processing:
Basecalls performed using Bcl2fastq (v2.17.1.14)
Short reads alignment tool Bowtie2 was used for mapping reads to ribosome RNA (rRNA) database. The rRNA mapped reads will be removed. The remaining reads were further used in assembly and analysis of transcriptome.
The rRNA removed reads of each sample were then mapped to reference genome by TopHat2 (version 2.0.3.12).
Genome_build: The reference genome sequences and gene model annotation files of P. yoelii were downloaded from PlasmoDB 36.
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Plasmodium yoelii yoelii

source_name: Female gametocytes

extract_protocol:
For gametocyte sorting, the gametocytes of the DFsc7 and DFsc7;Δap2-o3 strains were enriched by centrifugation (1,900×g for 10 min) on a 48% Nycodenz solution, and then applied for cell sorting using MoFlo Astrios EQS (Beckman Coulter). Female gametocytes were sorted out through the signal of mCherry. After sorting, the purity of cells was assessed by FACS analysis. Total RNA of parasites was extracted using TRIzol reagent (Invitrogen, #15596026).
After extraction of total RNA from purified female gametocytes, mRNA was isolated by Oligo(dT) beads and further enriched by removing rRNA using Ribo-ZeroTM Magnetic Kit (Epicentre, #MRZG126). The enriched mRNA was first fragmented using fragmentation buffer and then reverse transcribed to cDNA with random primers. Second-strand cDNA was synthesized by DNA polymerase I, RNase H, dNTP, and buffer. Then the cDNA fragments were purified with QiaQuick PCR extraction kit, end-repaired, poly(A) added, and ligated with Illumina sequencing adapters. The ligation products were size-selected by agarose gel electrophoresis, PCR amplified, and sequenced using Illumina HiSeqTM 2500 by Gene Denovo Biotechnology (Guangzhou, China).

value: Plasmodium yoelii yoelii 17XNL

tag: developmental stage

value: Female gametocytes


title: KO-rep1

description: All gene expression.txt


title: KO-rep2

description: All gene expression.txt


title: AML_test_A31

tag: tissue


title: WT-rep3

description: All gene expression.txt

value: wildtype


title: AML_test_A33


title: AML_test_A30


title: WT-rep2

description: All gene expression.txt


title: AML_test_A32


title: AML_test_A37


title: AML_test_A39


title: AML_test_A28


title: AML_test_A26


title: WT-rep1

description: All gene expression.txt


title: AML_test_A27


title: MR-1 wt rep5


title: AML_test_A64


title: HA-IP rep2

data_processing:
Basecalls performed using Bcl2fastq (v2.17.1.14)
pass filter data of fastq format were processed by Cutadapt (version 1.9.1) to obtain high quality clean data
The clean data were aligned with reference genome via software Bowtie
peak-calling:The mapping data (immunoprecipitated and input) were analyzed with the MACS2 (V2)
Genome_build: The reference genome sequences and gene model annotation files of P. yoelii were downloaded from PlasmoDB 36.
Supplementary_files_format_and_content: bigwig files

source_name: gametocytes

extract_protocol:
Mice infected with parasite were treated with sulfadiazine in drinking water for 24-32 hours to kill asexual stage parasites. Blood with high gametocytemia was collected from mouse orbital sinus into heparin tubes and depleted of leukocytes using NWF Filter (ZhiXing Bio, China). Gametocytes were immediately fixed with 1% of methanol-free formaldehyde (Pierce, #28906) at room temperature for 10 min with gentle shaking for crosslinking DNA-proteins. Fixed cells were subjected to lysis in 0.84% NH4Cl for 10 min on ice and then washed twice with gametocyte maintenance buffer (GMB, containing 137 mM sodium chloride, 4 mM potassium chloride, 1 mM calcium chloride, 20 mM HEPES, 20 mM Glucose, 4 mM sodium bicarbonate, 0.1% w/v bovine serum albumin, pH 7.25). The gametocytes were further enriched in a 60% Nycodenz gradient centrifugation and harvested for ChIP.ChIP assays were performed using SimpleChIP Plus Sonication Chromatin IP Kit (Cell Signaling Technology, #56383). The crosslinked cells were lysed and followed by chromatin-shearing using Covaris M220 focused ultrasonicator (Covaris, Inc) with the procedures: peak power 75W, 20% duty factor, 200 cycles per burst and total treatment time of 600 sec. The distribution and concentration of sheared chromatin were detected by agarose gel electrophoresis and Nanodrop 2000 (Thermo Fisher). 10 μg of chromatin was immunoprecipitated with anti-HA rabbit antibodies (Cell Signaling Technology, AB_1549585). As a control, the same amount of IgG antibody (Cell Signaling Technology, AB_1031062) was used. Immunoprecipitated chromatin collected with A+G magnetic beads was extensively washed and eluted with elution buffer. The input and ChIP samples were reverse cross-linked overnight at 65°C in the presence of Proteinase K (Thermo Fisher, #AM2546) and purified using the QIAquick Gel Extraction Kit (QIAGEN, #28704).
ChIP samples were quantified using a Qubit 2.0 Fluorometer (Invitrogen, USA) and qualified by Agilent Bioanalyzer 2100 (Agilent Technologies, USA). For each sample, At least 5 ng ChIP product was used for library preparation using VAHTS Universal Pro DNA Library Prep Kit (Vazyme, #ND-608). The ChIP product was treated with End Prep Enzyme Mix for end repairing, 5’ Phosphorylation, and dA-tailing in one reaction, followed by ligation to adaptors with a “T” base overhang. Adaptor-ligated DNA was recovered using AxyPrep Mag PCR Clean-up (Axygen, #MAG-PCR-CL-50) and amplified by PCR for 10 cycles using P5 and P7 primers, with both primers carrying sequences which can anneal with flowcell to perform bridge PCR and P7 primer carrying a six-base index allowing for multiplexing. PCR products were cleaned using AxyPrep Mag PCR Clean-up, validated using an Agilent 2100 Bioanalyzer, and quantified by Qubit 2.0 Fluorometer.

tag: chip antibody

value: HA-Tag (C29F4) Rabbit mAb #3724


title: Input rep2


title: Input rep1


title: HA-IP rep1


title: AML_test_A24


title: ER-/PR- [320039]

city: Dijon

first: Romain

last: Boidot

address: 1, rue Pr Marion

country: France

institute: CGFL

data_processing:
The abundance of transcripts from RNA seq data was quantified through the Kallisto program. This program is based on pseudo alignment for rapidly determining the compatibility of reads with targets, without the need for alignment. The Kallisto transcript index used as reference was built from merged human cDNA and ncDNA files from GRCh37 assembly ENSEMBL. Gene level count matrices were then created with the DESeq2 library. Low count genes were pre filtered by removing genes with too few reads.
Genome_build: hg19
Supplementary_files_format_and_content: excel file

source_name: Breast cancer

extract_protocol:
Total RNA was extracted from slices obatined from FFPE tumors by using the Maxwell 16 LEV RNA FFPE Purification kit (Pomega) following manufacturer's protocol.
Libraries were prepared with the TruSeq RNA library prep kit according to the manufacturer's instructions (Illumina). Briefly, RNA was heat fragmented and double strand cDNA synthesis was performed in 2 steps. After purification, the double strand cDNA was end repaired and then adenylated. After adapter ligation, DNA was PCR amplified for 12 cycles and library fragments of ~300 bp (insert plus adaptor and PCR primer sequences) were obtained. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on a NextSeq500 device following the manufacturer's protocols with paired-end 76-base pair reads.

tag: group

value: ER-/PR-


title: AML_test_A25


title: AML_test_A22


title: AML_test_A23


title: AML_test_A21


title: ER-/PR- [47222]


title: AML_test_A29


title: ER-/PR- [11397]


title: AML_test_A20


title: AML_test_A19


title: scRNAseq Late Lung (LL) DCCs

city: New York

first: Julio

last: Aguirre-Ghiso

address: 1468 Madison Avenue, A24-64e

institute: Icahn School of Medicine at Mount Sinai

data_processing:
Single-cell datasets were clustered using an unsupervised clustering algorithm previously described (Martin et al., 2019). In this EM-like algorithm, parameters for multinomial cell-type specific gene-expression models are learned together with a parameter for the fraction of background noise that is associated with cells in each sample
Mitochondrial genes, Malat1 were excluded from the clustering process.
The clustering parameters were chosen to accommodate the different UMI and cell counts between the experiments. The minimum number of UMI per cell was 800, k was set to 20, and (P1,P2) =(0th,20th) percentiles.
Genome_build: mm10
Supplementary_files_format_and_content: tsv and mtx files with barcodes, genes and matrix per sample

growth_protocol: MMTV-HER2/Neu mice were maintained on FvB background and bred and crossed in our facilities. All experimental procedures were approved by the Institutional Animal Care and Use Committee (IACUC) of Icahn School of Medicine at Mount Sinai.

extract_protocol:
Lungs from ‘early’ and ‘late stage’ mice (eL and LL) were dissected and digested. Cancer cells (CD45- HER2+) and non-cancer lung cells (CD45-HER2-) were sorted. Cells were encapsulated using the 10X Chromium 3’ v3 and chemistry kit according to manufacturer instructions.
Sequencing, libraries were prepared according to manufacturer instructions. QC of cDNA and final libraries was performed by CyberGreen qPCR library quantification assay (KAPA). Samples were sequenced on an Illumina Nextseq 550 using the 75-cycle kit to a depth of 100 million reads per library.

value: FvB

tag: tumor stage

value: With primary tumor(s)

value: lungs

tag: cell tyoe

value: breast cancer cells


title: AML_test_A17

value: acute myeloid leukemia

value: whole blood


title: scRNAseq Non-cancer lung cells

value: No palpable tumor

value: non-cancer lung cells


title: ER-/PR- [6368]


title: ER-/PR+ [6252]

value: ER-/PR+


title: AML_test_A14

value: female


title: scRNAseq Early Lung (eL) DCCs


title: AML_test_A18

value: male


title: AML_test_A16


title: AML_test_A13


title: ER-/PR- [5963]


title: AML_test_A11


title: AML_test_A15


title: Late Lung (LL) DCCs

data_processing:
Single-cell datasets were clustered using an unsupervised clustering algorithm previously described (Martin et al., 2019). In this EM-like algorithm, parameters for multinomial cell-type specific gene-expression models are learned together with a parameter for the fraction of background noise that is associated with cells in each sample.
Mitochondrial genes, Malat1 were excluded from the clustering process.
The clustering parameters were chosen to accommodate the different UMI and cell counts between the experiments. The minimum number of UMIs per cell was 300, the number of clusters k was 12, and (P1,P2) =(30th,60th) percentiles.
Genome_build: mm10
Supplementary_files_format_and_content: tsv and mtx files with barcodes, genes and matrix per sample

extract_protocol:
Mammary glands of ‘early stage’ mice (EL), primary tumors from ‘late stage’ mice (PT) and lungs from ‘early’ and ‘late stage’ mice (eL and LL) were dissected and digested. After sorting, cancer cells (CD45- HER2+) were encapsulated using the 10X Chromium 3’ v2 and chemistry kit according to manufacturer instructions.
Sequencing, libraries were prepared according to manufacturer instructions. QC of cDNA and final libraries was performed by CyberGreen qPCR library quantification assay (KAPA). Samples were sequenced on an Illumina Nextseq 550 using the 75-cycle kit to a depth of 100 million reads per library.


title: Primary tumor (PT) cells

value: breast tumor


title: Early lesion (EL) cells

value: mammary gland


title: AML_test_A10


title: AML_test_A9


title: AML_test_A8


title: AML_test_A7


title: ER-/PR- [5795]


title: ER-/PR- [5541]


title: Early Lung (eL) DCCs


title: RAW_shSMRT_pro_bait_rp2

city: Nanjing

first: Zhiqiang

last: Huang

state: Jiangsu

address: Hankou 22

department: Medical School

institute: Nanjing University

description:
genomic DNA (bait PCR)
4C-seq_Sample

data_processing:
Library strategy: 4C-seq
ChIP-seq raw files (fastq or txt files, single-end) were aligned to the NCBI37/mm9 version of the mouse reference genome, using Bowtie2 with default parameters. HOMER were then used for the tag directories construction from SAM files, duplicated reads removal, peak calling, peaks annotation, raw tag counts extraction and Bed file generation. Only peaks with fold enrichment over input tag count and local tag count > 4 and fdr< 0.001 (default -F -L -C -fdr) are kept.
Genome_build: mm9
Supplementary_files_format_and_content: Bedgraph files contain the genomic coordinates and p value of each peak.
ChIP-seq raw files (fastq, paired-end) were aligned to the NCBI37/mm9 version of the mouse reference genome, using Bowtie2 with default parameters. HOMER were then used for the tag directories construction from SAM files, duplicated reads removal, peak calling, peaks annotation, raw tag counts extraction and Bed file generation. Only peaks with fold enrichment over input tag count and local tag count > 4 and fdr< 0.001 (default -F -L -C -fdr) are kept.
Genome_build: mm9
Supplementary_files_format_and_content: Bedgraph files contain the genomic coordinates and p value of each peak.
GRO-seq raw files (fastq, single-end) were aligned to the NCBI37/mm9 version of the mouse reference genome, using bwa with default parameters. HOMER were then used for the tag directories construction from SAM files, duplicated reads removal, peak calling, peaks annotation, raw tag counts extraction and Bed file generation. Only peaks with fold enrichment over input tag count and local tag count > 4 and fdr< 0.001 (default -F -L -C -fdr) are kept.
Genome_build: mm9
Supplementary_files_format_and_content: Bedgraph files contain the genomic coordinates and p value of each peak.
4C-seq raw files (fastq, paired-end) were performed by the standard 4Cseqpipe protocol. The primer sequences were trimmed from the raw reads. The trimmed reads were mapped to the mm9 reference fragmented genome. The contact intensity was normalized by the fragment counts. The cis-interacting DNA contact profiles around the baits were plotted in the same chromosome window.
Genome_build: mm9
Supplementary_files_format_and_content: 4C-seq analysis does not provide processed data file.
RNA-seq raw files (fastq, single-end) were aligned to the NCBI37/mm9 version of the mouse reference genome, using HISAT2 with default parameters. Read counts were imported by HOMER and analyzed using analyzeRepeats with the option rna and parameters -noadj -condenseGenes and -count exons for four replicates per condition.  Differential gene expression was performed with DESeq2 using HOMER’s getDiffExpression.pl using default parameter. Transcripts with an adjusted p-value < 0.05 were considered as differentially expressed genes.
Genome_build: mm9
Supplementary_files_format_and_content: Bedgraph files contain the tags for each condense gene
ATAC-seq raw files (fastq, paired-end) were aligned to the NCBI37/mm9 version of the mouse reference genome, using Bowtie2 with default parameters. MACS2 was used for the peak calling. The differential changed peaks was done in R using edgeR.
Genome_build: mm9
Supplementary_files_format_and_content: Bedgraph files contain the genomic coordinates and p value of each peak.

source_name: RAW264.7 cells

growth_protocol: RAW264.7 cells were maintained normal 10% FBS DMEM medium

extract_protocol:
WT or LNA control cells, CRISPR KO cells , Ccl2 E1 eRNA knockdown cells and GPS2/SMRT knockdown cells  were re-suspended with 10 ml lysis buffer containing 50 mM Tris-HCl, 150 mM NaCl, 5 mM EDTA, 0.5% NP-40, 1% TX-100, for 10 minutes. Nuclei were re-suspended into 440 l Milli-Q water and 60 l of digestion buffer (15 l 10% SDS and 75 l 20% Triton X-100) was added. The cell lysis mixture was then incubated at 37 C for 2 hours in the shaker (900 RPM). 200U DpnII (NEB, R0543M) was added into the mixture three times. The lysis mixture was then incubated in the shaker overnight. The reaction mix was inactivated after overnight digestion by incubating at 65C for 20 min. The samples were then transferred to 50 ml Falcon tubes with 700 l ligation buffer and 5.5 ml Milli-Q water. The samples were then supplemented with 100 U T4 ligase (NEB, M0202M) and incubated overnight at room temperature.  After that, samples were de-crosslinked at 65C for 12 hours. The ligated DNA was then purified by phenol-chloroform method, and further digested with NlaIII (NEB, R0125L) at 37 C overnight. The restriction enzyme was then inactivated for 20 min at 65 C. The DNA was further ligated at room temperature overnight. After the second ligation, the DNA was purified by QIAquick PCR purification kit
PCR purified DNA (by baits) was processed using Takara SMRTer ThruPLEX DNA-seq Kit. Briefly, DNA was end-repaired and ligated to stem-loop adaptors. Then DNA was PCR amplified with Illumina-compatible primers for 7-11 cycles and library fragments of 200 to 400 bp were selected using Ampure XP beads.

treatment_protocol: RAW264.7 cells were treated with/without LPS (2 hours)

tag: cell type

value: Macrophage

value: BALB/c

tag: agent

value: No treatment


title: AML_test_A12


title: AML_test_A6


title: RAW_shSMRT_pro_bait_rp1

description:
genomic DNA (bait PCR)
4C-seq_Sample


title: ER-/PR- [5459]

value: ER-/PR-


title: AML_test_A5


title: RAW_shSMRT_e2_bait_rp2

description:
genomic DNA (bait PCR)
4C-seq_Sample


title: AML_test_A2


title: ER-/PR- [5828]


title: AML_test_A4


title: ER-/PR- [5429]


title: AML_test_A1


title: AML_test_A3


title: RAW_shSMRT_e2_bait_rp1

description:
genomic DNA (bait PCR)
4C-seq_Sample


title: HealthyDonor11

value: healthy donor


title: RAW_shSMRT_e1_bait_rp1

description:
genomic DNA (bait PCR)
4C-seq_Sample


title: RAW_shSMRT_e1_bait_rp2

description:
genomic DNA (bait PCR)
4C-seq_Sample


title: ER-/PR+ [5240]


title: HealthyDonor5


title: HealthyDonor10


title: HealthyDonor9


title: HealthyDonor8


title: HealthyDonor4


title: RAW_shGPS2_pro_bait_rp1

description:
genomic DNA (bait PCR)
4C-seq_Sample


title: ER-/PR+ [5074]


title: HealthyDonor3


title: HealthyDonor6


title: ER-/PR- [4982]


title: HealthyDonor2


title: ER-/PR+ [4955]


title: ER-/PR- [5045]


title: ER+/PR+ [4923]

value: ER+/PR+


title: RAW_shGPS2_e2_bait_rp1

description:
genomic DNA (bait PCR)
4C-seq_Sample


title: RAW_shGPS2_e1_bait_rp2

description:
genomic DNA (bait PCR)
4C-seq_Sample


title: RAW_shGPS2_e1_bait_rp1

description:
genomic DNA (bait PCR)
4C-seq_Sample


title: ER-/PR+ [5272]


title: RAW_shGPS2_pro_bait_rp2

description:
genomic DNA (bait PCR)
4C-seq_Sample


title: ER-/PR+ [4828]


title: HealthyDonor7


title: RAW_shGFP_pro_bait_rp2

description:
genomic DNA (bait PCR)
4C-seq_Sample


title: RAW_shGPS2_e2_bait_rp2

description:
genomic DNA (bait PCR)
4C-seq_Sample


title: RAW_shGFP_pro_bait_rp1

description:
genomic DNA (bait PCR)
4C-seq_Sample


title: RAW_shGFP_e2_bait_rp2

description:
genomic DNA (bait PCR)
4C-seq_Sample


title: HealthyDonor1


title: ER-/PR- [4427]


title: ER+/PR+ [4450]


title: RAW_shGFP_e2_bait_rp1

description:
genomic DNA (bait PCR)
4C-seq_Sample


title: ER-/PR+ [4911]


title: RAW_shGFP_e1_bait_rp2

description:
genomic DNA (bait PCR)
4C-seq_Sample


title: ER-/PR+ [4412]


title: 3998675101_E

city: London

first: Long

last: Hoang

address: Dovehouse Street

department: Genomic Medicine

institute: Imperial College London

description:
RNA was isolated using 1.5 ml whole blood and the MagMAX-96 Blood RNA Isolation Kit (Applied Biosystems/Ambion)
3998675101_E

hyb_protocol: For each sample, seven hundred and fifty nanograms of labelled cRNA were hybridised overnight to Illumina Human HT12 V4 BeadChip arrays (Illumina), which contained greater than 47,000 probes. The arrays were washed, blocked, stained and scanned on an Illumina iScan, as per the manufacturer’s instructions.

scan_protocol: The arrays were scanned on an Illumina iScan, as per the manufacturer’s instructions.

data_processing: GenomeStudio (Illumina) was used to perform quality control and generate signal intensity values.

label: Biotin

source_name: Whole blood

extract_protocol: RNA was isolated using 1.5 ml whole blood and the MagMAX-96 Blood RNA Isolation Kit (Applied Biosystems/Ambion), as per the manufacturer’s instructions. 250 g of isolated total RNA was globin-reduced using the GLOBINclear 96-well format kit (Applied Biosystems/Ambion) according to the manufacturer’s instructions. Total and globin-reduced RNA integrity was assessed using an Agilent 2100 Bioanalyzer (Agilent Technologies). RNA yield was assessed using a NanoDrop8000 spectrophotometer (NanoDrop Products, Thermo Fisher Scientific). High-quality (>6.5 RIN) whole blood RNA was successfully obtained and processed by microarray in all cases. Biotinylated, amplified antisense complementary RNA (cRNA) targets were prepared from 200-250 ng of globin-reduced RNA using the Illumina CustomPrep RNA amplification kit (Applied Biosystems/Ambion).

tag: title

tag: sampledate at t0

tag: dosanjh

tag: diagnosis

value: Chest Infection

tag: eptborptb

value: OD

tag: smear microscopy

value: FALSE

value: Male

tag: height (cm)

tag: weight (kg)

tag: bmi

value: Indian

tag: hiv positive

value: Clinical Features

tag: tst

tag: pcr

tag: qtf-git

value: POSITIVE

value: NEGATIVE


title: 3998675101_D

description:
RNA was isolated using 1.5 ml whole blood and the MagMAX-96 Blood RNA Isolation Kit (Applied Biosystems/Ambion)
3998675101_D

label_protocol: Biotinylated, amplified antisense complementary RNA (cRNA) targets were prepared from 200-250 ng of globin-reduced RNA using the Illumina CustomPrep RNA amplification kit (Applied Biosystems/Ambion).

value: Other

tag: culture result

value: Negative

tag: age

tag: gender

value: Female


title: ER-/PR+ [3992]

tag: group

value: ER-/PR+


title: 3998703001_L

description:
RNA was isolated using 1.5 ml whole blood and the MagMAX-96 Blood RNA Isolation Kit (Applied Biosystems/Ambion)
3998703001_L

tag: title

value: TRUE


title: 3998720100_A

description:
RNA was isolated using 1.5 ml whole blood and the MagMAX-96 Blood RNA Isolation Kit (Applied Biosystems/Ambion)
3998720100_A

tag: sampledate at t0

tag: site of infection

value: Brain

value: Black

value: OTHER

value: INDETERMINATE


title: ER-/PR+ [4516]


title: 3998734086_F

description:
RNA was isolated using 1.5 ml whole blood and the MagMAX-96 Blood RNA Isolation Kit (Applied Biosystems/Ambion)
3998734086_F

tag: dosanjh

tag: diagnosis


title: 3998703044_A

description:
RNA was isolated using 1.5 ml whole blood and the MagMAX-96 Blood RNA Isolation Kit (Applied Biosystems/Ambion)
3998703044_A

tag: eptborptb

tag: smear microscopy

value: Mixed


title: 3998734064_K

description:
RNA was isolated using 1.5 ml whole blood and the MagMAX-96 Blood RNA Isolation Kit (Applied Biosystems/Ambion)
3998734064_K

value: Other, Pneumonia

value: OD

value: Lung

tag: height (cm)

tag: weight (kg)

value: Clinical Features, OTHER

tag: tst result


title: 3998734069_G

description:
RNA was isolated using 1.5 ml whole blood and the MagMAX-96 Blood RNA Isolation Kit (Applied Biosystems/Ambion)
3998734069_G

value: Sarcoidosis

tag: bmi

tag: hiv positive

value: FALSE

value: Clinical Features

tag: tst


title: 3998675040_A

description:
RNA was isolated using 1.5 ml whole blood and the MagMAX-96 Blood RNA Isolation Kit (Applied Biosystems/Ambion)
3998675040_A

value: Other

value: Lymph node

tag: culture result

value: Male

value: Indian

value: Clinical Features, Imaging, OTHER

tag: pcr

tag: qtf-git

value: NEGATIVE


title: 3998734087_E

description:
RNA was isolated using 1.5 ml whole blood and the MagMAX-96 Blood RNA Isolation Kit (Applied Biosystems/Ambion)
3998734087_E

tag: age

tag: gender

value: Female

value: Black

value: POSITIVE


title: 3998675068_L

description:
RNA was isolated using 1.5 ml whole blood and the MagMAX-96 Blood RNA Isolation Kit (Applied Biosystems/Ambion)
3998675068_L

tag: title

tag: sampledate at t0

value: URTI

value: TRUE

value: Negative


title: 3998675040_L

description:
RNA was isolated using 1.5 ml whole blood and the MagMAX-96 Blood RNA Isolation Kit (Applied Biosystems/Ambion)
3998675040_L

tag: dosanjh

value: Pneumonia

value: OD

tag: site of infection

value: Lung


title: 3998675118_C

description:
RNA was isolated using 1.5 ml whole blood and the MagMAX-96 Blood RNA Isolation Kit (Applied Biosystems/Ambion)
3998675118_C

tag: diagnosis

tag: eptborptb

value: FALSE

value: OTHER


title: ER-/PR- [3803]

tag: group

value: ER-/PR-


title: ER+/PR+ [3775]

value: ER+/PR+


title: RAW_LNA_ctrl_LPS2h_pro_bait_rp1

description:
genomic DNA (bait PCR)
4C-seq_Sample

tag: cell type

value: Macrophage

tag: strain

value: BALB/c

tag: agent

value: LPS

tag: time point

value: 2 hours


title: 3998734086_B

description:
RNA was isolated using 1.5 ml whole blood and the MagMAX-96 Blood RNA Isolation Kit (Applied Biosystems/Ambion)
3998734086_B

value: Other

value: Intestine, OTHER

tag: smear microscopy

value: Female

tag: height (cm)

tag: weight (kg)

tag: bmi

value: Indian

tag: hiv positive

tag: tst

tag: tst result

value: NEGATIVE


title: 3998734063_L

description:
RNA was isolated using 1.5 ml whole blood and the MagMAX-96 Blood RNA Isolation Kit (Applied Biosystems/Ambion)
3998734063_L

tag: title

tag: sampledate at t0

value: URTI

value: TRUE

tag: culture result

value: Negative

tag: age

tag: gender

value: Male

value: Black

value: Clinical Features, Imaging, OTHER

tag: pcr

tag: qtf-git

value: POSITIVE


title: RAW_shGFP_e1_bait_rp1

description:
genomic DNA (bait PCR)
4C-seq_Sample

tag: cell type

tag: strain

value: No treatment


title: 3998675049_I

description:
RNA was isolated using 1.5 ml whole blood and the MagMAX-96 Blood RNA Isolation Kit (Applied Biosystems/Ambion)
3998675049_I

tag: dosanjh

tag: diagnosis

tag: eptborptb

value: OD

tag: site of infection

value: Lung

value: FALSE

value: OTHER

tag: pcr result


title: ER-/PR- [3890]

tag: group

value: ER-/PR-


title: RAW_LNA_ctrl_LPS2h_e2_bait_rp2

description:
genomic DNA (bait PCR)
4C-seq_Sample

value: Macrophage

value: BALB/c

tag: agent

value: LPS

tag: time point

value: 2 hours


title: RAW_LNA_ctrl_LPS2h_e2_bait_rp1

description:
genomic DNA (bait PCR)
4C-seq_Sample


title: 3998734102_J

description:
RNA was isolated using 1.5 ml whole blood and the MagMAX-96 Blood RNA Isolation Kit (Applied Biosystems/Ambion)
3998734102_J

tag: title

value: Other

tag: smear microscopy

value: Indeterminate

value: Female

tag: height (cm)

tag: weight (kg)

tag: bmi

value: Indian

tag: hiv positive

value: Clinical Features

tag: tst


title: 3998734087_A

description:
RNA was isolated using 1.5 ml whole blood and the MagMAX-96 Blood RNA Isolation Kit (Applied Biosystems/Ambion)
3998734087_A

tag: sampledate at t0

value: Other, Pneumonia

value: Bones, Lung

tag: age

tag: gender

value: Male

value: White

value: TRUE

tag: tst result

tag: pcr

tag: qtf-git

value: NEGATIVE


title: RAW_LNA_ctrl_LPS2h_pro_bait_rp2

description:
genomic DNA (bait PCR)
4C-seq_Sample

tag: cell type

tag: strain


title: ER-/PR- [3736]

tag: group


title: 3998734071_J

description:
RNA was isolated using 1.5 ml whole blood and the MagMAX-96 Blood RNA Isolation Kit (Applied Biosystems/Ambion)
3998734071_J

tag: dosanjh

tag: diagnosis

tag: eptborptb

value: OD

tag: site of infection

value: Lung, Spine

tag: culture result

value: Negative

value: Asian

value: FALSE

value: OTHER


title: ER-/PR- [3712]

value: ER-/PR-


title: RAW_LNA_ctrl_LPS2h_e1_bait_rp2

description:
genomic DNA (bait PCR)
4C-seq_Sample

value: Macrophage

value: BALB/c

tag: agent

value: LPS

tag: time point

value: 2 hours


title: RAW_LNA_ctrl_LPS2h_e1_bait_rp1

description:
genomic DNA (bait PCR)
4C-seq_Sample


title: ER-/PR- [3559]


title: ER-/PR+ [3364]

value: ER-/PR+


title: 3998734078_G

description:
RNA was isolated using 1.5 ml whole blood and the MagMAX-96 Blood RNA Isolation Kit (Applied Biosystems/Ambion)
3998734078_G

tag: title

value: LRTI

value: Lung

tag: smear microscopy

value: Female

tag: weight (kg)

value: Indian

tag: hiv positive

value: Clinical Features

tag: tst

value: INDETERMINATE


title: ER-/PR- [3345]


title: RAW_LNA_ctrl_con_pro_bait_rp2

description:
genomic DNA (bait PCR)
4C-seq_Sample

value: No treatment


title: 3998734071_F

description:
RNA was isolated using 1.5 ml whole blood and the MagMAX-96 Blood RNA Isolation Kit (Applied Biosystems/Ambion)
3998734071_F

tag: sampledate at t0

value: Other

value: OD

value: TRUE

value: Negative

tag: age

tag: gender

value: Male

value: Culture

tag: tst result

tag: pcr

value: NEGATIVE


title: 3998734071_L

description:
RNA was isolated using 1.5 ml whole blood and the MagMAX-96 Blood RNA Isolation Kit (Applied Biosystems/Ambion)
3998734071_L

tag: dosanjh

value: Other, Pneumonia

value: FALSE

value: Clinical Features, OTHER

tag: qtf-git


title: 3998734064_C

description:
RNA was isolated using 1.5 ml whole blood and the MagMAX-96 Blood RNA Isolation Kit (Applied Biosystems/Ambion)
3998734064_C

tag: diagnosis

tag: eptborptb

value: Spine

value: Black


title: 3998675114_C

description:
RNA was isolated using 1.5 ml whole blood and the MagMAX-96 Blood RNA Isolation Kit (Applied Biosystems/Ambion)
3998675114_C

tag: site of infection

value: Chest or Thorax

tag: culture result


title: RAW_LNA_ctrl_con_pro_bait_rp1

description:
genomic DNA (bait PCR)
4C-seq_Sample

tag: cell type

value: Macrophage

tag: strain

value: BALB/c

tag: agent


title: 3998675118_L

description:
RNA was isolated using 1.5 ml whole blood and the MagMAX-96 Blood RNA Isolation Kit (Applied Biosystems/Ambion)
3998675118_L

tag: title

value: Pneumonia

tag: smear microscopy

value: Female

tag: weight (kg)

value: White

value: Clinical Features, Imaging

value: MISSING


title: 200683670009_L

description:
RNA was isolated using 1.5 ml whole blood and the MagMAX-96 Blood RNA Isolation Kit (Applied Biosystems/Ambion)
200683670009_L

tag: sampledate at t0

value: Cancer

value: OD

value: Lung

value: TRUE

value: Negative

value: Indian

tag: hiv positive

value: Histology, Imaging

tag: tst

tag: pcr result


title: 3998720114_K

description:
RNA was isolated using 1.5 ml whole blood and the MagMAX-96 Blood RNA Isolation Kit (Applied Biosystems/Ambion)
3998720114_K

tag: age

tag: gender

value: FALSE

value: Clinical Features, Imaging, OTHER

tag: tst result

tag: pcr

value: NEGATIVE


title: 3998675081_G

description:
RNA was isolated using 1.5 ml whole blood and the MagMAX-96 Blood RNA Isolation Kit (Applied Biosystems/Ambion)
3998675081_G

tag: dosanjh

tag: diagnosis

tag: eptborptb

tag: qtf-git


title: 3998675081_A

description:
RNA was isolated using 1.5 ml whole blood and the MagMAX-96 Blood RNA Isolation Kit (Applied Biosystems/Ambion)
3998675081_A

value: URTI

tag: site of infection

tag: culture result

value: Male

tag: height (cm)

tag: bmi

value: OTHER

value: POSITIVE


title: ER-/PR- [2650]

tag: group

value: ER-/PR-


title: ER-/PR+ [3109]

value: ER-/PR+


title: 3998675081_E

description:
RNA was isolated using 1.5 ml whole blood and the MagMAX-96 Blood RNA Isolation Kit (Applied Biosystems/Ambion)
3998675081_E

tag: title

tag: sampledate at t0

value: Other

value: Lymph node, Neck

tag: smear microscopy

value: Female

tag: weight (kg)

value: Clinical Features, OTHER


title: ER-/PR- [2534]


title: 3998720114_L

description:
RNA was isolated using 1.5 ml whole blood and the MagMAX-96 Blood RNA Isolation Kit (Applied Biosystems/Ambion)
3998720114_L

value: OD

value: Lung

value: TRUE

tag: age

tag: hiv positive

value: Imaging

tag: tst


title: RAW_LNA_ctrl_con_e2_bait_rp1

description:
genomic DNA (bait PCR)
4C-seq_Sample

tag: cell type

value: Macrophage

tag: strain

value: BALB/c

tag: agent

value: No treatment


title: RAW_LNA_ctrl_con_e2_bait_rp2

description:
genomic DNA (bait PCR)
4C-seq_Sample


title: 3998675081_C

description:
RNA was isolated using 1.5 ml whole blood and the MagMAX-96 Blood RNA Isolation Kit (Applied Biosystems/Ambion)
3998675081_C

tag: dosanjh

tag: diagnosis

value: Sarcoidosis

tag: eptborptb

value: Negative

tag: gender

value: Indian

value: FALSE

value: Clinical Features, Imaging

tag: tst result

tag: pcr

value: NEGATIVE


title: ER-/PR- [2439]

tag: group

value: ER-/PR-


title: 200683670009_C

description:
RNA was isolated using 1.5 ml whole blood and the MagMAX-96 Blood RNA Isolation Kit (Applied Biosystems/Ambion)
200683670009_C

tag: title

value: Other

value: Male

tag: qtf-git


title: 3998734071_A

description:
RNA was isolated using 1.5 ml whole blood and the MagMAX-96 Blood RNA Isolation Kit (Applied Biosystems/Ambion)
3998734071_A

tag: sampledate at t0

tag: site of infection

value: Hearth

tag: smear microscopy

tag: culture result

value: Female

value: Clinical Features


title: 3998720114_A

description:
RNA was isolated using 1.5 ml whole blood and the MagMAX-96 Blood RNA Isolation Kit (Applied Biosystems/Ambion)
3998720114_A

value: LRTI

value: OD

value: Lung

value: TRUE

tag: age

tag: weight (kg)

tag: hiv positive

value: Clinical Features, Imaging, OTHER

tag: tst


title: RAW_LNA_ctrl_con_e1_bait_rp1

description:
genomic DNA (bait PCR)
4C-seq_Sample

tag: cell type

value: Macrophage

tag: strain

value: BALB/c

tag: agent

value: No treatment


title: RAW_Ccl2_LNA_LPS2h_pro_bait_rp2

description:
genomic DNA (bait PCR)
4C-seq_Sample

value: LPS

tag: time point

value: 2 hours


title: 3998720114_F

description:
RNA was isolated using 1.5 ml whole blood and the MagMAX-96 Blood RNA Isolation Kit (Applied Biosystems/Ambion)
3998720114_F

tag: dosanjh

tag: diagnosis

tag: eptborptb

value: Lymph node

value: Negative

tag: gender

value: Indian

value: FALSE

tag: tst result

value: NEGATIVE


title: RAW_Ccl2_LNA_LPS2h_pro_bait_rp1

description:
genomic DNA (bait PCR)
4C-seq_Sample


title: 3998720106_H

description:
RNA was isolated using 1.5 ml whole blood and the MagMAX-96 Blood RNA Isolation Kit (Applied Biosystems/Ambion)
3998720106_H

tag: title

tag: sampledate at t0

value: Other

value: Female

value: Imaging

tag: pcr

tag: qtf-git


title: 3998675091_K

description:
RNA was isolated using 1.5 ml whole blood and the MagMAX-96 Blood RNA Isolation Kit (Applied Biosystems/Ambion)
3998675091_K

value: LRTI, Other

value: OD

tag: smear microscopy

tag: culture result

tag: age

value: Male

value: Clinical Features


title: ER-/PR+ [2460]

tag: group

value: ER-/PR+


title: 3998720114_C

description:
RNA was isolated using 1.5 ml whole blood and the MagMAX-96 Blood RNA Isolation Kit (Applied Biosystems/Ambion)
3998720114_C

value: LRTI

value: TRUE

tag: weight (kg)

value: White

tag: hiv positive

tag: tst


title: 200681360009_E

description:
RNA was isolated using 1.5 ml whole blood and the MagMAX-96 Blood RNA Isolation Kit (Applied Biosystems/Ambion)
200681360009_E

value: Pneumonia

tag: site of infection

value: Lung

tag: pcr result

value: INDETERMINATE


title: ER-/PR+ [2207]


title: RAW_LNA_ctrl_con_e1_bait_rp2

description:
genomic DNA (bait PCR)
4C-seq_Sample

tag: cell type

value: Macrophage

tag: strain

value: BALB/c

tag: agent

value: No treatment


title: ER-/PR- [2177]

value: ER-/PR-


title: ER-/PR- [2206]


title: RAW_Ccl2_LNA_LPS2h_e2_bait_rp1

description:
genomic DNA (bait PCR)
4C-seq_Sample

value: LPS

tag: time point

value: 2 hours


title: RAW_Ccl2_LNA_LPS2h_e2_bait_rp2

description:
genomic DNA (bait PCR)
4C-seq_Sample


title: RAW_Ccl2_LNA_LPS2h_e1_bait_rp2

description:
genomic DNA (bait PCR)
4C-seq_Sample


title: 3998734087_H

description:
RNA was isolated using 1.5 ml whole blood and the MagMAX-96 Blood RNA Isolation Kit (Applied Biosystems/Ambion)
3998734087_H

tag: title

tag: dosanjh

tag: diagnosis

value: Sarcoidosis

tag: eptborptb

value: Negative

tag: gender

value: Female

value: Indian

value: FALSE

value: Histology

tag: tst result

value: NEGATIVE


title: 3998675092_A

description:
RNA was isolated using 1.5 ml whole blood and the MagMAX-96 Blood RNA Isolation Kit (Applied Biosystems/Ambion)
3998675092_A

tag: sampledate at t0

value: LTBI - treatment indicated, Pneumonia

value: OD

tag: smear microscopy

value: TRUE

tag: culture result

tag: age

value: OTHER

tag: pcr

tag: qtf-git


title: 200681360014_D

description:
RNA was isolated using 1.5 ml whole blood and the MagMAX-96 Blood RNA Isolation Kit (Applied Biosystems/Ambion)
200681360014_D

value: Other

value: Male

tag: weight (kg)

tag: hiv positive

tag: tst


title: 3998703013_G

description:
RNA was isolated using 1.5 ml whole blood and the MagMAX-96 Blood RNA Isolation Kit (Applied Biosystems/Ambion)
3998703013_G

value: Chest Infection

tag: site of infection

value: Lung

value: Imaging


title: 200681360014_I

description:
RNA was isolated using 1.5 ml whole blood and the MagMAX-96 Blood RNA Isolation Kit (Applied Biosystems/Ambion)
200681360014_I

value: Black

value: Culture


title: 3998703001_J

description:
RNA was isolated using 1.5 ml whole blood and the MagMAX-96 Blood RNA Isolation Kit (Applied Biosystems/Ambion)
3998703001_J

value: Negative

value: INDETERMINATE


title: 3998675092_F

description:
RNA was isolated using 1.5 ml whole blood and the MagMAX-96 Blood RNA Isolation Kit (Applied Biosystems/Ambion)
3998675092_F

value: Pneumonia

value: Female

value: Indian

value: POSITIVE


title: RAW_Ccl2_LNA_LPS2h_e1_bait_rp1

description:
genomic DNA (bait PCR)
4C-seq_Sample

tag: cell type

value: Macrophage

tag: strain

value: BALB/c

tag: agent

value: LPS

tag: time point

value: 2 hours


title: 3998703001_H

description:
RNA was isolated using 1.5 ml whole blood and the MagMAX-96 Blood RNA Isolation Kit (Applied Biosystems/Ambion)
3998703001_H

tag: title

tag: dosanjh

tag: diagnosis

value: Other

tag: eptborptb

value: OD

value: FALSE

value: Clinical Features, Imaging

value: TRUE


title: CRISPR_ProKO_LPS2h_Ccl2_pro_bait_rp1

description:
genomic DNA (bait PCR)
4C-seq_Sample


title: CRISPR_ProKO_LPS2h_Ccl2_e2_bait_rp2

description:
genomic DNA (bait PCR)
4C-seq_Sample


title: ER-/PR- [1736]

tag: group

value: ER-/PR-


title: ER-/PR+ [1786]

value: ER-/PR+


title: CRISPR_ProKO_LPS2h_Ccl2_pro_bait_rp2

description:
genomic DNA (bait PCR)
4C-seq_Sample


title: ER-/PR+ [1682]


title: ER-/PR+ [1669]


title: CRISPR_ProKO_LPS2h_Ccl2_e2_bait_rp1

description:
genomic DNA (bait PCR)
4C-seq_Sample


title: ER-/PR- [1989]


title: 3998675065_K

description:
RNA was isolated using 1.5 ml whole blood and the MagMAX-96 Blood RNA Isolation Kit (Applied Biosystems/Ambion)
3998675065_K

tag: sampledate at t0

value: Sarcoidosis

value: Lymph node

tag: smear microscopy

tag: culture result

value: Negative

tag: gender

value: Male

tag: height (cm)

tag: bmi

value: White

value: Histology

tag: tst result

tag: pcr result

value: NEGATIVE


title: 3998675029_H

description:
RNA was isolated using 1.5 ml whole blood and the MagMAX-96 Blood RNA Isolation Kit (Applied Biosystems/Ambion)
3998675029_H

value: Pneumonia

tag: age

value: Female

tag: weight (kg)

value: Indian

tag: hiv positive

value: Clinical Features, Culture

tag: tst

tag: pcr

tag: qtf-git


title: 3998675069_C

description:
RNA was isolated using 1.5 ml whole blood and the MagMAX-96 Blood RNA Isolation Kit (Applied Biosystems/Ambion)
3998675069_C

tag: title

tag: dosanjh

tag: diagnosis

value: Other

value: OD

tag: site of infection

value: Breast

value: Culture, Histology


title: 3998675043_E

description:
RNA was isolated using 1.5 ml whole blood and the MagMAX-96 Blood RNA Isolation Kit (Applied Biosystems/Ambion)
3998675043_E

tag: sampledate at t0

value: Chest Infection

tag: eptborptb

value: Lung

tag: smear microscopy

value: TRUE

value: FALSE


title: 3998675027_D

description:
RNA was isolated using 1.5 ml whole blood and the MagMAX-96 Blood RNA Isolation Kit (Applied Biosystems/Ambion)
3998675027_D

tag: gender

value: Clinical Features


title: 3998720107_L

description:
RNA was isolated using 1.5 ml whole blood and the MagMAX-96 Blood RNA Isolation Kit (Applied Biosystems/Ambion)
3998720107_L

value: Cancer

value: Axilla (left)

tag: culture result

value: Negative

value: Male

value: Clinical Features, Histology, Response to Treatment

value: POSITIVE


title: ER+/PR+ [1553]

tag: group

value: ER+/PR+


title: 3998720107_B

description:
RNA was isolated using 1.5 ml whole blood and the MagMAX-96 Blood RNA Isolation Kit (Applied Biosystems/Ambion)
3998720107_B

tag: height (cm)

value: Indian

value: Clinical Features, Culture

value: NEGATIVE


title: 3998675027_F

description:
RNA was isolated using 1.5 ml whole blood and the MagMAX-96 Blood RNA Isolation Kit (Applied Biosystems/Ambion)
3998675027_F

value: Other

value: OD

value: Breast

tag: age

value: Female

value: MiddleEast


title: 3998675029_C

description:
RNA was isolated using 1.5 ml whole blood and the MagMAX-96 Blood RNA Isolation Kit (Applied Biosystems/Ambion)
3998675029_C

value: Sarcoidosis

value: Lung

value: TRUE

tag: weight (kg)

value: Black

value: FALSE

value: Histology

tag: pcr result


title: 3998675092_I

description:
RNA was isolated using 1.5 ml whole blood and the MagMAX-96 Blood RNA Isolation Kit (Applied Biosystems/Ambion)
3998675092_I

value: OTHER

value: Negative

value: Male

tag: hiv positive

value: Clinical Features, OTHER

tag: tst

tag: tst result


title: CRISPR_ProKO_LPS2h_Ccl2_e1_bait_rp2

description:
genomic DNA (bait PCR)
4C-seq_Sample

tag: cell type

value: Macrophage

tag: strain

value: BALB/c

tag: agent

value: LPS

tag: time point

value: 2 hours


title: 3998720107_F

description:
RNA was isolated using 1.5 ml whole blood and the MagMAX-96 Blood RNA Isolation Kit (Applied Biosystems/Ambion)
3998720107_F

tag: title

tag: sampledate at t0

tag: dosanjh

tag: diagnosis

value: Other

value: OD

tag: site of infection

value: Culture

tag: pcr

tag: qtf-git

value: NEGATIVE


title: 3998675120_E

description:
RNA was isolated using 1.5 ml whole blood and the MagMAX-96 Blood RNA Isolation Kit (Applied Biosystems/Ambion)
3998675120_E

value: Pneumonia

tag: eptborptb

value: Lung

tag: smear microscopy

tag: culture result

tag: age

tag: gender

value: Indian

value: Clinical Features


title: ER-/PR+ [1551]

tag: group

value: ER-/PR+


title: ER-/PR- [1215]

value: ER-/PR-


title: 3998720112_A

description:
RNA was isolated using 1.5 ml whole blood and the MagMAX-96 Blood RNA Isolation Kit (Applied Biosystems/Ambion)
3998720112_A

value: TRUE

value: Negative

tag: height (cm)

tag: weight (kg)

tag: bmi

tag: hiv positive

value: FALSE

value: Histology

tag: tst


title: 3998675101_J

description:
RNA was isolated using 1.5 ml whole blood and the MagMAX-96 Blood RNA Isolation Kit (Applied Biosystems/Ambion)
3998675101_J

tag: title

tag: sampledate at t0

value: LRTI

value: Male

tag: tst result

value: INDETERMINATE


title: CRISPR_E2KO_LPS2h_Ccl2_e2_bait_rp3

description:
genomic DNA (bait PCR)
4C-seq_Sample

tag: cell type

value: Macrophage

tag: strain

value: BALB/c

tag: agent

value: LPS

tag: time point

value: 2 hours


title: 3998703044_I

description:
RNA was isolated using 1.5 ml whole blood and the MagMAX-96 Blood RNA Isolation Kit (Applied Biosystems/Ambion)
3998703044_I

tag: dosanjh

tag: diagnosis

value: Other

tag: eptborptb

value: OD

tag: smear microscopy

value: Female

value: Black

tag: pcr

tag: qtf-git

value: NEGATIVE


title: CRISPR_E2KO_LPS2h_Ccl2_e2_bait_rp2

description:
genomic DNA (bait PCR)
4C-seq_Sample


title: CRISPR_ProKO_LPS2h_Ccl2_e1_bait_rp1

description:
genomic DNA (bait PCR)
4C-seq_Sample


title: ER+/PR+ [1053]

tag: group

value: ER+/PR+


title: ER-/PR+ [1505]

value: ER-/PR+


title: CRISPR_E2KO_LPS2h_Ccl2_pro_bait_rp3

description:
genomic DNA (bait PCR)
4C-seq_Sample


title: ER-/PR+ [1271]


title: 3998703004_L

description:
RNA was isolated using 1.5 ml whole blood and the MagMAX-96 Blood RNA Isolation Kit (Applied Biosystems/Ambion)
3998703004_L

tag: age

tag: gender

value: White

value: OTHER

value: TRUE

value: POSITIVE


title: CRISPR_E2KO_LPS2h_Ccl2_pro_bait_rp2

description:
genomic DNA (bait PCR)
4C-seq_Sample


title: 3998675120_K

description:
RNA was isolated using 1.5 ml whole blood and the MagMAX-96 Blood RNA Isolation Kit (Applied Biosystems/Ambion)
3998675120_K

tag: site of infection

value: Kidneys

tag: culture result

value: negative

value: Male

tag: height (cm)

tag: weight (kg)

tag: bmi

tag: hiv positive

value: FALSE

value: Clinical Features

tag: tst


title: ER+/PR+ [1006]


title: ER-/PR+ [1225]


title: 3998675102_F

description:
RNA was isolated using 1.5 ml whole blood and the MagMAX-96 Blood RNA Isolation Kit (Applied Biosystems/Ambion)
3998675102_F

tag: title

tag: sampledate at t0

value: Negative

value: Indian

value: Clinical Features, Imaging