title: D8_1287_CTTGTA [1287]

tag: subject id

tag: subject group

value: Orang Asli (indigenous) study village resident

value: M

tag: time point (before or after anthelmintic treatment)

value: Before

tag: trichuris egg count

tag: ascaris egg count

tag: hookworm infection (yes/no)

tag: treatment responder or not

value: NA (not paired)

value: blood

tag: kilocalories

tag: protein

tag: carbohydrate

tag: cholesterol

tag: tryptophan

tag: threonine

tag: isoleucine

tag: leucine

tag: lysine

tag: methionine

tag: cystine

tag: phenylalanine

tag: tyrosine

tag: valine

tag: histidine

tag: thiamin

tag: riboflavin

tag: niacin

tag: pyridoxine

tag: folate

tag: cobalamin

tag: biotin

tag: pantothenic

tag: iron

tag: magnesium

tag: zinc

tag: copper

tag: manganese

tag: selenium

tag: chromium

tag: molybdenum

tag: fat

tag: fruit

tag: vegetable

value: Mild

value: Normal


title: D4_969_TGACCA [969]

status: Public on Oct 01 2019

type: SRA

city: New York

first: Alice

middle: V

last: Easton

state: NY

address: 430 E 29th St

department: Microbiology

country: USA

institute: NYU Langone

library_source: transcriptomic

data_processing:
CEL-Seq
Three lanes of a paired-end 50 Illumina HiSeq 4000 run
Per-read per-lane FASTQ files were generated using the bcl2fastq2 Conversion software (v.2.2.0) to convert per-cycle BCL base call output files produced by the sequencing instrument into the FASTQ format, and the FASTQ files were then further split based on corresponding CEL-seq barcodes for each sample using the CEL-Seq demultiplexer, “bc_demultiplex”.
Bowtie2 (v.2.3.4.1), was used for mapping reads of 264 demultiplexed human CEL-Seq samples to the human reference genome hg19; and the CEL-Seq wrapper for the HTSeq-count script of the Python (v.2.7.15) package, HTSeq, was used to generate the matrix of read counts for annotated genomic features.
This resulted in a final median read depth of 1,707,022 mapped reads per sample, covering a median of 10,210 genes per sample. PCA was performed using 1835 genes with high variance, defined using the varFilter function in the genefilter package with default parameters, which keeps only features with variance inter-quartile range > 0.85. Gene Ontology annotation terms associated with each of the genes were fetched through the R package GO.db
Genome_build: hg19
Supplementary_files_format_and_content: counts

molecule: total RNA

organism: Homo sapiens

source_name: Orang Asli (indigenous) study village resident_Before treatment

extract_protocol:
PAXgene RNA extraction kit
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: subject id

tag: subject group

tag: gender

tag: time point (before or after anthelmintic treatment)

tag: age

tag: trichuris egg count

tag: ascaris egg count

tag: hookworm infection (yes/no)

tag: treatment responder or not

tag: tissue

tag: kilocalories

tag: protein

tag: carbohydrate

tag: cholesterol

tag: tryptophan

tag: threonine

tag: isoleucine

tag: leucine

tag: lysine

tag: methionine

tag: cystine

tag: phenylalanine

tag: tyrosine

tag: valine

tag: histidine

tag: thiamin

tag: riboflavin

tag: niacin

tag: wasting

tag: stunting

tag: underweight


title: C50 Pre placebo

type: RNA

city: Jena

first: Amol

last: Kolte

address: Am Klinikum 1

country: Germany

institute: Center for Sepsis Control and Care, University Clinic, Jena

description:
C50 Pre placebo
1705168046_A

hyb_protocol: 1.5 µg cRNA of each sample was hybridized on Human-WG6-V3 BeadChips. Hybridization was performed according to the Gene Expression on Sentrix® Arrays Direct Hybridization System Manual (Illumina Inc.). After 16 h hybridization time at a temperature of 58° C for a volume of 30 µl, label incorporation was performed by staining of hybridized arrays with 1µg/µl Streptavidin-Cy3 (FluoroLink® Cy3, GE Biosciences). Arrays were washed, dried and scanned immediately.

scan_protocol: Arrays were scanned on an Illumina BeadArray Reader (MIAME compliant file). BeadChips were scanned by Gene Expression Module v3.2 according to the protocol of the manufacturer (Revision A). Arrays were readout with the detection system iScan from Illumina.

data_processing: Raw data was pre-processed using GenomeStudio (v 1.9.0). Microarray normalization and statistical analysis were performed using R/Bioconductor (www.r-project.org). Probes with a detection significance P ≤ 0.05 were selected for further analysis. The data was log2 transformed followed by quantile normalization using the lumi package. Probe annotations were processed using lumiHumanIDMapping and lumiHumanAll.db to get HGNC symbols via Illumina nuIDs.

label: biotin

source_name: C50 Pre placebo

label_protocol: Biotinylated probes were prepared from total RNA, using the TargetAmp™-Nano Labeling Kit for Illumina® Expression BeadChip®.

extract_protocol: Blood was drawn on (pre) and 24 h after admission (post) and prepared with PAXgene reagent (PreAnalytix®, Qiagen, Hilden, Germany).

tag: individual

value: Pid C50

tag: timepoint

value: Pre

tag: treatment

value: placebo

tag: acth

value: Non responder

tag: survival (28 days)

value: survived

tag: age

tag: gender

value: male

tag: pre-treatment ifng il10 ratio

value: high

tag: disease

value: septic shock

tag: cell type

value: blood leukocytes


title: 111049_Naive_v2

city: New York City

first: Ramin

last: Herati

address: 429 E. 29th Street, room 308

institute: NYU School of Medicine

description: CD4+CD45RA+CD27+ T cells one week after vaccination

data_processing:
FASTQ files were trimmed using Trimmomatic 0.32.
Trimmed FASTQ files were aligned using STAR 2.5.2a against the HG38 reference genome.
The aligned files were processed using PORT 0.8.5 gene-based normalization (https://github.com/itmat/Normalization).
Variance-stabilizing transformation and differential expression analysis were performed using DESeq2 1.20.0.
Genome_build: HG38
Supplementary_files_format_and_content: Counts data

molecule: polyA RNA

source_name: Naïve CD4 T cells

extract_protocol:
Peripheral blood mononuclear cells were isolated from patient samples by density centrifugation using Ficoll (GE catalog #17144003), followed by cell sorting on a BD Aria II sorter. Sorted cells were lysed and RNA isolated using the Rneasy Plus Micro kit (Qiagen catalog #74034 ) using the standard protocol.
cDNA was produced and amplified using Clontech SMARTer v3, followed by Nextera XT for library preparation according to standard protocols.

tag: tissue

value: PBMC

tag: time point

value: Post-vaccine day 7

tag: cohort

value: Young


title: D5_995_CTTGTA [995]

tag: subject id

tag: subject group

value: Orang Asli (indigenous) study village resident

value: F

tag: time point (before or after anthelmintic treatment)

value: Before

tag: trichuris egg count

tag: ascaris egg count

tag: hookworm infection (yes/no)

tag: treatment responder or not

tag: kilocalories

tag: protein

tag: carbohydrate

tag: cholesterol

tag: tryptophan

tag: threonine

tag: isoleucine

tag: leucine

tag: lysine

tag: methionine

tag: cystine

tag: phenylalanine

tag: tyrosine

tag: valine

tag: histidine

tag: thiamin

tag: riboflavin

tag: niacin

tag: pyridoxine

tag: folate

tag: cobalamin

tag: biotin

tag: pantothenic

tag: iron

tag: magnesium

tag: zinc

tag: copper

tag: manganese

tag: selenium

tag: chromium

tag: molybdenum

tag: fat

tag: fruit

tag: vegetable


title: 111049_Naive_v1

description: CD4+CD45RA+CD27+ T cells before vaccination

tag: tissue

tag: time point

value: Post-vaccine day 0

tag: cohort


title: E3_1999_CGTACG [1999]

tag: subject id

tag: subject group

tag: gender

tag: time point (before or after anthelmintic treatment)

tag: age

tag: trichuris egg count

tag: ascaris egg count

tag: hookworm infection (yes/no)

tag: treatment responder or not

value: NA (not paired)

value: blood

tag: kilocalories

tag: protein

tag: carbohydrate

tag: cholesterol

tag: tryptophan

tag: threonine

tag: isoleucine

tag: leucine

tag: lysine

tag: methionine

tag: cystine

tag: phenylalanine

tag: tyrosine

tag: valine

tag: histidine

tag: thiamin

tag: riboflavin

tag: niacin

tag: pyridoxine

tag: folate

tag: cobalamin

tag: wasting

value: Mild

tag: stunting

value: Significant

tag: underweight


title: C49 Post(24h) placebo

description:
C49 Post(24h) placebo
1705168017_F

source_name: C49 Post(24h) placebo

tag: individual

value: Pid C49

tag: timepoint

tag: treatment

value: placebo

tag: acth

value: Non responder

tag: survival (28 days)

tag: age

tag: gender

tag: pre-treatment ifng il10 ratio

tag: disease

tag: cell type


title: C49 Pre placebo

description:
C49 Pre placebo
1705168017_E

source_name: C49 Pre placebo

value: Pre

value: survived

value: male

value: high


title: 111049_LoLo_v2

description: CD4+CXCR5+PD1+ICOS-CD38- T cells one week after vaccination

source_name: Quiescent Tfh

tag: tissue

value: PBMC

tag: time point

value: Post-vaccine day 7

tag: cohort


title: C48 Post(24h) hydrocortisone

description:
C48 Post(24h) hydrocortisone
1705168017_D

source_name: C48 Post(24h) hydrocortisone

value: Pid C48

value: hydrocortisone

value: Responder

value: female

value: septic shock

value: blood leukocytes


title: C57 Pre hydrocortisone

description:
C57 Pre hydrocortisone
1705168046_E

source_name: C57 Pre hydrocortisone

value: Pid C57


title: C50 Post(24h) placebo

description:
C50 Post(24h) placebo
1705168046_B

source_name: C50 Post(24h) placebo

value: Pid C50


title: C47 Post(24h) placebo

description:
C47 Post(24h) placebo
1705168017_B

source_name: C47 Post(24h) placebo

value: Pid C47

value: low


title: C47 Pre placebo

description:
C47 Pre placebo
1705168017_A

source_name: C47 Pre placebo

value: placebo

value: Non responder


title: C48 Pre hydrocortisone

description:
C48 Pre hydrocortisone
1705168017_C

source_name: C48 Pre hydrocortisone

value: Pre

value: survived


title: A12_C13_GTCCGC [C13]

source_name: Urban resident_Before treatment

tag: subject id

tag: subject group

value: Urban resident

value: F

tag: time point (before or after anthelmintic treatment)

value: Before

tag: trichuris egg count

tag: ascaris egg count

tag: hookworm infection (yes/no)

tag: treatment responder or not

value: NA (not treated)

value: blood

tag: kilocalories

tag: protein

tag: carbohydrate

tag: cholesterol

tag: tryptophan

tag: threonine

tag: isoleucine

tag: leucine

tag: lysine

tag: methionine

tag: cystine

tag: phenylalanine

tag: tyrosine

tag: valine

tag: histidine

tag: thiamin

tag: riboflavin

tag: niacin

tag: pyridoxine

tag: folate

tag: cobalamin

tag: biotin

tag: pantothenic

tag: iron

tag: magnesium

tag: zinc

tag: copper

tag: manganese

tag: selenium

tag: chromium

tag: molybdenum

tag: fat

tag: fruit

tag: vegetable

value: Overweight

value: Obese class I


title: C46 Post(24h) hydrocortisone

description:
C46 Post(24h) hydrocortisone
1705168088_F

source_name: C46 Post(24h) hydrocortisone

tag: individual

value: Pid C46

tag: timepoint

tag: treatment

value: hydrocortisone

tag: acth

tag: survival (28 days)

tag: age

tag: gender

value: male

tag: pre-treatment ifng il10 ratio

tag: disease

value: septic shock

tag: cell type


title: 111049_LoLo_v1

description: CD4+CXCR5+PD1+ICOS-CD38- T cells before vaccination

tag: tissue

value: PBMC

tag: time point

value: Post-vaccine day 0

tag: cohort

value: Young


title: C44 Post(24h) hydrocortisone

description:
C44 Post(24h) hydrocortisone
1705168088_B

source_name: C44 Post(24h) hydrocortisone

value: Pid C44

value: Responder

value: high

value: blood leukocytes


title: C46 Pre hydrocortisone

description:
C46 Pre hydrocortisone
1705168088_E

source_name: C46 Pre hydrocortisone

value: Pre

value: Non responder

value: survived

value: low


title: CHX_BY4741_rep1

city: Solna

first: Vicent

last: Pelechano

address: Nobels väg 16

department: MTC

country: Sweden

institute: ScilifeLab - Karolinska Institutet

data_processing:
Base-calling was done using bcl2fastq v2.20.0.422  with one mismatch
For each read we trimmed the first 8 nt (UMI, unique molecular identifier) and align the rest to S. cerevisiae genome (version R64-1-1) using STAR 2.5.3a default settings except AlignIntronMax(2500). Reads with the same 5’mapping site and UMI were considered PCR duplicates and omitted from the analysis.
Genome_build: S. cerevisiae R64-1-1
Supplementary_files_format_and_content: Bedgraph files for UMI collapsed reads for positive and negative strand

organism: Saccharomyces cerevisiae

source_name: yeast cells

growth_protocol: Saccharomyces cerevisiae  grown in YPD at 30°C.

extract_protocol:
RNA was extracted from yeast cells using the hot phenol procedure. The amount of RNA was quantified in a Nanodrop 2000 Spectrophotometer (Thermo Scientific) and RNA integrity was checked by agarose gel electrophoresis.
5PSeq methods was performed as previously described (PMID: 26820793). 6µg of total RNA was used as input. In brief a RNA oligo (rP5_RND) containing an Illumina adaptor and unique molecular identifiers (UMI) was ligated to the intermediates of mRNA co-translation degradation (5’P). Ribosomal RNA was depleted using Ribo-Zero Magnetic Gold Kit (Illumina).Libraries were PCR amplified (14 cycles). Ampure beads size selected libraries with a length of 300-500 nt were sent for sequencing (llumina NextSeq 500 instrument).

treatment_protocol: Cells were incubated with 0.1 mg/ml final cycloheximide  for 10 minutes prior to harvesting.

tag: genotype

tag: parental strain

value: BY4741(MATa his3[delta]1 leu2[delta]0 met15[delta]0 ura3[delta]0)

value: Cycloheximide treatment


title: C45 Post(24h) placebo

description:
C45 Post(24h) placebo
1705168088_D

source_name: C45 Post(24h) placebo

value: Pid C45

value: placebo

value: died


title: C45 Pre placebo

description:
C45 Pre placebo
1705168088_C

source_name: C45 Pre placebo

value: male

value: septic shock


title: C44 Pre hydrocortisone

description:
C44 Pre hydrocortisone
1705168088_A

source_name: C44 Pre hydrocortisone

value: hydrocortisone


title: 222065_Naive_v1

source_name: Naïve CD4 T cells

value: PBMC

value: Post-vaccine day 0

value: Elderly


title: 111049_HiHi_v2

description: CD4+CXCR5+PD1+ICOS+CD38+ T cells one week after vaccination

source_name: Activated Tfh

value: Post-vaccine day 7

value: Young


title: 111049_HiHi_v1

description: CD4+CXCR5+PD1+ICOS+CD38+ T cells before vaccination


title: B7_C20_CGATGT [C20]

tag: subject id

tag: subject group

value: Urban resident

value: M

tag: time point (before or after anthelmintic treatment)

value: Before

tag: trichuris egg count

tag: ascaris egg count

tag: hookworm infection (yes/no)

tag: treatment responder or not

value: NA (not treated)

value: blood

tag: kilocalories

tag: protein

tag: carbohydrate

tag: cholesterol

tag: tryptophan

tag: threonine

tag: isoleucine

tag: leucine

tag: lysine

tag: methionine

tag: cystine

tag: phenylalanine

tag: tyrosine

tag: valine

tag: histidine

tag: thiamin

tag: riboflavin

tag: niacin

tag: pyridoxine

tag: folate

tag: cobalamin

tag: biotin

tag: pantothenic

tag: iron

tag: magnesium

tag: zinc

tag: copper

tag: manganese

tag: selenium

tag: chromium

tag: molybdenum

tag: fat

tag: fruit

value: Normal

tag: wasting

tag: stunting

tag: underweight


title: DMT1

type: genomic

city: Münster

first: Christian

last: Thomas

address: Pottkamp 2

institute: Institute of Neuropathology Münster, Germany

description:
desmoplastic myxoid tumor
3998919099_R04C02

hyb_protocol: bisulphite converted DNA was hybridised to either the Illumina HumanMethylation450 BeadChip array or the MethylationEPIC BeadChip array.

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing:
R environment (version 3.6.0)
Samples were normalized using the MNPpreprocessIllumina R function (https://github.com/mwsill/mnp_training)
Unmethylated and methylated signal intensities

label: Cy3, Cy5

molecule: genomic DNA

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from formalin-fixed paraffin-embedded tumor samples using the Maxwell 16 FFPE Tissue LEV DNA Purification Kit (Promega).

tag: gender

value: female

tag: sample type

value: cancer tissue


title: DMT6

description:
desmoplastic myxoid tumor
9373551108_R01C02


title: 111043_Naive_v2

tag: tissue

tag: time point

tag: cohort


title: A11_C12_GATCAG [C12]

tag: subject id

tag: subject group

value: F

tag: time point (before or after anthelmintic treatment)

tag: age

tag: trichuris egg count

tag: ascaris egg count

tag: hookworm infection (yes/no)

tag: treatment responder or not

tag: kilocalories

tag: protein

tag: carbohydrate

tag: cholesterol

tag: tryptophan

tag: threonine

tag: isoleucine

tag: leucine

tag: lysine

tag: methionine

tag: cystine

tag: phenylalanine

tag: tyrosine

tag: valine

tag: histidine

tag: thiamin

tag: riboflavin

tag: niacin

tag: pyridoxine

tag: folate

tag: cobalamin

tag: biotin

tag: pantothenic

tag: iron

tag: magnesium

tag: vegetable


title: A9_C10_GTCCGC [C10]

tag: subject id

tag: subject group

tag: gender

tag: time point (before or after anthelmintic treatment)

tag: age

tag: trichuris egg count

tag: ascaris egg count

tag: hookworm infection (yes/no)

tag: treatment responder or not

tag: tissue

tag: kilocalories

tag: protein

tag: carbohydrate

tag: cholesterol

tag: tryptophan

tag: threonine

tag: isoleucine

tag: leucine

tag: lysine

tag: methionine

tag: zinc

tag: copper

tag: manganese

tag: selenium

tag: chromium

tag: molybdenum

tag: fat

tag: fruit

tag: wasting

tag: stunting

tag: underweight


title: 111043_Naive_v1

tag: tissue

tag: time point

tag: cohort


title: A8_C9_GATCAG [C9]

tag: subject id

tag: subject group

tag: gender

tag: time point (before or after anthelmintic treatment)

tag: age

tag: trichuris egg count

tag: ascaris egg count

tag: hookworm infection (yes/no)

tag: treatment responder or not

tag: kilocalories

tag: protein

tag: carbohydrate

tag: cholesterol

tag: tryptophan

tag: threonine

tag: isoleucine

tag: leucine

tag: cystine

tag: phenylalanine

tag: tyrosine

tag: valine

tag: histidine

tag: thiamin

tag: riboflavin

tag: niacin

tag: pyridoxine

tag: folate

tag: cobalamin

tag: biotin

tag: pantothenic

tag: iron

tag: magnesium

tag: vegetable

value: Underweight

value: Moderate thinness


title: non_involved_lung_tissue_patient_89 9983140109_A_Expression

city: Milan

first: Matteo

last: Dugo

address: via Olgettina 60

department: Department of Medical Oncology

country: Italy

institute: IRCCS Ospedale San Raffaele

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Primary microarray data were collected using BeadStudio v3 software package. Raw data were log2-transformed and normalized using the robust spline normalization method, implemented in the lumi R/Bioconductor package. Batch effects were removed using ComBat function implemented in the sva R/Bioconductor package.

source_name: Non-involved (apparently normal) lung parenchyma

label_protocol: RNA was reverse transcribed, labeled with biotin and amplified overnight using the Illumina TotalPrep RNA Amplification Kit (Life Technologies).

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit.

tag: Sex

tag: age

tag: smoking status

value: never-smoker

tag: batch


title: 111043_LoLo_v2

source_name: Quiescent Tfh

tag: tissue

value: PBMC

tag: time point

tag: cohort


title: A7_C8_ATCACG [C8]

tag: subject id

tag: subject group

tag: gender

tag: time point (before or after anthelmintic treatment)

tag: trichuris egg count

tag: ascaris egg count

tag: hookworm infection (yes/no)

tag: treatment responder or not

tag: kilocalories

tag: protein

tag: carbohydrate

tag: cholesterol

tag: tryptophan

tag: threonine

tag: isoleucine

tag: leucine

tag: lysine

tag: methionine

tag: cystine

tag: phenylalanine

tag: tyrosine

tag: valine

tag: histidine

tag: thiamin

tag: riboflavin

tag: zinc

tag: copper

tag: manganese

tag: selenium

tag: chromium

tag: molybdenum

tag: fat

tag: fruit

value: Overweight

value: Obese class I

tag: wasting

tag: stunting

tag: underweight


title: 111043_LoLo_v1

tag: tissue

tag: time point

value: Post-vaccine day 0

tag: cohort


title: C43 Pre hydrocortisone

description:
C43 Pre hydrocortisone
1705168004_E

source_name: C43 Pre hydrocortisone

tag: individual

value: Pid C43

tag: timepoint

value: Pre

tag: treatment

value: hydrocortisone

tag: acth

value: Non responder

tag: survival (28 days)

value: survived

tag: age

tag: gender

tag: pre-treatment ifng il10 ratio

value: high

tag: disease

value: septic shock

tag: cell type

value: blood leukocytes


title: C41 Pre hydrocortisone

description:
C41 Pre hydrocortisone
1705168004_C

source_name: C41 Pre hydrocortisone

value: Pid C41

value: Responder

value: died

value: male


title: C41 Post(24h) hydrocortisone

description:
C41 Post(24h) hydrocortisone
1705168004_D

source_name: C41 Post(24h) hydrocortisone


title: C43 Post(24h) hydrocortisone

description:
C43 Post(24h) hydrocortisone
1705168004_F

source_name: C43 Post(24h) hydrocortisone

value: female


title: C40 Post(24h) placebo

description:
C40 Post(24h) placebo
1705168004_B

source_name: C40 Post(24h) placebo

value: Pid C40

value: placebo


title: B6_C19_GTGAAA [C19]

source_name: Urban resident_Before treatment

tag: subject id

tag: subject group

value: Urban resident

value: F

tag: time point (before or after anthelmintic treatment)

value: Before

tag: trichuris egg count

tag: ascaris egg count

tag: hookworm infection (yes/no)

tag: treatment responder or not

value: NA (not treated)

value: blood

tag: kilocalories

tag: protein

tag: carbohydrate

tag: cholesterol

tag: tryptophan

tag: threonine

tag: isoleucine

tag: leucine

tag: lysine

tag: methionine

tag: cystine

tag: phenylalanine

tag: tyrosine

tag: valine

tag: histidine

tag: thiamin

tag: riboflavin

tag: niacin

tag: pyridoxine

tag: folate

tag: cobalamin

tag: biotin

tag: pantothenic

tag: iron

tag: magnesium

tag: zinc

tag: copper

tag: manganese

tag: selenium

tag: chromium

tag: molybdenum

tag: fat

tag: fruit

tag: vegetable

value: Normal


title: C40 Pre placebo

description:
C40 Pre placebo
1705168004_A

source_name: C40 Pre placebo

tag: individual

tag: timepoint

value: Pre

tag: treatment

tag: acth

tag: survival (28 days)

value: survived

tag: age

tag: gender

tag: pre-treatment ifng il10 ratio

tag: disease

tag: cell type


title: 111043_HiHi_v2

tag: tissue

value: PBMC

tag: time point

value: Post-vaccine day 7

tag: cohort

value: Young


title: A10_C11_ATCACG [C11]

tag: subject id

tag: subject group

tag: time point (before or after anthelmintic treatment)

tag: trichuris egg count

tag: ascaris egg count

tag: hookworm infection (yes/no)

tag: treatment responder or not

tag: kilocalories

tag: protein

tag: carbohydrate

tag: cholesterol

tag: tryptophan

tag: threonine

tag: isoleucine

tag: leucine

tag: lysine

tag: methionine

tag: cystine

tag: phenylalanine

tag: tyrosine

tag: valine

tag: histidine

tag: thiamin

tag: riboflavin

tag: niacin

tag: pyridoxine

tag: folate

tag: cobalamin

tag: biotin

tag: pantothenic

tag: iron

tag: magnesium

tag: zinc

tag: copper

tag: manganese

tag: selenium

tag: chromium

tag: molybdenum

tag: wasting

tag: stunting

tag: underweight


title: B4_C17_CGATGT [C17]

tag: subject id

tag: subject group

tag: gender

value: M

tag: time point (before or after anthelmintic treatment)

tag: age

tag: trichuris egg count

tag: ascaris egg count

tag: hookworm infection (yes/no)

tag: treatment responder or not

tag: tissue

tag: kilocalories

tag: protein

tag: carbohydrate

tag: cholesterol

tag: tryptophan

tag: threonine

tag: isoleucine

tag: leucine

tag: lysine

tag: methionine

tag: cystine

tag: phenylalanine

tag: tyrosine

tag: valine

tag: histidine

tag: thiamin

tag: riboflavin

tag: niacin

tag: fat

tag: fruit

tag: vegetable


title: 111043_HiHi_v1

tag: tissue

tag: time point

value: Post-vaccine day 0

tag: cohort


title: A6_C7_GTCCGC [C7]

tag: subject id

tag: subject group

tag: gender

tag: time point (before or after anthelmintic treatment)

tag: age

tag: trichuris egg count

tag: ascaris egg count

tag: hookworm infection (yes/no)

tag: treatment responder or not

tag: kilocalories

tag: protein

tag: carbohydrate

tag: cholesterol

tag: tryptophan

tag: threonine

tag: isoleucine

tag: leucine

tag: pyridoxine

tag: folate

tag: cobalamin

tag: biotin

tag: pantothenic

tag: iron

tag: magnesium

tag: zinc

tag: copper

tag: manganese

tag: selenium

tag: chromium

tag: molybdenum

tag: wasting

tag: stunting

tag: underweight


title: 111039_Naive_v1

tag: tissue

tag: time point

tag: cohort


title: C39 Pre hydrocortisone

description:
C39 Pre hydrocortisone
1674120006_E

source_name: C39 Pre hydrocortisone

tag: individual

value: Pid C39

tag: timepoint

tag: treatment

value: hydrocortisone

tag: acth

value: Responder

tag: survival (28 days)

tag: age

tag: gender

value: male

tag: pre-treatment ifng il10 ratio

value: high

tag: disease

value: septic shock

tag: cell type

value: blood leukocytes


title: A5_C6_GATCAG [C6]

tag: subject id

tag: subject group

value: Urban resident

value: F

tag: time point (before or after anthelmintic treatment)

value: Before

tag: trichuris egg count

tag: ascaris egg count

tag: hookworm infection (yes/no)

tag: treatment responder or not

value: NA (not treated)

tag: kilocalories

tag: protein

tag: carbohydrate

tag: cholesterol

tag: tryptophan

tag: threonine

tag: isoleucine

tag: leucine

tag: lysine

tag: methionine

tag: cystine

tag: phenylalanine

tag: tyrosine

tag: valine

tag: histidine

tag: thiamin

tag: riboflavin

tag: niacin

tag: pyridoxine

tag: folate

tag: cobalamin

tag: biotin

tag: pantothenic

tag: iron

tag: magnesium

tag: zinc

tag: copper

tag: manganese

tag: selenium

tag: chromium

tag: molybdenum

tag: fat

tag: fruit

tag: vegetable

value: Underweight

value: Mild thinness


title: C39 Post(24h) hydrocortisone

description:
C39 Post(24h) hydrocortisone
1674120006_F

source_name: C39 Post(24h) hydrocortisone

tag: individual

tag: timepoint

tag: treatment

tag: acth

tag: survival (28 days)

value: survived

tag: age

tag: gender

tag: pre-treatment ifng il10 ratio

tag: disease

tag: cell type


title: 111039_LoLo_v2

tag: tissue

value: PBMC

tag: time point

value: Post-vaccine day 7

tag: cohort

value: Young


title: B5_C18_TAGCTT [C18]

tag: subject id

tag: subject group

tag: time point (before or after anthelmintic treatment)

tag: trichuris egg count

tag: ascaris egg count

tag: hookworm infection (yes/no)

tag: treatment responder or not

value: blood

tag: kilocalories

tag: protein

tag: carbohydrate

tag: cholesterol

tag: tryptophan

tag: threonine

tag: isoleucine

tag: leucine

tag: lysine

tag: methionine

tag: cystine

tag: phenylalanine

tag: tyrosine

tag: valine

tag: histidine

tag: thiamin

tag: riboflavin

tag: niacin

tag: pyridoxine

tag: folate

tag: cobalamin

tag: biotin

tag: pantothenic

tag: iron

tag: magnesium

tag: zinc

tag: copper

tag: manganese

tag: selenium

tag: chromium

tag: molybdenum

value: Normal

tag: wasting

tag: stunting

tag: underweight


title: C37 Post(24h) hydrocortisone

description:
C37 Post(24h) hydrocortisone
1674120006_D

source_name: C37 Post(24h) hydrocortisone

tag: individual

value: Pid C37

tag: timepoint

tag: treatment

value: hydrocortisone

tag: acth

value: Non responder

tag: survival (28 days)

value: died

tag: age

tag: gender

tag: pre-treatment ifng il10 ratio

tag: disease

tag: cell type


title: B2_C15_TAGCTT [C15]

tag: subject id

tag: subject group

tag: time point (before or after anthelmintic treatment)

tag: trichuris egg count

tag: ascaris egg count

tag: hookworm infection (yes/no)

tag: treatment responder or not

tag: tissue

tag: kilocalories

tag: protein

tag: carbohydrate

tag: cholesterol

tag: tryptophan

tag: threonine

tag: isoleucine

tag: leucine

tag: lysine

tag: methionine

tag: cystine

tag: phenylalanine

tag: tyrosine

tag: valine

tag: histidine

tag: thiamin

tag: riboflavin

tag: niacin

tag: pyridoxine

tag: folate

tag: cobalamin

tag: biotin

tag: pantothenic

tag: iron

tag: magnesium

tag: zinc

tag: copper

tag: manganese

tag: fat

tag: fruit

tag: vegetable


title: A4_C5_ATCACG [C5]

tag: subject id

tag: subject group

tag: gender

tag: time point (before or after anthelmintic treatment)

tag: age

tag: trichuris egg count

tag: ascaris egg count

tag: hookworm infection (yes/no)

tag: treatment responder or not

tag: tissue

tag: kilocalories

tag: protein

tag: carbohydrate

tag: cholesterol

tag: tryptophan

tag: threonine

tag: isoleucine

tag: leucine

tag: lysine

tag: methionine

tag: cystine

tag: phenylalanine

tag: tyrosine

tag: valine

tag: histidine

tag: selenium

tag: chromium

tag: molybdenum

tag: wasting

tag: stunting

tag: underweight


title: C37 Pre hydrocortisone

description:
C37 Pre hydrocortisone
1674120006_C

source_name: C37 Pre hydrocortisone

tag: individual

tag: timepoint

value: Pre

tag: treatment

tag: acth

tag: survival (28 days)

tag: age

tag: gender

value: male

tag: pre-treatment ifng il10 ratio

value: high

tag: disease

value: septic shock

tag: cell type

value: blood leukocytes


title: 111039_Naive_v2

tag: tissue

tag: time point

tag: cohort


title: 111039_HiHi_v2


title: 111039_LoLo_v1

value: Post-vaccine day 0


title: C35 Post(24h) hydrocortisone

description:
C35 Post(24h) hydrocortisone
1674120006_B

source_name: C35 Post(24h) hydrocortisone

value: Pid C35

value: Responder


title: B1_C14_CGATGT [C14]

tag: subject id

tag: subject group

value: Urban resident

value: F

tag: time point (before or after anthelmintic treatment)

value: Before

tag: trichuris egg count

tag: ascaris egg count

tag: hookworm infection (yes/no)

tag: treatment responder or not

value: NA (not treated)

tag: kilocalories

tag: protein

tag: carbohydrate

tag: cholesterol

tag: tryptophan

tag: threonine

tag: isoleucine

tag: leucine

tag: lysine

tag: methionine

tag: cystine

tag: phenylalanine

tag: tyrosine

tag: valine

tag: histidine

tag: thiamin

tag: riboflavin

tag: niacin

tag: pyridoxine

tag: folate

tag: cobalamin

tag: biotin

tag: pantothenic

tag: iron

tag: magnesium

tag: zinc

tag: copper

tag: manganese

tag: selenium

tag: chromium

tag: molybdenum

tag: fat

tag: fruit

tag: vegetable


title: C33 Post(24h) hydrocortisone

description:
C33 Post(24h) hydrocortisone
1674120168_E

source_name: C33 Post(24h) hydrocortisone

tag: individual

value: Pid C33

tag: timepoint

tag: treatment

tag: acth

tag: survival (28 days)

value: survived

tag: age

tag: gender

tag: pre-treatment ifng il10 ratio

tag: disease

tag: cell type


title: A3_C4_GTCCGC [C4]

tag: subject id

tag: subject group

tag: time point (before or after anthelmintic treatment)

tag: trichuris egg count

tag: ascaris egg count

tag: hookworm infection (yes/no)

tag: treatment responder or not

tag: tissue

value: blood

tag: kilocalories

tag: protein

tag: carbohydrate

tag: cholesterol

tag: tryptophan

tag: threonine

tag: isoleucine

tag: leucine

tag: lysine

tag: methionine

tag: cystine

tag: phenylalanine

tag: tyrosine

tag: valine

tag: histidine

tag: thiamin

tag: riboflavin

tag: niacin

tag: pyridoxine

tag: folate

tag: cobalamin

tag: biotin

tag: pantothenic

tag: iron

tag: magnesium

tag: zinc

tag: copper

tag: manganese

value: Normal

tag: wasting

tag: stunting

tag: underweight


title: C35 Pre hydrocortisone

description:
C35 Pre hydrocortisone
1674120006_A

source_name: C35 Pre hydrocortisone

tag: individual

tag: timepoint

tag: treatment

value: hydrocortisone

tag: acth

tag: survival (28 days)

value: died

tag: age

tag: gender

tag: pre-treatment ifng il10 ratio

tag: disease

tag: cell type


title: C33 Pre hydrocortisone

description:
C33 Pre hydrocortisone
1674120168_D

source_name: C33 Pre hydrocortisone

value: Pre

value: Non responder

value: male


title: C31 Pre placebo

description:
C31 Pre placebo
1705168288_E

source_name: C31 Pre placebo

value: Pid C31

value: placebo

value: female

value: high

value: septic shock

value: blood leukocytes


title: A1_C2_ATCACG [C2]

tag: subject id

tag: subject group

value: Urban resident

value: F

tag: time point (before or after anthelmintic treatment)

value: Before

tag: trichuris egg count

tag: ascaris egg count

tag: hookworm infection (yes/no)

tag: treatment responder or not

tag: tissue

tag: kilocalories

tag: protein

tag: carbohydrate

tag: cholesterol

tag: tryptophan

tag: threonine

tag: isoleucine

tag: leucine

tag: lysine

tag: methionine

tag: cystine

tag: phenylalanine

tag: tyrosine

tag: valine

tag: histidine

tag: thiamin

tag: riboflavin

tag: niacin

tag: pyridoxine

tag: folate

tag: cobalamin

tag: biotin

tag: pantothenic

tag: iron

tag: magnesium

tag: selenium

tag: chromium

tag: molybdenum

tag: fat

tag: fruit

tag: vegetable


title: C28 Post(24h) hydrocortisone

description:
C28 Post(24h) hydrocortisone
1705168288_B

source_name: C28 Post(24h) hydrocortisone

tag: individual

value: Pid C28

tag: timepoint

tag: treatment

tag: acth

tag: survival (28 days)

value: survived

tag: age

tag: gender

tag: pre-treatment ifng il10 ratio

tag: disease

tag: cell type


title: 111005_Naive_v2

description: CD4+CD45RA+CD27+ T cells one week after vaccination

source_name: Naïve CD4 T cells

tag: tissue

value: PBMC

tag: time point

value: Post-vaccine day 7

tag: cohort

value: Young


title: 111005_LoLo_v2

description: CD4+CXCR5+PD1+ICOS-CD38- T cells one week after vaccination

source_name: Quiescent Tfh


title: A2_C3_GATCAG [C3]

tag: subject id

tag: subject group

tag: time point (before or after anthelmintic treatment)

tag: trichuris egg count

tag: ascaris egg count

tag: hookworm infection (yes/no)

tag: treatment responder or not

value: NA (not treated)

value: blood

tag: kilocalories

tag: protein

tag: carbohydrate

tag: cholesterol

tag: tryptophan

tag: threonine

tag: isoleucine

tag: leucine

tag: lysine

tag: methionine

tag: cystine

tag: phenylalanine

tag: tyrosine

tag: valine

tag: histidine

tag: thiamin

tag: riboflavin

tag: niacin

tag: pyridoxine

tag: folate

tag: cobalamin

tag: biotin

tag: pantothenic

tag: iron

tag: magnesium

tag: zinc

tag: copper

tag: manganese

tag: selenium

tag: chromium

tag: molybdenum

value: Normal

tag: wasting

tag: stunting

tag: underweight


title: 111039_HiHi_v1

source_name: Activated Tfh

tag: tissue

tag: time point

value: Post-vaccine day 0

tag: cohort


title: H9_463AF_ATTCCT [463AF]

source_name: Orang Asli (indigenous) study village resident_After treatment

tag: subject id

tag: subject group

tag: gender

tag: time point (before or after anthelmintic treatment)

value: After

tag: age

tag: trichuris egg count

tag: ascaris egg count

tag: hookworm infection (yes/no)

tag: treatment responder or not

value: Resistant

tag: kilocalories

tag: protein

tag: carbohydrate

tag: cholesterol

tag: tryptophan

tag: threonine

tag: isoleucine

tag: leucine

tag: lysine

tag: methionine

tag: cystine

tag: phenylalanine

tag: tyrosine

tag: valine

tag: histidine

tag: thiamin

tag: riboflavin

tag: niacin

tag: pyridoxine

tag: folate

tag: cobalamin

tag: fat

tag: fruit

tag: vegetable

value: Mild


title: 111005_Naive_v1

description: CD4+CD45RA+CD27+ T cells before vaccination

tag: tissue

tag: time point

tag: cohort


title: 111005_LoLo_v1


title: 111005_HiHi_v2


title: C31 Post(24h) placebo

description:
C31 Post(24h) placebo
1705168288_F

source_name: C31 Post(24h) placebo

tag: individual

value: Pid C31

tag: timepoint

tag: treatment

value: placebo

tag: acth

value: Responder

tag: survival (28 days)

tag: age

tag: gender

value: female

tag: pre-treatment ifng il10 ratio

value: high

tag: disease

value: septic shock

tag: cell type


title: tumor biopsy PCNSL_19

city: Ulm

first: Julia

last: Vogt

address: Albert-Einstein Allee 11

department: Institute of Human Genetics

institute: Ulm University

description: tumor sample

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium HumanMethylation450 BeadChip

scan_protocol: Arrays were imaged using iScan using standard recommended Illumina scanner setting

data_processing:
GenomeStudio software v2011.1; methylation module 1.9.0
160919_allCpG_detpval0.01

label: Cy5 and Cy3

source_name: FFPE tumor

extract_protocol: genomic DNA was extracted and purified from tumor FFPE-biopsies using Promega Maxwell 16 FFPE Plus LEV DNA Purification kit/QIAamp DNA FFPE Tissue Kit (Qiagen) and tumor from cryo-preserved biopsies using Genomic-tip 100/G (Qiagen)

value: tumor

tag: disease state

value: PCNSL


title: tumor biopsy PCNSL_18

description: tumor sample


title: C29 Post(24h) placebo

description:
C29 Post(24h) placebo
1705168288_D

source_name: C29 Post(24h) placebo

value: Pid C29

value: survived

value: male

value: blood leukocytes


title: tumor biopsy PCNSL_17

description: tumor sample


title: tumor biopsy PCNSL_24

description: tumor sample


title: 111005_HiHi_v1

value: PBMC

value: Young


title: C28 Pre hydrocortisone

description:
C28 Pre hydrocortisone
1705168288_A

source_name: C28 Pre hydrocortisone

value: Pid C28

value: Pre

value: hydrocortisone

value: Non responder


title: C26 Pre hydrocortisone

description:
C26 Pre hydrocortisone
1705168287_E

source_name: C26 Pre hydrocortisone

value: Pid C26


title: C29 Pre placebo

description:
C29 Pre placebo
1705168288_C

source_name: C29 Pre placebo

value: placebo

value: Responder


title: H6_20109AF_ATTCCT [20109AF]

tag: subject id

tag: subject group

value: Orang Asli (indigenous) study village resident

value: M

tag: time point (before or after anthelmintic treatment)

value: After

tag: trichuris egg count

tag: ascaris egg count

tag: hookworm infection (yes/no)

tag: treatment responder or not

value: Resistant

value: blood

tag: kilocalories

tag: protein

tag: carbohydrate

tag: cholesterol

tag: tryptophan

tag: threonine

tag: isoleucine

tag: leucine

tag: lysine

tag: methionine

tag: cystine

tag: phenylalanine

tag: tyrosine

tag: valine

tag: histidine

tag: thiamin

tag: riboflavin

tag: niacin

tag: pyridoxine

tag: folate

tag: cobalamin

tag: biotin

tag: pantothenic

tag: iron

tag: magnesium

tag: zinc

tag: copper

tag: manganese

tag: selenium

tag: chromium

tag: molybdenum

tag: fat

tag: wasting

value: Mild

tag: stunting

value: Significant

tag: underweight


title: 111004_Naive_v2

tag: tissue

tag: time point

value: Post-vaccine day 7

tag: cohort


title: H4_8107AF_ACTTGA [8107AF]

tag: subject id

tag: subject group

tag: gender

tag: time point (before or after anthelmintic treatment)

tag: age

tag: trichuris egg count

tag: ascaris egg count

tag: hookworm infection (yes/no)

tag: treatment responder or not

tag: kilocalories

tag: protein

tag: carbohydrate

tag: cholesterol

tag: tryptophan

tag: threonine

tag: isoleucine

tag: leucine

tag: lysine

tag: methionine

tag: cystine

tag: phenylalanine

tag: tyrosine

tag: valine

tag: histidine

tag: thiamin

tag: riboflavin

tag: niacin

tag: pyridoxine

tag: folate

tag: cobalamin

tag: biotin

tag: fruit

tag: vegetable

value: Normal


title: 111004_Naive_v1

tag: tissue

value: PBMC

tag: time point

value: Post-vaccine day 0

tag: cohort

value: Young


title: H3_5113AF_ATTCCT [5113AF]

tag: subject id

tag: subject group

tag: gender

value: F

tag: time point (before or after anthelmintic treatment)

tag: age

tag: trichuris egg count

tag: ascaris egg count

tag: hookworm infection (yes/no)

tag: treatment responder or not

tag: kilocalories

tag: protein

tag: carbohydrate

tag: cholesterol

tag: tryptophan

tag: threonine

tag: isoleucine

tag: leucine

tag: lysine

tag: methionine

tag: cystine

tag: pantothenic

tag: iron

tag: magnesium

tag: zinc

tag: copper

tag: manganese

tag: selenium

tag: chromium

tag: molybdenum

tag: fat

value: Overweight

value: Pre-obese

tag: wasting

tag: stunting

tag: underweight


title: H5_19100AF_CCGTCC [19100AF]

tag: subject id

tag: subject group

tag: gender

tag: time point (before or after anthelmintic treatment)

tag: age

tag: trichuris egg count

tag: ascaris egg count

tag: hookworm infection (yes/no)

tag: treatment responder or not

tag: tissue

tag: kilocalories

tag: protein

tag: carbohydrate

tag: cholesterol

tag: tryptophan

tag: threonine

tag: isoleucine

tag: leucine

tag: phenylalanine

tag: tyrosine

tag: valine

tag: histidine

tag: thiamin

tag: riboflavin

tag: niacin

tag: pyridoxine

tag: folate

tag: cobalamin

tag: biotin

tag: fruit

tag: vegetable


title: C25 Post(24h) hydrocortisone

description:
C25 Post(24h) hydrocortisone
1705168287_D

source_name: C25 Post(24h) hydrocortisone

tag: individual

value: Pid C25

tag: timepoint

tag: treatment

value: hydrocortisone

tag: acth

tag: survival (28 days)

value: died

tag: age

tag: gender

value: female

tag: pre-treatment ifng il10 ratio

value: high

tag: disease

value: septic shock

tag: cell type

value: blood leukocytes


title: H2_2093AF_CCGTCC [2093AF]

tag: subject id

tag: subject group

value: Orang Asli (indigenous) study village resident

value: M

tag: time point (before or after anthelmintic treatment)

value: After

tag: trichuris egg count

tag: ascaris egg count

tag: hookworm infection (yes/no)

tag: treatment responder or not

value: Responder

tag: tissue

value: blood

tag: kilocalories

tag: protein

tag: carbohydrate

tag: cholesterol

tag: tryptophan

tag: threonine

tag: isoleucine

tag: leucine

tag: lysine

tag: methionine

tag: cystine

tag: phenylalanine

tag: tyrosine

tag: valine

tag: histidine

tag: thiamin

tag: riboflavin

tag: niacin

tag: pantothenic

tag: iron

tag: magnesium

tag: zinc

tag: copper

tag: manganese

tag: selenium

tag: chromium

tag: molybdenum

tag: fat

tag: wasting

tag: stunting

tag: underweight


title: 111004_LoLo_v1

description: CD4+CXCR5+PD1+ICOS-CD38- T cells before vaccination

tag: tissue

value: PBMC

tag: time point

value: Post-vaccine day 0

tag: cohort


title: tumor biopsy PCNSL_22

description: tumor sample

tag: gender

value: tumor

tag: disease state

value: PCNSL


title: 111004_LoLo_v2

value: Post-vaccine day 7

value: Young


title: tumor biopsy PCNSL_20

description: tumor sample


title: 111004_HiHi_v2


title: C25 Pre hydrocortisone

description:
C25 Pre hydrocortisone
1705168287_C

source_name: C25 Pre hydrocortisone

tag: individual

value: Pid C25

tag: timepoint

value: Pre

tag: treatment

value: hydrocortisone

tag: acth

tag: survival (28 days)

tag: age

tag: pre-treatment ifng il10 ratio

tag: disease

tag: cell type


title: H11_1533AF_CCGTCC [1533AF]

tag: subject id

tag: subject group

tag: time point (before or after anthelmintic treatment)

tag: trichuris egg count

tag: ascaris egg count

tag: hookworm infection (yes/no)

tag: treatment responder or not

value: Resistant

tag: kilocalories

tag: protein

tag: carbohydrate

tag: cholesterol

tag: tryptophan

tag: threonine

tag: isoleucine

tag: leucine

tag: lysine

tag: methionine

tag: cystine

tag: phenylalanine

tag: tyrosine

tag: valine

tag: histidine

tag: thiamin

tag: riboflavin

tag: niacin

tag: pyridoxine

tag: folate

tag: cobalamin

tag: biotin

tag: pantothenic

tag: iron

tag: magnesium

tag: zinc

tag: copper

tag: manganese

tag: selenium

tag: chromium

tag: molybdenum

tag: fat

tag: fruit

tag: vegetable

value: Normal

tag: wasting


title: C24 Pre hydrocortisone

description:
C24 Pre hydrocortisone
1705168287_A

source_name: C24 Pre hydrocortisone

tag: individual

value: Pid C24

tag: timepoint

tag: treatment

tag: acth

value: Non responder

tag: survival (28 days)

value: survived

tag: age

tag: gender

value: male

tag: pre-treatment ifng il10 ratio

value: high

tag: disease

value: septic shock

tag: cell type

value: blood leukocytes


title: H12_511AF_ATTCCT [511AF]

tag: subject id

tag: subject group

value: Orang Asli (indigenous) study village resident

value: M

tag: time point (before or after anthelmintic treatment)

value: After

tag: trichuris egg count

tag: ascaris egg count

tag: hookworm infection (yes/no)

tag: treatment responder or not

value: Responder

tag: tissue

value: blood

tag: kilocalories

tag: protein

tag: carbohydrate

tag: cholesterol

tag: tryptophan

tag: threonine

tag: isoleucine

tag: leucine

tag: lysine

tag: methionine

tag: cystine

tag: phenylalanine

tag: tyrosine

tag: valine

tag: histidine

tag: thiamin

tag: riboflavin

tag: niacin

tag: pyridoxine

tag: folate

tag: cobalamin

tag: biotin

tag: pantothenic

tag: iron

tag: magnesium

tag: zinc

tag: copper

tag: manganese

tag: selenium

tag: stunting

tag: underweight


title: C24 Post(24h) hydrocortisone

description:
C24 Post(24h) hydrocortisone
1705168287_B

source_name: C24 Post(24h) hydrocortisone

tag: individual

tag: timepoint

tag: treatment

tag: acth

tag: survival (28 days)

tag: age

tag: gender

tag: pre-treatment ifng il10 ratio

tag: disease

tag: cell type


title: 111004_HiHi_v1

tag: tissue

value: PBMC

tag: time point

value: Post-vaccine day 0

tag: cohort

value: Young


title: H10_1259AF_ACTTGA [1259AF]

tag: subject id

tag: subject group

tag: time point (before or after anthelmintic treatment)

tag: trichuris egg count

tag: ascaris egg count

tag: hookworm infection (yes/no)

tag: treatment responder or not

value: Resistant

tag: kilocalories

tag: protein

tag: carbohydrate

tag: cholesterol

tag: tryptophan

tag: threonine

tag: isoleucine

tag: leucine

tag: lysine

tag: methionine

tag: cystine

tag: phenylalanine

tag: tyrosine

tag: valine

tag: histidine

tag: thiamin

tag: riboflavin

tag: niacin

tag: pyridoxine

tag: folate

tag: cobalamin

tag: biotin

tag: pantothenic

tag: iron

tag: magnesium

tag: zinc

tag: copper

tag: manganese

tag: chromium

tag: molybdenum

tag: fat

tag: fruit

tag: vegetable

tag: wasting


title: H1_1889AF_ACTTGA [1889AF]

tag: subject id

tag: subject group

tag: gender

value: F

tag: time point (before or after anthelmintic treatment)

tag: age

tag: trichuris egg count

tag: ascaris egg count

tag: hookworm infection (yes/no)

tag: treatment responder or not

tag: tissue

tag: kilocalories

tag: protein

tag: carbohydrate

tag: cholesterol

tag: tryptophan

tag: threonine

tag: isoleucine

tag: leucine

tag: lysine

tag: methionine

tag: cystine

tag: phenylalanine

tag: tyrosine

tag: valine

tag: histidine

tag: thiamin

tag: riboflavin

tag: niacin

tag: selenium

value: Overweight

value: Pre-obese

tag: stunting

tag: underweight


title: tumor biopsy PCNSL_14

description: tumor sample

tag: gender

tag: tissue

value: tumor

tag: disease state

value: PCNSL


title: 23787_H1299-Ko2_S16_L999_R1_001

city: duarte

first: LU

last: YANG

address: 1500 duarte rd

institute: city of hope

description: RNA subjected to RNAseq

data_processing:
Illumina RTA was used to create .bcl files, and bcl2fastq v2.20.0.422 software was used for base calling (for samples split between flowcells and later merged per run)
Sequenced reads were mapped to hg19 whole genome using STAR_2.6.0a
Aligned reads was normalized by edgeR bioconductor package and outputed as rpkm.txt file
Genome_build: Genome Reference Consortium GRCh37
Supplementary_files_format_and_content: rpkm(normalized counts) in txt format for all 8 samples

source_name: Lung

growth_protocol: Cells were routinely cultured in DMEM/RPMI medium with 10% FBS and  1% PenStrep (100 U/mL )

extract_protocol: Transcriptome libraries were constructed with TruSeq RNA Sample Preparation Kit V2  (Illumia, San Diego, USA) with minor modifications.

treatment_protocol: Crispr/Cas9 sgRNAs mediated USP22 knockout

tag: cell type

value: Non-small cell lung cancer

tag: sirna knockdown

value: USP22 knockout clone 2

tag: cell line


title: C23 Pre hydrocortisone

description:
C23 Pre hydrocortisone
1705168049_C

source_name: C23 Pre hydrocortisone

tag: individual

value: Pid C23

tag: timepoint

value: Pre

tag: treatment

value: hydrocortisone

tag: acth

value: Non responder

tag: survival (28 days)

value: died

tag: age

value: male

tag: pre-treatment ifng il10 ratio

value: high

tag: disease

value: septic shock

value: blood leukocytes


title: C19 Post(24h) placebo

description:
C19 Post(24h) placebo
1705168049_B

source_name: C19 Post(24h) placebo

value: Pid C19

value: placebo

value: Responder

value: survived

value: female

value: low


title: 23786_H1299-Ko1_S39_L999_R1_001

description: RNA subjected to RNAseq

value: Non-small cell lung cancer

value: USP22 knockout clone 1


title: C26 Post(24h) hydrocortisone

description:
C26 Post(24h) hydrocortisone
1705168287_F

source_name: C26 Post(24h) hydrocortisone

value: Pid C26


title: tumor biopsy PCNSL_15

description: tumor sample

value: Male

value: tumor

value: PCNSL


title: C19 Pre placebo

description:
C19 Pre placebo
1705168049_A

source_name: C19 Pre placebo

value: Pre


title: 16107_H1299-P2_S53_L999_R1_001

description: RNA subjected to RNAseq

value: Parental cell sample 2


title: G9_1612AF_ACTGAT [1612AF]

tag: subject id

tag: subject group

value: Orang Asli (indigenous) study village resident

value: F

tag: time point (before or after anthelmintic treatment)

value: After

tag: trichuris egg count

tag: ascaris egg count

tag: hookworm infection (yes/no)

tag: treatment responder or not

value: Resistant

value: blood

tag: kilocalories

tag: protein

tag: carbohydrate

tag: cholesterol

tag: tryptophan

tag: threonine

tag: isoleucine

tag: leucine

tag: lysine

tag: methionine

tag: cystine

tag: phenylalanine

tag: tyrosine

tag: valine

tag: histidine

tag: thiamin

tag: riboflavin

tag: niacin

tag: pyridoxine

tag: folate

tag: cobalamin

tag: biotin

tag: pantothenic

tag: iron

tag: magnesium

tag: zinc

tag: copper

tag: manganese

tag: selenium

tag: chromium

tag: molybdenum

tag: fat

tag: fruit

tag: vegetable

value: Overweight

value: Obese class I

tag: wasting


title: 16106_H1299-P1_S52_L999_R1_001

description: RNA subjected to RNAseq

tag: cell type

tag: sirna knockdown

value: Parental cell sample 1

tag: cell line


title: H8_145AF_CCGTCC [145AF]

tag: subject id

tag: subject group

tag: gender

tag: time point (before or after anthelmintic treatment)

tag: age

tag: trichuris egg count

tag: ascaris egg count

tag: hookworm infection (yes/no)

tag: treatment responder or not

tag: tissue

tag: kilocalories

tag: protein

tag: carbohydrate

tag: cholesterol

tag: tryptophan

tag: threonine

tag: isoleucine

tag: leucine

tag: lysine

tag: methionine

tag: cystine

tag: phenylalanine

tag: tyrosine

tag: valine

tag: histidine

tag: thiamin

tag: riboflavin

tag: niacin

tag: pyridoxine

tag: folate

tag: cobalamin

tag: biotin

value: Normal

tag: stunting

tag: underweight


title: G8_1248AF_ATGTCA [1248AF]

tag: subject id

tag: subject group

tag: gender

tag: time point (before or after anthelmintic treatment)

tag: age

tag: trichuris egg count

tag: ascaris egg count

tag: hookworm infection (yes/no)

tag: treatment responder or not

tag: tissue

tag: kilocalories

tag: protein

tag: carbohydrate

tag: cholesterol

tag: tryptophan

tag: threonine

tag: isoleucine

tag: leucine

tag: pantothenic

tag: iron

tag: magnesium

tag: zinc

tag: copper

tag: manganese

tag: selenium

tag: chromium

tag: molybdenum

tag: fat

tag: fruit

tag: vegetable

tag: wasting


title: tumor biopsy PCNSL_9

description: tumor sample

tag: gender

tag: tissue

tag: disease state


title: EN3_S5_L001_R1_001

city: Moscow

first: Daniil

last: Nikitin

address: Miklucho-Maklaya

country: Russia

institute: Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry

data_processing:
RNA sequencing FASTQ files were processed with STAR aligner30 in ‘GeneCounts’ mode with the Ensembl human transcriptome annotation (Build version GRCh38 and transcript annotation GRCh38.89).
Genome_build: GRCh38
Supplementary_files_format_and_content: Read counts table generated by merging of STAR output. Ensembl gene IDs were converted to HGNC gene symbols using Complete HGNC dataset (https://www.genenames.org, database version of July 13, 2017). In total, read counts values were established for 37233 annotated genes with corresponding HGNC identifiers.

source_name: healthy endometrium

extract_protocol:
Tissue specimens were immediately stabilized in RNAlater (Qiagen, Germany) and then stored at -70 °C. RNA extraction was performed immediately before the preparation of sequencing libraries using Direct-zol™ RNA MiniPrep (Zymo Research) with TRI Reagent (MRC) following the manufacturer’s protocol.
KAPA RNA Hyper with RiboErase (KAPA Biosystem) Kit was used for depletion of ribosomal RNA and library preparation.

tag: subject status

value: healthy control

value: healthy endometrium


title: E5_5112_AGTCAA [5112]

source_name: Orang Asli (indigenous) study village resident_Before treatment

tag: subject id

tag: subject group

tag: time point (before or after anthelmintic treatment)

value: Before

tag: age

tag: trichuris egg count

tag: ascaris egg count

tag: hookworm infection (yes/no)

tag: treatment responder or not

value: NA (not paired)

tag: kilocalories

tag: protein

tag: carbohydrate

tag: cholesterol

tag: tryptophan

tag: threonine

tag: isoleucine

tag: leucine

tag: lysine

tag: methionine

tag: cystine

tag: phenylalanine

tag: tyrosine

tag: valine

tag: histidine

tag: thiamin

tag: riboflavin

tag: niacin

tag: pyridoxine

tag: folate

tag: cobalamin

tag: biotin

tag: pantothenic

tag: stunting

tag: underweight


title: tumor biopsy PCNSL_10

description: tumor sample

tag: gender

value: Male

tag: tissue

value: tumor

tag: disease state


title: C23 Post(24h) hydrocortisone

description:
C23 Post(24h) hydrocortisone
1705168049_D

source_name: C23 Post(24h) hydrocortisone

tag: individual

value: Pid C23

tag: timepoint

tag: treatment

value: hydrocortisone

tag: acth

value: Non responder

tag: survival (28 days)

value: died

tag: age

value: male

tag: pre-treatment ifng il10 ratio

value: high

tag: disease

value: septic shock

tag: cell type

value: blood leukocytes


title: G6_953AF_ACTGAT [953AF]

source_name: Orang Asli (indigenous) study village resident_After treatment

tag: subject id

tag: subject group

value: M

tag: time point (before or after anthelmintic treatment)

value: After

tag: trichuris egg count

tag: ascaris egg count

tag: hookworm infection (yes/no)

tag: treatment responder or not

value: Resistant

value: blood

tag: kilocalories

tag: protein

tag: carbohydrate

tag: cholesterol

tag: tryptophan

tag: threonine

tag: isoleucine

tag: leucine

tag: lysine

tag: methionine

tag: cystine

tag: phenylalanine

tag: tyrosine

tag: valine

tag: histidine

tag: thiamin

tag: riboflavin

tag: niacin

tag: pyridoxine

tag: folate

tag: cobalamin

tag: iron

tag: magnesium

tag: zinc

tag: copper

tag: manganese

tag: selenium

tag: chromium

tag: molybdenum

tag: fat

tag: fruit

tag: vegetable

tag: wasting

value: Mild


title: G5_941AF_ATGTCA [941AF]

tag: subject id

tag: subject group

value: Orang Asli (indigenous) study village resident

tag: gender

tag: time point (before or after anthelmintic treatment)

tag: age

tag: trichuris egg count

tag: ascaris egg count

tag: hookworm infection (yes/no)

tag: treatment responder or not

tag: tissue

tag: kilocalories

tag: protein

tag: carbohydrate

tag: cholesterol

tag: tryptophan

tag: threonine

tag: isoleucine

tag: leucine

tag: lysine

tag: methionine

tag: cystine

tag: phenylalanine

tag: tyrosine

tag: valine

tag: histidine

tag: thiamin

tag: riboflavin

tag: biotin

tag: pantothenic

tag: stunting

tag: underweight

value: Significant


title: 23784_A549-Ko1_S44_L999_R1_001

description: RNA subjected to RNAseq

tag: cell type

value: Non-small cell lung cancer

tag: sirna knockdown

value: USP22 knockout clone 1

tag: cell line


title: EN1_S3_L001_R1_001

tag: subject status

value: healthy control

tag: tissue

value: healthy endometrium


title: tumor biopsy PCNSL_5

description: tumor sample

source_name: FFPE tumor

tag: gender

value: Female

value: tumor

tag: disease state

value: PCNSL


title: 16103_A549-P2_S49_L999_R1_001

description: RNA subjected to RNAseq

value: Parental cell sample 2


title: tumor biopsy PCNSL_7

description: tumor sample

value: Male


title: C18 Pre hydrocortisone

description:
C18 Pre hydrocortisone
1705168041_E

source_name: C18 Pre hydrocortisone

tag: individual

value: Pid C18

tag: timepoint

value: Pre

tag: treatment

value: hydrocortisone

tag: acth

value: Responder

tag: survival (28 days)

value: survived

tag: age

value: male

tag: pre-treatment ifng il10 ratio

value: low

tag: disease

value: septic shock

value: blood leukocytes


title: E62_S15_L008_R1_001


title: C16 Post(24h) placebo

description:
C16 Post(24h) placebo
1705168041_B

source_name: C16 Post(24h) placebo

value: Pid C16

value: placebo


title: tumor biopsy PCNSL_8

description: tumor sample


title: 23785_A549-Ko2_S45_L999_R1_001

description: RNA subjected to RNAseq

value: Non-small cell lung cancer

value: USP22 knockout clone 2


title: G4_930AF_CAGATC [930AF]

tag: subject id

tag: subject group

value: Orang Asli (indigenous) study village resident

value: F

tag: time point (before or after anthelmintic treatment)

value: After

tag: trichuris egg count

tag: ascaris egg count

tag: hookworm infection (yes/no)

tag: treatment responder or not

value: Resistant

value: blood

tag: kilocalories

tag: protein

tag: carbohydrate

tag: cholesterol

tag: tryptophan

tag: threonine

tag: isoleucine

tag: leucine

tag: lysine

tag: methionine

tag: cystine

tag: phenylalanine

tag: tyrosine

tag: valine

tag: histidine

tag: thiamin

tag: riboflavin

tag: niacin

tag: pyridoxine

tag: folate

tag: cobalamin

tag: biotin

tag: pantothenic

tag: iron

tag: magnesium

tag: zinc

tag: copper

tag: manganese

tag: selenium

tag: chromium

tag: molybdenum

tag: fat

tag: fruit

tag: vegetable

tag: wasting

tag: stunting

value: Mild

value: Significant


title: E9_S20_R1_001

source_name: tissue sample from patient with endometriosis

tag: subject status

value: patient with endometriosis

tag: tissue

value: endometrial samples and lesions


title: C16 Pre placebo

description:
C16 Pre placebo
1705168041_A

source_name: C16 Pre placebo

tag: individual

tag: timepoint

value: Pre

tag: treatment

tag: acth

value: Responder

tag: survival (28 days)

value: survived

tag: age

tag: gender

value: male

tag: pre-treatment ifng il10 ratio

tag: disease

tag: cell type


title: Ad-SREBP2 3 ATAC-Seq

city: La Jolla

first: John

last: Shyy

state: California

address: 9500 Gilman Dr., BRF2 Rm 1217 Bay LL

department: Medicine

institute: University of California, San Diego

library_source: genomic

data_processing:
Base calling and quality scoring were performed by an updated implementation of Real-Time Analysis (RTA), termed RTA v2, on theIllumina HiSeq 2000. bcl2fastq Conversion Software v1.8.4 was used to demultiplex data and convert BCL files to FASTQ file formats.
Reads were aligned to the Human GRCh38 genome using bowtie2. After read alignment, SAMtools, Picard's MarkDuplicates, and bedtools were used to remove multi-mapped reads (MAPQ < 30), remove PCR duplicates reads, and convert alignment BAM format to tagAlign format, respectively.
The retained alignment results were used to call peaks by MACS2 with the false discovery rate (FDR) threshold of 0.01. Results of peak signal were imported into WashU Epigenome Browser for further visualization and analysis.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each sample

source_name: HUVEC

growth_protocol: Human umbelical vein endothelial cells (HUVECs) between 6-8 passages were grown to confluence in M199 media supplemented with 15% fetal bovine serum, 5 ng/mL b-endothelial cell growth factor, 4 U/mL haparin, and 100 U/mL penicillin-streptomycin.

extract_protocol:
Nuclei were isolated by resuspending ~5000 cells in 50 ul cold lysis buffer (10 mM Tris-HCl, 10 mM NaCl, 3 mM MgCl2, and 0.1% NP-40). The nuclear pellets were resuspended in 50 uL transposition buffer in Nextera DNA Library Preparation Kit (Illumina Inc. San Diego, CA).
ATAC libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: HUVECs were grown to 70% confluency and infected with adenovirus containing SREBP2 (Ad-SREBP2) or empty vector control (Ad-null) for 72 hr.

value: Umbilical vein endothelial cells

tag: passage


title: G3_762AF_ACTGAT [762AF]

tag: subject id

tag: subject group

tag: time point (before or after anthelmintic treatment)

tag: trichuris egg count

tag: ascaris egg count

tag: hookworm infection (yes/no)

tag: treatment responder or not

tag: kilocalories

tag: protein

tag: carbohydrate

tag: cholesterol

tag: tryptophan

tag: threonine

tag: isoleucine

tag: leucine

tag: lysine

tag: methionine

tag: cystine

tag: phenylalanine

tag: tyrosine

tag: valine

tag: histidine

tag: thiamin

tag: riboflavin

tag: niacin

tag: pyridoxine

tag: folate

tag: cobalamin

tag: biotin

tag: pantothenic

tag: iron

tag: magnesium

tag: zinc

tag: copper

tag: manganese

tag: selenium

tag: chromium

tag: molybdenum

tag: fat

tag: fruit

tag: underweight

value: Normal


title: E8_S21_L006_R1_001

tag: subject status

tag: tissue


title: G2_634AF_ATGTCA [634AF]

tag: subject id

tag: subject group

tag: gender

tag: time point (before or after anthelmintic treatment)

tag: age

tag: trichuris egg count

tag: ascaris egg count

tag: hookworm infection (yes/no)

tag: treatment responder or not

tag: kilocalories

tag: protein

tag: carbohydrate

tag: cholesterol

tag: tryptophan

tag: threonine

tag: isoleucine

tag: leucine

tag: lysine

tag: methionine

tag: cystine

tag: phenylalanine

tag: tyrosine

tag: valine

tag: histidine

tag: thiamin

tag: riboflavin

tag: niacin

tag: pyridoxine

tag: folate

tag: vegetable

tag: wasting

tag: stunting


title: 16102_A549-P1_S48_L999_R1_001

description: RNA subjected to RNAseq

tag: cell type

value: Non-small cell lung cancer

tag: sirna knockdown

value: Parental cell sample 1

tag: cell line


title: E75_S2_L001_R1_001

tag: subject status

tag: tissue


title: G12_1875AF_ACTGAT [1875AF]

tag: subject id

tag: subject group

value: Orang Asli (indigenous) study village resident

tag: gender

tag: time point (before or after anthelmintic treatment)

tag: age

tag: trichuris egg count

tag: ascaris egg count

tag: hookworm infection (yes/no)

tag: treatment responder or not

tag: kilocalories

tag: protein

tag: carbohydrate

tag: cholesterol

tag: tryptophan

tag: threonine

tag: isoleucine

tag: leucine

tag: lysine

tag: methionine

tag: cystine

tag: phenylalanine

tag: cobalamin

tag: biotin

tag: pantothenic

tag: iron

tag: magnesium

tag: zinc

tag: copper

tag: manganese

tag: selenium

tag: chromium

tag: molybdenum

tag: fat

tag: fruit

tag: underweight


title: Ad-Null 3 ATAC-Seq

tag: cell type

tag: passage


title: C08 Post(24h) hydrocortisone

description:
C08 Post(24h) hydrocortisone
1705168238_F

source_name: C08 Post(24h) hydrocortisone

tag: individual

value: Pid C08

tag: timepoint

tag: treatment

value: hydrocortisone

tag: acth

tag: survival (28 days)

tag: age

tag: gender

value: female

tag: pre-treatment ifng il10 ratio

value: low

tag: disease

value: septic shock

value: blood leukocytes


title: C08 Pre hydrocortisone

description:
C08 Pre hydrocortisone
1705168238_E

source_name: C08 Pre hydrocortisone


title: G10_1719AF_CAGATC [1719AF]

tag: subject id

tag: subject group

value: F

tag: time point (before or after anthelmintic treatment)

value: After

tag: trichuris egg count

tag: ascaris egg count

tag: hookworm infection (yes/no)

tag: treatment responder or not

tag: tissue

value: blood

tag: kilocalories

tag: protein

tag: carbohydrate

tag: cholesterol

tag: tryptophan

tag: threonine

tag: isoleucine

tag: leucine

tag: lysine

tag: methionine

tag: cystine

tag: phenylalanine

tag: tyrosine

tag: valine

tag: histidine

tag: thiamin

tag: riboflavin

tag: niacin

tag: pyridoxine

tag: folate

tag: cobalamin

tag: biotin

tag: pantothenic

tag: iron

tag: magnesium

tag: zinc

tag: copper

tag: manganese

tag: selenium

tag: vegetable

tag: wasting

tag: stunting


title: E74_S1_L001_R1_001

tag: subject status

value: patient with endometriosis

tag: tissue

value: endometrial samples and lesions


title: C18 Post(24h) hydrocortisone

description:
C18 Post(24h) hydrocortisone
1705168041_F

source_name: C18 Post(24h) hydrocortisone

tag: individual

value: Pid C18

tag: timepoint

tag: treatment

tag: acth

value: Responder

tag: survival (28 days)

value: survived

tag: age

tag: gender

value: male

tag: pre-treatment ifng il10 ratio

tag: disease

tag: cell type


title: tumor biopsy PCNSL_2

description: tumor sample

value: Male

value: tumor

tag: disease state

value: PCNSL


title: tumor biopsy PCNSL_1

description: tumor sample

source_name: cryo-preserved tumor

value: Female


title: C07 Post(24h) placebo

description:
C07 Post(24h) placebo
1705168238_D

source_name: C07 Post(24h) placebo

value: Pid C07

value: placebo

value: female

value: high


title: G7_1097AF_CAGATC [1097AF]

tag: subject id

tag: subject group

value: Orang Asli (indigenous) study village resident

value: F

tag: time point (before or after anthelmintic treatment)

tag: trichuris egg count

tag: ascaris egg count

tag: hookworm infection (yes/no)

tag: treatment responder or not

tag: kilocalories

tag: protein

tag: carbohydrate

tag: cholesterol

tag: tryptophan

tag: threonine

tag: isoleucine

tag: leucine

tag: lysine

tag: methionine

tag: cystine

tag: phenylalanine

tag: tyrosine

tag: valine

tag: histidine

tag: thiamin

tag: riboflavin

tag: niacin

tag: pyridoxine

tag: folate

tag: cobalamin

tag: biotin

tag: pantothenic

tag: iron

tag: magnesium

tag: zinc

tag: copper

tag: manganese

tag: selenium

tag: chromium

tag: molybdenum

tag: fat

tag: fruit

value: Mild

tag: underweight

value: Normal


title: E71_S2_L002_R1_001

tag: subject status

value: patient with endometriosis

tag: tissue

value: endometrial samples and lesions


title: Ad-SREBP2 1 ATAC-Seq

tag: cell type

value: Umbilical vein endothelial cells

tag: passage


title: E72_S21_L004_R1_001


title: G1_442AF_CAGATC [442AF]

tag: subject id

tag: subject group

tag: gender

value: M

tag: time point (before or after anthelmintic treatment)

value: After

tag: age

tag: trichuris egg count

tag: ascaris egg count

tag: hookworm infection (yes/no)

tag: treatment responder or not

value: Responder

value: blood

tag: kilocalories

tag: protein

tag: carbohydrate

tag: cholesterol

tag: tryptophan

tag: threonine

tag: isoleucine

tag: leucine

tag: lysine

tag: methionine

tag: cystine

tag: phenylalanine

tag: tyrosine

tag: valine

tag: histidine

tag: thiamin

tag: riboflavin

tag: niacin

tag: pyridoxine

tag: folate

tag: cobalamin

tag: biotin

tag: vegetable

tag: wasting

tag: stunting


title: tumor biopsy PCNSL_3

description: tumor sample

tag: gender

value: Male

tag: tissue

value: tumor

tag: disease state

value: PCNSL


title: F9_218AF_GAGTGG [218AF]

tag: subject id

tag: subject group

tag: time point (before or after anthelmintic treatment)

tag: age

tag: trichuris egg count

tag: ascaris egg count

tag: hookworm infection (yes/no)

tag: treatment responder or not

tag: kilocalories

tag: protein

tag: carbohydrate

tag: cholesterol

tag: tryptophan

tag: threonine

tag: isoleucine

tag: leucine

tag: lysine

tag: methionine

tag: cystine

tag: phenylalanine

tag: pantothenic

tag: iron

tag: magnesium

tag: zinc

tag: copper

tag: manganese

tag: selenium

tag: chromium

tag: molybdenum

tag: fat

tag: fruit

tag: underweight


title: Ad-Null 1 ATAC-Seq

tag: cell type

tag: passage


title: C07 Pre placebo

description:
C07 Pre placebo
1705168238_C

source_name: C07 Pre placebo

tag: individual

value: Pid C07

tag: timepoint

value: Pre

tag: treatment

value: placebo

tag: acth

tag: survival (28 days)

value: survived

tag: age

tag: gender

tag: pre-treatment ifng il10 ratio

tag: disease

value: septic shock

value: blood leukocytes


title: E70_S2_L002_R1_001

tag: subject status

tag: tissue


title: F8_181AF_AGTTCC [181AF]

tag: subject id

tag: subject group

value: Orang Asli (indigenous) study village resident

value: F

tag: time point (before or after anthelmintic treatment)

tag: trichuris egg count

tag: ascaris egg count

tag: hookworm infection (yes/no)

tag: treatment responder or not

tag: kilocalories

tag: protein

tag: carbohydrate

tag: cholesterol

tag: tryptophan

tag: threonine

tag: isoleucine

tag: leucine

tag: lysine

tag: methionine

tag: cystine

tag: phenylalanine

tag: tyrosine

tag: valine

tag: histidine

tag: thiamin

tag: riboflavin

tag: niacin

tag: pyridoxine

tag: folate

tag: cobalamin

tag: biotin

tag: pantothenic

tag: iron

tag: magnesium

tag: zinc

tag: copper

tag: manganese

tag: selenium

tag: chromium

tag: molybdenum

tag: vegetable

value: Overweight

value: Obese class I

tag: wasting

tag: stunting


title: C06 Post(24h) placebo

description:
C06 Post(24h) placebo
1705168238_B

source_name: C06 Post(24h) placebo

tag: individual

value: Pid C06

tag: timepoint

tag: treatment

tag: acth

tag: survival (28 days)

value: died

tag: age

tag: gender

value: male

tag: pre-treatment ifng il10 ratio

value: high

tag: disease

tag: cell type


title: E68_S3_L008_R1_001

tag: subject status

value: patient with endometriosis

tag: tissue

value: endometrial samples and lesions


title: F7_166AF_GCCAAT [166AF]

tag: subject id

tag: subject group

value: M

tag: time point (before or after anthelmintic treatment)

value: After

tag: trichuris egg count

tag: ascaris egg count

tag: hookworm infection (yes/no)

tag: treatment responder or not

value: Resistant

value: blood

tag: kilocalories

tag: protein

tag: carbohydrate

tag: cholesterol

tag: tryptophan

tag: threonine

tag: isoleucine

tag: leucine

tag: lysine

tag: methionine

tag: cystine

tag: phenylalanine

tag: tyrosine

tag: valine

tag: histidine

tag: thiamin

tag: riboflavin

tag: niacin

tag: pyridoxine

tag: folate

tag: cobalamin

tag: biotin

tag: pantothenic

tag: iron

tag: magnesium

tag: zinc

tag: copper

tag: manganese

tag: selenium

tag: chromium

tag: fat

tag: fruit

value: Normal

tag: underweight


title: C05 Post(24h) hydrocortisone

description:
C05 Post(24h) hydrocortisone
1705168236_F

source_name: C05 Post(24h) hydrocortisone

tag: individual

value: Pid C05

tag: timepoint

tag: treatment

value: hydrocortisone

tag: acth

value: Responder

tag: survival (28 days)

value: survived

tag: age

tag: gender

value: female

tag: pre-treatment ifng il10 ratio

value: low

tag: disease

value: septic shock

tag: cell type


title: Ad-Null 2 ATAC-Seq

value: Umbilical vein endothelial cells

tag: passage


title: E67_S18_L008_R1_001

tag: subject status

tag: tissue


title: C06 Pre placebo

description:
C06 Pre placebo
1705168238_A

source_name: C06 Pre placebo

value: Pid C06

value: Pre

value: placebo

value: died

value: male

value: blood leukocytes


title: F6_135AF_GAGTGG [135AF]

tag: subject id

tag: subject group

value: Orang Asli (indigenous) study village resident

value: M

tag: time point (before or after anthelmintic treatment)

value: After

tag: trichuris egg count

tag: ascaris egg count

tag: hookworm infection (yes/no)

tag: treatment responder or not

tag: kilocalories

tag: protein

tag: carbohydrate

tag: cholesterol

tag: tryptophan

tag: threonine

tag: isoleucine

tag: leucine

tag: lysine

tag: methionine

tag: cystine

tag: phenylalanine

tag: tyrosine

tag: valine

tag: histidine

tag: thiamin

tag: riboflavin

tag: niacin

tag: pyridoxine

tag: folate

tag: cobalamin

tag: biotin

tag: pantothenic

tag: iron

tag: magnesium

tag: zinc

tag: copper

tag: manganese

tag: selenium

tag: chromium

tag: molybdenum

tag: vegetable

value: Underweight

value: Severe thinness

tag: wasting

tag: stunting

value: Significant


title: Mm_PU1_BMDC_ST_ChIPSeq

city: Oviedo

first: Laura

last: Gutiérrez

state: Asturias

address: Avenida de Roma S/N

country: Spain

institute: ISPA - University of Oviedo

data_processing:
peaks were called using  macs version 1.4.1 20110622 with the following settings: bandwidth 125 and a lower and upper M-fold cutoff of 8 and 30 respectively.
Genome_build: GRCh37 (hg19) (human moDC) or mm9 (mouse BMDC)
Supplementary_files_format_and_content: annotated peaks.txt

organism: Mus musculus

source_name: mouse inflammatory DC immature

growth_protocol: BMDC were cultured at a density of 0.5x10E6 cells/ml in RPMI-1640 supplemented with 5% FCS, 1% Pen/Strep, 5microM 2-mercaptoethanol, in the presence of 20 ng/ml GM-CSF.

extract_protocol:
After crosslinking the chromatin of 2x10E8 cell lysates, sonicated nuclei and PU.1-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions.

treatment_protocol: At day 7, BMDC were stimulated or not with 500 ng/ml LPS, and collected at day 10.

tag: culture type

value: bone marrow derived DC

tag: cell type

value: dendritic cells (DC)

tag: treatment and collection date

value: no LPS added, collection day 10

tag: culture conditions

value: GM-CSF

tag: antibody

value: PU.1 (T-21, Santa Cruz)


title: F5_119AF_AGTTCC [119AF]

source_name: Orang Asli (indigenous) study village resident_After treatment

tag: subject id

tag: subject group

tag: gender

tag: time point (before or after anthelmintic treatment)

tag: age

tag: trichuris egg count

tag: ascaris egg count

tag: hookworm infection (yes/no)

tag: treatment responder or not

value: Resistant

tag: tissue

value: blood

tag: kilocalories

tag: protein

tag: carbohydrate

tag: cholesterol

tag: tryptophan

tag: threonine

tag: isoleucine

tag: leucine

tag: lysine

tag: methionine

tag: cystine

tag: phenylalanine

tag: tyrosine

tag: valine

tag: histidine

tag: thiamin

tag: riboflavin

tag: niacin

tag: pyridoxine

tag: folate

tag: cobalamin

tag: biotin

tag: pantothenic

tag: fat

tag: fruit

value: Mild thinness

tag: underweight


title: Z1119

city: Dallas

first: Sara

middle: K

last: Hildebrand

state: TX

address: 5323 Harry Hines blvd

department: Center for the Genetics of Host Defense

institute: UT Southwestern Medical Center

description:
Treat_Mut_SC27
EL4_gene_exp.diff

data_processing:
fastq files were aligned to version mm10 of mouse reference genome using tophat v2.0.10
BAM files resulting from the alignments were run through cuffdiff v2.1.1 for differential expression
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: EL4 cells

growth_protocol: Wild-type and Snrnp40-KO EL4 cells were routinely maintained in DMEM medium with 10% horse serum (cultures typically between 1 x 10e5 and 1 x 10e6 cells/mL).

extract_protocol:
Total RNAs from the cells were extracted using the RNeasy Plus kit with genomic DNA elimination (Qiagen), according to the manufacturer’s instructions.
Libraries were prepared using the KAPA Stranded RNA-Seq kit with RiboErase (HMR) (Kapa Biosystems), according to the manufacturer’s instructions.

treatment_protocol: EL4 cells were untreated or treated with PMA/ionomycin (50 ng/ml PMA and 1 ug/ml ionomycin) for 4 h. No treatment for primary HSPCs and T cells.

tag: background strain

tag: genotype

tag: treatment

value: treated with PMA/ionomycin


title: Z1118

description:
Treat_Mut_SC24
EL4_gene_exp.diff


title: E64_S16_L008_R1_001

tag: subject status

value: patient with endometriosis

tag: tissue

value: endometrial samples and lesions


title: C04 Post(24h) hydrocortisone

description:
C04 Post(24h) hydrocortisone
1705168236_D

source_name: C04 Post(24h) hydrocortisone

tag: individual

value: Pid C04

tag: timepoint

value: hydrocortisone

tag: acth

value: Responder

tag: survival (28 days)

value: died

tag: age

tag: gender

value: female

tag: pre-treatment ifng il10 ratio

value: low

tag: disease

value: septic shock

tag: cell type

value: blood leukocytes


title: C05 Pre hydrocortisone

description:
C05 Pre hydrocortisone
1705168236_E

source_name: C05 Pre hydrocortisone

value: Pid C05

value: Pre

value: survived


title: E60_S14_L008_R1_001

source_name: tissue sample from patient with endometriosis


title: Z1117

description:
Treat_WT_SC5
EL4_gene_exp.diff

value: wild-type


title: C01 Post(24h) placebo

description:
C01 Post(24h) placebo
1705168236_B

source_name: C01 Post(24h) placebo

value: Pid C01

value: placebo

value: Non responder

value: male

value: high


title: F3_101AF_GAGTGG [101AF]

tag: subject id

tag: subject group

value: Orang Asli (indigenous) study village resident

value: F

tag: time point (before or after anthelmintic treatment)

value: After

tag: trichuris egg count

tag: ascaris egg count

tag: hookworm infection (yes/no)

tag: treatment responder or not

value: blood

tag: kilocalories

tag: protein

tag: carbohydrate

tag: cholesterol

tag: tryptophan

tag: threonine

tag: isoleucine

tag: leucine

tag: lysine

tag: methionine

tag: cystine

tag: phenylalanine

tag: tyrosine

tag: valine

tag: histidine

tag: thiamin

tag: riboflavin

tag: niacin

tag: pyridoxine

tag: folate

tag: cobalamin

tag: biotin

tag: pantothenic

tag: iron

tag: magnesium

tag: zinc

tag: copper

tag: manganese

tag: selenium

tag: chromium

tag: molybdenum

tag: fat

tag: vegetable

tag: wasting

tag: stunting

value: Mild

value: Normal


title: F4_102AF_GCCAAT [102AF]

tag: subject id

tag: subject group

tag: gender

tag: time point (before or after anthelmintic treatment)

tag: age

tag: trichuris egg count

tag: ascaris egg count

tag: hookworm infection (yes/no)

tag: treatment responder or not

value: Responder

tag: tissue

tag: kilocalories

tag: protein

tag: carbohydrate

tag: cholesterol

tag: tryptophan

tag: threonine

tag: isoleucine

tag: leucine

tag: lysine

tag: methionine

tag: cystine

tag: phenylalanine

tag: tyrosine

tag: valine

tag: histidine

tag: thiamin

tag: riboflavin

tag: niacin

tag: pyridoxine

tag: fruit

value: Overweight

value: Obese class I

tag: underweight


title: Mm_PU1_BMDC_LPS_ChIPSeq

source_name: mouse inflammatory DC LPS stimulated

tag: culture type

value: bone marrow derived DC

tag: cell type

value: dendritic cells (DC)

tag: treatment and collection date

value: LPS added at day 7, collection day 10

tag: culture conditions

value: GM-CSF

tag: antibody

value: PU.1 (T-21, Santa Cruz)


title: Z1116

description:
Treat_WT_Pool
EL4_gene_exp.diff

tag: background strain

tag: genotype

value: wild-type

tag: treatment

value: treated with PMA/ionomycin


title: F2_98AF_AGTTCC [98AF]

tag: subject id

tag: subject group

tag: gender

tag: time point (before or after anthelmintic treatment)

tag: age

tag: trichuris egg count

tag: ascaris egg count

tag: hookworm infection (yes/no)

tag: treatment responder or not

tag: tissue

tag: kilocalories

tag: protein

tag: carbohydrate

tag: cholesterol

tag: tryptophan

tag: threonine

tag: isoleucine

tag: leucine

tag: lysine

tag: methionine

tag: cystine

tag: phenylalanine

tag: tyrosine

tag: folate

tag: cobalamin

tag: biotin

tag: pantothenic

tag: iron

tag: magnesium

tag: zinc

tag: copper

tag: manganese

tag: selenium

tag: chromium

tag: molybdenum

tag: fat

tag: vegetable

tag: wasting

tag: stunting


title: tm1473_NGM_3

city: Salt lake city

first: Elizabeth

middle: A

last: Leibold

state: Utah

address: 15 North 2030 East

department: Molecular Medicine

institute: University of Utah

data_processing:
Basecalls performed using CASAVA version 1.4
RNA-seq reads were aligned to Ce10 (Wormbase Build 220) using Novoalign
Differentially expressed reads were determined by Useq 8.7.4
DESeq's log2 ratio for differential expression, log2(mean(varCorT1,varCorT2, ...)/mean(varCorC1,varCorC2,...)). Note these varCor values will differ somewhat from the blinded varCor values exported to the spreadsheet since they use a different variance estimation.
DESeq's negative binomial p-value following the Benjamini and Hochberg multiple testing correction.
Genome_build: Ce10 Wormbase Build 220

organism: Caenorhabditis elegans

source_name: L4 Larvae

growth_protocol: N2 wild-type and nhr-14 (tm1473) mutants were synchronized by hypochlorite treatment at the L1 larval stage, and grown to the L4 larval stage on NGM plates seeded with OP50 E. coli before RNA extraction.

extract_protocol:
Worms were rinsed with M9 buffer and RNA was extracted using a modified Trizol protocol.
Library construction was performed using the Illumina TruSeq RNA Sample Preparation Kit v2 with oligo dT selection (RS-122-2001 and RS-122-2002), and was sequenced with the Illumina HiSeq (50 cycle, single read).

treatment_protocol: Worms were grown on NGM plates seeded with OP50 E. coli

tag: cell type

value: Whole Organism

tag: passages

value: Synchronized L4 Larvae

tag: strain

value: tm1473 allele backcrossed to N2 Bristol


title: E6_S19_R1_001

tag: subject status

value: patient with endometriosis

tag: tissue

value: endometrial samples and lesions


title: Z1114

description:
Mut_SC24
EL4_gene_exp.diff

tag: background strain

tag: genotype

tag: treatment

value: untreated


title: E65_S17_L008_R1_001


title: tm1473_NGM_1


title: tm1473_NGM_2


title: Z1115

description:
Mut_SC27
EL4_gene_exp.diff


title: F12_351AF_GAGTGG [351AF]

tag: subject id

tag: subject group

value: Orang Asli (indigenous) study village resident

tag: gender

value: M

tag: time point (before or after anthelmintic treatment)

value: After

tag: age

tag: trichuris egg count

tag: ascaris egg count

tag: hookworm infection (yes/no)

tag: treatment responder or not

value: blood

tag: kilocalories

tag: protein

tag: carbohydrate

tag: cholesterol

tag: tryptophan

tag: threonine

tag: isoleucine

tag: leucine

tag: lysine

tag: methionine

tag: cystine

tag: phenylalanine

tag: tyrosine

tag: valine

tag: histidine

tag: thiamin

tag: riboflavin

tag: niacin

tag: pyridoxine

tag: folate

tag: cobalamin

tag: biotin

tag: pantothenic

tag: iron

tag: magnesium

tag: zinc

tag: copper

tag: fruit

value: Significant

tag: underweight


title: E59_S13_L008_R1_001

tag: subject status

tag: tissue


title: E57_S12_L008_R1_001


title: N2_NGM_3

tag: cell type

tag: passages

tag: strain

value: N2 Bristol


title: F11_221AF_AGTTCC [221AF]

tag: subject id

tag: subject group

tag: gender

tag: time point (before or after anthelmintic treatment)

tag: age

tag: trichuris egg count

tag: ascaris egg count

tag: hookworm infection (yes/no)

tag: treatment responder or not

value: Responder

tag: kilocalories

tag: protein

tag: carbohydrate

tag: cholesterol

tag: tryptophan

tag: threonine

tag: isoleucine

tag: leucine

tag: lysine

tag: methionine

tag: cystine

tag: phenylalanine

tag: tyrosine

tag: valine

tag: histidine

tag: thiamin

tag: riboflavin

tag: niacin

tag: manganese

tag: selenium

tag: chromium

tag: molybdenum

tag: fat

tag: vegetable

value: Normal

tag: wasting

tag: stunting


title: E56_S11_L008_R1_001

tag: subject status

tag: tissue


title: Z1113

description:
WT_SC5
EL4_gene_exp.diff

tag: background strain

tag: genotype

tag: treatment


title: C04 Pre hydrocortisone

description:
C04 Pre hydrocortisone
1705168236_C

source_name: C04 Pre hydrocortisone

tag: individual

value: Pid C04

tag: timepoint

value: Pre

value: hydrocortisone

tag: acth

tag: survival (28 days)

value: died

tag: age

tag: gender

value: female

tag: pre-treatment ifng il10 ratio

value: low

tag: disease

value: septic shock

tag: cell type

value: blood leukocytes


title: N2_NGM_2

value: Whole Organism

tag: passages

value: Synchronized L4 Larvae

tag: strain


title: F10_220AF_GCCAAT [220AF]

tag: subject id

tag: subject group

value: Orang Asli (indigenous) study village resident

value: M

tag: time point (before or after anthelmintic treatment)

tag: trichuris egg count

tag: ascaris egg count

tag: hookworm infection (yes/no)

tag: treatment responder or not

value: Resistant

tag: kilocalories

tag: protein

tag: carbohydrate

tag: cholesterol

tag: tryptophan

tag: threonine

tag: isoleucine

tag: leucine

tag: lysine

tag: methionine

tag: cystine

tag: phenylalanine

tag: tyrosine

tag: valine

tag: histidine

tag: thiamin

tag: riboflavin

tag: niacin

tag: pyridoxine

tag: folate

tag: cobalamin

tag: biotin

tag: pantothenic

tag: iron

tag: magnesium

tag: zinc

tag: copper

tag: manganese

tag: selenium

tag: chromium

tag: molybdenum

tag: fat

tag: fruit

tag: vegetable

tag: wasting

tag: stunting

tag: underweight


title: Z1112

description:
WT_Pool
EL4_gene_exp.diff

tag: background strain

tag: genotype

value: wild-type

tag: treatment

value: untreated


title: E55_S30_L006_R1_001

tag: subject status

value: patient with endometriosis

tag: tissue

value: endometrial samples and lesions


title: N2_NGM_1

tag: cell type

tag: passages

tag: strain

value: N2 Bristol


title: E53_S29_L006_R1_001


title: E9_19100_CGTACG [19100]

source_name: Orang Asli (indigenous) study village resident_Before treatment

tag: subject id

tag: subject group

tag: gender

tag: time point (before or after anthelmintic treatment)

value: Before

tag: age

tag: trichuris egg count

tag: ascaris egg count

tag: hookworm infection (yes/no)

tag: treatment responder or not

value: Responder

value: blood

tag: kilocalories

tag: protein

tag: carbohydrate

tag: cholesterol

tag: tryptophan

tag: threonine

tag: isoleucine

tag: leucine

tag: lysine

tag: methionine

tag: cystine

tag: phenylalanine

tag: tyrosine

tag: valine

tag: histidine

tag: thiamin

tag: riboflavin

tag: niacin

tag: pyridoxine

tag: folate

tag: cobalamin

tag: biotin

tag: pantothenic

tag: iron

tag: magnesium

tag: zinc

tag: copper

tag: manganese

tag: selenium

value: Significant


title: E51_S27_L006_R1_001

tag: subject status

tag: tissue


title: E52_S28_L006_R1_001


title: E7_8107_ACAGTG [8107]

tag: subject id

tag: subject group

tag: gender

tag: time point (before or after anthelmintic treatment)

tag: age

tag: trichuris egg count

tag: ascaris egg count

tag: hookworm infection (yes/no)

tag: treatment responder or not

tag: kilocalories

tag: protein

tag: carbohydrate

tag: cholesterol

tag: tryptophan

tag: threonine

tag: isoleucine

tag: leucine

tag: lysine

tag: methionine

tag: cystine

tag: phenylalanine

tag: tyrosine

tag: valine

tag: histidine

tag: chromium

tag: molybdenum

tag: fat

tag: fruit

tag: vegetable

tag: wasting

tag: stunting

value: Mild

tag: underweight

value: Normal


title: C01 Pre placebo

description:
C01 Pre placebo
1705168236_A

source_name: C01 Pre placebo

tag: individual

value: Pid C01

tag: timepoint

value: Pre

tag: treatment

value: placebo

tag: acth

value: Non responder

tag: survival (28 days)

value: survived

tag: age

tag: gender

value: male

tag: pre-treatment ifng il10 ratio

value: high

tag: disease

value: septic shock

tag: cell type

value: blood leukocytes


title: KLF4-M-ChIP-WT2

first: Priscillia

last: Lhoumaud

address: 550 first avenue Smilow 307

department: Pathology

institute: NYU Langone Health

description:
KLF4 ChIP-seq with methylated adaptors and bisulfite converted
WT-Klf4-BC_merged_R1_bismark_bt2_pe.bismark.cov, WT-Klf4-BC_merged_R1_bismark_bt2_pe.bedGraph.gz

data_processing:
Reads were trimmed using trim-galore/0.4.4
Reads were aligned to the mm10 assembly of mouse genome using bowtie2 for ChIP-seq and ATAC-seq, and using Bismark/0.18.1 (bowtie2) for M-ChIP and M-ATAC to account for bisulfite conversion.
Reads with quality < 30 and duplicates were removed using Samtools/1.3
Peaks were called using PeakDeck
Bigwigs were generated from bam files with RPKM (Reads Per Kilobase per Megabase) normalization using Deeptools
Genome_build: mm10
Supplementary_files_format_and_content: bigwigs and peak files were generated from bam files for data visualization. Methylation was extracted using bismark as coverage (.cov) and bedgraph files. Tsv files correspond to subsampling of methylation from coverage files inside peak regions.

source_name: emrbyonic stem cells

growth_protocol: KH2 embryonic stem cells (ESCs) were cultured on irradiated feeder cells in KO-DMEM (Invitrogen) supplemented with L-glutamine, penicillin/streptomycin, nonessential amino acids, β-mercaptoethanol, 1,000 U/mL LIF, and 15% FBS (ESC medium). To remove feeder cells from ESCs, cells were trypsin digested and pre-plated in ESC medium for 30 mins. Supernatant containing ESCs was used for further experiments.

extract_protocol:
For ATAC-seq (converted or not) nuclei were prepared from 50,000 cells for each transposition reaction. For ChIP-seq (converted or not), Lysates were clarified from sonicated nuclei and KLF4-bound chromatin was isolated with KLF4 antibody.
For ATAC-seq and ChIP-seq, sequencing libraries were constructed using the Illumina Nextera DNA Sample prep kit. For bisulfite converted samples, a transposome was assembled with methylated adaptors for transposition reaction.

tag: strain

value: emrbyonic stem cells

tag: genotype

value: KLF4 -/- that re-express WT Klf4

tag: chip antibody


title: E6_5113_CGTACG [5113]

tag: subject id

tag: subject group

value: Orang Asli (indigenous) study village resident

value: F

tag: time point (before or after anthelmintic treatment)

value: Before

tag: trichuris egg count

tag: ascaris egg count

tag: hookworm infection (yes/no)

tag: treatment responder or not

value: Resistant

tag: tissue

tag: kilocalories

tag: protein

tag: carbohydrate

tag: cholesterol

tag: tryptophan

tag: threonine

tag: isoleucine

tag: leucine

tag: lysine

tag: methionine

tag: cystine

tag: phenylalanine

tag: tyrosine

tag: valine

tag: histidine

tag: thiamin

tag: riboflavin

tag: niacin

tag: pyridoxine

tag: folate

tag: cobalamin

tag: biotin

tag: pantothenic

tag: iron

tag: magnesium

tag: zinc

tag: copper

tag: manganese

tag: selenium

tag: chromium

tag: molybdenum

tag: fat

tag: fruit

tag: vegetable

value: Overweight

value: Pre-obese


title: KLF4-M-ChIP-Mut2

description:
KLF4 ChIP-seq with methylated adaptors and bisulfite converted
Mut-Klf4-BC_merged_R1_bismark_bt2_pe.bismark.cov, Mut-Klf4-BC_merged_R1_bismark_bt2_pe.bedGraph.gz

tag: strain

tag: cell type

tag: genotype

value: KLF4 -/- that re-express R462A mutant Klf4

tag: chip antibody


title: KLF4-M-ChIP-Mut1


title: KLF4-M-ChIP-WT1


title: E5_S7_L008_R1_001

tag: subject status

value: patient with endometriosis

tag: tissue

value: endometrial samples and lesions


title: KLF4-ChIP-KO2

description: KLF4 ChIP-seq


title: F1_88AF_GCCAAT [88AF]

tag: subject id

tag: subject group

tag: gender

value: M

tag: time point (before or after anthelmintic treatment)

value: After

tag: age

tag: trichuris egg count

tag: ascaris egg count

tag: hookworm infection (yes/no)

tag: treatment responder or not

value: Responder

value: blood

tag: kilocalories

tag: protein

tag: carbohydrate

tag: cholesterol

tag: tryptophan

tag: threonine

tag: isoleucine

tag: leucine

tag: lysine

tag: methionine

tag: cystine

tag: phenylalanine

tag: tyrosine

tag: valine

tag: histidine

tag: thiamin

tag: riboflavin

tag: niacin

tag: pyridoxine

tag: folate

tag: cobalamin

tag: biotin

tag: pantothenic

tag: iron

tag: wasting

value: Mild

tag: stunting

value: Significant

tag: underweight


title: E2_1889_AGTCAA [1889]

tag: subject id

tag: subject group

tag: gender

tag: time point (before or after anthelmintic treatment)

tag: age

tag: trichuris egg count

tag: ascaris egg count

tag: hookworm infection (yes/no)

tag: treatment responder or not

tag: tissue

tag: kilocalories

tag: protein

tag: carbohydrate

tag: cholesterol

tag: tryptophan

tag: threonine

tag: isoleucine

tag: leucine

tag: lysine

tag: methionine

tag: cystine

tag: magnesium

tag: zinc

tag: copper

tag: manganese

tag: selenium

tag: chromium

tag: molybdenum

tag: fat

tag: fruit

tag: vegetable


title: E48_S25_L006_R1_001

tag: subject status

tag: tissue


title: E12_52AF_CGTACG [52AF]

tag: subject id

tag: subject group

tag: gender

tag: time point (before or after anthelmintic treatment)

tag: age

tag: trichuris egg count

tag: ascaris egg count

tag: hookworm infection (yes/no)

tag: treatment responder or not

tag: kilocalories

tag: protein

tag: carbohydrate

tag: cholesterol

tag: tryptophan

tag: threonine

tag: isoleucine

tag: phenylalanine

tag: tyrosine

tag: valine

tag: histidine

tag: thiamin

tag: riboflavin

tag: niacin

tag: pyridoxine

tag: folate

tag: cobalamin

tag: biotin

tag: pantothenic

tag: iron

tag: wasting

tag: stunting

value: Normal

tag: underweight


title: non_involved_lung_tissue_patient_85 9983140102_I_Expression

source_name: Non-involved (apparently normal) lung parenchyma

tag: Sex

tag: age

tag: smoking status

value: never-smoker

tag: batch


title: M-ATAC-Mut2

description:
ATAC-seq with methylated adaptors and bisulfite converted
ATAC-BS-MUTmerged_R1_bismark_bt2_pe.bismark.cov, ATAC-BS-MUTmerged_R1_bismark_bt2_pe.bedGraph.gz

tag: strain

tag: cell type

value: emrbyonic stem cells

tag: genotype


title: E47_S10_L004_R1_001

tag: subject status

tag: tissue


title: non_involved_lung_tissue_patient_86 9983140102_J_Expression

value: F

value: ever-smoker


title: non_involved_lung_tissue_patient_87 9983140102_K_Expression


title: non_involved_lung_tissue_patient_84 9983140102_F_Expression


title: E46_S24_L006_R1_001


title: M-ATAC-Mut1


title: E44_S23_L006_R1_001


title: E11_37AF_AGTCAA [37AF]

tag: subject id

tag: subject group

value: Orang Asli (indigenous) study village resident

tag: gender

tag: time point (before or after anthelmintic treatment)

tag: trichuris egg count

tag: ascaris egg count

tag: hookworm infection (yes/no)

tag: treatment responder or not

tag: kilocalories

tag: protein

tag: carbohydrate

tag: cholesterol

tag: tryptophan

tag: threonine

tag: isoleucine

tag: leucine

tag: lysine

tag: methionine

tag: cystine

tag: phenylalanine

tag: tyrosine

tag: valine

tag: histidine

tag: thiamin

tag: riboflavin

tag: niacin

tag: pyridoxine

tag: folate

tag: magnesium

tag: zinc

tag: copper

tag: manganese

tag: selenium

tag: chromium

tag: molybdenum

tag: fat

tag: fruit

tag: vegetable


title: E4_2093_ACAGTG [2093]

tag: subject id

tag: subject group

tag: gender

tag: time point (before or after anthelmintic treatment)

value: Before

tag: age

tag: trichuris egg count

tag: ascaris egg count

tag: hookworm infection (yes/no)

tag: treatment responder or not

tag: tissue

tag: kilocalories

tag: protein

tag: carbohydrate

tag: cholesterol

tag: tryptophan

tag: threonine

tag: isoleucine

tag: leucine

tag: lysine

tag: methionine

tag: cystine

tag: phenylalanine

tag: tyrosine

tag: valine

tag: cobalamin

tag: biotin

tag: pantothenic

tag: iron

tag: wasting

tag: stunting

tag: underweight


title: M-ATAC-WT2

description:
ATAC-seq with methylated adaptors and bisulfite converted
ATAC-BS-WTmerged_R1_bismark_bt2_pe.bismark.cov, ATAC-BS-WTmerged_R1_bismark_bt2_pe.bedGraph.gz

tag: strain

tag: cell type

tag: genotype

value: KLF4 -/- that re-express WT Klf4


title: E49_S26_L006_R1_001

tag: subject status

tag: tissue


title: E1_1875_ACAGTG [1875]

tag: subject id

tag: subject group

tag: gender

tag: time point (before or after anthelmintic treatment)

tag: age

tag: trichuris egg count

tag: ascaris egg count

tag: hookworm infection (yes/no)

tag: treatment responder or not

tag: kilocalories

tag: protein

tag: carbohydrate

tag: cholesterol

tag: tryptophan

tag: threonine

tag: isoleucine

tag: leucine

tag: lysine

tag: methionine

tag: histidine

tag: thiamin

tag: riboflavin

tag: niacin

tag: pyridoxine

tag: folate

tag: magnesium

tag: zinc

tag: copper

tag: manganese

tag: selenium

tag: chromium

tag: molybdenum

tag: fat

tag: fruit

tag: vegetable


title: E10_20109_ACAGTG [20109]

tag: subject id

tag: subject group

tag: gender

tag: time point (before or after anthelmintic treatment)

tag: age

tag: trichuris egg count

tag: ascaris egg count

tag: hookworm infection (yes/no)

tag: treatment responder or not

value: Resistant

tag: tissue

tag: kilocalories

tag: protein

tag: carbohydrate

tag: cholesterol

tag: tryptophan

tag: threonine

tag: isoleucine

tag: leucine

tag: lysine

tag: methionine

tag: cystine

tag: phenylalanine

tag: tyrosine

tag: valine

tag: cobalamin

tag: biotin

tag: pantothenic

tag: iron

tag: wasting

tag: stunting

tag: underweight


title: KLF4-ChIP-KO1

description: KLF4 ChIP-seq

tag: strain

tag: cell type

tag: genotype

tag: chip antibody


title: M-ATAC-WT1


title: E43_S22_L006_R1_001

tag: subject status

value: patient with endometriosis

tag: tissue


title: D7_1248_TGACCA [1248]

tag: subject id

tag: subject group

tag: gender

tag: time point (before or after anthelmintic treatment)

tag: age

tag: trichuris egg count

tag: ascaris egg count

tag: hookworm infection (yes/no)

tag: treatment responder or not

tag: kilocalories

tag: protein

tag: carbohydrate

tag: cholesterol

tag: tryptophan

tag: threonine

tag: isoleucine

tag: leucine

tag: lysine

tag: methionine

tag: cystine

tag: histidine

tag: thiamin

tag: riboflavin

tag: niacin

tag: pyridoxine

tag: folate

tag: magnesium

tag: zinc

tag: copper

tag: manganese

tag: selenium

tag: chromium

tag: molybdenum

tag: fat

tag: fruit

tag: vegetable


title: E42_S21_L006_R1_001

tag: subject status

tag: tissue

value: endometrial samples and lesions


title: non_involved_lung_tissue_patient_83 9983140102_E_Expression

tag: Sex

value: M

tag: age

tag: smoking status

tag: batch


title: non_involved_lung_tissue_patient_82 9983140102_C_Expression


title: non_involved_lung_tissue_patient_81 9983140102_B_Expression


title: non_involved_lung_tissue_patient_79 9983140095_L_Expression


title: non_involved_lung_tissue_patient_80 9983140102_A_Expression


title: E40_S20_L005_R1_001


title: E38_S18_L005_R1_001