title: D2_941_CTTGTA [941]

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: niacin

tag: pyridoxine

tag: folate

tag: cobalamin

tag: biotin

tag: pantothenic

tag: iron

tag: wasting

tag: stunting

tag: underweight


title: E39_S19_L005_R1_001

status: Public on Oct 01 2019

type: SRA

city: Moscow

first: Daniil

last: Nikitin

address: Miklucho-Maklaya

country: Russia

institute: Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry

library_source: transcriptomic

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.

molecule: polyA RNA

organism: Homo sapiens

source_name: tissue sample from patient with endometriosis

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: patient with endometriosis

tag: tissue

value: endometrial samples and lesions


title: D3_953_GTTTCG [953]

city: New York

first: Alice

middle: V

last: Easton

state: NY

address: 430 E 29th St

department: Microbiology

country: USA

institute: NYU Langone

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

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

value: M

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: 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: magnesium

tag: zinc

tag: copper

tag: manganese

tag: selenium

tag: chromium

tag: molybdenum

tag: fat

tag: fruit

tag: vegetable

value: Mild

value: Normal


title: E37_S17_L005_R1_001

tag: subject status

tag: tissue


title: EN2_S4_L001_R1_001

source_name: healthy endometrium

value: healthy control

value: healthy endometrium


title: D12_511_GTTTCG [511]

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

value: Responder

tag: kilocalories

tag: protein

tag: carbohydrate

tag: cholesterol

tag: tryptophan

tag: threonine

tag: isoleucine

tag: leucine

tag: lysine

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

tag: underweight


title: Old 3 Kidney

city: South San Francisco

first: Jacob

middle: Cameron

last: Kimmel

state: CA

address: 1170 Veterans Blvd

department: Computing

institute: Calico Life Sciences, LLC

description:
10X Chromium 3' Single Cell Transcriptome v2 Single cell RNA-sequencing
kidney.h5ad

data_processing:
Basecalling with Illumina bcl2fastq
Read alignment, cell barcode demultiplexing, and UMI demultiplexing using cellranger 3.0.2
Cell barcodes were filtered if they contained less than 1000 UMIs, less than 500 unique genes, or >10% mitochondrial mRNA content.
Samples were joined between animals of the same tissue, discarding any genes not detected across samples
Genome_build: mm10
Supplementary_files_format_and_content: h5ad

organism: Mus musculus

source_name: Old kidney

growth_protocol: Mice were maintained on a 12 hour light/dark cycle with ad libitum feeding.

extract_protocol:
Single cell suspensions for each tissue were prepared after dissecting tissues with a razor blade into small pieces. Kidney and lung were digested in liberase DL while speen further mechanically dissociated with a plunger. Cells suspensions were filtered through 100 um, 70 um, and 40 um filters before treatment with ACK Lysing Buffer. Cells were washed 2 times in cold PBS, counted on a TC20 Cell Counter, and diluted to 1e6 cells / mL. 6,000 cells/sample were then loaded onto each of two lanes in a 10X Chromium v2 Single Cell Transcriptomics microfluidics chip and emulsified.
Libraries were constructed following the 10X Genomics 3' Single Cell transcriptome v2 protocol.

tag: strain

tag: Sex

value: Male

tag: age

value: 93 weeks


title: Old 3 Spleen

description:
10X Chromium 3' Single Cell Transcriptome v2 Single cell RNA-sequencing
spleen.h5ad

source_name: Old spleen


title: Old 2 Spleen

value: 91 weeks


title: D11_1719_CTTGTA [1719]

tag: subject id

tag: subject group

tag: gender

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: 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: magnesium

tag: zinc

tag: copper

tag: manganese

tag: selenium

tag: chromium

tag: molybdenum

tag: fat

tag: fruit

tag: vegetable


title: non_involved_lung_tissue_patient_78 9983140095_K_Expression

type: RNA

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.

label: biotin

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: ever-smoker

tag: batch


title: D6_1097_GTTTCG [1097]

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: 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: histidine

tag: thiamin

tag: riboflavin

tag: niacin

tag: pyridoxine

tag: folate

tag: cobalamin

tag: biotin

tag: pantothenic

tag: iron

tag: wasting

tag: stunting

tag: underweight


title: D10_1612_TGACCA [1612]

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: tyrosine

tag: valine

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: E34_S16_L005_R1_001

tag: subject status

value: patient with endometriosis

tag: tissue

value: endometrial samples and lesions


title: Ad-SREBP2 2 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

molecule: genomic DNA

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.

tag: cell type

value: Umbilical vein endothelial cells

tag: passage


title: Old 3 Lung

description:
10X Chromium 3' Single Cell Transcriptome v2 Single cell RNA-sequencing
lung.h5ad

source_name: Old lung

tag: strain

tag: Sex

tag: age


title: C17 Pre hydrocortisone

city: Jena

first: Amol

last: Kolte

address: Am Klinikum 1

country: Germany

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

description:
C17 Pre hydrocortisone
1705168041_C

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.

source_name: C17 Pre hydrocortisone

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 C17

tag: timepoint

value: Pre

tag: treatment

value: hydrocortisone

tag: acth

value: Non responder

tag: survival (28 days)

value: survived

tag: gender

value: male

tag: pre-treatment ifng il10 ratio

value: high

tag: disease

value: septic shock

value: blood leukocytes


title: Old 2 Lung

value: Male

value: 91 weeks


title: non_involved_lung_tissue_patient_76 9983140095_I_Expression

value: M

tag: smoking status

value: ever-smoker

tag: batch


title: C17 Post(24h) hydrocortisone

description:
C17 Post(24h) hydrocortisone
1705168041_D

source_name: C17 Post(24h) hydrocortisone


title: D1_930_TGACCA [930]

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

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

tag: underweight

value: Significant


title: non_involved_lung_tissue_patient_74 9983140095_G_Expression

tag: Sex

tag: age

tag: smoking status

tag: batch


title: non_involved_lung_tissue_patient_73 9983140095_F_Expression


title: Old 2 Kidney

tag: strain


title: C9_351_GTGGCC [351]

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

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: folate

tag: cobalamin

tag: biotin

tag: pantothenic

tag: iron

tag: magnesium

tag: zinc


title: E31_S14_L005_R1_001

tag: subject status

value: patient with endometriosis

tag: tissue

value: endometrial samples and lesions


title: E30_S13_L005_R1_001


title: Old 1 Spleen

tag: strain

tag: Sex

tag: age

value: 88 weeks


title: Old 1 Lung


title: non_involved_lung_tissue_patient_75 9983140095_H_Expression

tag: smoking status

tag: batch


title: C7_220_TTAGGC [220]

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: copper

tag: manganese

tag: selenium

tag: chromium

tag: molybdenum

tag: fat

tag: fruit

tag: vegetable

value: Normal

tag: wasting

tag: stunting

tag: underweight


title: C8_221_GGCTAC [221]

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: niacin

tag: pyridoxine

tag: folate

tag: cobalamin

tag: biotin

tag: pantothenic

tag: iron

tag: magnesium

tag: zinc


title: E33_S15_L005_R1_001

tag: subject status

tag: tissue


title: non_involved_lung_tissue_patient_72 9983140095_E_Expression

tag: Sex

tag: age

tag: smoking status

tag: batch


title: E29_S12_L005_R1_001


title: C6_218_GTGGCC [218]

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: tyrosine

tag: valine

tag: histidine

tag: thiamin

tag: riboflavin

tag: copper

tag: manganese

tag: selenium

tag: chromium

tag: molybdenum

tag: fat

tag: fruit

tag: vegetable

tag: wasting

tag: stunting

tag: underweight


title: non_involved_lung_tissue_patient_71 9983140095_D_Expression

tag: Sex

tag: age

tag: smoking status

tag: batch


title: non_involved_lung_tissue_patient_70 9983140095_C_Expression


title: E28_S11_L005_R1_001

tag: subject status

tag: tissue


title: Young 4 Spleen

source_name: Young spleen

tag: strain

value: 34 weeks


title: E3_S20_L006_R1_001


title: C5_181_GGCTAC [181]

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: niacin

tag: pyridoxine

tag: folate

tag: cobalamin

tag: biotin

tag: pantothenic

tag: iron

tag: magnesium

tag: zinc

tag: copper

tag: manganese

value: Overweight

value: Obese class I


title: non_involved_lung_tissue_patient_77 9983140095_J_Expression

tag: Sex

tag: age

tag: smoking status

tag: batch


title: C4_166_TTAGGC [166]

tag: subject id

tag: subject group

tag: gender

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

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: selenium

tag: chromium

tag: molybdenum

tag: fat

tag: fruit

tag: vegetable

tag: wasting

tag: stunting

tag: underweight


title: E27_S10_L004_R1_001

tag: subject status

tag: tissue


title: Old 1 Kidney

tag: strain

tag: Sex

value: Male

tag: age


title: Young 4 Kidney

source_name: Young kidney


title: non_involved_lung_tissue_patient_68 9983140095_A_Expression

tag: smoking status

value: ever-smoker

tag: batch


title: E26_S9_L004_R1_001


title: non_involved_lung_tissue_patient_67 9983140094_L_Expression

value: F

value: never-smoker


title: E23_S8_L004_R1_001


title: Young 3 Spleen


title: C3_135_GTGGCC [135]

tag: subject id

tag: subject group

value: Orang Asli (indigenous) study village resident

tag: gender

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

value: Underweight

value: Severe thinness


title: E22_S7_L004_R1_001

tag: subject status

tag: tissue


title: non_involved_lung_tissue_patient_66 9983140094_K_Expression

tag: Sex

tag: age

tag: smoking status

tag: batch


title: non_involved_lung_tissue_patient_65 9983140094_J_Expression


title: Young 3 Lung

source_name: Young lung

tag: strain


title: non_involved_lung_tissue_patient_69 9983140095_B_Expression


title: C12_762_GTGGCC [762]

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

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: selenium

tag: chromium

tag: molybdenum

tag: fat

tag: fruit

tag: vegetable

tag: wasting

tag: stunting

value: Mild

tag: underweight


title: C2_119_GGCTAC [119]

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: folate

tag: cobalamin

tag: biotin

tag: pantothenic

tag: iron

tag: magnesium

tag: zinc

tag: copper

tag: manganese

value: Mild thinness


title: E21_S6_L004_R1_001

tag: subject status

value: patient with endometriosis

tag: tissue

value: endometrial samples and lesions


title: C11_634_GGCTAC [634]

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: tyrosine

tag: valine

tag: histidine

tag: thiamin

tag: riboflavin

tag: niacin

tag: pyridoxine

tag: selenium

tag: chromium

tag: molybdenum

tag: fat

tag: fruit

tag: vegetable

tag: wasting

tag: stunting

value: Normal

tag: underweight


title: Young 3 Kidney

tag: strain

tag: Sex

tag: age

value: 34 weeks


title: Young 4 Lung

value: Male


title: non_involved_lung_tissue_patient_64 9983140094_I_Expression

value: M

tag: smoking status

value: ever-smoker

tag: batch


title: E20_S5_L004_R1_001

tag: subject status

tag: tissue


title: Young 2 Spleen

value: 31 weeks


title: E2_S2_L002_R1_001


title: C10_442_TTAGGC [442]

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: cobalamin

tag: biotin

tag: pantothenic

tag: iron

tag: magnesium

tag: zinc

tag: copper

tag: manganese


title: C1_102_TTAGGC [102]

tag: subject id

tag: subject group

tag: gender

value: F

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: selenium

tag: chromium

tag: molybdenum

tag: fat

tag: fruit

tag: vegetable

value: Overweight

value: Obese class I

tag: wasting

tag: stunting

tag: underweight


title: Young 2 Lung

tag: strain

tag: Sex

tag: age


title: Young 2 Kidney


title: Young 1 Spleen

value: 29 weeks


title: E19_S4_L004_R1_001

tag: subject status

tag: tissue


title: B9_52_GTGAAA [52]

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

value: blood

tag: kilocalories

tag: protein

tag: carbohydrate

tag: cholesterol

tag: tryptophan

tag: threonine

tag: isoleucine

tag: leucine

tag: lysine

tag: methionine

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


title: non_involved_lung_tissue_patient_61 9983140094_E_Expression

tag: Sex

tag: age

tag: smoking status

tag: batch


title: E15_S2_L004_R1_001

tag: subject status

tag: tissue


title: Young 1 Lung

tag: strain


title: B3_1892AF_GTGAAA [1892AF]

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: 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: selenium

tag: chromium

tag: molybdenum

tag: fat

tag: fruit

tag: vegetable

tag: wasting

tag: stunting

value: Mild

tag: underweight


title: non_involved_lung_tissue_patient_63 9983140094_H_Expression

tag: Sex

tag: age

tag: smoking status

tag: batch


title: E14_S1_L004_R1_001

tag: subject status

value: patient with endometriosis

tag: tissue

value: endometrial samples and lesions


title: Young 1 Kidney

tag: strain


title: non_involved_lung_tissue_patient_59 9983140094_C_Expression


title: non_involved_lung_tissue_patient_62 9983140094_G_Expression


title: B12_101_GTGAAA [101]

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

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: pyridoxine

tag: folate

tag: cobalamin

tag: biotin

tag: pantothenic

tag: iron

tag: magnesium

tag: zinc

tag: copper

tag: manganese

value: Normal


title: non_involved_lung_tissue_patient_60 9983140094_D_Expression

tag: Sex

tag: age

tag: smoking status

value: never-smoker

tag: batch


title: non_involved_lung_tissue_patient_58 9983140094_B_Expression

value: M

value: ever-smoker


title: B11_98_TAGCTT [98]

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: 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: selenium

tag: chromium

tag: molybdenum

tag: fat

tag: fruit

tag: vegetable

tag: wasting

tag: stunting

tag: underweight


title: E12_S21_R1_001

tag: subject status

tag: tissue


title: E11_S8_L008_R1_001


title: E16_S3_L004_R1_001


title: B10_88_CGATGT [88]

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: riboflavin

tag: niacin

tag: pyridoxine

tag: folate

tag: cobalamin

tag: biotin

tag: pantothenic

tag: iron

tag: magnesium

tag: zinc

tag: copper

tag: manganese

value: Significant


title: B8_37_TAGCTT [37]

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: phenylalanine

tag: tyrosine

tag: valine

tag: histidine

tag: thiamin

tag: selenium

tag: chromium

tag: molybdenum

tag: fat

tag: fruit

tag: vegetable

tag: wasting

tag: stunting

tag: underweight


title: CTCF-ChIP-rep2

first: Priscillia

last: Lhoumaud

address: 550 first avenue Smilow 307

department: Pathology

institute: NYU Langone Health

description: CTCF ChIP-seq with Nextera adaptors

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 Macs/2.1.0 and narrow peaks were considered for further analysis.
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 CTCF ChIP-seq (converted or not), Lysates were clarified from sonicated nuclei and CTCF-bound chromatin was isolated with CTCF antibody.
For ATAC-seq and CTCF 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

tag: cell type

value: emrbyonic stem cells

tag: treatment

value: Nextera adaptors

tag: chip antibody

value: CTCF (Millipore 07-729)


title: CTCF-ChIP-rep1

description: CTCF ChIP-seq with Nextera adaptors


title: CTCF-M-ChIP-NC-rep1

description: CTCF ChIP-seq with methylated adaptors not converted

value: methylated adaptors not converted


title: non_involved_lung_tissue_patient_56 9983140075_L_Expression

tag: Sex

value: F

tag: age

tag: smoking status

tag: batch


title: non_involved_lung_tissue_patient_57 9983140094_A_Expression


title: non_involved_lung_tissue_patient_55 9983140075_K_Expression


title: E1_S2_L002_R1_001

tag: subject status

tag: tissue


title: CTCF-M-ChIP-rep2

description: CTCF ChIP-seq with methylated adaptors and bisulfite converted


title: non_involved_lung_tissue_patient_54 9983140075_J_Expression


title: C2_REST_sh-PA_PB-Day24_3

city: Lund

first: Johan

last: Jakobsson

address: Solvegatan 17

country: Sweden

institute: Lund University

data_processing:
Raw basecalls were converted to Fastq using bcl2fastq program provided by Illumina.
Reads were aligned to genome using STAR mapper.
mRNA expression was quantified using the subread package FeatureCounts quantifying to NCBI annotation (GRCh38).
Abundance estiamtes were combined using tximport and normalized using edgeR/limma
Genome_build: GRCh38
Supplementary_files_format_and_content: TSV of raw and normalised counts for all genes

extract_protocol:
RNA was extracted using miRNAeasy mini kit (Qiagen) with DNase treatment
cDNA libraries were prepared using the KAPA Stranded mRNA-Seq Kit from KAPAbiosystems.
Single-end 50 base-pair RNA sequencing sample reads were generated in one batch. Sequencing was performed using Illumina HiSeq3000 sequencer.

value: induced human neurons from fibroblasts

value: Control


title: non_involved_lung_tissue_patient_52 9983140075_H_Expression


title: C2_REST_sh-PA_PB-Day24_2


title: 7_S7_ensembl [445]

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

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: Mild


title: E10_S22_L006_R1_001

tag: subject status

value: patient with endometriosis

tag: tissue

value: endometrial samples and lesions


title: CTCF-M-ChIP-rep1

tag: strain

tag: cell type

tag: treatment

value: methylated adaptors and bisulfite converted

tag: chip antibody


title: C2_REST_sh-PA_PB-Day24_1


title: ATAC-rep2

description: ATAC-seq with Nextera adaptors


title: 5_S5_ensembl [780AF]

tag: subject id

tag: subject group

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

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

tag: wasting

tag: stunting

tag: underweight

value: Normal


title: C2_REST_sh-PBmPA-Day24_3

tag: tissue

tag: treatment

value: Treated with miRNA


title: ATAC-rep1

description: ATAC-seq with Nextera adaptors

tag: strain

tag: cell type


title: M-ATAC-NC-rep2

description: ATAC-seq with methylated adaptors not converted


title: 4_S4_ensembl [463]

tag: subject id

tag: subject group

value: Orang Asli (indigenous) study village resident

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: 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: biotin

tag: pantothenic

tag: iron

tag: magnesium

tag: zinc

tag: copper

tag: manganese

tag: selenium

tag: chromium

tag: molybdenum


title: CTCF-M-ChIP-NC-rep2

tag: strain

tag: cell type

value: emrbyonic stem cells

tag: treatment

tag: chip antibody

value: CTCF (Millipore 07-729)


title: 9_S9_ensembl [1533]

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: thiamin

tag: riboflavin

tag: niacin

tag: pyridoxine

tag: folate

tag: cobalamin

tag: fat

tag: fruit

tag: vegetable

tag: wasting

tag: stunting

tag: underweight


title: non_involved_lung_tissue_patient_53 9983140075_I_Expression

tag: Sex

tag: age

tag: smoking status

value: ever-smoker

tag: batch


title: non_involved_lung_tissue_patient_50 9983140075_F_Expression

value: F


title: non_involved_lung_tissue_patient_49 9983140075_E_Expression


title: 3_S3_ensembl [1892]

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: 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: biotin

tag: pantothenic

tag: iron

tag: magnesium

tag: zinc

tag: copper

tag: manganese

tag: selenium

tag: chromium

tag: molybdenum


title: M-ATAC-NC-rep1

tag: strain

tag: cell type

tag: treatment

value: methylated adaptors not converted


title: C2_REST_sh-PBmPA-Day24_1

tag: tissue

value: induced human neurons from fibroblasts


title: 8_S8_ensembl [1998AF]

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: tyrosine

tag: thiamin

tag: riboflavin

tag: niacin

tag: pyridoxine

tag: folate

tag: cobalamin

tag: fat

tag: fruit

tag: vegetable

tag: wasting

tag: stunting

tag: underweight


title: 2_S2_ensembl [445AF]

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: tissue

tag: kilocalories

tag: protein

tag: carbohydrate

tag: cholesterol

tag: tryptophan

tag: threonine

tag: isoleucine

tag: leucine

tag: lysine

tag: valine

tag: histidine

tag: biotin

tag: pantothenic

tag: iron

tag: magnesium

tag: zinc

tag: copper

tag: manganese

tag: selenium

tag: chromium

tag: molybdenum

value: Mild


title: non_involved_lung_tissue_patient_51 9983140075_G_Expression

tag: Sex

tag: age

tag: smoking status

value: never-smoker

tag: batch


title: non_involved_lung_tissue_patient_47 9983140075_C_Expression


title: 15_S15_ensembl [1383AF]

tag: subject id

tag: subject group

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

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: thiamin

tag: riboflavin

tag: niacin

tag: pyridoxine

tag: folate

tag: cobalamin

tag: fat

tag: fruit

tag: vegetable

value: Overweight

value: Obese class I

tag: wasting

tag: stunting

tag: underweight


title: lncRNA-AK096729 siRNA_T3

city: Shanghai

first: Haoyan

last: Chen

state: Shanghai

address: 145 Shandong Road

country: China

institute: Renji Hospital

data_processing:
Sequence reads were mapped to the human genome (hg19) using TopHat v2.0.11 with the default options with a TopHat transcript index built from Ensembl_GRCh37.
Count files of the aligned sequencing reads were generated by the htseq-count script from the Python package HTSeq with union mode, using the GTF annotation file
Genome_build: hg19
Supplementary_files_format_and_content: count file

source_name: SW480 cells

growth_protocol: The human SW480 colorectal cancer cell were cultured in RPMI-1640 medium (Gibco, USA) supplemented with 10 % fetal bovine serum at 37 °C in an atmosphere of 5 % CO2.

extract_protocol:
total RNA of SW480 cells with different treatment was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The human lncRNA-AK096729 siRNA were introduced into the SW480 colorectal cells, while nonspecific siRNA was used as negative controls.  lncRNA GenBank ID is AK096729

tag: cell line

tag: cell type

value: human colorectal cancer cells

tag: passage

tag: genotype

value: lncRNA-AK096729 siRNA


title: 6_S6_ensembl [1259]

tag: subject id

tag: subject group

value: Orang Asli (indigenous) study village resident

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: histidine

tag: biotin

tag: pantothenic

tag: iron

tag: magnesium

tag: zinc

tag: copper

tag: manganese

tag: selenium

tag: chromium

tag: molybdenum

value: Normal


title: M-ATAC-rep3

description: ATAC-seq with methylated adaptors and bisulfite converted

tag: strain

tag: cell type

value: emrbyonic stem cells

tag: treatment


title: M-ATAC-rep4

value: methylated adaptors and bisulfite converted


title: lncRNA-AK096729 siRNA_T2

tag: cell line

tag: passage

tag: genotype


title: 13_S13_ensembl [1998]

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: folate

tag: cobalamin

tag: fat

tag: fruit

tag: vegetable

tag: wasting

tag: stunting

tag: underweight


title: M-ATAC-rep2

tag: strain

tag: cell type

tag: treatment


title: 14_S14_ensembl [1383]

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: biotin

tag: pantothenic

tag: iron

tag: magnesium

tag: zinc

tag: copper

tag: manganese

tag: selenium

tag: chromium

tag: molybdenum


title: lncRNA-AK096729 siRNA_T1

tag: cell line

tag: cell type

tag: passage

tag: genotype


title: Control siRNA_N3

value: Control siRNA


title: M-ATAC-rep1

tag: strain

tag: treatment


title: Control siRNA_N2


title: 12_S12_ensembl [780]

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

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: fat

tag: fruit

tag: vegetable

tag: wasting

tag: stunting

value: Significant

tag: underweight


title: 11_S11_ensembl [145]

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: biotin

tag: pantothenic

tag: iron

tag: magnesium

tag: zinc

tag: copper

tag: manganese

tag: selenium

tag: chromium

tag: molybdenum


title: PAX8 3

city: Chicago

first: Matthew

middle: J.

last: Schipma

state: IL

address: 750 N. Lake Shore Drive

department: Biochemistry and Molecular Genetics

institute: Northwestern University

data_processing:
Adapters were trimmed from reads using cutadapt version 1.13
Trimmed reads were aligned to mm10 using STAR version 020201
Gene counting was performed using htseq-count version 0.6.1p1
Differential expression was performed using DESeq2
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited file with read counts per gene

source_name: Murine ovarian surface epithelial cells

growth_protocol: MOSE-NEO and MOSE-PAX8 cells were maintained as stable cell lines by selection with G418 (0.05mg/mL).

extract_protocol:
Total RNA was extracted using Trizol reagent, treated with DNase I, and purified with Qiagen RNeasy Mini cleanup.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Not applicable.

tag: cell line


title: PAX8 2


title: Control siRNA_N1

tag: cell type

tag: passage

tag: genotype


title: 10_S10_ensembl [96]

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: 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

tag: wasting

tag: stunting

tag: underweight

value: Mild


title: PAX8 1

tag: cell line


title: non_involved_lung_tissue_patient_48 9983140075_D_Expression

tag: Sex

tag: age

tag: smoking status

value: ever-smoker

tag: batch


title: 1_S1_ensembl [96AF]

tag: subject id

tag: subject group

tag: gender

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

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: biotin

tag: pantothenic

tag: iron

tag: magnesium

tag: zinc

tag: copper

tag: manganese

tag: selenium

tag: chromium

tag: molybdenum


title: non_involved_lung_tissue_patient_44 9983140068_L_Expression

tag: Sex

tag: age

tag: smoking status

tag: batch


title: non_involved_lung_tissue_patient_42 9983140068_J_Expression


title: non_involved_lung_tissue_patient_46 9983140075_B_Expression


title: NEO 3

tag: cell line

value: MOSE-NEO


title: non_involved_lung_tissue_patient_41 9983140068_H_Expression


title: non_involved_lung_tissue_patient_43 9983140068_K_Expression


title: NEO 2


title: NEO 1


title: GD2-28z CAR T cells

city: Stanford

first: Zinaida

last: Good

address: 265 Campus Drive, Room G2105

department: Stanford Cancer Institute, Department of Biomedical Data Science

institute: Stanford University School of Medicine

data_processing:
Cell Ranger pipeline v1.2.0
We performed read-depth normalization using Cell Ranger R Kit software v2.0.0 (10X Genomics) to remove batch effects, and then combined individual samples into 1 file.
The Cell Ranger cell-gene UMI count matrices were processed using Cell Ranger R Kit software v2.0.0. Briefly, we first selected genes expressed in ≥1 cell (12,491 genes). For downstream analysis, we selected T cells (CD3D+), followed by either CD4 T cells (CD4+ CD8A-) or CD8 T cells (CD4- CD8A+). We performed differential expression analysis on UMI count data using DESeq2 1.22.2 pipleline. We next normalized UMI count sums for each cell to median and log-transformed cell-gene matrix for downstream applications, including visualizing the data and transcription factor network anaysis.
Genome_build: hg19
Supplementary_files_format_and_content: An h5 file containing Cell Ranger pipeline output for filtered cell-gene data: columns contain non-batch-normalized UMI counts across cells (804 CD19-28z cells or 726 GD2-28z cells); rows contain genes.
Supplementary_files_format_and_content: An HTML file containing Cell Ranger alignment summary for CD19-28z and GD2-28z CAR T cells.

source_name: T cells from a healthy donor engineered to express CAR

extract_protocol:
Droplet-based single-cell RNA-sequencing on 10X Genomics Chromium platform.
10X Genomics Single Cell 3' v2 Kit
Data is paired-end, but read1 (26bp) only contains cell barcode and UMI data (sample index is 8 bp), and only read2 (98bp) contains transcript data.

tag: car construct

tag: sample type

value: Human (healthy donor)


title: T,biological rep3

city: Wuhan

first: Di

last: Liu

state: Hubei

address: 1277 Jiefang Road

department: Department of Urology

institute: Union Hospital

description:
A1090
miRNA expression data from piperlongumine treated bladder cancer T24 cells

hyb_protocol: 900 ng of biotin labeled RNA was hybridized to Affymetrix GeneChip® miRNA 4.0 Arrays at 48 °C and 60 rpm for 16-18 h.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G.

data_processing: Data were collected using Affymetrix Command Console Software.

source_name: bladder cancer T24 cells treated with piperlongumine

label_protocol: 1000 ng of total RNA was labeled using Affymetrix Flashtag Biotin HSR RNA Labeling kit (P/N 901910, Affymetrix, Santa Clara, CA, USA) according to the manufacturer's instructions.

growth_protocol: T24 cells in logarithmic growth phase were seeded in 60 mm dishes at a density of 4 × 104 cell/cm2 and incubated overnight.

extract_protocol: After drug treatment, total RNA was extracted from bladder cancer cell using Trizol reagent (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s protocol.

treatment_protocol: T24 cells was subsequently treated with PL 20 μM or 0 μM (DMSO control)

tag: cell type

value: bladder cancer cell line

tag: treated with

value: Piperlongumine (PL)


title: non_involved_lung_tissue_patient_39 9983140068_E_Expression

value: never-smoker


title: CD19-28z CAR T cells


title: non_involved_lung_tissue_patient_45 9983140075_A_Expression


title: non_involved_lung_tissue_patient_40 9983140068_F_Expression


title: non_involved_lung_tissue_patient_38 9983140068_D_Expression


title: STAT5B-ko, replicate 3

city: Vienna

first: Veronika

last: Sexl

address: Veterinaerplatz 1

department: Pharmacology / Toxikology

country: Austria

institute: University of Veterinary Medicine Vienna

description:
expression profile of BCR/ABLp185+ bone marrow wt cell lines, replicate 3
STAT5B-ko-3

data_processing:
Alignment to genome version GRCm38 using STAR
Adapter trimming and removing of low quality bases was performed using Trimmomatic
Counting of reads was done using featureCounts
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: raw count file (tab delimited)

source_name: BCR/ABLp185+ bone marrow STAT5B-ko cell lines

growth_protocol: Cells were cultured in RPMI incl. 10% FCS,50 μmol/l 2-mercaptoethanol, 100 u/ml penicillin and 100 μg/ml streptomycin

extract_protocol:
QIAGEN RNeasy extraction kit
RNA-seq: SENSE mRNA-Seq Library Prep kit, 50 bp single-end

tag: background strain

tag: tissue

value: bone marrow

value: BCR/ABLp185+ transformed bone marrow cell lines

tag: genotype


title: JUN-overexpressing Her2-BBz CAR T cells

data_processing:
Cell Ranger pipeline v3.0.2, including batch effect removal that includes combining individual samples into 1 file with read-depth normalization (10X Genomics aggr pipleline).
The Cell Ranger cell-gene UMI count matrix was processed using Seurat software. Briefly, we first selected genes expressed in ≥50 cells (12,491 genes) and cells with >500 genes and <10% mitochondrial gene expression (to remove apoptotic cells). To remove cell doublets, we excluded cells with >20,000 UMI counts (16,161 cells). UMI counts were then normalized using the SCTransform pipeline. Next, we selected T cells (99.3%, 16,046 cells) based on CD3 gene expression (CD3G, CD3D, CD3E, or CD247). Finally, we selected CD4 T cells (8.3%; CD4+ CD8A-) and CD8 T cells (70.3%; CD4- CD8A+). For downstream analysis, we performed cell cycle analysis, PCA and UMAP embedding, and cell clustering.
Genome_build: GRCh38
Supplementary_files_format_and_content: An h5 file containing Cell Ranger pipeline output for filtered cell-gene data: columns contain batch-normalized UMI counts across cells (10,985 JUN-overexpressing Her2-BBz cells, followed by 6,946 control Her2-BBz cells); rows contain genes.
Supplementary_files_format_and_content: An RDS file containing Seurat object with SCTransform-normalized data for all filtered cells (mx-norm.rds), all T cells (T.rds), CD4+ T cells (CD4T.rds), or CD8+ T cells (CD8T.rds).
Supplementary_files_format_and_content: An HTML file containing Cell Ranger alignment summary for Control (Control-Her2-BBz-summary-HGWGGBGX7.html) and JUN-overexpressing (JUN-Her2-BBz-summary-HGWGGBGX7.html) Her2-BBz CAR T cells; an HTML file containing Cell Ranger aggregation statistics for both samples (JUN-Her2-BBz-and-Control-Her2-BBz-aggr_summary.html).
Supplementary_files_format_and_content: A TXT file containing genes that were used to define S and G2/M cell cycle stages (from Tirosh et al. 2016).

source_name: Live human CD45+ tumor-infiltrating lymphocytes

extract_protocol:
Droplet-based single-cell RNA-sequencing on 10X Genomics Chromium platform.
10X Genomics Single Cell 3' v2 Kit
*Data is paired-end, but read1 (26bp) only contains cell barcode and UMI data (sample index is 8 bp), and only read2 (98bp) contains transcript data.

tag: disease state

value: healthy donor


title: Control Her2-BBz CAR T cells

value: Live human CD45+ tumor-infiltrating lymphocytes


title: STAT5B-ko, replicate 1

description:
expression profile of BCR/ABLp185+ bone marrow wt cell lines, replicate 1
STAT5B-ko-1


title: STAT5B-ko, replicate 2

description:
expression profile of BCR/ABLp185+ bone marrow wt cell lines, replicate 2
STAT5B-ko-2


title: T,biological rep2

description:
A1089
miRNA expression data from piperlongumine treated bladder cancer T24 cells


title: C,biological rep2

description:
A1086
miRNA expression data from DMSO treated bladder cancer T24 cells

source_name: bladder cancer T24 cells treated with DMSO

value: DMSO


title: T,biological rep1

description:
A1088
miRNA expression data from piperlongumine treated bladder cancer T24 cells


title: non_involved_lung_tissue_patient_37 9983140068_C_Expression

source_name: Non-involved (apparently normal) lung parenchyma


title: non_involved_lung_tissue_patient_35 9983140068_A_Expression

value: F


title: non_involved_lung_tissue_patient_36 9983140068_B_Expression


title: non_involved_lung_tissue_patient_34 9983140064_L_Expression


title: tRNA-HySeq, paf1∆1

city: New Delhi

first: G Aneeshkumar

last: Arimbasseri

state: Delhi

address: Aruna Asaf Ali Marg

department: Molecular Genetics Laboratory

country: India

institute: National Institute of Immunology

description:
Size selected tRNA
tRNA was hydroyzed and the fragments ranging 19-35 nt were selected for sequencing

data_processing:
Data was analyzed using Galaxy. Adapter sequences were clipped using NGS: QC and manipulation/Clip, specifying a minimum length of 25 nt, and enter a custom adapter sequence 5′-CTGTAGGCACCATCAAT-3′
Trimmed the adapter sequence using NGS: QC and Manipulation/Trim sequences
Mapped the sequences to a custom genome file consisting of all unique mature tRNA sequences in S. cerevisiae using Bowtie for illumina tool in Galaxy.
Count table was prepared using Idxstats in Samtools.
Genome_build: Custom genome file including all unique mature tRNA sequences in S. cerevisiae.
Supplementary_files_format_and_content: Tabular format with raw counts for each of the tRNA sequences.

organism: Saccharomyces cerevisiae

source_name: DAS516, Log-phase cells in the 1X YEP with 2% dextrose

growth_protocol: Different yeast strains were grown up to A600: 0.6-0.8 in YEP medium at 30°C

extract_protocol:
Total RNA was isolated using Trizol method, followed by gel purification of tRNAs by size.
Samples were processed using the protocol described in Ingolia, N.T., Brar, G.A., Rouskin, S., Mcgeachy, A.M., and Weissman, J.S. (2012). The ribosome profiling strategy for monitoring translation in vivo by deep sequencing of ribosome-protected mRNA fragments. Nat. Protoc. 7, 1534–1550.

tag: genotype/variation

tag: strain


title: BGC823_miR-194_mimics

city: Shiyan

first: Qin

last: Shanshan

address: Renmin Road 30, Maojian District

institute: Institute of Basic Medical Sciences, School of Basic Medical Sciences, Hubei University of Medicine

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing poly-N and low quality reads from raw data.
Paired-end clean reads were aligned to the reference genome using HISAT2 v2.1.0 with default parameters.
HTSeq v0.6.1 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text file include count and FPKM values for each Sample

source_name: gastric cancer cell

growth_protocol: The human gastric cancer cell line BGC823 and SGC7901 were purchased from the Shanghai Cell Bank of Chinese Academy of Sciences (Shanghai, China). The two gastric cancer cell lines were cultured in DMEM medium containing 10% fetal bovine serum (FBS), 100 U/mL penicillin, 100 U/mL streptomycin and 0.03% glutamine at 37 oC in 5% CO2.

extract_protocol:
Gastric cancer cells were grown in 6-well plates and transfected with NC siRNAs and miR-194-5p mimics. After 48 hours, remove the medium and directly add 800μL Trizol into the 6-well plate to harvest samples. Total RNA was extracted using Trizol reagent (Invitrogen, USA) according to the manufacturer’s instructions. The RNA purity and concentration was checked using the NanoPhotometer spectrophotometer (IMPLEN, CA, USA).
A total amount of 1.5 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext Ultra RNA Library Prep Kit for Illumina (NEB, USA) following manufacturer's recommendations and index codes were added to attribute sequences to each sample.

treatment_protocol: Two different GC cell lines were seeded into 6-well plates and grown overnight. The next day, when the cell plating density reached 20%-30%, GC cells were transfected with NC siRNAs and miR-194-5p mimics (final concentration, 50 nM) by Lipofectamine 2000 (Invitrogen) according to the manufacturer’s instructions. At 48 h post-transfection, cells were harvested for RNA sequencing.

value: gastric cancer cell

tag: transfection

value: miR-194-5p mimics


title: tRNA-HySeq, paf1∆2


title: BGC823_NC

value: negative control siRNAs


title: STAT5A-ko, replicate 2

description:
expression profile of BCR/ABLp185+ bone marrow wt cell lines, replicate 2
STAT5A-ko-2

source_name: BCR/ABLp185+ bone marrow STAT5A-ko cell lines


title: STAT5A-ko, replicate 3

description:
expression profile of BCR/ABLp185+ bone marrow wt cell lines, replicate 3
STAT5A-ko-3


title: non_involved_lung_tissue_patient_32 9983140064_J_Expression

value: M


title: non_involved_lung_tissue_patient_33 9983140064_K_Expression

value: ever-smoker


title: SGC7901_NC


title: tRNA-HySeq, WT2

source_name: DAS217, Log-phase cells in the 1X YEP with 2% dextrose

value: Wild type


title: C,biological rep1

description:
A1085
miRNA expression data from DMSO treated bladder cancer T24 cells


title: SGC7901_miR-194_mimics


title: tRNA-HySeq, rtf1∆2

source_name: DAS549, Log-phase cells in the 1X YEP with 2% dextrose


title: tRNA-HySeq, rtf1∆1


title: C,biological rep3

description:
A1087
miRNA expression data from DMSO treated bladder cancer T24 cells


title: wild-type, replicate 3

description:
expression profile of BCR/ABLp185+ bone marrow wt cell lines, replicate 3
wt-3

source_name: BCR/ABLp185+ bone marrow wt cell lines

value: wt


title: non_involved_lung_tissue_patient_31 9983140064_I_Expression


title: non_involved_lung_tissue_patient_28 9983140064_F_Expression


title: non_involved_lung_tissue_patient_29 9983140064_G_Expression


title: RN16_G_P58

city: Cambridge

first: Ralitsa

middle: Radostinova

last: Madsen

address: Addenbrookes Treatment Centre, Keith Day Road

department: Metabolic Research Laboratories, Clinical Biochemistry

country: United Kingdom

institute: University of Cambridge

data_processing:
The raw reads were mapped to the human genome build GRCh38.
Gene level counts were performed using Spliced Transcripts Alignment to a Reference (STAR) v2.5.
All subsequent data analyses steps were performed in R using RStudio. Briefly, the edgeR package was used to calculate counts per million (CPM) for each gene and sample. Genes were included for further analysis if expressed at CPM > 0.3 in at least 1/3 of all samples. Sample library size was normalised by the TMM (trimmed mean of M values) method (Robinson and Oshlack, 2010 Genome Biology), followed by differential gene expression analysis with voom(), lmFit() and eBayes() according to the limma analysis pipeline described by Ritchie et al. (2015 Nucleic Acid Research).
Genome_build: GRCh38
Supplementary_files_format_and_content: Each sample is associated with 6 fastq files corresponding to paired-end sequencing across 3 sequencing lanes (s_1, s_2 and s_3 in the file names; r_1 and r_2 in the file names indicate read 1 and read 2). The alignment output results  are provided as a single processed file (raw_gene_count.tsv) containing the counts for all samples.

source_name: Induced pluripotent stem cell

growth_protocol: The cells were cultured in 6-well plates coated with hESC-qualified Geltrex (Thermo Fisher Scien- tific # A1413302) diluted 1:100 in DMEM/F12 (Sigma # D6421). Cells were maintained in Essential 8 Flex medium (Thermo Fisher Scientific # A2858501) and passaged every four days when 80-90 % confluent, with split ratios ranging from 1:10 to 1:15. ReLeSR (Stem Cell Technologies # 5872) was used to dissociate the cells non- enzymatically, and 1X RevitaCell (Thermo Fisher Scientific # A2644501) was included during the first 24 hours to promote survival.

extract_protocol:
Cells were washed in DPBS and lysed with QIAzol. The RNA was extracted with the Direct-zol RNA Miniprep Kit (ZymoResearch # R2051) according to the manufacturer's instructions (eluted in 50 μl nuclease-free water). The quality of the RNA was confirmed on an Agilent 2100 Bioanalyzer using the RNA 6000 Nano Kit (Agilent # 5067-1511) according to the manufacturer’s instructions, with all samples pre-diluted to 300 ng/μl in nuclease-free water. All samples had high RNA Integrity Number (RIN) scores of 9.9-10.
A total of 1 μg RNA per sample was used as input to prepare indexed, 300-bp-long paired-end mRNA libraries with Illumina's TruSeq Stranded mRNA Library Prep Kit (# 20020594) and TruSeq RNA Single Indexes Set A (# 20020492) according to the manufacturer's instructions. The integrity and quantity of the libraries were determined on the Agilent Bioanalyzer using the DNA 12000 Kit (Agilent # 5067-1508).

treatment_protocol: The cells were replenished with fresh Essential 8 Flex medium 3 hours before collection for RNA extraction.

tag: passage


title: RN18_F_P56


title: RN17_F_P56


title: RN15_G_P57


title: non_involved_lung_tissue_patient_30 9983140064_H_Expression

tag: Sex


title: wild-type, replicate 2

description:
expression profile of BCR/ABLp185+ bone marrow wt cell lines, replicate 2
wt-2


title: Phf21b_ChIP_mESC_pDox_Replicate1

city: Mainz

first: Hyobin

last: Jeong

state: Germany

address: Richard shirrmann Str 12.

institute: IMB

description: ChIP-seq in mESC

data_processing:
For the ChIP-Seq samples, sequenced reads were aligned to the mouse reference genome (mm9) using Bowtie v0.12.9 and each read was aligned to maximally one position in the genome. SAMTOOLS v0.1.19 was used to convert the SAM file into BAM format and to sort and index the BAM file. Sorted BAM files were used for peak calling using MACS2 v2.0.10 with default parameters. For the UCSC genome browser track visualization, WIG files were obtained using the QuasR package .
Genome_build: mm9
Supplementary_files_format_and_content: For the RNA-Seq samples, tab-delimited text files include DESeq normalized read counts for each Sample. For the ChIP-Seq and ATAC-Seq samples, wig files for UCSC genome browser track were provided.

growth_protocol:
For ES cell experiments, ES159 cells on feeders were splitted every 2 days onto tissue culture dishes coated with 0.2% gelatin, and the media was changed daily. All ES cell experiments were performed at feeder-free five stage. In vitro neuronal differentiation was performed as described by Bibel et al (2004, 2007) where ES cells were directly plated on PORN/Laminin-coated tissue culture dishes and cultivated for 2 days in N2 media followed by complete media for induced neuron (iTN) formation.
Murine Neuro2a cells (N2a cells)  were cultured at 37°C in 7% CO2 and 88% relative humidity in 10 ml of DMEM supplemented with 10% fetal calf serum, 1× NEAA and 2 mM L-glutamine. Neuronal differentiation in N2A cells was induced by adding 20 μM retinoic acid in DMEM supplemented with 2% FBS, 1% Glutamine and 1% NEAA.  For ES cell experiments, ES159 cells on feeders were splitted every 2 days onto tissue culture dishes coated with 0.2% gelatin, and the media was changed daily. All ES cell experiments were performed at feeder-free five stage. In vitro neuronal differentiation was performed as described by Bibel et al (2004, 2007) where ES cells were directly plated on PORN/Laminin-coated tissue culture dishes and cultivated for 2 days in N2 media followed by complete media for induced neuron (iTN) formation.

extract_protocol:
For ChIP seq lysates were clarified from sonicated nuclei. For inducible ES ChIP, abcam HA antibody was used while for ChIP from N2a cells origene Phf21b endogenous antibody was used.
The library for ChIPseq samples were prepared using standard illumina library preparation kit.

treatment_protocol: (1) For ES cell ChIP and RNA seq: Transgenic A2lox ES cells harboring the murine Phf21b fused to an N-terminal HA-tag under the control of a doxycycline-inducible promoter were generated according to Iacovino et al (2011). Ectopic induction of Phf21b was achieved with 500 ng/ml doxycycline for 24 hours.2) ChIP-seq, ATAC seq and RNA seq  from  N2a day2  neuronal differentiation in N2A cells was induced by adding 20 μM retinoic acid in DMEM supplemented with 2% FBS, 1% Glutamine and 1% NEAA. (3) For all siRNA-mediated knockdown experiments, cells were seeded and pre-depleted for two days by transfecting with ON-TARGETplus SMARTpool siRNAs (i.e., a mixture of 4 siRNAs provided as a single reagent from Dharmacon) every second day. For siRNA transfections, Lipofectamine RNAiMax was used according to the manufacturer's instructions. For N2a differentiation pre-depleted cells were differentiated by adding retinoic acid along with siRNAs for two days in N2a differentiation media.

value: mESC

tag: replicate

tag: developmental stage

value: Undifferentiated


title: tRNA-HySeq, WT1


title: STAT5A-ko, replicate 1

description:
expression profile of BCR/ABLp185+ bone marrow wt cell lines, replicate 1
STAT5A-ko-1


title: Phf21b_RNA_N2A_Day5_Diff_Replicate3

description:
RNA-seq in N2A
Normalized_counts_N2a.txt
N2A_Day5_Diff_Replicate3

data_processing:
For the RNA-Seq samples, sequenced reads were aligned to the mouse reference genome (mm9) with UCSC’s annotations using TopHat v2.0.8. SAMTOOLS v0.1.19 was used to convert the BAM output to SAM format and to sort the BAM file. From the aligned BAM files, the read counts per gene were calculated using the HTSeq program v0.5.4p1. Read counts from HTSeq program was normalized using DESeq program.
Genome_build: mm9
Supplementary_files_format_and_content: For the RNA-Seq samples, tab-delimited text files include DESeq normalized read counts for each Sample. For the ChIP-Seq and ATAC-Seq samples, wig files for UCSC genome browser track were provided.

growth_protocol:
Murine Neuro2a cells (N2a cells)  were cultured at 37°C in 7% CO2 and 88% relative humidity in 10 ml of DMEM supplemented with 10% fetal calf serum, 1× NEAA and 2 mM L-glutamine. Neuronal differentiation in N2A cells was induced by adding 20 μM retinoic acid in DMEM supplemented with 2% FBS, 1% Glutamine and 1% NEAA.
Murine Neuro2a cells (N2a cells)  were cultured at 37°C in 7% CO2 and 88% relative humidity in 10 ml of DMEM supplemented with 10% fetal calf serum, 1× NEAA and 2 mM L-glutamine. Neuronal differentiation in N2A cells was induced by adding 20 μM retinoic acid in DMEM supplemented with 2% FBS, 1% Glutamine and 1% NEAA.  For ES cell experiments, ES159 cells on feeders were splitted every 2 days onto tissue culture dishes coated with 0.2% gelatin, and the media was changed daily. All ES cell experiments were performed at feeder-free five stage. In vitro neuronal differentiation was performed as described by Bibel et al (2004, 2007) where ES cells were directly plated on PORN/Laminin-coated tissue culture dishes and cultivated for 2 days in N2 media followed by complete media for induced neuron (iTN) formation.

extract_protocol:
Total RNA of cultured cells was prepared using TRIzol reagent (Invitrogen)
RNA libraries for N2a cells were prepared for sequencing using standard Illumina protocols.

value: Day5 differentiated


title: rrp6_polysome_rep1

city: Solna

first: Vicent

last: Pelechano

address: Nobels väg 16

department: MTC

institute: ScilifeLab - Karolinska Institutet

data_processing:
Library strategy: 5'cap-seq
For polyribosomes 5’ cap sequencing reads, random barcodes were first extracted and added to the reads name. The reads were aligned to yeast genome with Novoalign (http://www.novocraft.com) using default setting.
For 5’PSeq 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 for 5PSeq. For polyribosome 5'cap sequencing both strands are in the same file.

source_name: yeast cells

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

extract_protocol:
For polyribosome analysis, cells resuspended on Lysis buffer were transferred to pre-cooled 1.5mL screw-tubes with 300 µL glass beads and supplemented with 100 units of RNAse inhibitor (RNAsin plus, Promega). Cells were lysed using a FastPrep-24 shaker (6.0m/s for 15 seconds, MP biomedicals). Supernatant was recovered after 5 minutes centrifugation at 2300g, and cleared with an additional centrifugation at 5900g. Extracts were supplemented with glycerol (5% final  v/v) and stored at -70C. 10-50% sucrose gradients were prepared with a Gradient Master BIOCOMP (Nycomed Pharma). Sucrose solution contains 20 mM Tris-HCl, pH 8, 140 mM KCl, 5 mM MgCl2 , 0.5 mM DTT, 100 µg/mL cycloheximide and sucrose (from 10 to 50 %). Cleared cell extracts were ultracentifuged at 34400 rpm for 2 hours 40 minutes at 4C using a C-1000 XP centrifuge with SW40 rotor (Beckman Coulter). Gradient UV absorption at 254 nm was measured and selected fractions were selected for 5’cap library preparation (5µg purified RNA per sample). Polyribosome fraction (i.e., 2n+) was compared with the total extract prior to fractionation).    For 5PSeq 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.
5’cap polyribosome fractioned libraries was performed as previously described (Pelechano et al. Nat Protocols. 2016  PMID: 26820793). In brief, 10µg total RNA was treated with Calf intestinal alkaline phosphatase (NEB)
to remove 5′P from fragmented and non-capped molecules. After purification, mRNA caps were removed using 3.75 units of Cap-Clip (Biozyme) exposing a 5’P in those molecules previously capped. Samples were ligated overnight at 16ºC with a DNA/RNA oligo (rP5_RND: TTTCCCTACACGACGCTCTTCCGATrCrUrNrNrNrNrNrNrNrN ) using T4 RNA ligase 1 (New England Biolabs). RNA integrity after ligation was assayed by agarose gel electrophoresis and polyA RNA was purified using oligo dT magnetic beads. After this, ligated mRNA was fragmented at 80ºC for 5 min in the presence of RNA fragmentation buffer (40 mM Tris-acetate, pH 8.1, 100 mM KOAc, 30 mM MgOAc). Ligated RNA was subjected to reverse transcription using random hexamers with Superscript II (Life Technologies) with the following program: 10 min at 25ºC, 50 min at 42ºC and heat inactivated for 15 min at 72ºC. Second strand cDNA synthesis was performed by a single PCR cycle (1 min at 98ºC; 2 min at 50ºC and 15 min at 72ºC) using Phusion High-Fidelity PCR Master Mix (New England Biolabs). A biotinilated oligo (BioNotI-P5-PET: [Btn]TATAGCGGCCGCAATGATACGGCGACCACCGAGATCTACACTCTTTCCCTAC ACGACGCTCTTCCGATCT) was added during the generation of the second cDNA strand. Double stranded cDNA was purified using Ampure XP (Beckman Coulter) or HighPrep (Magbio) beads. After the samples were bound to streptavidin coated magnetic beads (M-280 Dynabeads, Life Technologies) and subjected to standard Illumina end-repair, dA addition and adapter ligation was performed as previously described. Libraries were enriched by PCR and sequenced in an Illumina HiSeq 2000 instrument.     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 an average length of 451 nt were sent for sequencing (llumina NextSeq 500 instrument).

treatment_protocol: For polyribosome analysis  100 mL of S. cerevisiae cells at OD600 ~1 were treated with cycloheximide for 5 minutes (100 µg/mL, final concentration), harvested by centrifugation and transferred to ice. Pellets were washed with ice-cold lysis buffer and resuspended in 700µL lysis buffer. Lysis buffer contains 20 mM Tris-HCl, pH 8, 140 mM KCl,  5 mM MgCl2 , 0.5 mM DTT, 1% Triton X-100, 100 µg/mL cycloheximide, 500 µg/mL heparin and complete EDTA-free protease inhibitor (1 tablet per 10 mL, Sigma Aldrich).    For 5PSeq cells were shifted for 5 minutes to YP media without glucose (1% yeast extract, 2% peptone) prior to harvesting.

tag: parental strain

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


title: Phf21b_RNA_N2A_Day5_Diff_Replicate2

description:
RNA-seq in N2A
Normalized_counts_N2a.txt
N2A_Day5_Diff_Replicate2

tag: cell line


title: wild-type, replicate 1

description:
expression profile of BCR/ABLp185+ bone marrow wt cell lines, replicate 1
wt-1

value: bone marrow


title: rrp6_total_rep2


title: Phf21b_ChIP_mESC_pDox_Replicate2

description: ChIP-seq in mESC


title: RN13_Het3_P59


title: rrp6_total_rep1


title: Phf21b_RNA_N2A_Day5_Diff_Replicate1

description:
RNA-seq in N2A
Normalized_counts_N2a.txt
N2A_Day5_Diff_Replicate1


title: RN8_H11_E1_P56

value: WT/WT


title: RN10_Het2_P58


title: RN11_Het3_P59


title: RN12_Het1_P55


title: non_involved_lung_tissue_patient_24 9983140064_B_Expression

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.

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: age

tag: smoking status

tag: batch


title: Phf21b_RNA_N2A_Day2_Diff_siRNA_Replicate2

description:
RNA-seq in N2A
Normalized_counts_N2a.txt
N2A_Day2_Diff_siRNA_Replicate2

value: Day2 differentiated


title: non_involved_lung_tissue_patient_23 9983140064_A_Expression

value: never-smoker


title: RN6_C_P59


title: non_involved_lung_tissue_patient_26 9983140064_D_Expression


title: rrp6_5cap_rep2

description:
rrp6.normalized.plus.bedGraph
rrp6.normalized.minus.bedGraph

data_processing:
Library strategy: 5'cap-seq
For 5’ cap sequencing reads, random barcodes were first extracted and added to the reads name. The reads were aligned to yeast genome  with Novoalign (http://www.novocraft.com) using default setting.
After read alignment, a customized script adapted from UMI-tools was used for removing PCR duplicates. Specifically we allowed 1 bp shifting at the beginning of 5’ ends. CAGEr was employed for clustering the 5’ cap TSSs of BY4741 wild-type strain and the mutants. TSS counts in different samples were normalized to match a common reference power-law distribution. Data provided as normalized BedGraph.  For polyribosome analysis reads PCR duplicateswere removed and assigned to CAGEr clusters. Data provided as UMI collapsed BedGraph.
Genome_build: S. cerevisiae R64-1-1
Supplementary_files_format_and_content: Bedgraph files for CAGE normalized reads for 5'cap- sequencing (independent filed for positive and negative strand), or UMI collapsed reads for polyribosome analysis (positive and negative strands in one file).

growth_protocol: Cells were grown in YPD (1% yeast extract, 2% peptone, 2% glucose and 40 mg/L adenine) and harvested at OD600 ~1.

extract_protocol:
For 5'cap-sequencing samples RNA was extracted from yeast cells using standar phenol procedure using glass beads and a FastPrep-24 shaker. The amount of RNA was quantified in a Nanodrop 2000 Spectrophotometer (Thermo Scientific) and RNA integrity was checked by agarose gel electrophoresis.  For polyribosome analysis, cells resuspended on Lysis buffer were transferred to pre-cooled 1.5mL screw-tubes with 300 µL glass beads and supplemented with 100 units of RNAse inhibitor (RNAsin plus, Promega). Cells were lysed using a FastPrep-24 shaker (6.0m/s for 15 seconds, MP biomedicals). Supernatant was recovered after 5 minutes centrifugation at 2300g, and cleared with an additional centrifugation at 5900g. Extracts were supplemented with glycerol (5% final  v/v) and stored at -70C. 10-50% sucrose gradients were prepared with a Gradient Master BIOCOMP (Nycomed Pharma). Sucrose solution contains 20 mM Tris-HCl, pH 8, 140 mM KCl, 5 mM MgCl2 , 0.5 mM DTT, 100 µg/mL cycloheximide and sucrose (from 10 to 50 %). Cleared cell extracts were ultracentifuged at 34400 rpm for 2 hours 40 minutes at 4C using a C-1000 XP centrifuge with SW40 rotor (Beckman Coulter). Gradient UV absorption at 254 nm was measured and selected fractions were selected for 5’cap library preparation (5µg purified RNA per sample). Polyribosome fraction (i.e., 2n+) was compared with the total extract prior to fractionation).
5’cap-libraries was performed as previously described (Pelechano et al. Nat Protocols. 2016  PMID: 26820793). In brief, 10µg total RNA was treated with Calf intestinal alkaline phosphatase (NEB)to remove 5′P from fragmented and non-capped molecules. After purification, mRNA caps were removed using 3.75 units of Cap-Clip (Biozyme) exposing a 5’P in those molecules previously capped. Samples were ligated overnight at 16ºC with a DNA/RNA oligo (rP5_RND: TTTCCCTACACGACGCTCTTCCGATrCrUrNrNrNrNrNrNrNrN ) using T4 RNA ligase 1 (New England Biolabs). RNA integrity after ligation was assayed by agarose gel electrophoresis and polyA RNA was purified using oligo dT magnetic beads. After this, ligated mRNA was fragmented at 80ºC for 5 min in the presence of RNA fragmentation buffer (40 mM Tris-acetate, pH 8.1, 100 mM KOAc, 30 mM MgOAc). Ligated RNA was subjected to reverse transcription using random hexamers with Superscript II (Life Technologies) with the following program: 10 min at 25ºC, 50 min at 42ºC and heat inactivated for 15 min at 72ºC. Second strand cDNA synthesis was performed by a single PCR cycle (1 min at 98ºC; 2 min at 50ºC and 15 min at 72ºC) using Phusion High-Fidelity PCR Master Mix (New England Biolabs). A biotinilated oligo (BioNotI-P5-PET: [Btn]TATAGCGGCCGCAATGATACGGCGACCACCGAGATCTACACTCTTTCCCTAC ACGACGCTCTTCCGATCT) was added during the generation of the second cDNA strand. Double stranded cDNA was purified using Ampure XP (Beckman Coulter) or HighPrep (Magbio) beads. After the samples were bound to streptavidin coated magnetic beads (M-280 Dynabeads, Life Technologies) and subjected to standard Illumina end-repair, dA addition and adapter ligation was performed as previously described. Libraries were enriched by PCR and sequenced in an Illumina HiSeq 2000 instrument.

treatment_protocol: No treatment for 5'cap-sequencing samples. For polyribosome analysis  100 mL of S. cerevisiae cells at OD600 ~1 were treated with cycloheximide for 5 minutes (100 µg/mL, final concentration), harvested by centrifugation and transferred to ice. Pellets were washed with ice-cold lysis buffer and resuspended in 700µL lysis buffer. Lysis buffer contains 20 mM Tris-HCl, pH 8, 140 mM KCl,  5 mM MgCl2 , 0.5 mM DTT, 1% Triton X-100, 100 µg/mL cycloheximide, 500 µg/mL heparin and complete EDTA-free protease inhibitor (1 tablet per 10 mL, Sigma Aldrich).

tag: transcription factor


title: non_involved_lung_tissue_patient_25 9983140064_C_Expression


title: RN3_G7_H4_P57


title: rrp6_polysome_rep2


title: Phf21b_RNA_N2A_Day2_Diff_siRNA_Replicate1

description:
RNA-seq in N2A
Normalized_counts_N2a.txt
N2A_Day2_Diff_siRNA_Replicate1


title: non_involved_lung_tissue_patient_22 9983140054_L_Expression


title: rrp6_5cap_rep1


title: rco1_5cap_rep1

description:
rco1.normalized.plus.bedGraph
rco1.normalized.minus.bedGraph


title: C2_REST_sh-PBmPA-Day24_2

value: induced human neurons from fibroblasts

tag: treatment

value: Treated with miRNA


title: non_involved_lung_tissue_patient_27 9983140064_E_Expression


title: Phf21b_RNA_N2A_Day2_Diff_Replicate2

description:
RNA-seq in N2A
Normalized_counts_N2a.txt
N2A_Day2_Diff_Replicate2


title: Phf21b_RNA_N2A_Day2_Diff_Replicate1

description:
RNA-seq in N2A
Normalized_counts_N2a.txt
N2A_Day2_Diff_Replicate1


title: rco1_5cap_rep2


title: eaf3_5cap_rep2

description:
eaf3.normalized.plus.bedGraph
eaf3.normalized.minus.bedGraph


title: eaf3_5cap_rep1


title: non_involved_lung_tissue_patient_21 9983140054_K_Expression


title: non_involved_lung_tissue_patient_20 9983140054_J_Expression

value: F


title: Phf21b_RNA_N2A_Untreated_Replicate2

description:
RNA-seq in N2A
Normalized_counts_N2a.txt
N2A_UntReplicateated_Replicate2


title: Phf21b_RNA_N2A_Untreated_Replicate1

description:
RNA-seq in N2A
Normalized_counts_N2a.txt
N2A_UntReplicateated_Replicate1


title: set2_5cap_rep1

description:
set2.normalized.plus.bedGraph
set2.normalized.minus.bedGraph


title: non_involved_lung_tissue_patient_19 9983140054_I_Expression


title: non_involved_lung_tissue_patient_17 9983140054_G_Expression


title: non_involved_lung_tissue_patient_18 9983140054_H_Expression


title: RN1_G7_H4_P56


title: D6_Macs_IL_10

first: Joseph

middle: C

last: Devlin

address: 430 East 29th Street

institute: New York University Langone Health

description: normalizedCounts.txt.gz

data_processing:
Reads were mapped by Bowtie (v2.3.1) to the hg38 reference genome
Uniquely mapped indices (UMI) determined by HTSeq-counts
Normalized count tables were generated in R (v3.5.1) using DESeq2 (v1.18.1)
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include normalized count values for each Sample

source_name: blood

growth_protocol: Primary human polymorphonuclear neutrophils (PMNs) and peripheral blood mononuclear cells (PBMCs) from anonymous, healthy donors (New York Blood Center) were isolated by Ficoll gradient separation as previously described. CD14+ monocytes were then isolated from the PBMC fraction by positive selection. In brief: PBMCs were resuspended in MACS buffer (PBS + 0.05% BSA + 2 mM EDTA) at a concentration of 1x108 PBMCs per 950 mL. 50 mL of CD14+ microbeads (Miltenyi Biotec) were added for every 1x108 PBMCs. Cells were incubated for 20 minutes at 4°C, washed, and filtered through a cell strainer. The cells were run on an AutoMACS Pro (Miltenyi Biotec) using the ‘Posselds’ program. Monocytes were used directly after sorting. Monocyte-derived dendritic cells (DCs), and Monocyte-derived macrophages were differentiated from CD14+ monocytes by culturing the cells for 4 days at 37°C and 5% CO2 in RPMI medium supplemented with 10% FBS, 10 mM HEPES, 100 U/mL penicillin, 100 mg/mL streptomycin with either 110 U/mL granulocyte-macrophage colony-stimulating factor (GM-CSF) (Leukine; Sanofi) and 282 U/mL interleukin-4 (IL-4) (Affymetrix, eBioscience) for DCs or 280 U/mL GM-CSF for macrophages. Media was replenished with fresh cytokine on day 2.

extract_protocol:
RNA for each donor was then isolated with the RNeasy Plus Mini Kit (Qiagen) following the protocol with on column DNAse Digestion (Qiagen).
RNA libraries were prepared using standard CelSeq2 protocols.

treatment_protocol: Differentiated cells were resuspended in clear RPMI + 10% FBS. 1x105 cells were added to each stimulation well. Stimulations comprised of buffer control (PBS + 0.01% Glycerol), 500 U/mL IFN-b1a (Carrier Free; R&D Systems), 10 ng/mL IFN-g (Carrier Free, R&D Systems), IFN-l2 (Carrier Free, R&D Systems), 1000 IU/mL IL-4 (Carrier Free, Life Technologies), 100 IU/mL IL-10 (Carrier Free, Life Technologies), and 100 IU/mL IL-13 (Carrier Free, R&D Systems). Plates were spun for 5 minutes at 1200 rpm and incubated for 4 hours at 37°C and 5% CO2. Cells were then washed with PBS. Cells were resuspended in RLT buffer (Qiagen) and vortexed for 1 minute before being placed at -80°C.

tag: donor

tag: cell type

value: Macs

tag: stimulation


title: Phf21b_RNA_mESC_pDox_Replicate5

description:
RNA-seq in mESC
Normalized_counts_mESC.txt
mESC_pDox_Replicate5

extract_protocol:
Total RNA of cultured cells was prepared using TRIzol reagent (Invitrogen)
RNA libraries for inducible ES cells were prepared for sequencing using standard Illumina protocols.


title: set1_5cap_rep2

description:
set1.normalized.plus.bedGraph
set1.normalized.minus.bedGraph

tag: genotype


title: D6_Macs_IFN_y

description: normalizedCounts.txt.gz

value: IFN-y


title: Phf21b_RNA_mESC_pDox_Replicate4

description:
RNA-seq in mESC
Normalized_counts_mESC.txt
mESC_pDox_Replicate4


title: D6_Macs_IFN_lambda2

description: normalizedCounts.txt.gz


title: D6_Macs_IL_13

description: normalizedCounts.txt.gz


title: set1_5cap_rep1


title: set2_5cap_rep2


title: D6_Macs_Buffer

description: normalizedCounts.txt.gz

value: Buffer


title: D6_Macs_IL_4

description: normalizedCounts.txt.gz


title: D6_Macs_IFN_B1a

description: normalizedCounts.txt.gz


title: Phf21b_RNA_mESC_pDox_Replicate2

description:
RNA-seq in mESC
Normalized_counts_mESC.txt
mESC_pDox_Replicate2


title: Phf21b_RNA_mESC_pDox_Replicate1

description:
RNA-seq in mESC
Normalized_counts_mESC.txt
mESC_pDox_Replicate1


title: D6_DCs_IL_13

description: normalizedCounts.txt.gz

value: DCs


title: BY4741_5cap_rep2

description:
BY4741.normalized.plus.bedGraph
BY4741.normalized.minus.bedGraph

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

tag: strain


title: non_involved_lung_tissue_patient_16 9983140054_E_Expression

value: ever-smoker


title: BY4741_total_rep2


title: Phf21b_RNA_mESC_pDox_Replicate3

description:
RNA-seq in mESC
Normalized_counts_mESC.txt
mESC_pDox_Replicate3

value: mESC


title: non_involved_lung_tissue_patient_15 9983140054_D_Expression


title: BY4741_total_rep1


title: non_involved_lung_tissue_patient_14 9983140054_C_Expression

value: M


title: non_involved_lung_tissue_patient_12 9983140054_A_Expression


title: non_involved_lung_tissue_patient_11 9983140008_L_Expression


title: D6_DCs_IL_10

description: normalizedCounts.txt.gz


title: Phf21b_RNA_mESC_mDox_Replicate4

description:
RNA-seq in mESC
Normalized_counts_mESC.txt
mESC_mDox_Replicate4

value: Undifferentiated


title: BY4741_polysome_rep1

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


title: non_involved_lung_tissue_patient_10 9983140008_K_Expression


title: Phf21b_RNA_mESC_mDox_Replicate2

description:
RNA-seq in mESC
Normalized_counts_mESC.txt
mESC_mDox_Replicate2


title: D6_DCs_IFN_y

description: normalizedCounts.txt.gz


title: Phf21b_RNA_mESC_mDox_Replicate1

description:
RNA-seq in mESC
Normalized_counts_mESC.txt
mESC_mDox_Replicate1


title: Hmgb2KO-CCL4-S15

city: Indianapolis

first: Zhihong

last: Yang

institute: Indiana University

data_processing:
HCS V2.2 software was used for sequencing Control
Sequenced read were trmmed for adaptor sequence and masked for low-compleity or low-quality sequence, then mapped to mm10 whole genome using bowtie
Differentially expressed genes was analyzed using DESeq2 and the hciR package on Github to simplify the R code.
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: excel file include counts and FPKM values for each sample

source_name: Liver

extract_protocol:
livers were flash frozen in liquid N2, and TruSeq Stranded Total RNA LT sample Prep Kit was used for library generation.
TruSeq Stranded Total RNA LT sample Prep Kit was used for library generation.
Library Protocol followed TruSeq Stranded Total RNA Sample Prep Guide, Part # 15031048 Rev. E


title: D6_DCs_IFN_lambda2

city: New York

description: normalizedCounts.txt.gz


title: D6_DCs_Buffer

description: normalizedCounts.txt.gz


title: non_involved_lung_tissue_patient_9 9983140008_J_Expression

first: Matteo

last: Dugo

institute: IRCCS Ospedale San Raffaele


title: non_involved_lung_tissue_patient_8 9983140008_H_Expression


title: D6_DCs_IFN_B1a

description: normalizedCounts.txt.gz


title: D6_Monos_IL_13

description: normalizedCounts.txt.gz

value: Monos


title: D6_DCs_IL_4

description: normalizedCounts.txt.gz


title: non_involved_lung_tissue_patient_7 9983140008_G_Expression


title: Hmgb2KO-CCL4-E24


title: Phf21b_RNA_mESC_mDox_Replicate3

description:
RNA-seq in mESC
Normalized_counts_mESC.txt
mESC_mDox_Replicate3


title: BY4741_polysome_rep2


title: D6_Monos_IL_10

description: normalizedCounts.txt.gz


title: Hmgb2KO-CCL4-E25


title: C12LHSL_plus_5

city: Berlin

first: Hans-Joachim

last: Mollenkopf

address: Charitéplatz 1

institute: Max-Planck-Institute for Infection Biology

description: biol.replicate 5

hyb_protocol: 750 ng Cy3-labelled cRNA was fragmented and hybridized following Agilents instructions. After hybridization, microarrays were washed with GE Wash Buffer (Agilent).

scan_protocol: Slides were scanned with extended dynamic range (XDR) and 5 µm resolution (4x44K) using a G2565CA high-resolution laser microarray scanner (Agilent)

data_processing: Microarray image data were processed with the Image Analysis/Feature Extraction software G2567AA v. A.11.5.1.1 (Agilent Technologies) using default settings and the GE1_1105_Oct12 extraction protocol

organism: Danio rerio

source_name: total fish larvae

label_protocol: Cy3 labeled cRNA was prepared from 200ng total RNA using the One-Color Low RNA Input Linear Amplification kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (Qiagen).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Wild type zebrafish (AB strain, https://zfin.org/action/genotype/view/ZDB-GENO-960809-7) were set up for mating overnight, in 3:2 ratios, females and males, respectively. Fertilized embryos from wildtype zebrafish AB strain were used for all experiments and kept in Embryo medium (E3, 5 mM NaCl, 0.17 mM KCl, 0.33 mM CaCl2, 0.33 mM MgSO4) in an incubator at 28ºC. At 1dpf, larvae were manually dechorionated under a stereomicroscope. At 2dpf, zebrafish larvae were divided randomly into the different experimental groups, at a density of 12 larvae per well of a 12 well plate (Corning) in 1.5mL of E3.

extract_protocol: After the desired exposure to diverse ligands, larvae were euthanized with Tricaine (MS-222, 300 µg/mL) and placed in Trizol for RNA isolation. RNA was isolated according the manufacturers instruction.

treatment_protocol: Three biological replicates of 12 larvae per condition were exposed to different conditions for 4 hours at 28 ºC: DMSO; DMSO + CH223191 (5mM); 3-o-C12-L-HSL (50mM); 3-o-C12-L-HSL (50mM) + CH223191 (5 mM ); 1-hydroxyphenazine (1-HP, 5mM); 1-HP (5mM) + CH223191(5mM) and 1-HP (5mM) + 3-o-C12-L-HSL (50mM).To mention, in experiments using the Aryl hydrocarbon Receptor inhibitor CH223191, larvae were pre-exposed to 5uM of the inhibitor for 2h prior to the start of the experiment and the inhibitor was kept during the experiment.

value: 3-o-C12-L-HSL stimulation

tag: additional treatment

value: plus CH223191 inhibitor


title: HPC12LHSL_plus_5

description: biol.replicate 5

value: 1-HP + 3-o-C12-L-HSL stimulation


title: non_involved_lung_tissue_patient_5 9983140008_E_Expression

city: Milan

address: via Olgettina 60


title: Hmgb2KO-Oil-S12

value: Oil


title: HP_plus_5

description: biol.replicate 5

value: 1-HP stimulation


title: non_involved_lung_tissue_patient_13 9983140054_B_Expression

value: F


title: D6_Monos_IL_4

description: normalizedCounts.txt.gz


title: non_involved_lung_tissue_patient_3 9983140008_C_Expression

value: never-smoker


title: D6_Monos_IFN_lambda2

description: normalizedCounts.txt.gz


title: DMSO_plus_5

description: biol.replicate 5

value: DMSO stimulation


title: C12LHSL_w/o_5

description: biol.replicate 5

value: w/o CH223191 inhibitor


title: WT-CCL4-S5

value: wild type


title: non_involved_lung_tissue_patient_2 9983140008_B_Expression


title: Hmgb2KO-Oil-S11


title: BY4741_5cap_rep1

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


title: D6_Monos_Buffer

description: normalizedCounts.txt.gz

value: Buffer