title: Round_spermatid_WT_IgG

city: Cincinnati

first: Iouri

last: Chepelev

state: OH

address: 3200 Vine St

institute: US Department of Veterans Affairs Medical Center

data_processing:
Sequenced tags were mapped to the mouse genome (mm8) using Bowtie algorithm with the option ‘-m 1’.  In order to reduce PCR amplification bias, at most one read was kept per genomic location. The resulting lists  of uniquely mapped non-redundant reads were used for all downstream analyses. UCSC genome browser  displayable BedGraph files for ChIP-Seq data were generated by counting tags in 200-bp windows across the  genome and normalizing window tag counts by 10 million total sequenced reads to make different libraries  directly comparable. BRDT binding sites from the ChIP-Seq data were identified using SICER software  (PMID: 19505939) using IgG data as control and a False Discovery Rate (FDR) threshold of 10%.
Genome_build: mm8
Supplementary_files_format_and_content: BedGraph files contain normalized ChIP-Seq counts as described above. BED files contain locations of BRDT peaks.

source_name: Round, spermatid, WT, IgG

extract_protocol:
The pachytene spermatocyte sample consisted of cellular suspensions obtained from testicular tubules isolated  from eighteen day old male mice following our laboratory's standard protocols as previously published (PMID: 2441396).  Briefly, testes were decapsulated and transferred to cold PBS, The tubules were manually sheared with  scissors and by pipetting, and then passed through a 40 μm filter. Although this population also includes  spermatogonia, leptotene/zygotene spermatocytes, and some Sertoli cells, these cells do not express BRDT.  Round spermatids were purified as previously described (PMID: 2441396). Briefly, testes were dissected from seven 129  Sv/Ev adult mice and were decapsulated. The tubular mass was transferred to a 50 ml Erlenmeyer flask  containing 25 ml of solution composed of 1.0 mg/ml collagenase (Sigma Cat# C0130) in RPMI buffer. The  tubules were then incubated at 33oC in a shaking water bath for ~7 min until dispersed. They were then allowed  to sediment to the bottom of the flask and the supernatant was removed by aspiration. Thetubules were washed  twice with 25 ml of RPMI, then resuspended in 25 ml of RPMI containing 0.25 mg/ml trypsin (Sigma  cat#T8003) and incubated at 33oC in a shaking water bath for 5 min. Cell aggregates and connective tissue were  removed by filtration through 74-pm nylon mesh (BD Falcon). The single cell suspension of germ cells was  separated using gravity sedimentation on a 2-4% BSA in DPBS gradient. Fractions containing round spermatids  were pooled to yield samples containing ≥90% round spermatids, as assessed by flow cytometric analysis   using propidium iodide (Sigma cat#P4170) staining and analysis on a BD FACSCalibur Cell Analyzer. All  steps of cell separation, fractionation and pooling were performed at 4oC in order to maintain cell viability and  maximize nucleic acid integrity.
To identify BRDT-containing complex binding sites, we prepared cross-linked chromatin samples for ChIP-Seq  analysis. Approximately 107 cells from the two cellular preparations were fixed with 1% formaldehyde for 10  min at room temperature. The chromatin template was then fragmented to a size of 150 to 200 bp by sonication. Aliquots of the chromatin samples were subjected to chromatin immunoprecipitation using a C-terminal  anti-BRDT antibody generated by our laboratory (PMID: 17728347) or anti-IgG as a control. This was followed by performing end repair and addition of “A” bases to the 3’ end of the DNA fragments, and ligation of adapters to the DNA  fragments. The resulting fragments were then size-selected for 150-350bp regions before generating the  library, which was enriched for the adapter-modified DNA fragments by PCR. The purified DNA samples were  subjected to analysis on the Ilumina Cluster Station and Genome Analyzer.

tag: strain

value: 129 Sv/Ev

tag: genotype

value: wild type

tag: cell type

value: Round spermatid

tag: chip antibody

value: anti-IgG (EMD Millipore, catalog #12-370)


title: Round_spermatid_WT_Brdt

status: Public on Jan 26 2021

type: SRA

country: USA

library_source: genomic

molecule: genomic DNA

organism: Mus musculus

source_name: Round, spermatid, WT, Brdt

value: anti-BRDT antibody generated by our laboratory (PMID:17728347)


title: 3998734087_F

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)
3998734087_F

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

organism: Homo sapiens

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: Active TB

tag: eptborptb

value: EPTB

tag: site of infection

value: Spine

tag: smear microscopy

value: TRUE

tag: culture result

value: Positive

tag: age

tag: gender

value: Female

tag: weight (kg)

value: Indian

tag: hiv positive

value: FALSE

value: Culture

tag: tst

tag: tst result

tag: pcr

tag: qtf-git

value: NEGATIVE

value: POSITIVE


title: 3998675114_G

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

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

value: Lymph node

value: MISSING


title: 200681360009_D

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

value: PTB

value: Lung

value: Male

tag: pcr result

value: Negative


title: 3998734064_E

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

tag: title

value: Active TB

value: Lung, Lymph node

value: Culture, PCR


title: Sperm_cells_rep3 [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

library_source: transcriptomic

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: 3998734064_A

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

tag: sampledate at t0

tag: dosanjh

tag: diagnosis

value: EPTB

value: TRUE

value: Positive

value: Asian


title: 3998734078_L

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

tag: eptborptb

tag: site of infection

value: Pleura

tag: smear microscopy

value: Female

value: Indian

value: FALSE

value: Culture


title: NB1_KO

city: Oulu

first: Nadiya

last: Byts

address: Aapistie 7C

department: FBMM

country: Finland

institute: Biocenter Oulu

description: gene expression data from the cortex of P4H-TM knockout mice

hyb_protocol: Biotinylated cRNA was cleaned with a GeneChip Sample Cleanup Module (Qiagen), fragmented to 35 to 200 nt, and hybridized to Affymetrix Mouse Genome 430_ 2.0 arrays according to manufacturer's instructions.

scan_protocol: GeneChips were scanned on Affymetrix GeneChip Scanner 3000

data_processing: Data were normalized using RMA algorithm with no variance stabilization in Chipster software.

label: biotin

source_name: cortical tissue

label_protocol: biotin-labeled cRNA was produced using an IVT labeling kit (Affymetrix) according to the manufacturer's instructions.

growth_protocol: 2.5 months old mice

extract_protocol: Total RNA was isolated from cortical tissue using TriPure isolation reagent (Roche Applied Science) and further purified with an EZNA total RNA kit (Omega Biotek)

treatment_protocol: naive mice

tag: strain

value: P4H-TM knockout

tag: tissue

value: cortical tissue


title: SAM24333438 RVH-421

city: South San Francisco

first: Robert

last: Piskol

state: CA

address: 1 DNA Way

department: gRED Computational Sciences

institute: Genentech Inc.

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: Skin

value: Melanoma

tag: treatment

value: siYAP + siTAZ


title: SAM24333436 RVH-421

value: siNTC


title: SAM24333437 RVH-421


title: Pachytene_spermatocytes_WT_Brdt

source_name: Pachytene, spermatocytes, WT, Brdt

value: 129 Sv/Ev

tag: cell type

value: Pachytene spermatocytes

tag: chip antibody

value: anti-BRDT antibody generated by our laboratory (PMID:17728347)


title: 3998675114_D

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

value: Active TB

value: PTB

value: Lung

value: TRUE

tag: culture result

tag: age

tag: gender

tag: weight (kg)

tag: hiv positive

value: Culture, Imaging, PCR

tag: tst

tag: tst result

tag: pcr

tag: qtf-git

value: POSITIVE


title: 3998720114_B

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

tag: title

tag: sampledate at t0

tag: dosanjh

tag: diagnosis

tag: eptborptb

tag: site of infection

value: Positive

value: Male

value: Indian

value: FALSE

value: Culture, PCR

tag: pcr result


title: Pachytene_spermatocytes_WT_IgG

source_name: Pachytene, spermatocytes, WT, IgG

tag: strain

tag: genotype

value: wild type

tag: cell type

tag: chip antibody

value: anti-IgG (EMD Millipore, catalog #12-370)


title: SAM24333435 RVH-421

tag: cell line

tag: tissue

value: Skin

value: Melanoma

tag: treatment

value: siNTC


title: ChIP_H3K4me3_EpiSC_WT

city: Santander

first: Alvaro

last: Rada-Iglesias

state: Cantabria

address: Albert Einstein 22, PCTCAN

country: Spain

institute: Institute of Biomedicine and Biotechnology of Cantabria (IBBTEC), CSIC/University of Cantabria

data_processing:
ChIP-seq single end reads were mapped to the mouse genome (mm10) using BWA. After duplication removal with the MarkDuplicates function from the Picard tools, reads within blacklisted regions were discarded and the aligned reads were normalized with deeptools to 1x sequencing depth (as RPGC: Reads per genomic content).
Genome_build: mm10
Supplementary_files_format_and_content: RPGC normalized bigWig

source_name: epiblast stem cells

growth_protocol: ESC were cultured on gelatin-coated plates using Knock-out DMEM supplemented with 15% FBS and LIF. Before each PGCLC differentiation, ESC were adapted to 2i+LIF media (serum-free N2B27 medium supplemented with MEK inhibitor PD0325901 [0.4 μM], GSK3β inhibitor CHIR99021 [3 μM], and LIF) for at least four days in gelatin-coated tissue culture plates. For the EpiLC differentiation, 6-well plates were coated with 15 µg ml-1 Fibronectin and 2 x 105 2i ESC were differentiated in N2B27 media supplemented with 20 ng ml-1 Activin A, 12 ng ml-1 bFGF and 10 µl ml-1 KSR for two days. For EpiSC differentiation, 2i ESC were plated at a density of 2.5 x 105 cells ml-1 on plates coated with 15 µg ml-1 Fibronectin and differentiated into EpiSC by passaging them in N2B27 media supplemented with 20 ng ml-1 Activin A and 12 ng ml-1 bFGF for at least eight days. For the PGCLC differentiation, d2 EpiLC were plated at a density of 2 x 104 cells ml-1 and cultured as embryoid bodies (EB) on Ultra-Low attachment multiwell plates (Corning® Costar®) in GK15 medium supplemented with growth factors (0.5 µg ml-1 BMP4, 0.1 µg ml-1 SCF, 1000 U ml-1 LIF and 50 ng ml-1 EGF, no BMP8a) for four days.

extract_protocol:
Cells were cross-linked with 1 % formaldehyde for 10 min, followed by quenching with 0.125 M glycine, harvesting and washing in PBS containing protease inhibitors. The cells were sequentially lysed in three buffers (lysis buffer 1: 50 mM HEPES, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% NP-40, 0.25% TX-100; lysis buffer 2: 10 mM Tris, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA; lysis Buffer 3: 10 mM Tris, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% Na-Deoxycholate, 0.5% N-lauroylsarcosine) with rotation for 10 min in between. Then, the chromatin was sonicated with the Epishear™ Probe Sonicator (Active Motif) with 20 s ON and 30 s OFF for 8 cycles. After centrifugation, the supernatant was divided into input and ChIP samples. The ChIP samples were incubated with specific antibodies (Supplementary Table 4) overnight, followed by immunoprecipitation with Dynabeads Protein G beads (invitrogen). Next, the beads were washed with RIPA buffer (50 mM Hepes, 500 mM LiCl, 1 mM EDTA, 1% NP-40, 0.7% Na-Deoxycholate) on a magnet, eluted (50 mM Tris, 10 mM EDTA, 1% SDS), and reverse crosslinked at 65 °C overnight in parallel with the input. Finally, DNAs were purified with the ChIP DNA Clean & Concentrator (Zymo Research).
Illumina TruSeq

value: EpiSC


title: 3998675114_I

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

value: Active TB

value: EPTB

value: Lymph node

tag: smear microscopy

tag: culture result

tag: age

tag: gender

tag: weight (kg)

tag: hiv positive

value: Culture

tag: tst

tag: tst result


title: 3998720114_H

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

tag: title

tag: sampledate at t0

tag: dosanjh

tag: diagnosis

tag: eptborptb

value: PTB

tag: site of infection

value: Lung

value: TRUE

value: White

value: Culture, PCR, Smear Microscopy

tag: pcr

tag: qtf-git

value: INDETERMINATE


title: dme2_rep1 [RNA-seq]

description: dme-2 heterozygous mutant pollen

source_name: Mature pollen

tag: ecotype

value: Col-gl

tag: genotype


title: ChIP_H3K4me3_EpiLC_dCD

source_name: epiblast-like cells

tag: cell line

value: d2 EpiLC

tag: strain

value: Mll3/4 dCD


title: NB2_WT

description: gene expression data from the cortex of P4H-TM wild-type mice

value: wild-type

tag: tissue

value: cortical tissue


title: 3998720114_I

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

tag: smear microscopy

tag: culture result

value: Positive

tag: age

tag: gender

value: Female

tag: weight (kg)

value: Indian

value: FALSE

value: NEGATIVE


title: 3998720106_L

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

tag: title

tag: sampledate at t0

value: Active TB

value: EPTB

value: Miliary TB (disseminated)

value: Male

tag: hiv positive

value: Culture

tag: tst

value: POSITIVE


title: 3998720106_F

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

tag: dosanjh

tag: diagnosis

tag: eptborptb

tag: site of infection

value: Pleura

value: TRUE

tag: tst result


title: 200683670009_E

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

value: Intestine, Lung, Peritoneum

value: Black

tag: pcr

tag: pcr result

tag: qtf-git


title: ChIP_H3K4me3_EpiSC_dCD

tag: cell line

value: EpiSC

tag: strain

tag: genotype

value: Mll3/4 dCD


title: ChIP_H3K4me3_EpiLC_WT

value: d2 EpiLC

value: wild type


title: 3998720114_D

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

value: PTB

value: Lung

tag: smear microscopy

tag: culture result

value: Positive

tag: age

tag: gender

value: Female


title: SAM24333432 SF268

tag: tissue

value: Brain

value: Glioma

tag: treatment

value: siYAP + siTAZ


title: SAM24333431 SF268

value: siNTC


title: 3998675095_H

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

tag: title

tag: sampledate at t0

tag: dosanjh

value: Active TB

value: Lung, Lymph node

value: Male

tag: weight (kg)

value: Indian

tag: hiv positive

value: FALSE

value: Culture, Histology, PCR

tag: tst

value: NEGATIVE

value: POSITIVE


title: 3998734102_I

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

tag: diagnosis

tag: eptborptb

tag: site of infection

value: Lung, Pleura

value: TRUE

value: Asian

value: Culture

tag: tst result

tag: pcr


title: ChIP_H3K4me3_ESC_dCD

source_name: embryonic stem cells

tag: cell line

value: 2i+LIF ESC

tag: strain

tag: genotype

value: Mll3/4 dCD


title: SAM24333433 SF268

value: Brain

value: Glioma


title: SAM24333434 SF268

value: siYAP + siTAZ


title: SAM24333430 SF268

value: siNTC


title: ChIP_H3K4me3_ESC_WT

value: wild type


title: 3998675092_H

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

value: Active TB

value: Lung, Pericardium, Pleura

tag: smear microscopy

tag: culture result

value: Positive

tag: age

tag: gender

value: Male

tag: pcr result

value: Negative

tag: qtf-git


title: 3998734071_B

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

tag: title

tag: sampledate at t0

tag: dosanjh

value: PTB

value: Lung

tag: weight (kg)

value: Indian

value: FALSE

value: POSITIVE


title: 200681360014_B

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

tag: diagnosis

tag: eptborptb

value: Lung, Lymph node, Pericardium

value: TRUE

tag: hiv positive

value: Culture

tag: tst


title: 3998675065_I

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

value: EPTB

tag: site of infection

value: Lymph node

tag: tst result

tag: pcr


title: 200681360014_K

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

tag: smear microscopy

value: White

value: Culture, PCR

value: INDETERMINATE


title: SAM24333428 HCC1954

tag: cell line

tag: tissue

value: Breast

value: Adenocarcinoma Ductal

tag: treatment

value: siYAP + siTAZ


title: scRNAseq_d4EB_WT

data_processing:
The 10x Genomics scRNA-seq data was generated for the d4 EB in R1 WT and dCD can be easily explored by opening the cloupe file with the Loupe Cell Browser (https://www.10xgenomics.com).
Genome_build: mm10
Supplementary_files_format_and_content: UMI_counts;cloupe_file

source_name: embryoid bodies

growth_protocol: ESC were cultured on gelatin-coated plates using Knock-out DMEM supplemented with 15% FBS and LIF. Before each PGCLC differentiation, ESC were adapted to 2i+LIF media (serum-free N2B27 medium supplemented with MEK inhibitor PD0325901 [0.4 μM], GSK3β inhibitor CHIR99021 [3 μM], and LIF) for at least four days in gelatin-coated tissue culture plates. For the EpiLC differentiation, 6-well plates were coated with 15 µg ml-1 Fibronectin and 2 x 105 2i ESC were differentiated in N2B27 media supplemented with 20 ng ml-1 Activin A, 12 ng ml-1 bFGF and 10 µl ml-1 KSR for two days.  For the PGCLC differentiation, d2 EpiLC were plated at a density of 2 x 104 cells ml-1 and cultured as embryoid bodies (EB) on Ultra-Low attachment multiwell plates (Corning® Costar®) in GK15 medium supplemented with growth factors (0.5 µg ml-1 BMP4, 0.1 µg ml-1 SCF, 1000 U ml-1 LIF and 50 ng ml-1 EGF, no BMP8a) for four days.

extract_protocol:
For single cell RNA sequencing, d4 EBs were dissociated with TripleExpress. Cells were then centrifuged and resuspended in PBS containing 0.04 % BSA. Next, cells were passed through a strainer, the cell concentration was determined and the single cell RNA sequencing libraries were prepared using the Chromium Single Cell Gene Expression (10x Genomics) according to the Single Cell 3’ Reagents Kit (v3 chemistry) protocol.
10x Genomics - Single Cell 3’ Reagents Kit (v3)

value: d4 EB

tag: strain

value: R1 WT

tag: genotype

value: wild type


title: 3998703013_B

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

tag: title

value: Active TB

value: Lung, Spine

tag: culture result

value: Positive

tag: age

tag: gender

value: Male

value: Indian

tag: qtf-git

value: NEGATIVE


title: SAM24333429 SF268

value: Brain

tag: diagnosis

value: Glioma

value: siNTC


title: SAM24333427 HCC1954


title: 3998734071_I

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

tag: sampledate at t0

tag: dosanjh

tag: eptborptb

value: PTB

value: Lung

value: TRUE

tag: weight (kg)

value: Black

tag: hiv positive

value: FALSE

value: Culture

value: POSITIVE


title: scRNAseq_d4EB_dCD

value: d4 EB

value: R1 WT

value: Mll3/4 dCD


title: G15_P1

city: cheonan

first: ji hoon

last: jeong

address: cheonan

country: South Korea

institute: Soonchunhyang Institute of Medi-bio Science

description: cell differentiated on GelMA with PSS

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 Tophat
Read count extraction and Quantile nomalization were performed using edgeR.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include read count values for each Sample

source_name: muscle

growth_protocol: c2c12 cells were cultured in tissue-culture plates at a density of 5 * 103 cells/cm2 with high-glucose Dulbecco’s modified Eagle’s medium supplemented with 10% fetal bovine serum, 1% L-glutamine, and 1% penicillin-streptomycin

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using SMARTER mRNA-Seq Library Prep Kit standard protocols.

treatment_protocol: When cells were reached to 80% confluency, growth medium was replaced with myogenic induction medium containing DMEM supplemented with 2% of horse serum and 1% penicillin-streptomycin to induce myogenic differentiation in 3 different cell culture substrate, Tissue culture plate, Methacarylated gelatin and 15% Methacarylated gelatin mixed with 1% PSS (poly sodium 4-styrenesulfonate).

tag: cell type

value: immortalized mouse myoblast cell line

tag: type of substrate


title: G15

description: cell differentiated on GelMA

value: Methacarylated gelatin


title: SAM24333426 HCC1954

tag: cell line

tag: tissue

value: Breast

value: Adenocarcinoma Ductal

value: siYAP + siTAZ


title: 3998675040_B

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

value: Active TB

tag: site of infection

tag: smear microscopy

value: Positive

value: Female

tag: height (cm)

tag: bmi

value: Indian

tag: tst

tag: tst result

tag: pcr

value: NEGATIVE


title: 3998675120_I

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

tag: title

tag: diagnosis

value: PTB

value: Lung

value: TRUE

tag: culture result

tag: age

tag: gender

value: Male

tag: pcr result

tag: qtf-git


title: 3998675049_L

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

tag: sampledate at t0

tag: dosanjh

tag: eptborptb

value: EPTB

value: OTHER

tag: weight (kg)

tag: hiv positive

value: FALSE

value: Culture

value: POSITIVE


title: 3998675119_G

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

tag: site of infection

value: Pleura

tag: smear microscopy

tag: height (cm)


title: 3998675119_I

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

tag: tst

value: INDETERMINATE


title: 3998675092_B

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

value: Bones, Lung, Lymph node

value: Culture, PCR

tag: tst result

tag: pcr


title: 3998675069_A

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

tag: title

tag: diagnosis

value: Active TB

value: Lymph node

value: Positive


title: SAM24333424 HCC1954

tag: cell line

tag: tissue

value: Breast

value: Adenocarcinoma Ductal

tag: treatment

value: siNTC


title: 3998720112_H

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

value: TRUE

tag: culture result

tag: age

tag: gender

tag: bmi

value: Indian

tag: pcr result

tag: qtf-git

value: NEGATIVE


title: SAM24333423 HCC1954


title: Primary tumor (PT) spheres - replicate 3

city: New York

first: Julio

last: Aguirre-Ghiso

state: NY

address: 1468 Madison Avenue, A24-64e

institute: Icahn School of Medicine at Mount Sinai

data_processing:
The RNA-Seq data was analyzed using Basepair software (https://urldefense.proofpoint.com/v2/url?u=https-3A__www.basepairtech.com_&d=DwIFaQ&c=shNJtf5dKgNcPZ6Yh64b-A&r=2eTrMIlet1N-adSlZc06oeRObUwVMmPYgdoyfpjVSin5Kgoy-anjqY2o5qXmg6s_&m=JP2DaO0EeJHYY-pErtgneKGYD4_scJPda-QP6fmXaok&s=Pk2IgzqD_rcZILd5PYdfYTol9LmHQNL3dNIMjv5M6bE&e= ) with a pipeline that included the following steps. Reads were aligned to the transcriptome derived from UCSC genome assembly (((hg19))) using STAR (Dobin et al., 2013) with default parameters.
Read counts for each transcript was measured using featureCounts (Liao et al., 2014).
Differentially expressed genes were determined using DESeq2 (Love et al., 2014) and a cut-off of 0.05 on adjusted p-value (corrected for multiple hypotheses testing) was used for creating lists and heatmaps.
Genome_build: mm10
Supplementary_files_format_and_content: txt, counts

molecule: polyA RNA

growth_protocol: MMTV-HER2/Neu mice were maintained on FvB background and bred and crossed in our facilities. All experimental procedures were approved by the Institutional Animal Care and Use Committee (IACUC) of Icahn School of Medicine at Mount Sinai. Mammary glands and primary tumors were digested and cells were cultured for 7-days in ultra-low adhesion plates in mammosphere media.

extract_protocol:
RNA was extracted using RNeasy protocol (Qiagen) following manufacturer instructions.
Sequencing libraries were prepared according to manufacturer instructions. Samples were sequenced on Illumina MiSeq.

tag: strain

value: FvB

tag: tumor stage

value: With primary tumor(s)

value: breast tumor

tag: cell tyoe

value: breast cancer cells


title: 3998703044_G

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

tag: sampledate at t0

tag: dosanjh

tag: eptborptb

value: EPTB

tag: site of infection

tag: smear microscopy

value: Female

tag: height (cm)

tag: weight (kg)

value: Black

tag: hiv positive

value: FALSE

value: Culture

tag: tst

value: POSITIVE


title: TCP

description: cell differentiated on TCP

tag: cell type

value: immortalized mouse myoblast cell line

tag: type of substrate

value: Tissue culture plate


title: SAM24333422 ES-2

tag: cell line

tag: tissue

value: Ovary

tag: diagnosis

value: Adenocarcinoma Clear Cell

tag: treatment

value: siYAP + siTAZ


title: Primary tumor (PT) spheres - replicate 1

tag: strain

tag: age

tag: tumor stage


title: 3998675102_A

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

tag: title

tag: sampledate at t0

tag: dosanjh

value: Active TB

value: PTB

value: Lung

value: TRUE

tag: culture result

value: Positive

tag: gender

value: Male

value: Indian

tag: tst result

tag: pcr

tag: qtf-git


title: 3998703022_K

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

tag: eptborptb

value: EPTB

tag: site of infection

value: Lymph node

tag: smear microscopy

tag: height (cm)

tag: weight (kg)

tag: bmi

tag: hiv positive

tag: tst

value: NEGATIVE


title: Early lesion (EL) spheres - replicate 3

tag: strain

value: FvB

tag: age

tag: tumor stage

value: No palpable tumor

tag: tissue

value: mammary lung

tag: cell tyoe

value: breast cancer cells


title: 3998703044_C

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

tag: title

tag: sampledate at t0

tag: dosanjh

tag: diagnosis

value: OTHER

tag: culture result

tag: gender

value: FALSE

value: Culture, Histology

value: POSITIVE

value: INDETERMINATE


title: SAM24333425 HCC1954

tag: cell line

value: Breast

value: Adenocarcinoma Ductal

tag: treatment

value: siNTC


title: SAM24333421 ES-2

value: Ovary

value: Adenocarcinoma Clear Cell

value: siYAP + siTAZ


title: 3998703022_C

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

value: Active TB

tag: eptborptb

value: EPTB

tag: site of infection

value: Lymph node, Spine

tag: smear microscopy

value: TRUE

value: Positive

value: Female

tag: weight (kg)

value: Indian

value: Culture

tag: pcr

tag: qtf-git

value: MISSING


title: Early lesion (EL) spheres - replicate 2

tag: strain

value: FvB

tag: age

tag: tumor stage

value: No palpable tumor

value: mammary lung

value: breast cancer cells


title: 3998734084_K

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

tag: title

value: PTB

value: Lung

value: Male

tag: hiv positive

value: FALSE

tag: tst

tag: pcr result

value: POSITIVE

value: NEGATIVE


title: SAM24333420 ES-2

tag: tissue

value: Ovary

tag: diagnosis

value: Adenocarcinoma Clear Cell

value: siYAP + siTAZ


title: 3998675101_A

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

tag: sampledate at t0

tag: dosanjh

value: Active TB

value: TRUE

tag: culture result

value: Positive

tag: gender

value: Female

value: White

tag: tst result


title: 3998675092_K

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

tag: eptborptb

tag: site of infection

value: Lung, Pleura

tag: smear microscopy

tag: weight (kg)

value: Indian

value: Culture


title: 3998734082_I

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

value: EPTB

value: Lymph node

tag: age

tag: height (cm)

tag: bmi

tag: pcr

tag: qtf-git


title: 3998703044_E

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

tag: title

value: Spine

value: Male

tag: hiv positive

value: Culture, Histology, Imaging

tag: tst

value: INDETERMINATE


title: Primary tumor (PT) spheres - replicate 2

tag: strain

value: FvB

tag: tumor stage

value: With primary tumor(s)

tag: tissue

value: breast tumor

tag: cell tyoe

value: breast cancer cells


title: Early lesion (EL) spheres - replicate 1

value: No palpable tumor

value: mammary lung


title: SAM24333419 ES-2

tag: cell line

value: Ovary

tag: diagnosis

value: Adenocarcinoma Clear Cell

tag: treatment

value: siNTC


title: SAM24333418 ES-2


title: SAM24333417 ES-2


title: NKTtotal spl rep1

city: San Diego

first: Mitchell

last: Kronenberg

address: 9420 Athena Circle

institute: La Jolla Institute for Immunology

data_processing:
Basecalls and demultiplexing performed in Illumina basespace
ATAC-seq reads were aligned to the mm9 genome assembly using bowtie v 1.0
Unmapped reads were trimmed to remove adapters and to 36nt length with trim_galore and remapped and merged with first bam file
Duplicate read pairs were removed using Picard (v1.94).
Bam files were filtered to extract fragments less than 100 nt, downsampled to a maximum of 5 million reads with Picard (v1.94) and peaks were identified using MACS2 with parameters "--nomodel --nolambda --keep-dup all --call-summits -q 0.0001"
NarrowPeak files from individual replicates of all conditions were merged into a global set of peaks, excluding those on the Y chromosome or overlapped the ENCODE blacklist, and condensed to non-overlapping regions with a uniform size of 500 bp using chromVAR readNarrowpeaks (v 1.8.0)
ATAC-seq reads overlapping peaks were computed with  chromVAR fragmentCounts (v1.8) and normalized with limma/voom (v3.40.6)
Genome_build: mm9
Supplementary_files_format_and_content: tsv containing ATAC-seq density

source_name: spleen

growth_protocol: Cells were sorted ex vivo from the indicated mouse tissues into 5% FCS

extract_protocol:
Cells representing specific iNKT subsets were sorted directly into 0.2 ml PCR tubes containing 8 µL of low-input lysis buffer (0.2% Triton-X-100 and RNase inhibitor) and stored at -80oC until processed further.  RNA extraction, reverse transcription, cDNA amplification, fragmentation, and additional PCR amplification was performed as previously described (Rosales et al. Methods Mol Biol 1799, p275).
iNKT cells (10,000) were sorted into 1.5 mL Eppendorf tubes containing PBS with 5% FCS.  Cells were centrifuged at 600g for 10 minutes at 4oC, washed with 50 mL PBS, then resuspended in 50 mL ATAC lysis buffer (10 mM Tris pH 7.5, 10 mM NaCl, 3 mM MgCl2, 0.1% NP-40).  Cells were centrifuged in lysis buffer for 10 minutes at 600g, 4oC.  Following lysis, the pellet was resuspended in 50 mL ATAC reaction mix (25uL 2X TD buffer, 2.5 mL Nextera Enzyme, 22.5 mL water, Illumina).  The transposase reaction was carried out at 37oC for 30 minutes.
Libraries were amplified using a KAPA HiFi real-time library amplification kit with barcoded primers for 11-12 cycles followed by 2x50 cycle paired-end sequencing.

treatment_protocol: Cells were isolated from either pools of tissues from 15-20 6 week old female C57Bl/6J mice, or from individual 6-7 week old female C57Bl/6J mice, as indicated in column C.  Mice were euthanized and perfused with 3-10ml liver perfusion media (Gibco) when liver or lung was harvested.  Thymus, spleen and liver cell suspensions were prepared by physical disaggregation, and sedimentation at 400xg.  Liver mononuclear cells were isolated by pelleting through centrifugation at 750g for 12’ in 34% Percoll/PBS.  Spleen and liver suspensions were treated with RBC lysis buffer (Sigma).  Lungs were homogenized in GentleMacs C tubes (Miltenyi Biotec) with 2 mL Spleen Dissociation Medium (STEMCELL Technologies) using the Miltenyi GentleMacs dissociator.  Cell suspensions for all tissues except liver were enriched for iNKT cells by negative selection using biotinylated antibodies against CD8b.2 (53–5.8, BD Biosciences), CD19 (1D3, Tonbo Biosciences), CD24 (M1/69, BD Biosciences), CD62L (MEL-14, Invitrogen), CD11b (M1/70, Tonbo Biosciences), CD11c (N418, Tonbo Biosciences), F4/80 (BM5.1, Tonbo Biosciences), EpCam(G8.8, Invitrogen), and TER-119 (TER-119, Tonbo Biosciences) together with Rapidspheres (StemCell technologies) and either the Big Easy or Easy eight magnets (StemCell technologies) using protocols from the manufacturer.  The cells were then suspended at up to 100 million cells/mL and incubated with 1 mg/mL of Streptavidin A (Sigma-Aldrich).  Cells were stained with tetramers of CD1d loaded with αGalCer (BV421, in house preparation), live/dead yellow (ThermoFisher Scientific), anti-TCRb-APC-eF780 (H57-597, ThermoFisher Scientific), anti-CD8a-PE CF594 (53-6.7, BD Biosciences) and anti-CD19-PE CF594 (1D3, BD Biosciences), anti-CD4-AF700 (GK1.5, BioLegend), together with one of the following antibody panels, as indicated in column H.  Panel A:  anti-IL-17RB-AF488 (FAB10402G, R&D Systems), anti-ICOS-PerCP Cy5.5 (C398.4A, BioLegend), anti-CD122-BV650 (5H4, BD Biosciences), anti-CXCR3-APC (CXCR3-173, BioLegend), anti-SDC1-PE (281-2, BioLegend), and anti-FR4-PE Cy7 (ebio12A5, ThermoFisher Scientific).  Panel B:  anti-CXCR5-PE (L138D7, BioLegend), and anti-PD-1-APC, clone RMP1-30, BioLegend.  Panel C:  anti-TCRgd-FITC (GL3, BD Biosciences), and anti NK1.1 (PK136, BD Biosciences).  Cells were sorted using a FACSAria III or a FACSAria Fusion.  All NKT cells were sorted as lymphocyte-gated single cells, viability dye-low, CD8a-, CD19- , CD1d-tetramer-staining, TCRb+, in addition to the criteria indicated in column H (total NKT cells required no additional sorting criteria).  gdT cells, CD4 T cells and NK cells were sorted as lymphocyte-gated single cells, viability dye-low, CD8a-, CD19- , and CD1d-tetramer-non-staining, in addition to the additional criteria indicated in column H.

tag: cell type

value: NKTtotal

value: spleen

tag: stimulation


title: NKTtotal spl rep2


title: SAM24317277 Detroit 562

source_name: Detroit 562

value: Detroit 562

value: Nasal Pharynx

value: Carcinoma

value: siYAP + siTAZ


title: 3998720107_G

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

tag: sampledate at t0

tag: dosanjh

value: Active TB

tag: eptborptb

value: EPTB

tag: site of infection

value: Miliary TB (disseminated)

tag: smear microscopy

value: TRUE

tag: culture result

value: Positive

tag: age

tag: gender

value: Female

tag: weight (kg)

value: White

value: FALSE

value: Culture

value: POSITIVE


title: 3998675027_C

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

tag: title

value: Pleura

value: Male

value: Indian

tag: hiv positive

tag: tst

tag: pcr

tag: qtf-git

value: INDETERMINATE


title: NKTtotal spl rep3

value: NKTtotal

tag: tissue

value: spleen

tag: strain


title: 3998720107_E

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

tag: diagnosis

value: PTB

value: Lung

tag: height (cm)

tag: bmi

tag: tst result


title: 3998720079_B

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

tag: sampledate at t0

tag: dosanjh

value: Active TB

tag: eptborptb

value: EPTB

tag: site of infection

value: NEGATIVE


title: SAM24317276 Detroit 562

tag: cell line

value: Detroit 562

value: Nasal Pharynx

value: Carcinoma

tag: treatment

value: siYAP + siTAZ


title: NKTtotal lung rep1

source_name: lung

tag: cell type

value: lung

tag: stimulation


title: NKTtotal lung rep2


title: 3998720079_I

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

tag: title

tag: smear microscopy

value: TRUE

tag: culture result

value: Positive

tag: age

tag: gender

tag: weight (kg)

value: Black

tag: hiv positive

value: FALSE

value: Culture

tag: tst

value: POSITIVE


title: 3998675070_G

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

tag: diagnosis

value: Abdomen, Lung, Lymph node, Neck, Peritoneum

value: Female

tag: height (cm)

tag: bmi

value: Indian

tag: tst result

tag: pcr

tag: qtf-git


title: 3998703044_H

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

tag: sampledate at t0

tag: dosanjh

value: Active TB

tag: eptborptb

value: PTB

tag: site of infection

value: Lung

value: Male

tag: pcr result

value: INDETERMINATE


title: 3998703044_D

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

tag: title

value: EPTB

value: Lymph node

tag: smear microscopy

tag: culture result

value: NEGATIVE


title: 3998675070_C

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

value: TRUE

tag: age

tag: gender

tag: weight (kg)


title: SAM24317275 Detroit 562

tag: cell line

value: Detroit 562

tag: tissue

value: Nasal Pharynx

tag: diagnosis

value: Carcinoma

tag: treatment

value: siYAP + siTAZ


title: 3998734070_J

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

value: Positive

tag: hiv positive

value: FALSE

value: Culture

tag: tst

tag: pcr

value: POSITIVE


title: 3998703004_C

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

tag: sampledate at t0

tag: dosanjh

value: Active TB

value: Indian

tag: qtf-git


title: SAM24317268 Detroit 562

value: siNTC


title: NKTnonFH spl6d aGC rep3

tag: cell type

value: NKTnonFH

value: spleen

tag: strain

tag: stimulation


title: SAM24317267 Detroit 562


title: NKTnonFH spl6d aGC rep2


title: SAM24317266 Detroit 562


title: 3998675065_F

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

tag: title

tag: eptborptb

value: PTB

tag: site of infection

value: Lung

tag: smear microscopy

tag: culture result

value: Male

value: White

tag: tst result


title: 3998675068_I

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

tag: diagnosis

value: TRUE

tag: age

tag: gender

tag: weight (kg)

value: Black


title: NKTnonFH spl6d aGC rep1

tag: tissue


title: 3998675106_C

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

tag: sampledate at t0

value: EPTB

value: Lymph node

tag: hiv positive

tag: tst

tag: pcr

value: INDETERMINATE


title: NKTFH spl6d aGC rep6

tag: cell type

value: NKTFH

tag: strain


title: 3998675106_I

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

tag: title

tag: dosanjh

value: Positive

value: FALSE

value: Culture

tag: qtf-git

value: NEGATIVE


title: NKTFH spl6d aGC rep4

tag: stimulation


title: NKTFH spl6d aGC rep5


title: 3998675118_B

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

value: Active TB

tag: eptborptb

tag: site of infection

tag: smear microscopy

tag: culture result

value: Female

value: Indian

value: POSITIVE


title: 3998675093_F

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

tag: diagnosis

value: PTB

value: Lung

tag: age

tag: gender


title: 3998734071_E

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

tag: sampledate at t0

value: Male

tag: weight (kg)

tag: tst result


title: 3998675118_K

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

value: TRUE

tag: hiv positive

tag: tst

tag: pcr


title: 3998734087_G

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

tag: title

tag: pcr result


title: 3998734070_C

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

tag: dosanjh

value: Negative

tag: qtf-git


title: NKTFH spl6d aGC rep1

tag: cell type

tag: tissue

value: spleen

tag: strain

tag: stimulation


title: NKTFH spl6d aGC rep3


title: NKT2 thy rep4

source_name: thymus

value: thymus


title: NKTFH spl6d aGC rep2


title: NKT2 thy rep3


title: NKT2 thy rep1


title: 3998720107_I

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

tag: diagnosis

tag: eptborptb

value: EPTB

tag: site of infection

value: Lymph node

tag: smear microscopy

tag: culture result


title: NKT2 thyCD44low rep1


title: NKT2 thy rep2


title: 3998734089_L

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

tag: sampledate at t0

value: Positive

tag: age

tag: gender

tag: weight (kg)

tag: tst result

value: Indeterminate


title: 3998734069_I

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

tag: title

value: Black

tag: hiv positive

value: FALSE

value: Culture

tag: tst

tag: pcr


title: 3998675096_H

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

tag: dosanjh

value: Active TB

tag: height (cm)

tag: bmi

value: Culture, PCR

tag: pcr result

tag: qtf-git


title: 3998675112_D

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

tag: diagnosis

tag: eptborptb

tag: site of infection

value: Asian

value: NEGATIVE

value: POSITIVE


title: 3998720079_L

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

tag: sampledate at t0

value: Bones, Lung

tag: smear microscopy

tag: culture result

value: Male


title: 3998675056_A

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

value: TRUE

tag: age

tag: gender

tag: weight (kg)

value: Indian


title: 3998720112_G

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

tag: title

value: PTB

value: Lung

tag: hiv positive


title: 3998675070_D

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

value: EPTB

value: Pericardium

tag: tst

tag: pcr

value: INDETERMINATE


title: 3998675074_K

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

tag: dosanjh

value: Positive

value: Female

tag: tst result


title: 3998675091_D

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

value: Lymph node

value: FALSE

value: Culture


title: 3998675108_A

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

value: Active TB


title: 3998675074_I

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

value: White

value: Culture, PCR

tag: pcr result


title: 3998675108_D

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

value: Asian

tag: qtf-git

value: POSITIVE


title: 3998734087_D

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

tag: diagnosis

value: TRUE

tag: height (cm)

tag: bmi


title: 3998720106_D

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

tag: sampledate at t0

tag: eptborptb

tag: site of infection

value: Lung, Spine

value: Male

value: Indian

value: Culture, Imaging

value: NEGATIVE


title: 3998675102_K

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

value: EPTB

tag: smear microscopy

tag: culture result

tag: age


title: 3998734102_F

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

tag: title

value: PTB

value: Lung

value: Positive

tag: gender

tag: weight (kg)


title: 3998675112_H

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

tag: hiv positive

value: FALSE

tag: tst

tag: pcr


title: 3998675106_D

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

tag: dosanjh

value: Abdomen, Lung, Miliary TB (disseminated)

value: Female

value: Black

value: Culture


title: 3998675086_J

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

value: Active TB

value: Lymph node

tag: tst result

tag: qtf-git


title: 3998675070_J

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

tag: diagnosis

value: Abdomen, Lymph node

value: TRUE

value: INDETERMINATE


title: NKT2 spl rep2

tag: cell type

tag: tissue

value: spleen

tag: strain

tag: stimulation


title: 3998675056_K

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

tag: sampledate at t0

tag: eptborptb

tag: site of infection

tag: smear microscopy

value: White

tag: pcr result

value: POSITIVE


title: ChIP Primary tumor (PT) spheres - replicate 3

data_processing:
ChIP was performed using EZ ChIP protocol (Millipore, Massachusetts, USA) with Zfp281 antibody (ab101318, Abcam)
ChIP-seq reads were aligned to the mm10 genome using bowtie2 (v2.3.4.3), followed by removing PCR duplicates using Picard with the parameter REMOVE_DUPLICATES=true.
ChIP-seq peaks were determined by the MACS program (v.2.1.2) using input ChIP-seq as the control data, and all other parameters followed the default setting.
Genome_build: mm10
Supplementary_files_format_and_content: Bed file of MACS called peaks.

extract_protocol:
RNA was extracted using RNeasy protocol (Qiagen) following manufacturer instructions.
One EL input, one PT input, three biological EL and three biological PT replicates ChIPed DNA were used to prepare ZFP281 ChIP-seq libraries. Massively parallel sequencing was performed with the Illumina HiSeq4000 according to the manufactory protocol, and paired-end 150 bp-length reads were produced.

value: FvB

tag: age

tag: tumor stage

value: With primary tumor(s)

value: breast tumor

value: breast cancer cells

tag: antibody


title: 3998675120_L

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

tag: title

value: PTB

value: Lung

tag: culture result

value: Positive

tag: gender

value: Male

tag: height (cm)

tag: weight (kg)

tag: bmi

value: Indian

tag: hiv positive

value: FALSE

tag: tst

tag: pcr

value: NEGATIVE


title: 3998675093_C

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

tag: sampledate at t0

tag: dosanjh

tag: diagnosis

value: Active TB

value: Culture

tag: qtf-git


title: ChIP Primary tumor (PT) spheres - replicate 2

tag: strain

tag: tissue

tag: cell type


title: NKT2 thyCD44hi rep1

value: thymus

tag: stimulation


title: ChIP Primary tumor (PT) spheres - replicate 1

tag: age

tag: tumor stage

tag: antibody


title: NKT2 spl rep1

value: spleen


title: NKT2 lung rep1

value: lung


title: ChIP Primary tumor (PT) spheres - input


title: NKT17 thy rep4


title: ChIP Early lesion (EL) spheres - replicate 3

value: No palpable tumor

value: mammary lung


title: ChIP Early lesion (EL) spheres - replicate 2

value: FvB


title: ChIP Early lesion (EL) spheres - replicate 1


title: NKT17 thy rep3


title: NKT17 thy rep1


title: ChIP Early lesion (EL) spheres - input


title: NKT17 spl rep3


title: 200681360009_L

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

tag: title

tag: eptborptb

value: EPTB

tag: site of infection

value: Lymph node

tag: smear microscopy

tag: culture result

tag: gender

tag: height (cm)

value: POSITIVE


title: NKT17 spl rep2


title: TtT-GF-Starvation-SAG3

city: Goettingen

first: Nadine

last: Brandes

address: Heinrich-Düker-Weg 12

department: Institute of Human Genetics

institute: University Medical Center Goettingen

data_processing:
Sequence images were transformed with Illumina software BaseCaller to BCL files, which was demultiplexed to fastq files with bcl2fastq v2.20.0.422. The sequencing quality was asserted using FastQC. FastQC A Quality Control tool for High Throughput Sequence Data. http://www.bioinformatics.babraham.ac.uk/projects/fastqc/)(version 0.11.5).
Sequences were aligned to the reference genome Mus musculus (Mus_musculus.GRCh38  Ensembl 96 , https://www.ensembl.org/Mus_musculus/Info/Index) using the STAR aligner (2.7.0f)
Afterwards, aligned reads were counted towards their features (genes) with rsem calculate expression (Li and Dewey 2011) (RSEM v1.1.1). The resulting expected counts were the baseline input for further analysis in the programming language R (3.6.1) using the limma + voom (Law et al. 2014) (limma version 3.40.6 ) package for differential gene expression analysis. Following GSEA utilising the clusterProfiler v3.12 (Guangchuang Yu and He 2012) package in R. For quality control during the analysis pipeline multiQC (Ewels et al. 2016) version 1.8, evaluating the output of fastqc (Andrews 2014) and the log files of STAR, was used.
The significance level was set to alpha = 5% for all statistical tests. All analyses were performed with the statistic software R (version 3.6.1, www.r-project.org)
Genome_build: mm10
Supplementary_files_format_and_content: text file includes gene expression for each sample

source_name: Folliculo-stellate cell line TtT/GF

growth_protocol: Cells were grown  in DMEM/HamF12 medium supplemented with 10% Horse serum and 2.5% FCS. 5x10^4 cells were seeded into one well of a 6 well plate

extract_protocol:
RNA was harvested using Trizol.
Libraries were prepared according to Illumina's instructions accompanying the TruSeq® RNA Sample Preparation v2 kit.

treatment_protocol: For treatment the cells the starved for 24 hours in medium containing 0.5% Horse serum and 0.125% FCS, afterwards the cells were treated for 48 hrs with 100nM SAG or DMSO (1:10000) in the starvation medium.

tag: treatment

value: Smoothened Agonist (SAG)

tag: cell line

value: TtT/GF cells


title: 3998734071_K

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

tag: sampledate at t0

tag: dosanjh

tag: diagnosis

value: TRUE

value: Positive

value: Male

tag: weight (kg)

tag: bmi

tag: hiv positive

tag: tst

tag: pcr

tag: qtf-git


title: NKT17 lung rep2

tag: cell type

tag: tissue

tag: strain

tag: stimulation


title: 3998675101_C

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

tag: title

tag: eptborptb

tag: site of infection

tag: smear microscopy

tag: culture result

tag: age

tag: gender

value: Female

value: Indian

value: FALSE

tag: tst result

value: INDETERMINATE


title: 200681360009_H

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

tag: sampledate at t0

tag: dosanjh

tag: diagnosis

value: Active TB

tag: height (cm)

tag: weight (kg)

tag: bmi

value: Histology

value: NEGATIVE


title: 3998675101_K

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

tag: hiv positive

value: Culture

tag: tst

tag: pcr

tag: qtf-git


title: TtT-GF-Starvation-SAG2

tag: treatment

tag: cell line


title: 3998734084_J

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

tag: title

tag: eptborptb

value: PTB

tag: site of infection

value: Lung

tag: smear microscopy


title: 3998720107_J

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

value: Central nervous system, Lung, Miliary TB (disseminated)

tag: culture result

tag: age

tag: gender

value: Culture, Imaging


title: NKT17 lung rep1

tag: cell type

tag: tissue

value: lung

tag: strain

tag: stimulation


title: 3998675110_F

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

tag: sampledate at t0

tag: dosanjh

tag: diagnosis

tag: height (cm)

tag: weight (kg)

tag: bmi

value: Black

tag: hiv positive

value: POSITIVE


title: 3998675070_B

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

tag: title

tag: eptborptb

value: EPTB

value: Ankle

value: TRUE

value: Positive

tag: tst

tag: pcr

tag: qtf-git


title: 3998675040_H

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

tag: site of infection

value: Lymph node

tag: smear microscopy

tag: culture result

tag: age

tag: gender

value: Female

value: Indian

value: FALSE


title: 3998675040_K

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

tag: sampledate at t0

value: Active TB


title: TtT-GF-Starvation-SAG1

tag: treatment

value: Smoothened Agonist (SAG)

tag: cell line

value: TtT/GF cells


title: 3998675091_H

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

tag: dosanjh

tag: diagnosis

value: Male

tag: height (cm)

value: NEGATIVE


title: 3998675081_H

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

tag: weight (kg)

tag: bmi

tag: hiv positive

value: Culture


title: NKT1 thy rep9

tag: cell type

tag: tissue

value: thymus

tag: strain

tag: stimulation


title: TtT-GF-Starvation-DMSO3

value: DMSO


title: 3998703044_F

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

tag: title

tag: eptborptb

value: PTB

tag: site of infection

value: Lung

tag: smear microscopy

value: Asian

tag: tst

tag: pcr

tag: qtf-git

value: POSITIVE


title: NKT1 thy rep7


title: 3998675043_D

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

tag: sampledate at t0

tag: dosanjh

value: EPTB

value: Omentum, Peritoneum

value: TRUE

tag: culture result

value: Positive

tag: age

tag: gender


title: 200681360014_F

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

tag: diagnosis

value: Female

tag: height (cm)

tag: weight (kg)

tag: bmi

value: Black

tag: hiv positive

value: FALSE

tag: pcr result


title: 3998675112_J

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

tag: title

value: Active TB

tag: eptborptb

value: Lymph node

value: Indian


title: NKT1 thy rep1

tag: cell type

tag: tissue

tag: strain

tag: stimulation


title: 200683670009_J

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

tag: sampledate at t0

tag: site of infection

tag: smear microscopy

value: Male

value: Culture

tag: tst

tag: pcr

tag: qtf-git


title: 3998720105_B

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

tag: dosanjh

tag: diagnosis

tag: culture result

tag: age

tag: gender

tag: height (cm)


title: TtT-GF-Starvation-DMSO1

tag: treatment

value: DMSO

tag: cell line

value: TtT/GF cells


title: 3998675086_C

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

tag: title

tag: eptborptb

value: PTB

value: Lung

tag: weight (kg)

tag: bmi

tag: hiv positive


title: 3998675112_C

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

tag: sampledate at t0

tag: site of infection

value: Lung, Pleural cavity

tag: smear microscopy

tag: pcr result

value: POSITIVE


title: NKT1 thy rep2

tag: cell type

tag: tissue

value: thymus

tag: strain

tag: stimulation


title: 3998675091_F

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

tag: dosanjh

tag: diagnosis

value: EPTB

value: Lymph node, Spine

value: TRUE

tag: culture result

tag: age

tag: gender

tag: tst

tag: pcr

tag: qtf-git

value: NEGATIVE


title: 3998675091_C

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

tag: title

tag: eptborptb

value: FALSE

value: Positive

tag: height (cm)

tag: weight (kg)

tag: bmi

tag: hiv positive


title: 3998675091_A

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

tag: sampledate at t0

value: Active TB

tag: site of infection

tag: smear microscopy

value: White

tag: pcr result

value: Negative


title: 3998675070_E

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

tag: dosanjh

tag: diagnosis

value: Female

value: Indian

value: Culture

tag: tst result


title: 3998734086_D

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

value: Lymph node

tag: culture result

tag: age

tag: gender

value: Male


title: NKT1 spl rep4

tag: cell type

tag: tissue

value: spleen

tag: strain

tag: stimulation


title: NKT1 spl rep3


title: Mutant HSPCs sample1

city: Guangzhou

first: Gaofei

last: Li

address: Guangzhou Higher Education Mega Centre, Panyu District

country: China

institute: South China University of Technology

data_processing:
Clean fastq files were applied to FASTQC for quality control.
After quality control, the clean reads were mapped to the zebrafish GRCz11 reference genome using STAR.
The mapped reads were then counted using FeatureCounts (from Rsubread).
The counts matrix was applied to DESeq2 for normalization, differentially expressed genes identification, and sample-to-sample distance analysis.
GO terms enrichment was performed using the online resource Metascape.
Genome_build: GRCz11
Supplementary_files_format_and_content: Normalized counts (TPM) matrix

organism: Danio rerio

source_name: Hematopoietic Stem/Progenitor Cell

growth_protocol: Zebrafish embroys were maintained in egg water in 28 °C till 4 dpf for sacrification.

extract_protocol:
The 4 dpf larvae were grind and enzyme-digested into single cells. The cells were then applied to FACS to sort the HSPCs.
Approximately 500  cells from each group were collected and applied to the Discover-sc WTA v2 kit (Vazyme, N711-03) for cell lysis, reverse transcription, amplification, and library construction.

treatment_protocol: The embryos underwent no further treatment.

value: AB

tag: genotype

value: Smu07 mutant

value: 4 dpf

tag: facs gate


title: Mutant HSPCs sample2


title: 3998703016_C

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

source_name: Whole blood

tag: title

tag: eptborptb

value: EPTB

tag: height (cm)

tag: weight (kg)

tag: bmi

value: Asian

tag: hiv positive

tag: tst

tag: pcr

tag: qtf-git

value: POSITIVE


title: 3998720112_L

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

tag: sampledate at t0

tag: dosanjh

tag: diagnosis

tag: site of infection

tag: smear microscopy

value: FALSE

tag: culture result

tag: age


title: TtT-GF-Starvation-DMSO2

tag: treatment

value: DMSO

tag: cell line

value: TtT/GF cells


title: Sibling HSPCs sample1

tag: strain

tag: genotype

value: Sibling

tag: facs gate


title: NKT1 lung rep4

tag: cell type

tag: tissue

value: lung

tag: stimulation


title: 3998675096_L

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

tag: title

value: Active TB

tag: eptborptb

value: Abdomen

value: Positive

tag: gender

tag: height (cm)

tag: weight (kg)

tag: bmi

tag: hiv positive

tag: tst

tag: pcr

value: NEGATIVE


title: NKT1 lung rep3


title: Sibling HSPCs sample2

tag: age


title: NKT1 lung rep2


title: H1299 cells-RIP-WT-2-D08-Input

city: Shanghai

first: Jianxiu

last: Yu

address: 280 South Chongqing Road, Shanghai 200025, China

department: Department of Biochemistry and Molecular Cell Biology

institute: shanghai jiaotong university school of medicine

description:
input RNA
H1299 cells-RIP-WT-2-D08-Input

data_processing:
3’ adaptor-trimming and low quality reads were removed by cutadapt software (v1.9.3)
clean reads of all libraries were aligned to the reference genome (hg19)  by Hisat2 software (v2.0.4).
Methylated sites on RNAs (peaks) were identified by MACS software
Differentially methylated sites were identified by diffReps. These peaks identified by both softwares overlapping with exons of mRNAs were figured out and choosed by home-made scripts.
cuffdiff software (v2.2.1, part of cufflinks) was used to get the transcript level and gene level FPKM, and fold change and p-value were calculated , differentially bound or expressed mRNAs were identified.
Genome_build: hg19
Supplementary_files_format_and_content: FPKM, counts

source_name: H1299 cells

extract_protocol:
MeRIP-seq:m6A RNA immunoprecipitation was performed with the GenSeqTM m6A RNA IP Kit (GenSeq,China) with anti-m6A antiboy. Both the input sample without immunoprecipitation and the m6A IP samples were used for library generation with  NEBNext® Ultra II  Directional RNA Library Prep Kit (New England Biolabs).
RIP-seq:RNA immunoprecipitation was performed with the GenSeqTM RIP Kit (GenSeq,China) with anti-Flag antiboy. RNA extracted by Trizol (Invitrogen, UK).rRNAs were removed from the immunoprecipitated RNA and input RNA samples by using Ribo-Zero™ rRNA Removal Kit (Illumina, San Diego,CA, USA).
RNA-seq:Total RNA harvested by Trizol reagent was used for removing the rRNAs with NEBNext rRNA Depletion Kit (New England Biolabs, Inc., Massachusetts, USA) following the manufacturer's instructions.
MeRIP-seq:The library quality was evaluated with BioAnalyzer 2100 system (Agilent Technologies, Inc., USA). Library sequencing was performed on an illumina Hiseq instrument with 150bp paired-end reads.
RIP-seq:Libraries were controlled for quality and uantified using the BioAnalyzer 2100 system (Agilent Technologies). Library sequencing was performed on the Illumina Hiseq instrument with 150bp paired-end reads according to the manufacturer’s instructions
RNA-seq:Libraries were controlled for quality and quantified using the BioAnalyzer 2100 system (Agilent Technologies, Inc., USA). Library sequencing was performed on an illumina NovaSeq 6000 instrument with 150bp paired end reads

treatment_protocol:
H1299-shYTHDF2-WT cells (endogenous YTHDF2 was silenced by shYTHDF2 and then re-expressed Flag-tagged YTHDF2-WT) were treated with Ginkgolic acid for 12h
H1299-shYTHDF2-WT cells (endogenous YTHDF2 was silenced by shYTHDF2 and then re-expressed Flag-tagged YTHDF2-WT) were treated with 2-D08 for 24h

tag: antibody/kit

tag: treatment

value: untreated


title: 3998675086_G

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

tag: sampledate at t0

tag: dosanjh

tag: diagnosis

value: PTB

tag: site of infection

value: Lung

tag: smear microscopy

value: TRUE

tag: culture result

value: Male

value: Black

value: Culture

tag: pcr result

tag: qtf-git


title: H1299 cells-RIP-WT-GA-Input

description:
input RNA
H1299 cells-RIP-WT-GA-Input

tag: tissue


title: H1299 cells-RIP-WT-Control-Input

description:
input RNA
H1299 cells-RIP-WT-Control-Input


title: 3998675098_A

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

tag: title

tag: eptborptb

value: EPTB

value: Lymph node

tag: gender

tag: height (cm)

tag: weight (kg)

value: Indian

tag: tst result

value: POSITIVE


title: H1299 cells-RIP-WT-2-D08-IP

description:
immunoprecipitated RNA
H1299 cells-RIP-WT-2-D08-IP

tag: antibody/kit

value: Flag(Sigma, lot F1804)

value: treated with 2-D08 for 24h


title: 3998734089_C

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

value: Active TB

tag: age

tag: bmi

tag: hiv positive

value: FALSE

tag: tst

tag: pcr


title: NKT1 liv rep1

source_name: liver

tag: cell type

value: liver

tag: strain

tag: stimulation


title: 3998675110_H

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

tag: sampledate at t0

tag: dosanjh

tag: diagnosis

tag: site of infection

tag: smear microscopy

tag: culture result

value: Positive

tag: qtf-git


title: NK lung rep2

value: NK

tag: tissue

value: lung


title: 3998720110_H

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

tag: title

tag: eptborptb

value: PTB

value: Lung

tag: gender

tag: height (cm)

tag: weight (kg)

tag: pcr result

value: NEGATIVE


title: 3998675120_J

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

value: TRUE

tag: age

value: Male

tag: hiv positive

tag: tst

tag: pcr

value: Negative


title: NKT1 liv rep2

tag: cell type

tag: strain

tag: stimulation


title: 3998734086_C

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

tag: sampledate at t0

tag: dosanjh

tag: diagnosis

tag: site of infection

tag: smear microscopy

value: Female

tag: bmi

value: Asian

value: Culture


title: 3998675049_K

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

tag: title

tag: eptborptb

tag: culture result

tag: gender

value: White

tag: qtf-git

value: INDETERMINATE

value: POSITIVE


title: H1299 cells-RIP-WT-Control-IP

description:
immunoprecipitated RNA
H1299 cells-RIP-WT-Control-IP

tag: tissue

tag: antibody/kit

value: Flag(Sigma, lot F1804)

tag: treatment

value: untreated


title: H1299 cells-RIP-WT-GA-IP

description:
immunoprecipitated RNA
H1299 cells-RIP-WT-GA-IP

value: treated with Ginkgolic acid for 12h


title: 3998675106_A

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

value: Active TB

value: Positive

tag: age

tag: height (cm)

tag: weight (kg)

value: Mixed

tag: hiv positive

value: FALSE

value: Culture, Smear Microscopy

tag: tst

tag: pcr


title: 3998703016_B

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

tag: sampledate at t0

tag: dosanjh

tag: diagnosis

value: PTB

tag: site of infection

value: Lung

value: TRUE

value: Black


title: H1299 cells-RIP-K571R-Input

description:
input RNA
H1299 cells-RIP-K571R-Input

value: lung


title: NK spl rep3

tag: cell type

value: NK

value: spleen

tag: strain

tag: stimulation


title: gdT spl rep2

value: gdT


title: H1299 cells-RIP-WT-Input

description:
input RNA
H1299 cells-RIP-WT-Input


title: gdT spl rep1


title: 3998675065_A

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

tag: title

tag: eptborptb

tag: smear microscopy

tag: culture result

tag: gender

value: Female

tag: bmi

value: White

tag: qtf-git

value: POSITIVE


title: 3998734064_L

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

tag: age

tag: weight (kg)

tag: hiv positive


title: H1299 cells-RIP-K571R-IgG

description:
immunoprecipitated RNA
H1299 cells-RIP-K571R-IgG

tag: tissue

tag: antibody/kit

value: IgG(Millipore, lot CS200623)

tag: treatment

value: untreated


title: 3998734064_J

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

tag: sampledate at t0

tag: dosanjh

tag: diagnosis

value: Active TB

tag: site of infection

value: Positive

value: Male

value: Indian

value: Culture

tag: tst

tag: pcr


title: H1299 cells-RIP-WT-IgG

description:
immunoprecipitated RNA
H1299 cells-RIP-WT-IgG

value: IgG(Millipore, lot CS200621)


title: gdT lung rep1

tag: cell type

tag: strain

tag: stimulation


title: gdT lung rep2


title: H1299 cells-RIP-K571R-IP

description:
immunoprecipitated RNA
H1299 cells-RIP-K571R-IP

value: Flag(Sigma, lot F1804)


title: 3998675049_C

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

tag: title

tag: eptborptb

value: PTB

value: Lung

tag: smear microscopy

value: TRUE

tag: culture result

tag: gender

tag: height (cm)

tag: bmi

value: FALSE

value: Culture, Smear Microscopy

value: MISSING


title: H1299 cells-RIP-WT-IP

description:
immunoprecipitated RNA
H1299 cells-RIP-WT-IP

tag: tissue

value: lung

tag: antibody/kit

tag: treatment


title: 3998675102_J

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

tag: sampledate at t0

tag: dosanjh

tag: diagnosis

tag: age

tag: weight (kg)

value: Black

tag: hiv positive

value: Smear Microscopy

tag: qtf-git

value: INDETERMINATE

value: POSITIVE


title: CD4 spl rep4

tag: cell type

value: spleen

tag: strain

tag: stimulation


title: gdT spl rep3

value: gdT


title: 3998675027_G

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

tag: title

value: Active TB

tag: eptborptb

tag: site of infection

tag: smear microscopy

tag: culture result

value: Positive

value: Male

tag: tst

tag: pcr


title: 3998675106_K

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

tag: sampledate at t0

value: EPTB

value: Lymph node

tag: gender

tag: height (cm)

tag: bmi

value: Indian

value: Culture

value: NEGATIVE


title: H1299 cells-MeRIP-K571R-Input

description:
input RNA
H1299 cells-MeRIP-K571R-Input

data_processing:
Library strategy: MeRIP-seq
3’ adaptor-trimming and low quality reads were removed by cutadapt software (v1.9.3)
clean reads of all libraries were aligned to the reference genome (hg19)  by Hisat2 software (v2.0.4).
Methylated sites on RNAs (peaks) were identified by MACS software
Differentially methylated sites were identified by diffReps. These peaks identified by both softwares overlapping with exons of mRNAs were figured out and choosed by home-made scripts.
cuffdiff software (v2.2.1, part of cufflinks) was used to get the transcript level and gene level FPKM, and fold change and p-value were calculated , differentially bound or expressed mRNAs were identified.
Genome_build: hg19
Supplementary_files_format_and_content: FPKM, counts

tag: tissue

tag: antibody/kit

tag: treatment

value: untreated


title: CD4 spl rep2

tag: cell type


title: CD4 spl rep1

tag: strain


title: 200681360011_E

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

tag: dosanjh

tag: diagnosis

value: PTB

value: Lung

value: TRUE

tag: age

tag: weight (kg)

tag: hiv positive

value: FALSE

tag: qtf-git


title: H1299 cells-MeRIP-WT-Input

description:
input RNA
H1299 cells-MeRIP-WT-Input

value: lung


title: CD4 lung rep2

tag: stimulation


title: CD4 lung rep1


title: H1299 cells-MeRIP-WT-IP

description:
immunoprecipitated RNA
H1299 cells-MeRIP-WT-IP

value: m6A RNA IP Kit(GenSeqTM)


title: H1299 cells-MeRIP-K571R-IP

description:
immunoprecipitated RNA
H1299 cells-MeRIP-K571R-IP


title: 3998675114_F

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

tag: title

tag: eptborptb

tag: site of infection

tag: smear microscopy

tag: culture result

value: Clinical Features, Culture

tag: tst

tag: pcr

tag: pcr result

value: Negative

value: POSITIVE


title: NKT17_lung_H

description:
069_69_17H_NKT_120417_200_IsEn12_E9
all_counts.tsv

data_processing:
Reads passing Illumina filters were further filtered for those mapping to tRNA, rRNA, adapters, and spike-in controls using Bowtie v1.0.0 (-S --fr).
Filtered reads were mapped against the mouse mm10 reference using Tophat v1.4.1 (--library-type fr-firststrand).
Reads mapping to the reference genome are further filtered to remove low-complexity reads with PRINSEQ v0.20.3 (-lc_method "dust" -lc_threshold 4).
Sequencing read coverage per gene was counted using HTSeq-count v0.7.1 (-m union -s yes -t exon -i gene_id) and features with 0 counts across all samples were removed.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: all_counts.tsv: Count matrix with rows as genes and columns as samples.

source_name: individual lung

growth_protocol: Cells were enriched and sorted ex vivo from the indicated mouse tissues into 0.2% Triton-x-100 without cell culture.

extract_protocol:
Cells representing specific iNKT subsets were sorted directly into 0.2 ml PCR tubes containing 8 µL of low-input lysis buffer (0.2% Triton-X-100 and RNase inhibitor) and stored at -80oC until processed further. RNA extraction, reverse transcription, cDNA amplification, fragmentation, and additional PCR amplification were performed as previously described (Rosales et al. Methods Mol Biol 1799, p275).
We followed the Smart-Seq2 protocol as described previously (Picelli et al., 2013; Rosales et al., 2018). Libraries were then pooled at equal molar concentration and sequenced using the HiSeq 2500 and NovaSeq6000 Illumina platform (Illumina).
Samples from the experiment comparing splenic NKTFH and NKTeff cells from aGalCer-challenged mice with unchallenged splenic iNKT cells were sequenced via a paired-end read method using the Novaseq6000 sequencer according to supplied protocols (Illumina). Sequencing for all other samples was performed according to a single-end strategy using the HiSeq2500 sequencer (Illumina).

treatment_protocol: Cells were isolated from either pools of tissues from 15-20 6-week-old female C57Bl/6J mice, or from individual 6-7 week-old female C57Bl/6J mice. Mice were euthanized and perfused with 3-10ml liver perfusion media (Gibco) when liver or lung was harvested. Thymus, spleen and liver cell suspensions were prepared by physical disaggregation, and sedimentation at 400xg. Liver mononuclear cells were isolated by pelleting through centrifugation at 750g for 12’ in 34% Percoll/PBS. Spleen and liver suspensions were treated with RBC lysis buffer (Sigma). Lungs were homogenized in GentleMacs C tubes (Miltenyi Biotec) with 2 mL Spleen Dissociation Medium (STEMCELL Technologies) using the Miltenyi GentleMacs dissociator. Cell suspensions for all tissues except liver were enriched for iNKT cells by negative selection using biotinylated antibodies against CD8b.2 (53–5.8, BD Biosciences), CD19 (1D3, Tonbo Biosciences), CD24 (M1/69, BD Biosciences), CD62L (MEL-14, Invitrogen), CD11b (M1/70, Tonbo Biosciences), CD11c (N418, Tonbo Biosciences), F4/80 (BM5.1, Tonbo Biosciences), EpCam(G8.8, Invitrogen), and TER-119 (TER-119, Tonbo Biosciences) together with Rapidspheres (StemCell technologies) and either the Big Easy or Easy eight magnets (StemCell technologies) using protocols from the manufacturer. The cells were then suspended at up to 100 million cells/mL and incubated with 1 mg/mL of Streptavidin A (Sigma-Aldrich). Cells were stained with tetramers of CD1d loaded with αGalCer (BV421, in house preparation), live/dead yellow (ThermoFisher Scientific), anti-TCRb-APC-eF780 (H57-597, ThermoFisher Scientific), anti-CD8a-PE CF594 (53-6.7, BD Biosciences) and anti-CD19-PE CF594 (1D3, BD Biosciences), anti-CD4-AF700 (GK1.5, BioLegend), together with one of the following antibody panels, as indicated in column H. Panel A: anti-IL-17RB-AF488 (FAB10402G, R&D Systems), anti-ICOS-PerCP Cy5.5 (C398.4A, BioLegend), anti-CD122-BV650 (5H4, BD Biosciences), anti-CXCR3-APC (CXCR3-173, BioLegend), anti-SDC1-PE (281-2, BioLegend), and anti-FR4-PE Cy7 (ebio12A5, ThermoFisher Scientific). Panel B: anti-CXCR5-PE (L138D7, BioLegend), and anti-PD-1-APC, clone RMP1-30, BioLegend. Panel C: anti-TCRgd-FITC (GL3, BD Biosciences), and anti NK1.1 (PK136, BD Biosciences). Cells were sorted using a FACSAria III or a FACSAria Fusion. All NKT cells were sorted as lymphocyte-gated single cells, viability dye-low, CD8a-, CD19- , CD1d-tetramer-staining, TCRb+, in addition to the criteria indicated in column H (total NKT cells required no additional sorting criteria). gdT cells, CD4 T cells and NK cells were sorted as lymphocyte-gated single cells, viability dye-low, CD8a-, CD19- , and CD1d-tetramer-non-staining, in addition to the additional criteria indicated in column H.

tag: Sex

value: Female

tag: cell type

tag: sorting scheme / criteria

value: A / CXCR3-ICOS+CD122-SDC1+IL-17RB+FR4-


title: NKT1_lung_H

description:
068_68_1H_NKT_120417_200_IsEn12_D9
all_counts.tsv

tag: strain

value: A / CXCR3+ICOS-CD122+SDC1-IL-17RB-


title: 3998734087_L

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

tag: sampledate at t0

tag: dosanjh

tag: diagnosis

value: Active TB

value: Positive

tag: age

tag: gender

tag: height (cm)

tag: bmi

value: White

tag: tst result


title: 3998734070_I

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

tag: title

tag: eptborptb

tag: site of infection

tag: smear microscopy

value: Male

tag: weight (kg)

value: Black

tag: hiv positive

value: Culture

tag: qtf-git


title: 3998675043_F

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

value: EPTB

value: Lymph node

tag: culture result

tag: tst

tag: pcr

value: INDETERMINATE


title: 3998675101_G

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

tag: sampledate at t0

tag: dosanjh

value: PTB

value: Lung

value: TRUE

value: MiddleEast

value: FALSE

tag: pcr result

value: NEGATIVE


title: 3998734078_I

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

tag: diagnosis

value: Chest or Thorax, Lymph node

tag: age

tag: gender

value: Asian

value: Culture, Smear Microscopy

value: POSITIVE


title: 3998675093_K

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

value: Active TB

value: Lymph node, Spine

value: Positive

tag: height (cm)

tag: bmi


title: 3998734063_C

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

tag: title

tag: eptborptb

value: Lung, Lymph node, Miliary TB (disseminated)

value: Male

value: White

value: Culture


title: primary human islets-IgG CUT&RUN [S369_neg]

city: Stanford

first: Romina

middle: J

last: Bevacqua

address: 279 Campus Drive W

department: Developmental Biology

institute: Stanford University

description:
S369-IgG
merged_S369_178_A385_peaks.bed

data_processing:
Library strategy: CUT&RUN
Trimmomatic (Bolger et al. 2014) was used for trimming.
Bowtie2 (Langmead and Salzberg 2012) was used for alignment.
HOMER (Heinz et al. 2010) was used for peak calling.
The GREAT algorithm was used for gene annotation (McLean et al. 2010).
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: bigWig files
Supplementary_files_format_and_content: *.bed: Peaks files.

source_name: primary human islets

growth_protocol: Primary human islets were disersed/ transduced with lentiviruses and cultured for 5 days.

extract_protocol:
Lysates were clarified from Protein A-micrococcal nuclease digested DNA. DNA fragments were released for 20 min at 37°C and purified using phenol/chloroform/isoamyl alcohol followed by chloroform extraction and precipitated with glycogen and ethanol. SIX2-Flag-DNA complexes were isolated with anti-Flag antibody.
NEBnext Ultra II library kit.
CUT&RUN (similar to ChIP-seq) and sequenced as 2 × 75 on HiSeq4000.

treatment_protocol: Lentiviruses expressing SIX2-Flag.

tag: cell type

value: Primary islet cells

tag: developmental stage

value: Adult

tag: genotype/variation

value: SIX2-Flag overexpression

tag: treatment

value: pA-MN; EpiCypher

tag: chip antibody

value: IgG (Millipore)


title: primary human islets-antiFlag CUT&RUN [S369]

description:
S369-S2rb
merged_S369_178_A385_peaks.bed

value: Flag (Sigma-Millipore F7425)


title: 3998720106_C

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

value: EPTB

tag: site of infection

value: Abdomen

tag: smear microscopy

value: TRUE

tag: culture result

tag: weight (kg)

value: Indian

tag: hiv positive

value: FALSE

tag: tst

tag: qtf-git

value: NEGATIVE


title: 200681360001_J

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

tag: sampledate at t0

tag: dosanjh

tag: diagnosis

value: Active TB

value: Brain, Lung, Miliary TB (disseminated)

value: Positive

tag: age

tag: gender

tag: pcr

tag: pcr result

value: POSITIVE


title: 3998703016_A

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

tag: title

tag: eptborptb

value: Miliary TB (disseminated)

value: Male

tag: height (cm)

tag: bmi

value: Black

value: Clinical Features, Culture, Imaging

value: Negative

value: INDETERMINATE


title: 3998675120_G

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

tag: site of infection

value: Lymph node

tag: smear microscopy

value: Culture


title: 3998675093_E

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

value: PTB

value: Lung

tag: culture result

tag: weight (kg)

value: MiddleEast


title: 200683670009_D

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

value: TRUE

value: White

tag: hiv positive

value: FALSE

tag: tst

tag: tst result


title: 3998720107_D

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

tag: sampledate at t0

tag: dosanjh

value: Active TB

value: Mixed

tag: qtf-git


title: SIX3 overexpression-Control

description:
E.ins.neon
six3-ox_neonatal_TPM_filter_table.csv

data_processing:
Barcodes were trimmed using Trimgalore_0.5.0.
Reads were aligned to the human genome index (hg19) using STAR v2.6.1d (Dobin et al. 2013).
Transcripts per million (TPM) were quantified using RSEM v1.3.0 (Li and Dewey 2011).
Differentially expressed genes with fold change were detected using the DESeq2 R package (Love et al. 2014).
Genome_build: hg19 (GRCh37) transcriptome
Supplementary_files_format_and_content: *_csv: Comma-separated text files include TPM values.

source_name: primary islet cells

extract_protocol:
SMART-seq v4 Ultra Low input RNA kit (Clontech).
Low Input library preparation kit v2 (Clontech).
Paired-end 150-bp reads on the Illumina HiSeq4000 platform.

treatment_protocol: Lentiviral shRNAs against SIX2 or SIX3 versus non-target shRNA control.

tag: cell type

value: Primary islet cells

tag: developmental stage

value: Juvenile

tag: genotype/variation

value: Control


title: 3998720112_J

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

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

tag: title

tag: diagnosis

value: EPTB

value: Positive

tag: age

tag: gender

value: Female

value: Clinical Features, Culture

tag: pcr

tag: pcr result

value: NEGATIVE


title: 3998703044_K

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

tag: eptborptb

tag: site of infection

tag: smear microscopy

tag: culture result

value: Male

tag: height (cm)

tag: bmi

value: Indian

value: Culture

value: POSITIVE


title: 3998734078_A

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

tag: sampledate at t0

tag: dosanjh

value: PTB

value: Lung

value: TRUE

tag: weight (kg)

value: Black

tag: hiv positive

tag: tst


title: 3998675093_I

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

tag: title

value: Active TB

value: Lymph node

value: FALSE

tag: qtf-git


title: 3998703004_D

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

tag: diagnosis

value: Eyes, Lymph node

tag: age

tag: tst result

value: Negative


title: SIX3 knockdown-Control_D3

description:
RB03
six3_TPM_3D_ordered.csv

tag: cell type

value: Primary islet cells

tag: developmental stage

value: Adult

tag: genotype/variation

value: Control


title: 200681360011_I

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

tag: eptborptb

value: EPTB

tag: site of infection

value: Miliary TB (disseminated)

tag: smear microscopy

value: Positive

tag: gender

tag: pcr


title: SIX3 overexpression

description:
SIX3.Flag.ins.neon
six3-ox_neonatal_TPM_filter_table.csv

value: Juvenile

value: SIX3 overexpression


title: 3998675093_B

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

tag: sampledate at t0

tag: dosanjh

value: Lung, Lymph node

tag: culture result

value: Male

tag: height (cm)

tag: bmi

value: Indian

value: Clinical Features, Culture

tag: pcr result

value: POSITIVE

value: NEGATIVE


title: NKT17_lung_F

description:
065_65_17F_NKT_120417_200_IsEn12_A9
all_counts.tsv

tag: strain

tag: Sex

value: Female

tag: stimulation

tag: sorting scheme / criteria

value: A / CXCR3-ICOS+CD122-SDC1+IL-17RB+FR4-


title: NKT1_lung_G

description:
066_66_1G_NKT_120417_200_IsEn12_B9
all_counts.tsv

tag: cell type

value: A / CXCR3+ICOS-CD122+SDC1-IL-17RB-