title: Veh_RPC_CA3_replicate7

first: Supriyo

last: De

state: Maryland

address: 251 Bayview Blvd

department: Laboratory of Genetics and Genomics

institute: NIA-IRP, NIH

hyb_protocol: Standard Illumina protocol. In short, a total of 0.75 μg of biotin-labeled cRNA was hybridized at 58°C for 16 hours to Illumina's HumanHT-12 V4.0 Expression Bead Chips (Illumina, San Diego, CA). Each BeadChip has more than 47,000 probes derived from the National Center for Biotechnology Information Reference Sequence (NCBI) RefSeq Release 38 (November 7, 2009) and other sources. The arrays were washed, blocked and the biotin labeled cRNA was detected by staining with streptavidin-Cy3.

scan_protocol: Arrays were scanned at a resolution of 0.54 μm using the Illumina iScan scanner.

data_processing: Data was extracted using the Illumina GenomeStudio software V2011.1, Gene expression module 1.9.0. Any spots at or below the background were filtered out using an Illumina detection Pvalue of 0.02 and above. The natural log of all remaining scores were used to find the avg and std of each array and the z-score normalization was calculated and presented below.  Z-score = (raw value - avg)/std.  Complete data including detection scores is supplied.

organism: Rattus norvegicus

label_protocol: Standard Illumina protocol using Illumina TotalPrep RNA Amplification Kit (Ambion; Austin, TX, cat # IL1791) In short, 0.5 μg of total RNA was first converted into single-stranded cDNA with reverse transcriptase using an oligo-dT primer containing the T7 RNA polymerase promoter site and then copied to produce double-stranded cDNA molecules. The double stranded cDNA was cleaned and concentrated with the supplied columns and used in an overnight in-vitro transcription reaction where single-stranded RNA (cRNA) was generated and labeled by incorporation of biotin-16-UTP.

growth_protocol: Twenty-eight young (7 months of age) male Fischer 344 × Brown Norway F1 hybrid rats (F344xBN) from the National Institute on Aging colony (Harlan Industries) were singly housed in standard cages in a climate-controlled vivarium maintained on a 12 h light/dark cycle. Food and water were available ad libitum. Subjects acclimated for 1 week and were handled for 5 min/d for a total of 3 d before treatment. Animal procedures followed the National Institutes of Health Guide for the Care and Use of Laboratory Animals (2011) and were approved by the Animal Care and Use Committee of the National Institute on Aging.  Standard water maze training was conducted for all rats, except for home cage controls. Briefly, training took place across eight consecutive days, three trials per day (each using a 90 s cutoff), with a 60 s intertrial interval. Every sixth trial was a probe test in which the escape platform was initially retracted to the bottom of the maze for 30 s and then made accessible to permit escape.

extract_protocol: Ninety minutes following injection of vehicle or SAHA, animals in all conditions were deeply anesthetized with isoflurane and sacrificed. Brains were removed, and freshly microdissected hippocampal subfields (CA1, CA3, and dentate gyrus [DG]) were frozen and stored at −80°C until RNA extraction using Trizol reagent and further purified using RNEasy mini columns (QIagen, Valencia, CA) according to the manufacturer’s instructions. RNA quantity and integrity was assessed using Nanodrop and Agilent Bioanalyzer RNA 6000 Chip(Agilent, Santa Clara, CA).

treatment_protocol: One week following standard spatial training (not for home cage controls), subjects used to examine the influence of recent experience on the response to HDACi administration were tested on a one session RPC variant of the Morris water maze, consistting of 17 trials (60 s cutoff), with a 15 s intertrial interval. During trials 1–9, 11, 13, 15, and 17, a black escape platform protruded above the water surface, rendering it visible; and on trials 10, 12, 14, and 16, the platform was hidden, submerged just below the water. A single 60 s probe trial was administered 85 min after the onset of training, immediately before death. Rats were injected with freshly prepared SAHA dissolved in 100% DMSO, administered at 50 mg/kg (final concentration delivered was 50 mg/ml i.p.) per rat, or with an equal volume of 100% DMSO vehicle (Veh). Vehicle and SAHA solutions were administered 10 min before RPC testing, 90 min before death.

tag: strain

value: Fischer 344 × Brown Norway F1 hybrid (F344xBN)

tag: Sex

value: Male

tag: age

value: 7 months

tag: tissue

value: Brain

tag: hippocampal region

tag: drug treatment

value: VEH

tag: behavioral group

value: RPC


title: Veh_RPC_CA3_replicate3

status: Public on Apr 15 2021

type: RNA

city: Baltimore

country: USA

molecule: total RNA


title: Veh_RPC_CA3_replicate2


title: Veh_RPC_DG_replicate2

value: DG


title: Veh_RPC_DG_replicate1


title: Cell 79 from renal allograft sample 1

type: SRA

city: Chicago

first: Yuta

last: Asano

state: IL

address: 924 E 57th Street

department: Medicine

institute: The University of Chicago

library_source: transcriptomic

data_processing:
Illumina bcl2fastq2 software was used for basecalling. Sequenced reads were trimmed for adaptor sequence.
Before mapping, reference human transcriptome was masked for low-complexity or low-quality sequence by RepeatMasker with -noint -norna -qq options.
Reads were mapped to masked human transcriptome by kallisto. For single-end reads, -l 200 -s 50 options were used.
High quality cells were selected by detected gene count (> 3,000 for the first, and > 1,000 for the second cohort) and antibody gene expression (sum of log2-cpm values of Ig heavy constant region genes > 5).
Data of the first cohort was normalized by RUVSeq using ERCC-mapped reads as negative controls, and normalized by log2-cpm. The second cohort data were also log2-cpm-normalized and combined with the first cohort data by ComBat and SCTransform in Seurat to generate the integrated data.
Genome_build: GRCh38
Supplementary_files_format_and_content: Csv files of the normalized first cohort and integrated data

organism: Homo sapiens

source_name: Kidney

extract_protocol:
Tissues were minced and digested by Liberase TL, stained and sorted by FACS Fusion at -80 ˚C and frozen until library preparation.
Smart-Seq 2
single-cell RNA-seq

tag: patient

value: Kidney 1

tag: plate

tag: well

tag: batch

value: Batch 2

tag: cohort

value: First


title: Veh_RPC_DG_replicate3


title: Cell 83 from renal allograft sample 1


title: C6 (scRRBS)

city: Cambridge

first: Ayush

middle: T

last: Raman

state: MA

address: 75 Ames St

department: Epigenomics Program

institute: Broad Institute of MIT and Harvard

description: day 0 dox+ DNMT1 KO

library_source: genomic

data_processing:
The quality of raw reads was assessed using FastQC (Andrews, 2010).
RRBS-seq libraries were aligned to the bisulfite converted GRCh38.p2 genome using Bismark5 (v.0.18.2) with bowtie2 (Langmead et al 2012)  as the aligner. The reads were trimmed using the Trim galore wrapper tool.
Bismark methylation extractor (-bedgraph --buffer_size 50%) was used to determine the methylation state of each individual CpG across both the strands. Duplicated reads were removed, followed by estimating the number of CpGs.
Genome_build: hg38
Supplementary_files_format_and_content: tab delimited file; bismark coverage output file

molecule: genomic DNA

source_name: embryonic stem cell

extract_protocol:
SPRI clean-up of poly(A)+ mRNA-depleted cell lysate
RRBS of MspI+HaeIII double-digested DNA
single cell Bisulfite-Seq (reduced representation)

tag: cell line

tag: time point

value: day 0

tag: genotype

value: inducible DNMT1 KO

tag: dox induction

value: No


title: Veh_RPC_CA1_replicate5


title: C9 (scRRBS)

description: day 0 dox+ DNMT1 KO


title: Veh_RPC_CA3_replicate6


title: C5 (scRRBS)

description: day 0 dox+ DNMT1 KO


title: Veh_RPC_CA3_replicate4


title: Cell 36 from renal allograft sample 2

value: Kidney 2


title: Veh_RPC_CA1_replicate4


title: Cell 80 from renal allograft sample 1


title: C4 (scRRBS)

description: day 0 dox+ DNMT1 KO


title: Veh_RPC_CA1_replicate3


title: Veh_DG_replicate7

value: HC


title: Veh_RPC_CA3_replicate1


title: Veh_RPC_CA1_replicate6


title: Cell 35 from renal allograft sample 2


title: Veh_DG_replicate6


title: Veh_RPC_CA3_replicate5


title: Veh_RPC_CA1_replicate1


title: Veh_DG_replicate5


title: C3 (scRRBS)

description: day 0 dox+ DNMT1 KO


title: Veh_RPC_CA1_replicate7


title: Veh_RPC_CA1_replicate2


title: Cell 34 from renal allograft sample 2


title: Veh_DG_replicate2


title: C2 (scRRBS)

description: day 0 dox+ DNMT1 KO


title: Cell 33 from renal allograft sample 2


title: C12 (scRRBS)

description: day 0 dox+ DNMT1 KO


title: C1 (scRRBS)

description: day 0 dox+ DNMT1 KO


title: Cell 31 from renal allograft sample 2


title: Veh_CA3_replicate7


title: Veh_CA3_replicate4


title: Veh_DG_replicate1


title: Veh_DG_replicate3


title: Veh_CA3_replicate3


title: C11 (scRRBS)

description: day 0 dox+ DNMT1 KO


title: Veh_DG_replicate4


title: Cell 78 from renal allograft sample 1


title: Veh_CA3_replicate6


title: C10 (scRRBS)

description: day 0 dox+ DNMT1 KO


title: B9 (scRRBS)

description: day 0 dox+ DNMT1 KO


title: Cell 77 from renal allograft sample 1


title: B8 (scRRBS)

description: day 0 dox+ DNMT1 KO


title: Cell 75 from renal allograft sample 1


title: B7 (scRRBS)

description: day 0 dox+ DNMT1 KO


title: Cell 32 from renal allograft sample 2


title: Veh_CA3_replicate2


title: Veh_CA3_replicate1


title: Veh_CA1_replicate6


title: Veh_CA1_replicate7


title: Veh_CA3_replicate5


title: Veh_CA1_replicate4


title: Veh_CA1_replicate3


title: SAHA_RPC_DG_replicate7

value: SAHA


title: Veh_CA1_replicate1


title: Cell 74 from renal allograft sample 1


title: Veh_CA1_replicate2


title: B6 (scRRBS)

description: day 0 dox+ DNMT1 KO


title: B5 (scRRBS)

description: day 0 dox+ DNMT1 KO


title: Cell 73 from renal allograft sample 1


title: Cell 30 from renal allograft sample 2


title: Cell 76 from renal allograft sample 1


title: B4 (scRRBS)

description: day 0 dox+ DNMT1 KO


title: Cell 29 from renal allograft sample 2


title: B3 (scRRBS)

description: day 0 dox+ DNMT1 KO


title: Cell 28 from renal allograft sample 2


title: Cell 27 from renal allograft sample 2


title: B2 (scRRBS)

description: day 0 dox+ DNMT1 KO


title: B12 (scRRBS)

description: day 0 dox+ DNMT1 KO


title: SAHA_RPC_DG_replicate1


title: B1 (scRRBS)

description: day 0 dox+ DNMT1 KO


title: Cell 25 from renal allograft sample 2


title: SAHA_RPC_DG_replicate5


title: SAHA_RPC_DG_replicate2


title: B11 (scRRBS)

description: day 0 dox+ DNMT1 KO


title: Cell 72 from renal allograft sample 1


title: SAHA_RPC_DG_replicate3


title: SAHA_RPC_CA3_replicate4


title: SAHA_RPC_CA3_replicate7


title: SAHA_RPC_CA3_replicate6


title: B10 (scRRBS)

description: day 0 dox+ DNMT1 KO


title: SAHA_RPC_CA3_replicate3


title: SAHA_RPC_CA1_replicate7


title: SAHA_RPC_CA3_replicate5


title: SAHA_RPC_DG_replicate4


title: Cell 71 from renal allograft sample 1


title: SAHA_RPC_CA1_replicate6


title: SAHA_RPC_CA1_replicate5


title: SAHA_RPC_CA3_replicate1


title: SAHA_RPC_CA3_replicate2


title: SAHA_RPC_DG_replicate6


title: SAHA_RPC_CA1_replicate4


title: Cell 26 from renal allograft sample 2


title: Cell 70 from renal allograft sample 1


title: SAHA_RPC_CA1_replicate2


title: A8 (scRRBS)

description: day 0 dox+ DNMT1 KO


title: Cell 69 from renal allograft sample 1


title: A7 (scRRBS)

description: day 0 dox+ DNMT1 KO


title: SAHA_RPC_CA1_replicate1


title: Cell 68 from renal allograft sample 1


title: SAHA_DG_replicate6


title: Cell 67 from renal allograft sample 1


title: SAHA_DG_replicate7


title: SAHA_RPC_CA1_replicate3


title: A3 (scRRBS)

description: day 0 dox+ DNMT1 KO


title: Cell 24 from renal allograft sample 2


title: A5 (scRRBS)

description: day 0 dox+ DNMT1 KO


title: Cell 23 from renal allograft sample 2


title: A9 (scRRBS)

description: day 0 dox+ DNMT1 KO


title: Cell 22 from renal allograft sample 2


title: SAHA_DG_replicate1


title: A4 (scRRBS)

description: day 0 dox+ DNMT1 KO


title: SAHA_DG_replicate5


title: A2 (scRRBS)

description: day 0 dox+ DNMT1 KO


title: A6 (scRRBS)

description: day 0 dox+ DNMT1 KO


title: Cell 21 from renal allograft sample 2


title: SAHA_DG_replicate3


title: SAHA_CA3_replicate3


title: SAHA_DG_replicate2


title: A12 (scRRBS)

description: day 0 dox+ DNMT1 KO


title: Cell 20 from renal allograft sample 2


title: Cell 19 from renal allograft sample 2


title: SAHA_CA3_replicate4


title: A1 (scRRBS)

description: day 0 dox+ DNMT1 KO


title: SAHA_DG_replicate4


title: A11 (scRRBS)

description: day 0 dox+ DNMT1 KO


title: SAHA_CA3_replicate7


title: SAHA_CA3_replicate2


title: SAHA_CA3_replicate6


title: SAHA_CA1_replicate5


title: SAHA_CA3_replicate1


title: SAHA_CA3_replicate5


title: SAHA_CA1_replicate4


title: SAHA_CA1_replicate7


title: H9 (scRNAseq)

description: day 0 dox+ DNMT1 KO

data_processing:
The quality of raw reads was assessed using FastQC (Andrews, 2010).
The raw reads were aligned to the Homo sapiens genome (GRCh38.p2 genome build (Ensembl v79)) using STAR v2.7.3a (Dobin et al., 2013). The raw counts were computed using quantMode function in STAR.
The obtained read counts are analogous to the expression level of each gene across all the samples. The single cell RNA-seq QC analysis was done using scater (McCarthy et al., 2017).
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files; raw counts file output from STAR

molecule: polyA RNA

extract_protocol:
poly(A)+ mRNA pulldown from cell lysate
SMART-seq2 Illumina Nextera XT
single cell RNA-Seq


title: Cell 66 from renal allograft sample 1


title: SAHA_CA1_replicate3


title: Veh_RPC_DG_replicate5


title: Cell 64 from renal allograft sample 1


title: SAHA_CA1_replicate2


title: Cell 63 from renal allograft sample 1


title: mut_7_B

city: Basel

first: Foivos

last: Gypas

address: Maulbeerstrasse 66

country: Switzerland

institute: FMI

data_processing:
3’adapters (AGATCGGAAGAGCACACGTCTGAACTCCAGTCA, AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT) were trimmed with cutadapt (version 2.3) (--error-rate 0.1, --minimum-length 15, --overlap 3)
Reads were mapped to the genome with STAR (version 2.7.0f)
Reads were counted with featureCounts (version 2.0.0) (-M -O --fraction -s 2 -p -B -P -C).
Genome_build: ce11
Supplementary_files_format_and_content: tsv file with counts

organism: Caenorhabditis elegans

source_name: whole worms

growth_protocol: The animals were grown on peptone rich plates with NA22 bacteria as a food source at 15C

extract_protocol:
After the animals were collecetd, the worms were transferred to 2 ml tubes (Sarstedt, Ref: 72.693.005) with Zirconia/Silica beads (Biospec, Cat. No. 110791052) in 1 ml of tri-reagent and snap frozen on dry ice. The worms were lysed using MP Biomedicals Fast Prep-24 5G bead beater for 16 cycles at 8m/Sec. Total RNA was then extracted.
Total RNA-seq libraries were generated using the TruSeq Illumina Total RNA-seq (stranded – high input) according to manufacturer’s protocol. Libraries were sequenced on the NextSeq HIGH-OUT 150 Cycle Paired-end (eg. 2 x 75bp).

tag: developmental stage

value: L4 staged animals


title: Cell 65 from renal allograft sample 1


title: Veh_RPC_DG_replicate6

tag: strain

value: Fischer 344 × Brown Norway F1 hybrid (F344xBN)


title: H8 (scRNAseq)

description: day 0 dox+ DNMT1 KO


title: H7 (scRNAseq)

description: day 0 dox+ DNMT1 KO


title: SAHA_CA1_replicate1

tag: Sex

value: Male


title: SAHA_CA1_replicate6

tag: age

value: 7 months


title: A10 (scRRBS)

description: day 0 dox+ DNMT1 KO


title: mut_2_B


title: mut_2_C


title: Veh_RPC_DG_replicate7

tag: tissue

value: Brain


title: Cell 61 from renal allograft sample 1


title: H6 (scRNAseq)

description: day 0 dox+ DNMT1 KO


title: mut_2_A


title: wild_type_I

value: Wild type


title: Cell 18 from renal allograft sample 2


title: wild_type_G


title: H5 (scRNAseq)

description: day 0 dox+ DNMT1 KO


title: mut_7_A


title: mut_7_C


title: Dpf_3_null_C


title: Cell 17 from renal allograft sample 2


title: wild_type_F


title: Cell 16 from renal allograft sample 2


title: H3 (scRNAseq)

description: day 0 dox+ DNMT1 KO


title: Veh_CA1_replicate5

tag: hippocampal region

value: VEH


title: Dpf_3_null_B


title: wild_type_D


title: H4 (scRNAseq)

description: day 0 dox+ DNMT1 KO


title: wild_type_H


title: H2 (scRNAseq)

description: day 0 dox+ DNMT1 KO


title: Cell 15 from renal allograft sample 2


title: wild_type_C


title: Cell 13 from renal allograft sample 2


title: H12 (scRNAseq)

description: day 0 dox+ DNMT1 KO


title: wild_type_E


title: wild_type_B


title: wild_type_A


title: H1 (scRNAseq)

description: day 0 dox+ DNMT1 KO


title: Veh_RPC_DG_replicate4

value: DG

tag: drug treatment

value: RPC


title: Dpf_3_null_A


title: H11 (scRNAseq)

description: day 0 dox+ DNMT1 KO


title: Cell 60 from renal allograft sample 1

value: Kidney 1

value: Batch 2


title: H10 (scRNAseq)

description: day 0 dox+ DNMT1 KO

value: day 0


title: GEMS15_um_dpi4_2

city: Nanjing

first: Xinsen

last: Ruan

address: Weigang #1

country: China

institute: Nanjing Agricultural University

data_processing:
Hisat2 software version 2.1.0 was applied to mapping read pairs to B73 AGPv4.59 reference genome
Stringtie software version 1.3.5(Pertea et al., 2015) was applied in assembling with B73 v4.59 reference genome annotation
R package DESeq2 was applied in maize gene counts data processing
Genome_build: maize NCBI B73 AGPv4.59
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Zea mays

source_name: U. maydis-infected 4dpi maize seedling leaf

growth_protocol: The seeds of maize lines resistance CML326 and susceptible GEMS15 to U. maydis were sown  and grown in potting soil (garden soil:vermiculite=1:1). The seedlings were grown 7 days in a temperature-controlled greenhouse with a 14-/10-h light-dark photoperiod, with the light flux density at 300μmol·m-2·s-1, and the temperature at 28/20°C (day/night).

extract_protocol:
Each three biological samples were pooled and ground in liquid nitrogen, and the RNA was extracted with TRIZOL (Invitrogen) by following the manufactory instruction.
RNA was subjected to quality control prior to library construction using Illumina TruSeq RNA library prep kit v2.

treatment_protocol: Maize 7 days seedlings of resistance CML326 and susceptible GEMS15 to U. maydis were inject with U. maydis at 1h before the light period as described above. Samples of the stem around inject site were collected at 0 hour (mock), 24 hours, 48 hours, and 96 hours post infection, and quickly frozen in liquid nitrogen.

tag: phenotype

value: susceptible

value: seedling leaf

tag: treatment

value: U. maydis-infected

tag: treat time

value: post inoculation day 4


title: GEMS15_um_dpi4_3


title: Cell 59 from renal allograft sample 1

tag: patient

tag: plate

tag: well

value: First


title: GEMS15_um_dpi4_1


title: Cell 14 from renal allograft sample 2

value: Kidney 2

tag: batch

tag: cohort


title: GEMS15_um_dpi2_3

source_name: U. maydis-infected 2dpi maize seedling leaf

value: post inoculation day 2


title: G9 (scRNAseq)

description: day 0 dox+ DNMT1 KO

tag: cell line

tag: time point

tag: genotype

value: inducible DNMT1 KO

value: No


title: Cell 58 from renal allograft sample 1


title: GEMS15_um_dpi2_1

tag: strain


title: GEMS15_um_dpi2_2


title: GEMS15_um_dpi1_3

source_name: U. maydis-infected 1dpi maize seedling leaf

value: post inoculation day 1


title: G8 (scRNAseq)

description: day 0 dox+ DNMT1 KO

tag: dox induction


title: GEMS15_um_dpi1_2


title: Cell 57 from renal allograft sample 1


title: GEMS15_um_dpi1_1


title: GEMS15_mock_3

source_name: mock-treated maize seedling leaf

value: mock

value: post inoculation day 0


title: G7 (scRNAseq)

description: day 0 dox+ DNMT1 KO


title: GEMS15_mock_1


title: Cell 56 from renal allograft sample 1


title: G6 (scRNAseq)

description: day 0 dox+ DNMT1 KO


title: GEMS15_mock_2


title: Cell 12 from renal allograft sample 2


title: CML326_um_dpi4_3

value: resistant


title: G5 (scRNAseq)

description: day 0 dox+ DNMT1 KO


title: CML326_um_dpi4_2


title: Cell 62 from renal allograft sample 1


title: CML326_um_dpi4_1


title: Cell 11 from renal allograft sample 2


title: CML326_um_dpi2_3


title: CML326_um_dpi2_2


title: Cell 10 from renal allograft sample 2


title: CML326_um_dpi2_1


title: G3 (scRNAseq)

description: day 0 dox+ DNMT1 KO


title: G2 (scRNAseq)

description: day 0 dox+ DNMT1 KO


title: CML326_um_dpi1_3


title: CML326_um_dpi1_2


title: Cell 9 from renal allograft sample 2


title: CML326_um_dpi1_1


title: G4 (scRNAseq)

description: day 0 dox+ DNMT1 KO


title: Cell 55 from renal allograft sample 1


title: G12 (scRNAseq)

description: day 0 dox+ DNMT1 KO


title: Cell 8 from renal allograft sample 2


title: G1 (scRNAseq)

description: day 0 dox+ DNMT1 KO


title: CML326_mock_3


title: CML326_mock_1


title: Cell 7 from renal allograft sample 2


title: Maxi

city: Davis

first: Alexander

middle: Star

last: Nord

state: CA

address: 1544 Newton Court

department: Center for Neuroscience

institute: University of California Davis

data_processing:
Library strategy: MPRA
PE reads were trimmed using Ngmerge (v0.2_dev) in adaptor removal mode.
Reads from were aligned to the human and mouse genomes (GRCh38, GRCm38) using bwa mem v0.7.17.
Aligned reads in SAM format were converted to BAM format, and duplicates were removed using Picard Tools MarkDuplicates, v2.23.3.
Reads per amplicon were counted using samtools view -F 0x0400 v1.10
Genome_build: GRCh38 and GRCm38
Supplementary_files_format_and_content: CSV, read counts per MPRA amplicon

molecule: other

organism: synthetic construct

source_name: plasmid DNA library

extract_protocol:
Bulk forebrains were dissected from postnatal day (P)7 mice injected with the viral library at P0. Dissection included whole forebrain, separated into left and right hemispheres, after removing surface tissue and skull. Hemispheres were stored in RNAlater Stabilization Solution (Thermo Fisher #AM7020) for downstream dual DNA and RNA collection. Hemispheres were then physically homogenized and processed using the AllPrep DNA/RNA Mini Kit (Qiagen #80204) to collect total RNA and genomic DNA from the same tissue. RNA was treated on-column with 1 µL RNase-Free DNase (Qiagen #79254). First strand cDNA was synthesized from purified total RNA using the SuperScript VILO cDNA Synthesis Kit (Invitrogen #11755050) with random primers.
We amplified the variable regions of the reporter library from cDNA and genomic (g)DNA using PCR with Phusion Hot Start II High Fidelity DNA polymerase (Invitrogen #F549S) using primers flanking the variable region within pscAAV-Hsp68-EGFP (forward primer, Amplicon PCR Primer F: GATCACTCTCGGCATGGAC; reverse primer, Amplicon PCR Primer R: GATGGCTGGCAACTAGAAGG). PCR consisted of 30 cycles (or 35, for technical replicate Sample 4-35) at 60 °C for annealing and 1 min for extension. PCRs were then loaded onto a 1.0% agarose gel, the ~1-1.1 kb fragment excised, and gel fragment purified using the Promega Gel & PCR Cleanup system (#A9282). Purified gel fragments were then re-purified using the Qiagen MinElute PCR Purification Kit (#28004) to remove residual chemical contamination, and concentration and quality assessed with Nanodrop and the Qubit dsDNA High Sensitivity assay kit (Thermo Fisher #Q33230). Purified amplicons were prepared for sequencing using the Nextera XT DNA Library Preparation Kit (Illumina #FC-131-1001) using 1 ng of purified amplicon library per sample. Quality and concentration of sequencing libraries was assessed using an Agilent BioAnalyzer instrument. Each library was quantified and pooled for sequencing on the Illumina HiSeq 4000 using a paired end 150-bp sequencing strategy. The miniMPRA was sequenced on a MiSeq instrument since lower coverage was required due to lower library complexity.

treatment_protocol: C57BL/6 mice from Jackson Laboratories were used for mouse experiments. All procedures were performed in accordance with the ARVO statement for the Use of Animals in Ophthalmic and Vision Research and were approved by the University of California Animal Care and Use Committee (AUP #R200-0913BC). Surgery was performed under anesthesia, and all efforts were made to minimize suffering. Neonatal mice (on a C57BL6/J background) were injected in the prefrontal cortex in 2 separate locations with 0.5 µL of virus. Only the left side of brain was injected. A beveled 34-gauge needle (Hamilton syringes) was used to push through the skull and to inject virus into the brain. Virus was delivered slowly by hand over the course of 1 min. Mice were anesthetized on ice for 3-4 min prior to injection, and after injection mice were heated on a warm pad before being returned to the cage.

tag: genetic material

value: plasmid DNA library

tag: developmental stage

tag: vehicle

value: AAV library


title: G11 (scRNAseq)

description: day 0 dox+ DNMT1 KO


title: Cell 54 from renal allograft sample 1

value: Kidney 1

value: Batch 2


title: CML326_mock_2

tag: tissue


title: Cell 53 from renal allograft sample 1


title: H2A.Z_lateS_ChIP-seq_rep2

city: Fukuoka

first: Yasuyuki

last: Ohkawa

address: 3-1-1 Maidashi

country: Japan

institute: Medical Institute of Bioregulation

data_processing:
The in-read unique-molecular-identifiers (tags) were extracted using UMI-tools (version 0.5.5) with the command: umi_tools extract --extract-method=regex --bc-pattern='(?P<umi_1>.{6})(?P<discard_1>.{0,3}GTAGCTCA){s<=2}'.
The extracted reads were mapped to human genome (GRCh38) using hisat2 (version 2.1.0). The PCR-duplicates were removed using umi_tools dedup.
The read counts on 15 chromatin states were calculated using BED-Tools (version 2.27.1). The definition of ChromHMM track was obtained from the consolidated data set of Roadmap Epigenomics project (E117_15_coreMarks_hg38lift_mnemonics.bed).
The bigWig files were created by 1 bp intervals on the genome, and then the counts were normalized as CPM (Reads Per Million reads) using deepTools (version 3.2.1) with the option: -bs 1 --normalizeUsing CPM --minMappingQuality 60 --ignoreDuplicates --normalizeUsing CPM.
Genome_build: GRCh38
Supplementary_files_format_and_content: The count matrix file (csv) contains the total read counts in each chromatin state.

source_name: HeLa cells

growth_protocol: HeLa cells were cultured in DMEM medium supplemented with 10% fetal bovine serum at 37°C in 5% CO2. For synchronizing cells, HeLa cells were cultured with 2 mM thymidine for 19 hours. Then, the medium was changed to remove the thymidine. After 9 hours culture without thymidine, HeLa cells were cultured with 2 mM thymidine again for 15 hours to synchronize HeLa cells in S phase.

extract_protocol:
After the assay, permeabilized cells were treated with 3% formaldehyde in PBS for 5 min at room temperature. Fixed chromatin of permeabilized cells was digested with MNase in ChIP buffer (10 mM Tris-HCl pH 8.0, 200 mM KCl, 1 mM CaCl2, 0.5% NP-40). The supernatant was incubated with mixed with 50 ml of anti-HA-tag mAb-Magnetic Beads at 4°C overnight with rotation. Then, beads were washed three times with ChIP buffer containing 500 mM KCl and TE. After washing beads, beads were resuspended with 100 ml of ChIP elution buffer (50 mM Tris-HCl pH8.0, 10 mM EDTA and 1% SDS) containing 25 mM NaCl and incubated at 65°C for overnight to reverse the cross-links. Then, DNA was eluted with 0.4 mg/ml Proteinase K. The eluted DNA samples were further purified with a NucleoSpin Gel and PCR clean-up kit (MACHEREY-NAGEL).
Libraries were prepared using SMARTer ThruPLEX Tag-seq Kit (Takara Bio).

treatment_protocol: Cell permeabilization was performed as described below. HeLa cells were chilled on ice and rinsed twice with ice-cold PBF (100 mM CH3COOK, 10 mM Na2HPO4, 30 mM KCl, 1 mM dithiothreitol, 1 mM MgCl2, 1 mM ATP and 5% Ficoll). Then, PBF containing 0.2% TritonX-100 were added to cells. After 5 min incubation on ice, permeabilized cells were rinsed twice with ice-cold PBF.  A reaction mixture containing 100 nM histone complex, 60% cellular extract, 2.5% Ficoll, 100 mM CH3COOK, 10 mM Na2HPO4, 30 mM KCl, 1 mM dithiothreitol, 1 mM MgCl2, 100 mM each of dNTP and NTP (Roche) was added to permeabilized cells. After 60 min at 30°C, cells were washed in PBS containing 0.05% Tween 20 (PBST) twice for 5 min at room temperature.

tag: cell cycle

value: late S

tag: chip antibody

value: Anti-HA-tag (TANA2, MBL)

value: HeLa


title: H2A.Z_lateS_input_rep1


title: H2A.Z_lateS_input_rep2


title: G10 (scRNAseq)

description: day 0 dox+ DNMT1 KO

value: day 0


title: F9 (scRNAseq)

description: day 0 dox+ DNMT1 KO


title: Cell 52 from renal allograft sample 1

value: First


title: H2A.Z_lateS_ChIP-seq_rep1


title: F8 (scRNAseq)

description: day 0 dox+ DNMT1 KO


title: H2A_lateS_input_rep2


title: Cell 51 from renal allograft sample 1


title: F7 (scRNAseq)

description: day 0 dox+ DNMT1 KO


title: H2A_lateS_input_rep1


title: Cell 50 from renal allograft sample 1


title: H2A_lateS_ChIP-seq_rep1


title: H2A.Z_earlyS_input_rep2

value: early S


title: F6 (scRNAseq)

description: day 0 dox+ DNMT1 KO


title: F5 (scRNAseq)

description: day 0 dox+ DNMT1 KO


title: H2A.Z_earlyS_input_rep1


title: Cell 6 from renal allograft sample 2

value: Kidney 2


title: Cell 49 from renal allograft sample 1


title: H2A.Z_earlyS_ChIP-seq_rep1


title: F4 (scRNAseq)

description: day 0 dox+ DNMT1 KO

value: inducible DNMT1 KO


title: Cell 5 from renal allograft sample 2


title: F3 (scRNAseq)

description: day 0 dox+ DNMT1 KO

value: No


title: H2A_earlyS_ChIP-seq_rep2


title: H2A_earlyS_input_rep2


title: H2A_earlyS_input_rep1


title: H2A.Z_asynchronous_input_rep2

value: asynchronous


title: F2 (scRNAseq)

description: day 0 dox+ DNMT1 KO


title: H2A_earlyS_ChIP-seq_rep1


title: Cell 3 from renal allograft sample 2


title: H2A.Z_asynchronous_input_rep1


title: Cell 4 from renal allograft sample 2


title: F12 (scRNAseq)

description: day 0 dox+ DNMT1 KO


title: Cell 2 from renal allograft sample 2


title: H2A_lateS_ChIP-seq_rep2


title: H2A.Z_asynchronous_ChIP-seq_rep2


title: H2A.Z_asynchronous_ChIP-seq_rep1


title: H2A_asynchronous_input_rep2


title: H2A.Z_earlyS_ChIP-seq_rep2


title: F1 (scRNAseq)

description: day 0 dox+ DNMT1 KO


title: H2A_asynchronous_input_rep1


title: H2A_asynchronous_ChIP-seq_rep2


title: F11 (scRNAseq)

description: day 0 dox+ DNMT1 KO


title: H2A_asynchronous_ChIP-seq_rep1


title: F10 (scRNAseq)

description: day 0 dox+ DNMT1 KO


title: Cell 47 from renal allograft sample 1

value: Batch 1


title: E9 (scRNAseq)

description: day 0 dox+ DNMT1 KO


title: Cell 1 from renal allograft sample 2


title: Cell 46 from renal allograft sample 1


title: E8 (scRNAseq)

description: day 0 dox+ DNMT1 KO


title: Cell 45 from renal allograft sample 1


title: E7 (scRNAseq)

description: day 0 dox+ DNMT1 KO


title: Cell 44 from renal allograft sample 1


title: whole blood of COVID-19 patient 400

type: genomic

city: Badalona

first: Manel

last: Esteller

state: Barcelona

address: Ctra. de Can Ruti, Cami de les Escoles s/n

department: Cancer and Leukemia Epigenetics and Biology Program (PEBCL)

country: Spain

institute: Josep Carreras Leukaemia Research Institute (IJC)

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridized to Illumina Infinium Human MethylationEPIC array using standard Illumina protocol

scan_protocol: Arrays were imaged using High Scan SQ using standard recommended Illumina scanner setting

data_processing: Minfi R package standard protocol. Normalization using ssNoob preprocessing method.

label: Cy5 and Cy3

source_name: Whole Blood

label_protocol: EPICOVID from 1 to 407

growth_protocol: Whole blood patient samples

extract_protocol: DNA extracted with Qiagen kit

tag: disease state

tag: individual id

value: Patient 400

tag: age

tag: gender

value: M

value: whole blood


title: whole blood of COVID-19 patient 403

value: Patient 403


title: whole blood of COVID-19 patient 399

value: Patient 399

value: F


title: whole blood of COVID-19 patient 404

value: Patient 404


title: whole blood of COVID-19 patient 405

value: Patient 405


title: whole blood of COVID-19 patient 406

value: Patient 406


title: whole blood of COVID-19 patient 398

value: Patient 398


title: Cell 43 from renal allograft sample 1

tag: patient

value: Kidney 1

tag: plate

tag: well

tag: batch

value: First


title: E6 (scRNAseq)

description: day 0 dox+ DNMT1 KO

tag: cell line

tag: time point

value: day 0

tag: genotype


title: whole blood of COVID-19 patient 396

value: Patient 396


title: E5 (scRNAseq)

description: day 0 dox+ DNMT1 KO

value: inducible DNMT1 KO

tag: dox induction

value: No


title: whole blood of COVID-19 patient 407

value: Patient 407


title: whole blood of COVID-19 patient 395

value: Patient 395


title: whole blood of COVID-19 patient 397

value: Patient 397

value: M


title: Cell 41 from renal allograft sample 1

value: Batch 1

tag: cohort


title: Cell 48 from renal allograft sample 1


title: E4 (scRNAseq)

description: day 0 dox+ DNMT1 KO


title: whole blood of COVID-19 patient 402

value: Patient 402

value: whole blood


title: whole blood of COVID-19 patient 392

value: Patient 392

value: F


title: E3 (scRNAseq)

description: day 0 dox+ DNMT1 KO


title: whole blood of COVID-19 patient 401

value: Patient 401


title: whole blood of COVID-19 patient 391

value: Patient 391


title: E2 (scRNAseq)

description: day 0 dox+ DNMT1 KO


title: whole blood of COVID-19 patient 390

value: Patient 390


title: whole blood of COVID-19 patient 386

value: Patient 386


title: whole blood of COVID-19 patient 388

value: Patient 388


title: E12 (scRNAseq)

description: day 0 dox+ DNMT1 KO

value: day 0


title: E1 (scRNAseq)

description: day 0 dox+ DNMT1 KO

value: inducible DNMT1 KO


title: Cell 37 from renal allograft sample 1

value: Kidney 1

value: First


title: whole blood of COVID-19 patient 385

value: Patient 385


title: Cell 42 from renal allograft sample 1


title: whole blood of COVID-19 patient 384

value: Patient 384


title: whole blood of COVID-19 patient 394

value: Patient 394

value: M


title: Cell 36 from renal allograft sample 1

value: Batch 1


title: whole blood of COVID-19 patient 383

value: Patient 383

value: whole blood


title: whole blood of COVID-19 patient 382

value: Patient 382


title: E10 (scRNAseq)

description: day 0 dox+ DNMT1 KO

value: No


title: whole blood of COVID-19 patient 393

value: Patient 393

value: F


title: Cell 40 from renal allograft sample 1


title: whole blood of COVID-19 patient 380

value: Patient 380


title: whole blood of COVID-19 patient 381

value: Patient 381


title: whole blood of COVID-19 patient 379

value: Patient 379


title: whole blood of COVID-19 patient 378

value: Patient 378


title: D9 (scRNAseq)

description: day 0 dox+ DNMT1 KO

value: day 0

value: inducible DNMT1 KO


title: D8 (scRNAseq)

description: day 0 dox+ DNMT1 KO


title: whole blood of COVID-19 patient 389

value: Patient 389


title: whole blood of COVID-19 patient 387

value: Patient 387


title: whole blood of COVID-19 patient 377

value: Patient 377


title: Cell 38 from renal allograft sample 1

value: Kidney 1

value: First


title: Cell 33 from renal allograft sample 1

value: Batch 1


title: Cell 35 from renal allograft sample 1


title: Cell 34 from renal allograft sample 1


title: whole blood of COVID-19 patient 376

value: Patient 376

value: whole blood


title: D7 (scRNAseq)

description: day 0 dox+ DNMT1 KO

value: No


title: E11 (scRNAseq)

description: day 0 dox+ DNMT1 KO


title: Cell 39 from renal allograft sample 1


title: whole blood of COVID-19 patient 375

value: Patient 375

value: M


title: whole blood of COVID-19 patient 373

value: Patient 373


title: Cell 31 from renal allograft sample 1


title: D5 (scRNAseq)

description: day 0 dox+ DNMT1 KO


title: D6 (scRNAseq)

description: day 0 dox+ DNMT1 KO


title: whole blood of COVID-19 patient 372

value: Patient 372


title: whole blood of COVID-19 patient 374

value: Patient 374

value: F


title: Cell 32 from renal allograft sample 1


title: Cell 30 from renal allograft sample 1


title: whole blood of COVID-19 patient 371

value: Patient 371


title: D4 (scRNAseq)

description: day 0 dox+ DNMT1 KO

value: day 0

value: inducible DNMT1 KO


title: whole blood of COVID-19 patient 370

value: Patient 370


title: whole blood of COVID-19 patient 369

value: Patient 369


title: Cell 29 from renal allograft sample 1

value: Kidney 1


title: whole blood of COVID-19 patient 368

value: Patient 368


title: D3 (scRNAseq)

description: day 0 dox+ DNMT1 KO


title: whole blood of COVID-19 patient 367

value: Patient 367


title: D2 (scRNAseq)

description: day 0 dox+ DNMT1 KO


title: Cell 28 from renal allograft sample 1

value: Batch 1

value: First


title: whole blood of COVID-19 patient 366

value: Patient 366

value: whole blood


title: D12 (scRNAseq)

description: day 0 dox+ DNMT1 KO

value: No


title: whole blood of COVID-19 patient 364

value: Patient 364

value: M


title: Cell 27 from renal allograft sample 1


title: whole blood of COVID-19 patient 365

value: Patient 365


title: whole blood of COVID-19 patient 363

value: Patient 363


title: Cell 26 from renal allograft sample 1


title: whole blood of COVID-19 patient 362

value: Patient 362


title: D1 (scRNAseq)

description: day 0 dox+ DNMT1 KO

value: day 0


title: Cell 25 from renal allograft sample 1


title: whole blood of COVID-19 patient 361

value: Patient 361

value: F


title: D11 (scRNAseq)

description: day 0 dox+ DNMT1 KO

value: inducible DNMT1 KO


title: whole blood of COVID-19 patient 359

value: Patient 359


title: whole blood of COVID-19 patient 358

value: Patient 358


title: whole blood of COVID-19 patient 360

value: Patient 360


title: whole blood of COVID-19 patient 357

value: Patient 357


title: Cell 23 from renal allograft sample 1

value: Kidney 1

value: Batch 1

value: First


title: Cell 24 from renal allograft sample 1


title: C9 (scRNAseq)

description: day 0 dox+ DNMT1 KO

value: No


title: whole blood of COVID-19 patient 356

value: Patient 356

value: whole blood


title: D10 (scRNAseq)

description: day 0 dox+ DNMT1 KO


title: whole blood of COVID-19 patient 355

value: Patient 355

value: M


title: Cell 22 from renal allograft sample 1


title: whole blood of COVID-19 patient 354

value: Patient 354


title: C8 (scRNAseq)

description: day 0 dox+ DNMT1 KO

value: day 0


title: whole blood of COVID-19 patient 353

value: Patient 353


title: Cell 21 from renal allograft sample 1


title: C7 (scRNAseq)

description: day 0 dox+ DNMT1 KO


title: whole blood of COVID-19 patient 352

value: Patient 352

value: F


title: whole blood of COVID-19 patient 351

value: Patient 351


title: Cell 19 from renal allograft sample 1


title: C6 (scRNAseq)

description: day 0 dox+ DNMT1 KO

value: inducible DNMT1 KO


title: C5 (scRNAseq)

description: day 0 dox+ DNMT1 KO


title: whole blood of COVID-19 patient 349

value: Patient 349


title: Cell 18 from renal allograft sample 1


title: whole blood of COVID-19 patient 347

value: Patient 347


title: C4 (scRNAseq)

description: day 0 dox+ DNMT1 KO


title: Cell 17 from renal allograft sample 1

value: Kidney 1


title: whole blood of COVID-19 patient 346

value: Patient 346


title: whole blood of COVID-19 patient 345

value: Patient 345


title: whole blood of COVID-19 patient 342

value: Patient 342


title: C3 (scRNAseq)

description: day 0 dox+ DNMT1 KO

value: No


title: whole blood of COVID-19 patient 344

value: Patient 344

value: whole blood


title: whole blood of COVID-19 patient 341

value: Patient 341


title: Cell 15 from renal allograft sample 1

value: Batch 1

value: First


title: Cell 16 from renal allograft sample 1


title: whole blood of COVID-19 patient 343

value: Patient 343

value: M


title: C2 (scRNAseq)

description: day 0 dox+ DNMT1 KO

value: day 0


title: whole blood of COVID-19 patient 340

value: Patient 340


title: whole blood of COVID-19 patient 339

value: Patient 339


title: C1 (scRNAseq)

description: day 0 dox+ DNMT1 KO

value: inducible DNMT1 KO


title: C12 (scRNAseq)

description: day 0 dox+ DNMT1 KO


title: Cell 14 from renal allograft sample 1


title: whole blood of COVID-19 patient 350

value: Patient 350


title: Cell 20 from renal allograft sample 1

value: Kidney 1


title: whole blood of COVID-19 patient 348

value: Patient 348


title: whole blood of COVID-19 patient 337

value: Patient 337


title: whole blood of COVID-19 patient 336

value: Patient 336


title: C11 (scRNAseq)

description: day 0 dox+ DNMT1 KO

value: No


title: whole blood of COVID-19 patient 334

value: Patient 334


title: Cell 12 from renal allograft sample 1


title: C10 (scRNAseq)

description: day 0 dox+ DNMT1 KO


title: Cell 11 from renal allograft sample 1


title: whole blood of COVID-19 patient 332

value: Patient 332

value: F

value: whole blood


title: Cell 10 from renal allograft sample 1

value: Batch 1

value: First


title: B9 (scRNAseq)

description: day 0 dox+ DNMT1 KO


title: whole blood of COVID-19 patient 331

value: Patient 331


title: whole blood of COVID-19 patient 333

value: Patient 333

value: M


title: B8 (scRNAseq)

description: day 0 dox+ DNMT1 KO

value: day 0


title: Cell 8 from renal allograft sample 1


title: whole blood of COVID-19 patient 329

value: Patient 329


title: whole blood of COVID-19 patient 327

value: Patient 327


title: B7 (scRNAseq)

description: day 0 dox+ DNMT1 KO

value: inducible DNMT1 KO


title: whole blood of COVID-19 patient 330

value: Patient 330


title: Cell 9 from renal allograft sample 1

value: Kidney 1


title: whole blood of COVID-19 patient 335

value: Patient 335


title: whole blood of COVID-19 patient 338

value: Patient 338


title: whole blood of COVID-19 patient 325

value: Patient 325


title: whole blood of COVID-19 patient 326

value: Patient 326


title: whole blood of COVID-19 patient 323

value: Patient 323


title: whole blood of COVID-19 patient 324

value: Patient 324

value: F

value: whole blood


title: whole blood of COVID-19 patient 321

value: Patient 321


title: whole blood of COVID-19 patient 322

value: Patient 322


title: Cell 7 from renal allograft sample 1

value: Batch 1

value: First


title: B4 (scRNAseq)

description: day 0 dox+ DNMT1 KO

value: day 0

value: No


title: Cell 5 from renal allograft sample 1


title: whole blood of COVID-19 patient 320

value: Patient 320


title: Cell 13 from renal allograft sample 1


title: Cell 6 from renal allograft sample 1


title: B5 (scRNAseq)

description: day 0 dox+ DNMT1 KO

value: inducible DNMT1 KO


title: B6 (scRNAseq)

description: day 0 dox+ DNMT1 KO


title: Cell 4 from renal allograft sample 1

value: Kidney 1


title: whole blood of COVID-19 patient 318

value: Patient 318


title: whole blood of COVID-19 patient 319

value: Patient 319


title: whole blood of COVID-19 patient 317

value: Patient 317


title: Cell 3 from renal allograft sample 1


title: B12 (scRNAseq)

description: day 0 dox+ DNMT1 KO


title: whole blood of COVID-19 patient 328

value: Patient 328


title: whole blood of COVID-19 patient 314

value: Patient 314


title: whole blood of COVID-19 patient 315

value: Patient 315


title: B1 (scRNAseq)

description: day 0 dox+ DNMT1 KO


title: B3 (scRNAseq)

description: day 0 dox+ DNMT1 KO


title: whole blood of COVID-19 patient 313

value: Patient 313

value: F


title: Cell 1 from renal allograft sample 1


title: whole blood of COVID-19 patient 312

value: Patient 312

value: whole blood


title: whole blood of COVID-19 patient 311

value: Patient 311


title: B2 (scRNAseq)

description: day 0 dox+ DNMT1 KO


title: whole blood of COVID-19 patient 309

value: Patient 309


title: whole blood of COVID-19 patient 306

value: Patient 306


title: InfantLiver_Rep4

city: Milwaukee

first: Sridhar

last: Rao

state: WI

address: 8727 Watertown Plank Road

department: Blood Research Institute

institute: BloodCenter of Wisconsin

data_processing:
The raw reads were mapped to HG19 using STAR alignment tool.
The FPKM values were calculated using Cufflinks
Differential Expression Analysis was done for Infant/Fetal and iHLC versus adult Liver using DESEQ2 in R.
The Signifincant genes were defined at adj P-value < 0.05 and |FC| of 2 .
Genome_build: HG19
Supplementary_files_format_and_content: FPKM value for genes across samples  in .txt format . DESEQ2 results for iHLC and Infant Liver versus Adult Liver in .txt format

source_name: Infant liver samples  from Tissue Bank

growth_protocol: Human iPSC from the SV7 cell line were cultured on a defined StemAdhere matrix and supplemented with 20% mouse embryonic fibroblast (MEF)-conditioned media and 20 ng/ml fibroblast growth factor (FGF), and maintained in hypoxic culture conditions at 37C, 4% O2/5% CO2.

extract_protocol:
iHLC were harvested in Trizol (Life Technologies; Carlsbad, CA) and total RNA isolated and purified using the same RNeasy Mini Kit with on-column DNase treatment . iHLC from 6 independent differentiations were used for RNA-sequencing RNA was stored at -80°C until library preparation and sequencing.
Libraries and next-generation sequencing of human fetal/infant liver samples were prepared by BGI Americas Corporation (University of California Davis, Sacramento, CA),

treatment_protocol: For differentiations, cells were transferred to Matrigel (Corning; Pittston, PA) coated plates, seeded at 500,000 cells/mL, and directly differentiated into hepatocyte-like cells (iHLC) following the 20-day procedure described by Si-Tayeb

value: Infant liver


title: B11 (scRNAseq)

description: day 0 dox+ DNMT1 KO

value: day 0

value: No


title: whole blood of COVID-19 patient 310

value: Patient 310


title: Cell 2 from renal allograft sample 1

value: Kidney 1

value: Batch 1

value: First


title: A8 (scRNAseq)

description: day 0 dox+ DNMT1 KO

value: inducible DNMT1 KO


title: InfantLiver_Rep2


title: A7 (scRNAseq)

description: day 0 dox+ DNMT1 KO


title: InfantLiver_Rep3


title: HD_Day20_Rep6

source_name: iPSC-derived hepatocyte-like cells

value: iPSC-derived hepatocyte-like cells


title: whole blood of COVID-19 patient 307

value: Patient 307


title: whole blood of COVID-19 patient 305

value: Patient 305


title: whole blood of COVID-19 patient 316

value: Patient 316

value: M


title: A6 (scRNAseq)

description: day 0 dox+ DNMT1 KO


title: whole blood of COVID-19 patient 302

value: Patient 302

value: F

value: whole blood


title: B10 (scRNAseq)

description: day 0 dox+ DNMT1 KO


title: whole blood of COVID-19 patient 303

value: Patient 303


title: whole blood of COVID-19 patient 301

value: Patient 301


title: InfantLiver_Rep1

value: Infant liver


title: A5 (scRNAseq)

description: day 0 dox+ DNMT1 KO

value: day 0

value: No


title: A9 (scRNAseq)

description: day 0 dox+ DNMT1 KO


title: whole blood of COVID-19 patient 308

value: Patient 308


title: whole blood of COVID-19 patient 300

value: Patient 300


title: HD_Day20_Rep4


title: whole blood of COVID-19 patient 299

value: Patient 299


title: whole blood of COVID-19 patient 298

value: Patient 298


title: A4 (scRNAseq)

description: day 0 dox+ DNMT1 KO

value: inducible DNMT1 KO


title: whole blood of COVID-19 patient 304

value: Patient 304


title: HD_Day20_Rep3

value: iPSC-derived hepatocyte-like cells


title: whole blood of COVID-19 patient 296

value: Patient 296


title: HD_Day20_Rep5


title: HD_Day20_Rep2


title: A3 (scRNAseq)

description: day 0 dox+ DNMT1 KO


title: whole blood of COVID-19 patient 295

value: Patient 295

value: M


title: whole blood of COVID-19 patient 297

value: Patient 297

value: F


title: A2 (scRNAseq)

description: day 0 dox+ DNMT1 KO


title: whole blood of COVID-19 patient 293

value: Patient 293

value: whole blood


title: whole blood of COVID-19 patient 291

value: Patient 291


title: Crb2 S267A- 4Dox (rep4)

city: Münster

first: Annika

last: Möller-Kerutt

address: Albert-Schweitzer-Campus 1, A14

department: Medical Dept. D

country: Germany

institute: University Clinics of Münster

description:
processed data file: norm_read_counts_S267AwoDox_vs_S267ADox.txt
processed data file: raw_read_counts_S267AwoDox_vs_S267ADox.txt

data_processing:
The sequences were demultiplexed (bcl2fastq2) to fastq data and quality controlled.
Trimmomatic (v. 0.38) was used for adapter trimming and read filtering. (Parameter: SE -phred33, ILLUMINACLIP:adapters/NEB-SE.fa:2:30:10, LEADING:3 TRAILING:3 MINLEN:15)
The resulted reads were aligned to the hg38 using Hisat2 (v.2.1.0; Parameter: default) and sorted using SAM tools (v. 1.9).
The sorted and aligned reads were counted into genes using HTSeq (v.0.11.1; Parameter: --minaqual 0, --stranded reverse).
Testing for differential expression was performed using DESeq2 r-package (v. 1.24.0).
Genome_build: GRCh38
Supplementary_files_format_and_content: raw_read_counts_S267AwoDox_vs_S267ADox.txt: Tab-delimited text file includes raw read counts.
Supplementary_files_format_and_content: norm_read_counts_S267AwoDox_vs_S267ADox.txt: Tab-delimited text file includes normalized read counts.

source_name: AB8 cell line

extract_protocol:
RNA was isolated from cell lines using GenElute™ Mammalian Total RNA Miniprep Kit (Sigma-Aldrich).
NEBNext Ultra Directional RNA II Library Prep kit was used for the construction of sequencing libraries, which were then sequenced with the Illumina NextSeq 500 System and NextSeq v2.5 sequencing reagent kit in a single read-mode with a read-length of 75 bp.

tag: cell type

value: podocyte-derived human cell line

tag: modification

tag: passage after modification

tag: induction

value: Yes


title: HD_Day20_Rep1

tag: tissue


title: whole blood of COVID-19 patient 294

tag: disease state

tag: individual id

value: Patient 294


title: whole blood of COVID-19 patient 289

value: Patient 289

tag: age

tag: gender


title: whole blood of COVID-19 patient 292

value: Patient 292


title: whole blood of COVID-19 patient 290

value: Patient 290


title: whole blood of COVID-19 patient 288

value: Patient 288


title: A12 (scRNAseq)

description: day 0 dox+ DNMT1 KO

value: day 0

value: inducible DNMT1 KO

value: No


title: Crb2 S267A- 3Dox (rep3)


title: A11 (scRNAseq)

description: day 0 dox+ DNMT1 KO


title: A1 (scRNAseq)

description: day 0 dox+ DNMT1 KO


title: Crb2 S267A- 2Dox (rep2)


title: whole blood of COVID-19 patient 286

value: Patient 286


title: whole blood of COVID-19 patient 287

value: Patient 287


title: A10 (scRNAseq)

description: day 0 dox+ DNMT1 KO


title: whole blood of COVID-19 patient 285

value: Patient 285


title: Crb2 S267A- 1Dox (rep1)


title: whole blood of COVID-19 patient 284

value: Patient 284

value: F


title: Crb2 S267A- 4woDox (control, rep4)


title: whole blood of COVID-19 patient 283

value: Patient 283

value: M

value: whole blood


title: whole blood of COVID-19 patient 282

value: Patient 282


title: 11374X7 doxycycline 48h

city: Salt Lake City

first: Sankar

last: Swaminathan

state: UT

institute: University of Utah

data_processing:
Sequenced reads were aligned to the human genome (hg19) and EBV Akata (KC207813).
Raw counts were estimated using USeq’s Defined Region Differential Seq (DRDS) application
Differentially expressed genes were identified using DESeq2 version 1.26.0
Enriched pathways were identified using gene set enrichment analysis (GSEA) and Ingenuity Pathway Analysis.
Genome_build: hg19
Supplementary_files_format_and_content: Raw counts from DRDS

source_name: AGSiZ/Akata cell line

growth_protocol: AGSiZ cells infected with Akata virus were maintained in 250µg/ml G-418 and 1µg/ml puromycin, inDMEM containing 10% charcoal stripped FBS (Sigma) and 1% glutamine.

extract_protocol:
Qiagen miRNA isolation kit
Libraries were prepared according to Illumina's instructions accompanying the TruSeq Stranded mRNA Library Prep Kit. Briefly, oligo-dT beads were used to capture RNA species containing a polyA tail. Following polyA RNA enrichment, the RNA was chemically fragmented and random primed for reverse transcription. The average insert size of libraries constructed with the TruSeq Stranded mRNA Library Prep Kit is 200 bp.

value: AGSiZ

tag: infected with

value: EBV strain Akata BX-1


title: Crb2 S267A- 3woDox (control, rep3)

value: podocyte-derived human cell line


title: whole blood of COVID-19 patient 281

value: Patient 281


title: whole blood of COVID-19 patient 280

value: Patient 280


title: whole blood of COVID-19 patient 279

value: Patient 279


title: 11374X8 doxycycline 48h


title: 11374X4 doxycycline 24h


title: Crb2 S267A- 2woDox (control, rep2)


title: 11374X1 Control


title: whole blood of COVID-19 patient 278

value: Patient 278


title: Crb2 S267A- 1woDox (control, rep1)

value: No


title: whole blood of COVID-19 patient 277

value: Patient 277


title: 11374X3 doxycycline 24h


title: EGF_48_C1_D_RNAseq

city: Portland

first: Laura

middle: M

last: Heiser

state: OR

address: 2730 S Moody Ave

department: Biomedical Engineering

institute: Oregon Health and Science University

data_processing:
Sequence preprocessing and alignment was performed using a Docker-based pipeline (Tatlow et al., 2016).
100-bp single-end reads trimmed of adapter sequences and low-quality base calls using TrimGalore (v 0.4.3), a wrapper for CutAdapt (v. 1.10) and FastQC (v. 0.11.5). Minimum 1-bp overlap with the adapter sequence (AGATCGGAAGAGC) required for trimming. Trimmed reads with a length < 35 bp were discarded.
Trimmed reads were aligned to GENCODE V24 (GRCh38.p5) transcript sequences using Kallisto (v. 0.43.0) using the following parameters: --bias -b 30 --pseudobam.
Kallisto transcript abundance estimates are provided for each sample, in units of estimated counts and transcripts-per-million (TPM).
Genome_build: hg38
Supplementary_files_format_and_content: abundance.tsv: tab-separated value table of per-sample transcript abundance estimates output by Kallisto, in units of estimated counts and transcripts-per-million

source_name: breast epilthelial cells

growth_protocol: Cells were cultured to 50-80% confluence in growth media (GM) composed of DMEM/F12, 5% horse serum, 20 ng/ml EGF, 0.5 µg/ml hydrocortisone, 100 ng/ml cholera toxin, 10 µg/ml insulin, and 1% Pen/Strep.

extract_protocol:
Total RNA was extracted from flash-frozen samples using a Qiagen RNeasy Mini kit.
Libraries were prepared using an Illumina TruSeq Stranded mRNA library preparation kit.

treatment_protocol: Cells were detached using 0.05% trypsin-EDTA, and 75,000 cells were seeded onto a collegen-1-coated eight-well plate. After approx. 7 hours., cells were washed with PBS and experimental media (EM) composed of DMEM/F12, 5% horse serum, 0.5 µg/ml hydrocortisone, 100 ng/ml cholera toxin, and 1% Pen/Strep was added. After 18 hours of incubation in EM, cells were treated with ligand in fresh EM.

value: normal breast epithelium

tag: treatment

value: EGF

tag: treatment concentration

value: 10 ng/ml

tag: timepoint


title: 11374X2 Control

tag: cell line


title: whole blood of COVID-19 patient 276

value: Patient 276

value: F


title: whole blood of COVID-19 patient 272

value: Patient 272


title: whole blood of COVID-19 patient 274

value: Patient 274

value: whole blood


title: whole blood of COVID-19 patient 273

value: Patient 273


title: whole blood of COVID-19 patient 275

value: Patient 275


title: whole blood of COVID-19 patient 271

value: Patient 271


title: whole blood of COVID-19 patient 269

value: Patient 269


title: EGF_48_C1_C_RNAseq


title: EGF_48_C1_B_RNAseq


title: whole blood of COVID-19 patient 268

value: Patient 268


title: whole blood of COVID-19 patient 267

value: Patient 267


title: whole blood of COVID-19 patient 266

value: Patient 266


title: EGF_48_C1_A_RNAseq


title: EGF_24_C1_D_RNAseq


title: whole blood of COVID-19 patient 264

value: Patient 264


title: whole blood of COVID-19 patient 265

value: Patient 265

value: M


title: whole blood of COVID-19 patient 263

value: Patient 263


title: whole blood of COVID-19 patient 259

value: Patient 259


title: whole blood of COVID-19 patient 261

value: Patient 261


title: whole blood of COVID-19 patient 258

value: Patient 258

value: F


title: EGF_24_C1_C_RNAseq

value: normal breast epithelium

value: EGF

value: 10 ng/ml


title: whole blood of COVID-19 patient 260

value: Patient 260

value: whole blood


title: whole blood of COVID-19 patient 262

value: Patient 262


title: whole blood of COVID-19 patient 255

value: Patient 255


title: whole blood of COVID-19 patient 257

value: Patient 257


title: whole blood of COVID-19 patient 254

value: Patient 254


title: OSM_48_C1_C_RNAseq

value: OSM


title: EGF_24_C1_A_RNAseq


title: whole blood of COVID-19 patient 270

value: Patient 270


title: OSM_48_C1_B_RNAseq


title: whole blood of COVID-19 patient 253

value: Patient 253


title: OSM_48_C1_A_RNAseq


title: whole blood of COVID-19 patient 251

value: Patient 251

value: M


title: whole blood of COVID-19 patient 249

value: Patient 249


title: OSM_24_C1_B_RNAseq


title: OSM_24_C1_C_RNAseq


title: whole blood of COVID-19 patient 250

value: Patient 250


title: whole blood of COVID-19 patient 248

value: Patient 248


title: whole blood of COVID-19 patient 246

value: Patient 246

value: F


title: whole blood of COVID-19 patient 244

value: Patient 244


title: HGF_48_C1_C_RNAseq

value: normal breast epithelium

value: HGF

value: 40 ng/ml


title: whole blood of COVID-19 patient 247

value: Patient 247

value: whole blood


title: whole blood of COVID-19 patient 245

value: Patient 245


title: OSM_24_C1_A_RNAseq

value: OSM

value: 10 ng/ml


title: whole blood of COVID-19 patient 243

value: Patient 243


title: whole blood of COVID-19 patient 256

value: Patient 256


title: whole blood of COVID-19 patient 242

value: Patient 242


title: whole blood of COVID-19 patient 252

value: Patient 252

value: M


title: HGF_48_C1_B_RNAseq


title: HGF_48_C1_A_RNAseq


title: whole blood of COVID-19 patient 239

value: Patient 239


title: HGF_24_C1_C_RNAseq


title: whole blood of COVID-19 patient 240

value: Patient 240


title: whole blood of COVID-19 patient 238

value: Patient 238


title: whole blood of COVID-19 patient 237

value: Patient 237

value: F


title: whole blood of COVID-19 patient 236

value: Patient 236


title: HGF_24_C1_A_RNAseq

value: normal breast epithelium

value: HGF

value: 40 ng/ml


title: whole blood of COVID-19 patient 233

value: Patient 233

value: whole blood


title: whole blood of COVID-19 patient 235

value: Patient 235


title: whole blood of COVID-19 patient 234

value: Patient 234


title: whole blood of COVID-19 patient 231

value: Patient 231


title: whole blood of COVID-19 patient 232

value: Patient 232


title: TGFB_48_C1_B_RNAseq

value: 10 ng/ml_10 ng/ml


title: whole blood of COVID-19 patient 230

value: Patient 230


title: whole blood of COVID-19 patient 229

value: Patient 229

value: M


title: whole blood of COVID-19 patient 228

value: Patient 228


title: whole blood of COVID-19 patient 227

value: Patient 227


title: whole blood of COVID-19 patient 226

value: Patient 226


title: whole blood of COVID-19 patient 225

value: Patient 225


title: TGFB_24_C1_C_RNAseq

value: normal breast epithelium


title: TGFB_24_C1_B_RNAseq


title: whole blood of COVID-19 patient 223

value: Patient 223

value: F


title: TGFB_24_C1_A_RNAseq


title: whole blood of COVID-19 patient 220

value: Patient 220


title: whole blood of COVID-19 patient 222

value: Patient 222

value: whole blood


title: IFNG_48_C1_C_RNAseq

value: 20 ng/ml_10 ng/ml


title: IFNG_48_C1_B_RNAseq


title: whole blood of COVID-19 patient 219

value: Patient 219


title: HGF_24_C1_B_RNAseq

value: HGF

value: 40 ng/ml


title: EGF_24_C1_B_RNAseq

value: EGF

value: 10 ng/ml


title: whole blood of COVID-19 patient 215

value: Patient 215

value: M


title: whole blood of COVID-19 patient 216

value: Patient 216


title: whole blood of COVID-19 patient 217

value: Patient 217


title: IFNG_48_C1_A_RNAseq


title: whole blood of COVID-19 patient 218

value: Patient 218


title: whole blood of COVID-19 patient 214

value: Patient 214


title: TGFB_48_C1_C_RNAseq

value: normal breast epithelium

value: 10 ng/ml_10 ng/ml


title: IFNG_24_C1_C_RNAseq


title: whole blood of COVID-19 patient 241

value: Patient 241


title: whole blood of COVID-19 patient 213

value: Patient 213

value: F


title: IFNG_24_C1_B_RNAseq

value: 20 ng/ml_10 ng/ml


title: TGFB_48_C1_A_RNAseq


title: whole blood of COVID-19 patient 211

value: Patient 211

value: whole blood


title: whole blood of COVID-19 patient 210

value: Patient 210


title: whole blood of COVID-19 patient 224

value: Patient 224


title: whole blood of COVID-19 patient 221

value: Patient 221


title: whole blood of COVID-19 patient 208

value: Patient 208


title: whole blood of COVID-19 patient 207

value: Patient 207


title: whole blood of COVID-19 patient 205

value: Patient 205


title: BMP2_24_C1_C_RNAseq


title: whole blood of COVID-19 patient 202

value: Patient 202

value: M


title: BMP2_48_C1_B_RNAseq


title: whole blood of COVID-19 patient 203

value: Patient 203


title: BMP2_48_C1_A_RNAseq

value: normal breast epithelium


title: whole blood of COVID-19 patient 199

value: Patient 199


title: whole blood of COVID-19 patient 204

value: Patient 204


title: BMP2_24_C1_B_RNAseq


title: whole blood of COVID-19 patient 198

value: Patient 198


title: BMP2_24_C1_A_RNAseq


title: whole blood of COVID-19 patient 212

value: Patient 212

value: F


title: PBS_48_C1_C_RNAseq

value: PBS

value: 0 ng/ml


title: IFNG_24_C1_A_RNAseq

value: 20 ng/ml_10 ng/ml


title: whole blood of COVID-19 patient 197

value: Patient 197

value: whole blood


title: whole blood of COVID-19 patient 195

value: Patient 195


title: whole blood of COVID-19 patient 194

value: Patient 194


title: whole blood of COVID-19 patient 209

value: Patient 209


title: whole blood of COVID-19 patient 193

value: Patient 193


title: whole blood of COVID-19 patient 192

value: Patient 192


title: PBS_48_C1_B_RNAseq


title: whole blood of COVID-19 patient 206

value: Patient 206

value: M


title: PBS_24_C1_C_RNAseq

value: normal breast epithelium


title: whole blood of COVID-19 patient 190

value: Patient 190


title: BMP2_48_C1_C_RNAseq


title: PBS_48_C1_A_RNAseq


title: whole blood of COVID-19 patient 191

value: Patient 191


title: whole blood of COVID-19 patient 201

value: Patient 201


title: whole blood of COVID-19 patient 189

value: Patient 189

value: F


title: PBS_24_C1_B_RNAseq

value: PBS

value: 0 ng/ml


title: whole blood of COVID-19 patient 187

value: Patient 187


title: PBS_24_C1_A_RNAseq


title: whole blood of COVID-19 patient 200

value: Patient 200

value: whole blood


title: whole blood of COVID-19 patient 188

value: Patient 188


title: whole blood of COVID-19 patient 182

value: Patient 182


title: whole blood of COVID-19 patient 183

value: Patient 183


title: ctrl_0_C1_D_RNAseq

value: 0 h


title: whole blood of COVID-19 patient 184

value: Patient 184


title: whole blood of COVID-19 patient 185

value: Patient 185


title: whole blood of COVID-19 patient 186

value: Patient 186


title: ctrl_0_C1_C_RNAseq

value: normal breast epithelium


title: whole blood of COVID-19 patient 179

value: Patient 179

value: M


title: ctrl_0_C1_B_RNAseq


title: whole blood of COVID-19 patient 180

value: Patient 180


title: whole blood of COVID-19 patient 178

value: Patient 178

value: F


title: whole blood of COVID-19 patient 177

value: Patient 177


title: ctrl_0_C1_A_RNAseq

value: PBS

value: 0 ng/ml


title: whole blood of COVID-19 patient 196

value: Patient 196

value: whole blood


title: whole blood of COVID-19 patient 181

value: Patient 181


title: whole blood of COVID-19 patient 175

value: Patient 175


title: whole blood of COVID-19 patient 176

value: Patient 176


title: EGF_48_C1_C_ATACseq

data_processing:
ATAC-seq data were pre-processed and aligned using the "ATACseq (1 -> 3)" workflow on the AnswerALS Galaxy server (answer.csbi.mit.edu).
Reads were trimmed of adapter sequences and low-quality bases using Trimmomatic (Galaxy version 0.36.5). Reads were trimmed of low-quality bases (Phred score < 15) at the read start or end, and Nextera adapter sequences (CTGTCTCTTATA) were trimmed from read ends (minimum of a 2-bp overlap required for trimming).
Reads were aligned to the human genome (hg38) using Bowtie2 (Galaxy version 2.3.4.1) in paired-end mode with otherwise default settings.
BAM files were filtered to remove secondary alignments, unmapped reads, and mitochondiral DNA alignments using ngsutils bam filter (Galaxy version 0.5.9).
PCR duplicates were detected and removed using Picard MarkDuplicates (Galaxy version 2.7.1.2).
Peaks were called from de-duplicated, filtered BAM files using MACS2 (Galaxy Version 2.1.1.20160309.5) using the following parameters: -format BAMPE -nomodel -extsize 200 -shift -100 -qvalue 0.01.
bigwig files were created from BAM files using deepTools bamCoverage (v. 3.1.2) using the following parameters: -of bigwig --normalizeUsing CPM
Genome_build: hg38
Supplementary_files_format_and_content: narrowPeak files contain significant (FDR q-value < 0.01) peaks called by MACS  in each sample. bigWig files contain CPM-normalized sample accessibility tracks computed from BAM files using deepTools bamCoverage.

extract_protocol:
ATAC-seq samples were prepared following the Omni-ATAC protocol published in Corces, et al. 2017.
MCF10A cells were washed with PBS and detached from plate using trypsin. 50,000 cells per sample were spun at 500 RCF for 5 min. The cell pellet was resuspended in 500 ul of PBS, spun at 500 RCF for 5 min, and resuspended in 50 µl of cold ATAC resuspension buffer (RSB) containing 0.1% NP40, 0.1% Tween-20, and 0.01% digitonin. After 3 min on ice, 1 ml of cold RSB containing 0.1% Tween-20 was added, and the tube was inverted three times to mix. Nuclei were pelleted by centrifugation at 500 RCF for 10 min at 4’C. The supernatant was carefully aspirated and the nuclei were resuspended in 50 µl of transposition buffer (25 µl 2x TD buffer (Illumina), 2.5 µl transposase (Illumina), 16.5 µl PBS, 0.5 µl 1% digitonin, 0.5 µl 10% Tween-20, and 5 µl H2O). Samples were placed in a pre-warmed (37˚C) thermomixer and mixed for 30 min at 100 RPM. Transposed fragments were then purified using a Qiagen MinElute column and frozen at -80C for further processing. DNA was pre-amplified with 5 rounds of PCR (72ºC for 5 min, 98ºC for 30 seconds, then 5 cycles of [ 98ºC for 10 sec, 63ºC for 30 sec, 72ºC for 1 min]). PCR reactions contained 20 µl eluate, 25 µl NEBNext 2x MasterMix, 2.5 µl 25 µM i5 primer and 2.5 µl 25 µM i7 primer. The DNA concentration of the pre-amplified samples was then assessed by qPCR. After calculating tagmented DNA concentrations, pre-amplified samples were diluted with buffer to a concentration of 5 µM. Six samples had an undiluted DNA concentration below 5 µM and were not diluted. 5 µM pre-amplified samples were amplified for 3 additional PCR cycles. 100bp PE reads were sequenced on an Illumina HiSeq 2500 Sequencer by the OHSU Massively Parallel Sequencing Shared Resource.

value: EGF

value: 10 ng/ml


title: EGF_48_C1_D_ATACseq


title: whole blood of COVID-19 patient 174

value: Patient 174


title: whole blood of COVID-19 patient 173

value: Patient 173


title: whole blood of COVID-19 patient 172

value: Patient 172


title: whole blood of COVID-19 patient 171

value: Patient 171


title: EGF_48_C1_B_ATACseq

value: normal breast epithelium


title: whole blood of COVID-19 patient 170

value: Patient 170


title: EGF_48_C1_A_ATACseq


title: whole blood of COVID-19 patient 169

value: Patient 169

value: M


title: EGF_24_C1_D_ATACseq


title: whole blood of COVID-19 patient 166

value: Patient 166

value: F


title: whole blood of COVID-19 patient 167

value: Patient 167


title: whole blood of COVID-19 patient 168

value: Patient 168

value: whole blood


title: whole blood of COVID-19 patient 165

value: Patient 165


title: EGF_24_C1_C_ATACseq


title: whole blood of COVID-19 patient 163

value: Patient 163


title: whole blood of COVID-19 patient 164

value: Patient 164


title: whole blood of COVID-19 patient 162

value: Patient 162


title: EGF_24_C1_B_ATACseq

value: EGF

value: 10 ng/ml


title: whole blood of COVID-19 patient 161

value: Patient 161


title: whole blood of COVID-19 patient 159

value: Patient 159


title: whole blood of COVID-19 patient 160

value: Patient 160


title: EGF_24_C1_A_ATACseq

value: normal breast epithelium


title: whole blood of COVID-19 patient 157

value: Patient 157


title: whole blood of COVID-19 patient 158

value: Patient 158

value: M


title: OSM_48_C1_C_ATACseq

value: OSM


title: OSM_48_C1_B_ATACseq


title: whole blood of COVID-19 patient 155

value: Patient 155

value: F


title: OSM_48_C1_A_ATACseq


title: whole blood of COVID-19 patient 154

value: Patient 154

value: whole blood


title: OSM_24_C1_C_ATACseq


title: whole blood of COVID-19 patient 153

value: Patient 153


title: whole blood of COVID-19 patient 152

value: Patient 152


title: whole blood of COVID-19 patient 151

value: Patient 151


title: OSM_24_C1_B_ATACseq


title: OSM_24_C1_A_ATACseq


title: whole blood of COVID-19 patient 147

value: Patient 147


title: HGF_48_C1_C_ATACseq

value: HGF

value: 40 ng/ml


title: whole blood of COVID-19 patient 149

value: Patient 149


title: HGF_48_C1_B_ATACseq


title: whole blood of COVID-19 patient 146

value: Patient 146


title: whole blood of COVID-19 patient 144

value: Patient 144


title: whole blood of COVID-19 patient 145

value: Patient 145


title: HGF_48_C1_A_ATACseq

value: normal breast epithelium


title: whole blood of COVID-19 patient 141

value: Patient 141

value: M


title: whole blood of COVID-19 patient 142

value: Patient 142


title: whole blood of COVID-19 patient 140

value: Patient 140

value: F


title: whole blood of COVID-19 patient 139

value: Patient 139

value: whole blood


title: whole blood of COVID-19 patient 156

value: Patient 156


title: whole blood of COVID-19 patient 138

value: Patient 138


title: whole blood of COVID-19 patient 137

value: Patient 137


title: HGF_24_C1_A_ATACseq

value: HGF


title: HGF_24_C1_B_ATACseq

value: 40 ng/ml


title: whole blood of COVID-19 patient 135

value: Patient 135


title: whole blood of COVID-19 patient 136

value: Patient 136


title: whole blood of COVID-19 patient 134

value: Patient 134


title: TGFB_48_C1_B_ATACseq

value: 10 ng/ml


title: TGFB_48_C1_C_ATACseq

value: normal breast epithelium


title: whole blood of COVID-19 patient 133

value: Patient 133


title: whole blood of COVID-19 patient 150

value: Patient 150

value: M


title: whole blood of COVID-19 patient 148

value: Patient 148


title: TGFB_48_C1_A_ATACseq


title: whole blood of COVID-19 patient 132

value: Patient 132


title: whole blood of COVID-19 patient 131

value: Patient 131


title: whole blood of COVID-19 patient 129

value: Patient 129

value: whole blood


title: whole blood of COVID-19 patient 143

value: Patient 143

value: F


title: whole blood of COVID-19 patient 128

value: Patient 128


title: HGF_24_C1_C_ATACseq

value: HGF

value: 40 ng/ml


title: TGFB_24_C1_C_ATACseq


title: TGFB_24_C1_B_ATACseq


title: whole blood of COVID-19 patient 125

value: Patient 125


title: whole blood of COVID-19 patient 124

value: Patient 124


title: TGFB_24_C1_A_ATACseq

value: 10 ng/ml


title: whole blood of COVID-19 patient 123

value: Patient 123


title: whole blood of COVID-19 patient 122

value: Patient 122


title: IFNG_48_C1_B_ATACseq

value: normal breast epithelium

value: 20 ng/ml


title: whole blood of COVID-19 patient 121

value: Patient 121

value: M


title: IFNG_48_C1_C_ATACseq


title: whole blood of COVID-19 patient 119

value: Patient 119


title: whole blood of COVID-19 patient 118

value: Patient 118


title: IFNG_48_C1_A_ATACseq


title: whole blood of COVID-19 patient 120

value: Patient 120

value: whole blood


title: IFNG_24_C1_B_ATACseq


title: whole blood of COVID-19 patient 117

value: Patient 117

value: F


title: IFNG_24_C1_C_ATACseq


title: whole blood of COVID-19 patient 115

value: Patient 115


title: IFNG_24_C1_A_ATACseq


title: whole blood of COVID-19 patient 130

value: Patient 130


title: whole blood of COVID-19 patient 114

value: Patient 114


title: whole blood of COVID-19 patient 127

value: Patient 127


title: whole blood of COVID-19 patient 113

value: Patient 113


title: BMP2_48_C1_C_ATACseq


title: whole blood of COVID-19 patient 126

value: Patient 126


title: whole blood of COVID-19 patient 111

value: Patient 111


title: whole blood of COVID-19 patient 110

value: Patient 110


title: whole blood of COVID-19 patient 116

value: Patient 116


title: whole blood of COVID-19 patient 109

value: Patient 109


title: BMP2_48_C1_A_ATACseq

value: normal breast epithelium

value: 20 ng/ml


title: whole blood of COVID-19 patient 105

value: Patient 105


title: whole blood of COVID-19 patient 103

value: Patient 103


title: BMP2_24_C1_B_ATACseq


title: whole blood of COVID-19 patient 104

value: Patient 104

value: whole blood


title: whole blood of COVID-19 patient 101

value: Patient 101

value: M


title: whole blood of COVID-19 patient 102

value: Patient 102

value: F


title: BMP2_24_C1_A_ATACseq


title: BMP2_24_C1_C_ATACseq


title: whole blood of COVID-19 patient 107

value: Patient 107


title: whole blood of COVID-19 patient 99

value: Patient 99


title: whole blood of COVID-19 patient 100

value: Patient 100


title: whole blood of COVID-19 patient 98

value: Patient 98


title: whole blood of COVID-19 patient 97

value: Patient 97


title: PBS_48_C1_B_ATACseq

value: PBS

value: 0 ng/ml


title: whole blood of COVID-19 patient 112

value: Patient 112


title: PBS_48_C1_C_ATACseq

value: normal breast epithelium


title: PBS_48_C1_A_ATACseq


title: BMP2_48_C1_B_ATACseq

value: 20 ng/ml


title: whole blood of COVID-19 patient 91

value: Patient 91


title: whole blood of COVID-19 patient 93

value: Patient 93


title: whole blood of COVID-19 patient 94

value: Patient 94

value: whole blood


title: whole blood of COVID-19 patient 95

value: Patient 95

value: M


title: whole blood of COVID-19 patient 108

value: Patient 108

value: F


title: PBS_24_C1_C_ATACseq


title: PBS_24_C1_B_ATACseq


title: whole blood of COVID-19 patient 106

value: Patient 106


title: PBS_24_C1_A_ATACseq


title: whole blood of COVID-19 patient 92

value: Patient 92


title: whole blood of COVID-19 patient 90

value: Patient 90


title: whole blood of COVID-19 patient 88

value: Patient 88


title: whole blood of COVID-19 patient 87

value: Patient 87


title: ctrl_0_C1_D_ATACseq

value: PBS

value: 0 ng/ml

value: 0 h


title: whole blood of COVID-19 patient 86

value: Patient 86


title: ctrl_0_C1_C_ATACseq

value: normal breast epithelium


title: whole blood of COVID-19 patient 89

value: Patient 89


title: whole blood of COVID-19 patient 85

value: Patient 85


title: whole blood of COVID-19 patient 84

value: Patient 84

value: whole blood


title: whole blood of COVID-19 patient 83

value: Patient 83


title: whole blood of COVID-19 patient 82

value: Patient 82


title: whole blood of COVID-19 patient 81

value: Patient 81

value: F


title: ctrl_0_C1_A_ATACseq


title: ctrl_0_C1_B_ATACseq


title: whole blood of COVID-19 patient 79

value: Patient 79


title: whole blood of COVID-19 patient 96

value: Patient 96

value: M


title: whole blood of COVID-19 patient 80

value: Patient 80


title: whole blood of COVID-19 patient 76

value: Patient 76


title: whole blood of COVID-19 patient 77

value: Patient 77


title: whole blood of COVID-19 patient 74

value: Patient 74


title: Heat stress_Rep4

city: Parkville

first: Weicheng

last: Zhao

state: Victoria

address: Building 184, Royal Parade

country: Australia

institute: The University of Melbourne

data_processing:
Quality control of sequencing reads was performed using FastQC software version 0.11.9. The raw reads were subjected to Illumina adaptor and low-quality base removals to obtain clean reads.
Clean reads were aligned/mapped to the pig reference genome (Sus scrofa 11.1) using Hisat2 version 2.1.0. The average alignment rate across all samples was 96.5 ± 0.15% (SD).
The aligned reads were then counted per gene using HTSeq software (version 0.11.3) with reversed strand interpretation.
Differential expression analysis using DESeq2 version 1.28.1.
Genome_build: Sus scrofa 11.1
Supplementary_files_format_and_content: Tab-delimited text files containing gene Ensembl ID and counts.

organism: Sus scrofa

source_name: Placenta

extract_protocol:
Placental total RNA was extracted using ReliaPrep RNA tissue Miniprep System (Cat# Z6111; Promega, Madison, WI, USA) as per the manufacturer’s instructions.
The sequencing library was constructed using the NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® (New England Biolabs, Ipswich, MA, USA) according to the manufacturer’s instructions.

treatment_protocol: On d40 of gestation, pregnant pigs were either exposed to thermoneutral control (CON; constant 20 °C) or cyclic heat stress (HS; 28 °C between 0900h and 1700h, and 33 °C between 1700h and 0900h) conditions for 3 weeks.

value: Placenta

tag: breed

value: Large White x Landrace

value: Heat stress

tag: developmental stage

value: d60 of gestation


title: Heat stress_Rep2


title: whole blood of COVID-19 patient 73

value: Patient 73


title: whole blood of COVID-19 patient 75

value: Patient 75

value: whole blood


title: Heat stress_Rep1


title: Heat stress_Rep5


title: whole blood of COVID-19 patient 78

value: Patient 78


title: whole blood of COVID-19 patient 71

value: Patient 71


title: Heat stress_Rep3


title: whole blood of COVID-19 patient 70

value: Patient 70

value: F


title: Control_Rep5

value: Control


title: whole blood of COVID-19 patient 69

value: Patient 69


title: whole blood of COVID-19 patient 68

value: Patient 68


title: whole blood of COVID-19 patient 67

value: Patient 67

value: M


title: Control_Rep4


title: whole blood of COVID-19 patient 66

value: Patient 66


title: Control_Rep3

value: Placenta


title: whole blood of COVID-19 patient 65

value: Patient 65


title: whole blood of COVID-19 patient 64

value: Patient 64


title: Control_Rep2

value: Large White x Landrace

value: d60 of gestation


title: whole blood of COVID-19 patient 63

value: Patient 63


title: Control_Rep1


title: whole blood of COVID-19 patient 61

value: Patient 61

value: whole blood


title: whole blood of COVID-19 patient 62

value: Patient 62


title: whole blood of COVID-19 patient 72

value: Patient 72


title: MHC-17-9

city: 昆明市

first: shaoxing

last: Dai

state: 云南

address: No.1 boda road chenggong, Kunming 650500 Yunnan,China

institute: Kunming University of Science and Technology

description: Chimera embryo cell of Macaca fascicularis

data_processing:
fastp was used to cut adapters and quality control
human and monkey cells were identified by two ways using the clean data. One way is to compare the number of identical hits of sequencing reads from each cell by blastp with the random selected 10000 reads against the human and monkey genome (Ensembl Homo_sapiens.GRCh38 and Macaca_fascicularis_5.0), respectively. Another way is to compare the reads counts of sequencing reads mapped to tdTomato vector.
hisat2  was used to map sequencing reads to the human or monkey genome with the default parameters.
The program stringtie with default parameters was used to assembly alignments into potential transcripts
Quantify the gene expression as transcripts per million mapped reads (TPM) value by the program stringtie
Genome_build: Homo_sapiens.GRCh38 and Macaca_fascicularis_5.0
Supplementary_files_format_and_content: tab-delimited text file include TPM matrix for all samples

organism: Macaca fascicularis

source_name: embryo cell

extract_protocol:
The single-cell was washed in 30µL micro-drop of PBS-BSA solution and individual cells were picked into 0.2mL PCR tubes by micropipette for modified Smart2-seq,all the cDNA were quantified on a 2100 Bioanalyzer (Agilent) and Qubit 3.0.
The scRNA-seq libraries were generated using the TruePrepTM DNA Library Prep Kit V2 for Illumina®(Vazyme) . Briefly, we use 5-50ng cDNA constructing the libraries according to the manufacturer’s instructions.  cDNA molecules were preamplified and pooled followed by library construction. All libraries were quantified on a 2100 Bioanalyzer (Agilent) and realtime quantitative PCR, and then subjected to 150 bp paired-end sequencing on an Illumina Xten platform (sequenced by Novogene and Annoroad).

value: embryo

tag: development stage

tag: lineage

value: EPI


title: whole blood of COVID-19 patient 59

value: Patient 59


title: whole blood of COVID-19 patient 58

value: Patient 58


title: whole blood of COVID-19 patient 60

value: Patient 60


title: whole blood of COVID-19 patient 57

value: Patient 57

value: M


title: MHC-17-8


title: MHC-17-7


title: whole blood of COVID-19 patient 55

value: Patient 55


title: whole blood of COVID-19 patient 54

value: Patient 54

value: F


title: whole blood of COVID-19 patient 56

value: Patient 56


title: whole blood of COVID-19 patient 53

value: Patient 53


title: MHC-17-71


title: whole blood of COVID-19 patient 51

value: Patient 51


title: MHC-17-72

value: EXMC


title: whole blood of COVID-19 patient 49

value: Patient 49

value: whole blood


title: MHC-17-6

value: PE


title: MHC-17-70

value: embryo


title: MHC-17-69


title: whole blood of COVID-19 patient 50

value: Patient 50


title: whole blood of COVID-19 patient 52

value: Patient 52


title: whole blood of COVID-19 patient 45

value: Patient 45


title: MHC-17-68

value: EPI


title: whole blood of COVID-19 patient 44

value: Patient 44


title: whole blood of COVID-19 patient 48

value: Patient 48

value: M


title: whole blood of COVID-19 patient 42

value: Patient 42


title: MHC-17-67


title: whole blood of COVID-19 patient 41

value: Patient 41

value: F


title: whole blood of COVID-19 patient 40

value: Patient 40


title: MHC-17-66


title: whole blood of COVID-19 patient 38

value: Patient 38


title: whole blood of COVID-19 patient 39

value: Patient 39


title: MHC-17-65

value: EXMC


title: whole blood of COVID-19 patient 35

value: Patient 35

value: whole blood


title: whole blood of COVID-19 patient 37

value: Patient 37


title: MHC-17-64

value: embryo


title: whole blood of COVID-19 patient 36

value: Patient 36


title: whole blood of COVID-19 patient 34

value: Patient 34


title: MHC-17-63

value: EPI


title: MHC-17-62


title: whole blood of COVID-19 patient 32

value: Patient 32


title: whole blood of COVID-19 patient 47

value: Patient 47


title: whole blood of COVID-19 patient 31

value: Patient 31

value: M


title: whole blood of COVID-19 patient 33

value: Patient 33


title: whole blood of COVID-19 patient 46

value: Patient 46


title: whole blood of COVID-19 patient 30

value: Patient 30


title: whole blood of COVID-19 patient 29

value: Patient 29


title: MHC-17-5


title: whole blood of COVID-19 patient 43

value: Patient 43


title: MHC-17-61


title: whole blood of COVID-19 patient 28

value: Patient 28


title: whole blood of COVID-19 patient 26

value: Patient 26

value: F


title: whole blood of COVID-19 patient 27

value: Patient 27

value: whole blood


title: MHC-17-59

value: embryo


title: whole blood of COVID-19 patient 25

value: Patient 25


title: MHC-17-58

value: EPI


title: whole blood of COVID-19 patient 24

value: Patient 24


title: whole blood of COVID-19 patient 23

value: Patient 23


title: whole blood of COVID-19 patient 22

value: Patient 22


title: whole blood of COVID-19 patient 17

value: Patient 17


title: MHC-17-55

value: PE


title: MHC-17-56


title: whole blood of COVID-19 patient 21

value: Patient 21


title: whole blood of COVID-19 patient 18

value: Patient 18

value: M


title: whole blood of COVID-19 patient 19

value: Patient 19


title: whole blood of COVID-19 patient 20

value: Patient 20


title: MHC-17-52

value: EXMC


title: MHC-17-54


title: whole blood of COVID-19 patient 15

value: Patient 15

value: F


title: MHC-17-53


title: whole blood of COVID-19 patient 13

value: Patient 13

value: whole blood


title: whole blood of COVID-19 patient 16

value: Patient 16


title: whole blood of COVID-19 patient 14

value: Patient 14


title: whole blood of COVID-19 patient 12

value: Patient 12


title: whole blood of COVID-19 patient 11

value: Patient 11


title: whole blood of COVID-19 patient 8

value: Patient 8


title: MHC-17-4

value: embryo

value: EPI


title: whole blood of COVID-19 patient 9

value: Patient 9


title: MHC-17-49


title: whole blood of COVID-19 patient 7

value: Patient 7


title: whole blood of COVID-19 patient 5

value: Patient 5

value: M


title: whole blood of COVID-19 patient 4

value: Patient 4


title: MHC-17-48


title: whole blood of COVID-19 patient 3

value: Patient 3


title: MHC-17-57


title: MHC-17-47


title: whole blood of COVID-19 patient 1

value: Patient 1


title: whole blood of COVID-19 patient 2

value: Patient 2

value: F


title: MHC-17-45


title: MHC-17-51

value: PE


title: whole blood of COVID-19 patient 10

value: Patient 10

value: whole blood


title: whole blood of COVID-19 patient 6

value: Patient 6


title: MHC-17-42

value: EXMC


title: MHC-17-44


title: MHC-17-40


title: MHC-17-46


title: MHC-17-39


title: MHC-17-43


title: MHC-17-41


title: MHC-17-37


title: MHC-17-3


title: MHC-17-36


title: MHC-17-38


title: MHC-17-35


title: MHC-17-34


title: MHC-17-33


title: FFPE colorectal cancer sample, IRI-res 2

city: Rionero in Vulture

first: Valentina

last: Condelli

state: PZ

address: Via Padre Pio, 1

country: Italy

institute: IRCCS CROB

description:
IRI-res 2
matrix_signal_Unmeth_Meth_DetPval_FOLFIRI.txt

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridized to Illumina Infinium Human Methylation 850 Beadchip using standard Illumina protocol

scan_protocol: Arrays were scanned using Illumina HiScanSQ system, using standard recommended Illumina scanner setting

data_processing: Illumina Infinium 850K Human Methylation data were processed by R/Bioconductor environment

source_name: FFPE colorectal cancer sample

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted and purified from formalin-fixed, paraffin-embedded (FFPE) CRC specimens using QIAamp DNA Mini kit according to standard instructions

value: metastatic CRC

tag: subgroup

value: first-line primary-resistant mCRC


title: FFPE colorectal cancer sample, IRI-sens 8

description:
IRI-sens 8
matrix_signal_Unmeth_Meth_DetPval_FOLFIRI.txt

value: drug-sensitive mCRC


title: FFPE colorectal cancer sample, IRI-sens 2

description:
IRI-sens 2
matrix_signal_Unmeth_Meth_DetPval_FOLFIRI.txt


title: FFPE colorectal cancer sample, IRI-res 8

description:
IRI-res 8
matrix_signal_Unmeth_Meth_DetPval_FOLFIRI.txt


title: MHC-17-32

value: embryo

value: EPI


title: FFPE colorectal cancer sample, IRI-sens 4

description:
IRI-sens 4
matrix_signal_Unmeth_Meth_DetPval_FOLFIRI.txt


title: FFPE colorectal cancer sample, IRI-res 4

description:
IRI-res 4
matrix_signal_Unmeth_Meth_DetPval_FOLFIRI.txt


title: FFPE colorectal cancer sample, IRI-res 1

description:
IRI-res 1
matrix_signal_Unmeth_Meth_DetPval_FOLFIRI.txt


title: FFPE colorectal cancer sample, IRI-sens 5

description:
IRI-sens 5
matrix_signal_Unmeth_Meth_DetPval_FOLFIRI.txt


title: FFPE colorectal cancer sample, IRI-res 5

description:
IRI-res 5
matrix_signal_Unmeth_Meth_DetPval_FOLFIRI.txt


title: FFPE colorectal cancer sample, OHP-res 6

description:
OHP-res 6
matrix_signal_Unmeth_Meth_DetPval_FOLFOX.txt


title: FFPE colorectal cancer sample, IRI-sens 3

description:
IRI-sens 3
matrix_signal_Unmeth_Meth_DetPval_FOLFIRI.txt


title: FFPE colorectal cancer sample, IRI-res 7

description:
IRI-res 7
matrix_signal_Unmeth_Meth_DetPval_FOLFIRI.txt


title: FFPE colorectal cancer sample, IRI-res 6

description:
IRI-res 6
matrix_signal_Unmeth_Meth_DetPval_FOLFIRI.txt


title: MHC-17-30


title: MHC-17-31


title: FFPE colorectal cancer sample, OHP-res 7

description:
OHP-res 7
matrix_signal_Unmeth_Meth_DetPval_FOLFOX.txt


title: MHC-17-2


title: FFPE colorectal cancer sample, OHP-res 11

description:
OHP-res 11
matrix_signal_Unmeth_Meth_DetPval_FOLFOX.txt


title: A11_Brain_nTg_Arg1++_LysMCreTg+_rep2

city: Lexington

first: Chao

last: Ma

state: KY

address: Sanders-Brown Bldg. R430, 800 S. Limestone St.

department: Department of Neuroscience

institute: University of Kentucky

hyb_protocol: Panel codeset probes were hybridized with 100 ng of total RNA per sample according to manufacturer’s protocol.

scan_protocol: Hybridized RNA samples were loaded, scanned, and counted by the nCounter® SPRINT Profiler, Moffitt Cancer Center, Tampa, FL, US) according to the manufacturer’s protocol.

data_processing: The NanoString nCounter data analysis was performed using the nSolver™ Analysis Software (v4.0, NanoString Technologies, Inc.) according to the user manuals (MAN-C0019-08, MAN-10030-03). The nSolver was used for analyzing the mouse neuropathology panel by loading with an RLF file (NS_Mm_NeuroPath_v1.0). We performed the basic features of the nSolver analysis to generate the heat maps of differentially expressed gene transcripts (DEGs) with agglomerative clustering based on the normalized data. We also used it to export all normalized data. We also performed the advanced nSolver analysis based on the downloaded and installed online R package (nCounter_Advanced_Analysis_2.0.134) and a modified probe annotation file based on the original one provided by NanoString (NS_Mm_NeuroPath_v1.0_ProbeAnnotations). All RNA samples passed system QC parameters on imaging (fields of view > 75), binding density (0.1-2.25), and positive control linearity (R2 > 0.95). All RNA data passed the positive control limit of detection QC (0.5fM > 2*standard deviations above the arithmetic mean of the negative controls). The following basic threshold criteria were applied. A threshold count value of 10 was calculated as the gene transcript expression background (arithmetic mean of negative controls + 2*standard deviation). An observation frequency of 0.5 was applied for the background, indicating gene transcripts with counts lower than 10 were omitted if it happened to more than 50% of the samples. Therefore, 648 genes were above the background, and 122 genes were removed for falling below the background too frequently. A total of 6 house-keeping genes (Aars, Ccdc127, Cnot10, Csnk2a2, Lars, Mto1) were selected for data normalization by the geNorm algorithm. The p-values were adjusted for multiple testing by the false discovery rate (FDR) method of Benjamini and Hochberg correction. The matrix remodeling pathway was dropped from pathway scoring analysis due to less than five detected gene transcripts. In gene set analysis, a directed global significance score at ±1.3 was set as the cut-off value to reflect the top changed pathways further.

label: Nanostring

organism: Mus musculus

source_name: Brain Posterior Cortex

label_protocol: All RNA samples were loaded and labeled with gene transcript specific probes built in the nCounter® mouse neuropathology panel (v1.0, XT-CSO-MNROP1-12, 12 Reactions, NanoString Technologies, Inc.), then analyzed by the nCounter® Analysis System (nCounter® SPRINT Profiler, Moffitt Cancer Center, Tampa, FL, US) according to the manufacturer’s procedures for hybridization, detection, and scanning.

growth_protocol: The Cre-recombinase mice (B6.129P2-Lyz2tm1(cre)/fo /J; LysMcre promoter, Stock No: 004781) and arginase 1 mice (C57BL/6-Arg1tm1Pmu /J (Arg1fl), Stock No: 008817) were purchased from the Jackson Laboratory. The APP Tg2576 mice (APP+/-), Arg1 floxed mice (Arg1fl/fl), and LysMcreTg/+ were bred according to the Institutional Animal Care and Use Committee (IACUC) approved protocols. Thus, four groups of mice were maintained (nTg/Arg1+/+/LysMcreTg/+, nTg/Arg1fl/+/LysMcreTg/+, APP+/-/Arg1+/+/LysMcreTg/+, and APP+/-/Arg1fl/+/LysMcreTg/+). All mice were subjected to behavioral tests at the age of 15 months, followed by euthanasia and perfusion at 16-month-old age.

extract_protocol: Total RNA of the posterior cortex was extracted using AllPrep DNA/RNA/Protein Mini Kit (QIAGEN, #80004) according to the manufacturer’s protocol.

value: Male


title: FFPE colorectal cancer sample, IRI-sens 6

description:
IRI-sens 6
matrix_signal_Unmeth_Meth_DetPval_FOLFIRI.txt


title: FFPE colorectal cancer sample, OHP-res 9

description:
OHP-res 9
matrix_signal_Unmeth_Meth_DetPval_FOLFOX.txt


title: FFPE colorectal cancer sample, OHP-res 8

description:
OHP-res 8
matrix_signal_Unmeth_Meth_DetPval_FOLFOX.txt


title: A12_Brain_nTg_Arg1++_LysMCreTg+_rep3

value: Female


title: FFPE colorectal cancer sample, OHP-res 3

description:
OHP-res 3
matrix_signal_Unmeth_Meth_DetPval_FOLFOX.txt


title: FFPE colorectal cancer sample, IRI-sens 7

description:
IRI-sens 7
matrix_signal_Unmeth_Meth_DetPval_FOLFIRI.txt


title: FFPE colorectal cancer sample, OHP-res 13

description:
OHP-res 13
matrix_signal_Unmeth_Meth_DetPval_FOLFOX.txt


title: FFPE colorectal cancer sample, OHP-res 15

description:
OHP-res 15
matrix_signal_Unmeth_Meth_DetPval_FOLFOX.txt


title: MHC-17-28

description: Chimera embryo cell of Macaca fascicularis


title: FFPE colorectal cancer sample, OHP-res 14

description:
OHP-res 14
matrix_signal_Unmeth_Meth_DetPval_FOLFOX.txt


title: A10_Brain_nTg_Arg1++_LysMCreTg+_rep1


title: MHC-17-29


title: FFPE colorectal cancer sample, IRI-res 3

description:
IRI-res 3
matrix_signal_Unmeth_Meth_DetPval_FOLFIRI.txt


title: A08_Brain_nTg_Arg1fl+_LysMCreTg+_rep2


title: FFPE colorectal cancer sample, OHP-res 16

description:
OHP-res 16
matrix_signal_Unmeth_Meth_DetPval_FOLFOX.txt


title: FFPE colorectal cancer sample, IRI-sens 1

description:
IRI-sens 1
matrix_signal_Unmeth_Meth_DetPval_FOLFIRI.txt


title: FFPE colorectal cancer sample, OHP-res 5

description:
OHP-res 5
matrix_signal_Unmeth_Meth_DetPval_FOLFOX.txt


title: A07_Brain_nTg_Arg1fl+_LysMCreTg+_rep1


title: A06_Brain_APP+-_Arg1++_LysMCreTg+_rep3


title: MHC-17-26


title: A04_Brain_APP+-_Arg1++_LysMCreTg+_rep1


title: FFPE colorectal cancer sample, OHP-res 10

description:
OHP-res 10
matrix_signal_Unmeth_Meth_DetPval_FOLFOX.txt


title: A03_Brain_APP+-_Arg1fl+_LysMCreTg+_rep3


title: MHC-17-24


title: MHC-17-27


title: A01_Brain_APP+-_Arg1fl+_LysMCreTg+_rep1


title: A09_Brain_nTg_Arg1fl+_LysMCreTg+_rep3


title: MHC-17-25


title: A05_Brain_APP+-_Arg1++_LysMCreTg+_rep2


title: FFPE colorectal cancer sample, OHP-res 12

description:
OHP-res 12
matrix_signal_Unmeth_Meth_DetPval_FOLFOX.txt


title: MHC-17-23


title: MHC-17-21