title: embryonic week 16 technical replicate 3

city: Rotterdam

first: Erwin

last: Brosens

state: - If in U.S, Select a State -

address: Dr molewaterplein 50

department: Clinical genetics

country: Netherlands

institute: ErasmusMC

description:
technical replicate sample 3
ENS_development_leanient_mapping
ENS_development_unique_mapping
HHFHLBBXX_102938-001-003_T3_GGTATAGG_L004_R1

data_processing:
libraries were prepared according to the Illumina TruSeq Stranded mRNA Library Prep Kit and protocol (Illumina Inc., San Diego, CA, USA)
CLC-Bio (Qiagen, Venlo, The Netherlands) was used for subsequent quality control, read trimming, alignment to the NCBI v37 H. sapiens reference genome, transcript quantification and differential expression analysis.
Reads were aligned using the following settings: mismatch cost 2, insertion/deletion cost 3, length fraction 0.8, similarity fraction 0.8, alignment to gene regions only. Paired reads were counted as one. Stringent analysis: reads can align to one location, lenient alignment: reads can align to a maximum of 10 locations
Trimmed mean of M values was used to normalize for sequencing depth across samples. Counts per Million (CPM) values were calculated for each gene, centered and scaled to unit-variance. Expression values were counted as total counts and Reads Per Kilobase of exon model per Million mapped reads (RPKM)
RPKM values were used for within sample gene expression comparison and pathway enrichment analysis.
Genome_build: hg19
Supplementary_files_format_and_content: Two excel files with all processed data (total counts, RKPM, CPM, and statistics), one for the lenient alignment and one for the stringent alignment

source_name: colon

growth_protocol: not applicable

extract_protocol: Total RNA from human foetal colonic samples were obtained sourced via the Joint MRC/Wellcome Trust Human Developmental Biology Resource under informed ethical consent

treatment_protocol: not applicable

value: embryonic week 16

tag: sample

tag: replicate

tag: tissue

value: colon


title: embryonic week 16 technical replicate 2

status: Public on Feb 20 2019

type: SRA

description:
technical replicate sample 3
ENS_development_leanient_mapping
ENS_development_unique_mapping
HHFHLBBXX_102938-001-002_T2_TCCATTGC_L004_R1

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

tag: age


title: Pat57T

city: Seoul

first: Jihae

last: Seo

address: 52 Ewhayeodae-gil, Seodaemun-Gu

department: Ewha Research Center for Systems BIology

country: South Korea

institute: Ewha Womans University

data_processing:
miRNA sequencing was performed on Illumina HiSeq 2000 platform using 1X50bp single-end runs.
For miRNA-Seq data, sequencing reads were mapped to the miRBase release 19 using Bowtie V.0.12.9 with the perfect match option after removing adapter sequences.
Genome_build: miRBase v19
Supplementary_files_format_and_content: Tab-delimited text files include read count values for each sample

source_name: lung adenocarcinoma tumor

extract_protocol:
cDNA size selection was carried out with the Sage Science’s Pippin prep electrophoresis platform. Sequencing of pooled libraries were performed on HiSeq 2000 sequencing system (Illumina) with the single end read of 50 bp length.
Small RNA sequencing libraries were prepared according to the manufacturer’s instructions using the Illumina Small RNA Prep kit.

tag: patient id

tag: disease

value: lung adenocarcinoma

tag: gender

value: Female

value: never smoker

tag: molecule subtype

value: microRNA

tag: tumor stage


title: sci3-me-036

city: Seattle

first: Junyue

last: Cao

state: WA

address: Foege Building S-210, 3720 15th Ave NE

department: Department of Genome Sciences

country: USA

institute: University of Washington

description: sci-RNA-seq3 library

data_processing:
For sc-RNA-seq processing, read alignment and gene count matrix generation for single cell RNA-seq of co-assay was the same with sci-RNA-seq ("J. Cao et al., Comprehensive single cell transcriptional profiling of a multicellular organism by combinatorial indexing. bioRxiv, 104844 (2017).") with minor modifications: Reads were mapped to a chimeric reference genome of human (hg19) and mouse (mm10) for RNA-seq from A594, HEK293T and NIH/3T3 cells, and mouse (mm10) only for RNA-seq from mouse kidney experiment with STAR/v 2.5.2b, with gene annotations (GENCODE V19 for human; GENCODE VM11 for mouse). For mixed-species experiment, the percentage of uniquely mapping reads for genomes of each species was calculated. Cells with over 80% of UMIs assigned to one species were regarded as species-specific cells, with the remaining cells classified as mixed cells or “collisions”.
Genome_build: mouse reference genome (mm10)
Supplementary_files_format_and_content: Processed data files include a cell annotation csv  file, gene annotation csv file, and a gene count sparse matrix file
Supplementary_files_format_and_content: Cell annotation file: sample is cell id of each single cell with the reverse transcription and ligation barcode attached; tsne_1 and tsne_2 are cell coordinates after t-SNE dimension reduction.
Supplementary_files_format_and_content: Gene annotation file including gene id, gene type and gene short name.
Supplementary_files_format_and_content: A sparse matrix file: each row corresponds to gene id (with gene information in the gene_annotation.csv; each column corresponds to each cell (with cell source information in the cell_annotation.csv); each value in the matrix corresponds to UMI count.

molecule: polyA RNA

organism: Mus musculus

source_name: mouse embryos

growth_protocol: The C57BL/6 mice were obtained from The Jackson Laboratory (Bar Harbor, ME) and plug matings were set up. Noon on the day of the vaginal plug was considered as embryonic day (E) 0.5. Dissections were done as previously described76 and all embryos were immediately snap frozen in liquid nitrogen. All animal procedures were in accordance with institutional, state, and government regulations (IACUC protocol 4378-01).

extract_protocol:
Mouse embryos from different development stages were processed together to reduce batch effect. Each mouse embryo was minced into small pieces by blade in 1 mL ice-cold cell lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2 and 0.1% IGEPAL CA-630 from77, modified to also include 1% SUPERase In and 1% BSA) and transferred to the top of a 40um cell strainer (Falcon). Tissues were homogenized with the rubber tip of a syringe plunger (5ml, BD) in 4ml cell lysis buffer. The filtered nuclei were then transferred to a new 15ml tube (Falcon) and pelleted by centrifuge at 500xg for 5min and washed once with 1ml cell lysis buffer. The nuclei were fixed in 4ml ice cold 4% paraformaldehyde (EMS) for 15min on ice. After fixation, the nuclei were washed twice in 1ml nuclei wash buffer (cell lysis buffer without IGEPAL), and re-suspended in 500ul nuclei wash buffer. The samples were split to two tubes with 250ul in each tube and flash frozen in liquid nitrogen. We estimated the nuclei extraction efficiency based on extracted nuclei number vs. expected total nuclei number in each embryo and the nuclei extraction efficiency range from 60% to 85%.
Thawed nuclei are permeabilized with 0.2% tritonX-100 (in nuclei wash buffer) for 3 minutes on ice, and briefly sonicated (Diagenode, 12s on low power mode) to reduce nuclei clumping.  The nuclei were then washed once with nuclei wash buffer and filtered through 1ml Flowmi cell strainer (Flowmi). Filtered nuclei were spun down at 500xg for 5min and resuspended in nuclei wash buffer.    Nuclei from each mouse embryo were then distributed into several individual wells in four 96-well plates. The links between well id and mouse embryo were recorded for downstream data processing. For each well, 80,000 nuclei (16 µL) were mixed with 8 µl of 25 µM anchored oligo-dT primer (5′- /5Phos/CAGAGCNNNNNNNN[10bp barcode]TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT-3′, where “N” is any base; IDT) and 2 µL 10 mM dNTP mix (Thermo), denatured at 55°C for 5 min and immediately placed on ice. 14 µL of first-strand reaction mix, containing 8 µL 5X Superscript IV First-Strand Buffer (Invitrogen), 2 µl 100 mM DTT (Invitrogen), 2 µl SuperScript IV reverse transcriptase (200 U/μl, Invitrogen), 2 μL RNaseOUT Recombinant Ribonuclease Inhibitor (Invitrogen), was then added to each well. Reverse transcription was carried out by incubating plates by gradient temperature (4°C 2 minutes, 10°C 2 minutes, 20°C 2 minutes, 30°C 2 minutes, 40°C 2 minutes, 50°C 2 minutes and 55°C 10 minutes).    After ligation reaction, 60µL nuclei dilution buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2 and 1% BSA) was added into each well. Nuclei from all wells were pooled together and spun down at 500xg for 10min. Nuclei were then resuspended in nuclei wash buffer and redistributed into another four 96-well plates with each well including  4µL T4 ligation buffer (NEB), 2µL T4 DNA ligase (NEB), 4µL Betaine solution (5M, Sigma-Aldrich), 6µL nuclei in nuclei wash buffer, 8µL barcoded ligation adaptor (100uM, 5’- GCTCTG[9bp or 10bp barcode A]/ideoxyU/ACGACGCTCTTCCGATCT[reverse complement of barcode A]-3’) and 16µL 40% PEG 8000 (Sigma-Aldrich). The ligation reaction was done at 16°C for 3 hours.    After RT reaction, 60µL nuclei dilution buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2 and 1% BSA) was added into each well. Nuclei from all wells were pooled together and spun down at 600xg for 10min. Nuclei were washed once with nuclei wash buffer and filtered with 1ml Flowmi cell strainer (Flowmi) twice, counted and redistributed into eight 96-well plates with each well including 2,500 nuclei in 5µL nuclei wash buffer and 5µL elution buffer (Qiagen). 1.33 μl mRNA Second Strand Synthesis buffer (NEB) and 0.66 μl mRNA Second Strand Synthesis enzyme (NEB) were then added to each well, and second strand synthesis was carried out at 16°C for 180 min.    For tagmentation, each well was mixed with 11 μL Nextera TD buffer (Illumina) and 1 μL i7 only TDE1 enyzme (62.5nM, Illumina), and then incubated at 55°C for 5 min to carry out tagmentation. The reaction was then stopped by adding 24 μL DNA binding buffer (Zymo) per well and incubating at room temperature for 5 min. Each well was then purified using 1.5x AMPure XP beads (Beckman Coulter). In the elution step, each well was added with 8µL nuclease free water, 1µL 10X USER buffer (NEB), 1µL USER enzyme (NEB) and incubated at 37°C for 15 min. Another 6.5µL elution buffer was added into each well. The AMPure XP beads were removed by magnetic stand and the elution product was transferred into a new 96-well plate.    For PCR amplification, each well (16µL product) was mixed with 2μL of 10 μM indexed P5 primer (5′-AATGATACGGCGACCACCGAGATCTACAC[i5]ACACTCTTTCCCTACACGACGCTCTTCCGATCT-3′; IDT), 2 μL of 10 μM P7 primer (5′-CAAGCAGAAGACGGCATACGAGAT[i7]GTCTCGTGGGCTCGG-3′, IDT), and 20 μL NEBNext High-Fidelity 2X PCR Master Mix (NEB). Amplification was carried out using the following program: 72°C for 5 min, 98°C for 30 sec, 12-14 cycles of (98°C for 10 sec, 66°C for 30 sec, 72°C for 1 min) and a final 72°C for 5 min.

tag: developmental stage

tag: genetic background

value: B6 background


title: sci3-me-040

description: sci-RNA-seq3 library


title: K31R_2

city: rochester

first: Zhenkun

last: Lou

state: mn

address: 200 1st street sw

institute: mayo clinic

data_processing:
Paired-end RNA-seq data was generated with the Illumina HiSeq 4000 platform following the Illumina protocol. The raw sequencing reads were aligned to human hg38 genome using star aligner (version v2.3.0e).
Following read alignment, featureCounts (v1.4.4) was used to quantify the gene expression at the gene level based on GENCODE gene annotation model GRCh38.p10 release 27.
Genes with 1 count per million in at least 1 sample were considered expressed and selected for further analysis, otherwise discarded.
The gene level read counts data was normalized using the trimmed mean of M-values normalization (TMM) method to adjust for sequencing library size difference. The data were transformed to log2 scale.
Genome_build: hg38

source_name: U2OS cells

growth_protocol: U2OS cells  were cultured in DMEM supplemented with 10% FBS and kept in a humidified 37°C 5% CO2 5%O2 incubator..

extract_protocol:
The transfected U2OS cells were flash frozen on dry ice, and RNA 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: U2OS cells were transfected with wildtype H4 plasmids or K31R H4 mutant.

tag: cell origin

value: osteosarcoma cells

tag: cell stock information

value: Parental U2OS odered from ATCC

tag: genotype

value: K31R mutant


title: sci3-me-037

description: sci-RNA-seq3 library


title: sci3-me-035

description: sci-RNA-seq3 library


title: Pat56N

source_name: lung adenocarcinoma normal


title: sci3-me-034

description: sci-RNA-seq3 library


title: sci3-me-033

description: sci-RNA-seq3 library


title: Pat56T


title: sci3-me-055

description: sci-RNA-seq3 library


title: Pat58N


title: sci3-me-032

description: sci-RNA-seq3 library


title: sci3-me-031

description: sci-RNA-seq3 library


title: embryonic week 14 technical replicate 3

description:
technical replicate sample 2
ENS_development_leanient_mapping
ENS_development_unique_mapping
HHFHLBBXX_102938-001-001_T3_ATAACGCC_L004_R1

value: embryonic week 14


title: sci3-me-030

description: sci-RNA-seq3 library


title: embryonic week 14 technical replicate 1

description:
technical replicate sample 2
ENS_development_leanient_mapping
ENS_development_unique_mapping
HHFHLBBXX_102938-001-001_T1_GTACCACA_L004_R1


title: Pat50T


title: sci3-me-029

description: sci-RNA-seq3 library


title: sci3-me-028

description: sci-RNA-seq3 library


title: Pat57N


title: sci3-me-027

description: sci-RNA-seq3 library


title: Pat49T


title: embryonic week 12 technical replicate 2

description:
technical replicate sample 1
ENS_development_leanient_mapping
ENS_development_unique_mapping
HHJTJBBXX_102938-001-003_T2_GTCGATTG_L003_R1

value: embryonic week 12


title: embryonic week 16 technical replicate 1

description:
technical replicate sample 3
ENS_development_leanient_mapping
ENS_development_unique_mapping
HHFHLBBXX_102938-001-003_T1_GTCCTTGA_L004_R1


title: sci3-me-024

description: sci-RNA-seq3 library


title: embryonic week 12 technical replicate 1

description:
technical replicate sample 1
ENS_development_leanient_mapping
ENS_development_unique_mapping
HHJTJBBXX_102938-001-002_T1_CGAATACG_L003_R1


title: Pat49N


title: Pat47T


title: embryonic week 14 technical replicate 2

description:
technical replicate sample 2
ENS_development_leanient_mapping
ENS_development_unique_mapping
HHFHLBBXX_102938-001-001_T2_CAGTGCTT_L004_R1


title: sci3-me-023

description: sci-RNA-seq3 library


title: Pat50N


title: sci3-me-021

description: sci-RNA-seq3 library


title: embryonic week 12 technical replicate 3

description:
technical replicate sample 1
ENS_development_leanient_mapping
ENS_development_unique_mapping
HHJTJBBXX_102938-001-002_T3_GCCTTAAC_L003_R1


title: sci3-me-020

description: sci-RNA-seq3 library


title: sci3-me-022

description: sci-RNA-seq3 library


title: Pat42T


title: Pat42N


title: sci3-me-019

description: sci-RNA-seq3 library


title: sci3-me-025

description: sci-RNA-seq3 library


title: sci3-me-015

description: sci-RNA-seq3 library


title: Pat40T


title: sci3-me-017

description: sci-RNA-seq3 library


title: Pat40N


title: sci3-me-016

description: sci-RNA-seq3 library


title: Pat38T


title: sci3-me-026

description: sci-RNA-seq3 library


title: sci3-me-014

description: sci-RNA-seq3 library


title: sci3-me-009

description: sci-RNA-seq3 library


title: Pat38N


title: sci3-me-012

description: sci-RNA-seq3 library


title: sci3-me-013

description: sci-RNA-seq3 library


title: Pat37T


title: proximal colon of Ercc1-/∆7 mouse treated with Akkermansia muciniphila, replicate 5

type: RNA

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

institute: Wageningen University

description: Ercc1-/∆7 with F1 C57Bl6J/FVB hybrid background

hyb_protocol: Hybridization and washing of the Affymetrix GeneChip Mouse Gene 2.1 ST peg arrays were performed on a GeneTitan Instrument according to the manufacturer's recommendations (Affymetrix, Santa Clara, CA, USA).

scan_protocol: Arrays were scanned on an Affymetrix GeneTitan instrument (Affymetrix, Santa Clara, CA, USA).

data_processing: Expression estimates were calculated applying the RMA algorithm in the Bioconductor library 'Oligo' (v1.46.0).

label: biotin

label_protocol: Total RNA (100ng per sample) was labeled with the Whole-Transcript Sense Target Assay (Affymetrix, Santa Clara, CA, USA; P/N 900652).

growth_protocol: The generation and characterization of Ercc1+/∆7 and Ercc1-/+ mice has been previously described [PMID: 9197240]. Ercc1-/∆7 mice were obtained by crossing Ercc1+/∆7 with Ercc1-/+ mice of pure C57Bl6/J and FVB backgrounds to yield Ercc1-/∆7 with an F1 C57Bl6J/FVB hybrid background.

extract_protocol: Total RNA was isolated from samples using the RNeasy kit (Qiagen) with a DNase digestion step according to the manufacturer’s protocol.

treatment_protocol: Akkermansia muciniphila were grown on MRS medium (Merck, Darmstadt, Germany) until stationary phase, frozen in glycerol, and stored in -80°C until use. Upon use, bacteria were thawed and 10x diluted in NaHCO3/PBS buffer. Around 2*10e8 CFU in 200 µL were administered to mice by gavage, three times per week. Treatment of mice started at 6 weeks of age until one day before sacrifice at 16 weeks or until death.

tag: Sex

value: female

tag: mouse id

tag: treatment

value: Akkermansia muciniphila

tag: background diet

value: semi-synthetic low fat diet (contains 10%E fat), D12450B, Research Diets

tag: age at sacrifice

value: 16 weeks

tag: strain

value: F1 C57Bl6J/FVB hybrid background


title: proximal colon of Ercc1-/∆7 mouse treated with Akkermansia muciniphila, replicate 6


title: proximal colon of Ercc1-/∆7 mouse treated with Akkermansia muciniphila, replicate 4


title: sci3-me-011

description: sci-RNA-seq3 library


title: proximal colon of Ercc1-/∆7 mouse treated with Akkermansia muciniphila, replicate 2


title: Pat37N

tag: age


title: proximal colon of Ercc1-/∆7 mouse treated with Akkermansia muciniphila, replicate 3


title: sci3-me-004

description: sci-RNA-seq3 library


title: proximal colon of Ercc1-/∆7 mouse treated with Akkermansia muciniphila, replicate 1


title: Pat47N

tag: patient id


title: Pat36T

tag: disease


title: proximal colon of Ercc1-/∆7 mouse treated with vehicle (NaHCO3/PBS buffer), replicate 3

value: vehicle (NaHCO3/PBS; 3x week)


title: sci3-me-018

description: sci-RNA-seq3 library


title: proximal colon of Ercc1-/∆7 mouse treated with vehicle (NaHCO3/PBS buffer), replicate 4


title: sci3-me-010

description: sci-RNA-seq3 library


title: sci3-me-008

description: sci-RNA-seq3 library


title: sci3-me-002

description: sci-RNA-seq3 library


title: sci3-me-007

description: sci-RNA-seq3 library


title: mass_M3 miRNA seq

city: Riverside

first: Genbo

last: Xu

address: 900 University Ave

institute: University of California, Riverside

data_processing:
Raw reads were trimmed off using the FASTX toolkit (Cambridge, UK), to obtain a mean Phred score ≥30.
The processed reads were mapped to the Fugu rubripes genome, and both known and novel miRNAs were identified using miRDeep2
Read counts generated from miRDeep2 were used for differential expression analysis using DESeq2.
Supplementary_files_format_and_content: Files with raw read counts and differential expression results

organism: Coryphaena hippurus

source_name: whole embryo

growth_protocol: Mahi-mahi broodstock were captured off the coast of Miami, FL using hook and line angling techniques and subsequently transferred to the University of Miami Experimental Hatchery (UMEH) where they were acclimated in 80 m3 fiberglass maturation tanks (typically 5-7 per tank).  Tanks were equipped with recirculating aquaculture systems for water quality and temperature control.  All embryos used in experiments were collected <8 h following a volitional (non-induced) spawn using standard UMEH methods (Stieglitz et al 2012).

extract_protocol:
miRNAs of pooled samples were isolated using the miRNeasy mini kit from Qiagen (Valencia, CA).  The quality and concentration of miRNA were determined using the Agilent 2100 small RNA chip (Santa Clara, CA).
miRNA libraries were made using the New England Biolabs NEBNext Multiplex Small RNA Sample Prep kit (Ipswich, MA) following the manufacturer’s protocol. The size distribution and concentration of the libraries were determined using the Agilent High Sensitivity DNA Assay Chip (Santa Clara, CA).

treatment_protocol: Bulk dilutions were prepared by adding the appropriate volume of slick or source oil HEWAF to 1 µm filtered, UV-sterilized seawater in 5 L glass bottles,  vigorously spinning for several minutes with a stir bar followed by decanting into each of the replicate 1 L glass beakers.   Freshly fertilized embryos were then gently added to each replicate using a glass transfer pipette and each beaker covered with a glass petri dish.  All exposures were static, non-renewal and performed in a temperature controlled environmental chamber at 27°C with a light cycle of 16:8 h light:dark.

tag: tissue

value: whole larva

tag: exposure

value: treated

tag: concentration


title: proximal colon of Ercc1-/∆7 mouse treated with vehicle (NaHCO3/PBS buffer), replicate 1


title: mass_H1 miRNA seq

tag: developmental stage


title: proximal colon of Ercc1-/∆7 mouse treated with vehicle (NaHCO3/PBS buffer), replicate 5


title: proximal colon of Ercc1-/∆7 mouse treated with vehicle (NaHCO3/PBS buffer), replicate 2


title: sci3-me-006

description: sci-RNA-seq3 library

tag: genetic background


title: mass_M2 miRNA seq


title: Pat32T

value: lung adenocarcinoma

tag: gender

value: Female

tag: molecule subtype

tag: tumor stage


title: sci3-me-005

description: sci-RNA-seq3 library


title: sci3-me-003

description: sci-RNA-seq3 library


title: mass_H3 miRNA seq


title: sci3-me-001

description: sci-RNA-seq3 library


title: Pat33T

value: never smoker

value: microRNA


title: mass_L2 miRNA seq


title: Pat36N


title: mass_H2 miRNA seq


title: Pat33N


title: Pat31T


title: mass_M1 miRNA seq


title: slick_M3 miRNA seq


title: Pat29T


title: slick_M1 miRNA seq


title: Pat31N


title: mass_L3 miRNA seq


title: Pat29N


title: mass_L1 miRNA seq


title: slick_H3 miRNA seq


title: Pat32N


title: slick_H2 miRNA seq


title: slick_H1 miRNA seq


title: Pat28T


title: distal ileum of Ercc1-/∆7 mouse treated with Akkermansia muciniphila, replicate 2

tag: Sex

tag: genotype


title: slick_M2 miRNA seq


title: distal ileum of Ercc1-/∆7 mouse treated with vehicle (NaHCO3/PBS buffer), replicate 5

tag: mouse id

tag: treatment


title: distal ileum of Ercc1-/∆7 mouse treated with Akkermansia muciniphila, replicate 4

tag: background diet

tag: age at sacrifice


title: distal ileum of Ercc1-/∆7 mouse treated with Akkermansia muciniphila, replicate 5

tag: strain


title: distal ileum of Ercc1-/∆7 mouse treated with Akkermansia muciniphila, replicate 6


title: C2 miRNA seq

value: control


title: slick_L2 miRNA seq


title: Pat28N

tag: patient id

tag: age


title: C3 miRNA seq

tag: tissue


title: slick_L3 miRNA seq

tag: exposure


title: slick_L1 miRNA seq

tag: concentration


title: mass_H3 mRNA-seq

description:
treated
mass_H

data_processing:
Raw sequences were trimmed off Illumina adapter sequences and filtered out sequences that did not meet the quality thresholds using Trimmomatic (version 0.33)
All reads were pooled and assembled de novo using Trinity (version 2.2.0) with k-mer length set at 25.
Reads were mapped to the Trinity assembled de novo mahi-mahi transcriptome to estimate the transcript/Unigene abundance using RSEM (RNA-Seq by Expectation-Maximization) (version 1.2.21)65 with the default aligner Bowtie (version 1.1.1)
Differential expression analysis using DESeq in Trinity (version 2.2.0)

extract_protocol:
Pooled larvae were homogenized with a Kontes Pellet Pestle Cordless Motor (Sigma-Aldrich, St. Louis, Missouri) in RNAzol (Molecular Research Center, Cincinnati, Ohio).Total RNA was isolated and purified with RNeasy Mini Kit (Qiagen, Valencia, California) and quantified by NanoDrop ND-1000 Spectrophotometer (Nanodrop Technologies, Wilmington, DE, USA).
200 ng of total RNA was used to prepare RNA-Seq libraries using the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina following the protocol described by the manufacturer (Ipswich, MA).

tag: developmental stage

value: source/mass


title: mass_H2 mRNA-seq

description:
treated
mass_H


title: distal ileum of Ercc1-/∆7 mouse treated with Akkermansia muciniphila, replicate 1


title: Pat27T

tag: disease


title: distal ileum of Ercc1-/∆7 mouse treated with Akkermansia muciniphila, replicate 3


title: distal ileum of Ercc1-/∆7 mouse treated with vehicle (NaHCO3/PBS buffer), replicate 2


title: mass_H1 mRNA-seq

description:
treated
mass_H


title: G2-2: Giardia lamblia cells arrested at the G2-phase by treatment with nocodazole

first: Juri

last: Kim

address: 50-1, Yonsei-ro, Seodaemun-gu

department: Environmental Medical Biology

institute: Yonsei University

data_processing:
bcl2fastq v1.8.4 package was used for basecalling.
Sequenced reads were trimmed for adaptor sequence and masked for low-complexity or low-quality sequence with Trimmomatic0.32.
To estimate expression levels, the RNA-Seq reads were mapped to the genome of Homo sapiens using Hisat2-2.0.5, which is capable of reporting split-read alignments across splice junctions and determined using Stringtie-1.3.3b software in default options.
The reference genome sequence of Giardia lamblia ATCC 50803 (GCF_000002435.1_GL2) and annotation data were downloaded from NCBI. The transcript counts in isoform level were calculated, and the relative transcript abundances were measured in FPKM (Fragments Per Kilobase of exon per Million fragments mapped) using Cufflinks.
Raw data (the reads for each transcript) were normalized by FPKM (Fragments Per Kilobase of exon model per Millon mapped fragments).
Genome_build: GCF_000002435.1_GL2
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Giardia lamblia ATCC 50803

source_name: Giardia lamblia Cell

extract_protocol:
RNAs were extracted from the cell of Homo Sapiens. Poly(A) mRNA using the Illumina TruSeq Stranded mRNA LT Sample Prep Kit, according to the manufacturer’s instructions.
Libraries were prepared for multiplex sequencing using Illumina TruSeq Stranded mRNA LT Sample Prep Kit , according to the manufacturer’s protocol.

tag: reference

value: Giardia lamblia Cell


title: G2-3: Giardia lamblia cells arrested at the G2-phase by treatment with nocodazole


title: mass_M3 mRNA-seq

description:
treated
mass_M


title: distal ileum of Ercc1-/∆7 mouse treated with vehicle (NaHCO3/PBS buffer), replicate 4


title: G2-1: Giardia lamblia cells arrested at the G2-phase by treatment with nocodazole


title: distal ileum of Ercc1-/∆7 mouse treated with vehicle (NaHCO3/PBS buffer), replicate 3


title: Pat27N

tag: gender

tag: molecule subtype


title: mass_M1 mRNA-seq

description:
treated
mass_M


title: Pat15T

tag: tumor stage


title: mass_L3 mRNA-seq

description:
treated
mass_L


title: Pat15N


title: G1-2: Giardia lamblia cells arrested at the G1-phase by treatment with nocodazole


title: Pat08T


title: distal ileum of Ercc1-/∆7 mouse treated with vehicle (NaHCO3/PBS buffer), replicate 1

tag: Sex

tag: genotype


title: mass_M2 mRNA-seq

description:
treated
mass_M


title: Pat17T


title: G1-3: Giardia lamblia cells arrested at the G1-phase by treatment with nocodazole


title: C1 miRNA seq


title: Pat17N


title: slick_H3 mRNA-seq

description:
treated
slick_H

value: slick


title: mass_L2 mRNA-seq

description:
treated
mass_L


title: Pat05N


title: Pat08N


title: Pat05T


title: slick_H2 mRNA-seq

description:
treated
slick_H


title: Pat02N


title: mass_L1 mRNA-seq

description:
treated
mass_L


title: G1-1: Giardia lamblia cells arrested at the G1-phase by treatment with nocodazole


title: slick_M2 mRNA-seq

description:
treated
slick_M


title: slick_H1 mRNA-seq

description:
treated
slick_H


title: Pat02T


title: slick_M3 mRNA-seq

description:
treated
slick_M


title: slick_L3 mRNA-seq

description:
treated
slick_L


title: Italia_ OI_ rep3

city: Turi

first: Maria Francesca

last: Cardone

state: Bari

address: via Casamassima 148

department: Centro di ricerca Viticoltura ed Enologia (CREA-VE)

country: Italy

institute: Consiglio per la ricerca in agricoltura e l’analisi dell’economia agraria (CREA)

description: Gene expression

hyb_protocol: Agilent Technologies_One-Color Microarray-based_Gene expression Analyses_protocol version 6.9.1,

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) _using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: Array images were analyzed using Agilent Feature Extraction software version 10.7.1.1 (Agilent Technologies, Santa Clara, CA) using default parameters (Protocol name_GE1_107_Sep09_grid name_028416_D_F_20100513) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Vitis vinifera

source_name: Italia, OI, rep3

extract_protocol: Total RNA was extracted from 0.1 g of shoot apex collected at 10% veraison with Total RNA Isolation Mini Kit (Agilent Technologies). RNA integrity was assessed by automated gel electrophoresis on 2100 Bioanalyzer (Agilent Technologies, Amstelveen, Netherlands).

value: leaf apex

tag: irrigation treatment

value: Over Irrigation (OI)

tag: cultivar

value: Italia


title: slick_M1 mRNA-seq

description:
treated
slick_M


title: Italia_ WD_ rep3

description: Gene expression

source_name: Italia, WD, rep3

label_protocol: Agilent Technologies_One-Color Microarray-based_Gene expression Analyses_protocol version 6.9.1,

value: Water Deficit (WD)


title: Autumn Royal_ WD_ rep4

description: Gene expression

source_name: Autumn Royal, WD, rep4

value: Autumn Royal


title: Italia_ FI_ rep3

description: Gene expression

source_name: Italia, FI, rep3

value: Full Irrigation (FI)


title: Autumn Royal_ WD_ rep2

description: Gene expression

source_name: Autumn Royal, WD, rep2


title: Italia_ WD_ rep2

description: Gene expression

source_name: Italia, WD, rep2


title: Autumn Royal_ WD_ rep3

description: Gene expression

source_name: Autumn Royal, WD, rep3


title: Pat01N


title: Autumn Royal_ FI_ rep2

description: Gene expression

source_name: Autumn Royal, FI, rep2


title: BERP35T4 REP2

city: Beijing

first: Chenghui

last: Zhao

address: Haidian Taiping Road 27

country: China

institute: Beijing Institute of Radiation Medicine

description: The BERP35T1 malignant transformant cell line was derived from BEP2D cells irradiated with 1.5 Gy of α-particle emitted from 238Pu source

data_processing:
mRNA-seq reads were aligned to the hg19 genome assembly using STAR(version 2.5.2b) with default parameter.
Duplicated reads that mapped to the same location were removed using Picard(version 1.141)(https://broadinstitute.github.io/picard/) with default parameter.
Reads with a mapping quality <20 were removed using samtools(version 1.3.1) with parameter '-q 20'.
Variants were called using the GATK(version 3.5.0) HaplotypeCaller tool with options stand_call_conf of 20 and stand_emit_conf of 0.
Candidate RNA editing site were called using the following filtering steps: (1) all variants present in dbSNP (except SNPs of molecular type “cDNA”, database version 137, http://www.ncbi.nlm.nih.gov/SNP/); (2) variants located in the first 6 bp from either end of a sequence read were discarded; (3) in non-Alu regions, we removed sites in simple repeats according to RepeatMasker annotation, discarded intronic candidates if they were located within 4 bp of all known splicing junctions according to Ensembl gene annotations, and removed sites in homopolymer runs of ≥5 bp; (4) variant sites in regions of high similarity to other parts of the genome were discarded using the BLAST-like alignment tool (BLAT); (5) the editing type of each site was inferred based on the strand of overlapping annotated genes and only A-to-I base changing editing sites were retainned.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files include basic information of identified A-to-I editing sites for each sample;  basic information includes chromosome, position, strand, reference base, altered base and editing level of each A-to-I editing site.

source_name: Bronchiolar epithelium

growth_protocol: The cells were cultured in serum‑free LHC‑8 medium (#1708341, Gibco, USA) at 37˚C under a 95% air/5% CO2 atmosphere.

extract_protocol:
Total RNAs were extracted from cells with RNAiso Plus (TaKaRa, Dalian, China) following the manufacturer’s instruction.
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.

value: Bronchiolar epithelium

tag: cell line

tag: passages


title: BERP35T4 REP3


title: Pat01T

tag: patient id


title: TTFs-2_GHMT/TGFb inhibitor

city: Tokyo

first: Naoto

last: Muraoka

address: 35 Shinanomachi, Shinjuku-ku

department: Department of Cardiology

country: Japan

institute: Keio University School of Medicine

description: SAMPLE 7

hyb_protocol: Fragmented and labeled ss-cDNA were hybridized for 16 hr at 45°C on GeneChip Clariom S Array. GeneChips were washed and stained in the GeneChip Fluidics Station 450.

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

data_processing: Raw data were processed with Affymetrix Expression Console software version 1.4 for normalization.

source_name: GHMT transduced TTFs with TGFb inhibitor

label_protocol: Biotinylated ss-cDNA were prepared according to the standard Affymetrix protocol from 100ng total RNA (GeneChip WT PLUS Reagent Kit User Manual,  Affymetrix).Biotinylated ss-cDNA yield were checked with the NanoDrop ND-2000c Spectrophotometer.

growth_protocol: Fibroblasts were transduced with the retrovirus mixtures as indicated and DMSO, diclofenac, EP4 antagonist, PGE2, TGFb inhibitor or Wnt inhibitor was added simultaneously. The medium was replaced with FBS medium, which contained DMEM (high glucose) with L-glutamate and phenol red (Wako, Tokyo, Japan, 044-29765); Medium199 with Earle’s Salts, L-glutamate and 22 g/L sodium bicarbonate (Gibco, 11150-059); and 10% Hyclone Characterized FBS (Thermo Scientific, SV30014.03), after 24 h of infection and changed every 3 days.

extract_protocol: RNA was extracted from GHMT-, GHMT/diclofenac-, GHMT/EP4 antagonist-, GHMT/diclofenac/PGE2-, GHMT/TGFb inhibitor- or GHMT/Wnt inhibitor-induced TTFs using the ReliaPrep RNA Cell Miniprep System (Promega, Z6012) quantified using a NanoDrop-2000c spectrophotometer. Quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

tag: cell type

value: postnatal tail-tip fibroblasts (TTFs)

tag: treated with

value: TGFb inhibitor


title: Italia_ WD_ rep1

description: Gene expression

source_name: Italia, WD, rep1

tag: tissue


title: TTFs-2_GHMT/Wnt inhibitor

description: SAMPLE 8

source_name: GHMT transduced TTFs with Wnt inhibitor

value: Wnt inhibitor


title: BERP35T4 REP1


title: C3 mRNA-seq

description: control

value: whole larva

tag: exposure

tag: concentration


title: BERP35T1 REP3


title: BERP35T1 REP1


title: Italia_ OI_ rep1

description: Gene expression

source_name: Italia, OI, rep1


title: slick_L1 mRNA-seq

description:
treated
slick_L

tag: developmental stage


title: BERP35T1 REP2


title: C1 mRNA-seq

description: control


title: TTFs-2_GHMT

description: SAMPLE 5

source_name: GHMT transduced TTFs


title: TTFs-1_GHMT/diclofenac/PGE2

description: SAMPLE 4

source_name: GHMT transduced TTFs with diclofenac plus PGE2

value: diclofenac plus PGE2


title: Italia_ OI_ rep2

description: Gene expression

source_name: Italia, OI, rep2


title: Autumn Royal_ FI_ rep3

description: Gene expression

source_name: Autumn Royal, FI, rep3


title: Autumn Royal_ WD_ rep1

description: Gene expression

source_name: Autumn Royal, WD, rep1


title: TTFs-2_GHMT/EP4 antagonist

description: SAMPLE 6

source_name: GHMT transduced TTFs with EP4 antagonist

value: EP4 antagonist


title: Genome-wide occupancy of Hog1p - Replicate 2

type: genomic

city: Montreal

first: Adnane

last: Sellam

address: 5000, rue Bélanger

country: Canada

institute: Universite de Montreal

description: Agilent-062560 C. albicans whole genome probe G4499A

hyb_protocol: The microarray slides were pre-hybridized for1 hours at 42°C with DIGeasy hybridization buffer (Roche) containing 0.5 ug/ul of yeast tRNA (Roche) and 0.5 ug/ul of salmon sperm DNA (Invitrogen) and subsequently washed with 0.1X SSC and air dried. The slides were then hybridized with labeled cDNAs overnight at 42°C in DIGeasy hybridization buffer with yeast tRNA and salmon sperm DNA. The slides were washed twice for 10 min at 42°C with 1× SSC, 0.1% SDS, twice for 10 min at 37°C with 0.1× SSC, 0.1% SDS, and finally, with quick consecutive washes in three 0.1× SSC baths. Slides were air-dried.

scan_protocol: Microarray slides were scanned with a ScanArray 5000 scanner (Perkin Elmer) at 10-µm resolution. The scanning was performed using GenePix4000B scanner for the ChIP-chip slides.

data_processing: Data were normalized as following : Signal intensity was quantified with QuantArray software (Perkin Elmer) and final Lowess normalization and inspection of the data was done with the GeneSpring package GX v.7.3 (Agilent Technologies).

molecule: genomic DNA

organism: Candida albicans

source_name: WT elutriated G1 cells  grown in YPD medium at 30°C for 10 min

label_protocol: Indirect labeling with Cy3 and Cy5 was performed as described by Lavoie et al. BMC Genomics 2008, 9:578. The labeled DNA was purified with QIAquick PCR Purification Kit (Qiagen). For expression profiling experiment, 20 µg of total RNA was reverse transcribed using oligo(dT)21 in the presence of either Cy3-dCTP or Cy5-dCTP (Perkin-Elmer-Cetus/NEN) and Superscript III reverse transcriptase (Invitrogen). Thereafter, template RNA was degraded by adding 2.5 units of RNase H (USB) and 1 ug of RNase A (Pharmacia) followed by incubation for 15 min at 37°C. The labeled cDNAs were purified with QIAquick PCR Purification Kit (Qiagen).

extract_protocol: ChIP-chip experiment was performed as described by Lavoie et al. BMC Genomics 2008, 9:578. Chromatin immunoprecipitation was performed by following the protocol available at http://www.ircm.qc.ca/microsites/francoisrobert/en/317.html with the following exceptions: chromatin was sonicated to an average 300 bp, and 700 μl of whole-cell extract (WCE) were incubated with IgG-Sepharose 6 beads Fast Flow (GE Healthcare, catalog number 17-0969-01beads). RNAs were extracted as described by Sellam et al. (2009) Eukaryotic Cell 8 (8), 1174–1183, using RNeasy Mini kit (Qiagen).

treatment_protocol: for both microarrays and Chip-chip experiments, overnight cultures of hog1 mutant and WT strains were diluted to an OD600 of 0.1 in 1 L fresh YPD-uridine medium, grown at 30°C to an OD600 of 0.8 and separated into size fractions by using the Beckman JE-5.0  elutriation system at 16°C. A total of 108 unbudded G1 phase cells were harvested, released into fresh YPD medium and grown for 10 min prior to harvesting by centrifugation and stored at -80°C.

tag: strains

source_name: Hog1p-TAP under yeast conditions (YPD 30oC)


title: Autumn Royal_ FI_ rep1

description: Gene expression

source_name: Autumn Royal, FI, rep1


title: BEP2D REP2

description: The BEP2D cell line is a human papilloma-virus (HPV18)-immortalized human bronchial epithelial cell line


title: Genome-wide occupancy of Hog1p - Replicate 1


title: TTFs-1_GHMT/diclofenac

description: SAMPLE 2

source_name: GHMT transduced TTFs with diclofenac

value: diclofenac


title: Italia_ FI_ rep2

description: Gene expression

source_name: Italia, FI, rep2


title: BEP2D REP1


title: slick_L2 mRNA-seq

description:
treated
slick_L

source_name: whole embryo


title: B6.Lm_3

status: Public on Feb 19 2019

city: Philadelphia

first: daniel

last: beiting

state: PA

address: 380 S. University Ave

department: Pathobiology

institute: University of Pennsylvania

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were quantile normalized without background subtraction using Illumina GenomeStudio V1.8

source_name: whole mouse ear with Leishmania lesion

label_protocol: Biotin labeled complementary RNA (cRNA) was made using the EpiCentre Nano Total-Amp kit

growth_protocol: 6-8wk old mice were infected with 105 metacyclic-enriched parasites.  Mice were killed at 4 weeks post-infection and the infected ear was recovered.

extract_protocol: RNAlater-preserved ear tissue was weighed, minced with a razor blade, and the entire ear was homogenized in 1ml of Qiazol (Qiagen) using 3 x 20 second pulses on a  FastPrep-24 MP homogenizer (MP Biomedicals), with 5 min on ice between each pulse.  Total RNA was isolated using the Qiagen miRNeasy kit.

treatment_protocol: Ear tissue was preserved in RNAlater reagent (Qiagen) and stored at -80c.

tag: strain of mouse

tag: species of leishmania

value: major

tag: susceptibility phenotype

value: resistant

value: whole mouse ear


title: B6.Lm_4


title: TTFs-1_GHMT

description: SAMPLE 1


title: TTFs-1_GHMT/EP4 antagonist

description: SAMPLE 3

source_name: GHMT transduced TTFs with EP4 antagonis


title: Italia_ FI_ rep1

description: Gene expression

source_name: Italia, FI, rep1

value: leaf apex


title: Input_shCTCF1_DOX_Rep3

city: Madison

first: Nathan

last: Damaschke

state: WI

address: 1111 Highland Ave Room 7048

department: Urology

institute: University of Wisconsin

description: Hybridized to CytoScanHD_Array

hyb_protocol: DNA was restriction digested, methylated DNA was immunoprecipitated by 5mC antibody and purified.  Input and methylated DNA samples were PCR amplified, fragmented, labeled, and hybridized to the array individually according to manufacturer's protocols.

scan_protocol: The arrays were washed using Affymetrix fluidics stations and scanned using the Gene Chip Scanner 3000.

data_processing: Array image was acquired using Affymetrix GeneChip Operating Software (GCOS version 1.4).  Raw intensity files were extracted from .CEL files using Affymetrix Power Tools.  Input subtraction was used to normalize for copy number specific effects.  Input subtracted Log2 intensity data was used for comparison of methylated DNA enrichment.  Statistical analysis was performed using LIMMA to identify regions of significantly altered enrichment.

label: Biotin

source_name: Immortalized prostate epithelial cells

label_protocol: Labling was performed according to manufacturer's protocols (CytoScan HD Array Manual)

growth_protocol: Cell lines were grown according to standard conditions.

extract_protocol: Genomic DNA was extracted using Qiagen Dneasy blood and tissue kit according to manufacturer's protocols. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer.

treatment_protocol: Controls were treated with vehicle only (DMSO) for 5 days, CTCF knockdown samples were treated with 2 micrograms/milliliter of Doxycycline to induce shRNA targeting CTCF for 5 days.

value: Immortalized prostate epithelial cells

tag: ctcf knockdown

value: CTCF knockdown

tag: sample fraction

value: Input Control


title: 5MC_shCTCF1_DOX_Rep2

description: Hybridized to CytoScanHD_Array

value: 5mC antibody enriched


title: C2 mRNA-seq

description: control

value: control


title: Input_shCTCF1_DMSO_Rep1

description: Hybridized to CytoScanHD_Array

value: No knockdown control


title: Balb.Lm_4

value: Balb/C

value: suseptible


title: B6.Lb_5

value: braziliensis


title: Balb.Lm_5


title: B6.Lm_1


title: 5MC_shCTCF1_DMSO_Rep2

description: Hybridized to CytoScanHD_Array


title: Balb.Lm_3


title: B6.Lb_3


title: Input_shCTCF1_DOX_Rep2

description: Hybridized to CytoScanHD_Array


title: Input_shCTCF1_DMSO_Rep3

description: Hybridized to CytoScanHD_Array


title: 5MC_shCTCF1_DOX_Rep1

description: Hybridized to CytoScanHD_Array


title: 5MC_shCTCF1_DMSO_Rep3

description: Hybridized to CytoScanHD_Array


title: Balb.Lb_3


title: 200277210003_R06C02: saliva_118

city: Iowa City

first: Gen

last: Shinozaki

state: IA

address: University of Iowa Hospitals and Clinics, 200 Hawkins Dr

department: Psychiatry

institute: University of Iowa

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 and EPIC Beadchips using standard Illumina protocol

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

data_processing: Background correction was performed with the Noob method in Minfi. Using RnBeads, probes were filtered out if they: 1) overlapped within 5 bp of a SNP, 2) had a detection P-value > 0.01 or were considered unreliable measures based on RnBeads’s greedy-cut algorithm, or 3) were context-specific sites. Samples were normalized with beta mixture quantile dilation (BMIQ).

label: Cy5 and Cy3

source_name: saliva from subject 118

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted with the MasterPureTM DNA extraction kit (Epicenter, MCD85201) following the respective protocols for each tissue type. DNA quality was assessed with NanoDrop spectrometry and quantified with the Qubit™ dsDNA Broad Range Assay Kit (ThermoFisher Scientific, Q32850).

tag: slide

tag: array

tag: subject

value: saliva

tag: Sex

tag: age

value: Male


title: 5MC_shCTCF1_DOX_Rep3

description: Hybridized to CytoScanHD_Array


title: 200078650139_R03C02: brain_118

source_name: brain from subject 118

value: Hippocampus


title: 5MC_shCTCF1_DMSO_Rep1

description: Hybridized to CytoScanHD_Array


title: Balb.Lm_2


title: 200078650093_R04C02: brain_116

source_name: brain from subject 116

value: Frontal lobe

value: Female


title: B6.naive_3

value: uninfected


title: 200078650139_R04C02: brain_118

value: Amygdala


title: 200277210003_R03C02: saliva_116

source_name: saliva from subject 116


title: B6.Lb_2

value: resistant

value: whole mouse ear


title: B6.naive_2


title: Balb.Lm_1

value: major


title: Balb.Lb_4


title: B6.Lb_1


title: Balb.Lb_2


title: BEP2D REP3

source_name: Bronchiolar epithelium

value: Bronchiolar epithelium

tag: cell line

tag: passages


title: Balb.Lb_1

tag: tissue


title: Balb.naive_1


title: 200277210003_R05C02: brain_118

value: Temporal cortex


title: BUC018_WB: Control_whole blood

city: Hong Kong

first: Brian

last: Chung

state: Hong Kong

address: 102 Pokfulam Road

department: Paediatrics and Adolescent Medicine

country: Hong Kong

institute: The University of Hong Kong

data_processing: Intensities were normalized using Illumina’s internal normalization probes and algorithms.

source_name: Control_whole blood

label_protocol: Standard Illumina labeling protocol

growth_protocol: Blood samples were kept at room temperature and processed within 30 min of the blood draw

extract_protocol: DNA was extracted from whole blood using FlexiGene DNA Kit according to the manufacturer’s protocol (Qiagen). DNA samples were then bisulfite converted using the EpiTect Bisulfite Kit according to the manufacturer’s protocol (Qiagen)

treatment_protocol: Peripheral blood mononuclear cells (PMBCs) were separated from red blood cells and polynuclear cells using Ficoll-Paque PLUS (GE Healthcare, Chicago, USA). Isolated PBMCs were sequentially incubated with anti-CD19, anti-CD8, and anti-CD4 microbeads (Miltenyi Biotec, Bergisch, Germany). Red blood cells and polynuclear cells were separated using 3% dextran (Fisher Scientific, Hampton, USA), as previously reported, and neutrophils were subsequently isolated using anti-CD16 microbeads (Miltenyi Biotec, Bergisch, Germany). The purity of each cell lineage was evaluated by flow cytometry.

tag: diagnosis

value: Control

tag: gender

value: whole blood


title: 200277210028_R04C02: brain_115

source_name: brain from subject 115


title: 200078650139_R06C01: brain_115


title: 200277210003_R04C02: blood_118

source_name: blood from subject 118

value: blood


title: Balb.naive_2

value: Balb/C


title: SLE023_WB: SLE patient_whole blood

source_name: SLE patient_whole blood

value: systemic lupus erythematosus (SLE)


title: Balb.naive_3


title: 200078650139_R05C01: brain_115


title: 200277210028_R06C02: saliva_115

source_name: saliva from subject 115

value: saliva


title: Input_shCTCF1_DMSO_Rep2

description: Hybridized to CytoScanHD_Array

value: Immortalized prostate epithelial cells

value: No knockdown control

value: Input Control


title: 200277210028_R03C02: blood_115

source_name: blood from subject 115

value: Male


title: Input_shCTCF1_DOX_Rep1

description: Hybridized to CytoScanHD_Array

value: CTCF knockdown


title: BUC023_WB: Control_whole blood

value: Female


title: 200277210003_R02C02: blood_116

source_name: blood from subject 116


title: BUC025_WB: Control_whole blood


title: BUC021_WB: Control_whole blood


title: 200277210028_R02C02: saliva_114

source_name: saliva from subject 114


title: 200078650139_R02C01: brain_114

source_name: brain from subject 114

value: Amygdala


title: 200277210028_R05C01: blood_114

source_name: blood from subject 114


title: 200277210028_R06C01: brain_114

value: Hippocampus


title: BUC026_8T: Control_purified CD8+ T cells

source_name: Control_purified CD8+ T cells

value: purified CD8+ T cells


title: 200277210028_R01C02: brain_114


title: 200277210003_R01C02: saliva_113

source_name: saliva from subject 113


title: BUC026_WB: Control_whole blood


title: SLE019_9B: SLE patient_purified B cells

source_name: SLE patient_purified B cells

value: purified B cells


title: BUC014_9B: Control_purified CD19+ B cells

source_name: Control_purified CD19+ B cells

value: purified CD19+ B cells


title: 200277210003_R05C01: brain_113

source_name: brain from subject 113

value: Frontal lobe


title: 200078650093_R02C02: saliva_111

source_name: saliva from subject 111


title: 200277210003_R04C01: blood_113

source_name: blood from subject 113


title: BUC014_6N: Control_purified CD16+ neutrophils

source_name: Control_purified CD16+ neutrophils

value: Control

value: purified CD16+ neutrophils


title: SLE022_4T: SLE patient_purified CD4+ T cells

source_name: SLE patient_purified CD4+ T cells

value: purified CD4+ T cells


title: SLE018_8T: SLE patient_purified CD8+ T cells

source_name: SLE patient_purified CD8+ T cells

value: systemic lupus erythematosus (SLE)


title: BUC022_WB: Control_whole blood

source_name: Control_whole blood

value: whole blood


title: SLE027_8T: SLE patient_purified CD8+ T cells


title: 200078650093_R06C01: brain_111

source_name: brain from subject 111


title: 3999142156_R04C02: brain_110

source_name: brain from subject 110

value: Insular cortex


title: SLE007_8T: SLE patient_purified CD8+ T cells


title: BUC020_6N: Control_purified CD16+ neutrophils


title: 200277210028_R01C01: blood_111

source_name: blood from subject 111

value: blood


title: B6.naive_1

source_name: whole mouse ear with Leishmania lesion

value: uninfected

value: whole mouse ear


title: 3999142156_R05C02: saliva_110

source_name: saliva from subject 110

value: saliva

value: Male


title: 3999142156_R06C02: blood_110

source_name: blood from subject 110


title: SLE026_WB: SLE patient_whole blood

source_name: SLE patient_whole blood

value: Female


title: SLE007_WB: SLE patient_whole blood


title: 3999119036_R05C02: saliva_109

source_name: saliva from subject 109


title: 200277210028_R03C01: brain_111

value: Temporal cortex


title: SLE011_6N: SLE patient_purified CD16+ neutrophils

source_name: SLE patient_purified CD16+ neutrophils


title: BUC024_4T: Control_purified CD4+ T cells

source_name: Control_purified CD4+ T cells


title: SLE020_8T: SLE patient_purified CD8+ T cells

value: purified CD8+ T cells


title: 3999119036_R03C02: brain_109

source_name: brain from subject 109

value: Hippocampus


title: 3999119036_R06C02: blood_109

source_name: blood from subject 109


title: BUC022_6N: Control_purified CD16+ neutrophils


title: 200277210028_R02C01: brain_111

value: Amygdala


title: SLE014_6N: SLE patient_purified CD16+ neutrophils


title: 200078650093_R04C01: saliva_107

source_name: saliva from subject 107


title: 200078650093_R02C01: brain_107

source_name: brain from subject 107


title: 200078650093_R03C01: brain_107


title: SLE008_WB: SLE patient_whole blood


title: BUC016_9B: Control_purified CD19+ B cells

source_name: Control_purified CD19+ B cells

value: purified CD19+ B cells


title: Case4

city: Barcelona

first: Joan

middle: Enric

last: Ramiz-Zaldivar

address: Rosselló, 153

department: Molecular Pathology Laboratory

country: Spain

institute: IDIBAPS

hyb_protocol: Samples were hybridized onto GenomeWideSNP_6 Affymetrix Genome-Wide Human SNP 6.0 Arrayand were washed and stained with GeneChip Fluidics Station 450 (Affymetrix)

scan_protocol: GeneChip Scanner 3000 7G (Affymetrix)

data_processing:
CHP file generated by Genotyping Console 4.1.3 (SNP6).
[Primary data description] Nexus biodiscovery 9.0 edition Software. Gains and losses were evaluated with visual inspection by 2 different observers using Nexus Biodiscovery software (Biodiscovery, Hawthorne CA, USA). The CNAs with a minimum size of 100kb were considered real. Loss of heterozygosity regions were considered when size was >5Mb. See "Global table of CN and CNN-LOH.xlsx" linked to the SuperSeries record.

source_name: Submaxilar Lymph Node

extract_protocol: DNAs from frozen tissues samples were extracted using the QIAamp DNA Mini Kit.

tag: disease state

value: Burkitt like lymphoma with 11q

value: female

value: Submaxilar Lymph Node

tag: sample type

value: frozen tissue


title: BUC019_4T: Control_purified CD4+ T cells

value: Control

value: purified CD4+ T cells


title: BUC016_WB: Control_whole blood

source_name: Control_whole blood

value: whole blood


title: 200277210003_R01C01: blood_107

source_name: blood from subject 107

value: blood


title: SLE021_9B: SLE patient_purified B cells

source_name: SLE patient_purified B cells

value: systemic lupus erythematosus (SLE)

value: purified B cells


title: B6.Lm_2

tag: strain of mouse

value: major

value: resistant

value: whole mouse ear


title: 3999119036_R05C01: brain_106

source_name: brain from subject 106

value: Frontal lobe

value: Male


title: SLE007_9B: SLE patient_purified B cells

value: Female


title: 3999119036_R01C02: saliva_106

source_name: saliva from subject 106

value: saliva


title: BUC021_6N: Control_purified CD16+ neutrophils

source_name: Control_purified CD16+ neutrophils

value: purified CD16+ neutrophils


title: BUC025_8T: Control_purified CD8+ T cells

source_name: Control_purified CD8+ T cells

value: purified CD8+ T cells


title: 3999142156_R02C02: saliva_105

source_name: saliva from subject 105


title: 3999142156_R06C01: brain_105

source_name: brain from subject 105

value: Temporal cortex


title: 3999119036_R01C01: brain_102

source_name: brain from subject 102


title: BUC015_4T: Control_purified CD4+ T cells

source_name: Control_purified CD4+ T cells


title: 3999119036_R04C01: blood_102

source_name: blood from subject 102


title: SLE010_8T: SLE patient_purified CD8+ T cells

source_name: SLE patient_purified CD8+ T cells


title: BUC023_9B: Control_purified CD19+ B cells

value: purified CD19+ B cells


title: 3999119036_R02C02: blood_106

source_name: blood from subject 106


title: SLE007_4T: SLE patient_purified CD4+ T cells

source_name: SLE patient_purified CD4+ T cells


title: 3999142156_R03C02: blood_105

source_name: blood from subject 105


title: 200277210003_R02C01: brain_107

source_name: brain from subject 107

value: Hippocampus


title: BUC016_6N: Control_purified CD16+ neutrophils

value: Control


title: BUC015_9B: Control_purified CD19+ B cells

source_name: Control_purified CD19+ B cells


title: SLE014_8T: SLE patient_purified CD8+ T cells


title: BUC018_9B: Control_purified CD19+ B cells


title: SLE017_6N: SLE patient_purified CD16+ neutrophils

source_name: SLE patient_purified CD16+ neutrophils


title: BUC021_9B: Control_purified CD19+ B cells


title: SLE008_6N: SLE patient_purified CD16+ neutrophils


title: SLE021_6N: SLE patient_purified CD16+ neutrophils


title: SLE011_WB: SLE patient_whole blood

source_name: SLE patient_whole blood

value: whole blood


title: SLE027_9B: SLE patient_purified B cells

source_name: SLE patient_purified B cells


title: SLE011_9B: SLE patient_purified B cells


title: 3999119036_R03C01: saliva_102

source_name: saliva from subject 102


title: SLE005_WB: SLE patient_whole blood


title: BUC026_9B: Control_purified CD19+ B cells


title: SLE022_9B: SLE patient_purified B cells


title: SLE023_6N: SLE patient_purified CD16+ neutrophils


title: SLE014_4T: SLE patient_purified CD4+ T cells

value: purified CD4+ T cells


title: B6.Lb_4

source_name: whole mouse ear with Leishmania lesion

tag: species of leishmania

value: braziliensis


title: BUC014_4T: Control_purified CD4+ T cells


title: SLE021_4T: SLE patient_purified CD4+ T cells

value: systemic lupus erythematosus (SLE)


title: BUC023_6N: Control_purified CD16+ neutrophils

source_name: Control_purified CD16+ neutrophils


title: BUC021_4T: Control_purified CD4+ T cells


title: SLE010_4T: SLE patient_purified CD4+ T cells


title: SLE022_WB: SLE patient_whole blood


title: SLE021_WB: SLE patient_whole blood


title: BUC019_6N: Control_purified CD16+ neutrophils


title: BUC026_4T: Control_purified CD4+ T cells


title: BUC016_4T: Control_purified CD4+ T cells


title: BUC024_6N: Control_purified CD16+ neutrophils


title: SLE020_6N: SLE patient_purified CD16+ neutrophils


title: BUC019_8T: Control_purified CD8+ T cells

source_name: Control_purified CD8+ T cells


title: SLE017_8T: SLE patient_purified CD8+ T cells


title: BUC028_WB: Control_whole blood

source_name: Control_whole blood


title: SLE011_4T: SLE patient_purified CD4+ T cells


title: SLE023_8T: SLE patient_purified CD8+ T cells


title: BUC018_4T: Control_purified CD4+ T cells


title: BUC023_4T: Control_purified CD4+ T cells


title: SLE013_4T: SLE patient_purified CD4+ T cells


title: SLE018_9B: SLE patient_purified B cells

value: purified B cells


title: SLE019_6N: SLE patient_purified CD16+ neutrophils


title: SLE023_9B: SLE patient_purified B cells


title: SLE010_9B: SLE patient_purified B cells


title: BUC028_6N: Control_purified CD16+ neutrophils


title: BUC024_WB: Control_whole blood


title: BUC018_6N: Control_purified CD16+ neutrophils


title: SLE018_WB: SLE patient_whole blood


title: SLE018_6N: SLE patient_purified CD16+ neutrophils


title: SLE008_8T: SLE patient_purified CD8+ T cells


title: BUC022_9B: Control_purified CD19+ B cells


title: BUC026_6N: Control_purified CD16+ neutrophils


title: SLE007_6N: SLE patient_purified CD16+ neutrophils


title: BUC020_8T: Control_purified CD8+ T cells


title: SLE010_6N: SLE patient_purified CD16+ neutrophils


title: SLE010_WB: SLE patient_whole blood


title: SLE017_WB: SLE patient_whole blood


title: BUC018_8T: Control_purified CD8+ T cells


title: SLE005_4T: SLE patient_purified CD4+ T cells


title: BUC028_8T: Control_purified CD8+ T cells


title: SLE008_4T: SLE patient_purified CD4+ T cells


title: BUC015_6N: Control_purified CD16+ neutrophils


title: SLE022_8T: SLE patient_purified CD8+ T cells


title: SLE020_WB: SLE patient_whole blood


title: BUC024_9B: Control_purified CD19+ B cells


title: SLE027_4T: SLE patient_purified CD4+ T cells


title: SLE021_8T: SLE patient_purified CD8+ T cells


title: BUC016_8T: Control_purified CD8+ T cells


title: SLE005_6N: SLE patient_purified CD16+ neutrophils


title: SLE018_4T: SLE patient_purified CD4+ T cells


title: SLE026_8T: SLE patient_purified CD8+ T cells


title: SLE020_4T: SLE patient_purified CD4+ T cells


title: SLE017_9B: SLE patient_purified B cells


title: BUC025_6N: Control_purified CD16+ neutrophils


title: SLE013_6N: SLE patient_purified CD16+ neutrophils


title: BUC020_4T: Control_purified CD4+ T cells


title: BUC014_8T: Control_purified CD8+ T cells


title: SLE013_8T: SLE patient_purified CD8+ T cells


title: SLE022_6N: SLE patient_purified CD16+ neutrophils


title: BUC014_WB: Control_whole blood


title: SLE014_9B: SLE patient_purified B cells


title: SLE019_8T: SLE patient_purified CD8+ T cells


title: SLE019_4T: SLE patient_purified CD4+ T cells


title: BUC028_4T: Control_purified CD4+ T cells


title: BUC025_4T: Control_purified CD4+ T cells


title: BUC028_9B: Control_purified CD19+ B cells


title: SLE027_WB: SLE patient_whole blood


title: SLE023_4T: SLE patient_purified CD4+ T cells


title: BUC023_8T: Control_purified CD8+ T cells


title: SLE026_9B: SLE patient_purified B cells


title: SLE013_9B: SLE patient_purified B cells


title: SLE005_8T: SLE patient_purified CD8+ T cells


title: BUC015_8T: Control_purified CD8+ T cells


title: SLE026_6N: SLE patient_purified CD16+ neutrophils


title: BUC022_4T: Control_purified CD4+ T cells


title: BUC021_8T: Control_purified CD8+ T cells


title: SLE017_4T: SLE patient_purified CD4+ T cells


title: BUC020_WB: Control_whole blood


title: SLE005_9B: SLE patient_purified B cells


title: SLE011_8T: SLE patient_purified CD8+ T cells


title: SLE013_WB: SLE patient_whole blood


title: SLE008_9B: SLE patient_purified B cells


title: BUC019_9B: Control_purified CD19+ B cells


title: BUC015_WB: Control_whole blood


title: SLE014_WB: SLE patient_whole blood


title: BUC024_8T: Control_purified CD8+ T cells


title: BUC025_9B: Control_purified CD19+ B cells


title: BUC020_9B: Control_purified CD19+ B cells


title: 201502850030_R04C01: brain_pos_113

source_name: brain_pos from subject 113

value: Hippocampus head


title: SLE027_6N: SLE patient_purified CD16+ neutrophils


title: 200607090089_R08C01: brain_pos_111

source_name: brain_pos from subject 111

value: Medial frontal ventral cortex


title: SLE019_WB: SLE patient_whole blood


title: 201502810025_R05C01: brain_pos_120

source_name: brain_pos from subject 120

value: Temporal pole


title: BUC022_8T: Control_purified CD8+ T cells


title: 201502810007_R02C01: brain_pos_109

source_name: brain_pos from subject 109

value: Occipital area

value: Male


title: 201502810025_R02C01: brain_neg_120

source_name: brain_neg from subject 120


title: 201502850007_R03C01: brain_neg_113

source_name: brain_neg from subject 113


title: BUC019_WB: Control_whole blood

value: Female


title: 201501980013_R03C01: brain_neg_115

source_name: brain_neg from subject 115


title: 201501980047_R01C01: brain_neg_114

source_name: brain_neg from subject 114

value: Lateral temporal cortex


title: 200607090089_R01C01: brain_pos_110

source_name: brain_pos from subject 110


title: 200607090061_R08C01: brain_neg_104

source_name: brain_neg from subject 104


title: 200607090075_R04C01: brain_neg_105

source_name: brain_neg from subject 105

value: Frontal cortex


title: 200607090061_R04C01: brain_neg_101

source_name: brain_neg from subject 101

value: Temporal cortex


title: 200607090075_R08C01: brain_neg_106

source_name: brain_neg from subject 106


title: 201502810041_R02C01: brain_whole_121

source_name: brain_whole from subject 121


title: 201502810007_R06C01: brain_neg_109

source_name: brain_neg from subject 109


title: SLE026_4T: SLE patient_purified CD4+ T cells

source_name: SLE patient_purified CD4+ T cells


title: SLE020_9B: SLE patient_purified B cells

source_name: SLE patient_purified B cells


title: 201502810025_R07C01: brain_whole_120

source_name: brain_whole from subject 120


title: 201502800040_R04C01: brain_neg_119

source_name: brain_neg from subject 119


title: BM2_30 [RHC6968]

city: Singapore

first: WENTING

last: LIU

address: #02-01 GENOME 60 BIOPOLIS STREET

country: Singapore

institute: Genome Institute of Singapore

data_processing:
Paired-end sequencing fastq files were processed using Bowtie2 2.3.0
Aligned to the H.sapiens NCBI GRCh38 reference genome using Spliced Transcripts Alignment to a Reference (STAR) software
SAMTools was used to extract the aligned reads
Gene expression counts were estimated using root square mean error (RSME)
Genome_build: NCBI GRCh38 reference genome
Supplementary_files_format_and_content: csv file

source_name: Bone marrow sample 2_hBMMSC

growth_protocol: hBMMSCs were cultured in commercial medium provided by the manufacturers.

extract_protocol:
RNA was extracted using 0.2% (vol/vol) Triton X-100 containing 1uL RNAse inhibitor.
Smart-seq2 protocol (Picelli et al., Nature Protocols, 2014: 9(1):171-180)

tag: tissue type/id#

value: Bone marrow sample 2

tag: cell type

value: Bone marrow mesenchymal stem cell (hBMMSC)


title: BM2_29 [RHC6967]


title: BM2_31 [RHC6969]


title: 201502800051_R02C01: brain_whole_118

source_name: brain_whole from subject 118


title: BM2_28 [RHC6966]


title: BM2_26 [RHC6964]


title: BM2_24 [RHC6962]


title: BM2_27 [RHC6965]


title: 201501980012_R05C01: brain_whole_116

source_name: brain_whole from subject 116


title: 201502800036_R04C01: brain_whole_117

source_name: brain_whole from subject 117

value: Inferior lateral temporal cortex


title: 201501980013_R01C01: brain_whole_115

source_name: brain_whole from subject 115

value: Hippocampus


title: BM2_25 [RHC6963]


title: 200607090086_R08C01: brain_neg_110

source_name: brain_neg from subject 110


title: BM2_22 [RHC6960]


title: BM2_21 [RHC6959]


title: 200607090089_R06C01: brain_neg_111

source_name: brain_neg from subject 111


title: BM2_23 [RHC6961]


title: BM2_20 [RHC6958]


title: BM2_19 [RHC6957]


title: 201502850030_R08C01: brain_whole_113

source_name: brain_whole from subject 113


title: 201501980013_R02C01: brain_whole_114

source_name: brain_whole from subject 114


title: BM2_18 [RHC6956]


title: 200392810089_R01C01: brain_whole_112

source_name: brain_whole from subject 112

value: Left frontal


title: BM2_16 [RHC6954]


title: BM2_17 [RHC6955]


title: BM2_15 [RHC6953]


title: 201502800036_R02C01: brain_whole_119

source_name: brain_whole from subject 119


title: 200607090089_R04C01: brain_whole_111

source_name: brain_whole from subject 111


title: BM2_14 [RHC6952]


title: BM2_13 [RHC6951]


title: BM2_11 [RHC6949]


title: BM2_10 [RHC6948]


title: BM2_9 [RHC6947]


title: 200392810022_R03C01: brain_whole_107

source_name: brain_whole from subject 107


title: 200392810022_R04C01: brain_whole_108

source_name: brain_whole from subject 108


title: BM2_8 [RHC6946]


title: BM2_7 [RHC6945]


title: 200607090075_R07C01: brain_whole_106

source_name: brain_whole from subject 106


title: BM2_3 [RHC6941]


title: BM2_4 [RHC6942]


title: BM2_6 [RHC6944]


title: 200607090075_R03C01: brain_whole_105

source_name: brain_whole from subject 105


title: BM1_32 [RHU299]

source_name: Bone marrow sample 1_hBMMSC

value: Bone marrow sample 1


title: BM2_1 [RHC6939]

source_name: Bone marrow sample 2_hBMMSC


title: 200607090061_R07C01: brain_whole_104

source_name: brain_whole from subject 104


title: BM1_31 [RHU298]


title: 200607090086_R07C01: brain_whole_110

source_name: brain_whole from subject 110


title: BM1_30 [RHU297]


title: 201502810008_R04C01: brain_whole_109

source_name: brain_whole from subject 109


title: BM2_12 [RHC6950]


title: BM1_29 [RHU296]


title: 200392800020_R04C01: brain_whole_103

source_name: brain_whole from subject 103


title: BM2_5 [RHC6943]


title: NSC Day 10 POU3F2oe dish 2 techrep 2

first: Jocelynn

middle: Renee

last: Pearl

state: Washington

address: 401 Terry Ave N

institute: Institute for Systems Biology

description: Gene expression of hNSCs 10 days after lentiviral transduction with POU3F2 overexpression virus and puromycin selection

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Human GE v2 8x60K Microarrays (G4852A) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by compressed air.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner using the Agilent G3-1-color scan setting for 8x60k arrays.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 39494_D_F_20120628).

source_name: neural stem cells

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 200 ng total RNA using Agilent’s Low Input Quick Amp One-Color Labeling Kit according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: NSC lines were grown in neural expansion media (NEM) supplemented with EGF and FGF-2 (20 ng/ml) (PeproTech) on laminin (Sigma L2020) -coated polystyrene plates and passaged as previously described81. Neural expansion media (NEM): NeuroCult NS-A Basal Medium (Stem Cell Technologies), DMEM/F12, Antibiotic-Antimycotic, GlutaMax, B-27 supplement, N-2 supplement, 1:1000 EGF, and 1:1000 FGF. Cells were detached from their plates using Accutase (Millipore).

extract_protocol: Total RNA was extracted using the miRNeasy extraction kit (Qiagen) at three days and ten days post-puromycin selection of lentiviral transduced hNSCs.  Two individual RNA extractions were performed from each plate at each time point, and each viral construct was transduced into two plates of cells.

treatment_protocol: VSV-G pseudotyped, self-inactivating lentivirus was prepared by transfecting 293T cells with 1.5 μg pVSV-G, 3 μg psPAX-2, and 6 μg pRRL lentiviral vectors - either lenti-SFFV-POU3F2-Myc-DDK or a control vector without the POU3F2-Myc-DDK cassette. Lentiviral supernatants were collected 48 hours later and transferred to human neural stem cells dishes (MOI = ~ 1).  Positively transduced cells were selected with 0.6 ug/mL puromycin for 3 days. Gene editing was evaluated using the SurveyorⓇ Assay (Integrated DNA Technologies).  Overexpression was evaluated using qRT-PCR and Western blotting.

tag: isolate

value: fetal

tag: source

value: primary isolates

tag: hyb slide id

tag: treatment

value: POU3F2 overexpression

tag: time

value: Day 10


title: BM1_28 [RHU295]


title: 200392800020_R07C01: brain_whole_102

source_name: brain_whole from subject 102

tag: slide

tag: array

tag: subject

tag: Sex

tag: age


title: NSC Day 10 POU3F2oe dish 2 techrep 1


title: BM2_2 [RHC6940]


title: NSC Day 10 POU3F2oe dish 1 techrep 1


title: BM1_27 [RHU294]


title: 200607090061_R03C01: brain_whole_101

source_name: brain_whole from subject 101

tag: tissue


title: NSC Day 10 POU3F2oe dish 1 techrep 2


title: BM1_26 [RHU293]


title: 201502810041_R04C01: blood_121

source_name: blood from subject 121

value: blood


title: BM1_24 [RHU291]


title: BM1_21 [RHU288]


title: BM1_22 [RHU289]


title: BM1_23 [RHU290]


title: 201502800040_R03C01: blood_119

source_name: blood from subject 119


title: BM1_20 [RHU287]


title: 201502810008_R03C01: blood_120

source_name: blood from subject 120


title: BM1_18 [RHU285]


title: BM1_19 [RHU286]


title: NSC Day 10 Control dish 1 techrep 1

description: Gene expression of hNSCs 10 days after lentiviral transduction with control virus and puromycin selection

value: control virus


title: BM1_17 [RHU284]


title: NSC Day 10 Control dish 1 techrep 2


title: NSC Day 10 Control dish 2 techrep 2


title: BM1_25 [RHU292]


title: BM1_15 [RHU282]


title: NSC Day 3 POU3F2oe dish 2 techrep 2

description: Gene expression of hNSCs 3 days after lentiviral transduction with POU3F2 overexpression virus and puromycin selection

value: Day 3


title: NSC Day 3 POU3F2oe dish 1 techrep 1


title: NSC Day 3 POU3F2oe dish 2 techrep 1


title: NSC Day 10 Control dish 2 techrep 1


title: BM1_16 [RHU283]


title: 201502800051_R06C01: blood_117

source_name: blood from subject 117

value: Female


title: NSC Day 3 Control dish 2 techrep 2

description: Gene expression of hNSCs 3 days after lentiviral transduction with control virus and puromycin selection


title: 201502800040_R05C01: blood_118

source_name: blood from subject 118

value: Male


title: 201501980047_R06C01: blood_116

source_name: blood from subject 116


title: NSC Day 3 POU3F2oe dish 1 techrep 2


title: BM1_14 [RHU281]


title: BM1_13 [RHU280]


title: BM1_11 [RHU278]


title: 201501980044_R06C01: blood_114

source_name: blood from subject 114


title: 201501980044_R04C01: blood_115

source_name: blood from subject 115


title: BM1_12 [RHU279]

source_name: Bone marrow sample 1_hBMMSC


title: NSC Day 3 Control dish 2 techrep 1


title: BM1_9 [RHU276]


title: BM1_7 [RHU274]


title: BM1_8 [RHU275]


title: BM1_6 [RHU273]


title: 200392810089_R02C01: blood_112

source_name: blood from subject 112


title: BM1_4 [RHU271]


title: BM1_5 [RHU272]


title: NSC Day 3 Control dish 1 techrep 1


title: NSC Day 3 Control dish 1 techrep 2


title: 200392810089_R05C01: blood_113

source_name: blood from subject 113


title: 200392810139_R06C01: blood_111

source_name: blood from subject 111


title: BM1_3 [RHU270]


title: BM1_10 [RHU277]


title: 200392810139_R02C01: blood_109

source_name: blood from subject 109


title: W2_30 [RHH6001]

source_name: Cord 2_hWJSC

growth_protocol: hWJSCs were cultured in the hWJSC medium that comprised of DMEM high glucose supplemented with 20% fetal bovine serum (FBS) (Hyclone), 1% non-essential amino acids, 2 mM L-glutamine, 0.1 mM β-mercaptoethanol, 1% insulin-transferrin-selenium (ITS), antibiotic-antimycotic mixture (Invitrogen) and 16 ng/ml basic fibroblast growth factor (bFGF) (Merck Millipore).

value: Cord 2

value: Whartons jelly stem cell (hWJSC)


title: BM1_1 [RHU268]


title: BM1_2 [RHU269]


title: W2_32 [RHH6003]


title: 200392810139_R03C01: blood_106

source_name: blood from subject 106


title: 200392810022_R06C01: blood_107

source_name: blood from subject 107


title: 200392810139_R05C01: blood_110

source_name: blood from subject 110


title: W2_28 [RHH5999]


title: W2_31 [RHH6002]


title: W2_27 [RHH5998]


title: W2_25 [RHH5996]


title: W2_23 [RHH5994]


title: W2_24 [RHH5995]


title: W2_22 [RHH5993]


title: 200392810139_R01C01: blood_104

source_name: blood from subject 104


title: W2_20 [RHH5991]


title: 200392810139_R04C01: blood_105

source_name: blood from subject 105


title: W2_18 [RHH5989]


title: W2_19 [RHH5990]


title: 200392810022_R08C01: blood_108

source_name: blood from subject 108


title: W2_17 [RHH5988]


title: 200392800020_R06C01: blood_102

source_name: blood from subject 102


title: W2_29 [RHH6000]


title: W2_14 [RHH5985]


title: W2_16 [RHH5987]


title: 200392800020_R01C01: blood_103

source_name: blood from subject 103


title: 200392810139_R08C01: blood_101

source_name: blood from subject 101


title: W2_15 [RHH5986]


title: W2_12 [RHH5983]


title: W2_13 [RHH5984]


title: W2_11 [RHH5982]


title: W2_10 [RHH5981]


title: 201502800036_R08C01: saliva_119

source_name: saliva from subject 119

value: saliva


title: W2_8 [RHH5979]


title: W2_6 [RHH5977]


title: 201502810007_R04C01: saliva_120

source_name: saliva from subject 120


title: W2_5 [RHH5976]


title: W2_9 [RHH5980]


title: W2_7 [RHH5978]


title: 201502800019_R08C01: saliva_117

source_name: saliva from subject 117


title: 201502800019_R03C01: saliva_118

source_name: saliva from subject 118


title: W2_2 [RHH5973]


title: W3_39 [RHH5946]

source_name: Cord 3_hWJSC

value: Cord 3


title: 201502810025_R08C01: saliva_121

source_name: saliva from subject 121


title: W3_38 [RHH5945]


title: W3_37 [RHH5944]


title: W3_40 [RHH5947]


title: W3_36 [RHH5943]


title: W3_33 [RHH5940]


title: 201501980044_R01C01: saliva_114

source_name: saliva from subject 114


title: 200392810089_R06C01: saliva_113

source_name: saliva from subject 113


title: W3_34 [RHH5941]


title: 200392810089_R04C01: saliva_112

source_name: saliva from subject 112


title: W3_31 [RHH5938]


title: W3_30 [RHH5937]


title: W3_32 [RHH5939]


title: W3_29 [RHH5936]


title: W3_28 [RHH5935]


title: 200607090089_R02C01: saliva_111

source_name: saliva from subject 111


title: W3_26 [RHH5933]


title: W3_27 [RHH5934]


title: 201501980013_R08C01: saliva_116

source_name: saliva from subject 116


title: W3_24 [RHH5931]


title: 200607090086_R01C01: saliva_109

source_name: saliva from subject 109


title: 201501980047_R04C01: saliva_115

source_name: saliva from subject 115


title: W3_23 [RHH5930]


title: 200392810022_R05C01: saliva_107

source_name: saliva from subject 107


title: 200392810022_R01C01: saliva_108

source_name: saliva from subject 108


title: W3_21 [RHH5928]


title: W3_22 [RHH5929]


title: W3_35 [RHH5942]


title: W3_19 [RHH5926]


title: W3_20 [RHH5927]


title: W3_18 [RHH5925]


title: 200607090075_R05C01: saliva_106

source_name: saliva from subject 106


title: W3_17 [RHH5924]


title: 200607090061_R05C01: saliva_104

source_name: saliva from subject 104


title: 200607090075_R01C01: saliva_105

source_name: saliva from subject 105


title: W3_16 [RHH5923]


title: 200392800020_R03C01: saliva_103

source_name: saliva from subject 103


title: 200607090086_R05C01: saliva_110

source_name: saliva from subject 110


title: W3_14 [RHH5921]


title: W3_13 [RHH5920]


title: W3_15 [RHH5922]


title: W3_12 [RHH5919]


title: 200392800020_R08C01: saliva_102

source_name: saliva from subject 102


title: W3_25 [RHH5932]

source_name: Cord 3_hWJSC


title: 200607090061_R01C01: saliva_101

source_name: saliva from subject 101


title: W3_11 [RHH5918]


title: W3_9 [RHH5916]


title: W3_10 [RHH5917]


title: W3_6 [RHH5913]


title: W3_7 [RHH5914]


title: W3_8 [RHH5915]


title: W3_5 [RHH5912]


title: W3_4 [RHH5911]


title: 201502810025_R01C01: buccal_120

source_name: buccal from subject 120

value: buccal


title: W3_3 [RHH5910]


title: 201502810041_R08C01: buccal_121

source_name: buccal from subject 121


title: 201502800019_R02C01: buccal_119

source_name: buccal from subject 119


title: 201502800040_R07C01: buccal_118

source_name: buccal from subject 118


title: W3_2 [RHH5909]


title: 201502800036_R03C01: buccal_117

source_name: buccal from subject 117


title: W1_30 [RHC6906]

source_name: Cord 1_hWJSC

value: Cord 1


title: W3_1 [RHH5908]


title: W1_31 [RHC6907]


title: W1_28 [RHC6904]


title: 201501980047_R05C01: buccal_116

source_name: buccal from subject 116


title: W1_27 [RHC6903]


title: 201501980044_R02C01: buccal_115

source_name: buccal from subject 115


title: W1_24 [RHC6900]


title: W1_29 [RHC6905]


title: 201501980012_R06C01: buccal_114

source_name: buccal from subject 114


title: W1_26 [RHC6902]


title: W1_23 [RHC6899]


title: 200392810089_R08C01: buccal_113

source_name: buccal from subject 113


title: W1_22 [RHC6898]


title: W1_25 [RHC6901]


title: 200392810089_R07C01: buccal_112

source_name: buccal from subject 112


title: W1_18 [RHC6894]


title: W1_19 [RHC6895]


title: W1_21 [RHC6897]


title: W1_20 [RHC6896]


title: 200607090086_R02C01: buccal_109

source_name: buccal from subject 109


title: 200607090086_R06C01: buccal_110

source_name: buccal from subject 110


title: 200392810139_R07C01: buccal_111

source_name: buccal from subject 111


title: W1_15 [RHC6891]


title: W1_16 [RHC6892]


title: W1_14 [RHC6890]


title: W1_13 [RHC6889]


title: W1_17 [RHC6893]


title: W1_12 [RHC6888]


title: W1_11 [RHC6887]


title: 200392810022_R07C01: buccal_108

source_name: buccal from subject 108


title: 200392810022_R02C01: buccal_107

source_name: buccal from subject 107


title: W1_9 [RHC6885]


title: W1_10 [RHC6886]


title: 200607090075_R06C01: buccal_106

source_name: buccal from subject 106


title: W1_8 [RHC6884]


title: W1_7 [RHC6883]


title: 200607090075_R02C01: buccal_105

source_name: buccal from subject 105


title: 200607090061_R06C01: buccal_104

source_name: buccal from subject 104


title: W1_6 [RHC6882]


title: W1_4 [RHC6880]


title: HMR1_testis_RNAseq: Ribo-depleted RNA-seq library

city: Moscow

first: Alexei

middle: A.

last: Kotov

address: 26 Vavilov Street

country: Russia

institute: Koltzov Institute of Developmental Biology of the Russian Academy of Sciences

data_processing:
Adapter sequences in small RNA sequencing and total RNA-seq libraries were removed using cutadapt 1.8.1
For analysis small RNA reads from yw library were passed through quality control and minimal length filter (>18 nt) and finally mapped to genomes of Drosophila melanogaster (dm6 assembly, UCSC Genome Browser, https://genome-euro.ucsc.edu/cgibin/hgGateway?redirect=manual&source=genome.ucsc.edu) without mismatches (0 mm) using bowtie 1.2.2.
For analysis small RNA reads (>15 nt) from interspecies hybrids libraries were mapped to the D. melanogaster dm6 and D. mauritiana (release 1.0 of MS17 strain, http://www.popoolation.at/mauritiana_genome/) genomes using bowtie 0.12.7.
Genome_build: dm6 and D. mauritiana (release 1.0 of MS17 strain, http://www.popoolation.at/mauritiana_genome/)
Supplementary_files_format_and_content: tab-delimited text and excel files include information about mapping individual reads

organism: Drosophila melanogaster

source_name: testes

extract_protocol:
Total RNA was isolated by Trizol (Invitrogene) and for small RNA libraries preparation were size-fractioned by PAGE (19-29 nt)
Testes were dissected from adult flies (0-5 d) and RNA was isolated with Trizol Reagent (Invitrogene). For small RNA librarires, 19-29 nt RNAs were isolated from total RNA of dissected testes using 12% polyacrylamide gels and cloned as described in previous studies (Aravin et al., 2008; Brennecke et al., 2007). For Ribo-depleted libraries, rRNA was depleted with Ribo-Zero™ rRNA Removal Kit. Standard RNA-seq libraries were generated using the NEBNext Ultra Directional RNA Library Prep kit (NEB #E7420) according to the manufacturer's instructions.

tag: strain

value: testes


title: 200392800020_R05C01: buccal_103

source_name: buccal from subject 103


title: W1_3 [RHC6879]


title: 200392800020_R02C01: buccal_102

source_name: buccal from subject 102


title: CTGATC_HmrI: small RNA library (18-29 nt)

tag: molecule subtype

value: small RNA (19-29 nt)


title: 200607090061_R02C01: buccal_101

source_name: buccal from subject 101


title: TTAGGC_yw: small RNA library (18-29 nt)


title: W1_2 [RHC6878]

source_name: Cord 1_hWJSC


title: GFP_positive

city: Baltimore

first: Dong Won

middle: Thomas

state: Maryland

address: 733 N.Broadway, MRB building (Rm 332)

department: Neuroscience

institute: Johns Hopkins University

description:
Bulk-RNA-seq
processed data file: GFP+ve_GFP-ve.xlsx

data_processing:
Bulk-RNA-Seq: Filtered sequencing reads were mapped to the mouse reference genome (mm10) using TopHat. FPKM value for each gene was estimated using Cufflink.
scRNA-Seq: Sequencing results were processed through the Cell Ranger pipeline (10x Genomics) with default parameters. Both treatment groups (saline and leptin) were aggregated together for downstream analysis. Seurat was used to perform downstream analysis following the standard pipeline using cells with more than 500 genes and 1000 UMI counts. Clusters were annotated based on previous literature, and differential gene expression test was performed in each cluster, between treatment groups.
Genome_build: mm10
Supplementary_files_format_and_content: scRNA-Seq: matrix file; Bulk-RNA-Seq Cuffdiff output

source_name: Hypothalamus

extract_protocol:
Bulk-RNA-Seq - polyadenylated RNA was purified from the total RNA samples using Oligo dT conjugated magnetic bead
scRNA-Seq -following the manufacturer's (10x Genomics)
Bulk-RNA-Seq (TruSeq SBS kit on NextSeq 500 system)
scRNA-Seq (Illumina NextSeq)

treatment_protocol: scRNA-Seq - brains were treated with aCSF or leptin 1 hour before collection

value: Adult

tag: genotype

value: wild type

value: Hypothalamus


title: GFP_negative


title: W1_1 [RHC6877]


title: aCSF-treated

description: scRNA-Seq

value: 8 weeks old


title: Leptin-treated

description: scRNA-Seq


title: W1_5 [RHC6881]


title: OL-2017-1447-03

first: Siok-Bian

last: Ng

address: National University Hospital, 5 Lower Kent Ridge Road, Main Building, level 3

department: Department of Pathology

institute: National University Health System, Singapore

description: Mixture of 30% MyLa T cells and 70% placental cells.

hyb_protocol: Arrays were hybridized, washed, and stained in GeneChip Fluidics Station 450 according to manufacturer's protocols.

scan_protocol: Arrays were scanned using the GeneChip 3000 7G scanner according to manufacturer's protocols.

data_processing: Data processed using Affymetrix OncoScan Console (v1.3) software.

label_protocol: MIP probe annealing and hybridization were performed according to manufacturer's protocols.

extract_protocol: Genomic DNAs were extracted according to manufacturer's standard protocols.

tag: disease

value: MF

value: T mixed

tag: preparation

value: Cell line


title: AB3630 (scRNA-Seq)

city: Rehovot

first: Ido

last: Amit

address: 234 Herzl st.

department: Immunology

country: Israel

institute: Weizmann Institute of Science

data_processing:
Note: Second read contained only cell and molecule barcodes. This information was appended to the fastq entry header
bcl2fastq/2.15.0.4
Sequences with RMT of low quality (defined as RMT with minimum Phred score of less than 27) were filtered out.
Pool-barcode and well-barcode-RMT were extracted from the first and second end of the read (respectively) and concatenated to the fastq header, delimited by a underscore i.e. POOL_BARCODE_WELL_BARCODE_RMT while "NNNNNN" was used as a place holders if plate barcode was not used.
Reads were separated by POOL_BARCODE_WELL_BARCODE header data, allowing 1 sequencing error. This process created a single fastq file for each source well.
Genome_build: mm9
Supplementary_files_format_and_content: [AB*.txt]  tab-delimited text files include mRNA molecule count values for each Sample
[metadata.txt]  file associating each single cell with its amplification batch and index sorting readouts

source_name: Auricular lymph node

growth_protocol: 6 to 8 weeks-old mice housed at the Weizmann Institute animal facility.

extract_protocol:
Mice were euthanized and auricular LNs were disected. Lymph nodes were digested in IMDM containing 100µg/mL Liberase TL and 100µg/mL DNase I for 20 minutes at 37°C. In the last 5 minutes of incubation, EDTA was added at a final concentration of 10mM. Cells were collected, filtered through a 70µm cell strainer, washed with IMDM and maintained strictly at 4°C. Cells were stained with FACS antibodies, then sorted into 384-well plates
Single-cell RNA-seq libraries were prepared as previously described {Jaitin, 2014}. In brief, mRNA from single cells sorted into capture plates were barcoded and converted into cDNA and then pooled using an automated pipeline. The pooled sample was linearly amplified by T7 in vitro transcription, and the resulting RNA was fragmented and converted into a sequencing-ready library by tagging the samples with pool barcodes and Illumina sequences during ligation, RT, and PCR. Each pool of cells was tested for library quality and concentration as described previously {Jaitin, 2014}
single cell RNA-seq for gene expression quantitation

treatment_protocol:
[treatment protocol (1)]  Mice were anesthetized and the indicated inactivated pathogens were administered by intradermal injection into the ear pinna. PBS was injected into the ear pinna of control animals.
[treatment protocol (2)]  mice were treated with depleting or neutralizing antibodies or their isotype controls: Anti-NK1.1 (200 µg/dose), anti-IFNγ (500 µg/dose), Mouse IgG2a Isotype control and Rat IgG1 Isotype control were injected 24 hours prior to immunization and on the day of immunization

value: Lymph node

tag: cell type

value: antigen-positive innate cells

tag: selection marker

value: CD45+, CD19-, CD3-, TCRb-, Antigen+

tag: infection

value: Mycobacterium smegmatis

tag: time point

value: Intradermal injection of inactivated pathogen

tag: replicate id

value: Ms day1 rep.4

tag: mouse age

value: 8 weeks


title: AB3628 (scRNA-Seq)

value: innate immune cells


title: AB3627 (scRNA-Seq)


title: OL-2017-1431-07

description: Monomorphic epitheliotropic intestinal T-cell lymphoma sample.

value: MEITL

value: T

value: FFPE


title: OL-2017-1431-08

description: High grade B-cell lymphoma sample.

source_name: High grade B-cell lymphoma

value: HGBCL

value: B


title: OL-2017-1431-06

source_name: Monomorphic epitheliotropic intestinal T-cell lymphoma


title: OL-2017-1447-04

description: L82, an anaplastic large cell lymphoma cell line.

source_name: L82 anaplastic large cell lymphoma cell line

tag: cell line

value: ALCL


title: OL-2017-1431-04

description: Small lymphocytic lymphoma sample.

source_name: Small lymphocytic lymphoma

value: SLL


title: AB3216 (scRNA-Seq)

value: anti-NK1.1+anti-IFNG injection

value: Ms+anti-NK1.1/IFNg antibodies, day2 rep.2


title: OL-2017-1431-05

description: Burkitt lymphoma sample.

source_name: Burkitt lymphoma

value: BL


title: AB3215 (scRNA-Seq)

value: Lymph node

value: antigen-positive innate cells


title: AB3629 (scRNA-Seq)

value: Mycobacterium smegmatis


title: OL-2017-1447-02

description: Mixture of 50% MyLa T cells and 50% placental cells.

value: MF

value: T mixed

value: Cell line


title: OL-2017-1447-01

description: MyLa, a mycosis fungoides cell line.

source_name: MyLa mycosis fungoides cell line

value: MyLa


title: OL-2017-1431-03

description: Follicular lymphoma sample.

source_name: Follicular lymphoma

value: FL


title: AB3217 (scRNA-Seq)

value: innate immune cells

value: Intradermal injection of inactivated pathogen

value: IgG2a + IgG1 isotype control injection

value: Ms+control antibody, day2 rep.2

value: 8 weeks


title: OL-2017-1431-02

description: Mixture of 30% normal T cells and 70% placental cells.

value: Normal

value: Blood


title: AB3214 (scRNA-Seq)

value: CD45+, CD19-, CD3-, TCRb-, Antigen+

value: anti-NK1.1+anti-IFNG injection

value: Ms+anti-NK1.1/IFNg antibodies, day2 rep.2


title: OL-2017-1431-01

description: Mixture of 10% normal T cells and 90% placental cells.


title: AB3211 (scRNA-Seq)

value: Lymph node


title: D7 (Agilent)

city: Houston

first: Hui

last: Yao

state: TX

address: 1515 Holcombe Blvd.

department: Bioinformatics and Computational Biology

institute: MD Anderson Cancer Center

description: Genomic DNA extracted from bladder samples was genotyped using a custom aCGH array.

hyb_protocol: Microarray from Agilent Technologies

scan_protocol: Agilent Technologies Scanner G2505B US23502362 using feature extraction 9.5

data_processing: Agilent Feature Extraction Software (9.1.3.1) was used for background subtraction and normalization.

source_name: Urothelial carcinoma (UC)

label_protocol: Agilent Oligonucleotide Array-Based CGH for Genomic DNA Analysis ULS Labeling for Blood, Cells, Tissues or FFPE (with a High Throughput option) Protocol Version 3.0

extract_protocol: DNA from each sample was extracted using Qiagen kit

tag: tumor stage

value: Urothelial carcinoma (UC)

value: Human bladder

source_name: Normal urothelium from ureter (reference)

value: Human ureter


title: AB3213 (scRNA-Seq)

value: Mycobacterium smegmatis


title: C9 (Agilent)

source_name: High-grade intraurothelial neoplasia (HGIN)


title: OL-2017-1430-08

description: Mixture of 70% normal T cells and 30% placental cells.

value: T mixed


title: OL-2017-1430-07

description: Mixture of 50% normal T cells and 50% placental cells.


title: B7 (Agilent)


title: C3 (Agilent)


title: AB3209 (scRNA-Seq)

value: Ms+anti-NK1.1/IFNg antibodies, day2 rep.1


title: AB3210 (scRNA-Seq)

value: innate immune cells

value: Ms+control antibody, day2 rep.1


title: AB3208 (scRNA-Seq)

value: antigen-positive innate cells

value: Intradermal injection of inactivated pathogen


title: D5 (Agilent)


title: AB3212 (scRNA-Seq)

value: IgG2a + IgG1 isotype control injection

value: Ms+control antibody, day2 rep.2

value: 8 weeks


title: OL-2017-1430-06

description: Mixture of 50% NK/T-cell lymphoma cell line SNT8 T cells and 50% placental cells.

value: Mixed

value: Cell line


title: D6 (Agilent)


title: D8 (Agilent)

value: High-grade intraurothelial neoplasia (HGIN)


title: C8 (Agilent)

source_name: Low-grade intraurothelial neoplasia (LGIN)


title: C6 (Agilent)


title: D9 (Agilent)

value: Low-grade intraurothelial neoplasia (LGIN)


title: E3 (Agilent)


title: C7 (Agilent)


title: C5 (Agilent)


title: E4 (Agilent)


title: OL-2017-1430-05

description: SNT8, an NK/T-cell lymphoma cell line.

source_name: SNT8 NK/T-cell lymphoma cell line

value: NKTL

value: T


title: D1 (Agilent)

value: Human bladder

value: Human ureter


title: OL-2017-1430-04

description: Peripheral T-cell lymphoma sample.

source_name: Peripheral T-cell lymphoma

value: PTCL

value: FFPE


title: C4 (Agilent)


title: Case17

description: Hybridized to Affymetrix OncoScan FFPE Assay

hyb_protocol: Samples were hybridized onto  Affymetrix OncoScan FFPE Assay ki arrays and were washed and stained with GeneChip Fluidics Station 450 (Affymetrix)

scan_protocol: Affymetrix® GeneChip® Scanner 3000G to detect target bound to Oncoscan array after staining with Biotin.

data_processing:
CHP files generated by Oncoscan console 1.3.
[Primary data description] Nexus biodiscovery 9.0 edition Software. Gains and losses were evaluated with visual inspection by 2 different observers using Nexus Biodiscovery software (Biodiscovery, Hawthorne CA, USA). The CNAs with a minimum size of 100kb were considered real. Loss of heterozygosity regions were considered when size was >5Mb.

source_name: Omentum

label_protocol: Affymetrix OncoScan™ FFPE Assay kit

extract_protocol: DNA from formalin-fixed paraffin-embedded (FFPE) tissue was extracted after dewaxing and proteinase K digestion applying standard phenol/chloroform purification procedures

tag: disease state

value: Burkitt like lymphoma with 11q

tag: gender

value: male

value: Omentum

tag: sample type


title: OL-2017-1430-03

description: Peripheral T-cell lymphoma sample.


title: AB3205 (scRNA-Seq)

tag: tissue

value: Lymph node

value: innate immune cells

value: Mycobacterium smegmatis

value: Intradermal injection of inactivated pathogen

value: Ms+control antibody, day2 rep.1


title: Case16

source_name: Laterocervical Lymph Node

value: Laterocervical Lymph Node


title: AB3207 (scRNA-Seq)

tag: strain

value: anti-NK1.1+anti-IFNG injection

value: Ms+anti-NK1.1/IFNg antibodies, day2 rep.1

value: 8 weeks


title: D4 (Agilent)

value: Low-grade intraurothelial neoplasia (LGIN)


title: Case15

source_name: Laterocervical mass

value: Laterocervical mass


title: AB2826 (scRNA-Seq)

source_name: Auricular lymph node

value: Nippostrongylus brasiliensis

value: Nb day2 rep.2


title: AB2827 (scRNA-Seq)

value: Ms day2 rep.2


title: OL-2017-1430-01

description: Follicular lymphoma sample.

value: FL

value: B

value: FFPE


title: Case14

value: Burkitt like lymphoma with 11q

value: male


title: AB2825 (scRNA-Seq)

value: Lymph node

value: innate immune cells

value: Candida albicans

value: Ca day1 rep,4


title: OL-2016-1423-20

description: SNK-6, an NK/T-cell lymphoma cell line.

source_name: SNK-6 NK/T-cell lymphoma cell line

value: NKTL

value: NK cell

value: Cell line


title: Case5

value: female

value: Laterocervical Lymph Node


title: AB2820 (scRNA-Seq)

value: PBS (control)

value: Intradermal injection of inactivated pathogen

value: PBS control rep.3

value: 8 weeks


title: AB3206 (scRNA-Seq)

value: antigen-positive innate cells

value: CD45+, CD19-, CD3-, TCRb-, Antigen+

value: Mycobacterium smegmatis

value: IgG2a + IgG1 isotype control injection

value: Ms+control antibody, day2 rep.1


title: Case6

source_name: Appendix

value: Burkitt like lymphoma with 11q

value: male

value: Appendix

value: FFPE


title: OL-2017-1430-02

source_name: Monomorphic epitheliotropic intestinal T-cell lymphoma

value: MEITL

value: T


title: Case3

source_name: Tonsil

value: female

value: Tonsil


title: OL-2016-1423-18

description: HANK-1, an NK/T-cell lymphoma cell line.

source_name: HANK-1 NK/T-cell lymphoma cell line

value: NKTL

value: NK cell

value: Cell line


title: OL-2016-1423-19

description: NK-YS, an NK/T-cell lymphoma cell line.

source_name: NK-YS NK/T-cell lymphoma cell line

value: NK-YS


title: AB2783 (scRNA-Seq)

value: Lymph node

value: innate immune cells

value: Intradermal injection of inactivated pathogen

value: Ms day4 rep.1

value: 8 weeks


title: AB2779 (scRNA-Seq)

value: Nippostrongylus brasiliensis

value: Nb day4 rep.2


title: OL-2016-1423-17

description: Normal NK cells.

source_name: Normal NK cells

value: Normal


title: E7 (Agilent)

source_name: Normal urothelium (NU)

value: Normal urothelium (NU)

value: Human bladder

value: Human ureter


title: C1 (Agilent)

value: Low-grade intraurothelial neoplasia (LGIN)

source_name: Normal urothelium from ureter (reference)


title: AB2778 (scRNA-Seq)

value: Nb day2 rep.5


title: C2 (Agilent)


title: E9 (Agilent)


title: E8 (Agilent)


title: OL-2016-1423-16

description: Normal B cells.

source_name: Normal B cells

value: B

value: Blood


title: OL-2016-1423-15

description: Normal T cells.

source_name: Normal T cells

value: T


title: E5 (Agilent)


title: AB2777 (scRNA-Seq)


title: B5 (Agilent)


title: OL-2016-1423-14

description: Mixture of 50% CD8+ T cells and 50% placental cells.

value: T mixed

value: FFPE