title: CRISPR_E2KO_LPS2h_Ccl2_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: ER-/PR+ [2358]

status: Public on Jan 26 2021

type: SRA

city: Dijon

first: Romain

last: Boidot

address: 1, rue Pr Marion

country: France

institute: CGFL

library_source: transcriptomic

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

molecule: total RNA

organism: Homo sapiens

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: 3998703022_B

type: RNA

city: London

first: Long

last: Hoang

address: Dovehouse Street

department: Genomic Medicine

country: United Kingdom

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)
3998703022_B

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: LTBI - treatment indicated

tag: eptborptb

value: OD

tag: smear microscopy

value: FALSE

tag: age

tag: gender

value: Male

tag: height (cm)

tag: weight (kg)

tag: bmi

value: Black

tag: hiv positive

value: Clinical Features, Imaging

tag: tst

value: TRUE

tag: tst result

tag: pcr

tag: qtf-git

value: POSITIVE

value: NEGATIVE


title: CRISPR_E2KO_LPS2h_Ccl2_e2_bait_rp1

city: Nanjing

first: Zhiqiang

last: Huang

state: Jiangsu

address: Hankou 22

department: Medical School

country: China

institute: Nanjing University

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

library_source: genomic

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.

molecule: genomic DNA

organism: Mus musculus

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

tag: strain

tag: agent

tag: time point


title: 3998675101_I

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

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).

tag: title

tag: sampledate at t0

tag: dosanjh

tag: diagnosis

value: Cancer

tag: site of infection

value: Brain, Lung

tag: culture result

value: Negative

value: Female

value: White

value: Histology, Imaging


title: 3998734084_F

description:
RNA was isolated using 1.5 ml whole blood and the MagMAX-96 Blood RNA Isolation Kit (Applied Biosystems/Ambion)
3998734084_F

value: Chest Infection

tag: eptborptb

tag: smear microscopy

tag: age

tag: gender

tag: height (cm)

tag: weight (kg)

value: Culture

value: INDETERMINATE


title: ER-/PR- [994]

tag: group

value: ER-/PR-


title: ER-/PR+ [900]

value: ER-/PR+


title: 3998675027_B

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

value: Other

value: OD

value: Lung

value: Male

tag: bmi

tag: hiv positive

value: FALSE

tag: tst

tag: tst result

tag: pcr

tag: qtf-git


title: CRISPR_E2KO_LPS2h_Ccl2_e1_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: CRISPR_E2KO_LPS2h_Ccl2_e1_bait_rp2

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


title: 3998675043_G

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

tag: title

tag: sampledate at t0

tag: dosanjh

tag: diagnosis

tag: eptborptb

value: TRUE

tag: culture result

value: Negative

value: Female

value: Indian

value: Clinical Features, Culture

value: NEGATIVE


title: ER-/PR+ [731]

tag: group


title: ER-/PR- [801]

value: ER-/PR-


title: ER-/PR- [788]


title: 3998734084_L

description:
RNA was isolated using 1.5 ml whole blood and the MagMAX-96 Blood RNA Isolation Kit (Applied Biosystems/Ambion)
3998734084_L

value: Pneumonia

tag: site of infection

tag: smear microscopy

tag: age

tag: gender

tag: weight (kg)

value: Black

value: Clinical Features

value: INDETERMINATE


title: CRISPR_E1.2KO_LPS2h_Ccl2_pro_bait_rp3

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


title: CRISPR_E2KO_LPS2h_Ccl2_e1_bait_rp1

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


title: 3998703004_J

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

value: Other

value: OD

tag: hiv positive

tag: tst

tag: pcr

tag: qtf-git


title: 3998675029_L

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

value: URTI

tag: height (cm)

tag: bmi

value: White

value: FALSE

tag: tst result

value: POSITIVE


title: 3998675027_K

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

tag: title

tag: sampledate at t0

tag: dosanjh

value: Cancer

value: TRUE

value: Male


title: 3998675027_H

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

tag: diagnosis

tag: eptborptb

value: Lung

tag: culture result

value: Negative

value: Indian

value: OTHER


title: ER+/PR+ [677]

tag: group

value: ER+/PR+


title: CRISPR_E1.2KO_LPS2h_Ccl2_pro_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: 3998675029_I

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

value: Other

value: OD

tag: smear microscopy

tag: age

tag: gender

tag: weight (kg)

tag: hiv positive

tag: tst

value: NEGATIVE


title: 3998675043_I

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

tag: title

value: White

value: FALSE

tag: pcr

tag: qtf-git


title: ER-/PR- [602]

value: ER-/PR-


title: 3998675043_K

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

tag: sampledate at t0

tag: dosanjh

tag: diagnosis

value: Cancer

value: TRUE

value: Female

value: Clinical Features, Imaging

tag: tst result


title: 3998734084_B

description:
RNA was isolated using 1.5 ml whole blood and the MagMAX-96 Blood RNA Isolation Kit (Applied Biosystems/Ambion)
3998734084_B

value: Sarcoidosis

tag: eptborptb

tag: culture result

value: Negative

value: Male

value: Indian

value: Culture

value: INDETERMINATE


title: 3998675029_E

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

value: Chest Infection

tag: height (cm)

tag: bmi

value: Clinical Features


title: CRISPR_E1.2KO_LPS2h_Ccl2_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: CRISPR_E1.2KO_LPS2h_Ccl2_e2_bait_rp2

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


title: CRISPR_E1.2KO_LPS2h_Ccl2_e2_bait_rp3

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


title: ER-/PR- [580]

tag: group

value: ER-/PR-


title: CRISPR_E1.2KO_LPS2h_Ccl2_e2_bait_rp1

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


title: 3998720079_E

description:
RNA was isolated using 1.5 ml whole blood and the MagMAX-96 Blood RNA Isolation Kit (Applied Biosystems/Ambion)
3998720079_E

value: LTBI - treatment indicated, URTI

value: OD

tag: smear microscopy

tag: age

tag: gender

tag: weight (kg)

value: Black

tag: hiv positive

value: FALSE

tag: tst

value: NEGATIVE


title: ER-/PR+ [559]

value: ER-/PR+


title: ER-/PR+ [673]


title: 3998720079_G

description:
RNA was isolated using 1.5 ml whole blood and the MagMAX-96 Blood RNA Isolation Kit (Applied Biosystems/Ambion)
3998720079_G

tag: title

tag: sampledate at t0

tag: dosanjh

tag: diagnosis

value: Other

tag: site of infection

value: Lymph node, Neck

value: TRUE

value: Negative

value: Male

tag: pcr

tag: qtf-git


title: 3998675068_F

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

value: Pneumonia

tag: eptborptb

value: Lung

tag: culture result

value: Indian

value: Culture

tag: tst result


title: 3998720079_F

description:
RNA was isolated using 1.5 ml whole blood and the MagMAX-96 Blood RNA Isolation Kit (Applied Biosystems/Ambion)
3998720079_F

value: Female

value: White

value: POSITIVE


title: 3998720105_I

description:
RNA was isolated using 1.5 ml whole blood and the MagMAX-96 Blood RNA Isolation Kit (Applied Biosystems/Ambion)
3998720105_I

value: Cancer

value: OD

value: Asian


title: CRISPR_E1.2KO_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: 3998675043_H

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

value: LTBI - treatment indicated, Other, URTI

tag: smear microscopy

value: TRUE

tag: age

tag: gender

tag: weight (kg)

value: FALSE

value: Clinical Features, OTHER

tag: pcr result


title: CRISPR_E1.2KO_LPS2h_Ccl2_e1_bait_rp1

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


title: 3998703044_J

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

tag: title

tag: sampledate at t0

tag: dosanjh

value: Pneumonia

value: Lung

value: Negative

value: Male

tag: hiv positive

value: Culture, Imaging

tag: tst

value: NEGATIVE


title: 3998675040_J

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

tag: diagnosis

value: Other

tag: eptborptb

tag: site of infection

value: Intestine, Peritoneum

value: Female

value: White

value: Clinical Features

tag: pcr

tag: qtf-git

value: POSITIVE


title: 3998703004_K

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

value: Cancer

value: OD

tag: culture result

tag: tst result

value: INDETERMINATE


title: 3998720106_G

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

value: Chest Infection, LTBI - treatment indicated

tag: smear microscopy

value: TRUE

value: Indian

value: FALSE


title: 3998703004_G

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

value: Spine

tag: age


title: ER-/PR- [525]

tag: group

value: ER-/PR-


title: 3998675069_K

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

value: Lung

value: Negative

tag: gender

value: Male

tag: weight (kg)


title: 3998675081_D

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

tag: title

value: Pneumonia

value: NEGATIVE


title: ER-/PR+ [504]

value: ER-/PR+


title: CRISPR_Con_LPS2h_Ccl2_pro_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: ER-/PR+ [546]


title: ER+/PR+ [496]

value: ER+/PR+


title: 3998720106_A

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

tag: sampledate at t0

tag: dosanjh

tag: diagnosis

value: Sarcoidosis

value: OD

value: Lung, Miliary TB (disseminated)

tag: hiv positive

value: Clinical Features

tag: tst


title: CRISPR_Con_LPS2h_Ccl2_pro_bait_rp2

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


title: ER+/PR+ [471]


title: CRISPR_Con_LPS2h_Ccl2_pro_bait_rp1

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


title: 3998734078_D

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

value: Other

tag: eptborptb

value: TRUE

tag: culture result

value: Indian

value: FALSE

tag: pcr

tag: qtf-git


title: CRISPR_Con_LPS2h_Ccl2_e2_bait_rp3

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


title: 3998720105_D

description:
RNA was isolated using 1.5 ml whole blood and the MagMAX-96 Blood RNA Isolation Kit (Applied Biosystems/Ambion)
3998720105_D

value: LRTI

tag: site of infection

value: Lung

tag: smear microscopy

tag: age

value: Male

tag: height (cm)

tag: bmi

value: OTHER

tag: tst result

value: POSITIVE


title: 3998675070_F

description:
RNA was isolated using 1.5 ml whole blood and the MagMAX-96 Blood RNA Isolation Kit (Applied Biosystems/Ambion)
3998675070_F

tag: title

value: Negative

tag: gender

value: Female

tag: weight (kg)

value: NEGATIVE


title: 3998675112_G

description:
RNA was isolated using 1.5 ml whole blood and the MagMAX-96 Blood RNA Isolation Kit (Applied Biosystems/Ambion)
3998675112_G

tag: sampledate at t0

tag: dosanjh

value: Lymph node

value: Response to Treatment


title: 3998720106_B

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

tag: diagnosis

value: Sarcoidosis

value: OD

tag: hiv positive

value: INDETERMINATE


title: ER+/PR+ [14]

tag: group

value: ER+/PR+


title: 3998703010_C

description:
RNA was isolated using 1.5 ml whole blood and the MagMAX-96 Blood RNA Isolation Kit (Applied Biosystems/Ambion)
3998703010_C

tag: eptborptb

value: TRUE

tag: culture result

value: Clinical Features

tag: tst

tag: pcr result


title: CRISPR_Con_LPS2h_Ccl2_e2_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_C

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

value: Other

tag: smear microscopy

tag: age

value: Male

tag: height (cm)

tag: bmi

value: Indian

value: FALSE

tag: pcr

tag: qtf-git


title: 3998703010_F

description:
RNA was isolated using 1.5 ml whole blood and the MagMAX-96 Blood RNA Isolation Kit (Applied Biosystems/Ambion)
3998703010_F

tag: title

tag: sampledate at t0

tag: dosanjh

tag: diagnosis

value: Negative

tag: gender

tag: weight (kg)

value: Asian

value: POSITIVE


title: 3998734069_L

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

tag: eptborptb

tag: site of infection

value: Pleura

value: Female

tag: hiv positive

tag: tst

tag: tst result

value: NEGATIVE


title: ER+/PR+ [13]

tag: group

value: ER+/PR+


title: 3998734086_I

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

value: Cancer, LTBI - treatment indicated

value: OD

tag: smear microscopy

value: TRUE

tag: culture result

tag: age


title: 3998675112_F

description:
RNA was isolated using 1.5 ml whole blood and the MagMAX-96 Blood RNA Isolation Kit (Applied Biosystems/Ambion)
3998675112_F

value: Cancer

value: Breast

value: Histology

tag: pcr


title: 3998675112_E

description:
RNA was isolated using 1.5 ml whole blood and the MagMAX-96 Blood RNA Isolation Kit (Applied Biosystems/Ambion)
3998675112_E

value: LTBI - treatment indicated

value: Clinical Features

tag: pcr result

tag: qtf-git


title: CRISPR_Con_LPS2h_Ccl2_e1_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: ER-/PR+ [380]

value: ER-/PR+


title: 3998675093_A

description:
RNA was isolated using 1.5 ml whole blood and the MagMAX-96 Blood RNA Isolation Kit (Applied Biosystems/Ambion)
3998675093_A

tag: title

tag: sampledate at t0

tag: dosanjh

tag: diagnosis

value: Other

value: Ankle

value: Negative

tag: gender

tag: weight (kg)

value: Indian

value: FALSE

value: Culture, Histology


title: 3998675056_B

description:
RNA was isolated using 1.5 ml whole blood and the MagMAX-96 Blood RNA Isolation Kit (Applied Biosystems/Ambion)
3998675056_B

tag: eptborptb

value: OD

value: TRUE

value: Female

value: Black

tag: hiv positive

tag: tst

tag: tst result

value: NEGATIVE


title: ER-/PR- [304]

tag: group

value: ER-/PR-


title: 3998675074_D

description:
RNA was isolated using 1.5 ml whole blood and the MagMAX-96 Blood RNA Isolation Kit (Applied Biosystems/Ambion)
3998675074_D

tag: smear microscopy

tag: culture result

tag: age

value: Male

tag: height (cm)

tag: bmi

value: White

value: Clinical Features

tag: pcr

value: POSITIVE


title: CRISPR_Con_LPS2h_Ccl2_e2_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: CRISPR_Con_LPS2h_Ccl2_e1_bait_rp2

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


title: ER+/PR+ [12]

value: ER+/PR+


title: 3998720100_I

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

tag: title

tag: sampledate at t0

tag: dosanjh

tag: diagnosis

value: Pneumonia

tag: site of infection

value: Lung

value: Negative

tag: gender

value: Imaging, OTHER

value: FALSE

tag: qtf-git

value: INDETERMINATE


title: ER+/PR+ [10]

tag: group


title: CRISPR_Con_Ccl2_pro_bait_rp3

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

value: No treatment


title: 3998720112_C

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

value: LTBI - treatment indicated

tag: eptborptb

value: OD

tag: smear microscopy

value: TRUE

tag: culture result

tag: weight (kg)

value: Asian

tag: hiv positive

value: Culture, Smear Microscopy

tag: tst

tag: tst result


title: CRISPR_Con_LPS2h_Ccl2_e1_bait_rp1

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

tag: cell type

value: Macrophage

tag: strain

tag: agent


title: SFN_NRF2KO_MED1

city: Tianjin

first: Zhiheng

last: Liu

state: Tianjin

address: No.22 Qixiangtai Road

department: Tianjin Research Center for Basic Medical Science

institute: Tianjin Medical University

data_processing:
Bowtie2 (version 2.3.4.1) was used to align paired-end 150 bp sequence reads to human (hg38) genome
HOMER (version 4.10) findPeaks command was used to call peak
BamCoverage within deeptools (version 3.3.0) were used to generate bigwig files from bam files.
Genome_build: hg38
Supplementary_files_format_and_content: Bigwig

source_name: WT 9-12_Nrf2 knockout_Nrf2 activator sulforaphane (SFN)

growth_protocol: WT 9-12 cells were cultured in DMEM/F-12 medium supplemented with 10% FBS

extract_protocol:
Cells were cross-linked with 1% formaldehyde in 1 mL PBS for 10 min at RT. The crosslink was quenched by adding 67 μL of 2.5 M glycine(150 mM final). Cells were washed with PBS and harvested using ChIP lysis buffer. Cells were then sonicated to obtain fragments (200-500 bp) with Sonicator. Immunoprecipitation was performed with indicated antibodies. After elution and reversal cross-linking, DNA was purified for library preparation.
Library construction were performed using VAHTS Universal DNA Library Prep Kit (Vazyme, ND607-02) and VATHS DNA Adapters set2 for Illumina (Vazyme Biotech, Cat.N802-01)

tag: cell line background

value: immortalized epithelial cell line obtained from patients with ADPKD

tag: genotype/variation

value: Nrf2 knockout

tag: treatment

value: Nrf2 activator sulforaphane (SFN)

tag: chip antibody

value: Bethyl, A300-793A


title: 3998675096_J

description:
RNA was isolated using 1.5 ml whole blood and the MagMAX-96 Blood RNA Isolation Kit (Applied Biosystems/Ambion)
3998675096_J

tag: title

tag: sampledate at t0

tag: dosanjh

tag: diagnosis

value: Other

tag: site of infection

tag: age

tag: gender

value: Female

value: Mixed

value: Clinical Features, Culture

tag: pcr

value: NEGATIVE


title: CRISPR_Con_Ccl2_pro_bait_rp2

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

value: BALB/c


title: SFN_NRF2KO_K27ac

value: Abcam, ab4729


title: 3998720110_D

description:
RNA was isolated using 1.5 ml whole blood and the MagMAX-96 Blood RNA Isolation Kit (Applied Biosystems/Ambion)
3998720110_D

tag: eptborptb

tag: smear microscopy

tag: culture result

value: Negative

tag: height (cm)

tag: weight (kg)

tag: bmi

value: Black

tag: hiv positive

value: Culture

tag: tst

value: FALSE

tag: qtf-git

value: POSITIVE


title: 3998703016_G

description:
RNA was isolated using 1.5 ml whole blood and the MagMAX-96 Blood RNA Isolation Kit (Applied Biosystems/Ambion)
3998703016_G

tag: title

value: OD

value: OTHER

value: TRUE

value: White

value: Histology, Imaging, PCR

value: INDETERMINATE


title: 3998675091_G

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

tag: sampledate at t0

value: Other

value: Lung

value: Male

value: Indian

value: Clinical Features, Culture, Imaging


title: CRISPR_Con_Ccl2_pro_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: ER+/PR+ [11]

tag: group

value: ER+/PR+


title: 3998675091_I

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

tag: dosanjh

tag: diagnosis

tag: site of infection

value: Negative

tag: age

tag: gender

value: Female

value: FALSE

value: Histology, OTHER

value: NEGATIVE


title: SFN_MED1

source_name: WT 9-12_control_Nrf2 activator sulforaphane (SFN)

tag: cell line background

value: immortalized epithelial cell line obtained from patients with ADPKD

tag: genotype/variation

value: control

tag: treatment

value: Nrf2 activator sulforaphane (SFN)

tag: chip antibody

value: Bethyl, A300-793A


title: 3998675114_H

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

value: LTBI - treatment indicated, Other

tag: eptborptb

value: OD

value: Lung

tag: smear microscopy

tag: height (cm)

tag: weight (kg)

tag: bmi

tag: hiv positive

value: Clinical Features, OTHER

tag: tst

tag: pcr


title: DMSO_NRF2KO_MED1

source_name: WT 9-12_Nrf2 knockout_vehicle

tag: cell type

value: Nrf2 knockout

value: DMSO


title: 3998675118_A

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

tag: title

tag: sampledate at t0

tag: dosanjh

tag: diagnosis

value: Pneumonia, Sarcoidosis

value: Chest or Thorax

value: TRUE

tag: culture result

value: Male

value: Asian

value: Imaging, OTHER

tag: qtf-git


title: CRISPR_Con_Ccl2_e2_bait_rp3

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

value: Macrophage

tag: strain

value: BALB/c

tag: agent

value: No treatment


title: 3998675118_G

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

value: Other

tag: eptborptb

value: FALSE

value: Negative

tag: age

tag: gender

value: Indian

value: OTHER

value: INDETERMINATE

value: NEGATIVE


title: CRISPR_Con_Ccl2_e2_bait_rp2

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


title: 3998675096_K

description:
RNA was isolated using 1.5 ml whole blood and the MagMAX-96 Blood RNA Isolation Kit (Applied Biosystems/Ambion)
3998675096_K

value: OD

tag: site of infection

value: Eye (left)

tag: smear microscopy

tag: height (cm)

tag: weight (kg)

value: Culture

value: POSITIVE


title: 3998675118_I

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

value: LRTI

value: TRUE

value: Male

tag: bmi

tag: hiv positive

tag: tst

tag: pcr


title: CRISPR_E1.2KO_LPS2h_Ccl2_e1_bait_rp3

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

tag: cell type

value: Macrophage

value: LPS

tag: time point

value: 2 hours


title: 3998720112_E

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

tag: title

tag: sampledate at t0

tag: dosanjh

tag: diagnosis

value: Chest Infection

tag: culture result

value: Female

value: Asian


title: 3998675093_L

description:
RNA was isolated using 1.5 ml whole blood and the MagMAX-96 Blood RNA Isolation Kit (Applied Biosystems/Ambion)
3998675093_L

value: Other

tag: eptborptb

value: Negative

tag: age

value: White

value: FALSE

value: Clinical Features

tag: qtf-git


title: DMSO_NRF2KO_K27ac

tag: cell line background

value: immortalized epithelial cell line obtained from patients with ADPKD

tag: genotype/variation

value: Nrf2 knockout

tag: treatment

value: DMSO

tag: chip antibody

value: Abcam, ab4729


title: 3998675029_F

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

value: OD

tag: site of infection

value: Axilla

tag: smear microscopy

tag: gender

tag: height (cm)

tag: weight (kg)

tag: bmi

tag: hiv positive

value: Histology

value: NEGATIVE


title: 3998703010_E

description:
RNA was isolated using 1.5 ml whole blood and the MagMAX-96 Blood RNA Isolation Kit (Applied Biosystems/Ambion)
3998703010_E

tag: title

tag: sampledate at t0

tag: dosanjh

value: Male

tag: tst

tag: pcr

value: INDETERMINATE


title: DMSO_MED1

source_name: WT 9-12_control_vehicle

tag: cell type

value: control

value: Bethyl, A300-793A


title: CRISPR_Con_Ccl2_e2_bait_rp1

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

value: Macrophage

tag: strain

value: BALB/c

tag: agent

value: No treatment


title: EV_3

city: Shanghai

first: Shanhe

last: Yu

address: 197# Rui Jin Road II

institute: Shanghai Institute of Hematology，Rui Jin Hospital

data_processing:
Raw data (raw reads) of fastq format were firstly processed through Cutadapt (v1.18) and Trimmomatic (v0.38) In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data.
Hisat2 (v2.1.0)  is used to align clean reads to reference genome.
Gene expression levels were estimated using FPKM (fragments per kilobase of exon per million fragments mapped) by StringTie (v1.3.4d). Gene counts were calculated from the Stringtie assemblies using the PrepDE.py script provided within the Stringtie package.
We applied edgeR algorithm to filter the differentially expressed genes, after the significant analysis and FDR analysis under the following criteria: i) |log2FC| > 1 ; ii) Pvalue < 0.05.
GO and KEGG enrichment analysis of differentially expressed genes
Genome_build: hg38
Supplementary_files_format_and_content: expression analysis result of  edgeR and annotation

source_name: HCCC9810_empty vector

growth_protocol: HCCC9810 cells were cultured in Dulbecco’s modified Eagle’s medium (Hyclone) supplemented with 10% fetal bovine serum (Gibco) plus Penicillin/ Streptomycin antibiotics (Invitrogen), with a 5% CO2 concentration at 37°C.

extract_protocol:
RNA was harvested using Trizol reagent.KAPA Stranded RNA-seq Kit (KK8401) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard KAPA Stranded RNA-seq Kit protocols

tag: cell line

tag: tissue

value: human cholangiocarcinoma cell line

tag: genotype/variation

value: transduced with empty vector


title: EV_2


title: CRISPR_Con_Ccl2_e1_bait_rp3

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


title: CRISPR_Con_Ccl2_e1_bait_rp1

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


title: CRISPR_Con_Ccl2_e1_bait_rp2

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


title: EV_1


title: CRISPR_GPS2_KO_ATAC_seq_rp3

data_processing:
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.

extract_protocol:
WT and GPS2 KO RAW264.7 cells were seeded with triplicates in the 12 wells plates with 2×105 cell number one day before the experiments. Cells were harvested (basal condition), washed with PBS and then resuspended in lysis buffer. Cell nuclei were spined down and transferred into the transposition reaction buffer and incubated at 37 °C for 30 minutes. Genomic DNA was extracted using Qiagen MinElute PCR Purification Kit. ATAC-seq library was done with the protocol as  previously reported (Buenrostro et al., 2015). The Purified ATAC-seq DNA library mix was sequenced on NextSeq 550 (Illumina, 75 SE reads) in BEA Core Facility (Karolinska Institutet, Huddinge, Sweden).
DNA was processed using Takara SMRTer ThruPLEX DNA-seq Kit.

treatment_protocol: Without any treatment


title: CRISPR_GPS2_KO_ATAC_seq_rp2


title: 3998734064_F

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

tag: diagnosis

value: Other

tag: eptborptb

tag: smear microscopy

value: TRUE

tag: culture result

value: Negative

tag: age

value: White

value: FALSE

value: Clinical Features, Imaging

tag: qtf-git


title: 3998675049_B

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

tag: title

value: OD

tag: site of infection

value: Lung

tag: gender

value: Female

tag: height (cm)

tag: weight (kg)

tag: bmi

tag: hiv positive

value: Histology


title: KDM5C_3

value: cells transduced with KDM5C-expression vector


title: 3998734063_E

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

tag: sampledate at t0

tag: dosanjh

value: Pneumonia

value: Male

value: Imaging

tag: tst

tag: pcr

value: INDETERMINATE

value: NEGATIVE


title: KDM5C_2

tag: cell line

tag: tissue

value: human cholangiocarcinoma cell line

tag: genotype/variation


title: 3998675056_H

description:
RNA was isolated using 1.5 ml whole blood and the MagMAX-96 Blood RNA Isolation Kit (Applied Biosystems/Ambion)
3998675056_H

tag: diagnosis

tag: eptborptb

value: Chest or Thorax

tag: smear microscopy

tag: culture result

value: Culture


title: 200681360009_J

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

tag: title

tag: site of infection

value: TRUE

value: Indeterminate

tag: age

tag: pcr result

value: Negative

tag: qtf-git


title: CRISPR_GPS2_KO_ATAC_seq_rp1

tag: cell type

value: Macrophage

tag: strain

value: BALB/c

tag: agent

value: No treatment


title: 200681360001_H

description:
RNA was isolated using 1.5 ml whole blood and the MagMAX-96 Blood RNA Isolation Kit (Applied Biosystems/Ambion)
200681360001_H

tag: sampledate at t0

tag: dosanjh

value: Sarcoidosis

value: OD

value: Lung

tag: gender

tag: height (cm)

tag: weight (kg)

tag: bmi

value: Indian

tag: hiv positive

value: FALSE

value: Imaging, OTHER

tag: tst


title: 3998675119_H

description:
RNA was isolated using 1.5 ml whole blood and the MagMAX-96 Blood RNA Isolation Kit (Applied Biosystems/Ambion)
3998675119_H

tag: diagnosis

value: Pneumonia

tag: eptborptb

tag: smear microscopy

tag: culture result

value: Male

tag: pcr


title: CRISPR_KO_Ctrl_ATAC_seq_rp3


title: 3998675065_B

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

tag: title

tag: site of infection

tag: age

value: White

value: OTHER

tag: qtf-git

value: NEGATIVE


title: NRF2KO_SFN_Input

tag: cell line background

tag: cell type

value: immortalized epithelial cell line obtained from patients with ADPKD

tag: genotype/variation

value: Nrf2 knockout

tag: treatment

value: Nrf2 activator sulforaphane (SFN)


title: 3998734063_A

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

tag: sampledate at t0

tag: dosanjh

value: Other, URTI

tag: gender

value: Female

tag: height (cm)

tag: weight (kg)

value: Imaging

value: POSITIVE


title: NRF2KO_SFN_P300

tag: chip antibody

value: Santa Cruz Biotechnology, sc-585


title: 3998675114_K

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

tag: diagnosis

value: Other

tag: eptborptb

value: OD

value: Ankle

tag: smear microscopy

value: TRUE

value: Negative

tag: bmi

tag: hiv positive

tag: tst


title: 3998734064_D

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

tag: title

tag: site of infection

value: Eyes

value: FALSE

tag: age

value: Indian

tag: pcr

tag: qtf-git


title: 3998734078_K

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

tag: sampledate at t0

value: Pneumonia

value: Lung

tag: culture result

value: Male

value: Culture, Imaging

value: NEGATIVE


title: SFN_Input

tag: cell line background

tag: cell type

value: immortalized epithelial cell line obtained from patients with ADPKD

tag: genotype/variation

value: control

tag: treatment

value: Nrf2 activator sulforaphane (SFN)


title: KDM5C_1

tag: cell line

tag: tissue

value: human cholangiocarcinoma cell line

value: cells transduced with KDM5C-expression vector


title: 3998675119_F

description:
RNA was isolated using 1.5 ml whole blood and the MagMAX-96 Blood RNA Isolation Kit (Applied Biosystems/Ambion)
3998675119_F

tag: dosanjh

tag: diagnosis

value: Other

tag: eptborptb

value: OD

value: Neck

tag: smear microscopy

tag: gender

value: Female

tag: height (cm)

tag: weight (kg)

value: Clinical Features


title: 3998734078_J

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

tag: title

tag: site of infection

value: FALSE

tag: age

tag: bmi

tag: hiv positive

value: Imaging

tag: tst

tag: pcr


title: 3998675081_B

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

tag: sampledate at t0

value: Indian

tag: qtf-git

value: INDETERMINATE


title: 3998734084_H

description:
RNA was isolated using 1.5 ml whole blood and the MagMAX-96 Blood RNA Isolation Kit (Applied Biosystems/Ambion)
3998734084_H

value: Lung

value: Male

value: Black

value: Clinical Features, OTHER

value: POSITIVE


title: 3998675074_C

description:
RNA was isolated using 1.5 ml whole blood and the MagMAX-96 Blood RNA Isolation Kit (Applied Biosystems/Ambion)
3998675074_C

value: IGRA, Imaging


title: CRISPR_KO_Ctrl_ATAC_seq_rp2

tag: cell type

value: Macrophage

tag: strain

value: BALB/c

tag: agent

value: No treatment


title: 3998675029_D

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

tag: dosanjh

tag: diagnosis

value: Other

tag: eptborptb

value: OD

value: Breast

value: TRUE

tag: culture result

value: Negative

value: White

value: NEGATIVE


title: CRISPR_KO_Ctrl_ATAC_seq_rp1


title: SFN_P300

tag: cell line background

value: immortalized epithelial cell line obtained from patients with ADPKD

tag: genotype/variation

value: control

tag: treatment

value: Nrf2 activator sulforaphane (SFN)

tag: chip antibody

value: Santa Cruz Biotechnology, sc-585


title: CRISPR_GPS2_KO_LPS_rp3

extract_protocol:
WT and GPS2 KO RAW cells were treated with 10 ng/ml LPS (6 hour).  Total RNA was extracted and followed with the PolyA  RNA-seq library  preparation protocol.
Total RNA was processed using NEBNext® Ultra™ II RNA Library Prep Kit for Illumina® (E7770, E7775)

treatment_protocol: RAW264.7 cells were treated with/without LPS (6 hours)

value: LPS

tag: time point

value: 6 hour


title: CRISPR_GPS2_KO_LPS_rp4


title: SFN_NRF2

value: Abcam, ab62352


title: 3998734070_G

description:
RNA was isolated using 1.5 ml whole blood and the MagMAX-96 Blood RNA Isolation Kit (Applied Biosystems/Ambion)
3998734070_G

tag: title

tag: smear microscopy

value: FALSE

tag: age

tag: gender

value: Female

tag: height (cm)

tag: weight (kg)

tag: bmi

value: Indian

tag: hiv positive

value: IGRA

value: POSITIVE


title: CRISPR_GPS2_KO_LPS_rp2

tag: cell type

value: Macrophage

tag: strain

value: BALB/c

tag: agent


title: 3998675070_K

description:
RNA was isolated using 1.5 ml whole blood and the MagMAX-96 Blood RNA Isolation Kit (Applied Biosystems/Ambion)
3998675070_K

tag: sampledate at t0

tag: dosanjh

tag: diagnosis

value: Other

tag: eptborptb

value: OD

tag: site of infection

value: Lung

value: Clinical Features

tag: tst

tag: pcr

tag: qtf-git


title: SFN_K4M3

tag: cell line background

value: immortalized epithelial cell line obtained from patients with ADPKD

tag: genotype/variation

value: control

tag: treatment

tag: chip antibody

value: Millipore, 05-745R


title: 3998734070_H

description:
RNA was isolated using 1.5 ml whole blood and the MagMAX-96 Blood RNA Isolation Kit (Applied Biosystems/Ambion)
3998734070_H

tag: title

value: Lymph node

tag: smear microscopy

value: TRUE

tag: culture result

value: Negative

tag: age

tag: gender

value: Male

tag: height (cm)

tag: weight (kg)

tag: bmi

value: Black

value: NEGATIVE


title: SFN_K4M1

tag: cell type

value: Nrf2 activator sulforaphane (SFN)

value: Abcam, ab8895


title: 3998675049_G

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

tag: sampledate at t0

tag: dosanjh

tag: diagnosis

tag: eptborptb

tag: site of infection

value: FALSE

value: Female

value: Indian

tag: hiv positive

value: Histology

value: INDETERMINATE


title: 3998675049_E

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

value: Pneumonia

value: OD

value: Lung

value: Clinical Features

tag: tst

tag: pcr

tag: qtf-git


title: SFN_K27ac

tag: cell line background

value: immortalized epithelial cell line obtained from patients with ADPKD

tag: genotype/variation

value: control

tag: treatment

tag: chip antibody

value: Abcam, ab4729


title: CRISPR_GPS2_KO_LPS_rp1

value: Macrophage

tag: strain

value: BALB/c

tag: agent

value: LPS

tag: time point

value: 6 hour


title: 3998734070_A

description:
RNA was isolated using 1.5 ml whole blood and the MagMAX-96 Blood RNA Isolation Kit (Applied Biosystems/Ambion)
3998734070_A

tag: title

value: Cancer

tag: smear microscopy

value: TRUE

tag: culture result

value: Negative

tag: age

tag: gender

value: Male

tag: weight (kg)

value: POSITIVE


title: 3998675081_J

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

tag: sampledate at t0

tag: dosanjh

tag: diagnosis

tag: eptborptb

tag: site of infection

value: Female

tag: height (cm)

tag: bmi

value: Indian

tag: hiv positive

value: FALSE

value: Imaging, Response to Treatment

value: NEGATIVE


title: 3998734082_H

description:
RNA was isolated using 1.5 ml whole blood and the MagMAX-96 Blood RNA Isolation Kit (Applied Biosystems/Ambion)
3998734082_H

value: Other

value: OD

value: Lung

value: Culture

tag: tst

tag: pcr

tag: qtf-git


title: 3998734084_E

description:
RNA was isolated using 1.5 ml whole blood and the MagMAX-96 Blood RNA Isolation Kit (Applied Biosystems/Ambion)
3998734084_E

tag: title

value: Pneumonia

value: White

value: Imaging

value: INDETERMINATE


title: NRF2KO_DMSO_Input

tag: cell line background

tag: cell type

value: immortalized epithelial cell line obtained from patients with ADPKD

tag: genotype/variation

value: Nrf2 knockout

tag: treatment

value: vehicle


title: 3998703009_B

description:
RNA was isolated using 1.5 ml whole blood and the MagMAX-96 Blood RNA Isolation Kit (Applied Biosystems/Ambion)
3998703009_B

tag: smear microscopy

value: TRUE

tag: culture result

value: Negative

tag: age

tag: gender

value: Male

tag: weight (kg)


title: CRISPR_GPS2_KO_rp4

value: Macrophage

tag: strain

value: BALB/c

tag: agent

value: No treatment


title: DMSO_P300

value: control

tag: chip antibody

value: Santa Cruz Biotechnology, sc-585


title: DMSO_Input


title: WT_LPS_rp4

value: LPS

tag: time point

value: 6 hour


title: 200681360011_L

description:
RNA was isolated using 1.5 ml whole blood and the MagMAX-96 Blood RNA Isolation Kit (Applied Biosystems/Ambion)
200681360011_L

tag: sampledate at t0

tag: dosanjh

tag: diagnosis

value: Pneumonia

tag: eptborptb

value: OD

tag: site of infection

value: Lung

tag: height (cm)

tag: bmi

value: Black

tag: hiv positive

value: Clinical Features

tag: tst

value: FALSE

tag: pcr result

value: NEGATIVE


title: CRISPR_GPS2_KO_rp2

tag: cell type


title: CRISPR_GPS2_KO_rp1


title: WT_LPS_rp3


title: 3998675093_H

description:
RNA was isolated using 1.5 ml whole blood and the MagMAX-96 Blood RNA Isolation Kit (Applied Biosystems/Ambion)
3998675093_H

tag: title

value: Sarcoidosis

tag: smear microscopy

value: TRUE

tag: culture result

tag: age

tag: gender

value: Female

value: Asian

tag: pcr

tag: qtf-git

value: INDETERMINATE


title: 200683670015_I

description:
RNA was isolated using 1.5 ml whole blood and the MagMAX-96 Blood RNA Isolation Kit (Applied Biosystems/Ambion)
200683670015_I

tag: sampledate at t0

tag: dosanjh

value: Negative

value: Male

tag: weight (kg)


title: 200681360009_G

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

tag: diagnosis

value: Other, URTI

tag: eptborptb

tag: site of infection

value: Indian

value: OTHER


title: 3998703009_D

description:
RNA was isolated using 1.5 ml whole blood and the MagMAX-96 Blood RNA Isolation Kit (Applied Biosystems/Ambion)
3998703009_D

value: Other

tag: height (cm)

tag: bmi

tag: hiv positive

tag: tst result


title: 200681360001_B

description:
RNA was isolated using 1.5 ml whole blood and the MagMAX-96 Blood RNA Isolation Kit (Applied Biosystems/Ambion)
200681360001_B

tag: title

value: Cancer

value: OD

value: Histology

tag: tst

value: POSITIVE


title: 3998720112_F

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

value: Pneumonia

value: Lung

tag: smear microscopy

value: FALSE

value: White

value: Clinical Features


title: 3998734063_K

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

value: TRUE

tag: culture result

tag: age

value: Culture

value: NEGATIVE


title: CRISPR_GPS2_KO_rp3

tag: cell type

value: Macrophage

tag: strain

value: BALB/c

tag: agent

value: No treatment


title: 3998703022_F

description:
RNA was isolated using 1.5 ml whole blood and the MagMAX-96 Blood RNA Isolation Kit (Applied Biosystems/Ambion)
3998703022_F

tag: sampledate at t0

tag: dosanjh

value: Negative

tag: gender

value: Female

value: Black

value: Clinical Features, OTHER

tag: pcr

tag: qtf-git


title: NRF2KO_DMSO_P300

tag: cell line background

value: immortalized epithelial cell line obtained from patients with ADPKD

tag: genotype/variation

value: Nrf2 knockout

tag: treatment

value: vehicle

tag: chip antibody

value: Santa Cruz Biotechnology, sc-585


title: DMSO_K4M3

value: control

value: Millipore, 05-745R


title: 3998675119_A

description:
RNA was isolated using 1.5 ml whole blood and the MagMAX-96 Blood RNA Isolation Kit (Applied Biosystems/Ambion)
3998675119_A

tag: title

tag: diagnosis

value: Cancer

tag: eptborptb

value: OD

tag: site of infection

value: Stomach

value: Male

tag: height (cm)

tag: weight (kg)

tag: bmi

value: Indian

tag: hiv positive

value: FALSE

value: Histology


title: DMSO_NRF2

tag: cell type

value: Abcam, ab62352


title: WT_LPS_rp2

value: Macrophage

tag: strain

value: BALB/c

tag: agent

value: LPS

tag: time point

value: 6 hour


title: WT_LPS_rp1


title: DMSO_K4M1

value: immortalized epithelial cell line obtained from patients with ADPKD

value: Abcam, ab8895


title: 3998734084_G

description:
RNA was isolated using 1.5 ml whole blood and the MagMAX-96 Blood RNA Isolation Kit (Applied Biosystems/Ambion)
3998734084_G

tag: sampledate at t0

tag: dosanjh

value: Other

value: Lung

tag: smear microscopy

tag: age

tag: gender

value: Clinical Features

tag: tst

tag: pcr

tag: qtf-git

value: NEGATIVE


title: 3998675086_L

description:
RNA was isolated using 1.5 ml whole blood and the MagMAX-96 Blood RNA Isolation Kit (Applied Biosystems/Ambion)
3998675086_L

tag: title

tag: diagnosis

tag: eptborptb

value: OD

tag: site of infection

value: Skin

value: Female

value: White


title: 3998734084_C

description:
RNA was isolated using 1.5 ml whole blood and the MagMAX-96 Blood RNA Isolation Kit (Applied Biosystems/Ambion)
3998734084_C

value: Pneumonia

value: TRUE

tag: height (cm)

tag: weight (kg)

tag: bmi

value: Black

tag: hiv positive

value: FALSE

tag: tst result


title: WT_Con_rp3

tag: cell type

value: Macrophage

tag: strain

value: BALB/c

tag: agent

value: No treatment


title: WT_Con_rp4


title: 3998675110_J

description:
RNA was isolated using 1.5 ml whole blood and the MagMAX-96 Blood RNA Isolation Kit (Applied Biosystems/Ambion)
3998675110_J

tag: sampledate at t0

tag: dosanjh

value: Throat

tag: smear microscopy

tag: age

value: Male


title: 3998675110_C

description:
RNA was isolated using 1.5 ml whole blood and the MagMAX-96 Blood RNA Isolation Kit (Applied Biosystems/Ambion)
3998675110_C

value: Sarcoidosis

tag: culture result

value: Negative

tag: gender

value: Mixed

value: OTHER

tag: tst

tag: pcr

tag: qtf-git


title: 3998675115_K

description:
RNA was isolated using 1.5 ml whole blood and the MagMAX-96 Blood RNA Isolation Kit (Applied Biosystems/Ambion)
3998675115_K

tag: title

tag: diagnosis

value: Other

tag: eptborptb

value: OD

tag: site of infection

tag: height (cm)

value: MiddleEast

value: Clinical Features

value: POSITIVE

value: NEGATIVE


title: 3998675098_K

description:
RNA was isolated using 1.5 ml whole blood and the MagMAX-96 Blood RNA Isolation Kit (Applied Biosystems/Ambion)
3998675098_K

value: Spine

value: Female

value: Black

tag: hiv positive

value: Imaging

value: INDETERMINATE


title: SW1-IgG plus combo (ceritinib-trametinib)

city: Tampa

first: Keiran

last: Smalley

state: FL

address: 12902 Magnolia Dr

country: USA

institute: Moffitt Cancer Center

data_processing:
Sequence reads for each sample were aligned and processed using cellranger/3.1.0
Individual samples are aggregated to create a combined dataset using cellranger/3.10
Genome_build: mm10
Supplementary_files_format_and_content: h5. filtered gene expression counts for called cells.

source_name: single cell suspension of tumor

growth_protocol: Mice were subcutaneously injected with 1.5 X 106 cells in Matrigel.

extract_protocol:
Tumors were collected, minced and single cell suspensions prepared by enzymatic digestion, using the MACS Tumor dissociation kit from Miltenyi Biotec, CA.
Sample were quantified and viability was analyzed using the Nexcelom Cellometer K2. The samples were then loaded onto 10X Genomics Chromium Single Cell Controller (10X Genomics, CA) to prepare single-cell RNA-sequencing libraries. Around 50,000 to 1,000,000 mean sequencing reads per cell were generated on Illumina NextSeq 500 instrument using v2.5 flow cells
scRNA-seq

treatment_protocol: IT: two doses of Anti-PD1 antibody (200 mg/100 ml) (clone RMP1-14) or IgG isotype control (200 mg/100 ml) from (BioXCell, NH) intra-peritoneal every 5 days. TT: On day 10, the immunotherapy was stopped and the mice received Ceritinib (25 mg/kg) and trametinib (1 mg/kg)  (Selleck Chemicals) combination via oral gavage

tag: disease state

value: SW1 murine melanoma model

tag: cell type

value: single cell suspension of tumor

tag: treatment

value: TT


title: DMSO_K27ac

tag: cell line background

value: immortalized epithelial cell line obtained from patients with ADPKD

tag: genotype/variation

value: control

value: vehicle

tag: chip antibody

value: Abcam, ab4729


title: SW1-IgG-Vehicle


title: WT_Con_rp2

value: Macrophage

tag: strain

value: BALB/c

tag: agent

value: No treatment


title: WT_Con_rp1


title: SW1-AntiPD1 plus combo (ceritinib-trametinib)

value: IT-TT


title: WT_LPS_CBP_rp2

growth_protocol: CRISPR/cas9-mediated enhancer/promoter knockout or lentivius-mediated gene knockdown  RAW264.7 cells were maintained normal 10% FBS DMEM medium

extract_protocol:
Fresh cells were crosslinked with 2 mM disuccinimidyl glutarate (DSG) for 30 min, followed by 1% formaldehyde for 10 min at room temperature. Nuclei were isolated, sonicated and incubated with magnetic bead-antibody complexes.
ChIPed DNA 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 or without LPS treatment (2 hours)

tag: antibody

value: CBP

value: LPS

tag: time point

value: 2 hours


title: WT_Ctrl_CBP_rp2


title: 3998675086_E

description:
RNA was isolated using 1.5 ml whole blood and the MagMAX-96 Blood RNA Isolation Kit (Applied Biosystems/Ambion)
3998675086_E

tag: sampledate at t0

tag: dosanjh

value: Other

value: OD

tag: smear microscopy

value: TRUE

tag: culture result

value: Negative

tag: age

tag: gender

value: Male

tag: weight (kg)

tag: bmi

value: Indian

value: FALSE

tag: tst

tag: pcr

tag: qtf-git

value: NEGATIVE


title: WT_Ctrl_CBP_rp1

tag: cell type


title: 3998734078_H

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

tag: title

tag: diagnosis

value: LTBI - treatment indicated, Other

tag: eptborptb

tag: site of infection

value: Lung

value: Female

tag: height (cm)

value: Hispanic

tag: hiv positive

value: Clinical Features, OTHER

tag: tst result

value: POSITIVE


title: 3998675115_E

description:
RNA was isolated using 1.5 ml whole blood and the MagMAX-96 Blood RNA Isolation Kit (Applied Biosystems/Ambion)
3998675115_E

tag: sampledate at t0

tag: dosanjh

tag: smear microscopy

value: Black

value: Culture


title: S_KO_Ctrl_CBP_rp2

value: Macrophage

tag: strain

value: BALB/c

tag: antibody

value: CBP

tag: agent

value: No treatment


title: 3998720110_L

description:
RNA was isolated using 1.5 ml whole blood and the MagMAX-96 Blood RNA Isolation Kit (Applied Biosystems/Ambion)
3998720110_L

value: Other

value: OD

value: TRUE

tag: culture result

value: Negative

tag: age

tag: gender

tag: weight (kg)

value: Clinical Features, Imaging

tag: tst


title: WT_LPS_CBP_rp1

tag: cell type

value: LPS

tag: time point

value: 2 hours


title: 13_0330_TIL_CD8

city: Buffalo

first: Sebastiano

last: Battaglia

state: NY

address: Elm and Carlton st

department: Department of Immunology

institute: Roswell Park Comprehensive Cancer Center

description:
cancer immunotherapy
*** Comment from submitter: "Adaptive ImmunoSeq, which is where the aligned TCR data are available, has no fastq files. the files uploaded here are what's being given to us." ***

data_processing:
Library strategy: ImmunoSeq
raw data were processed using the standard ImmunoSeq pipeline from Adaptive Biotechnology
processed data were further analyzed downstream using Lymphoseq
Genome_build: mm10
Supplementary_files_format_and_content: tsv, aminoacid and nucleotide sequences of CDR3 regions, cdj alleles, counts

source_name: tumor

extract_protocol: Sequencing libraries are generated using the immunoSeq kit from Adaptive Biotechnologies.  Input DNA amounts are determined using the recommendations in the kit based on the anticipated percentage of T cells for the sample type.  The first round of PCR is accomplished using the proprietary PCR primer mix included with the kit.  A positive control reaction, provided in the kit, and a negative control reaction are included with each sample batch.  A second round of PCR is performed to generate uniquely barcoded sequencing libraries utilizing the barcode primer plate included in the kit.  Final libraries are validated for appropriate size on a 4200 TapeStation D1000 Screentape (Agilent Technologies, Inc.).  Samples are pooled volumetrically and the final pool is then loaded into NextSeq500 MidOutput 150 cycle Reagent cartridge and sequenced on a NextSeq500 following the manufacturer’s recommended protocol (Illumina Inc.) utilizing the custom primers included in the immunoSeq kit.

tag: Sex

value: Female

tag: tumor type

value: CD8 TILs

tag: treatment

value: anti-CTLA-4 Ab/anti-PD-L1 Ab


title: 200681360011_F

description:
RNA was isolated using 1.5 ml whole blood and the MagMAX-96 Blood RNA Isolation Kit (Applied Biosystems/Ambion)
200681360011_F

tag: title

tag: diagnosis

value: Cancer

tag: eptborptb

tag: site of infection

value: OTHER

tag: height (cm)

tag: bmi

tag: hiv positive

value: FALSE

tag: pcr

tag: qtf-git

value: INDETERMINATE

value: NEGATIVE


title: 15_0413_TIL_CD8

tag: strain


title: 11_0413_sp_CR1hi

source_name: Spleen

value: splenic CX3CR1hi CD8 T cells


title: 14_0406_TIL_CD8


title: 3998675120_H

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

tag: sampledate at t0

tag: dosanjh

value: Lung

tag: smear microscopy

tag: age

tag: gender

value: Male

tag: weight (kg)

value: Indian

value: Imaging

tag: tst result


title: 3998703009_H

description:
RNA was isolated using 1.5 ml whole blood and the MagMAX-96 Blood RNA Isolation Kit (Applied Biosystems/Ambion)
3998703009_H

tag: title

value: Other

value: OD

value: TRUE

tag: tst


title: 3998703009_J

description:
RNA was isolated using 1.5 ml whole blood and the MagMAX-96 Blood RNA Isolation Kit (Applied Biosystems/Ambion)
3998703009_J

tag: diagnosis

tag: eptborptb


title: 3998675095_B

description:
RNA was isolated using 1.5 ml whole blood and the MagMAX-96 Blood RNA Isolation Kit (Applied Biosystems/Ambion)
3998675095_B

value: Pneumonia

tag: height (cm)

value: Mixed


title: 3998703010_K

description:
RNA was isolated using 1.5 ml whole blood and the MagMAX-96 Blood RNA Isolation Kit (Applied Biosystems/Ambion)
3998703010_K

value: Sarcoidosis

tag: bmi


title: 200681360011_G

description:
RNA was isolated using 1.5 ml whole blood and the MagMAX-96 Blood RNA Isolation Kit (Applied Biosystems/Ambion)
200681360011_G

tag: site of infection

tag: culture result

value: Negative

value: Female

value: Black

tag: hiv positive

value: Culture, Histology


title: 3998675115_G

description:
RNA was isolated using 1.5 ml whole blood and the MagMAX-96 Blood RNA Isolation Kit (Applied Biosystems/Ambion)
3998675115_G

value: Asian

value: FALSE

value: Culture

tag: pcr

tag: qtf-git

value: POSITIVE


title: 3998675102_C

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

tag: sampledate at t0

tag: dosanjh

value: Lung

value: Clinical Features, OTHER

value: NEGATIVE


title: S_KO_Ctrl_CBP_rp1

tag: cell type

value: Macrophage

tag: strain

value: BALB/c

tag: antibody

value: CBP

tag: agent

value: No treatment


title: SW1-AntiPD1-Vehicle

tag: disease state

value: SW1 murine melanoma model

value: single cell suspension of tumor

tag: treatment

value: IT


title: 200681360011_D

description:
RNA was isolated using 1.5 ml whole blood and the MagMAX-96 Blood RNA Isolation Kit (Applied Biosystems/Ambion)
200681360011_D

tag: title

tag: diagnosis

value: Cancer

value: OD

value: Lymph node

tag: smear microscopy

value: Negative

tag: age

tag: gender

value: Male

tag: weight (kg)

value: White

value: TRUE

value: Histology

tag: tst


title: 200681360011_A

description:
RNA was isolated using 1.5 ml whole blood and the MagMAX-96 Blood RNA Isolation Kit (Applied Biosystems/Ambion)
200681360011_A

value: Pneumonia

tag: eptborptb

tag: site of infection

value: Lung

tag: culture result

tag: height (cm)

tag: bmi

tag: hiv positive

value: Clinical Features

value: FALSE

tag: pcr

value: POSITIVE


title: 200683670015_K

description:
RNA was isolated using 1.5 ml whole blood and the MagMAX-96 Blood RNA Isolation Kit (Applied Biosystems/Ambion)
200683670015_K

tag: sampledate at t0

tag: dosanjh

tag: qtf-git

value: NEGATIVE

value: INDETERMINATE


title: 10_0406_sp_CR1hi

tag: strain

tag: Sex

value: Female

tag: tumor type

tag: cell type

value: splenic CX3CR1hi CD8 T cells

tag: treatment

value: anti-CTLA-4 Ab/anti-PD-L1 Ab


title: 200681360011_B

description:
RNA was isolated using 1.5 ml whole blood and the MagMAX-96 Blood RNA Isolation Kit (Applied Biosystems/Ambion)
200681360011_B

tag: title

tag: diagnosis

value: LRTI

value: OD

tag: smear microscopy

tag: age

tag: gender

tag: weight (kg)

value: Response to Treatment


title: 3998703016_J

description:
RNA was isolated using 1.5 ml whole blood and the MagMAX-96 Blood RNA Isolation Kit (Applied Biosystems/Ambion)
3998703016_J

tag: eptborptb

tag: site of infection

tag: culture result

value: Negative

value: Male

tag: height (cm)

tag: tst


title: 09_0330_sp_CR1hi


title: E_KO_Ctrl_CBP_rp2

value: Macrophage

value: BALB/c

tag: antibody

value: CBP

tag: agent

value: No treatment


title: E_KO_Ctrl_CBP_rp1

tag: strain


title: 07_0413_sp_CR1lo

tag: Sex

tag: tumor type

value: splenic CD27hiCX3CR1lo CD8 T cells


title: 3998734069_A

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

tag: sampledate at t0

tag: dosanjh

value: Other

value: Intestine, Urinary tract

value: FALSE

tag: bmi

value: Asian

tag: hiv positive

tag: pcr

tag: qtf-git


title: 06_0406_sp_CR1lo

value: Female

tag: cell type

tag: treatment


title: WT_LPS_GPS2_rp2

value: LPS

tag: time point

value: 2 hours


title: 05_0330_sp_CR1lo

value: anti-CTLA-4 Ab/anti-PD-L1 Ab


title: WT_Ctrl_GPS2_rp1


title: WT_Ctrl_GPS2_rp2


title: WT_LPS_GPS2_rp1


title: 3998675043_A

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

tag: title

tag: diagnosis

tag: eptborptb

value: OD

tag: site of infection

value: Lymph node

tag: smear microscopy

value: TRUE

tag: culture result

tag: age

tag: gender

tag: weight (kg)

value: Indian

value: Culture, Smear Microscopy

value: NEGATIVE


title: 03_0413_sp_CD27lo

description:
cancer immunotherapy
*** Comment from submitter: "Adaptive ImmunoSeq, which is where the aligned TCR data are available, has no fastq files. the files uploaded here are what's being given to us." ***

tag: strain

tag: Sex

tag: tumor type

value: splenic CD27loCX3CR1lo CD8 T cells


title: shSMRT_Ctrl_GPS2_rp2

value: Macrophage

value: BALB/c

tag: antibody

tag: agent

value: No treatment


title: 200683670015_B

description:
RNA was isolated using 1.5 ml whole blood and the MagMAX-96 Blood RNA Isolation Kit (Applied Biosystems/Ambion)
200683670015_B

tag: dosanjh

value: LRTI, Other

value: Negative

value: Male

tag: height (cm)

tag: bmi

value: Black

tag: hiv positive

value: Clinical Features, Imaging

tag: tst

tag: pcr

tag: qtf-git

value: POSITIVE


title: shSMRT_Ctrl_GPS2_rp1

tag: cell type


title: 3998703016_L

description:
RNA was isolated using 1.5 ml whole blood and the MagMAX-96 Blood RNA Isolation Kit (Applied Biosystems/Ambion)
3998703016_L

tag: title

tag: sampledate at t0

tag: diagnosis

value: Other

tag: eptborptb

tag: site of infection

value: Pelvis

tag: smear microscopy

tag: culture result

value: Female

value: Response to Treatment

value: FALSE


title: 200681360009_K

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

value: OD

value: Urinary tract

value: TRUE

tag: age

tag: gender

tag: weight (kg)

value: Indian

value: Clinical Features


title: shGFP_Ctrl_GPS2_rp2

value: Macrophage

tag: strain

value: BALB/c

tag: antibody

tag: agent

value: No treatment


title: 3998675068_G

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

tag: dosanjh

value: Male

tag: height (cm)

tag: bmi

tag: hiv positive

value: Imaging

tag: tst

value: NEGATIVE


title: 3998734063_H

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

tag: title

tag: sampledate at t0

value: Imaging, OTHER

tag: pcr

tag: qtf-git


title: 3998734086_A

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

tag: diagnosis

value: Other

tag: eptborptb

tag: smear microscopy

value: Negative

value: Black

value: OTHER

value: POSITIVE


title: 3998675092_C

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

value: Pneumonia

value: OD

tag: site of infection

value: Lung

tag: culture result

tag: age

tag: gender

value: Female

value: White

value: FALSE

value: Culture


title: Lung_P14_2

city: Ottawa

first: David

last: Cook

state: ON

address: 501 Smyth Rd

department: Cancer Therapeutics Program

country: Canada

institute: Ottawa Hospital Research Institute

description: 10x Genomics library of a MULTI-seq pool of P14 lung tissue from control and hyperoxia-exposed animals (n=3 lung samples per condition).

data_processing:
Raw sequencing reads were processed using CellRanger v3.0.2. The mm10 build of the mouse genome was used for both. Except for explicitly setting --expect-cells=25000, default parameters were used for all samples.
Sample demultiplexing was performed using the deMULTIplex R package v1.0.2.
Genome_build: mm10
Supplementary_files_format_and_content: Cell metadata table: Various metadata (sample ID, cluster, etc) for each cell contained in the UMI count matrix. UMI count matrix: Matrix containing UMI counts for all cells passing quality control filters. MULTI-seq barcode UMI count matrix: Cell-by-barcode matrix of MULTI-seq barcode counts for each cell that was used to demultiplex samples.

growth_protocol: Developing pups designated for single-cell RNA sequencing (scRNA-seq) and Fluorescence activated cell sorting (FACS) analyses were euthanized at P3, P7 or P14 by 10 μl/g i.p. injection of pentobarbital sodium (CDMV, Saint-Hyacinthe, QC, Canada) and received an additional i.p. injection of 10 mU/g (in 10 μl/g volume) heparin sodium (LEO Pharma INc., Thornhill, ON, Canada). Following euthanasia, the chest was opened and the abdominal aorta and vena cava were cut above the liver. The left atrium was perforated and lungs were perfused through the right ventricle with 5 ml of 25 U/ml Heparin Sodium until completely white. Lungs were removed, dissected into individual lobes, and shortly rinsed with Dulbecco’s PBS (DPBS, Lonza, Basel, Switzerland). Dissected lungs were than digested in 5 ml of enzyme mixture at 37°C by gentleMACS™ Octo Dissociator (Miltenyi Biotech, Bergisch Gladbach, Germany). Following costumed dissociation program was used for the digestion: loop 6× (spin 300rpm, 10''; spin -300rpm, 10''); loop 2× (spin 150rpm, 5''; spin -150rpm, 5''); loop 2× (spin 20rpm, 5' 0''; spin -20rpm, 5' 0''); loop 6× (ramp 360rpm, 15''; ramp -360rpm, 15'').  The following customized enzymatic mixture was used for lung digestion: i) 2500U Collagenase I (Wothington Biochem., Lakewood, NJ, USA), 30U Neutral Protease (Wothington Biochem., Lakewood, NJ, USA), 500U Deoxyribonuclease (DNAse) I (Sigma-Aldrich, Oakville, ON, Canada); ii) Elastase (Wothington Biochem., Lakewood, NJ, USA), 500U DNAse I; iii) 2500U Collagenase I, 500U DNase I; iv) Collagenase/Dispase (Sigma-Aldrich, Oakville, ON, Canada), 500U DNAse I. All enzyme mixtures were diluted in 5 ml of DPBS supplemented with Mg2+/Ca2+ (Thermofischer Scientific, Burlington, ON, Canada). Combination of Collagenase I, Neutral Proteasem and DNase (i) resulted in the most equal distribution and was used in all following experiments. The resulting suspension was filtered through a 100 μm nylon mesh (Thermofisher Scientific, Burlington, ON, Canada) and the enzymatic reaction was terminated by 0.9 mM EDTA. The cell suspension was than centrifuged and the resulting pellet was resuspended in 5 ml DPBS (Lonza, Basel, Switzerland), thoroughly filtered through 40 μm filter (Corning Life Sciences, Tewksbury, MA, USA) and centrifuged again. According to its size, the resulting pellet was resuspended in 500 - 1000 μl of cold RBC lysis buffer (Thermofischer Scientific, Burlington, ON, Canada) for 3-5 minutes until white appearance of the suspension was achieved. The cell suspension was than diluted by DPBS (Lonza, Basel, Switzerland) to a total volume of 5ml, centrifuged and washed twice. Cells were counted using both, the Scepter™ automated cell counter (Millipore-Sigma, Burlington, MA, USA) and a manual hematocyter (Bright-Line™ Hematocyter; Sigma-Aldrich, Oakville, ON, Canada).

extract_protocol:
Cells were lysed in droplets in the 10x Genomics Chromium system.
cDNA synthesis and library construction was performed using the 10x Genomics Single Cell 3' Reagent Kit v3

tag: strain

tag: developmental stage

tag: tissue


title: Lung_P14_1


title: 200681360009_C

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

tag: dosanjh

value: TRUE

tag: weight (kg)

value: Culture, OTHER, Smear Microscopy


title: 3998675065_L

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

value: Cancer

tag: height (cm)

tag: bmi

value: Indian

tag: hiv positive

value: Histology

tag: tst


title: 3998675040_E

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

tag: title

tag: sampledate at t0

value: URTI

value: Chest or Thorax

value: Male

value: Clinical Features

tag: pcr

tag: qtf-git

value: NEGATIVE


title: 3998675043_B

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

tag: diagnosis

value: Other

tag: eptborptb

tag: site of infection

tag: smear microscopy

value: Negative

value: OTHER


title: 3998703013_A

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

value: Pneumonia

value: OD

value: Lung

tag: culture result

tag: age

tag: gender

value: Female

value: POSITIVE


title: Lung_P7_1

description: 10x Genomics library of a MULTI-seq pool of P7 lung tissue from control and hyperoxia-exposed animals (n=3 lung samples per condition).

tag: strain

tag: developmental stage

tag: tissue


title: shGFP_Ctrl_GPS2_rp1

tag: cell type

value: Macrophage

value: BALB/c

tag: antibody

tag: agent

value: No treatment


title: S_KO_Ctrl_GPS2_rp2


title: 3998675092_L

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

tag: title

tag: dosanjh

value: LTBI - treatment indicated

value: TRUE

tag: height (cm)

tag: weight (kg)

tag: bmi

value: Indian

tag: hiv positive

value: FALSE

value: Culture

tag: tst

tag: tst result


title: 3998675029_A

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

tag: sampledate at t0

tag: diagnosis

tag: eptborptb

tag: site of infection

tag: smear microscopy

tag: culture result

value: Male

value: Imaging

tag: pcr

tag: qtf-git

value: NEGATIVE


title: Lung_P3_2

description: 10x Genomics library of a MULTI-seq pool of P3 lung tissue from control and hyperoxia-exposed animals (n=3 lung samples per condition).

tag: strain

tag: developmental stage

tag: tissue


title: S_KO_Ctrl_GPS2_rp1

tag: cell type

tag: antibody

tag: agent


title: 3998720112_K

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

tag: title

tag: dosanjh

value: Other

tag: age

tag: gender

tag: height (cm)

tag: weight (kg)

tag: bmi

value: White

tag: hiv positive


title: 3998675074_A

description:
RNA was isolated using 1.5 ml whole blood and the MagMAX-96 Blood RNA Isolation Kit (Applied Biosystems/Ambion)
3998675074_A

tag: sampledate at t0

tag: diagnosis

value: LRTI, Other

tag: eptborptb

value: OD

tag: site of infection

tag: smear microscopy

tag: culture result

value: Negative

value: OTHER

tag: tst


title: 3998675095_F

description:
RNA was isolated using 1.5 ml whole blood and the MagMAX-96 Blood RNA Isolation Kit (Applied Biosystems/Ambion)
3998675095_F

tag: tst result

tag: pcr

tag: qtf-git

value: POSITIVE


title: 3998703010_A

description:
RNA was isolated using 1.5 ml whole blood and the MagMAX-96 Blood RNA Isolation Kit (Applied Biosystems/Ambion)
3998703010_A

tag: title

tag: dosanjh

value: Lung

value: Female

value: IGRA


title: 3998675065_E

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

value: Pneumonia

value: TRUE

tag: age

tag: gender

value: Clinical Features


title: 3998734084_D

description:
RNA was isolated using 1.5 ml whole blood and the MagMAX-96 Blood RNA Isolation Kit (Applied Biosystems/Ambion)
3998734084_D

value: Lymph node

tag: height (cm)

tag: weight (kg)

value: Black

value: FALSE

value: Culture


title: GPS2_KO_Ctrl_GPS2_rp2

tag: cell type

value: Macrophage

tag: strain

value: BALB/c

tag: antibody

tag: agent

value: No treatment


title: 3998720107_H

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

tag: sampledate at t0

tag: diagnosis

value: Sarcoidosis

tag: eptborptb

value: OD

tag: bmi

value: Indian

tag: hiv positive

value: NEGATIVE


title: Lung_P3_P7_1

description: 10x Genomics library of a MULTI-seq pool of P3 and P7 lung tissue from control and hyperoxia-exposed animals (n=3 lung samples per condition and time point).

tag: developmental stage

value: P3 and P7

tag: tissue

value: Lung


title: 3998675029_J

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

tag: title

value: LTBI - treatment indicated

tag: site of infection

tag: smear microscopy

tag: culture result

value: Negative

value: Female

value: White

tag: tst

tag: pcr

tag: qtf-git

value: POSITIVE


title: GPS2_KO_Ctrl_GPS2_rp1

tag: cell type

tag: strain


title: 3998720107_A

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

tag: dosanjh

value: Other

value: TRUE

tag: age

tag: gender

value: Male

tag: height (cm)

tag: weight (kg)

tag: tst result


title: E_KO_Ctrl_GPS2_rp2

value: Macrophage

tag: antibody

tag: agent


title: Lung_P3_P7_2

tag: developmental stage

tag: tissue


title: Severe_SYH_17

city: Daejeon

first: Galam

last: Leem

address: 291 Daehakro Yusunggu

country: South Korea

institute: KAIST

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to hg19 whole genome using Bowtie2
Fastq files were mapped to hg19 whole genome using STAR.
Genome_build: hg19
Supplementary_files_format_and_content: Normalized read counts processed by DESeq2

molecule: polyA RNA

source_name: PBMC (NK cells)

growth_protocol: NK cells were sorted from PBMC by ARIA sorter.

extract_protocol:
RNA was extracted from cells with TRIzol RNA isolation reagents.
Poly(A) RNA Selection + SMARTer stranded RNA-Seq kit HT; QuantSeq 3' mRNA-Seq Library Prep Kit FWD

treatment_protocol: Untreated

value: PBMC

value: NK cells

tag: treatment

value: Untreated

tag: disease state

tag: disease severity

value: Severe


title: Severe_SYH_05


title: 3998720079_K

description:
RNA was isolated using 1.5 ml whole blood and the MagMAX-96 Blood RNA Isolation Kit (Applied Biosystems/Ambion)
3998720079_K

tag: title

tag: sampledate at t0

tag: diagnosis

tag: eptborptb

value: OD

tag: smear microscopy

tag: culture result

tag: bmi

value: Indian

tag: hiv positive

value: FALSE

value: Clinical Features

tag: tst

tag: pcr


title: E_KO_Ctrl_GPS2_rp1

tag: cell type

tag: strain

value: BALB/c

tag: antibody

value: No treatment


title: 02_0406_sp_CD27lo

description:
cancer immunotherapy
*** Comment from submitter: "Adaptive ImmunoSeq, which is where the aligned TCR data are available, has no fastq files. the files uploaded here are what's being given to us." ***

tag: Sex

value: Female

tag: tumor type

value: splenic CD27loCX3CR1lo CD8 T cells

value: anti-CTLA-4 Ab/anti-PD-L1 Ab


title: Severe_SYH_23

tag: tissue

tag: treatment

tag: disease state


title: WT_Ctrl_H3K27me3

tag: agent


title: 3998675112_A

description:
RNA was isolated using 1.5 ml whole blood and the MagMAX-96 Blood RNA Isolation Kit (Applied Biosystems/Ambion)
3998675112_A

tag: title

tag: sampledate at t0

tag: dosanjh

tag: diagnosis

value: Other

tag: site of infection

value: Lung

value: Negative

tag: age

tag: gender

tag: height (cm)

tag: weight (kg)

value: White

value: IGRA

tag: qtf-git

value: NEGATIVE


title: 3998703044_B

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

tag: eptborptb

tag: smear microscopy

tag: hiv positive

value: Imaging

tag: tst

tag: pcr


title: 3998675065_C

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

value: Pneumonia

value: TRUE

tag: culture result

tag: bmi

value: Culture


title: Severe_SJY_26

tag: tissue

value: PBMC

tag: cell type

value: NK cells

tag: treatment

value: Untreated

tag: disease state

tag: disease severity

value: Severe


title: S_KO_Ctrl_H3K27me3

value: Macrophage

tag: strain

value: BALB/c

tag: antibody

tag: agent

value: No treatment


title: 3998675106_B

description:
RNA was isolated using 1.5 ml whole blood and the MagMAX-96 Blood RNA Isolation Kit (Applied Biosystems/Ambion)
3998675106_B

tag: title

tag: sampledate at t0

tag: dosanjh

tag: diagnosis

value: Other

value: OD

tag: site of infection

value: Lymph node, OTHER

tag: age

tag: gender

value: Female

tag: height (cm)

tag: weight (kg)

value: Black

value: FALSE


title: Severe_SJY_19

tag: tissue


title: 3998675106_F

description:
RNA was isolated using 1.5 ml whole blood and the MagMAX-96 Blood RNA Isolation Kit (Applied Biosystems/Ambion)
3998675106_F

tag: eptborptb

value: Lung

tag: smear microscopy

tag: culture result

value: Negative

value: Male

tag: bmi

value: Indian

tag: hiv positive

value: Clinical Features

tag: tst

tag: pcr

tag: qtf-git

value: POSITIVE


title: 3998720106_E

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

tag: title

tag: sampledate at t0

value: Pneumonia

value: TRUE

value: Culture

value: NEGATIVE


title: 3998675069_B

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

value: No date

tag: dosanjh

tag: diagnosis

value: INDETERMINATE


title: 01_0330_sp_CD27lo

tag: strain

tag: Sex

tag: tumor type

tag: cell type

value: splenic CD27loCX3CR1lo CD8 T cells

tag: treatment

value: anti-CTLA-4 Ab/anti-PD-L1 Ab


title: 3998734102_H

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

value: LTBI - treatment indicated

tag: eptborptb

value: OD

tag: age

tag: gender

tag: height (cm)

tag: weight (kg)

tag: tst result


title: 3998734069_J

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

value: LTBI - treatment indicated, Other

tag: site of infection

value: Pleura

tag: smear microscopy

tag: culture result

value: White

tag: hiv positive

value: FALSE

tag: tst

tag: pcr


title: E_KO_Ctrl_H3K27me3

value: Macrophage

tag: strain

value: BALB/c

tag: antibody

tag: agent

value: No treatment


title: Severe_SJY_10

tag: tissue

value: PBMC

tag: cell type

value: NK cells

value: Untreated

tag: disease state

tag: disease severity

value: Severe


title: WT_LPS_JunB_rp2

value: JunB

value: LPS

tag: time point

value: 2 hours


title: Severe_SJY_05

tag: treatment


title: WT_LPS_JunB_rp1


title: Severe_LNK_24


title: WT_Ctrl_JunB_rp2


title: Severe_LNK_13


title: Severe_LNK_05


title: WT_Ctrl_JunB_rp1


title: Severe_LHD_24


title: S_KO_Ctrl_JunB_rp1


title: S_KO_Ctrl_JunB_rp2


title: Severe_LHD_10


title: GPS2_KO_LPS_JunB_rp2


title: GPS2_KO_LPS_JunB_rp1


title: 3998675086_D

description:
RNA was isolated using 1.5 ml whole blood and the MagMAX-96 Blood RNA Isolation Kit (Applied Biosystems/Ambion)
3998675086_D

tag: title

tag: sampledate at t0

tag: dosanjh

tag: diagnosis

value: Other

tag: eptborptb

value: Lung

value: TRUE

value: Negative

tag: age

tag: gender

value: Male

tag: height (cm)

tag: weight (kg)

tag: bmi

value: Indian

value: Culture

tag: qtf-git

value: NEGATIVE


title: Severe_KYJ_27

tag: tissue


title: GPS2_KO_Ctrl_JunB_rp2

tag: cell type

value: Macrophage

tag: strain

value: BALB/c

tag: antibody

tag: agent


title: Severe_LHD_05

value: PBMC

tag: treatment

tag: disease state

tag: disease severity


title: Severe_KYJ_18

value: NK cells


title: Severe_KYJ_10

value: Untreated


title: 3998703016_E

description:
RNA was isolated using 1.5 ml whole blood and the MagMAX-96 Blood RNA Isolation Kit (Applied Biosystems/Ambion)
3998703016_E

tag: title

tag: sampledate at t0

tag: dosanjh

value: OD

tag: site of infection

tag: smear microscopy

tag: culture result

value: Black

tag: hiv positive

value: Clinical Features, Imaging

tag: tst

value: FALSE

tag: pcr

tag: pcr result

value: INDETERMINATE


title: E_KO_Ctrl_JunB_rp2

tag: cell type

value: JunB

value: No treatment


title: 3998720100_E

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

tag: diagnosis

value: Other

tag: eptborptb

value: Lung

value: TRUE

value: Negative

tag: age

tag: gender

value: Female

tag: height (cm)

tag: weight (kg)

tag: bmi

value: White

tag: qtf-git

value: POSITIVE


title: 3998675110_I

description:
RNA was isolated using 1.5 ml whole blood and the MagMAX-96 Blood RNA Isolation Kit (Applied Biosystems/Ambion)
3998675110_I

tag: title

tag: sampledate at t0

tag: dosanjh

value: Mixed

value: Culture, Imaging

tag: tst result

value: NEGATIVE


title: GPS2_KO_Ctrl_JunB_rp1

value: Macrophage

tag: strain

value: BALB/c

tag: antibody

tag: agent


title: Severe_KDS_24

tag: tissue

value: PBMC

value: NK cells

tag: treatment

value: Untreated

tag: disease state

tag: disease severity

value: Severe


title: 3998720100_K

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

tag: diagnosis

value: Pneumonia

tag: eptborptb

value: OD

tag: site of infection

tag: smear microscopy

tag: culture result

tag: age

value: Male

tag: hiv positive

value: Clinical Features, Smear Microscopy

tag: tst

value: FALSE

tag: pcr

tag: pcr result

value: INDETERMINATE


title: 3998675114_B

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

tag: title

tag: sampledate at t0

tag: dosanjh

value: Other

value: TRUE

value: Negative

tag: gender

tag: height (cm)

tag: weight (kg)

tag: bmi

value: White

value: Culture

tag: qtf-git


title: 3998703010_L

description:
RNA was isolated using 1.5 ml whole blood and the MagMAX-96 Blood RNA Isolation Kit (Applied Biosystems/Ambion)
3998703010_L

tag: diagnosis

value: Cancer

tag: eptborptb

value: Lung

value: Black

value: Histology, Smear Microscopy

value: NEGATIVE


title: 3998675096_D

description:
RNA was isolated using 1.5 ml whole blood and the MagMAX-96 Blood RNA Isolation Kit (Applied Biosystems/Ambion)
3998675096_D

value: Sarcoidosis

tag: smear microscopy

value: Indian

value: Clinical Features

tag: tst result


title: 3998734063_F

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

value: OD

tag: site of infection

tag: culture result

tag: age

value: Male

value: Clinical Features, Imaging


title: 3998734071_G

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

value: Pneumonia

value: Female

tag: hiv positive

value: FALSE

tag: tst

tag: pcr

value: INDETERMINATE


title: 200683670009_B

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

tag: title

tag: sampledate at t0

value: Other, Sarcoidosis

value: TRUE

value: Negative

tag: pcr result

value: POSITIVE


title: 3998675093_D

description:
RNA was isolated using 1.5 ml whole blood and the MagMAX-96 Blood RNA Isolation Kit (Applied Biosystems/Ambion)
3998675093_D

tag: dosanjh

value: Other

tag: gender

value: Black


title: 200681360001_L

description:
RNA was isolated using 1.5 ml whole blood and the MagMAX-96 Blood RNA Isolation Kit (Applied Biosystems/Ambion)
200681360001_L

tag: height (cm)

tag: weight (kg)

tag: bmi

value: OTHER

value: NEGATIVE


title: 3998734087_I

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

tag: diagnosis

tag: eptborptb

value: White

tag: qtf-git


title: 200683670009_I

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

tag: smear microscopy

value: Indian

value: Clinical Features

tag: tst result


title: 3998675056_D

description:
RNA was isolated using 1.5 ml whole blood and the MagMAX-96 Blood RNA Isolation Kit (Applied Biosystems/Ambion)
3998675056_D

value: OD

tag: culture result

tag: age

value: Male

value: Clinical Features, Culture, Imaging


title: 3998720100_C

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

tag: site of infection

value: Urinary tract

value: Female

tag: hiv positive

tag: tst


title: 3998675101_H

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

tag: title

tag: sampledate at t0

value: Sarcoidosis

value: Lung, Mediastinum

value: FALSE

value: Clinical Features, Histology, Imaging

tag: pcr


title: 3998675065_J

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

tag: dosanjh

value: LTBI - treatment indicated, Other

tag: gender

value: Clinical Features, Imaging

value: INDETERMINATE


title: 3998675092_E

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

value: Cancer

value: TRUE

value: Negative

tag: height (cm)

tag: weight (kg)

value: Black

value: Histology, IGRA

tag: pcr result

value: POSITIVE


title: 3998675068_A

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

tag: diagnosis

value: Other

tag: eptborptb

value: OD

value: Lung

tag: bmi

value: Clinical Features, OTHER

value: NEGATIVE


title: 3998734063_D

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

value: Sarcoidosis

tag: smear microscopy

value: Male

value: Asian

tag: qtf-git


title: 3998675027_L

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

tag: culture result

tag: age

value: FALSE

value: Clinical Features, Imaging, OTHER

tag: tst result


title: 3998675106_J

description:
RNA was isolated using 1.5 ml whole blood and the MagMAX-96 Blood RNA Isolation Kit (Applied Biosystems/Ambion)
3998675106_J

value: Female

value: White

tag: hiv positive

value: Clinical Features

tag: tst


title: Severe_KDS_10

tag: tissue

value: PBMC

tag: cell type

value: NK cells

tag: treatment

value: Untreated

tag: disease state

tag: disease severity

value: Severe


title: 3998720110_B

description:
RNA was isolated using 1.5 ml whole blood and the MagMAX-96 Blood RNA Isolation Kit (Applied Biosystems/Ambion)
3998720110_B

tag: title

tag: sampledate at t0

tag: dosanjh

value: Other

value: TRUE

value: Negative

tag: gender

tag: height (cm)

tag: weight (kg)

tag: pcr


title: 3998734064_H

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

tag: diagnosis

value: Pneumonia

tag: eptborptb

value: OD

tag: site of infection

value: Lung

tag: smear microscopy

tag: culture result

tag: bmi

tag: qtf-git


title: 3998675049_D

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

tag: age

value: Male

value: Black

tag: hiv positive

tag: tst

value: POSITIVE

value: NEGATIVE


title: 200681360014_G

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

tag: title

value: Female

value: Indian

value: FALSE

value: Clinical Features, Imaging

tag: tst result

tag: pcr result


title: 3998675119_D

description:
RNA was isolated using 1.5 ml whole blood and the MagMAX-96 Blood RNA Isolation Kit (Applied Biosystems/Ambion)
3998675119_D

tag: sampledate at t0

tag: dosanjh

value: Sarcoidosis

value: Lymph node

tag: gender

value: Histology


title: WT_LPS_MED1_rp2

tag: cell type

value: Macrophage

tag: strain

value: BALB/c

tag: antibody

tag: agent

value: LPS

tag: time point

value: 2 hours