title: NHP2.H004.a1.media

description:
Donor replicate 2; 04 hours post infection; Treatment: media; Seq-well array 1
Data for a given Seq-Well array for a specific biological sample
PBMC purification: We centrifuged whole blood in K3EDTA tubes at 1800 x g for 10 min at room temperature, removed EDTA plasma, and added phosphate buffered saline (PBS, Thermo Fisher Scientific, Waltham, MA, USA) to the pelleted cells to double the original whole blood volume. We gently poured the PBS-blood cell mixture into an Accuspin tube containing Histopaque (Sigma-Aldrich, St. Louis, MO, USA) and centrifuged at 1000 x g for 10 min at room temperature with the brake set to 1. Following centrifugation, we removed the top, clear supernatant layer to within 0.5 cm of the cloudy white layer containing PBMCs. We transferred the cloudy PBMC layer to a clean 15 mL conical tube and increased the volume to 10 mL using PBS supplemented with 2% heat-inactivated fetal bovine serum (PBS/2%HI-FBS) and mixed by inversion. We then centrifuged at 300 x g for 10 min at 4 °C with the brake set to 1. Following centrifugation, we removed the supernatant, resuspended the cell pellet with PBS/2%HI-FBS to a final volume of 10 mL, and mixed using gentle raking to wash the cells. We repeated the wash step 2 more times with the centrifuge set to 200 x g for 10 min at 4 °C with the brake set to 1. We then resuspended the cell pellet in 9.5mL PBS/2%HI-FBS for counting using the Countess Cell Counting system (Thermo Fisher Scientific). We aliquoted 0.5 mL for Seq-Well, and used the remaining 9 mL volume for CyTOF.
Seq-Well: We performed Seq-Well as described previously (Gierahn et al., 2017), with the S3 protocol (Hughes et al., 2019) and some controls and modifications to adhere to the BSL-4 environment. After loading and sealing beads and cells in Seq-Well arrays, we placed them in a -80 °C freezer until further processing – this step was required due to time constraints in the BSL-4. Later, we removed sealed Seq-Well arrays from the -80 °C freezer, placed them in 4-well dishes, and allowed them to equilibrate to room temperature for at least 30 min. We then covered arrays in 5 mL Seq-Well Lysis Buffer per protocol. We performed RNA hybridization and RT as specified in the protocol (Hughes et al., 2019). After RT, we collected beads by centrifugation at 1000 x g for 1 min at room temperature. We resuspended beads with GeneXpert Lysis Buffer (Cepheid, Sunnyvale, CA, USA) for inactivation, which was required prior to removal from the BSL-4 laboratory according to standard operating procedures. After removal, we washed beads thrice with TE buffer containing 0.01% Tween 20 and shipped at 4 °C for further library construction and sequencing.


title: N113E15-Ts1Cje-Powder

status: Public on Sep 23 2020

type: RNA

city: Bethesda

first: Faycal

last: Guedj

state: Maryland

address: 35A Convent DR

department: NHGRI

country: USA

institute: National Institute of Health

hyb_protocol: Arrays were washed and stained with streptavidin-phycoerythrin using the Affymetrix GeneChip Hybridization, Wash and Stain Kit according to the manufacturer's instructions (Affymetrix, Santa Clara, CA).

scan_protocol: Arrays were scanned on a GeneArray Scanner 3000 7G, using the GeneChip Microarray Suite 5.0 (Affymetrix, Santa Clara, CA).

data_processing: Quality control and normalization were performed using the pipeline at the www.arrayanalysis.org website (Maastricht University, the Netherlands). Normalization was done using the Robust Multichip Average (RMA) algorithm and the MBNI custom CDF (http://brainarray.mbni.med.umich.edu/) version #14 for the mouse gene 1.0 ST array. Normalization output consisted of data for 21225 probe sets each corresponding to unique Entrez Gene IDs.

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: Forebrain from day 15 embryo

label_protocol: Samples were labeled with Biotin Allonamide Triphosphate according to the GeneChip Whole Transcriptome Labeling and Hybridization protocol (http://www.affymetrix.com) the Affymetrix GeneChip WT PLUS Reagent Kit (Thermo Fisher Scientific, Waltham, MA).

growth_protocol: Mice were housed in standard cages with food and water ad libitum under a controlled environment (temperature = 20°C; humidity = 60%) and a light/dark cycle of 12h. Ts1Cje (Jax Stock 004838) males were crossed to C57Bl/6J (Jax Stock 000664) females. For embryonic studies, the presence of a vaginal plug was defined as embryonic day 0.5 (E0.5) and 10-15% weight gain at embryonic day 10 was used to confirm pregnancy. Pregnant females were anesthetized with 2.5% isoflurane in a 3/7 02/N2O mixture and euthanized by decapitation at embryonic day E15.5 (E15.5). Embryos were extracted and decapitated in ice-cold phosphate-buffered-saline (PBS1X). Embryonic brains were rapidly removed and brain hemispheres dissected on a cold platform and snap frozen in liquid nitrogen before storage at -80°C. For adult studies, 6-7 month old animals were euthanaized as described above and brains were removed and dissected on a cold platform. Cerebral cortex, hippocampus and cerebellum were snap frozen in liquid nitrogen before storage at -80°C.

extract_protocol: Total RNA was isolated using the NucleoSpin RNA II kits following the manufacturer’s instructions (Macherey-Nagel, Bethlehem, PA). RNA concentrations were measured as absorbance at 260 nm on the Nanodrop instrument (Thermo Fisher Scientific, Waltham, MA). RNA quality was analyzed with the Bioanalyzer (Agilent Biotechnologies, Santa Clara, CA) using the RNA 6000 Nano kit according to the manufacturer’s instructions. Only samples displaying an A260/A280 ratio of 2.0-2.1 and a RIN (RNA Integrity Number) > 9 were used for hybridization to the arrays.

treatment_protocol: Breeding pairs received either purified powdered (Pow) chow F3197 (Bioserv, Flemington, NJ) or 333-400 mg/kg/day of apigenin (Apig) (2 g of apigenin in 1 kg of purified powdered chow) (SelleckChem, Houston, TX). Treatment was given as powdered chow with apigenin starting at the time of mating and continuing throughout pregnancy and lactation until all behavioral and biochemical studies in adulthood were completed.

tag: tissue

value: forebrain

tag: developmental stage

tag: genotype

tag: treatment

value: Powder


title: whole blood, control 24, year 1

city: Leicester

first: Christopher

last: Mitchell

address: University Road

department: Neuroscience, Psychology & Behaviour

country: United Kingdom

institute: University of Leicester

description: Gene expression data from peripheral whole blood of control individual

hyb_protocol: Affymetrix Eukaryotic Target Hybridization protocol (Affymetrix GeneChip® Expression Analysis Technical Manual).

scan_protocol: Affymetrix® GeneChip® Scanner 3000 (Affymetrix GeneChip® Expression Analysis Technical Manual).

data_processing: Probe sets were normalised using robust multi-array averaging (RMA) with the R/Bioconductor package affy.

organism: Homo sapiens

source_name: Peripheral whole blood

label_protocol: Year 1 Samples: The Ovation Whole Blood Kit and Encore Biotin Module (Nugen, Inc.) was used according to the manufacturer’s protocol.    Year 3 Samples: The Ovation RNA Amplification System V2 (Nugen, Inc.) was used according to the manufacturer’s protocol.

extract_protocol: Blood was stored in PAX Gene tubes from which RNA was extracted using the PAX RNA isolation kit according to manufacturer’s protocol.

tag: year

tag: Sex

value: Male

tag: age at year 1

tag: location

value: london

tag: disease stage

value: Control

tag: expanded allele cag repeat count

tag: uhdrs tms

tag: uhdrs tfc


title: whole blood, preHD A 02, year 3

description: Gene expression data from peripheral whole blood of pre-symptomatic Huntingtin gene change carrier

value: vancouver

value: preHD A


title: whole blood, control 24, year 3


title: Teosinte WGBS_JRIAL2P

type: SRA

city: Lincoln

first: GEN

last: XU

state: Nebraska

address: 383 Plant Science Hall  Department of Agronomy and Horticulture

institute: University of Nebraska-Lincoln

description:
Whole genome bisulfite sequencing
Table_S1_DMR.bed

library_source: genomic

data_processing:
Whole genome sequencing reads were aligned to the B73 reference genome using BWA; Bisulfite sequencing data analysis was conducted using Bismark
Duplicate reads were removed by picard
We conducted SNP calling using Genome Analysis Toolkit’s(GATK, version 4) HaplotypeCaller
We used a software package ‘metilene’ for DMR detection between two populations
We calculated XPCLR to detect selective signals
Genome_build: B73 reference genome
Supplementary_files_format_and_content: bed files include selective sweeps and differentially methylated regions.

molecule: genomic DNA

organism: Zea mays

growth_protocol: Plants were growed in greenhouse

extract_protocol:
CTAB method for DNA extraction
Libraries were prepared for sequencing using standard Illumina protocols

value: 3rd leaf

tag: Stage

value: seedling

tag: population

value: Teosinte


title: Teosinte WGBS_JRIAL2Q


title: N115E15-Ts1Cje-Powder

value: WT


title: whole blood, preHD A 01, year 3

value: Female


title: N94E15-Ts1Cje-Powder


title: whole blood, control 23, year 1


title: whole blood, control 22, year 1


title: whole blood, preHD A 01, year 1


title: NHP2.H004.a1.live

city: Cambridge

first: Dylan

last: Kotliar

state: MA

address: 4 Garnder Rd, Apt 2

department: Viral genomics

institute: Broad Institute

description:
Donor replicate 2; 04 hours post infection; Treatment: live; Seq-well array 1
Data for a given Seq-Well array for a specific biological sample
PBMC purification: We centrifuged whole blood in K3EDTA tubes at 1800 x g for 10 min at room temperature, removed EDTA plasma, and added phosphate buffered saline (PBS, Thermo Fisher Scientific, Waltham, MA, USA) to the pelleted cells to double the original whole blood volume. We gently poured the PBS-blood cell mixture into an Accuspin tube containing Histopaque (Sigma-Aldrich, St. Louis, MO, USA) and centrifuged at 1000 x g for 10 min at room temperature with the brake set to 1. Following centrifugation, we removed the top, clear supernatant layer to within 0.5 cm of the cloudy white layer containing PBMCs. We transferred the cloudy PBMC layer to a clean 15 mL conical tube and increased the volume to 10 mL using PBS supplemented with 2% heat-inactivated fetal bovine serum (PBS/2%HI-FBS) and mixed by inversion. We then centrifuged at 300 x g for 10 min at 4 °C with the brake set to 1. Following centrifugation, we removed the supernatant, resuspended the cell pellet with PBS/2%HI-FBS to a final volume of 10 mL, and mixed using gentle raking to wash the cells. We repeated the wash step 2 more times with the centrifuge set to 200 x g for 10 min at 4 °C with the brake set to 1. We then resuspended the cell pellet in 9.5mL PBS/2%HI-FBS for counting using the Countess Cell Counting system (Thermo Fisher Scientific). We aliquoted 0.5 mL for Seq-Well, and used the remaining 9 mL volume for CyTOF.
Seq-Well: We performed Seq-Well as described previously (Gierahn et al., 2017), with the S3 protocol (Hughes et al., 2019) and some controls and modifications to adhere to the BSL-4 environment. After loading and sealing beads and cells in Seq-Well arrays, we placed them in a -80 °C freezer until further processing – this step was required due to time constraints in the BSL-4. Later, we removed sealed Seq-Well arrays from the -80 °C freezer, placed them in 4-well dishes, and allowed them to equilibrate to room temperature for at least 30 min. We then covered arrays in 5 mL Seq-Well Lysis Buffer per protocol. We performed RNA hybridization and RT as specified in the protocol (Hughes et al., 2019). After RT, we collected beads by centrifugation at 1000 x g for 1 min at room temperature. We resuspended beads with GeneXpert Lysis Buffer (Cepheid, Sunnyvale, CA, USA) for inactivation, which was required prior to removal from the BSL-4 laboratory according to standard operating procedures. After removal, we washed beads thrice with TE buffer containing 0.01% Tween 20 and shipped at 4 °C for further library construction and sequencing.

library_source: transcriptomic

data_processing:
Library strategy: scRNA-Seq
Raw sequencing files were demultiplexed and converted to fastq using bcl2fastq version 2.20.
Reads were then trimmed, aligned to a reference transcriptome, and parsed into a digital gene expression matrix using the previously published Dropseq-tools pipeline (Macosko et al., 2015)
The scRNA-Seq data was preprocessed, clustered, and visualized using Scanpy (Wolf et al., 2018). We removed cells with <300 genes detected, >10% of their UMIs derived from mitochondrial genes, or >95% of UMIs mapped to non-genic regions. We excluded ribosomal genes, genes correlated with the percentage of UMIs assigned to mitochondrial genes (Pearson R > 0.1), and HBB as these were largely driven by the technical covariate of whether cells had loaded into Seq-Well arrays fresh or had undergone a freeze-thaw cycle with cryoprotectant. We also excluded EBOV genes and cell-cycle genes (defined by correlation with TOP2A, Pearson R > 0.1) prior to clustering so that these signals would not influence identification of cell types.
See https://www.biorxiv.org/content/10.1101/2020.06.12.148957v2 for details
Genome_build: hybrid of Mmul_8.01 and KU182905.1
Supplementary_files_format_and_content: digital gene expression matrix were generated using the previously published Dropseq-tools pipeline

organism: Macaca mulatta

source_name: Peripheral blood mononuclear cells (PBMC)

extract_protocol: Library construction and sequencing was performed with the S3 protocol (Hughes et al., 2019). We sequenced all libraries on either NextSeq 550 High Output or NovaSeq 6000 S2 flowcells (Illumina, San Diego, CA, USA), with 20 cycles for Read 1 (cell barcode and unique molecular index [UMI]) and 88 cycles for Read 2 (cDNA of interest). In some cases, we merged fastq files from multiple sequencing runs for increased coverage.

value: live


title: whole blood, control 21, year 1


title: Teosinte WGBS_JRIAL2O


title: NHP2.H004.a1.irrad

description:
Donor replicate 2; 04 hours post infection; Treatment: irrad; Seq-well array 1
Data for a given Seq-Well array for a specific biological sample
PBMC purification: We centrifuged whole blood in K3EDTA tubes at 1800 x g for 10 min at room temperature, removed EDTA plasma, and added phosphate buffered saline (PBS, Thermo Fisher Scientific, Waltham, MA, USA) to the pelleted cells to double the original whole blood volume. We gently poured the PBS-blood cell mixture into an Accuspin tube containing Histopaque (Sigma-Aldrich, St. Louis, MO, USA) and centrifuged at 1000 x g for 10 min at room temperature with the brake set to 1. Following centrifugation, we removed the top, clear supernatant layer to within 0.5 cm of the cloudy white layer containing PBMCs. We transferred the cloudy PBMC layer to a clean 15 mL conical tube and increased the volume to 10 mL using PBS supplemented with 2% heat-inactivated fetal bovine serum (PBS/2%HI-FBS) and mixed by inversion. We then centrifuged at 300 x g for 10 min at 4 °C with the brake set to 1. Following centrifugation, we removed the supernatant, resuspended the cell pellet with PBS/2%HI-FBS to a final volume of 10 mL, and mixed using gentle raking to wash the cells. We repeated the wash step 2 more times with the centrifuge set to 200 x g for 10 min at 4 °C with the brake set to 1. We then resuspended the cell pellet in 9.5mL PBS/2%HI-FBS for counting using the Countess Cell Counting system (Thermo Fisher Scientific). We aliquoted 0.5 mL for Seq-Well, and used the remaining 9 mL volume for CyTOF.
Seq-Well: We performed Seq-Well as described previously (Gierahn et al., 2017), with the S3 protocol (Hughes et al., 2019) and some controls and modifications to adhere to the BSL-4 environment. After loading and sealing beads and cells in Seq-Well arrays, we placed them in a -80 °C freezer until further processing – this step was required due to time constraints in the BSL-4. Later, we removed sealed Seq-Well arrays from the -80 °C freezer, placed them in 4-well dishes, and allowed them to equilibrate to room temperature for at least 30 min. We then covered arrays in 5 mL Seq-Well Lysis Buffer per protocol. We performed RNA hybridization and RT as specified in the protocol (Hughes et al., 2019). After RT, we collected beads by centrifugation at 1000 x g for 1 min at room temperature. We resuspended beads with GeneXpert Lysis Buffer (Cepheid, Sunnyvale, CA, USA) for inactivation, which was required prior to removal from the BSL-4 laboratory according to standard operating procedures. After removal, we washed beads thrice with TE buffer containing 0.01% Tween 20 and shipped at 4 °C for further library construction and sequencing.

value: irrad

value: Peripheral blood mononuclear cells (PBMC)


title: Teosinte WGBS_JRIAL2N


title: NHP1.H024.a4.live

description:
Donor replicate 1; 24 hours post infection; Treatment: live; Seq-well array 4
Data for a given Seq-Well array for a specific biological sample
PBMC purification: We centrifuged whole blood in K3EDTA tubes at 1800 x g for 10 min at room temperature, removed EDTA plasma, and added phosphate buffered saline (PBS, Thermo Fisher Scientific, Waltham, MA, USA) to the pelleted cells to double the original whole blood volume. We gently poured the PBS-blood cell mixture into an Accuspin tube containing Histopaque (Sigma-Aldrich, St. Louis, MO, USA) and centrifuged at 1000 x g for 10 min at room temperature with the brake set to 1. Following centrifugation, we removed the top, clear supernatant layer to within 0.5 cm of the cloudy white layer containing PBMCs. We transferred the cloudy PBMC layer to a clean 15 mL conical tube and increased the volume to 10 mL using PBS supplemented with 2% heat-inactivated fetal bovine serum (PBS/2%HI-FBS) and mixed by inversion. We then centrifuged at 300 x g for 10 min at 4 °C with the brake set to 1. Following centrifugation, we removed the supernatant, resuspended the cell pellet with PBS/2%HI-FBS to a final volume of 10 mL, and mixed using gentle raking to wash the cells. We repeated the wash step 2 more times with the centrifuge set to 200 x g for 10 min at 4 °C with the brake set to 1. We then resuspended the cell pellet in 9.5mL PBS/2%HI-FBS for counting using the Countess Cell Counting system (Thermo Fisher Scientific). We aliquoted 0.5 mL for Seq-Well, and used the remaining 9 mL volume for CyTOF.
Seq-Well: We performed Seq-Well as described previously (Gierahn et al., 2017), with the S3 protocol (Hughes et al., 2019) and some controls and modifications to adhere to the BSL-4 environment. After loading and sealing beads and cells in Seq-Well arrays, we placed them in a -80 °C freezer until further processing – this step was required due to time constraints in the BSL-4. Later, we removed sealed Seq-Well arrays from the -80 °C freezer, placed them in 4-well dishes, and allowed them to equilibrate to room temperature for at least 30 min. We then covered arrays in 5 mL Seq-Well Lysis Buffer per protocol. We performed RNA hybridization and RT as specified in the protocol (Hughes et al., 2019). After RT, we collected beads by centrifugation at 1000 x g for 1 min at room temperature. We resuspended beads with GeneXpert Lysis Buffer (Cepheid, Sunnyvale, CA, USA) for inactivation, which was required prior to removal from the BSL-4 laboratory according to standard operating procedures. After removal, we washed beads thrice with TE buffer containing 0.01% Tween 20 and shipped at 4 °C for further library construction and sequencing.


title: Teosinte WGBS_JRIAL2M


title: Teosinte WGBS_JRIAL2L


title: Teosinte WGBS_JRIAL2K


title: NHP1.H024.a2.live

description:
Donor replicate 1; 24 hours post infection; Treatment: live; Seq-well array 2
Data for a given Seq-Well array for a specific biological sample
PBMC purification: We centrifuged whole blood in K3EDTA tubes at 1800 x g for 10 min at room temperature, removed EDTA plasma, and added phosphate buffered saline (PBS, Thermo Fisher Scientific, Waltham, MA, USA) to the pelleted cells to double the original whole blood volume. We gently poured the PBS-blood cell mixture into an Accuspin tube containing Histopaque (Sigma-Aldrich, St. Louis, MO, USA) and centrifuged at 1000 x g for 10 min at room temperature with the brake set to 1. Following centrifugation, we removed the top, clear supernatant layer to within 0.5 cm of the cloudy white layer containing PBMCs. We transferred the cloudy PBMC layer to a clean 15 mL conical tube and increased the volume to 10 mL using PBS supplemented with 2% heat-inactivated fetal bovine serum (PBS/2%HI-FBS) and mixed by inversion. We then centrifuged at 300 x g for 10 min at 4 °C with the brake set to 1. Following centrifugation, we removed the supernatant, resuspended the cell pellet with PBS/2%HI-FBS to a final volume of 10 mL, and mixed using gentle raking to wash the cells. We repeated the wash step 2 more times with the centrifuge set to 200 x g for 10 min at 4 °C with the brake set to 1. We then resuspended the cell pellet in 9.5mL PBS/2%HI-FBS for counting using the Countess Cell Counting system (Thermo Fisher Scientific). We aliquoted 0.5 mL for Seq-Well, and used the remaining 9 mL volume for CyTOF.
Seq-Well: We performed Seq-Well as described previously (Gierahn et al., 2017), with the S3 protocol (Hughes et al., 2019) and some controls and modifications to adhere to the BSL-4 environment. After loading and sealing beads and cells in Seq-Well arrays, we placed them in a -80 °C freezer until further processing – this step was required due to time constraints in the BSL-4. Later, we removed sealed Seq-Well arrays from the -80 °C freezer, placed them in 4-well dishes, and allowed them to equilibrate to room temperature for at least 30 min. We then covered arrays in 5 mL Seq-Well Lysis Buffer per protocol. We performed RNA hybridization and RT as specified in the protocol (Hughes et al., 2019). After RT, we collected beads by centrifugation at 1000 x g for 1 min at room temperature. We resuspended beads with GeneXpert Lysis Buffer (Cepheid, Sunnyvale, CA, USA) for inactivation, which was required prior to removal from the BSL-4 laboratory according to standard operating procedures. After removal, we washed beads thrice with TE buffer containing 0.01% Tween 20 and shipped at 4 °C for further library construction and sequencing.


title: whole blood, control 22, year 3


title: NHP1.H024.a1.live

description:
Donor replicate 1; 24 hours post infection; Treatment: live; Seq-well array 1
Data for a given Seq-Well array for a specific biological sample
PBMC purification: We centrifuged whole blood in K3EDTA tubes at 1800 x g for 10 min at room temperature, removed EDTA plasma, and added phosphate buffered saline (PBS, Thermo Fisher Scientific, Waltham, MA, USA) to the pelleted cells to double the original whole blood volume. We gently poured the PBS-blood cell mixture into an Accuspin tube containing Histopaque (Sigma-Aldrich, St. Louis, MO, USA) and centrifuged at 1000 x g for 10 min at room temperature with the brake set to 1. Following centrifugation, we removed the top, clear supernatant layer to within 0.5 cm of the cloudy white layer containing PBMCs. We transferred the cloudy PBMC layer to a clean 15 mL conical tube and increased the volume to 10 mL using PBS supplemented with 2% heat-inactivated fetal bovine serum (PBS/2%HI-FBS) and mixed by inversion. We then centrifuged at 300 x g for 10 min at 4 °C with the brake set to 1. Following centrifugation, we removed the supernatant, resuspended the cell pellet with PBS/2%HI-FBS to a final volume of 10 mL, and mixed using gentle raking to wash the cells. We repeated the wash step 2 more times with the centrifuge set to 200 x g for 10 min at 4 °C with the brake set to 1. We then resuspended the cell pellet in 9.5mL PBS/2%HI-FBS for counting using the Countess Cell Counting system (Thermo Fisher Scientific). We aliquoted 0.5 mL for Seq-Well, and used the remaining 9 mL volume for CyTOF.
Seq-Well: We performed Seq-Well as described previously (Gierahn et al., 2017), with the S3 protocol (Hughes et al., 2019) and some controls and modifications to adhere to the BSL-4 environment. After loading and sealing beads and cells in Seq-Well arrays, we placed them in a -80 °C freezer until further processing – this step was required due to time constraints in the BSL-4. Later, we removed sealed Seq-Well arrays from the -80 °C freezer, placed them in 4-well dishes, and allowed them to equilibrate to room temperature for at least 30 min. We then covered arrays in 5 mL Seq-Well Lysis Buffer per protocol. We performed RNA hybridization and RT as specified in the protocol (Hughes et al., 2019). After RT, we collected beads by centrifugation at 1000 x g for 1 min at room temperature. We resuspended beads with GeneXpert Lysis Buffer (Cepheid, Sunnyvale, CA, USA) for inactivation, which was required prior to removal from the BSL-4 laboratory according to standard operating procedures. After removal, we washed beads thrice with TE buffer containing 0.01% Tween 20 and shipped at 4 °C for further library construction and sequencing.


title: Teosinte WGBS_JRIAL2I


title: NHP1.H024.a1.irrad

description:
Donor replicate 1; 24 hours post infection; Treatment: irrad; Seq-well array 1
Data for a given Seq-Well array for a specific biological sample
PBMC purification: We centrifuged whole blood in K3EDTA tubes at 1800 x g for 10 min at room temperature, removed EDTA plasma, and added phosphate buffered saline (PBS, Thermo Fisher Scientific, Waltham, MA, USA) to the pelleted cells to double the original whole blood volume. We gently poured the PBS-blood cell mixture into an Accuspin tube containing Histopaque (Sigma-Aldrich, St. Louis, MO, USA) and centrifuged at 1000 x g for 10 min at room temperature with the brake set to 1. Following centrifugation, we removed the top, clear supernatant layer to within 0.5 cm of the cloudy white layer containing PBMCs. We transferred the cloudy PBMC layer to a clean 15 mL conical tube and increased the volume to 10 mL using PBS supplemented with 2% heat-inactivated fetal bovine serum (PBS/2%HI-FBS) and mixed by inversion. We then centrifuged at 300 x g for 10 min at 4 °C with the brake set to 1. Following centrifugation, we removed the supernatant, resuspended the cell pellet with PBS/2%HI-FBS to a final volume of 10 mL, and mixed using gentle raking to wash the cells. We repeated the wash step 2 more times with the centrifuge set to 200 x g for 10 min at 4 °C with the brake set to 1. We then resuspended the cell pellet in 9.5mL PBS/2%HI-FBS for counting using the Countess Cell Counting system (Thermo Fisher Scientific). We aliquoted 0.5 mL for Seq-Well, and used the remaining 9 mL volume for CyTOF.
Seq-Well: We performed Seq-Well as described previously (Gierahn et al., 2017), with the S3 protocol (Hughes et al., 2019) and some controls and modifications to adhere to the BSL-4 environment. After loading and sealing beads and cells in Seq-Well arrays, we placed them in a -80 °C freezer until further processing – this step was required due to time constraints in the BSL-4. Later, we removed sealed Seq-Well arrays from the -80 °C freezer, placed them in 4-well dishes, and allowed them to equilibrate to room temperature for at least 30 min. We then covered arrays in 5 mL Seq-Well Lysis Buffer per protocol. We performed RNA hybridization and RT as specified in the protocol (Hughes et al., 2019). After RT, we collected beads by centrifugation at 1000 x g for 1 min at room temperature. We resuspended beads with GeneXpert Lysis Buffer (Cepheid, Sunnyvale, CA, USA) for inactivation, which was required prior to removal from the BSL-4 laboratory according to standard operating procedures. After removal, we washed beads thrice with TE buffer containing 0.01% Tween 20 and shipped at 4 °C for further library construction and sequencing.


title: Teosinte WGBS_JRIAL2H


title: Teosinte WGBS_JRIAL2G


title: N111E15-Ts1Cje-Powder


title: Teosinte WGBS_JRIAL2F


title: NHP1.H024.a3.live

description:
Donor replicate 1; 24 hours post infection; Treatment: live; Seq-well array 3
Data for a given Seq-Well array for a specific biological sample
PBMC purification: We centrifuged whole blood in K3EDTA tubes at 1800 x g for 10 min at room temperature, removed EDTA plasma, and added phosphate buffered saline (PBS, Thermo Fisher Scientific, Waltham, MA, USA) to the pelleted cells to double the original whole blood volume. We gently poured the PBS-blood cell mixture into an Accuspin tube containing Histopaque (Sigma-Aldrich, St. Louis, MO, USA) and centrifuged at 1000 x g for 10 min at room temperature with the brake set to 1. Following centrifugation, we removed the top, clear supernatant layer to within 0.5 cm of the cloudy white layer containing PBMCs. We transferred the cloudy PBMC layer to a clean 15 mL conical tube and increased the volume to 10 mL using PBS supplemented with 2% heat-inactivated fetal bovine serum (PBS/2%HI-FBS) and mixed by inversion. We then centrifuged at 300 x g for 10 min at 4 °C with the brake set to 1. Following centrifugation, we removed the supernatant, resuspended the cell pellet with PBS/2%HI-FBS to a final volume of 10 mL, and mixed using gentle raking to wash the cells. We repeated the wash step 2 more times with the centrifuge set to 200 x g for 10 min at 4 °C with the brake set to 1. We then resuspended the cell pellet in 9.5mL PBS/2%HI-FBS for counting using the Countess Cell Counting system (Thermo Fisher Scientific). We aliquoted 0.5 mL for Seq-Well, and used the remaining 9 mL volume for CyTOF.
Seq-Well: We performed Seq-Well as described previously (Gierahn et al., 2017), with the S3 protocol (Hughes et al., 2019) and some controls and modifications to adhere to the BSL-4 environment. After loading and sealing beads and cells in Seq-Well arrays, we placed them in a -80 °C freezer until further processing – this step was required due to time constraints in the BSL-4. Later, we removed sealed Seq-Well arrays from the -80 °C freezer, placed them in 4-well dishes, and allowed them to equilibrate to room temperature for at least 30 min. We then covered arrays in 5 mL Seq-Well Lysis Buffer per protocol. We performed RNA hybridization and RT as specified in the protocol (Hughes et al., 2019). After RT, we collected beads by centrifugation at 1000 x g for 1 min at room temperature. We resuspended beads with GeneXpert Lysis Buffer (Cepheid, Sunnyvale, CA, USA) for inactivation, which was required prior to removal from the BSL-4 laboratory according to standard operating procedures. After removal, we washed beads thrice with TE buffer containing 0.01% Tween 20 and shipped at 4 °C for further library construction and sequencing.


title: whole blood, control 19, year 1


title: NHP1.H004.a3.live

description:
Donor replicate 1; 04 hours post infection; Treatment: live; Seq-well array 3
Data for a given Seq-Well array for a specific biological sample
PBMC purification: We centrifuged whole blood in K3EDTA tubes at 1800 x g for 10 min at room temperature, removed EDTA plasma, and added phosphate buffered saline (PBS, Thermo Fisher Scientific, Waltham, MA, USA) to the pelleted cells to double the original whole blood volume. We gently poured the PBS-blood cell mixture into an Accuspin tube containing Histopaque (Sigma-Aldrich, St. Louis, MO, USA) and centrifuged at 1000 x g for 10 min at room temperature with the brake set to 1. Following centrifugation, we removed the top, clear supernatant layer to within 0.5 cm of the cloudy white layer containing PBMCs. We transferred the cloudy PBMC layer to a clean 15 mL conical tube and increased the volume to 10 mL using PBS supplemented with 2% heat-inactivated fetal bovine serum (PBS/2%HI-FBS) and mixed by inversion. We then centrifuged at 300 x g for 10 min at 4 °C with the brake set to 1. Following centrifugation, we removed the supernatant, resuspended the cell pellet with PBS/2%HI-FBS to a final volume of 10 mL, and mixed using gentle raking to wash the cells. We repeated the wash step 2 more times with the centrifuge set to 200 x g for 10 min at 4 °C with the brake set to 1. We then resuspended the cell pellet in 9.5mL PBS/2%HI-FBS for counting using the Countess Cell Counting system (Thermo Fisher Scientific). We aliquoted 0.5 mL for Seq-Well, and used the remaining 9 mL volume for CyTOF.
Seq-Well: We performed Seq-Well as described previously (Gierahn et al., 2017), with the S3 protocol (Hughes et al., 2019) and some controls and modifications to adhere to the BSL-4 environment. After loading and sealing beads and cells in Seq-Well arrays, we placed them in a -80 °C freezer until further processing – this step was required due to time constraints in the BSL-4. Later, we removed sealed Seq-Well arrays from the -80 °C freezer, placed them in 4-well dishes, and allowed them to equilibrate to room temperature for at least 30 min. We then covered arrays in 5 mL Seq-Well Lysis Buffer per protocol. We performed RNA hybridization and RT as specified in the protocol (Hughes et al., 2019). After RT, we collected beads by centrifugation at 1000 x g for 1 min at room temperature. We resuspended beads with GeneXpert Lysis Buffer (Cepheid, Sunnyvale, CA, USA) for inactivation, which was required prior to removal from the BSL-4 laboratory according to standard operating procedures. After removal, we washed beads thrice with TE buffer containing 0.01% Tween 20 and shipped at 4 °C for further library construction and sequencing.


title: whole blood, control 20, year 1


title: NHP1.H004.a2.live

description:
Donor replicate 1; 04 hours post infection; Treatment: live; Seq-well array 2
Data for a given Seq-Well array for a specific biological sample
PBMC purification: We centrifuged whole blood in K3EDTA tubes at 1800 x g for 10 min at room temperature, removed EDTA plasma, and added phosphate buffered saline (PBS, Thermo Fisher Scientific, Waltham, MA, USA) to the pelleted cells to double the original whole blood volume. We gently poured the PBS-blood cell mixture into an Accuspin tube containing Histopaque (Sigma-Aldrich, St. Louis, MO, USA) and centrifuged at 1000 x g for 10 min at room temperature with the brake set to 1. Following centrifugation, we removed the top, clear supernatant layer to within 0.5 cm of the cloudy white layer containing PBMCs. We transferred the cloudy PBMC layer to a clean 15 mL conical tube and increased the volume to 10 mL using PBS supplemented with 2% heat-inactivated fetal bovine serum (PBS/2%HI-FBS) and mixed by inversion. We then centrifuged at 300 x g for 10 min at 4 °C with the brake set to 1. Following centrifugation, we removed the supernatant, resuspended the cell pellet with PBS/2%HI-FBS to a final volume of 10 mL, and mixed using gentle raking to wash the cells. We repeated the wash step 2 more times with the centrifuge set to 200 x g for 10 min at 4 °C with the brake set to 1. We then resuspended the cell pellet in 9.5mL PBS/2%HI-FBS for counting using the Countess Cell Counting system (Thermo Fisher Scientific). We aliquoted 0.5 mL for Seq-Well, and used the remaining 9 mL volume for CyTOF.
Seq-Well: We performed Seq-Well as described previously (Gierahn et al., 2017), with the S3 protocol (Hughes et al., 2019) and some controls and modifications to adhere to the BSL-4 environment. After loading and sealing beads and cells in Seq-Well arrays, we placed them in a -80 °C freezer until further processing – this step was required due to time constraints in the BSL-4. Later, we removed sealed Seq-Well arrays from the -80 °C freezer, placed them in 4-well dishes, and allowed them to equilibrate to room temperature for at least 30 min. We then covered arrays in 5 mL Seq-Well Lysis Buffer per protocol. We performed RNA hybridization and RT as specified in the protocol (Hughes et al., 2019). After RT, we collected beads by centrifugation at 1000 x g for 1 min at room temperature. We resuspended beads with GeneXpert Lysis Buffer (Cepheid, Sunnyvale, CA, USA) for inactivation, which was required prior to removal from the BSL-4 laboratory according to standard operating procedures. After removal, we washed beads thrice with TE buffer containing 0.01% Tween 20 and shipped at 4 °C for further library construction and sequencing.


title: Teosinte WGBS_JRIAL2E


title: whole blood, control 20, year 3


title: Teosinte WGBS_JRIAL2J


title: whole blood, control 18, year 1


title: whole blood, control 18, year 3


title: NHP1.H024.a1.media

description:
Donor replicate 1; 24 hours post infection; Treatment: media; Seq-well array 1
Data for a given Seq-Well array for a specific biological sample
PBMC purification: We centrifuged whole blood in K3EDTA tubes at 1800 x g for 10 min at room temperature, removed EDTA plasma, and added phosphate buffered saline (PBS, Thermo Fisher Scientific, Waltham, MA, USA) to the pelleted cells to double the original whole blood volume. We gently poured the PBS-blood cell mixture into an Accuspin tube containing Histopaque (Sigma-Aldrich, St. Louis, MO, USA) and centrifuged at 1000 x g for 10 min at room temperature with the brake set to 1. Following centrifugation, we removed the top, clear supernatant layer to within 0.5 cm of the cloudy white layer containing PBMCs. We transferred the cloudy PBMC layer to a clean 15 mL conical tube and increased the volume to 10 mL using PBS supplemented with 2% heat-inactivated fetal bovine serum (PBS/2%HI-FBS) and mixed by inversion. We then centrifuged at 300 x g for 10 min at 4 °C with the brake set to 1. Following centrifugation, we removed the supernatant, resuspended the cell pellet with PBS/2%HI-FBS to a final volume of 10 mL, and mixed using gentle raking to wash the cells. We repeated the wash step 2 more times with the centrifuge set to 200 x g for 10 min at 4 °C with the brake set to 1. We then resuspended the cell pellet in 9.5mL PBS/2%HI-FBS for counting using the Countess Cell Counting system (Thermo Fisher Scientific). We aliquoted 0.5 mL for Seq-Well, and used the remaining 9 mL volume for CyTOF.
Seq-Well: We performed Seq-Well as described previously (Gierahn et al., 2017), with the S3 protocol (Hughes et al., 2019) and some controls and modifications to adhere to the BSL-4 environment. After loading and sealing beads and cells in Seq-Well arrays, we placed them in a -80 °C freezer until further processing – this step was required due to time constraints in the BSL-4. Later, we removed sealed Seq-Well arrays from the -80 °C freezer, placed them in 4-well dishes, and allowed them to equilibrate to room temperature for at least 30 min. We then covered arrays in 5 mL Seq-Well Lysis Buffer per protocol. We performed RNA hybridization and RT as specified in the protocol (Hughes et al., 2019). After RT, we collected beads by centrifugation at 1000 x g for 1 min at room temperature. We resuspended beads with GeneXpert Lysis Buffer (Cepheid, Sunnyvale, CA, USA) for inactivation, which was required prior to removal from the BSL-4 laboratory according to standard operating procedures. After removal, we washed beads thrice with TE buffer containing 0.01% Tween 20 and shipped at 4 °C for further library construction and sequencing.

value: media


title: whole blood, control 17, year 3


title: NHP1.H004.a1.media

description:
Donor replicate 1; 04 hours post infection; Treatment: media; Seq-well array 1
Data for a given Seq-Well array for a specific biological sample
PBMC purification: We centrifuged whole blood in K3EDTA tubes at 1800 x g for 10 min at room temperature, removed EDTA plasma, and added phosphate buffered saline (PBS, Thermo Fisher Scientific, Waltham, MA, USA) to the pelleted cells to double the original whole blood volume. We gently poured the PBS-blood cell mixture into an Accuspin tube containing Histopaque (Sigma-Aldrich, St. Louis, MO, USA) and centrifuged at 1000 x g for 10 min at room temperature with the brake set to 1. Following centrifugation, we removed the top, clear supernatant layer to within 0.5 cm of the cloudy white layer containing PBMCs. We transferred the cloudy PBMC layer to a clean 15 mL conical tube and increased the volume to 10 mL using PBS supplemented with 2% heat-inactivated fetal bovine serum (PBS/2%HI-FBS) and mixed by inversion. We then centrifuged at 300 x g for 10 min at 4 °C with the brake set to 1. Following centrifugation, we removed the supernatant, resuspended the cell pellet with PBS/2%HI-FBS to a final volume of 10 mL, and mixed using gentle raking to wash the cells. We repeated the wash step 2 more times with the centrifuge set to 200 x g for 10 min at 4 °C with the brake set to 1. We then resuspended the cell pellet in 9.5mL PBS/2%HI-FBS for counting using the Countess Cell Counting system (Thermo Fisher Scientific). We aliquoted 0.5 mL for Seq-Well, and used the remaining 9 mL volume for CyTOF.
Seq-Well: We performed Seq-Well as described previously (Gierahn et al., 2017), with the S3 protocol (Hughes et al., 2019) and some controls and modifications to adhere to the BSL-4 environment. After loading and sealing beads and cells in Seq-Well arrays, we placed them in a -80 °C freezer until further processing – this step was required due to time constraints in the BSL-4. Later, we removed sealed Seq-Well arrays from the -80 °C freezer, placed them in 4-well dishes, and allowed them to equilibrate to room temperature for at least 30 min. We then covered arrays in 5 mL Seq-Well Lysis Buffer per protocol. We performed RNA hybridization and RT as specified in the protocol (Hughes et al., 2019). After RT, we collected beads by centrifugation at 1000 x g for 1 min at room temperature. We resuspended beads with GeneXpert Lysis Buffer (Cepheid, Sunnyvale, CA, USA) for inactivation, which was required prior to removal from the BSL-4 laboratory according to standard operating procedures. After removal, we washed beads thrice with TE buffer containing 0.01% Tween 20 and shipped at 4 °C for further library construction and sequencing.


title: whole blood, control 16, year 3


title: whole blood, control 17, year 1


title: whole blood, control 19, year 3


title: Teosinte WGBS_JRIAL2D


title: whole blood, control 15, year 3


title: NHP1.H004.a1.live

description:
Donor replicate 1; 04 hours post infection; Treatment: live; Seq-well array 1
Data for a given Seq-Well array for a specific biological sample
PBMC purification: We centrifuged whole blood in K3EDTA tubes at 1800 x g for 10 min at room temperature, removed EDTA plasma, and added phosphate buffered saline (PBS, Thermo Fisher Scientific, Waltham, MA, USA) to the pelleted cells to double the original whole blood volume. We gently poured the PBS-blood cell mixture into an Accuspin tube containing Histopaque (Sigma-Aldrich, St. Louis, MO, USA) and centrifuged at 1000 x g for 10 min at room temperature with the brake set to 1. Following centrifugation, we removed the top, clear supernatant layer to within 0.5 cm of the cloudy white layer containing PBMCs. We transferred the cloudy PBMC layer to a clean 15 mL conical tube and increased the volume to 10 mL using PBS supplemented with 2% heat-inactivated fetal bovine serum (PBS/2%HI-FBS) and mixed by inversion. We then centrifuged at 300 x g for 10 min at 4 °C with the brake set to 1. Following centrifugation, we removed the supernatant, resuspended the cell pellet with PBS/2%HI-FBS to a final volume of 10 mL, and mixed using gentle raking to wash the cells. We repeated the wash step 2 more times with the centrifuge set to 200 x g for 10 min at 4 °C with the brake set to 1. We then resuspended the cell pellet in 9.5mL PBS/2%HI-FBS for counting using the Countess Cell Counting system (Thermo Fisher Scientific). We aliquoted 0.5 mL for Seq-Well, and used the remaining 9 mL volume for CyTOF.
Seq-Well: We performed Seq-Well as described previously (Gierahn et al., 2017), with the S3 protocol (Hughes et al., 2019) and some controls and modifications to adhere to the BSL-4 environment. After loading and sealing beads and cells in Seq-Well arrays, we placed them in a -80 °C freezer until further processing – this step was required due to time constraints in the BSL-4. Later, we removed sealed Seq-Well arrays from the -80 °C freezer, placed them in 4-well dishes, and allowed them to equilibrate to room temperature for at least 30 min. We then covered arrays in 5 mL Seq-Well Lysis Buffer per protocol. We performed RNA hybridization and RT as specified in the protocol (Hughes et al., 2019). After RT, we collected beads by centrifugation at 1000 x g for 1 min at room temperature. We resuspended beads with GeneXpert Lysis Buffer (Cepheid, Sunnyvale, CA, USA) for inactivation, which was required prior to removal from the BSL-4 laboratory according to standard operating procedures. After removal, we washed beads thrice with TE buffer containing 0.01% Tween 20 and shipped at 4 °C for further library construction and sequencing.


title: NHP1.H004.a4.live

description:
Donor replicate 1; 04 hours post infection; Treatment: live; Seq-well array 4
Data for a given Seq-Well array for a specific biological sample
PBMC purification: We centrifuged whole blood in K3EDTA tubes at 1800 x g for 10 min at room temperature, removed EDTA plasma, and added phosphate buffered saline (PBS, Thermo Fisher Scientific, Waltham, MA, USA) to the pelleted cells to double the original whole blood volume. We gently poured the PBS-blood cell mixture into an Accuspin tube containing Histopaque (Sigma-Aldrich, St. Louis, MO, USA) and centrifuged at 1000 x g for 10 min at room temperature with the brake set to 1. Following centrifugation, we removed the top, clear supernatant layer to within 0.5 cm of the cloudy white layer containing PBMCs. We transferred the cloudy PBMC layer to a clean 15 mL conical tube and increased the volume to 10 mL using PBS supplemented with 2% heat-inactivated fetal bovine serum (PBS/2%HI-FBS) and mixed by inversion. We then centrifuged at 300 x g for 10 min at 4 °C with the brake set to 1. Following centrifugation, we removed the supernatant, resuspended the cell pellet with PBS/2%HI-FBS to a final volume of 10 mL, and mixed using gentle raking to wash the cells. We repeated the wash step 2 more times with the centrifuge set to 200 x g for 10 min at 4 °C with the brake set to 1. We then resuspended the cell pellet in 9.5mL PBS/2%HI-FBS for counting using the Countess Cell Counting system (Thermo Fisher Scientific). We aliquoted 0.5 mL for Seq-Well, and used the remaining 9 mL volume for CyTOF.
Seq-Well: We performed Seq-Well as described previously (Gierahn et al., 2017), with the S3 protocol (Hughes et al., 2019) and some controls and modifications to adhere to the BSL-4 environment. After loading and sealing beads and cells in Seq-Well arrays, we placed them in a -80 °C freezer until further processing – this step was required due to time constraints in the BSL-4. Later, we removed sealed Seq-Well arrays from the -80 °C freezer, placed them in 4-well dishes, and allowed them to equilibrate to room temperature for at least 30 min. We then covered arrays in 5 mL Seq-Well Lysis Buffer per protocol. We performed RNA hybridization and RT as specified in the protocol (Hughes et al., 2019). After RT, we collected beads by centrifugation at 1000 x g for 1 min at room temperature. We resuspended beads with GeneXpert Lysis Buffer (Cepheid, Sunnyvale, CA, USA) for inactivation, which was required prior to removal from the BSL-4 laboratory according to standard operating procedures. After removal, we washed beads thrice with TE buffer containing 0.01% Tween 20 and shipped at 4 °C for further library construction and sequencing.


title: Teosinte WGBS_JRIAL2C


title: NHP1.H004.a1.irrad

description:
Donor replicate 1; 04 hours post infection; Treatment: irrad; Seq-well array 1
Data for a given Seq-Well array for a specific biological sample
PBMC purification: We centrifuged whole blood in K3EDTA tubes at 1800 x g for 10 min at room temperature, removed EDTA plasma, and added phosphate buffered saline (PBS, Thermo Fisher Scientific, Waltham, MA, USA) to the pelleted cells to double the original whole blood volume. We gently poured the PBS-blood cell mixture into an Accuspin tube containing Histopaque (Sigma-Aldrich, St. Louis, MO, USA) and centrifuged at 1000 x g for 10 min at room temperature with the brake set to 1. Following centrifugation, we removed the top, clear supernatant layer to within 0.5 cm of the cloudy white layer containing PBMCs. We transferred the cloudy PBMC layer to a clean 15 mL conical tube and increased the volume to 10 mL using PBS supplemented with 2% heat-inactivated fetal bovine serum (PBS/2%HI-FBS) and mixed by inversion. We then centrifuged at 300 x g for 10 min at 4 °C with the brake set to 1. Following centrifugation, we removed the supernatant, resuspended the cell pellet with PBS/2%HI-FBS to a final volume of 10 mL, and mixed using gentle raking to wash the cells. We repeated the wash step 2 more times with the centrifuge set to 200 x g for 10 min at 4 °C with the brake set to 1. We then resuspended the cell pellet in 9.5mL PBS/2%HI-FBS for counting using the Countess Cell Counting system (Thermo Fisher Scientific). We aliquoted 0.5 mL for Seq-Well, and used the remaining 9 mL volume for CyTOF.
Seq-Well: We performed Seq-Well as described previously (Gierahn et al., 2017), with the S3 protocol (Hughes et al., 2019) and some controls and modifications to adhere to the BSL-4 environment. After loading and sealing beads and cells in Seq-Well arrays, we placed them in a -80 °C freezer until further processing – this step was required due to time constraints in the BSL-4. Later, we removed sealed Seq-Well arrays from the -80 °C freezer, placed them in 4-well dishes, and allowed them to equilibrate to room temperature for at least 30 min. We then covered arrays in 5 mL Seq-Well Lysis Buffer per protocol. We performed RNA hybridization and RT as specified in the protocol (Hughes et al., 2019). After RT, we collected beads by centrifugation at 1000 x g for 1 min at room temperature. We resuspended beads with GeneXpert Lysis Buffer (Cepheid, Sunnyvale, CA, USA) for inactivation, which was required prior to removal from the BSL-4 laboratory according to standard operating procedures. After removal, we washed beads thrice with TE buffer containing 0.01% Tween 20 and shipped at 4 °C for further library construction and sequencing.


title: Teosinte WGBS_JRIAL2B


title: Teosinte WGBS_JRIAL2A


title: Landrace WGBS_PI-628514

value: Landrace


title: Landrace WGS_PI-628503

description:
Whole genome sequencing
Table_S2_Selective_sweep.bed

data_processing:
Library strategy: WGS-Seq
Whole genome sequencing reads were aligned to the B73 reference genome using BWA; Bisulfite sequencing data analysis was conducted using Bismark
Duplicate reads were removed by picard
We conducted SNP calling using Genome Analysis Toolkit’s(GATK, version 4) HaplotypeCaller
We used a software package ‘metilene’ for DMR detection between two populations
We calculated XPCLR to detect selective signals
Genome_build: B73 reference genome
Supplementary_files_format_and_content: bed files include selective sweeps and differentially methylated regions.


title: Landrace WGBS_PI-620860


title: Landrace WGBS_PI-628503


title: Landrace WGS_PI-620860


title: Landrace WGBS_PI-620859


title: Landrace WGS_PI-620856


title: WT_0hpa_NOFACS [S1]

city: Seattle

first: Anneke

middle: Dixie

last: Kakebeen

state: WA

address: 5611 9th Ave NW

department: Biochemistry

institute: University of Washington

data_processing:
Trim Galore!
Trim sequencing adaptors from fastq files
trim_galore --paired --phred33 --trim1 --nextera ${fastqDIR}${file}_R1_001.fastq.gz ${fastqDIR}${file}_R2_001.fastq.gz --output_dir
Bowtie2
align reads to the genome
bowtie2 --very-sensitive -x ${GenomeDIR} -X 2000 2>> ${BAMDIR}bowtie_log.txt -p 1 -1 ${fastqDIR}trimmed/${file}_R1_001_val_1.fq.gz -2 ${fastqDIR}trimmed/${file}_R2_001_val_2.fq.gz | samtools view -Sb - | samtools sort - -o ${BAMDIR}${file}.bam
MACS2
call peaks on aligned reads
macs2 callpeak -t ${BAMDIR}${file}.bam --nomodel --shift -100 --extsize 200 -g 1.7e9 -f BAM -n ${file} --outdir ${MACSDIR}${file}
GenomicRanges
annotated peaks to nearest transcription start site
used:  Xtropicalisv9.0.Named.primaryTrs.gff3 for annotation
Rsubread
make counts matrix for all samples
featureCounts(isPairedEnd=TRUE, maxFragLength=2000)
Genome_build: Xtropicalis9.0
Supplementary_files_format_and_content: peak counts

organism: Xenopus tropicalis

source_name: tadpole tail tissue

growth_protocol: Xenopus were reared in 1/9 Modified Ringers solution at 23C.

extract_protocol: The regenerated tail was isolated from the tadpole and cells were dissociated into single cell suspension using Liberase, washed in PBS and sorted for fluoresence through an Aria III cell sorter.

treatment_protocol: The posterior third of an anestitized tadpole tail was amputated at NF stage 41. Tadpoles were replaced in media without anesthetiz and allowed to regenerated until desired collection timepoint.

value: Wildtype

tag: regeneration timepoint

value: tadpole tail tissue

tag: facs

value: No FACS


title: WT_0hpa_FACS [S2]

value: FACS


title: Landrace WGBS_PI-620856


title: Landrace WGS_PI-620859


title: Landrace WGBS_PI-620846


title: Landrace WGS_PI-620846


title: Landrace WGS_PI-620842


title: whole blood, control 14, year 1

description: Gene expression data from peripheral whole blood of control individual

value: Male

value: london

value: Control


title: Landrace WGS_PI-628514

value: 3rd leaf


title: whole blood, control 12, year 3

value: vancouver


title: Landrace WGBS_PI-620842

description:
Whole genome bisulfite sequencing
Table_S1_DMR.bed

value: seedling


title: Landrace WGS_PI-620834


title: whole blood, control 16, year 1


title: whole blood, preHD A 09, year 1

description: Gene expression data from peripheral whole blood of pre-symptomatic Huntingtin gene change carrier

value: preHD A


title: Landrace WGBS_PI-620821


title: Landrace WGBS_PI-620834


title: whole blood, control 13, year 1

value: Female


title: Landrace WGS_PI-620821


title: NHP14.D000.fresh.a1

description:
Animal: NHP14; Day post infection: D000; Fresh or freeze-thawed: fresh; MDCK Spike in: False; Array number: a1
Data for a given Seq-Well array for a specific biological sample
PBMC purification: We centrifuged whole blood in K3EDTA tubes at 1800 x g for 10 min at room temperature, removed EDTA plasma, and added phosphate buffered saline (PBS, Thermo Fisher Scientific, Waltham, MA, USA) to the pelleted cells to double the original whole blood volume. We gently poured the PBS-blood cell mixture into an Accuspin tube containing Histopaque (Sigma-Aldrich, St. Louis, MO, USA) and centrifuged at 1000 x g for 10 min at room temperature with the brake set to 1. Following centrifugation, we removed the top, clear supernatant layer to within 0.5 cm of the cloudy white layer containing PBMCs. We transferred the cloudy PBMC layer to a clean 15 mL conical tube and increased the volume to 10 mL using PBS supplemented with 2% heat-inactivated fetal bovine serum (PBS/2%HI-FBS) and mixed by inversion. We then centrifuged at 300 x g for 10 min at 4 °C with the brake set to 1. Following centrifugation, we removed the supernatant, resuspended the cell pellet with PBS/2%HI-FBS to a final volume of 10 mL, and mixed using gentle raking to wash the cells. We repeated the wash step 2 more times with the centrifuge set to 200 x g for 10 min at 4 °C with the brake set to 1. We then resuspended the cell pellet in 9.5mL PBS/2%HI-FBS for counting using the Countess Cell Counting system (Thermo Fisher Scientific). We aliquoted 0.5 mL for Seq-Well, and used the remaining 9 mL volume for CyTOF.
Seq-Well: We performed Seq-Well as described previously (Gierahn et al., 2017), with the S3 protocol (Hughes et al., 2019) and some controls and modifications to adhere to the BSL-4 environment. After loading and sealing beads and cells in Seq-Well arrays, we placed them in a -80 °C freezer until further processing – this step was required due to time constraints in the BSL-4. Later, we removed sealed Seq-Well arrays from the -80 °C freezer, placed them in 4-well dishes, and allowed them to equilibrate to room temperature for at least 30 min. We then covered arrays in 5 mL Seq-Well Lysis Buffer per protocol. We performed RNA hybridization and RT as specified in the protocol (Hughes et al., 2019). After RT, we collected beads by centrifugation at 1000 x g for 1 min at room temperature. We resuspended beads with GeneXpert Lysis Buffer (Cepheid, Sunnyvale, CA, USA) for inactivation, which was required prior to removal from the BSL-4 laboratory according to standard operating procedures. After removal, we washed beads thrice with TE buffer containing 0.01% Tween 20 and shipped at 4 °C for further library construction and sequencing.

tag: fresh_vs_freezethawed (frz)

value: fresh

value: FALSE

tag: library_treatment (standard, dash, dashx2 if dash was applied sequentially, or mixed if dash-treated and standard libraries were combined)

value: std


title: Landrace WGBS_PI-620819

tag: tissue


title: whole blood, control 10, year 1


title: whole blood, control 15, year 1


title: whole blood, control 12, year 1


title: whole blood, control 10, year 3


title: Landrace WGBS_PI-620797


title: Landrace WGS_PI-620797


title: whole blood, control 11, year 1


title: whole blood, control 07, year 3


title: whole blood, control 09, year 1


title: whole blood, control 08, year 1


title: whole blood, control 09, year 3


title: Landrace WGS_PI-620785


title: whole blood, control 13, year 3


title: Landrace WGBS_PI-620785


title: Landrace WGS_PI-620784


title: whole blood, control 11, year 3


title: Landrace WGS_PI-620774


title: BB1174 T21 AP2

source_name: Apigenin treated human amniocytes derived from live a fetus with Trisomy 21

growth_protocol: Amniotic fluid was obtained during amniocentesis diagnostic procedure for 14 live fetuses with the following metaphase karyotypes: 47, XX, +21 (N=3); 47, XY, +21 (N=4); 46, XX (N=3); 46, XY (N=4). Gestational ages ranged from 15 3/7 to 20 2/7 weeks. Samples were matched for sex and gestational age (seven pairs were analyzed). Amniotic fluid was centrifuged at 1000 RPM for 5 min, cells were washed with DMEM/F12 and resuspended in Amniomax complete media (Amniomax basal media + Amniomax supplement) and incubated at 37°C and 5 % CO2.

treatment_protocol: Cells were plated at 10+6 in T25 flasks. Twenty four hours adter plating (DIV 1), amniocytes were either treated with apigenin at 2 uM in Amniomax complete media or supplemented only with Amniomax complete media for three consecutive days. Apigenin containing medid or regular media were changed daily. On DIV 4, total RNA was extracted and used for gene expression studies.

value: amniocytes

tag: pair

tag: karyotype

value: Apigenin


title: JL779 T21 AP2

tag: treatment


title: whole blood, control 06, year 3

tag: year

tag: Sex


title: Landrace WGBS_PI-620774

value: Landrace


title: whole blood, control 07, year 1

tag: age at year 1

tag: location


title: Landrace WGBS_PI-620773


title: Landrace WGS_PI-620773


title: Landrace WGS_PI-620767


title: Landrace WGBS_AMES-8235


title: BB16-225-T21-AP2


title: whole blood, control 06, year 1

tag: disease stage

tag: expanded allele cag repeat count


title: Landrace WGBS_PI-620767


title: SG01-T21-AP2


title: SZ16-201-T21-AP2


title: Landrace WGBS_PI-620784


title: Landrace WGS_AMES-8235


title: whole blood, control 04, year 3

tag: uhdrs tms

tag: uhdrs tfc


title: CG16-467-T21-AP2


title: Teosinte WGS_JRIAL2T

tag: Stage

tag: population

value: Teosinte


title: DD206 Memory cDC

city: New York

first: Daniel

last: Paik

state: NY

address: 650 W 168th Street

department: Microbiology and Immunology

institute: Columbia University Medical Center

description:
est_counts_genes_kallisto.txt
tpm_values_genes_kallisto.txt
normalized_data.csv

data_processing:
FASTq raw data were mapped to GRCm38 using kallisto (0.44.0) default parameters
Non-protein coding genes were removed, and of the remaining genes, genes in the bottom third of abundance (as determined by gene counts) were filtered out
DESeq2 was used to  normalize read counts using Variance Stabilizing Transformation and determine differentially expressed genes
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text files include read counts and tpm values as well as normalized data for each sample

source_name: mediastinal lymph node

extract_protocol:
CD45+ CD11c+ I-A/I-E+ zbtb46+ GFP+ cells were sorted from medLN cells and cells were flash frozen on dry ice.
RNA extracted usin Qiagen RNAEasy Mini kit
Clontech SMART-Seq v4 Ultra low Input RNA kit

tag: strain

value: C57BL/6 zbtb46-GFP

tag: infection status

value: Previously infected


title: DD205 Naïve cDC

value: Uninfected


title: Teosinte WGS_JRIAL2S


title: JG16-213 T21 AP2


title: BB1174 T21 UNTR

source_name: Untreated human amniocytes derived from live a fetus with Trisomy 21


title: Teosinte WGS_JRIAL2R


title: whole blood, control 04, year 1

value: Male


title: whole blood, control 03, year 3

value: london

value: Control


title: whole blood, control 05, year 1

value: vancouver


title: whole blood, control 03, year 1


title: SG01-T21-UNTR


title: JL779 T21 UNTR


title: DD203 Memory cDC


title: DD202 Memory cDC


title: DD204 Naïve cDC


title: Teosinte WGS_JRIAL2Q

value: 3rd leaf

value: seedling


title: Teosinte WGS_JRIAL2P


title: BB16-225-T21-UNTR


title: Teosinte WGS_JRIAL2O


title: whole blood, control 02, year 3

value: Female


title: SZ16-201-T21-UNTR


title: DD201 Naïve cDC


title: Teosinte WGS_JRIAL2N


title: LY96 siRNA-treated cell stimulated with HDM extract, sample 3

city: Tokyo

first: Takashi

last: Ishii

address: 7-3-1, Hongo, BUnkyo-ku

country: Japan

institute: The University of Tokyo

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using HISAT2 software (version 2.2.0)
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

source_name: airway epithelial cells

growth_protocol: BEAS-2b cell were maintained in BEGM medium (Lonza, Basel, Switzerland)

extract_protocol:
24 hours after stimulation, cells were harvested and Total RNA was extracted with a NucleoSpin RNA XS isolation and purification kit (Takara, Tokyo, Japan)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 24 hours before stimulation, Meidum was changed for BEBM medium (Lonza). PBS or HDM extract was used for stimulation.

tag: cell type

value: airway epithelial cells (cell-line)

tag: sirna

value: LY96 siRNA

value: HDM extract

tag: cell line


title: Teosinte WGS_JRIAL2M

tag: tissue


title: CG16-467-T21-UNTR

value: amniocytes

tag: pair

tag: karyotype

tag: treatment


title: LY96 siRNA-treated cell stimulated with HDM extract, sample 1


title: LY96 siRNA-treated cell stimulated with HDM extract, sample 2


title: whole blood, control 01, year 3

tag: year

tag: Sex

tag: age at year 1


title: CEMBA181023_6B_3_CEMBA181023_6B_4_H9_ad008

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

data_processing:
Library strategy: snmC-seq2
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted mm10 reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column

source_name: C57BL/6J Male P56 Mouse Brain

growth_protocol: All mice are C57BL/6J Male, brain dissected in P56

extract_protocol:
the brain of P56 male C57BL/6J mouse will be removed and cut into 600 microns thick coronal sections using a tissue matrix. Then each region will be microdissected from the coronal tissue sections based on identified landmarks and brain atlas coordinates, as defined in Allen brain atlas CCF3 (Avaliable at: http://atlas.brain-map.org). For each dissection region, the tissue from several littermate mice will be combined together into to separate replicate groups. The number of animals in a replicate depends on the size of the tissue. Nuclei preparation will be stained with the fluorescently labeled anti-NeuN body and nucleic acid stain Hoechst 33342.
Library prepared following protocol discribed in Luo, Chongyuan, Angeline Rivkin, Jingtian Zhou, Justin P. Sandoval, Laurie Kurihara, Jacinta Lucero, Rosa Castanon, et al. 2018. “Robust Single-Cell DNA Methylome Profiling with snmC-seq2.” Nature Communications 9 (1): 3824.

tag: brain region

value: SSp

value: male

tag: age


title: ML181 2N AP2

source_name: Apigenin treated human amniocytes derived from live euploid a fetus

value: Apigenin


title: Teosinte WGS_JRIAL2L

value: Teosinte


title: LC847-2N-AP2


title: whole blood, control 01, year 1

tag: location

tag: disease stage

tag: expanded allele cag repeat count

tag: uhdrs tms

tag: uhdrs tfc


title: whole blood, control 02, year 1


title: LY96 siRNA-treated cell stimulated with PBS

tag: cell type

value: PBS


title: ER48 2N AP2


title: Teosinte WGS_JRIAL2K

tag: Stage

tag: population


title: CEMBA181023_6B_3_CEMBA181023_6B_4_H9_ad007

tag: strain


title: control siRNA-treated cell stimulated with HDM extract, sample 3

tag: sirna

value: control

tag: cell line


title: CEMBA181023_6B_3_CEMBA181023_6B_4_H9_ad010


title: CEMBA181023_6B_3_CEMBA181023_6B_4_H9_ad012


title: control siRNA-treated cell stimulated with HDM extract, sample 2

tag: treatment


title: control siRNA-treated cell stimulated with HDM extract, sample 1


title: Teosinte WGS_JRIAL2J

tag: tissue


title: Teosinte WGS_JRIAL2I


title: CEMBA181023_6B_3_CEMBA181023_6B_4_H9_ad006

tag: Sex


title: Teosinte WGS_JRIAL2H


title: CEMBA181023_6B_3_CEMBA181023_6B_4_H9_ad002


title: control siRNA-treated cell stimulated with PBS


title: CEMBA181023_6B_3_CEMBA181023_6B_4_H9_ad004


title: CV1166-2N-AP2

tag: pair

tag: karyotype


title: JT1275 2N AP2


title: KM1170 2N AP2


title: CEMBA181023_6B_3_CEMBA181023_6B_4_H8_ad001

tag: brain region

tag: age


title: Teosinte WGS_JRIAL2G


title: Teosinte WGS_JRIAL2F


title: CEMBA181023_6B_3_CEMBA181023_6B_4_H8_ad012


title: JJ1298-2N-AP2


title: Teosinte WGS_JRIAL2E


title: ML181 2N UNTR

source_name: Untreated human amniocytes derived from live euploid a fetus


title: LC847-2N-UNTR


title: Teosinte WGS_JRIAL2C


title: ER48 2N UNTR


title: CEMBA181023_6B_3_CEMBA181023_6B_4_H8_ad007


title: CEMBA181023_6B_3_CEMBA181023_6B_4_H8_ad006


title: CEMBA181023_6B_3_CEMBA181023_6B_4_H8_ad008


title: Teosinte WGS_JRIAL2D


title: Teosinte WGS_JRIAL2B


title: CV1166-2N-UNTR


title: CEMBA181023_6B_3_CEMBA181023_6B_4_H8_ad002


title: KM1170 2N UNTR


title: Teosinte WGS_JRIAL2A


title: CEMBA181023_6B_3_CEMBA181023_6B_4_H7_ad002


title: CEMBA181023_6B_3_CEMBA181023_6B_4_H7_ad008


title: JT1275 2N UNTR


title: CEMBA181023_6B_3_CEMBA181023_6B_4_H7_ad004


title: JJ1298-2N-UNTR


title: FGF19 #2

city: Urbana

first: Young-Chae

last: Kim

state: IL

address: 394 Burrill Hall  407 S. Goodwin Ave

department: MIP

institute: University of Illinois at Urbana-Champaign

data_processing:
Using a HiSeq SBS sequencing kit version 4, Fastq files were generated and demultiplexed with with the bcl2fastq v2.17.1.14 Conversion Software (Illumina).
Trimmomatic ver 0.36 was used to remove sequence adapters and low-quality bases and quality control was checked by FastQC ver 0.11.5
Sequencing alignment was performed by STAR ver 2.5.3a.
The differential expression profiles of RNA-seq were analyzed by the edgeR-based R (ver 3.4.1) pipeline
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include fold change, FDR between two conditions generated by edgeR and gene read count

source_name: Liver

extract_protocol:
RNA from the livers was isolated with the RNeasy Kit (Qiagen)
RNA libraries were prepared for sequencing using standard Illumina protocols. The cDNA library was sequenced using an Illumina HiSeq2000 (Illumina, San Diego, CA) to produce paired-end 100 bp reads.

treatment_protocol: Eight week-old C57BL/6 mice were fasted overnight and treated with1 mg/kg FGF19 or vehicle for 6 h with continued fasting.

value: Liver

value: 8 weeks


title: FGF19 #3


title: P3_Female_80_days

city: Birmingham

first: julia

last: constantinou

address: Edgebaston

department: Biosciences

institute: University of Birmingham

data_processing:
The reads were mapped to reference genome of Daphnia magna (GCA_001632505.1) with TopHat2 (2.1.1) with preset b2-sensitive.
The read counts were extracted with Rsubread (1.30.9), with default settings, using the reference gene models (GCA_001632505.1).
Expression changes were analysed at gene levels using DESeq2 (1.20) with default settings. Genes  with significant expression difference between males and females, chages during normal ageing or interaction with sex and age are reported in processed files.
Genome_build: GCA_001632505.1
Supplementary_files_format_and_content: csv (differential expression analysis results at gene level: RSeq_results_age only_age in days_ordered by padj.csv.gz, RSeq_results_sex-age_interaction_age in days_ordered by padj.csv.gz, RSeq_results_sex only_age in days_ordered by padj.csv.gz)
Supplementary_files_format_and_content: csv (read counts at gene level: readcounts_combined.csv.gz)

organism: Daphnia magna

source_name: whole organism

growth_protocol: Cultures of Daphnia magna, strain Bham2, were maintained in a 16:8 h light:dark photoperiod and temperature of 20 ± 1 °C, in high hardness COMBO medium (COMBO). Media were prepared using a protocol adapted from Kilham et al. (1998), and renewed every other day. Animals were fed every other day with Chlorella vulgaris at a concentration of ~27,550 cells of algae per individual Daphnia. Daphnia samples were monitored every 2 hours during the light period once the appropriate age was reached.

extract_protocol:
Total RNA was extracted from the samples using RNeasy micro kit ((Qiagen Ltd, UK) according to the manufactures protocol.
The RNA-seq libraries were prepared using the Illumina TruSeq standard mRNA kit and sequenced (2x100bp) using Illumina Hi-Seq 4000 platform at BGI, Denmark.

treatment_protocol: Samples were flash frozen in liquid nitrogen when brood pouch was empty and stored in -80C until further use.

value: whole organism

tag: gender

tag: notes

value: Maintained under normal conditions

tag: culturing media

value: High Hardness COMBO


title: P2_Female_80_days


title: CEMBA181023_6B_3_CEMBA181023_6B_4_H7_ad010


title: FGF19 #1


title: Vehicle #3

value: Vehicle


title: P1_Female_80_days

value: Female


title: N3_Female_50_days


title: RANKL with LE_(A. distichum dataset)_rep1

city: Cheongju

first: Kyunghwan

address: Rm #202a, Bldg. S1-5, 1 chungdae-ro

country: South Korea

institute: Chungbuk National University

data_processing:
mRNA-Seq reads were mapped to reference mouse genome (mm10 assembly) using HISAT2 with default parameters.
RNA expression was quantified using analyzeRepeats.pl command in HOMER
DEGs was assessed with DESeq2 using getDiffExpression.pl in HOMER.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: Bone marrow-derived macrophage cells

growth_protocol: Bone marrow (BM) cells were collected by flushing femurs and tibias from 6- to 8-week-old C57BL/6 mice. Cells were cultured in α-minimum essential medium (α-MEM) supplemented with 10% FBS and M-CSF (5 ng/ml) for 16 h.  Non-adherent cells were harvested and cultured with M-CSF (30 ng/ml) for 3 days. Floating cells were removed and adherent cells were used as bone marrow-derived macrophage (BMM) cells.

extract_protocol:
Total RNA was isolated using the TRIzol reagent according to the manufacturer's instructinos.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Osteoclast precursor cells were cultured in 48-well plates with 30 ng/mL of macrophage colony-stimulating factor (M-CSF) and 100 ng/mL of receptor activator of nuclear factor kappaB ligand (RANKL), in the absence or presence of LE (10 μg/ml).

value: Primary cells

value: 6-8 weeks


title: RANKL with LE_(A. distichum dataset)_rep2


title: CEMBA181023_6B_3_CEMBA181023_6B_4_H6_ad001


title: N2_Female_50_days


title: iPSC, 585B1-BTAG

type: genomic

city: Kyoto

first: Yukihiro

last: Yabuta

state: Kyoto

address: Yoshida-Konoe-cho, Sakyo-ku

department: Anatomy and Cell Biology

institute: Kyoto University, Graduate school of medicine

hyb_protocol: Labeled genomic DNA was hybridized on SurePrint G3 Human CGH Microarray 8 × 60K (Agilent Technologies, G4450A) at 60°C for 24 hr at 20 rpm.

scan_protocol: After washing, the slide was scanned with SureScan Microarray Scanner G2600D (Agilent Technologies).

data_processing: The acquired images were processed with Feature Extraction 12.1.0.3 (Agilent Technologies). aCGH raw data were analyzed with CytoGenomics 5.0.2.5 (Agilent Technologies) with the analysis method “Default Analysis Method - CGH v2” which detects aberrant intervals with the algorithm ADM2. Additionally, “Fuzzy Zero” correction was applied to mitigate the erroneous calls of aberrant intervals. Log2 ratios of all probes were acquired as outputs of CytoGenomics and were subjected to the visualization.

source_name: iPSC, from 585-BTAG iPSC

label_protocol: aCGH experiment and image processing of the microarray was performed with SureTag Complete DNA Labeling Kit (Agilent Technologies, 5190-4240) by TaKaRa Bio. Human Reference DNA Male (Agilent Technologies) was used for the sex-matched reference genomic DNA. Briefly, 200 ng genomic DNA was digested with Alu1 and Rsa1, and then labeled with Cyanine 3 (reference genomic DNA) or Cyanine 5.

growth_protocol: The defined hPGCLC expansion culture medium is: DMEM (1.0 g/L glucose; GIBCO, 11054-020) with 15% of KSR, 2.5% of FBS, 1% of NEAA, 2mM of GlutaMAX (GIBCO, 35050-061), 1% penicillin & streptomycin, and 0.1 mM of 2-Mercaptoethanol (GIBCO, 21985-023) supplemented with 10 µM of forskolin, 100 ng/mL of SCF and 20 ng/mL of bFGF.

extract_protocol: For extracting genomic DNA, cells were collected in Cellotion and pelleted, and genomic DNA extraction was performed with NucleoSpin Tissue (MACHEREY-NAGEL, U0952Q) according to the manufacturer’s instruction.

value: iPSC

source_name: Human Reference DNA Male

tag: sample type

value: reference


title: N1_Female_50_days


title: RANKL_R1_(A. distichum dataset)_rep1

tag: cell type


title: No RANKL_C2_(A. distichum dataset)_rep2


title: RANKL_R2_(A. distichum dataset)_rep2


title: CEMBA181023_6B_3_CEMBA181023_6B_4_H7_ad012

value: SSp


title: c70 expanded hPGCLC

source_name: expanded hPGCLC derived from 585B1-BTAG iPSC, BT+AG+ cells were collected at expansion culture day 70

value: expanded PGCLC

value: male


title: CEMBA181023_6B_3_CEMBA181023_6B_4_H6_ad007


title: Bone marrow Lin-negative, Tet2+/-;Ins2Akita/+-rep3

city: INDIANAPOLIS

first: Xiaoyu

last: Lu

state: IN

address: 410W 10TH ST

department: school of medicine

institute: INDIANA UNIVERSITY

data_processing:
Demultiplexing of the reads was performed with bcl2fastq pipeline
Adapters and low quality bases were trimmed using Trimmomatic (version 0.32) with following specific parameters ILLUMINACLIP:<adapters.fa>:2:20:5 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:16. Custom perl scripts along with FASTX-Toolkit version 0.0.14 with the following parameters, “-l 17 -v -M 1 -i “, were used to look for partial adapters within the reads
Reads were mapped against GRCm38 using TopHat2 version 2.1.1 with parameters “--b2-very-sensitive --read-edit-dist 2 --max-multihits 100.
Read counts for each gene were created using custom perl scripts and Gencode M10 as the annotation.
Genome_build: GRCm38
Supplementary_files_format_and_content: Gene counts for each sample in tab-delimited format

source_name: bone marrow Lin-negative

growth_protocol: All the animal experiments were approved by the institutional IACUC (protocol #12204) and mouse colonies were maintained by Laboratory Animal Resource Center at Indiana University School of Medicine under standard husbandry condition.

extract_protocol: RNA libraries were prepared for sequencing using standard protocols

tag: genotype

value: bone marrow

value: Lin-negative


title: Vehicle #2


title: No RANKL_C1_(A. distichum dataset)_rep1


title: MS3_Male_8_days

value: Male


title: Vehicle #1

value: Liver


title: CEMBA181023_6B_3_CEMBA181023_6B_4_H6_ad012


title: Bone marrow Lin-negative, Tet2+/-;Ins2Akita/+-rep2


title: CITED2-KO_IL4_3

city: Cleveland

first: Ernest

last: Chan

state: OH

address: 10900 Euclid Ave, Robbins E211

department: PQHS

institute: CWRU

data_processing:
Illumina reads were mapped to mouse genome release mm10 using TopHat v2.2.1 program.
The expression levels of genes were determined using Cufflinks v2.2.1 and presented as FPKM
Differential expression analysis was done using Cuffdiff from Cufflinks package
Genome_build: GRCm38
Supplementary_files_format_and_content: Gene count matrix in FPKM

source_name: BMDMs

extract_protocol:
Total RNA was isolated from indicated samples using the High Pure RNA Isolation Kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: BMDMs

value: Postnatal week 10


title: CEMBA181023_6B_3_CEMBA181023_6B_4_H5_ad001


title: MS1_Male_8_days

value: whole organism

value: Maintained under normal conditions


title: CEMBA181023_6B_3_CEMBA181023_6B_4_H5_ad008


title: Landrace WGS_PI-620819

value: 3rd leaf

tag: Stage

value: seedling

tag: population

value: Landrace


title: CITED2-KO_IL4_2

tag: strain


title: MS2_Male_8_days

value: High Hardness COMBO


title: Bone marrow Lin-negative, Ins2Akita/+-rep2


title: CITED2-KO_IL4_1


title: MR3_H2_Male_10_days

value: technical replicate of MR3


title: CEMBA181023_6B_3_CEMBA181023_6B_4_H6_ad002


title: Wild Type-IL4_-3

value: Wild Type


title: MR3_E10_Male_10_days


title: Bone marrow Lin-negative, Tet2+/--rep3


title: Wild Type-IL4_-2


title: CEMBA181023_6B_3_CEMBA181023_6B_4_H5_ad007

value: SSp


title: MR2_Male_10_days


title: Bone marrow Lin-negative, Tet2+/--rep2


title: whole blood, control 05, year 3

source_name: Peripheral whole blood

tag: year

tag: age at year 1

tag: location

value: vancouver

tag: disease stage

value: Control

tag: expanded allele cag repeat count

tag: uhdrs tms

tag: uhdrs tfc


title: MR1_Male_10_days

tag: tissue

tag: age

tag: treatment


title: Bone marrow Lin-negative, Ins2Akita/+-rep1

value: bone marrow


title: CEMBA181023_6B_3_CEMBA181023_6B_4_H5_ad012

tag: brain region

tag: Sex

value: male


title: Bone marrow Lin-negative, Tet2+/-;Ins2Akita/+-rep1

tag: cell type

value: Lin-negative


title: Bone marrow Lin-negative, Tet2+/-;Ins2Akita/+-rep4

tag: genotype


title: Bone marrow Lin-negative, Tet2+/--rep1


title: CEMBA181023_6B_3_CEMBA181023_6B_4_H4_ad001


title: MP3_Male_15_days

tag: gender

value: Male

tag: notes

tag: culturing media


title: CITED2-KO_IFNg_2

tag: strain

value: BMDMs

value: IFNg


title: MP2_Male_15_days

value: whole organism


title: CEMBA181023_6B_3_CEMBA181023_6B_4_H4_ad012


title: Bone marrow Lin-negative, WT-rep2

value: WT


title: CEMBA181023_6B_3_CEMBA181023_6B_4_H5_ad004


title: Wild Type-IFNg_-3

value: Postnatal week 10


title: CEMBA181023_6B_3_CEMBA181023_6B_4_H4_ad010


title: Wild Type-IL4_-1


title: CEMBA181023_6B_3_CEMBA181023_6B_4_H5_ad002


title: CEMBA181023_6B_3_CEMBA181023_6B_4_H4_ad008


title: Wild Type-IFNg_-2


title: KO-3

city: Qingdao

first: Peng

last: Chen

address: 308 Ningxia road, Qingdao

country: China

institute: Qingdao University

data_processing:
Paired-end reads were harvested from Illumina HiSeq 4000 sequencer, and were quality controlled by Q30. After 3’ adaptor-trimming and low quality reads removing by cutadapt software (v1.9.3). The high quality trimmed reads were used to analyse circRNAs and mRNAs.
circRNA: The high quality reads were aligned to the reference genome/transcriptome with STAR software (v2.5.1b) and circRNAs were detected and identified with DCC software (v0.4.4). edgeR software (v3.16.5) was used to normalized the data and perform differentially expressed circRNA analysis. GO and KEGG analysis were performed for the differentially expressed circRNA-associated genes.
mRNA: The high quality reads were aligned to the mouse reference genome (UCSC MM10) with hisat2 software (v2.0.4). Then, guided by the Ensembl gtf gene annotation file, cuffdiff software (v2.2.1, part of cufflinks) was used to get the FPKM as the expression profiles of mRNA, and fold change and p-value were calculated based on FPKM, differentially expressed LncRNA and mRNA were identified. GO and Pathway enrichment analysis were performed based on the differentially expressed mRNAs.
Genome_build: MM10
Supplementary_files_format_and_content: excel format

source_name: Lacrimal gland

extract_protocol:
Lacrimal glands were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent.Sequencing library was determined by Agilent 2100 Bioanalyzer using the Agilent DNA 1000 chip kit (Agilent, part # 5067-1504)
Briefly, total RNA was used for removing the rRNAs with NEBNext rRNA Depletion Kit (New England Biolabs, Inc., Massachusetts, USA) following the manufacturer's instructions. RNA libraries were constructed by using NEBNext® Ultra™ II Directional RNA Library Prep Kit (New England Biolabs, Inc., Massachusetts,USA) according to the manufacturer’s instructions. Libraries were controlled for quality and quantified using the BioAnalyzer 2100 system (Agilent Technologies, Inc., USA). Library sequencing was performed on an illumina Hiseq instrument with 150bp paired end reads.

value: lacrimal gland

value: 6 month


title: MN2_Male_18_days

value: Maintained under normal conditions

value: High Hardness COMBO


title: CITED2-KO_IFNg_3


title: CEMBA181023_6B_3_CEMBA181023_6B_4_H4_ad007


title: KO-2


title: Wild Type-IFNg_-1

value: Wild Type


title: MN1_Male_18_days


title: KO-1


title: CEMBA181023_6B_3_CEMBA181023_6B_4_H4_ad006

value: SSp


title: CITED2-KO_LPS_3

value: LPS


title: Bone marrow Lin-negative, WT-rep3


title: CEMBA181023_6B_3_CEMBA181023_6B_4_H4_ad002


title: MI3_Male_23_days


title: MP1_Male_15_days


title: CITED2-KO_LPS_2


title: MI2_Male_23_days


title: WT-3

value: wild type


title: CITED2-KO_IFNg_1


title: CITED2-KO_LPS_1


title: Bone marrow Lin-negative, WT-rep1

value: bone marrow


title: CEMBA181023_6B_3_CEMBA181023_6B_4_H3_ad008

value: male


title: MI1_Male_23_days


title: JG16-213 T21 UNTR

value: amniocytes

tag: pair

tag: karyotype

value: Control


title: WT-2


title: Wild Type-LPS_-3

value: BMDMs


title: MN3_Male_18_days

value: Male


title: WT-1


title: MH3_Male_30_days

value: whole organism


title: Met-B-5

city: Shanghai

first: Hailiang

last: Liu

address: NO 1239, siping road

institute: Tongji university

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence and low-quality sequence, then mapped to GRCm38.84 whole genome using tophat2
Genes expression level is quantified by cuffquant.
Reads aligned to genes were calculated using cufflinks.
Genome_build: GRCm38.84
Supplementary_files_format_and_content: Read count and FPKM ( Fragments Per Kilobase Million) for each Sample

source_name: blood

extract_protocol:
Total RNA was extracted using the TRIZOL(LS) following the manufacturer's instructions.
Libraries were prepared according to Nextera® XT DNA Library Prep Kit for Illumina

value: blood

value: adult

value: Metformin treatment 30 days


title: CEMBA181023_6B_3_CEMBA181023_6B_4_H3_ad004


title: CEMBA181023_6B_3_CEMBA181023_6B_4_H3_ad002


title: Met-B-4


title: Wild Type-LPS_-1

value: Postnatal week 10


title: MH2_Male_30_days

value: Maintained under normal conditions


title: MH1_Male_30_days

value: High Hardness COMBO


title: CITED2-KO_Control_3

value: control


title: CEMBA181023_6B_3_CEMBA181023_6B_4_H3_ad012

value: SSp


title: Met-B-3


title: MG3_Male_28_days


title: CEMBA181023_6B_3_CEMBA181023_6B_4_H2_ad001


title: Met-B-2


title: Met-B-1


title: MG2_Male_28_days


title: CITED2-KO_Control_1


title: CEMBA181023_6B_3_CEMBA181023_6B_4_H2_ad010


title: CITED2-KO_Control_2


title: CEMBA181023_6B_3_CEMBA181023_6B_4_H2_ad008


title: Ctrl-B-5

value: PBS treatment 30 days


title: CEMBA181023_6B_3_CEMBA181023_6B_4_H3_ad006


title: Wild Type-LPS_-2

value: Wild Type

value: LPS


title: Ctrl-B-4


title: MF2_Male_25_days


title: MF3_Male_25_days

value: mislabelled samples, excluded


title: CEMBA181023_6B_3_CEMBA181023_6B_4_H2_ad012

value: male


title: CEMBA181023_6B_3_CEMBA181023_6B_4_H2_ad007


title: Wild Type-Control-2


title: Wild Type-Control-3


title: Ctrl-B-3


title: Wild Type-Control-1


title: Ctrl-B-2


title: CEMBA181023_6B_3_CEMBA181023_6B_4_H2_ad006


title: Il1r1_ko_R3

city: Mainz

first: Ari

last: Waisman

address: Obere Zahlbacher Straße 67

country: Germany

institute: Institute for Molecular Medicine

description: RiboTag: actively transcribed (ribosome-engaged) mRNA

data_processing:
Sequenced reads were mapped to the mouse genome reference sequence with STAR (version 2.4.0j)
The ENSEMBL Mus_musculus.GRCm38 was chosen as reference genome, alignments were processed with the featureCounts function of the Rsubread package. The corresponding gtf annotation for the reference (ENSEMBL v76) was used.
Exploratory data analysis was performed with the pcaExplorer package (version version 2.8.0, Marini et al., 2019)
Differential expression analysis was performed with DESeq2 (version 1.22.1), setting the False Discovery Rate to 0.05
Accurate estimation of the effect sizes (in terms of log fold change) is performed using the apeglm shrinkage estimator (version 1.4.1)
Further analyses included Gene Ontology pathway enrichment of DEG using topGO (v2.34.0) and goseq (v1.34.0) (with all expressed genes set as background) were performed using the ideal package (version 1.6.0) [Marini et al. 2020].
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text file includes raw counts as input matrix to DESeq2

molecule: polyA RNA

source_name: Spinal cord endothelial cells

growth_protocol: C57Bl/6 background, housed under specific-pathogen-free conditions

extract_protocol:
RiboTag: Ribosomal enrichment
isolated ribosomes were processed for RNA extraction using the Qiagen RNeasy Plus mini kit according to manufacturer’s instructions.
RNA quality and concentration were measured using a NanoDropTM (Thermo Fisher Scientific). For sequencing, RNA quality and integrity was determined using a Qbit and Bioanalyzer. Only samples with a RIN value of 8.0 and above were taken for further processing.
cDNA libraries were prepared with 200ng from each sample using the NEBNext Ultra II RNA Library Prep Kit for Illumina

treatment_protocol: 2mg Tamoxifen at P14 and P16

tag: condition

value: 12 weeks


title: MF1_Male_25_days


title: Il1r1_ko_R2


title: Ctrl-B-1


title: CEMBA181023_6B_3_CEMBA181023_6B_4_H2_ad004


title: ME2_Male_40_days


title: MG1_Male_28_days


title: Il1r1_ko_R1


title: CEMBA181023_6B_3_CEMBA181023_6B_4_H2_ad002


title: control_R2

value: HASLC


title: ME1_Male_40_days

value: Male


title: CEMBA181023_6B_3_CEMBA181023_6B_4_H12_ad004


title: MD3_Male_38_days

value: whole organism


title: CEMBA181023_6B_3_CEMBA181023_6B_4_H12_ad012


title: MD2_Male_38_days


title: control_R1


title: pSG_H3K27Ac Input

city: Buffalo

first: Jonathan

middle: E

last: Bard

state: New York

address: 701 Ellicott Street

department: Genomics and Bioinformatics Core

institute: University at Buffalo

data_processing:
Reads were mapped to the Mus musculus genome (mm9 build) using Bowtie (v1.1.1).
macs2 (v2.1.0) was used to call peaks
Genome_build: mm9
Supplementary_files_format_and_content: macs2 peak-calling output

source_name: Primary Mouse Epithelial Progenitor Cells

extract_protocol: IP performed using the iDeal ChIP-Seq Kit on the Diagenode SX-G8 IP-Star Compact System.

value: Adult (12wk)

value: Salivary Gland

tag: antibodies

tag: genotype/variation

value: p63 WildType mouse


title: CEMBA181023_6B_3_CEMBA181023_6B_4_H12_ad008


title: ME3_Male_40_days


title: MD1_Male_38_days


title: CEMBA181023_6B_3_CEMBA181023_6B_4_H12_ad007


title: MC3_Male_33_days


title: CEMBA181023_6B_3_CEMBA181023_6B_4_H12_ad006


title: CEMBA181023_6B_3_CEMBA181023_6B_4_H12_ad001


title: MC2_Male_33_days


title: MC1_Male_33_days


title: CEMBA181023_6B_3_CEMBA181023_6B_4_H11_ad010


title: PSECS_4A4

value: 4A4 mouse monoclonal anti-p63


title: MB3_Male_20_days

value: Maintained under normal conditions


title: CEMBA181023_6B_3_CEMBA181023_6B_4_H11_ad004


title: MB2_Male_20_days

value: High Hardness COMBO


title: pSG_H3K27Ac

value: H3K27ac (Diagenode:C15410174)


title: CEMBA181023_6B_3_CEMBA181023_6B_4_H11_ad012

value: SSp


title: Epitope-decreased

first: Guangan

last: Hu

address: 500 Main Street

department: Koch Institute

institute: MIT

data_processing:
Illumina Casava software used for basecalling.
Raw sequences were processed using the pRESTO (version 0.5.13) toolkit. The paired-ends MiSeq data firstly assembled into a full-length Ig sequence. Follow by removing the low quality reads, annotating Ig isotype (IgD, IgM and IgG), masking the primer regions and yielding the final repertoire comprised of unique sequence with at least two representative reads. The IMGT/High was used to determine germline V(D)J assignments and functionality with the Change-O (version 0.4.6) tool .
Genome_build: IMGT/High
Supplementary_files_format_and_content: tab-delimited text file include each Ig sequnce, VDJ calls and length, CDR/FWR, clone assignment, germline info, sample anntation

source_name: C57BL/6J (B6)  Mouse B cells

extract_protocol:
RNA was extracted from sorted cells by RNeasy Micro Kit (Qiagen) and the quality of RNA was assessed by Nanodrop and quantified by Qubit Fluorometer. RNA was reverse transcribed into cDNA by 10× SMARTScribe Reverse Transcriptase (Clontech). The cDNA was purified using a MinElute PCR Purification Kit (Qiagen).
The RNA-seq library preparation was executed by NEBNext Ultra II DNA Library Prep kit following manufacturer’s instruction.

tag: group

value: Sequential group, 2 weeks after final dose

value: Dengue-specific B cells


title: MB1_Male_20_days

tag: tissue


title: CEMBA181023_6B_3_CEMBA181023_6B_4_H11_ad007

source_name: C57BL/6J Male P56 Mouse Brain

tag: age


title: PSECS_4A4 Input


title: MA3_Male_35_days

tag: treatment


title: Repeated

value: Repeated group, 2 weeks after final dose


title: CEMBA181023_6B_3_CEMBA181023_6B_4_H11_ad006

tag: brain region


title: 78_SMG_WT_S29

data_processing:
Reads were mapped to the Mus musculus genome (mm9 build) with TopHat2 (v2.1.1),using Bowtie2 (v2.2.6) as the underlying aligner.
Reads aligning to the UCSC mm9 build were quantified with featureCounts (v1.5.1) , which disregarded any read/read pair that aligned to more than one location, or more than one gene at a single location.
DESeq2 (v1.20.0) was used to normalize the read counts, and TPM values were calculated by normalising read counts were further normalised by gene length and total counts to generate Transcript Per Million (TPM) values.
Genome_build: mm9
Supplementary_files_format_and_content: TPM values were generated by normalizing raw counts for both library size and gene length.

source_name: Mouse Submandilar Salivary Gland

extract_protocol:
Mouse submandibular salivary gland epithelial cells were isolated from adult wildtype  and p63 knockout mice and RNA was extracted using the Direct-zol RNA Mini-Prep kit.
Library preparation was carried out using the Illumina TruSeq RNA Sample Prep Kit protocol. 1 ug of total RNA from each sample was used in the the construction of sequencing libraries.


title: 6593_WT_SMG_S19

description: TPM values were generated by normalizing raw counts for both library size and gene length.


title: IL-7α high fresh_2

city: Seoul

first: Hang-Rae

address: 103 Daehak-ro, Jongno-gu

institute: Seoul National University College of Medicine

description: healthy individual 2

hyb_protocol: 600ng of each labeled cRNA was fragmented by adding 5 μl 10 x blocking agent and 1 μl of 25 x fragmentation buffer, and then heated at 60°C for 30 min. Finally 25 μl 2 x GE hybridization buffer was added to dilute the labeled cRNA. 50μl of hybridization solution was dispensed into the gasket slide and assembled to Agilent-014850 Whole Human Genome Microarray 4x44K G4112F. The slides were incubated for 17 h at 65°C in an Agilent hybridization oven. then washed at room temperature by using the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology, V 6.5, 2010).

scan_protocol: The hybridized array was immediately scanned with an Agilent SureScan Microarray Scanner(Agilent Technologies, Inc.)

data_processing: The scanned raw data were quantile normalized. The probes with low intensity were excluded from further analyses: only the probes that showed at least 10% brighter intensity than the 95th percentile of the negative control probes on more than two arrays were used.

source_name: resting IL-7Rα high

label_protocol: RNA labeling and hybridization were performed by using the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology, V 6.5, 2010). Briefly, 200ng of total RNA from each sample was linearly amplified and labeled with Cy3-dCTP. The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000(NanoDrop, Wilmington, USA).

extract_protocol: Total RNA was extracted using Trizol (Invitrogen Life Technologies, Carlsbad, USA), purified using RNeasy columns (Qiagen, Valencia, USA) according to the manufacturers’ protocol. After processing with DNase digestion, clean-up procedures, RNA samples were quantified, aliquot and stored at -80°C until use. For the quality control, RNA purity and integrity were evaluated by OD 260/280 ratio, and analyzed by Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, USA).

value: peripheral blood

value: effector memory (EM) CD8+ T cells

tag: sample type

value: resting IL-7Rα high


title: IL-7α high activated 1

description: healthy individual 1

source_name: activated IL-7Rα high

value: male

tag: cell type

value: activated IL-7Rα high


title: IL-7α high fresh_1

description: healthy individual 1


title: IL-7α high activated 3

description: healthy individual 3


title: IL-7α low activated 1

description: healthy individual 1

source_name: activated IL-7Rα low

value: activated IL-7Rα low


title: IL-7α low activated 3

description: healthy individual 3


title: MKN28_LKO

city: Hsinchu

first: Lin-Lu

last: Tseng

state: Taiwan

address: 101, Section 2 Kuang Fu Road

department: Life Science

country: Taiwan

institute: National Tsing Hua University

description: Gene expression profiles by Affymetrix microarray

hyb_protocol: Following fragmentation, 10 μg of cRNA were hybridized for 16 hr at 45°C on the Affymetrix GeneChip Human Gene 2.0 ST Array using Affymetrix hybridization kit materials. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChip Scanner 3000

data_processing: Data were processing using Transcriptome Analysis Console (TAC) Software. Robust Multi-array Average (RMA) method was used to background correction and normalization.

source_name: MKN28 cells infected with lentivirus containing LKO control

label_protocol: Not provided

growth_protocol: MKN28 cells (JCRB0253) were cultured in RPMI 1640 medium contained with 10% fetal bovine serum at 37OC  in 5% CO2.

extract_protocol: Total RNAs were extracted with TRIzol reagent following manufacturer's instructions.

treatment_protocol: MKN28 cells were infected with lentivirus contained LKO control or PHF8-targeted shRNA.

tag: cell line

value: Human gastric cancer cell line


title: IL-7α low fresh_1

description: healthy individual 1

source_name: resting IL-7Rα low

tag: gender

value: resting IL-7Rα low


title: CEMBA181023_6B_3_CEMBA181023_6B_4_H11_ad002

tag: Sex


title: MKN28_shPHF8

source_name: MKN28 cells infected with lentivirus containing PHF8-targeted shRNA


title: IL-7α low fresh_2

description: healthy individual 2