title: Severe_KDS_05

tag: tissue

value: PBMC

value: NK cells

tag: treatment

value: Untreated

tag: disease state

tag: disease severity

value: Severe


title: Severe_KC_23

status: Public on Jan 26 2021

type: SRA

city: Daejeon

first: Galam

last: Leem

address: 291 Daehakro Yusunggu

country: South Korea

institute: KAIST

library_source: transcriptomic

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

organism: Homo sapiens

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

tag: cell type


title: WT_LPS_MED1_rp1

city: Nanjing

first: Zhiqiang

last: Huang

state: Jiangsu

address: Hankou 22

department: Medical School

country: China

institute: Nanjing University

library_source: genomic

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.

molecule: genomic DNA

organism: Mus musculus

source_name: RAW264.7 cells

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)

value: Macrophage

tag: strain

value: BALB/c

tag: antibody

tag: agent

value: LPS

tag: time point

value: 2 hours


title: Severe_KC_03


title: WT_Ctrl_MED1_rp1

value: No treatment


title: WT_Ctrl_MED1_rp2


title: Severe_KC_07


title: S_KO_Ctrl_MED1_rp2


title: S_KO_Ctrl_MED1_rp1


title: 3998675027_J

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)
3998675027_J

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

molecule: total RNA

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: Other

tag: eptborptb

value: OD

tag: site of infection

value: Lung

tag: smear microscopy

value: TRUE

tag: culture result

value: Negative

tag: age

tag: gender

value: Female

tag: height (cm)

tag: weight (kg)

tag: bmi

value: MiddleEast

tag: hiv positive

value: FALSE

value: OTHER

tag: tst

tag: pcr

tag: pcr result

tag: qtf-git

value: POSITIVE

value: NEGATIVE


title: Severe_CHR_14

tag: tissue

value: PBMC

tag: cell type

value: NK cells

tag: treatment

value: Untreated

tag: disease state

tag: disease severity

value: Severe


title: 3998675069_D

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

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

tag: title

tag: sampledate at t0

tag: dosanjh

tag: diagnosis

value: Sarcoidosis

tag: eptborptb

tag: site of infection

value: Lung, Lymph node

tag: smear microscopy

value: Male

value: Black

value: Imaging


title: 3998675101_L

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

value: Pneumonia

value: OD

value: Chest or Thorax

value: TRUE

tag: culture result

tag: age

tag: gender

tag: height (cm)

tag: weight (kg)

tag: bmi

value: White

tag: hiv positive

value: Culture


title: 3998675029_K

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

value: Other

value: Negative

value: FALSE

value: Clinical Features

tag: tst

tag: tst result

tag: pcr

tag: qtf-git

value: MISSING


title: 3998703013_K

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

tag: title

tag: sampledate at t0

value: OTHER

value: Female

value: POSITIVE


title: 3998703013_I

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

tag: dosanjh

tag: diagnosis

value: Sarcoidosis

value: Male

value: Indian

tag: pcr result

value: NEGATIVE


title: GPS2_KO_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


title: 3998675093_G

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

tag: eptborptb

value: OD

tag: site of infection

value: Lung

tag: smear microscopy

value: TRUE

tag: culture result

tag: age

tag: gender

tag: height (cm)

tag: weight (kg)

value: White

value: Histology


title: E_KO_Ctrl_JunB_rp1

value: JunB

value: No treatment


title: GPS2_KO_LPS_MED1_rp1


title: 3998675120_C

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

tag: title

tag: sampledate at t0

value: Chest Infection

value: Negative

value: Female

tag: bmi

tag: hiv positive

value: FALSE

value: Clinical Features, Culture

tag: tst

tag: pcr

value: Indeterminate

tag: qtf-git


title: Severe_CHR_23

tag: tissue

value: PBMC

tag: cell type

value: NK cells

tag: treatment

value: Untreated

tag: disease state

tag: disease severity

value: Severe


title: 3998703022_J

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

tag: dosanjh

tag: diagnosis

value: Pneumonia

tag: eptborptb

value: OD

tag: site of infection

tag: smear microscopy

value: Male

value: Culture

tag: tst result

value: INDETERMINATE

value: NEGATIVE


title: 3998675029_B

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

tag: title

tag: sampledate at t0

value: Other

value: OTHER

tag: age

tag: gender

tag: height (cm)

tag: weight (kg)

value: Black

value: Clinical Features, Imaging

value: POSITIVE


title: E_KO_Ctrl_MED1_rp2

value: Macrophage

tag: strain

value: BALB/c

tag: antibody

tag: agent

value: No treatment


title: 3998703022_G

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

value: Sarcoidosis

value: Lung

value: TRUE

tag: culture result

value: Negative

value: Female

tag: bmi

value: White

tag: hiv positive

value: FALSE

value: Histology

tag: tst

tag: pcr

tag: qtf-git


title: 3998675068_C

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

tag: dosanjh

tag: diagnosis

tag: eptborptb

value: OD

tag: site of infection

value: Throat

tag: smear microscopy

value: Male

value: MiddleEast

value: Clinical Features

value: NEGATIVE


title: E_KO_Ctrl_MED1_rp1

tag: cell type

value: Macrophage


title: Mild_YTY_14

tag: tissue

value: PBMC

value: NK cells

tag: treatment

value: Untreated

tag: disease state

tag: disease severity

value: mild


title: 3998675040_F

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

tag: title

tag: sampledate at t0

value: Pneumonia

value: Lung

value: TRUE

tag: age

tag: gender

tag: height (cm)

tag: weight (kg)

value: Black


title: 3998734070_E

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

value: Sarcoidosis

value: Chest or Thorax, Lung

tag: culture result

value: Negative

tag: bmi

value: Indian

tag: hiv positive

value: FALSE

tag: tst

tag: pcr

tag: pcr result

tag: qtf-git


title: 3998675119_K

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

tag: dosanjh

tag: diagnosis

value: Other

tag: eptborptb

value: OD

tag: smear microscopy

value: Male

value: Clinical Features, Imaging


title: 3998675040_G

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

tag: title

value: Cancer, LTBI - treatment indicated

value: Female

value: MiddleEast

value: OTHER

tag: tst result

value: POSITIVE


title: 3998703004_B

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

tag: sampledate at t0

value: LRTI

tag: site of infection

value: Lung

tag: age

value: Culture

value: NEGATIVE


title: Mild_YTY_07

tag: tissue

value: PBMC

tag: cell type

value: NK cells

tag: treatment

value: Untreated

tag: disease state

tag: disease severity

value: mild


title: Mild_YSH_14


title: WT_LPS_PolII_rp2

value: Macrophage

tag: strain

value: BALB/c

tag: antibody

value: PolII

tag: agent

value: LPS

tag: time point

value: 2 hours


title: Mild_YSH_07


title: WT_LPS_PolII_rp1


title: 3998703013_J

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

tag: dosanjh

tag: diagnosis

value: Other

value: OD

value: TRUE

tag: culture result

value: Negative

tag: gender

value: Male

tag: weight (kg)

tag: hiv positive

value: FALSE

tag: tst

tag: pcr

tag: qtf-git


title: WT_Ctrl_PolII_rp2

tag: cell type

value: No treatment


title: 3998734069_B

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

tag: title

tag: sampledate at t0

tag: eptborptb

tag: site of infection

value: Lymph node

tag: smear microscopy

tag: age

value: Female

tag: height (cm)

tag: bmi

value: Indian

value: Clinical Features, Culture

tag: pcr result

value: NEGATIVE

value: POSITIVE


title: 3998675106_L

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

tag: dosanjh

tag: diagnosis

value: Lung, Lymph node

tag: culture result

value: Histology


title: WT_Ctrl_PolII_rp1

value: Macrophage

tag: strain

value: BALB/c

tag: antibody

value: PolII

tag: agent


title: Mild_YTY_01

tag: tissue

value: PBMC

value: NK cells

tag: treatment

value: Untreated

tag: disease state

tag: disease severity

value: mild


title: Mild_YKS_13

tag: cell type


title: 200681360011_H

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

tag: title

tag: sampledate at t0

value: Pneumonia

tag: eptborptb

value: OD

tag: site of infection

value: Lung

value: TRUE

value: Negative

tag: gender

tag: weight (kg)

value: Mixed

tag: hiv positive

value: Clinical Features

tag: tst

value: FALSE

tag: pcr

tag: qtf-git

value: INDETERMINATE


title: Mild_YKS_07


title: S_KO_LPS_PolII_rp2

tag: strain

tag: antibody

value: LPS

tag: time point

value: 2 hours


title: Mild_YSH_01

tag: tissue

tag: treatment


title: 3998675081_L

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

tag: dosanjh

tag: diagnosis

value: Other

tag: smear microscopy

tag: culture result

tag: age

value: Male

tag: height (cm)

tag: bmi

value: White

value: NEGATIVE

value: POSITIVE


title: Mild_YKS_01

value: PBMC

tag: cell type

value: NK cells

value: Untreated

tag: disease state

tag: disease severity

value: mild


title: Mild_YCJ_14


title: S_KO_Ctrl_KO_PolII_rp2

value: Macrophage

value: BALB/c

value: PolII

tag: agent

value: No treatment


title: 3998734069_K

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

tag: title

tag: sampledate at t0

value: Cancer

tag: eptborptb

value: OD

tag: site of infection

value: Lung

value: TRUE

tag: gender

value: Female

tag: weight (kg)

value: Black

tag: hiv positive

value: FALSE

value: Histology

tag: tst

tag: pcr

tag: qtf-git


title: 3998734069_E

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

tag: dosanjh

tag: diagnosis

value: Other, Sarcoidosis

tag: smear microscopy

tag: culture result

value: Negative

tag: age

value: Indian

value: OTHER

tag: pcr result

value: NEGATIVE


title: 3998734069_C

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

value: Other

value: Male

value: White


title: 3998675102_H

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

value: POSITIVE


title: 3998675119_B

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

value: Sarcoidosis

value: Lymph node

tag: height (cm)

value: MiddleEast

value: INDETERMINATE


title: 3998675092_J

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

tag: title

value: Cancer

value: OD

value: Lung

tag: bmi

value: Asian


title: Mild_YCJ_07

tag: tissue

value: PBMC

tag: cell type

value: NK cells

tag: treatment

value: Untreated

tag: disease state

tag: disease severity

value: mild


title: 3998675102_D

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

tag: sampledate at t0

value: Pneumonia

tag: eptborptb

tag: site of infection

value: TRUE

value: Negative

tag: gender

tag: weight (kg)

value: Indian

tag: hiv positive

value: FALSE

value: Culture

tag: tst


title: 3998703010_J

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

tag: dosanjh

tag: diagnosis

tag: smear microscopy

tag: culture result

tag: age

value: Male

value: Black

tag: pcr

tag: qtf-git

value: NEGATIVE


title: 3998675102_G

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

tag: title

value: Other

value: Throat

tag: height (cm)

tag: bmi

value: Imaging

value: POSITIVE


title: 3998675112_L

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

tag: sampledate at t0

value: Cancer

value: OD

value: Lung

value: Histology


title: 3998675056_I

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

value: Pneumonia

tag: eptborptb

value: MiddleEast

value: Clinical Features


title: 3998675112_K

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

tag: site of infection

value: TRUE

value: Negative

value: Indian


title: S_KO_Ctrl_KO_PolII_rp1

tag: cell type

value: Macrophage

tag: strain

value: BALB/c

tag: antibody

value: PolII

tag: agent

value: No treatment


title: GPS2_KO_LPS_PolII_rp2

value: LPS

tag: time point

value: 2 hours


title: 3998675102_L

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

tag: dosanjh

tag: diagnosis

value: Other

tag: gender

value: Male

tag: weight (kg)

tag: hiv positive

value: FALSE

tag: tst

tag: pcr result

value: POSITIVE


title: Mild_YCJ_01

tag: tissue

value: PBMC

value: NK cells

tag: treatment

value: Untreated

tag: disease state

tag: disease severity

value: mild


title: 3998675074_F

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

tag: title

tag: sampledate at t0

value: LRTI

tag: eptborptb

value: OD

tag: smear microscopy

value: TRUE

tag: culture result

tag: age

value: Female

tag: height (cm)

tag: bmi

value: White

value: OTHER

tag: tst result

tag: pcr

tag: qtf-git


title: Mild_SWK_24

tag: cell type


title: S_KO_LPS_PolII_rp1

value: Macrophage

tag: strain

value: BALB/c

tag: antibody

value: PolII

tag: agent

tag: time point


title: GPS2_KO_LPS_PolII_rp1

value: LPS

value: 2 hours


title: Mild_SWK_07

tag: tissue

tag: treatment

tag: disease state

tag: disease severity


title: E_KO_LPS_PolII_rp2


title: E_KO_LPS_PolII_rp1


title: E_KO_Ctrl_KO_PolII_rp2

value: No treatment


title: 3998675091_J

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

tag: title

tag: sampledate at t0

tag: dosanjh

tag: diagnosis

value: Cancer

tag: eptborptb

tag: site of infection

value: Lung

tag: smear microscopy

value: Negative

tag: gender

tag: weight (kg)

tag: hiv positive

value: FALSE

value: Histology

tag: tst

value: NEGATIVE


title: 3998675086_B

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

value: Chest Infection, Other

value: OD

tag: culture result

tag: age

value: Male

tag: height (cm)

tag: bmi

value: Clinical Features

tag: tst result

tag: pcr

tag: pcr result

tag: qtf-git


title: Mild_SWK_01

tag: tissue

value: PBMC

tag: cell type

value: NK cells

tag: treatment

value: Untreated

tag: disease state

tag: disease severity

value: mild


title: 3998720105_F

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

tag: title

tag: sampledate at t0

tag: dosanjh

tag: diagnosis

value: Pneumonia

tag: eptborptb

tag: site of infection

tag: smear microscopy

value: TRUE

tag: gender

value: Female

value: MiddleEast


title: 3998734089_B

description:
RNA was isolated using 1.5 ml whole blood and the MagMAX-96 Blood RNA Isolation Kit (Applied Biosystems/Ambion)
3998734089_B

value: Other

value: Lung

tag: culture result

tag: age

tag: height (cm)

tag: weight (kg)

tag: bmi

value: Indian

tag: hiv positive

value: Smear Microscopy

tag: tst


title: Mild_PHS_14

tag: tissue

tag: cell type

tag: treatment

tag: disease state


title: 3998734082_J

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

tag: title

tag: sampledate at t0

tag: dosanjh

value: Negative

value: White

value: FALSE

value: Culture, Imaging

tag: pcr

tag: pcr result

tag: qtf-git

value: POSITIVE

value: NEGATIVE


title: Mild_PHS_07

value: PBMC

value: NK cells

tag: disease severity


title: 3998734089_I

description:
RNA was isolated using 1.5 ml whole blood and the MagMAX-96 Blood RNA Isolation Kit (Applied Biosystems/Ambion)
3998734089_I

tag: diagnosis

value: Sarcoidosis

tag: eptborptb

value: OD

tag: smear microscopy

tag: age

tag: gender

value: Male

tag: tst result


title: E_KO_Ctrl_KO_PolII_rp1

value: Macrophage

tag: strain

value: BALB/c

tag: antibody

value: PolII

tag: agent

value: No treatment


title: WT_LPS_RUNX1_rp2

tag: cell type

value: LPS

tag: time point

value: 2 hours


title: Severe_CHR_08

tag: tissue

tag: treatment

value: Untreated

tag: disease state

value: Severe


title: 3998675098_E

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

tag: title

tag: sampledate at t0

tag: dosanjh

tag: site of infection

value: Lymph node

value: TRUE

tag: culture result

value: Negative

value: Female

tag: height (cm)

tag: weight (kg)

tag: bmi

value: White

tag: hiv positive

value: FALSE

value: OTHER

tag: tst

tag: pcr

tag: pcr result


title: Mild_LSM_14

value: PBMC

tag: cell type

value: NK cells

tag: disease severity

value: mild


title: WT_LPS_RUNX1_rp1

value: Macrophage

tag: strain

value: BALB/c

tag: antibody

tag: agent

tag: time point


title: 3998734082_K

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

tag: title

tag: sampledate at t0

tag: diagnosis

value: Other

tag: eptborptb

value: OD

tag: smear microscopy

tag: age

tag: gender

value: Male

value: Black

tag: qtf-git

value: POSITIVE


title: Mild_LSM_07

tag: tissue

tag: treatment

value: Untreated

tag: disease state


title: 3998675098_G

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

tag: dosanjh

value: Chest Infection, Other

tag: site of infection

value: Lung

value: TRUE

tag: culture result

tag: height (cm)

tag: weight (kg)

tag: bmi

tag: hiv positive

value: Clinical Features, Imaging

tag: tst

tag: pcr


title: 3998675096_E

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

tag: title

tag: sampledate at t0

tag: diagnosis

value: Sarcoidosis

tag: eptborptb

value: FALSE

value: Negative

value: Indian

value: Histology, Imaging

value: NEGATIVE


title: Mild_LSM_01

value: PBMC

tag: cell type

value: NK cells

tag: disease severity

value: mild


title: 3998675115_L

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

value: Other

value: OD

tag: smear microscopy

tag: age

tag: gender

value: Female

value: Clinical Features, Histology

tag: tst result

tag: pcr result

tag: qtf-git


title: Mild_PHS_01

tag: tissue

tag: treatment

value: Untreated

tag: disease state


title: 3998675096_F

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

tag: dosanjh

value: Pneumonia

tag: site of infection

value: Lung

tag: culture result

value: Male

value: Black

tag: hiv positive

value: Culture

tag: tst

value: POSITIVE

value: INDETERMINATE


title: 3998675108_L

description:
RNA was isolated using 1.5 ml whole blood and the MagMAX-96 Blood RNA Isolation Kit (Applied Biosystems/Ambion)
3998675108_L

tag: title

tag: sampledate at t0

tag: diagnosis

value: Cancer

tag: eptborptb

value: FALSE

value: Negative

tag: height (cm)

tag: weight (kg)

tag: bmi

value: White

value: Histology

tag: pcr


title: WT_Ctrl_RUNX1_rp1

tag: cell type

value: Macrophage

tag: strain

value: BALB/c

tag: antibody

tag: agent

value: No treatment


title: S_KO_Ctrl_RUNX1_rp2


title: Mild_KYM_17

tag: tissue

value: PBMC

value: NK cells

tag: treatment

tag: disease state

tag: disease severity

value: mild


title: 3998675108_H

description:
RNA was isolated using 1.5 ml whole blood and the MagMAX-96 Blood RNA Isolation Kit (Applied Biosystems/Ambion)
3998675108_H

tag: dosanjh

value: Pneumonia

value: OD

tag: site of infection

value: Lung

tag: smear microscopy

value: TRUE

tag: culture result

tag: age

tag: gender

tag: hiv positive

tag: tst

tag: qtf-git

value: NEGATIVE


title: WT_Ctrl_RUNX1_rp2

tag: cell type


title: S_KO_Ctrl_RUNX1_rp1

tag: strain


title: 3998675098_I

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

tag: title

tag: sampledate at t0

tag: diagnosis

value: Other

tag: eptborptb

value: Female

tag: height (cm)

tag: weight (kg)

tag: bmi

value: Indian

value: Clinical Features

tag: pcr


title: 200683670009_A

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

tag: dosanjh

tag: site of infection

tag: smear microscopy

value: FALSE

value: White

value: Clinical Features, Imaging

value: POSITIVE


title: 3998675108_J

description:
RNA was isolated using 1.5 ml whole blood and the MagMAX-96 Blood RNA Isolation Kit (Applied Biosystems/Ambion)
3998675108_J

value: Lymph node

tag: culture result

value: Negative

tag: age

tag: gender

value: Histology

tag: pcr result


title: Mild_KYM_10

tag: tissue

value: PBMC

tag: cell type

value: NK cells

tag: treatment

value: Untreated

tag: disease state

tag: disease severity

value: mild


title: 3998675108_F

description:
RNA was isolated using 1.5 ml whole blood and the MagMAX-96 Blood RNA Isolation Kit (Applied Biosystems/Ambion)
3998675108_F

tag: title

tag: sampledate at t0

tag: diagnosis

value: Sarcoidosis

tag: eptborptb

value: OD

value: TRUE

tag: hiv positive

tag: tst

tag: qtf-git


title: E_KO_Ctrl_RUNX1_rp2

value: Macrophage

tag: strain

value: BALB/c

tag: antibody

tag: agent

value: No treatment


title: 3998734078_C

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

tag: dosanjh

value: Other

tag: smear microscopy

tag: culture result

tag: age

tag: gender

value: Female

tag: weight (kg)

value: Black

value: FALSE

tag: tst result

tag: pcr


title: 3998675096_C

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

tag: title

tag: sampledate at t0

value: Pneumonia

tag: site of infection

value: Lung

value: Male

tag: height (cm)

tag: bmi

value: Culture

value: NEGATIVE


title: 3998703009_F

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

tag: diagnosis

tag: eptborptb

value: Negative

value: Unknown

tag: hiv positive

value: Culture, Imaging

tag: tst

tag: qtf-git


title: Mild_KYM_03

tag: tissue

value: PBMC

tag: cell type

value: NK cells

tag: treatment

value: Untreated

tag: disease state

tag: disease severity

value: mild


title: 3998734063_G

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

tag: dosanjh

value: OD

tag: smear microscopy

value: TRUE

tag: culture result

tag: age

tag: gender

tag: weight (kg)

value: Indian

value: Clinical Features

tag: tst result


title: 3998675102_B

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

tag: title

tag: sampledate at t0

tag: diagnosis

value: Other

tag: site of infection

value: Female

value: Black

value: FALSE

value: Clinical Features, Culture

tag: pcr

tag: pcr result


title: 3998675043_L

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

tag: eptborptb

value: Lung

value: Male

tag: height (cm)

tag: bmi

tag: hiv positive

value: Culture

tag: tst

tag: qtf-git

value: NEGATIVE


title: Mild_KoYS_14

tag: tissue

value: PBMC

tag: cell type

tag: treatment

tag: disease state

tag: disease severity


title: 3998675081_F

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

tag: title

tag: dosanjh

tag: smear microscopy

tag: culture result

value: Negative

tag: age

tag: gender

tag: weight (kg)

value: White

value: Histology

value: INDETERMINATE


title: 3998675095_L

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

tag: sampledate at t0

tag: diagnosis

tag: eptborptb

value: OD

tag: site of infection

value: TRUE

tag: height (cm)

value: MiddleEast

value: Culture, Response to Treatment

tag: tst result

tag: pcr

tag: pcr result


title: E_KO_Ctrl_RUNX1_rp1

tag: cell type

value: Macrophage

tag: strain

value: BALB/c

tag: antibody

tag: agent

value: No treatment


title: WT_LPS_SMRT_rp2

value: SMRT

value: LPS

tag: time point

value: 2 hours


title: Mild_KoYS_01

tag: tissue

value: NK cells

tag: treatment

value: Untreated

tag: disease state

tag: disease severity

value: mild


title: WT_LPS_SMRT_rp1


title: Mild_KimYS_14

value: PBMC


title: Mild_KimYS_07


title: WT_Ctrl_SMRT_rp1


title: S_KO_LPS_SMRT_rp2


title: Mild_KimYS_01


title: Mild_KoYS_07


title: S_KO_LPS_SMRT_rp1


title: 3998675095_I

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

tag: title

tag: sampledate at t0

tag: dosanjh

value: Other

value: Lung

tag: smear microscopy

tag: culture result

value: Negative

tag: age

tag: gender

value: Male

tag: weight (kg)

tag: bmi

value: White

tag: hiv positive

value: FALSE

value: Culture

tag: tst

tag: qtf-git

value: NEGATIVE


title: Mild_KHS_07

tag: cell type


title: 3998675043_C

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

tag: diagnosis

tag: eptborptb

value: OD

tag: site of infection

tag: height (cm)

value: Clinical Features

value: TRUE

tag: tst result

tag: pcr


title: 3998675074_G

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

tag: title

tag: sampledate at t0

tag: dosanjh

value: LRTI

value: Female

value: Histology


title: WT_Ctrl_SMRT_rp2

value: Macrophage

tag: strain

value: BALB/c

tag: antibody

value: SMRT

tag: agent

value: No treatment


title: S_KO_Ctrl_SMRT_rp2


title: 3998703010_B

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

value: Other

tag: smear microscopy

tag: age

tag: gender

tag: weight (kg)

tag: bmi

value: Black

value: POSITIVE


title: 3998675102_E

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

tag: diagnosis

value: Cancer

value: Lung

tag: culture result

value: Negative

value: Male

value: White

tag: hiv positive

tag: tst

tag: qtf-git


title: 3998675120_F

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

tag: eptborptb

value: OD

tag: site of infection

value: FALSE

tag: height (cm)

value: Mixed

tag: pcr

value: NEGATIVE


title: 3998720112_I

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

tag: title

tag: sampledate at t0

tag: dosanjh

value: Pneumonia

value: TRUE

value: Clinical Features, OTHER


title: 3998675098_J

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

value: Sarcoidosis

tag: smear microscopy

value: MiddleEast

value: Histology, Response to Treatment

tag: tst result

tag: pcr result


title: 3998675095_C

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

tag: age

tag: gender

tag: weight (kg)

value: Histology


title: 3998675095_D

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

tag: diagnosis

value: Active TB

value: PTB

tag: culture result

tag: bmi

value: Indian

value: Clinical Features

value: POSITIVE


title: S_KO_Ctrl_SMRT_rp1

tag: cell type

value: Macrophage

tag: strain

value: BALB/c

tag: antibody

value: SMRT

tag: agent

value: No treatment


title: E_KO_LPS_SMRT_rp2

value: LPS

tag: time point

value: 2 hours


title: Mild_KHJ_21

tag: tissue

value: PBMC

value: NK cells

tag: treatment

value: Untreated

tag: disease state

tag: disease severity

value: mild


title: Mild_KHS_20


title: 3998675095_E

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

tag: title

tag: sampledate at t0

tag: dosanjh

value: Pneumonia

tag: eptborptb

value: OD

tag: site of infection

value: Lung

tag: smear microscopy

value: TRUE

value: Negative

value: Female

tag: height (cm)

value: White

tag: hiv positive

value: FALSE

tag: tst

tag: pcr

tag: qtf-git

value: NEGATIVE


title: 3998675114_A

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

tag: diagnosis

value: Active TB

value: PTB

tag: culture result

tag: age

tag: gender

value: Male

tag: weight (kg)

value: Indian

value: OTHER

value: POSITIVE


title: 3998675119_L

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

value: EPTB

value: Clinical Features, IGRA, OTHER


title: E_KO_Ctrl_SMRT_rp2

tag: cell type

value: Macrophage

tag: strain

value: BALB/c

tag: antibody

value: SMRT

tag: agent

value: No treatment


title: E_KO_LPS_SMRT_rp1

value: LPS

tag: time point

value: 2 hours


title: 3998675095_A

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

tag: title

tag: sampledate at t0

tag: dosanjh

value: Other

tag: eptborptb

value: OD

tag: site of infection

value: Lung

value: TRUE

value: Negative

tag: bmi

value: Imaging

tag: tst result


title: Mild_KHJ_07

tag: tissue

value: PBMC

value: NK cells

tag: treatment

value: Untreated

tag: disease state

tag: disease severity

value: mild


title: 3998675110_D

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

tag: diagnosis

tag: smear microscopy

tag: culture result

tag: age

tag: gender

value: Male

tag: height (cm)

tag: weight (kg)

value: White

tag: hiv positive

value: FALSE

value: Clinical Features

tag: tst

tag: pcr

tag: qtf-git

value: NEGATIVE


title: 3998720105_K

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

tag: title

tag: sampledate at t0

tag: dosanjh

value: Active TB

tag: eptborptb

value: EPTB

tag: site of infection

value: Lymph node

value: Female

tag: bmi

value: Clinical Features, Histology


title: Mild_KHJ_01

tag: tissue

tag: cell type

tag: treatment

tag: disease state

tag: disease severity


title: 3998675069_I

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

tag: diagnosis

value: Pericardium

tag: smear microscopy

value: TRUE

tag: culture result

tag: age

tag: gender

tag: height (cm)

value: Black

value: POSITIVE


title: 3998734086_J

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

tag: title

value: Negative

value: Indian

tag: hiv positive

value: Histology

tag: tst

tag: pcr

tag: qtf-git


title: 3998675119_C

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

tag: sampledate at t0

tag: dosanjh

tag: eptborptb

value: PTB

tag: site of infection

value: Lung

value: Male

tag: weight (kg)

tag: bmi

value: Imaging

tag: tst result


title: 3998734086_H

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

tag: diagnosis

value: Bowel, OTHER

tag: smear microscopy

value: FALSE


title: 3998675049_H

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

value: Active TB

value: EPTB

tag: culture result

tag: age

value: PCR

tag: pcr result

value: Positive


title: E_KO_Ctrl_SMRT_rp1

tag: cell type

value: Macrophage

tag: strain

value: BALB/c

tag: antibody

value: SMRT

tag: agent

value: No treatment


title: 200683670009_H

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

tag: title

value: TRUE

value: Negative

tag: gender

value: Female

tag: hiv positive

tag: tst

tag: pcr

tag: qtf-git

value: POSITIVE


title: 3998734102_G

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

tag: sampledate at t0

tag: dosanjh

tag: eptborptb

tag: site of infection

value: Lymph node

tag: weight (kg)

value: Indian

value: Histology


title: WT_LPS_PU_1_rp2

value: LPS

tag: time point

value: 2 hours


title: Mild_JHY_13

tag: tissue

value: PBMC

value: NK cells

tag: treatment

value: Untreated

tag: disease state

tag: disease severity

value: mild


title: Mild_JHY_05

tag: cell type


title: WT_Ctrl_PU_1_rp2

value: Macrophage

tag: strain

tag: antibody

tag: agent


title: WT_LPS_PU_1_rp1

value: BALB/c


title: Mild_JHY_17


title: Healthy_SJ

value: Healthy


title: WT_Ctrl_PU_1_rp1

value: No treatment


title: Healthy_SIH


title: Healthy_SEC


title: S_KO_Ctrl_PU_1_rp1


title: 3998720105_A

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

tag: title

tag: diagnosis

value: Active TB

value: EPTB

value: Lymph node, Pleura

tag: smear microscopy

value: TRUE

tag: culture result

tag: age

tag: gender

tag: hiv positive

value: FALSE

tag: tst

tag: tst result


title: 3998720114_J

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

tag: sampledate at t0

tag: dosanjh

tag: eptborptb

tag: site of infection

value: Lymph node

value: Negative

value: Male

tag: weight (kg)

value: Indian

tag: pcr

tag: qtf-git

value: POSITIVE

value: INDETERMINATE


title: 3998675114_E

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

value: Female

value: Histology, Smear Microscopy

value: MISSING


title: Healthy_PSH

tag: tissue

value: PBMC

tag: cell type

value: NK cells

tag: treatment

value: Untreated

tag: disease state

tag: disease severity


title: 3998734071_H

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

tag: title

tag: diagnosis

value: Active TB

value: Brain, Pleura

tag: smear microscopy

tag: culture result

tag: age

value: Imaging


title: 3998720079_J

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

tag: sampledate at t0

value: PTB

value: Lung

value: TRUE

tag: gender

value: White

tag: hiv positive

tag: tst

tag: tst result

value: NEGATIVE


title: 3998734070_L

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

tag: dosanjh

tag: eptborptb

tag: site of infection

value: FALSE

value: Male

tag: height (cm)

tag: weight (kg)

tag: bmi

value: Indian

tag: pcr


title: 3998703022_D

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

tag: title

value: EPTB

value: Lymph node

value: Negative

value: Female

value: Clinical Features

tag: qtf-git

value: POSITIVE


title: 3998675119_E

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

tag: diagnosis

value: Active TB

tag: smear microscopy

value: Black

tag: pcr result


title: 3998675070_A

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

tag: sampledate at t0

value: Pleura

tag: culture result

tag: age


title: 3998703013_C

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

value: Spine

tag: gender

tag: hiv positive

value: Imaging

tag: tst


title: 3998720107_K

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

tag: dosanjh

tag: eptborptb

value: TRUE

tag: tst result


title: 3998675092_D

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

tag: site of infection

tag: weight (kg)

value: Asian

value: Histology


title: Healthy_LJS

tag: tissue

value: PBMC

tag: cell type

value: NK cells

tag: treatment

value: Untreated

tag: disease state

value: Healthy

tag: disease severity


title: GPS2_KO_LPS_PU_1_rp1

value: Macrophage

tag: strain

value: BALB/c

tag: antibody

tag: agent

value: LPS

tag: time point

value: 2 hours


title: S_KO_Ctrl_PU_1_rp2

value: No treatment


title: 3998675065_D

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

tag: title

tag: sampledate at t0

tag: diagnosis

value: Active TB

value: EPTB

value: Lymph node, Pleura

tag: smear microscopy

tag: culture result

value: Negative

tag: age

tag: gender

value: Female

value: Indian

value: FALSE

value: Clinical Features, Histology

tag: pcr

tag: qtf-git

value: POSITIVE


title: Healthy_KJG

tag: tissue

value: PBMC

tag: cell type

value: NK cells


title: 3998675106_H

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

tag: dosanjh

tag: eptborptb

tag: site of infection

value: Spine

value: TRUE

tag: weight (kg)

tag: hiv positive

value: Clinical Features, Imaging

tag: tst

tag: tst result


title: 3998720110_J

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

tag: title

tag: sampledate at t0

value: Pericardium

value: Male

value: Black

value: Clinical Features

value: INDETERMINATE


title: GPS2_KO_Ctrl_PU_1_rp2

value: Macrophage

tag: strain

value: BALB/c

tag: antibody

tag: agent

value: No treatment


title: GPS2_KO_LPS_PU_1_rp2

value: LPS

tag: time point

value: 2 hours


title: Healthy_JSJ

tag: treatment

value: Untreated

tag: disease state

value: Healthy

tag: disease severity


title: GPS2_KO_Ctrl_PU_1_rp1

tag: cell type


title: 3998703004_A

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

tag: dosanjh

tag: diagnosis

value: Active TB

value: EPTB

value: Lymph node, OTHER

tag: smear microscopy

value: FALSE

tag: age

tag: gender

value: Female

value: Indian

value: Imaging

tag: pcr

tag: qtf-git

value: NEGATIVE


title: Healthy_CSJ

tag: tissue

value: PBMC

value: NK cells


title: 3998720105_E

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

tag: title

tag: sampledate at t0

tag: eptborptb

tag: site of infection

value: Lymph node

value: TRUE

tag: culture result

value: Negative

tag: height (cm)

tag: weight (kg)

tag: bmi

tag: hiv positive

value: Response to Treatment

tag: tst

tag: tst result

value: POSITIVE


title: 3998675068_D

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

tag: dosanjh

tag: diagnosis

tag: smear microscopy

value: Male

value: Clinical Features, Culture, PCR

tag: pcr result

value: Positive

value: INDETERMINATE


title: E_KO_Ctrl_PU_1_rp2

tag: cell type

value: Macrophage

tag: strain

value: BALB/c

tag: antibody

tag: agent

value: No treatment


title: 3998734069_H

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

tag: title

tag: sampledate at t0

value: Active TB

tag: eptborptb

value: EPTB

value: Spine

value: FALSE

tag: age

tag: gender

value: Female

value: Indian

value: Clinical Features

tag: pcr

tag: qtf-git


title: 3998703013_H

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

tag: site of infection

value: Skin

value: TRUE

tag: culture result

value: Negative

tag: weight (kg)

tag: hiv positive

tag: tst


title: E_KO_Ctrl_PU_1_rp1


title: 3998720106_I

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

tag: dosanjh

tag: diagnosis

value: Lymph node

tag: smear microscopy

value: Histology

tag: tst result

tag: pcr result

value: POSITIVE


title: HBMVEC hypoxia + siHIF1 - 2

city: Boston

first: Bradley

last: Maron

state: MA

address: 77 Avenue Louis Pasteur

department: Medicine

country: USA

institute: Brigham & Women's Hospital

data_processing:
Illumina NextSeq 500 was used for sequencing, with a High-Output 150-cycle kit to obtain Paired-End 75bp reads
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using the Star package; Raw count data were obtained using HTSeq.
Genome_build: hg19
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Human brain microvascular endothelal cells

growth_protocol: none needed/used

extract_protocol: RNeasy Fibrous Tissue Mini Kit (Qiagen, #74704)

treatment_protocol: none needed/used

tag: cell type


title: CBP_CRISPR_E_KO_LPS_2_hour

tag: strain

tag: antibody

value: CBP

tag: agent

value: LPS

tag: time point

value: 2 hours


title: HPAEC hypoxia + siHIF1 - 3

source_name: Human pulmonary artery endothelial cells


title: CBP_CRISPR_S_KO_LPS_2_hour

value: Macrophage

value: BALB/c


title: HBMVEC hypoxia + siHIF1 - 3

value: Human brain microvascular endothelal cells


title: HPAEC hypoxia + siHIF1 - 2

value: Human pulmonary artery endothelial cells


title: CBP_CRISPR_WT_LPS_2_hour


title: 3998734086_L

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

tag: title

tag: sampledate at t0

value: Active TB

tag: eptborptb

value: EPTB

tag: age

tag: gender

value: Male

value: FALSE

value: PCR

tag: pcr

value: Positive

value: NEGATIVE


title: LNA_Ccl2_eRNA_LPS_2_hour_CBP


title: HPAEC hypoxia + siHIF1 - 1


title: Mild_KHS_01

tag: tissue

value: PBMC

value: NK cells

tag: treatment

value: Untreated

tag: disease state

tag: disease severity

value: mild


title: HBMVEC hypoxia + siHIF1 - 1


title: 3998720110_I

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

tag: dosanjh

tag: diagnosis

tag: site of infection

value: Brain

tag: smear microscopy

value: TRUE

tag: culture result

value: Negative

value: Female

tag: height (cm)

tag: weight (kg)

tag: bmi

value: Black

tag: hiv positive

value: Histology

tag: tst

tag: qtf-git

value: POSITIVE


title: 3998720110_K

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

tag: title

tag: sampledate at t0

value: Active TB

tag: eptborptb

value: PTB

value: Lung

tag: age

tag: gender

value: Asian

value: Imaging

value: INDETERMINATE


title: LNA_control_LPS_2_hour_CBP

tag: cell type

value: Macrophage

tag: strain

value: BALB/c

tag: antibody

value: CBP

tag: agent

value: LPS

tag: time point

value: 2 hours


title: 3998703010_H

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

tag: dosanjh

tag: diagnosis

value: EPTB

tag: site of infection

value: Lymph node

tag: smear microscopy

value: TRUE

value: Male

value: Indian

value: FALSE

tag: pcr


title: 3998675108_I

description:
RNA was isolated using 1.5 ml whole blood and the MagMAX-96 Blood RNA Isolation Kit (Applied Biosystems/Ambion)
3998675108_I

value: Active TB

tag: culture result

value: Negative

value: Female

tag: weight (kg)

value: Black

tag: hiv positive

value: OTHER

tag: tst

tag: tst result

value: POSITIVE


title: 3998734102_K

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

tag: title

tag: sampledate at t0

tag: eptborptb

value: PTB

value: Lung

tag: age

tag: height (cm)

tag: bmi

value: Histology

tag: qtf-git


title: 3998675027_A

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

tag: dosanjh

value: Brain, Lung, Spine

tag: gender

value: Imaging


title: 3998675092_G

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

tag: diagnosis

value: EPTB

tag: site of infection

value: Central nervous system

value: Clinical Features

value: NEGATIVE


title: 3998734087_C

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

value: Pleura

tag: smear microscopy

value: TRUE

tag: pcr


title: 3998734087_B

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

value: Active TB

value: Lymph node

tag: culture result

value: Male

tag: weight (kg)

value: Indian

value: FALSE


title: 3998675040_D

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

value: Negative

value: Female

tag: hiv positive

tag: tst

value: POSITIVE


title: HBMVEC hypoxia 3

tag: cell type

value: Human brain microvascular endothelal cells


title: GPS2_CRISPR_E_KO_LPS_2_hour

value: Macrophage

tag: strain

value: BALB/c

tag: antibody

tag: agent

value: LPS

tag: time point

value: 2 hours


title: 200681360011_K

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

tag: title

tag: sampledate at t0

tag: eptborptb

value: Lung, Lymph node

tag: age

tag: height (cm)

tag: bmi

value: Black

value: Imaging

value: INDETERMINATE


title: HBMVEC hypoxia 2


title: GPS2_CRISPR_S_KO_LPS_2_hour


title: LNA_control_LPS_2_hour_H3K27ac


title: LNA_Ccl2_eRNA_LPS_2_hour_H3K27ac


title: HBMVEC hypoxia 1


title: JunB_CRISPR_E_KO_LPS_2_hour

value: JunB


title: JunB_CRISPR_S_KO_LPS_2_hour


title: JunB_CRISPR_WT_LPS_2_hour


title: HBMVECs normoxia 2


title: HPAEC hypoxia 2

value: Human pulmonary artery endothelial cells


title: HBMVECs normoxia 3


title: HPAEC hypoxia 3


title: HBMVECs normoxia 1


title: MED1_CRISPR_S_KO_LPS_2_hour


title: MED1_CRISPR_E_KO_LPS_2_hour


title: HPAEC hypoxia 1


title: 3998703022_I

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

tag: dosanjh

tag: diagnosis

value: Active TB

value: EPTB

tag: site of infection

value: Lymph node

tag: smear microscopy

value: TRUE

tag: gender

value: Histology

tag: qtf-git


title: 3998703044_L

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

value: FALSE

tag: culture result

value: Negative

value: Female

tag: weight (kg)

value: Indian

tag: hiv positive

tag: tst

tag: pcr

value: NEGATIVE

value: POSITIVE


title: 3998703022_A

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

tag: title

value: Lung, Lymph node

value: Male


title: 3998675110_E

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

tag: sampledate at t0

value: PTB

value: Lung

value: White

value: Imaging


title: 3998720112_D

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

value: Active TB

tag: eptborptb


title: PU.1_CRISPR_E_KO_LPS_2_hour

tag: cell type

value: Macrophage

tag: strain

value: BALB/c

tag: antibody

tag: agent

value: LPS

tag: time point

value: 2 hours


title: 200681360014_H

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

tag: dosanjh

tag: diagnosis

value: EPTB

tag: site of infection

value: Lymph node

value: FALSE

tag: age

tag: height (cm)

tag: bmi

value: Histology


title: 3998734070_F

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

value: Lung, Peritoneum

tag: smear microscopy

value: TRUE

tag: culture result

value: Negative

tag: gender

value: Female

tag: weight (kg)

value: Indian

tag: hiv positive

tag: qtf-git

value: NEGATIVE

value: INDETERMINATE


title: MED1_CRISPR_WT_LPS_2_hour

tag: cell type


title: 3998675120_B

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

tag: title

tag: sampledate at t0

tag: eptborptb

value: Liver

value: Male

value: Black

tag: tst

tag: pcr


title: 3998675086_A

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

tag: dosanjh

tag: diagnosis

value: Active TB

value: Bones


title: 3998675070_L

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

tag: site of infection

value: Kidneys, Peritoneum

tag: age

value: Imaging


title: 3998720079_A

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

value: EPTB

value: Lymph node

tag: height (cm)

tag: bmi

value: Histology, IGRA

value: POSITIVE


title: 200683670015_D

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

value: Lung, Pleura

tag: smear microscopy

value: TRUE

tag: culture result

value: Histology

value: FALSE


title: HPAEC normoxia 1

value: Human pulmonary artery endothelial cells


title: 3998675096_A

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

value: Lymph node, Pleura

value: Negative

tag: gender

value: Female

tag: weight (kg)

value: Indian

value: Histology, Imaging


title: 3998675074_H

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

value: Active TB

value: Chest or Thorax, Spine

value: Male

tag: hiv positive

tag: qtf-git

value: MISSING


title: HPAEC normoxia 2

tag: cell type


title: 3998675098_H

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

tag: title

tag: sampledate at t0

value: PTB

value: Lung

value: White

value: Imaging

value: NEGATIVE


title: 3998675091_E

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

tag: eptborptb

value: EPTB

value: Lymph node

value: Histology

tag: tst

value: POSITIVE


title: 3998675098_D

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

tag: dosanjh

value: FALSE

value: Negative

value: Clinical Features

tag: pcr


title: 3998720106_J

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

tag: diagnosis

tag: site of infection

value: Skin

value: Indian


title: PU.1_CRISPR_Promoter_KO_LPS_2_hour

value: Macrophage

tag: strain

value: BALB/c

tag: antibody

tag: agent

value: LPS

tag: time point

value: 2 hours


title: 3998675112_B

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

value: Active TB

value: Abdomen, Liver, Lung

tag: smear microscopy

value: TRUE

tag: culture result

tag: age

tag: gender

value: Female

tag: height (cm)

tag: bmi

tag: tst result


title: 3998675086_K

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

tag: title

tag: sampledate at t0

tag: eptborptb

value: EPTB

value: Male

tag: hiv positive

tag: qtf-git


title: PU.1_CRISPR_S_KO_LPS_2_hour

tag: cell type


title: HPAEC normoxia 3

value: Human pulmonary artery endothelial cells


title: HUVEC_well_W14

city: Nijmegen

first: Nael

last: Nadif Kasri

address: Geert Grooteplein Zuid 10

department: Department of Human Genetics

country: Netherlands

institute: Radboudumc

description:
Cultured on 24-well plate
Count_table_HUVEC.txt

data_processing:
Base calls converted to fastq and demultiplexed using Illumina's bcl2fastq conversion software (v2.16.0.10)
Reads trimmed using Trimmomatic (version 0.33)
Mapping performed with STAR with default settings (--outReadsUnmapped None, --outFilterType Normal, --outFilterScoreMin 0, outFilterMultimapNmax 10, --outFilterMismatchNmax 10, --alignIntronMin 21, --alignIntroMax 0, --alignMatesGapMax 0, --alignSJoverhangMin 5, --alignSJDBoverhangMin 3, --sjdbOverhang 100).
Uniquely mapped reads (mapping quality = 255) extracted
Htseq count (version 0.9.1) was performed to generate count matrices (parameters: --order=pos, --stranded=yes, --mode=union, --type=exon, --idattr=gene_id)
The samples for which the fastq files are not demultiplexed are RNA-seq samples from co-cultures, i.e. human iNeurons and rat astrocytes. I cannot separate these samples using demultiplexing because the libraries have the same library barcodes, but they are separated further in the pipeline when mapping to a combined human and rat genome. Reads mapping to the human genome represent iNeuron reads and reads mapping to the rat genome represent astrocyte reads.
Genome_build: GRCh38.p12 for HUVECs, combined GRCh38.p12/Rnor6.0 for iNeurons and astrocytes
Supplementary_files_format_and_content: Count tables with raw gene counts for every gene and every sample

source_name: HUVEC

growth_protocol: HUVECs were seeded to the top surface of a 20 μg/ml rhlaminin-coated well of a 24-well plate. Fresh endothelial cell growth medium was used. Cells were cultured for 24 hours during which medium was changed twice.

extract_protocol:
RNA was isolated and purified using the Quick-RNA Microprep kit (Zymo Research, R1051)
RNA-seq libraries were prepared using the SMARTer Stranded Total RNA Sample Prep Kit (low input mammalian) (Takara Bio, 634861)

tag: origin

value: Umbilical vein endothelial cells

tag: treatment

value: untreated

tag: disease state/genotype

value: healthy


title: HUVEC_well_W13


title: HUVEC_chip_C32

description:
Cultured on microfluidic chip
Count_table_HUVEC.txt

growth_protocol: HUVECs were seeded to the top surface of a 20 μg/ml rhlaminin-coated bottom channel of the microfluidic chip. The microfluidic chips were inverted after cells were added to the channel for at least half an hour. The medium in the channel was replaced with fresh endothelial cell growth medium and microfluidic chips were placed back to the normal upright position. Cells were cultured for 24 hours during which medium was changed twice.


title: RUNX1_CRISPR_E_KO_LPS_2_hour

tag: strain

tag: antibody

tag: agent

tag: time point


title: HUVEC_chip_C31


title: 3998703016_D

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

tag: dosanjh

tag: diagnosis

value: PTB

tag: site of infection

value: Lung

tag: smear microscopy

tag: culture result

value: Negative

tag: age

tag: gender

tag: weight (kg)

value: Black

value: Clinical Features

tag: tst

value: FALSE

tag: pcr

value: POSITIVE


title: 3998703022_E

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

tag: title

tag: sampledate at t0

value: Active TB

tag: eptborptb

value: Lymph node

value: Indian

tag: hiv positive

tag: tst result

tag: qtf-git


title: RUNX1_CRISPR_S_KO_LPS_2_hour

tag: cell type

value: Macrophage

tag: strain

value: BALB/c

tag: antibody

tag: agent

value: LPS

tag: time point

value: 2 hours


title: iNeurons_astrocytes_well_W10

description:
Cultured on 24-well plate
Count_table_iNeurons_astrocytes.txt

source_name: iNeurons

growth_protocol: On DIV0, well plates were coated with 20 µg/ml laminin and 20,000 iPSCs were seeded per well of a 24-well plate using Essential E8 Flex Basal medium (Gibco), supplemented with 1x RevitaCell™ Supplement (Gibco), and 4 µg/ml doxycyclin (Sigma Aldrich). On DIV1 cell medium was changed to DMEM/F12 medium (Gibco), supplemented with 0.1 mg/ml primocin (InvivoGen), 4 µg/ml doxycyclin, 1x N-2 (Gibco),  1x MEM Non-Essential Amino Acids Solution (NEAA, GIbco), 10 ng/ml NT-3 Recombinant Human Protein (NT-3, Promocell) and 10 ng/ml BDNF Recombinant Human Protein (BDNF, Promocell). On DIV2, the rat astrocytes (isolated according to earlier described protocols26) were added in a 1:1 ratio with the hiPSCs, similar to the hiPSC seeding. On DIV3, medium was removed and switched to Neurobasal medium (Gibco) supplemented with 0.1 mg/ml primocin, 1X B-27 Supplement, serum free (Gibco),  1X GlutaMAX™ Supplement (Gibco), 4 µg/ml doxycyclin, 10 ng/ml NT-3, 10 ng/ml BDNF and 2 µM Cytosine β-D-arabinofuranoside hydrochloride (Sigma Aldrich). Starting from day 5, 50% of the medium was refreshed every 2 days with Neurobasal medium, supplemented with 0.1 mg/ml primocin, 1X B-27,  1X GlutaMAX™, 4 µg/ml doxycyclin, 10 ng/ml NT-3 and 10 ng/ml BDNF. From DIV9 onwards, medium was refreshed every 2 day with this medium, which was then supplemented with Fetal Calf Serum (Sigma Aldrich) to sustain the rat astrocytes. iNeurons were kept in culture up to DIV38.

tag: origin

value: iPSC-derived neurons (co-cultured with rat astrocytes)

tag: treatment

tag: disease state/genotype


title: 3998675029_G

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

tag: dosanjh

tag: diagnosis

value: EPTB

tag: site of infection

tag: smear microscopy

value: TRUE

tag: culture result

tag: age

tag: gender

value: Male

tag: height (cm)

tag: weight (kg)

tag: bmi

value: Asian

value: Histology

value: NEGATIVE


title: 3998675101_F

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

tag: title

tag: sampledate at t0

tag: eptborptb

value: PTB

value: Lung

value: Negative

tag: hiv positive

value: Clinical Features

tag: tst

tag: tst result

tag: pcr

tag: qtf-git


title: 3998720110_G

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

tag: dosanjh

tag: diagnosis

value: Active TB, Other

value: Spine

value: White

value: FALSE

value: POSITIVE

value: INDETERMINATE


title: Det ATACseq siYAPandTAZ3

city: South San Francisco

first: Robert

last: Piskol

state: CA

address: 1 DNA Way

department: gRED Computational Sciences

institute: Genentech Inc.

description: HIPPO_Detroit_ATACseq_peaks_counts_genomloc.csv

data_processing:
Reads were aligned to the human reference genome (NCBI Build 38) using GSNAP31 version ‘2013-10-10’, allowing a maximum of two mismatches per read sequence (parameters: ‘-M 2 -n 10 -B 2 -i 1–pairmax-dna = 1000–terminal-threshold = 1000–gmap-mode = none–clip-overlap’). Reads aligning to locations in the human genome that contain substantial sequence homology to the MT chromosome or to blacklisted regions identified by the ENCODE consortium were omitted from downstream analyses.
Properly paired reads derived from non-duplicate sequencing fragments were used to quantify chromatin accessibility according to the ENCODE pipeline standards with minor modifications as follows. Accessible genomic locations were identified by calling peaks with Macs2 (PMID: 18798982) using insertion-centred pseudo-fragments (73 bp; community standard) generated on the basis of the start positions of the mapped reads.
Accessible peak locations were identified as described: in brief, we called peaks on a group-level pooled sample containing all pseudo-fragments observed in all samples within each group.
Peaks in the pooled sample that were independently identified in two or more of the constituent biological replicates were retained for downstream analysis, using the union of all group-level reproducible peaks (https://www.encodeproject.org/atac-seq/#standards).
We quantified the level of chromatin accessibility within each peak for each replicate as the number of pseudo-fragments that overlapped the peak in question and normalized these estimates using the TMM method (PMID: 20196867).
Genome_build: GRCh38
Supplementary_files_format_and_content: csv, count matrix

source_name: Detroit 562

growth_protocol: RPMI 1640 supplemented with 10% FBS and 2 mM L-Glutamine

extract_protocol:
Tagmented DNA was isolated by MinElute PCR Purification Kit (Qiagen)
Libraries were generated using previously published protocols (PMID: 25559105; PMID: 28846090) and sequenced on NextSeq500 (Illumina).

treatment_protocol: Detroit-562/Patu-8902  cells (100,000) transduced with siNTC, siYAP1+WWTR1 were pelleted and pellets were washed with PBS. Cell were resuspended in 100 μL of ATAC-resuspension buffer (10 mM Tris HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2), and nuclei were pelleted by centrifugation. The nuclei were resuspended in 50 μL reaction buffer containing Tn5 transposase (2.5 μL Tn5 transposase, 25 μL 2× TD buffer, 16.5 μL PBS, 0.5 μL 1% digitonin, 0.5 μL 10% Tween-20, 5 μL H2O) (Illumina). The reaction was carried out at 37°C for 30 minutes.

tag: tissue

value: Nasal Pharynx

value: Carcinoma

tag: treatment

value: siYAP + siTAZ


title: Sperm_cells_rep2 [re-analysis]

city: Tübingen

first: Michael

last: Borg

address: Max Planck Ring 5

department: Algal Development & Evolution

country: Germany

institute: Max Planck Insititue for Biology

data_processing:
Raw, unaligned BAM files were first sorted with samtools sort -n and then converted to fastq files with bedtools bamtofastq.
Adapter trimming was performed using TrimGalore version 0.4.1.
Reads were aligned to the Arabidopsis genome (TAIR10) using the STAR aligner version 2.5.2a.
Transcripts per million (TPM) values were generated using Kallisto version 0.43.1 (21) with an index built on TAIR10 cDNA sequences.
Differential gene expression analysis of WT and dme-2/+ was performed using DESeq2 1.22.2 for transcripts that had 10 counts or more in at least one sample.
Differentially expressed genes (DEGs) were classified as having a p-value < 0.1 after correction for multiple testing (i.e. adjusted p-value).
Genome_build: TAIR10 cDNA sequences (Arabidopsis_thaliana.TAIR10.cdna.all.fa.gz)
Supplementary_files_format_and_content: *.tsv: Kallisto quantification abundance.tsv output
Supplementary_files_format_and_content: *.txt: TPM values for VN and Sperm

organism: Arabidopsis thaliana

source_name: Sperm cells

extract_protocol:
For analysis of dme-2/+ pollen, dry pollen was harvested from Col-gl and BASTA-sprayed dme-2/+ plants using a method published previously. Pollen grains were disrupted in a Precellys tissue homogenizer (Bertin Instruments) and total RNA isolated using an RNeasy Micro Kit (Qiagen). For vegetative cell nuclei, FACS-isolated nuclei from the ProVCK:NTF line were sorted directly into Trizol reagent and precipitated with isopropanol.
RNA-seq libraries were generated from the resulting RNA with Smart-seq2 using independent biological replicates. The libraries were sequenced on an Illumina Hiseq 2500 using 50 bp paired-end and single-end reads for VN and pollen samples, respectively.

tag: ecotype

tag: genotype

value: wild type


title: 200683670009_F

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

value: Active TB

value: EPTB

tag: site of infection

value: Intestine, Peritoneum, Pleura

tag: smear microscopy

value: TRUE

tag: culture result

tag: age

tag: gender

value: Female

tag: height (cm)

value: Black

value: Clinical Features, Imaging

tag: pcr result


title: 3998703004_H

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

tag: title

tag: sampledate at t0

tag: eptborptb

value: Pleura

value: Negative

value: Male

tag: weight (kg)

value: Indian

tag: hiv positive

value: OTHER

tag: tst

value: NEGATIVE


title: 3998675081_K

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

tag: dosanjh

tag: diagnosis

value: Eye (left)

value: FALSE

tag: bmi

value: Clinical Features

tag: tst result

tag: pcr

tag: qtf-git

value: POSITIVE


title: 3998734089_K

description:
RNA was isolated using 1.5 ml whole blood and the MagMAX-96 Blood RNA Isolation Kit (Applied Biosystems/Ambion)
3998734089_K

value: Active TB

tag: site of infection

value: Lymph node

tag: smear microscopy

tag: culture result


title: 3998675106_E

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

value: EPTB

tag: age

tag: gender

value: Clinical Features, Histology, Response to Treatment


title: 3998675120_D

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

tag: title

value: Abdomen, Lymph node

value: TRUE

value: Female

tag: height (cm)

value: Histology


title: RUNX1_CRISPR_WT_LPS_2_hour

tag: cell type

value: Macrophage

tag: strain

value: BALB/c

tag: antibody

tag: agent

value: LPS

tag: time point

value: 2 hours


title: 3998675115_B

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

tag: sampledate at t0

tag: dosanjh

tag: diagnosis

tag: eptborptb

value: Negative

value: Male

tag: weight (kg)

value: Indian

tag: hiv positive

tag: tst

tag: pcr result

value: NEGATIVE


title: 3998734078_F

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

tag: site of infection

value: Lung, Pleura

tag: smear microscopy

tag: culture result

tag: age

tag: bmi

value: FALSE

value: Clinical Features

tag: tst result

tag: pcr

tag: qtf-git


title: 3998703016_F

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

tag: title

value: Active TB

value: EPTB

value: Lymph node

tag: gender

tag: height (cm)

value: White

value: INDETERMINATE


title: Det ATACseq siYAPandTAZ2

tag: tissue

value: Nasal Pharynx

tag: diagnosis

value: Carcinoma

tag: treatment

value: siYAP + siTAZ


title: 3998703016_K

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

tag: sampledate at t0

tag: dosanjh

tag: eptborptb

value: TRUE

tag: weight (kg)

value: Black

tag: hiv positive

value: PCR

value: Positive

value: POSITIVE


title: 3998720106_K

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

tag: site of infection

tag: smear microscopy

value: Female

value: Indian

tag: tst


title: 3998675115_D

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

value: PTB

value: Lung

tag: culture result

value: Negative

tag: age

tag: bmi

value: FALSE

value: Histology, Imaging

tag: pcr result

value: NEGATIVE


title: Det ATACseq siNTC3

value: siNTC


title: Sperm_cells_rep1 [re-analysis]

tag: ecotype

tag: genotype

value: wild type


title: 3998675108_C

description:
RNA was isolated using 1.5 ml whole blood and the MagMAX-96 Blood RNA Isolation Kit (Applied Biosystems/Ambion)
3998675108_C

tag: title

value: Active TB

value: EPTB

value: Lymph node

tag: gender

value: Male

tag: height (cm)

value: White

value: Smear Microscopy

tag: pcr

tag: qtf-git


title: dme2_rep3 [RNA-seq]

description: dme-2 heterozygous mutant pollen

source_name: Mature pollen

value: Col-gl


title: 200681360011_C

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

tag: sampledate at t0

tag: dosanjh

tag: diagnosis

tag: eptborptb

value: Brain

value: TRUE

value: Black

value: Clinical Features


title: dme2_rep2 [RNA-seq]

description: dme-2 heterozygous mutant pollen


title: 200681360001_F

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

tag: site of infection

tag: smear microscopy

value: Negative

tag: weight (kg)

value: Indian

tag: hiv positive

value: Histology

tag: tst result

value: INDETERMINATE

value: POSITIVE


title: 3998675110_G

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

value: PTB

value: Lung

tag: culture result

tag: age

tag: bmi

value: FALSE

value: Histology, Imaging

tag: tst


title: PATU_8902_siYAP+TAZ_2

description: HIPPO_PATU_ATACseq_peaks_counts_genomloc.csv

source_name: PATU 8902

tag: tissue

value: Pancreas

value: PDAC

tag: treatment

value: siYAP + siTAZ


title: 200681360001_D

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

tag: title

value: Active TB

value: EPTB

value: Eyes

tag: gender

value: Female

tag: height (cm)

value: OTHER

tag: pcr

tag: pcr result


title: 3998720105_G

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

tag: dosanjh

tag: diagnosis

tag: eptborptb

value: Spine

value: Positive

value: Male

value: Asian

value: Culture

tag: qtf-git


title: 3998675102_I

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

tag: sampledate at t0

tag: site of infection

value: Lymph node

tag: smear microscopy

value: Negative

tag: weight (kg)

value: Indian

tag: hiv positive

value: Histology

value: TRUE

value: NEGATIVE


title: PATU_8902_siYAP+TAZ_3

value: Pancreas

value: PDAC

value: siYAP + siTAZ


title: PATU_8902_siNTC_3

value: siNTC


title: WT_rep2 [RNA-seq]

description: wild type pollen

tag: ecotype

value: Col-gl

tag: genotype

value: wild type


title: Det ATACseq siNTC2

description: HIPPO_Detroit_ATACseq_peaks_counts_genomloc.csv

tag: tissue

value: Nasal Pharynx

value: Carcinoma

tag: treatment


title: PATU_8902_siNTC_2


title: WT_rep3 [RNA-seq]

description: wild type pollen


title: SAM24333452 OVCAR-8

data_processing:
RNA-seq reads were first aligned to ribosomal RNA sequences to remove ribosomal reads. The remaining reads were aligned to the reference genome using GSNAP version “2013-10-10,” allowing a maximum of two mismatches per 75 base sequence (parameters: ‘-M 2 -n 10 -B 2 -i 1 -N 1 -w 200000 -E 1 --pairmax-rna=200000 --clip-overlap)(Wu and Nacu, 2010b; Wu et al., 2016b). Transcript annotation was based on the Ensembl genes database (release 77). To quantify gene expression levels, the number of reads mapped to the exons of each RefSeq gene was calculated.
Differential gene expression was performed with DESeq2(Love et al., 2014). A prefilter was applied, so that only genes with at least a median RPKM (reads per kilobase per million mapped reads) value of 10 in one condition were analyzed. P-values for other genes were simply set to 1 and log fold changes were set to 0 for visualization purposes, but such genes were not included in the multiple testing correction. Q-values were obtained by correcting P-values for multiple hypotheses using the Benjamini-Hochberg procedure. Genes were considered if they had a Q-value of less than 0.05 and were protein-coding. Counts were transformed to log2 counts per million, quantile-normalized, and precision-weighted with the “voom” function of the limma package(Law et al., 2014).
Genome_build: GRCh38
Supplementary_files_format_and_content: csv, count matrix

extract_protocol:
Tumors and cell lines were dissociated and lysed for RNA isolation using RNAeasy kit (Qiagen).
Total RNA was extracted using the Qiagen RNAeasy kit with the on-column DNA elimination. The concentration was identified using NanoDrop 8000 (Thermo Fisher Scientific). Quality control was done by determine RNA integrity with Bioanalyzer 2100(Agilent Technologies). About 500 ng of RNA was used for library synthesis using the TrueSeq RNA Sample Preparation kit v2 (Illumina).
Size of the libraries was confirmed using 2200 TapeStation and High Sensitivity D1K screen tape (Agilent Technologies), and the concentration was determined by a qPCR-based method using the Library Quantification Kit (KAPA). The libraries were multiplexed and then sequenced on Illumina HiSeq2500 (Illumina) to generate 30M of single-end 50–base pair reads.

treatment_protocol: transfection of siRNA, 2D culture, 48 hours

tag: cell line

value: Ovary

value: Adenocarcinoma


title: 3998703016_I

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

tag: title

value: Active TB

value: EPTB

tag: culture result

tag: age

tag: gender

value: Female

tag: height (cm)

tag: bmi

value: Clinical Features

tag: tst

value: FALSE

value: POSITIVE


title: WT_rep1 [RNA-seq]

description: wild type pollen


title: 3998675119_J

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

tag: sampledate at t0

tag: dosanjh

tag: diagnosis

tag: eptborptb

value: PTB

value: Lung

value: TRUE

value: Positive

value: Male

value: Black

value: Culture

tag: pcr

tag: qtf-git


title: 3998703009_L

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

tag: site of infection

value: Pleura

tag: smear microscopy

tag: hiv positive


title: SAM24333451 OVCAR-8

tag: cell line

tag: tissue

tag: treatment

value: siYAP + siTAZ


title: 3998675112_I

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

tag: title

tag: culture result

tag: age

tag: weight (kg)

tag: tst result

tag: pcr result


title: 3998703022_L

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

tag: sampledate at t0

tag: dosanjh

value: Lymph node

tag: gender

tag: height (cm)

tag: bmi

value: Indian

tag: tst


title: VN_rep2 [RNA-seq]

description:
total nuclear RNA
Vegetative cell nuclei
Pollen_TPM_counts.txt

source_name: Vegetative cell nuclei

tag: ecotype

tag: genotype


title: 3998675070_I

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

tag: diagnosis

value: Active TB

tag: eptborptb

tag: site of infection

tag: smear microscopy

tag: hiv positive

value: Clinical Features, Culture

tag: pcr

tag: qtf-git


title: SAM24333450 OVCAR-8

tag: cell line

tag: tissue

value: Ovary

value: Adenocarcinoma

tag: treatment


title: 3998703022_H

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

tag: title

tag: sampledate at t0

tag: dosanjh

value: EPTB

tag: culture result

value: Negative

tag: age

value: Female

tag: weight (kg)

value: FALSE

value: Clinical Features, Culture, Imaging

tag: tst result


title: VN_rep1 [RNA-seq]

tag: ecotype

tag: genotype


title: VN_rep3 [RNA-seq]


title: SAM24333449 OVCAR-8

tag: diagnosis

value: siNTC


title: 3998720079_D

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

tag: eptborptb

value: PTB

tag: site of infection

value: Lung

tag: smear microscopy

value: TRUE

value: Positive

tag: gender

value: Male

tag: height (cm)

tag: bmi

value: White

tag: tst

value: NEGATIVE


title: 3998675027_E

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

tag: title

value: Active TB

value: Indian

tag: hiv positive

value: Clinical Features, Imaging

tag: pcr

tag: qtf-git


title: 3998675049_J

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

tag: sampledate at t0

tag: dosanjh

value: Lymph node

tag: culture result

tag: age

value: Culture

value: POSITIVE


title: 3998675120_A

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

value: EPTB

value: Female

tag: weight (kg)

value: Hispanic


title: SAM24333448 OVCAR-8

tag: cell line

tag: tissue

value: Ovary

tag: diagnosis

value: Adenocarcinoma

tag: treatment

value: siNTC


title: 3998734102_B

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

tag: eptborptb

tag: site of infection

value: OTHER

tag: smear microscopy

value: TRUE

tag: gender

value: FALSE

tag: tst result


title: 3998703016_H

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

tag: title

value: Positive

tag: height (cm)

tag: bmi

value: Black

tag: hiv positive

tag: tst


title: 3998675118_E

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

tag: sampledate at t0

tag: dosanjh

value: Active TB

value: PTB

value: Lung

tag: culture result

value: Male

tag: pcr

tag: qtf-git

value: NEGATIVE


title: 3998675081_I

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

tag: diagnosis

tag: age

tag: weight (kg)

value: Culture

value: POSITIVE


title: SAM24333447 OVCAR-8

tag: cell line

tag: tissue

tag: treatment


title: PU.1_CRISPR_WT_LPS_2_hour

tag: cell type

value: Macrophage

tag: strain

value: BALB/c

tag: antibody

tag: agent

value: LPS

tag: time point

value: 2 hours


title: 3998734102_C

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

tag: title

tag: eptborptb

value: EPTB

tag: site of infection

value: Bones, Lymph node, Miliary TB (disseminated), Spine

tag: smear microscopy

tag: gender

value: Indian

tag: hiv positive

tag: tst

tag: tst result

value: INDETERMINATE


title: 200683670009_K

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

tag: sampledate at t0

tag: dosanjh

tag: diagnosis

value: TRUE

tag: culture result

value: Positive

tag: age

tag: weight (kg)

value: FALSE

tag: pcr

tag: pcr result

value: Negative

tag: qtf-git


title: 3998734087_J

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

tag: title

value: Active TB

value: Lymph node


title: MSP_rep3

description:
GSE155344_MSP.ATACseq.bw
GSE155344_SPOsp.peaks.bed
GSE155344_common.peaks.bed

data_processing:
Raw, unaligned BAM files were first sorted with samtools sort -n and then converted to fastq files with bedtools bamtofastq.
Adapter trimming was performed using cutadapt version 1.9.
Reads were mapped to the Arabidopsis genome (TAIR10) using Bowtie2 version 2.1.0.
Reads were filtered for duplicate reads using Picard tools MarkDuplicates version 1.141.
Biological replicates were subsequently merged for downstream analysis after confirming high correlation among replicates.
For data visualization, log2 ratio bigwig coverage files relative to input were generated using the deepTools version 2.2.4 utility bamCoverage with a bin size of 10 bp.
Peaks were called using the MACS2 version 2.1.0 callpeak function using -B -q 1e-5 -f BAMPE
Genome_build: TAIR10 (Arabidopsis thaliana)
Supplementary_files_format_and_content: *.bw: ATAC-seq coverage normalised to 1x Arabidopsis genome coverage. Data is generated from merged replicates.
Supplementary_files_format_and_content: *.bed: Peak BED files of different ATAC-seq peaks groups

source_name: Microspores

extract_protocol:
For GN, SN and VN ATAC-seq, ~50,000 FACS-purified nuclei were immediately resuspended in 25 ul transposase reaction mix (12.5 ul 2x TD buffer, 2.0 ul Nextera Tn5 [Illumina Cat #FC-121-1030] and nuclease-free water). For microspore ATAC-seq, FACS-purified spores were centrifuged at 800 g for 5 minutes at 4°C and the spore pellet resuspended in 500 ul lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 1 % IGEPAL CA-630). The microspores were pelleted once more at 500 g for 10 minutes at 4°C and ~50,000 added to a 25 ul transposase reaction mix (12.5 ul 2x TD buffer, 2.0 ul Nextera Tn5 [Illumina Cat #FC-121-1030] and nuclease-free water). The Tn5 reaction mixes were incubated at 37°C for 1 hour and tagmented DNA fragments recovered with a MinElute PCR Purification Kit (Qiagen).
Sequencing-ready libraries were generated as described previously (Buenrostro et al., 2015). The libraries were sequenced on an Illumina Hiseq 2500 using 50 bp paired-end reads. All ATAC-seq profiles were generated with at least two independent biological replicates.

tag: ecotype

tag: genotype

value: wild type


title: SAM24333446 SKG-II

source_name: SKG-II

tag: cell line

value: SKG-II

tag: tissue

value: Cervix

value: Carcinoma Large Cell

tag: treatment

value: siYAP + siTAZ


title: MSP_rep2


title: SN_rep2

description:
GSE155344_SN.ATACseq.bw
GSE155344_SNsp.peaks.bed
GSE155344_common.peaks.bed

source_name: Sperm nuclei


title: MSP_rep1


title: SAM24333445 SKG-II


title: 3998675068_J

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

tag: eptborptb

tag: site of infection

tag: smear microscopy

tag: gender

value: Male

tag: hiv positive

value: Culture

tag: tst

value: NEGATIVE

value: POSITIVE


title: 3998734078_B

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

tag: sampledate at t0

tag: dosanjh

tag: diagnosis

value: EPTB

tag: culture result

tag: age

tag: height (cm)

tag: bmi

value: Indian


title: 3998720114_E

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

tag: title

value: Ankle

value: TRUE

tag: weight (kg)

tag: pcr

tag: qtf-git


title: SAM24333444 SKG-II

tag: cell line

tag: tissue

tag: treatment


title: 3998675040_C

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

tag: eptborptb

value: PTB

tag: site of infection

value: Lung

tag: smear microscopy

value: Positive

tag: gender

value: FALSE

tag: tst result


title: 3998734087_K

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

tag: sampledate at t0

tag: dosanjh

tag: diagnosis

value: Active TB

value: White

tag: hiv positive

tag: tst


title: 3998734063_J

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

tag: title

value: Intestine, Lymph node, Peritoneum, Stomach

tag: culture result

tag: age

value: Culture, PCR

tag: pcr result


title: VN_rep2

description:
GSE155344_VN.ATACseq.bw
GSE155344_VNsp.peaks.bed
GSE155344_common.peaks.bed

tag: ecotype

tag: genotype


title: SN_rep1


title: VN_rep1


title: 3998720105_C

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

value: Female

tag: weight (kg)

tag: pcr

tag: qtf-git


title: SAM24333443 SKG-II

tag: cell line

value: SKG-II

tag: tissue

value: Cervix

value: Carcinoma Large Cell

tag: treatment

value: siNTC


title: 3998734064_G

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

tag: sampledate at t0

tag: eptborptb

value: EPTB

tag: site of infection

value: Breast, Lymph node

tag: smear microscopy

tag: gender

value: Culture

tag: tst result

value: POSITIVE


title: SAM24333441 SKG-II

tag: diagnosis


title: SAM24333440 RVH-421

value: Skin

value: Melanoma

value: siYAP + siTAZ


title: 3998675068_B

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

tag: title

tag: dosanjh

value: Lymph node, OTHER

value: TRUE

tag: culture result

value: Positive

tag: age

value: Male

value: Indian

tag: hiv positive

value: FALSE

tag: tst


title: SAM24333439 RVH-421


title: SAM24333442 SKG-II

value: SKG-II


title: 3998675049_A

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

value: Active TB

value: Lung, Lymph node

tag: weight (kg)

tag: pcr

tag: qtf-git

value: MISSING