title: control_treated_w_mock_6hr_rep1


title: EMPTY_G22_OE015_x6_S4

status: Public on Oct 01 2021

type: SRA

city: Seattle

first: Alice

last: Berger

state: WA

address: 1100 Fairview Ave N

country: USA

institute: Fred Hutchinson Cancer Center

description: processed data file: transcript_quants_log2TPM_EMPTY-EGFP.csv

library_source: transcriptomic

data_processing:
Illumina HiSeq 4000 reads were aligned by STAR v2.5.3a to BAM files.
Picard tools v.1.114 used mark duplicate reads, add read group info, and reorder BAMs.
BAMs are indexed using samtools v.0.1.19
FeatureCounts from Subread v.1.5.3 was used to quantify gene transcripts
EdgeR v.3.22.3 was used to normalize read counts and obtain CPM and RPKM values.
CPM values were used to filter the gene list  down to the 12,887 genes with average log2CPM >0.1 across all samples. RPKM values were converted into TPM values.
Genome_build: hg19/GRCh37
Supplementary_files_format_and_content: transcript_quants_log2TPM_EMPTY-EGFP.csv is a comma-separated values file of the log2 of TPM values of the negative control samples. Each row is a gene transcript and each column is a sample.
Supplementary_files_format_and_content: transcript_quants_log2TPM_KRAS-TP53.csv is a comma-separated values file of the log2 of TPM values. Each row is a gene transcript and each column is a sample.

molecule: polyA RNA

organism: Homo sapiens

source_name: cell line

growth_protocol: Cells were cultured for one day before and 96 hours after treatment.

extract_protocol:
Cells were lysed and RNA extracted with TRIzol (Invitrogen)
Nextera XT Index Kit v2, 75bp paired-end pre-pooled libraries

treatment_protocol: Cells were transduced with the ORF construct (if applicable) one day after plating. Infection efficiency is assessed at 24 hours post-infection with antibody selection.

tag: cell line

tag: cell type

value: lung adenocarcinoma

tag: genetic perturbation

tag: genotype/variation

value: Negative control sample with no ectopic gene expression


title: EMPTY_G17_OE015_x6_S4


title: combi-2#2

type: RNA

city: Mannheim

first: Carolina

last: Delatorre

address: Theodor-Kutzer-Ufer 1-3

country: Germany

institute: University Heidelberg

description: Gene expression of HuCCT-1 cells transfected with siRNAs YAP2/TAZ3

hyb_protocol: Hybridization (16h x 45°C) was processed according to the standard Affymetrix protocol.

scan_protocol: Affymetrix GeneArray Scanner3000

data_processing: The data were analyzed with a commercial software called JMP Genomics, version 6, from SAS. Gene expression profiling was performed using arrays of human Clariom D from Affymetrix. A Custom CDF Version 22 with Entrez based gene definitions was used to annotate the arrays. The Raw fluorescence intensity values were normalized applying quantile normalization, RMA background correction and Medianpolish Probeset Summary

label: Biotin

molecule: total RNA

source_name: HuCCT-1 cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol.

growth_protocol: Cells were cultured in RPMI (Sigma Aldrich, Steinheim, Germany) or DMEM (Gibco/Thermo Fisher Scientific, Waltham USA) containing 10% fetal bovine serum and 1% penicillin/streptomycin at 37°C in a 5% CO2 atmosphere. Cells were routinely tested for mycoplasma contamination and authentication was performed by short tandem repeat (STR) analysis (DSMZ, Braunschweig, Germany).

extract_protocol: Total RNA was isolated using the NucleoSpin RNA II kit (Macherey-Nagel, Düren, Germany).

treatment_protocol: Gene-specific small interfering RNAs (siRNAs) were obtained from Eurofins MWG Operon (Ebersberg, Germany). For siRNA inhibition assays, cells were directly transfected after trypsination. Scrambled siRNA-treated cells served as control. Gene-specific siRNAs (final concentration of 40 nM for combinations of two siRNAs for YAP and TAZ) and the transfection reagent Lipofectamine RNAiMAX (Gibco/Thermo Fisher Scientific) were diluted, mixed in Opti-MEM (Gibco/Thermo Fisher Scientific) and incubated at room temperature, before being distributed onto the cells. Twenty-four hours after transfection, fresh medium was added.

tag: treatment

value: siRNAs YAP2/TAZ3


title: control_treated_w_mock_6hr_rep4

city: Tsukuba

first: Nobutaka

last: Mitsuda

state: Ibaraki

address: Central 6 Higashi 1-1-1

department: Bioproduction Research Institute

country: Japan

institute: National Institute of Advanced Industrial Science and Technology

hyb_protocol: Hybridized using Gene Expression Hybridization kit (Agilent) and washed by Gene Expression wash pack (Agilent).

scan_protocol: Scanned on an Agilent G2505B scanner.

data_processing: Agilent Feature Extraction Software (v 9.1.3.1) was used for background subtraction. After that, signal of each probe was divided by median value of filter-passed probes.

organism: Arabidopsis thaliana

source_name: Arabidopsis Col-0 10-day seedlings treated with DMSO for 6 hours

label_protocol: 200 ng of total RNA was used for labeling procedure using Low Input Quick Amp Labeling kit (One-color) (Agilent).

growth_protocol: All plants were grown on MS-based agar media in growth chamber at 22 Celsius degree in 16h/8h day/night cycle.

extract_protocol: Plant RNeasy Mini kit (QIAGEN) was used to isolate total RNA.

treatment_protocol: Seedling was treated with 10 micro M estradiol or DMSO (mock).

tag: genotype

value: Wild type Col-0

tag: tissue

value: Seedling

value: DMSO (mock)

tag: treatment duration

value: 6 hours


title: EMPTY_D20_OE015_x6_S4


title: control_treated_w_mock_3hr_rep3

source_name: Arabidopsis Col-0 10-day seedlings treated with DMSO for 3 hours

value: 3 hours


title: EMPTY_G17_OE015_x5_S4


title: EMPTY_G22_OE015_x5_S4


title: EMPTY_C18_OE015_x6_S4


title: EMPTY_D23_OE015_x5_S4


title: 10X VDJ Library

city: Cambridge

first: Rebecca

middle: H

last: Herbst

state: MA

address: 415 Main Street

department: Klarman Cell Observatory

institute: Broad Institute of MIT and Harvard

description:
5' 10X reads
processed data file: n10X_cell_meta_data.tsv

data_processing:
10X - Sample demultiplexing, barcode processing, alignment, filtering, UMI counting, and csv files of TCR clonality were performed using the Cell Ranger analysis pipeline (v3.0.2)
Smart-Seq2 - BAM files were converted to de-multiplexed FASTQs using Illumina’s Bcl2Fastq software package v2.17.1.14.
Genome_build: mm10
Supplementary_files_format_and_content: Unique molecular identifiers (UMI) counts table (mtx file), with separate file for cell barcodes and genes. Exported for single-cell and single-nucleus RNA-seq data separatel.

organism: Mus musculus

source_name: lung resident T cells

growth_protocol: KP mice were infected with 25,000 titer/units of lentivirus expressing the LucOS construct (Dupage et al 2012).

extract_protocol:
10x: H-2Kb/SIINFEKL specific CD8+ T cells from KrasG12D+/-  Trp53-/- lung adenocarcinoma bearing lungs at different timepoints were sorted and loaded into the 10X Chromium Controller using the Chromium Single Cell 5' Library and Gel Bead Kit (10X Genomics)
Smart-Seq2: H-2Kb/SIINFEKL specific CD8+ T cells from KrasG12D+/-  Trp53-/- lung adenocarcinoma bearing lungs at different timepoints were sorted into 96-well plates with 5 µl lysis buffer comprised of Buffer TCL (Qiagen 1031576) plus 1% 2-mercaptoethanol (Sigma 63689). Following sorting, plates were spun down for one minute at 3,000 rpm and immediately frozen at −80°C.
10X: 10X Chromium Single Cell V(D)J kits (5' gene expression with paired T cell receptor sequencing, and for some samples Feature Barcode detection); Smart-Seq2: For preparation of single-cell libraries we thawed the cells and purified them with 2.2x RNAClean SPRI beads (Beckman Coulter Genomics) without final elution (Shalek et al., 2013). The RNA captured beads were air-dried and processed immediately for cDNA synthesis. We performed SMART-seq2 following the published protocol (Picelli et al., 2013).

treatment_protocol: Mice did not receive any treatments.

tag: strain

tag: mouse id

value: multiple-mice

value: lung resident T cells

value: TetPos


title: EMPTY_C21_OE015_x5_S4


title: 10X RNA Library

description:
5' 10X reads
processed data file: n10X_rna_counts_data.mtx


title: EMPTY_C18_OE015_x5_S4


title: NTC#3

description: Gene expression of HuCCT-1 cells

value: control


title: EMPTY_D20_OE015_x5_S4


title: Old liver ATAC_rep2

city: Boston

first: Yi

last: Zhang

address: 200 Longwood Ave

department: PCMM

institute: Boston Children's Hospital

library_source: genomic

data_processing:
Sequencing adapters and low quality reads were removed from the raw RNA-seq and ATAC-seq  reads with Trimmomatic (V0.39).
Reads from RNA-seq were aligned to mm10 with Hisat2 (V2.2.1). Reads from ATAC-seq were aligned to mm10 using Bowtie2 (V2.3.5.1).
For RNA-seq, HTSeq-count (V0.12.4) was used to calculate the count of reads for each gene. For ATAC-seq, MACS2 was used to call peaks, and DiffBind (V2.12.0) was used for filtration and feature count of peaks.
Genome_build: mm10

molecule: genomic DNA

source_name: liver from old(23-25 month old) mice

extract_protocol:
TRIzol reagent (Invitrogen) was used to extract total RNA according to the manufacturer’s instructions.
Libraries of RNA-seq and ATAC-seq were prepared for sequencing using standard Illumina protocols

value: liver

value: untreated


title: Old liver ATAC_rep3


title: control_treated_w_mock_3hr_rep4


title: control_treated_w_estrogen_6hr_rep4

source_name: Arabidopsis Col-0 10-day seedlings treated with 10 micro M estradiol for 6 hours

value: 10 micro M estradiol


title: control_treated_w_estrogen_1hr_rep3

source_name: Arabidopsis Col-0 10-day seedlings treated with 10 micro M estradiol for 1 hour

value: 1 hour


title: Old liver ATAC_rep1


title: control_treated_w_mock_3hr_rep1


title: NTC#2

description: Gene expression of HuCCT-1 cells


title: EMPTY_D19_OE014_x8_S3


title: EMPTY_D19_OE014_x7_S3


title: EMPTY_D20_OE014_x7_S3


title: EMPTY_G22_0E015_x3_F12


title: EMPTY_D23_0E015_x3_D12


title: EMPTY_D20_OE014_x8_S3


title: EMPTY_G17_0E015_x3_E12


title: control_treated_w_mock_3hr_rep2


title: EMPTY_D20_0E015_x3_C12


title: Young liver ATAC_rep2

source_name: liver from young(2.5 month old) mice


title: EMPTY_C18_0E015_x3_A12


title: EMPTY_C21_0E015_x3_B12


title: control_treated_w_mock_1hr_rep4

source_name: Arabidopsis Col-0 10-day seedlings treated with DMSO for 1 hour


title: Young liver ATAC_rep1


title: EMPTY_G17_0E015_x2_E6


title: EMPTY_G22_0E015_x2_F6


title: combi-1#1

description: Gene expression of HuCCT-1 cells transfected with siRNAs YAP1/TAZ2

value: siRNAs YAP1/TAZ2


title: eWAT-AKO11

city: Shanghai

first: Yijun

last: Lin

address: Yueyang Road

country: China

institute: Shanghai Institute of Nutrition and Health

data_processing:
RNA-seq transcriptome library was prepared following TruSeqTM RNA sample preparation Kit and and then sequenced on the Illumina HiSeq xtenvaSeq 6000 sequencer (2×150bp read length).
The raw paired end reads were trimmed and quality controlled by SeqPrep and Sickle with default parameters.
The clean reads were separately aligned to reference genome with orientation mode using HISAT2 software.
Differentially expressed genes were analyzed using DESeq2 with TPM as the expression level.
Genome_build: mm9
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: epididymal white adipose tissue

extract_protocol:
eWATs were removed, flash frozen with liquid nitrogen, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 2 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: HFD induced obesity


title: Old kidney ATAC_rep3

source_name: kidney from old(23-25 month old) mice

value: kidney


title: NTC#1

description: Gene expression of HuCCT-1 cells


title: Old kidney ATAC_rep2


title: EMPTY_D23_0E015_x2_D6

value: lung adenocarcinoma

value: Negative control sample with no ectopic gene expression


title: Young liver ATAC_rep3


title: control_treated_w_mock_1hr_rep2

value: Wild type Col-0

value: Seedling


title: control_treated_w_mock_1hr_rep3

value: DMSO (mock)


title: control_treated_w_mock_1hr_rep1


title: control_0hr_rep2

source_name: Arabidopsis Col-0 10-day seedlings


title: control_0hr_rep3


title: eWAT-AKO8


title: control_0hr_rep4


title: control_0hr_rep1


title: Old kidney ATAC_rep1


title: EMPTY_C18_0E015_x2_A6


title: eWAT-AKO3


title: control_treated_w_mock_24hr_rep4

source_name: Arabidopsis Col-0 10-day seedlings treated with DMSO for 24 hours

value: 24 hours


title: Young kidney ATAC_rep3

source_name: kidney from young(2.5 month old) mice


title: eWAT-AKO9


title: A549_EMPTY_D11_C2


title: A549_EMPTY_C12_B2


title: eWAT-WT5

value: Slc16a1 flox/flox


title: eWAT-WT4


title: A549_EMPTY_C11_A2


title: Young kidney ATAC_rep2


title: Young kidney ATAC_rep1


title: EMPTY_D20_0E015_x2_C6


title: EMPTY_C21_0E015_x2_B6


title: eWAT-WT2


title: healthy control 7

city: Houston

first: Gena

last: Tribble

state: Texas

address: 1941 East Road, BBS 5324

institute: UTHealth

data_processing:
Cutadapt®,and perl scripts® were used to remove reads containing undetermined bases, low quality bases, or those that contained adaptor contamination
FastQC® was used to verify sequence quality.
Bowtie2® and Tophat2® were used to map reads to the Homo sapiens genome.
StringTie® was used to assemble the reads.
Transcriptomes from all samples were merged to construct a comprehensive transcriptome using perlscript® and gffcompare®. The expression levels of all transcripts were estimated using StringTie® and Ballgown®.
Genome_build: GRCh38
Supplementary_files_format_and_content: text file; gene expression by fpkm values

source_name: alveolar bone

extract_protocol:
Bone fragments homogenized in a bone mill, in Trizol in a bullet blender, and RNA purified with RNaEasy (Qiagen)
Ribosomal RNA was removed via Epicentre Ribo-Zero Gold Kit. The ribo-minus RNA was purified and then fragmented using divalent ions under elevated temperatures. The RNA fragments were reverse transcribed to form the final cDNA library via deoxyuridine triphosphate (dUTP).

value: oral/craniofacial bone

tag: Sex

value: Female

tag: smoking

value: smoker

tag: disease

value: healthy control


title: healthy control 8

value: non-smoker


title: healthy control 9


title: healthy control 5

value: Male


title: healthy control 4


title: healthy control 6


title: healthy control 10


title: A549_EMPTY_D12_D2


title: eWAT-WT3


title: polyA Enriched RNA-sequencing_p28_Rnaseh2b_Atm_CB_5

city: Memphis

first: Peter

middle: J

last: McKinnon

state: Tennessee

address: 262 Danny Thomas Place

department: Center for Pediatric Neurological Disease Research

institute: St. Jude Children's Research Hospital

description:
AA850_G1_p28_Rnaseh2b_Atm_CB_5
processed data file: p28_log2CPM.txt
processed data file: p28_FPKM.txt

data_processing:
Read trimming using TrimGalore.
Read alignment using STAR and BWA.
Gene quantification using HTSEQ.
Differential expression modelled by limma-voom.
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: Text files of FPKM and log2CPM.

source_name: Whole Cerebellum

extract_protocol:
Total RNA was isolated from tissue with TRIzol (Invitrogen).
Library preparation using TruSeq Stranded Total RNA Kit (Illumina).
Double stranded cDNA fragments were ligated with Illumina paired-end adaptors, followed by size selection (~200bp) and libraries were analyzed using a HiSeq 2000 sequencing system (Illumina).

value: Cerebellum

tag: age

value: RnaseH2B,Atm Nes-cre

tag: rna sequencing

value: Poly A mRNA Seq


title: healthy control 3


title: polyA Enriched RNA-sequencing_p28_Rnaseh2b_Atm_CB_4

description:
AA849_G1_p28_Rnaseh2b_Atm_CB_4
processed data file: p28_log2CPM.txt
processed data file: p28_FPKM.txt


title: healthy control 2


title: healthy control 1


title: polyA Enriched RNA-sequencing_p28_Rnaseh2b_Atm_CB_3

description:
AA848_G1_p28_Rnaseh2b_Atm_CB_3
processed data file: p28_log2CPM.txt
processed data file: p28_FPKM.txt


title: P7 mice fibroblasts ATAC-seq_rep1

data_processing:
Sequencing adapters and low quality reads were removed from the raw RNA-seq and ATAC-seq  reads with Trimmomatic (V0.39) and from the RRBS reads with Trim Galore (V0.6.6).
Reads from RNA-seq were aligned to mm10 with Hisat2 (V2.2.1). Reads from ATAC-seq were aligned to mm10 using Bowtie2 (V2.3.5.1). Reads from RRBS were aligned to mm10 using Bismark (v0.22.3).
For RNA-seq, HTSeq-count (V0.12.4) was used to calculate the count of reads for each gene. For ATAC-seq, MACS2 was used to call peaks, and DiffBind (V2.12.0) was used for filtration and feature count of peaks. For RRBS, DSS (V2.34.0) was used to identify DMRs and DMSs.
Genome_build: mm10

source_name: P7 mice fibroblasts ATAC-seq

extract_protocol:
Total DNA was extracted from cells using the MasterPureTM Complete DNA & RNA Purification Kit (Cat.No. MC85200). TRIzol reagent (Invitrogen) was used to extract total RNA according to the manufacturer’s instructions.
Libraries of RNA-seq, ATAC-seq and RRBS were prepared for sequencing using standard Illumina protocols

tag: tissue/cell type

value: skin fibroblast

value: untreated


title: diabetic subject 6

value: diabetic


title: P5 mice fibroblasts ATAC-seq_rep2

source_name: P5 mice fibroblasts ATAC-seq


title: P7 mice fibroblasts ATAC-seq_rep2


title: P7 mice fibroblasts ATAC-seq_rep3


title: diabetic subject 8


title: diabetic subject 7


title: polyA Enriched RNA-sequencing_p28_Atm_CB_5

description:
AA847_G1_p28_Atm_CB_5
processed data file: p28_log2CPM.txt
processed data file: p28_FPKM.txt

value: Atm Nes-cre


title: P5 mice fibroblasts ATAC-seq_rep1


title: diabetic subject 4


title: diabetic subject 3


title: P3 mice fibroblasts ATAC-seq_rep3

source_name: P3 mice fibroblasts ATAC-seq


title: P3 mice fibroblasts ATAC-seq_rep1


title: polyA Enriched RNA-sequencing_p28_Atm_CB_4

description:
AA844_G1_p28_Atm_CB_4
processed data file: p28_log2CPM.txt
processed data file: p28_FPKM.txt


title: polyA Enriched RNA-sequencing_p28_Rnaseh2b_Atm_CB_1

description:
AA845_G1_p28_Rnaseh2b_Atm_CB_1
processed data file: p28_log2CPM.txt
processed data file: p28_FPKM.txt


title: diabetic subject 2


title: P3 mice fibroblasts ATAC-seq_rep2


title: diabetic subject 1


title: P5 mice fibroblasts ATAC-seq_rep3


title: P1 mice fibroblasts ATAC-seq_rep4

source_name: P1 mice fibroblasts ATAC-seq


title: polyA Enriched RNA-sequencing_p28_Rnaseh2b_Atm_CB_2

description:
AA846_G1_p28_Rnaseh2b_Atm_CB_2
processed data file: p28_log2CPM.txt
processed data file: p28_FPKM.txt


title: 1081_T2

city: Gainesville

first: VIJAYENDRAN

last: CHANDRAN

state: FL

address: Assistant Professor, Department of Pediatrics,  University of Florida, School of Medicine, 1600 SW Archer Road, Box 100296

institute: University of Florida

data_processing:
Bluebee’s genomics analysis platform
Sequencing targeted mean three million 65-nt single-stranded reads per sample, which were mapped to the human transcriptome and quantified as transcripts per million mapped reads using the STAR aligner. Briefly, all sequencing data were uploaded to Illumina’s BaseSpace in real-time for downstream analysis of quality control. Raw Illumina (fastq.gz) sequencing files were downloaded from BaseSpace, and uploaded to Bluebee’s genomics analysis platform (https://www.bluebee.com) to align reads against the human genome and to obtain raw read counts.
Supplementary_files_format_and_content: Three csv file contains: (1) raw read counts, (2) normalized read counts with batch correction, and (3) normalized read counts with batch correction and cell type correction for every gene and every sample.

source_name: T2 (before meditation)_whole blood

extract_protocol:
The human blood samples collected into PAXgene Blood RNA Tubes were removed from the -80°C freezer and incubated overnight at room temperature before RNA extraction. RNA was harvested using the RNeasy Tissue Mini Kit (Qiagen), according to manufacturer’s instructions. RNA was reverse transcribed to complementary DNA (Lexogen QuantSeq 3′ FWD), and sequenced on a HiSeq 4000 instrument (Illumina).
RNA libraries were prepared for sequencing using  manufacturer’s instructions  (Lexogen QuantSeq 3′ FWD)

value: T2 (before meditation)

value: Whole Blood


title: 1111_T4

source_name: T4 (three months after meditation)_whole blood

value: T4 (three months after meditation)


title: 1036_T4


title: P1 mice fibroblasts ATAC-seq_rep3


title: 1083_T4

value: Data not available


title: 1128_T1

source_name: T1 (baseline)_whole blood

value: T1 (baseline)


title: 1036_T1


title: 1091_T3

source_name: T3 (after meditation) _whole blood

value: Female

value: T3 (after meditation)


title: 1081_T4


title: diabetic subject 5

value: oral/craniofacial bone


title: 1036_T2


title: P1 mice fibroblasts ATAC-seq_rep1


title: polyA Enriched RNA-sequencing_p28_CNTRL_CB_R1_5

description:
AA840_G1_p28_CNTRL_CB_R1_5
processed data file: p28_log2CPM.txt
processed data file: p28_FPKM.txt

value: Control


title: polyA Enriched RNA-sequencing_p28_Atm_CB_1

description:
AA841_G1_p28_Atm_CB_1
processed data file: p28_log2CPM.txt
processed data file: p28_FPKM.txt


title: 1118_T1

value: Male


title: polyA Enriched RNA-sequencing_p28_Atm_CB_3

description:
AA843_G1_p28_Atm_CB_3
processed data file: p28_log2CPM.txt
processed data file: p28_FPKM.txt

value: Cerebellum


title: polyA Enriched RNA-sequencing_p28_CNTRL_CB_R1_4

description:
AA839_G1_p28_CNTRL_CB_R1_4
processed data file: p28_log2CPM.txt
processed data file: p28_FPKM.txt


title: polyA Enriched RNA-sequencing_p28_Atm_CB_2

description:
AA842_G1_p28_Atm_CB_2
processed data file: p28_log2CPM.txt
processed data file: p28_FPKM.txt


title: 1111_T1


title: 1024_T4


title: 1051_T4


title: WT/DK210+ABRA-rep2

first: Bin

last: Li

address: Dong'an Road

department: Department of Physiology and Pathophysiology

institute: Fudan University

data_processing:
none provided by the submitter
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited text files include gene counts for every gene and every sample.

source_name: Heart

extract_protocol:
Total mRNAs were isolated from  3 month mice hearts using TRIZOL (Invitrogen) according to the directions. 1 ug of total RNA for the construction of sequencing libraries.
1 ug of total RNA was enriched for the Poly-A mRNA and reversed to cDNA, which was end-repaired, 3' ends adenylated, and barcoded with multiplex adapters.

treatment_protocol: CTnT-DK210 neonatal mice were intraperitoneal injected with control AAV9-Luciferase or AAV9-ABRA viruses. Heart tissues were collected at 3 months.

value: BALB/c

value: Heart

value: 3 Month


title: WT/DK210+ABRA-rep1


title: polyA Enriched RNA-sequencing_p28_CNTRL_CB_R1_2

description:
AA837_G1_p28_CNTRL_CB_R1_2
processed data file: p28_log2CPM.txt
processed data file: p28_FPKM.txt

value: Poly A mRNA Seq


title: WT/DK210+ABRA-rep3


title: 1126_T1


title: P1 mice fibroblasts ATAC-seq_rep2

value: skin fibroblast

value: untreated


title: 1056_T3


title: polyA Enriched RNA-sequencing_p28_Rnaseh2b_CB_5

description:
AA835_G1_p28_Rnaseh2b_CB_5
processed data file: p28_log2CPM.txt
processed data file: p28_FPKM.txt

value: RnaseH2B Nes-cre


title: 1138_T1

value: Whole Blood


title: 1110_T2

value: T2 (before meditation)


title: polyA Enriched RNA-sequencing_p28_CNTRL_CB_R1_1

description:
AA836_G1_p28_CNTRL_CB_R1_1
processed data file: p28_log2CPM.txt
processed data file: p28_FPKM.txt


title: WT/DK210-rep2


title: 1110_T4

value: T4 (three months after meditation)


title: polyA Enriched RNA-sequencing_p28_Rnaseh2b_CB_4

description:
AA834_G1_p28_Rnaseh2b_CB_4
processed data file: p28_log2CPM.txt
processed data file: p28_FPKM.txt


title: WT/DK210-rep3


title: polyA Enriched RNA-sequencing_p28_Rnaseh2b_CB_3

description:
AA833_G1_p28_Rnaseh2b_CB_3
processed data file: p28_log2CPM.txt
processed data file: p28_FPKM.txt


title: 1111_T2


title: 1032_T3


title: WT/DK210-rep1


title: 1034_T3


title: polyA Enriched RNA-sequencing_p28_CNTRL_CB_R1_3

description:
AA838_G1_p28_CNTRL_CB_R1_3
processed data file: p28_log2CPM.txt
processed data file: p28_FPKM.txt


title: 1006_T2


title: polyA Enriched RNA-sequencing_p28_Rnaseh2b_CB_2

description:
AA832_G1_p28_Rnaseh2b_CB_2
processed data file: p28_log2CPM.txt
processed data file: p28_FPKM.txt


title: 1118_T4


title: 1042_T3

value: Data not available


title: WT-rep2

value: wild type


title: polyA Enriched RNA-sequencing_p28_Rnaseh2b_CB_1

description:
AA831_G1_p28_Rnaseh2b_CB_1
processed data file: p28_log2CPM.txt
processed data file: p28_FPKM.txt


title: 1061_T3

value: Female

value: T3 (after meditation)


title: 1108_T2


title: Total Stranded RNA-sequencing_p5_Rnaseh2b_p53_CB_4

description:
AA58_G1_p5_Rnaseh2b_p53_CB_4
processed data file: p5_log2CPM.txt
processed data file: p5_FPKM.txt

value: RnaseH2B,p53 Nes-cre

value: Total RNA seq


title: METTL3-knock-out-2

city: Wuhan

first: Shan

last: Zhong

address: Donghu Road 185

institute: Wuhan University

data_processing:
Data were filtered using Trimmomatic version 0.36.
RNA-seq reads were aligned to the mm10 genome assembly using STAR version 2.7.
CircRNA were calculated using CircSplice.pl from Feng, J., et al., Molecular Cancer, 2019.
Counts were calculated using  HTSeq version 0.11.2.
Genome_build: mm10
Supplementary_files_format_and_content: raw read counts

source_name: embryonic stem cell

growth_protocol: Mouse embryonic stem cell E14TG2a cell was cultured with N2B27 medium as described.

extract_protocol:
Total RNA was extracted using TRNzol (Tiangen, China). rRNA was removed using QIAGEN QIAseq FastSelect RNA Removal Kit.
RNA library was generated using NEBNext Ultra Directional RNA Library Prep Kit.Sequencing was carried out on Illumina Hiseq Xten platform following the manufacturers instruction.

treatment_protocol: METTL3 knockout cell line was generated via CRISPR/Cas9 targeted disruption of the endogenous METTL3. METTL3 D395A mutation cell line was generated by CRISPR/Cas9-mediated target integration using homology-mediated end joining.

value: embryonic stem cell


title: 1096_T4


title: Total Stranded RNA-sequencing_p5_Rnaseh2b_p53_CB_3

description:
AA57_G1_p5_Rnaseh2b_p53_CB_3
processed data file: p5_log2CPM.txt
processed data file: p5_FPKM.txt

value: Cerebellum


title: 1032_T2

value: Male


title: 1034_T4


title: 1107_T2


title: 1061_T2


title: 1143_T4


title: WT-rep3

value: BALB/c

value: Heart

value: 3 Month


title: METTL3-knock-out-1


title: Total Stranded RNA-sequencing_p5_Rnaseh2b_p53_CB_2

description:
AA56_G1_p5_Rnaseh2b_p53_CB_2
processed data file: p5_log2CPM.txt
processed data file: p5_FPKM.txt


title: Total Stranded RNA-sequencing_p5_Rnaseh2b_p53_CB_1

description:
AA55_G1_p5_Rnaseh2b_p53_CB_1
processed data file: p5_log2CPM.txt
processed data file: p5_FPKM.txt


title: D395A-mutation-2

value: METTL3 D395A


title: 1110_T1

value: T1 (baseline)


title: D395A-mutation-1


title: 1096_T2

value: Whole Blood


title: 1143_T3


title: 1042_T1


title: 1099_T4


title: WT-1

value: WT


title: WT-2


title: 1022_T1


title: Total Stranded RNA-sequencing_p5_Rnaseh2b_Atm_CB_3

description:
AA53_G1_p5_Rnaseh2b_Atm_CB_3
processed data file: p5_log2CPM.txt
processed data file: p5_FPKM.txt

value: RnaseH2B,Atm Nes-cre


title: 1005_T2

value: T2 (before meditation)


title: WT-rep1

value: wild type


title: Total Stranded RNA-sequencing_p5_Rnaseh2b_Atm_CB_4

description:
AA54_G1_p5_Rnaseh2b_Atm_CB_4
processed data file: p5_log2CPM.txt
processed data file: p5_FPKM.txt


title: 1096_T1

value: Female


title: 1032_T1


title: MM181_S8_L004_R1_001

city: Moscow

first: Daniil

last: Nikitin

address: Miklucho-Maklaya

country: Russia

institute: Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry

data_processing:
RNA sequencing FASTQ files were processed with STAR aligner in ‘GeneCounts’ mode with the Ensembl human transcriptome annotation
Ensembl gene IDs were converted to HGNC gene symbols using Complete HGNC dataset (https://www.genenames.org, database version of July 13, 2017
Additional quality control (QC) metrics for obtained data were generated using NCBI MAGIC software
Genome_build: Build version GRCh38 and transcript annotation GRCh38.89
Supplementary_files_format_and_content: DESeq2 normalized read counts

source_name: multiple myeloma

extract_protocol:
For RNA extraction, cells were resuspended in TRI Reagent (MRC) and then Direct-zol RNA MiniPrep (Zymo Research) was used for the RNA extraction. RNA was quantified using Nanodrop (Thermo Fisher Scientific), ethanol-precipitated, and stored in liquid nitrogen until sequencing.
For library preparation, RNA Integrity Number (RIN) was measured using Agilent 2100 bioanalyzer. Agilent RNA 6000 Nano or Qubit RNA Assay Kits were used to measure RNA concentration. For depletion of ribosomal RNA, we used KAPA RNA Hyper with RiboErase Kit (KAPA Biosystems). Different adaptors were used for multiplexing samples in one sequencing run. Library concentrations and quality were measured using Qubit ds DNA HS Assay kit (Life Technologies) and Agilent Tapestation (Agilent).

value: multiple myeloma

value: male

value: VCD (bortezomib + cyclophosphamide + dexamethasone) 4


title: 1128_T3

value: T3 (after meditation)


title: Total Stranded RNA-sequencing_p5_Rnaseh2b_Atm_CB_1

description:
AA51_G1_p5_Rnaseh2b_Atm_CB_1
processed data file: p5_log2CPM.txt
processed data file: p5_FPKM.txt

value: Cerebellum

value: Total RNA seq


title: 1051_T3

value: Male


title: 1006_T4

value: T4 (three months after meditation)


title: MM180_S7_L004_R1_001


title: MM179_S6_L004_R1_001

value: female

value: VCD (bortezomib + cyclophosphamide + dexamethasone) 6


title: Total Stranded RNA-sequencing_p5_Atm_CB_3

description:
AA50_G1_p5_Atm_CB_3
processed data file: p5_log2CPM.txt
processed data file: p5_FPKM.txt

value: Atm Nes-cre


title: 1126_T2

value: Whole Blood


title: Total Stranded RNA-sequencing_p5_Atm_CB_1

description:
AA48_G1_p5_Atm_CB_1
processed data file: p5_log2CPM.txt
processed data file: p5_FPKM.txt


title: 1107_T4


title: 1010_T1

value: T1 (baseline)


title: Total Stranded RNA-sequencing_p5_p53_CB_3

description:
AA47_G1_p5_p53_CB_3
processed data file: p5_log2CPM.txt
processed data file: p5_FPKM.txt

value: p53 Nes-cre


title: MM178_S5_L004_R1_001

value: VCD (bortezomib + cyclophosphamide + dexamethasone) 7


title: 1108_T3


title: MM174_S44_L008_R1_001

value: VCD (bortezomib + cyclophosphamide + dexamethasone) 5


title: 1126_T4


title: MM173_S3_L004_R1_001


title: Total Stranded RNA-sequencing_p5_Rnaseh2b_Atm_CB_2

description:
AA52_G1_p5_Rnaseh2b_Atm_CB_2
processed data file: p5_log2CPM.txt
processed data file: p5_FPKM.txt

value: RnaseH2B,Atm Nes-cre


title: Total Stranded RNA-sequencing_p5_p53_CB_2

description:
AA46_G1_p5_p53_CB_2
processed data file: p5_log2CPM.txt
processed data file: p5_FPKM.txt


title: 1091_T2

value: Female

value: T2 (before meditation)


title: 1108_T1


title: 1034_T1


title: MM175_S4_L004_R1_001

value: multiple myeloma


title: 1107_T1


title: Total Stranded RNA-sequencing_p5_p53_CB_1

description:
AA45_G1_p5_p53_CB_1
processed data file: p5_log2CPM.txt
processed data file: p5_FPKM.txt


title: 1126_T3

value: T3 (after meditation)


title: 1091_T1


title: Total Stranded RNA-sequencing_p5_Atm_CB_2

description:
AA49_G1_p5_Atm_CB_2
processed data file: p5_log2CPM.txt
processed data file: p5_FPKM.txt

value: Cerebellum


title: 1056_T1


title: Total Stranded RNA-sequencing_p5_Rnaseh2b_CB_3

description:
AA44_G1_p5_Rnaseh2b_CB_3
processed data file: p5_log2CPM.txt
processed data file: p5_FPKM.txt

value: RnaseH2B Nes-cre

value: Total RNA seq


title: 1005_T3


title: 1128_T4

value: T4 (three months after meditation)


title: 1091_T4


title: 1010_T3

value: Male


title: 1110_T3


title: MM170_S42_L008_R1_001

value: male


title: Total Stranded RNA-sequencing_p5_Rnaseh2b_CB_1

description:
AA42_G1_p5_Rnaseh2b_CB_1
processed data file: p5_log2CPM.txt
processed data file: p5_FPKM.txt


title: MM169_S17_L004_R1_001

value: female

value: VCD (bortezomib + cyclophosphamide + dexamethasone) 9


title: Total Stranded RNA-sequencing_p5_CNTRL_CB_3

description:
AA41_G1_p5_CNTRL_CB_3
processed data file: p5_log2CPM.txt
processed data file: p5_FPKM.txt

value: Control


title: 1051_T1

value: T1 (baseline)

value: Whole Blood


title: MM167_S19_L006_R1_001

value: VCD (bortezomib + cyclophosphamide + dexamethasone) 6


title: 1138_T2


title: 1056_T4


title: 1143_T2


title: Total Stranded RNA-sequencing_p5_CNTRL_CB_1

description:
AA39_G1_p5_CNTRL_CB_1
processed data file: p5_log2CPM.txt
processed data file: p5_FPKM.txt


title: MM166_S18_L006_R1_001

value: VCD (bortezomib + cyclophosphamide + dexamethasone) 5


title: Total Stranded RNA-sequencing_p5_CNTRL_CB_2

description:
AA40_G1_p5_CNTRL_CB_2
processed data file: p5_log2CPM.txt
processed data file: p5_FPKM.txt


title: 1006_T3


title: 1143_T1

value: Female


title: 1096_T3


title: 1062_T2

value: T2 (before meditation)


title: Total Stranded RNA-sequencing_9wk_Rnaseh2b_CB_7

description:
AA58_G1_9wk_Rnaseh2b_CB_7
processed data file: 9wk_log2CPM.txt
processed data file: 9wk_FPKM.txt

value: 9 weeks


title: MM172_S43_L008_R1_001

value: multiple myeloma


title: MM171_S2_L004_R1_001


title: MM163_S10_L004_R1_001


title: Total Stranded RNA-sequencing_p5_Rnaseh2b_CB_2

description:
AA43_G1_p5_Rnaseh2b_CB_2
processed data file: p5_log2CPM.txt
processed data file: p5_FPKM.txt

value: Cerebellum


title: 1061_T1


title: Total Stranded RNA-sequencing_9wk_Rnaseh2b_CB_6

description:
AA57_G1_9wk_Rnaseh2b_CB_6
processed data file: 9wk_log2CPM.txt
processed data file: 9wk_FPKM.txt

value: RnaseH2B Nes-cre


title: 1128_T2


title: 1056_T2


title: MM162_S16_L004_R1_001


title: MM161_S11_L007_R1_001

value: VCD (bortezomib + cyclophosphamide + dexamethasone) 3


title: 1062_T1


title: Total Stranded RNA-sequencing_9wk_Rnaseh2b_CB_5

description:
AA56_G1_9wk_Rnaseh2b_CB_5
processed data file: 9wk_log2CPM.txt
processed data file: 9wk_FPKM.txt

value: Total RNA seq


title: 1081_T3

value: Male

value: T3 (after meditation)


title: Total Stranded RNA-sequencing_9wk_Rnaseh2b_CB_4

description:
AA55_G1_9wk_Rnaseh2b_CB_4
processed data file: 9wk_log2CPM.txt
processed data file: 9wk_FPKM.txt


title: MM160_S15_L004_R1_001

value: female

value: VCD (bortezomib + cyclophosphamide + dexamethasone) 10


title: MM165_S41_L008_R1_001

value: male


title: Total Stranded RNA-sequencing_9wk_CNTRL_CB_7

description:
AA53_G1_9wk_CNTRL_CB_7
processed data file: 9wk_log2CPM.txt
processed data file: 9wk_FPKM.txt

value: Control


title: MM159_S40_L007_R1_001


title: 1099_T3

value: Whole Blood


title: Total Stranded RNA-sequencing_9wk_CNTRL_CB_6

description:
AA52_G1_9wk_CNTRL_CB_6
processed data file: 9wk_log2CPM.txt
processed data file: 9wk_FPKM.txt


title: 1111_T3


title: 1022_T2


title: MM158_S39_L007_R1_001

value: VCD (bortezomib + cyclophosphamide + dexamethasone) 4


title: 1010_T2


title: 1034_T2


title: 1061_T4

value: T4 (three months after meditation)


title: 1081_T1

value: T1 (baseline)


title: Total Stranded RNA-sequencing_9wk_CNTRL_CB_4

description:
AA50_G1_9wk_CNTRL_CB_4
processed data file: 9wk_log2CPM.txt
processed data file: 9wk_FPKM.txt


title: MM156_S38_L007_R1_001

value: VCD (bortezomib + cyclophosphamide + dexamethasone) 5


title: 1099_T2

value: Female

value: T2 (before meditation)


title: Total Stranded RNA-sequencing_9wk_CNTRL_CB_5

description:
AA51_G1_9wk_CNTRL_CB_5
processed data file: 9wk_log2CPM.txt
processed data file: 9wk_FPKM.txt

value: Cerebellum

value: 9 weeks


title: MM155_S37_L007_R1_001

value: multiple myeloma

value: VCD (bortezomib + cyclophosphamide + dexamethasone) 8


title: 1138_T4


title: Total Stranded RNA-sequencing_9wk_CNTRL_CB_3

description:
AA16_G1_9wk_CNTRL_CB_3
processed data file: 9wk_log2CPM.txt
processed data file: 9wk_FPKM.txt

value: Total RNA seq


title: MM154_S20_L006_R1_001

value: PAD (bortezomib + doxorubicin + dexamethasone) 4


title: 1010_T4

value: Male


title: 1118_T2


title: Total Stranded RNA-sequencing_9wk_CNTRL_CB_2

description:
AA15_G1_9wk_CNTRL_CB_2
processed data file: 9wk_log2CPM.txt
processed data file: 9wk_FPKM.txt


title: 1022_T3

value: T3 (after meditation)


title: Total Stranded RNA-sequencing_9wk_CNTRL_CB_1

description:
AA14_G1_9wk_CNTRL_CB_1
processed data file: 9wk_log2CPM.txt
processed data file: 9wk_FPKM.txt


title: MM153_S17_L006_R1_001

value: female

value: PAD (bortezomib + doxorubicin + dexamethasone) 4, VCD (bortezomib + cyclophosphamide + dexamethasone) 2


title: MM152_S36_L007_R1_001


title: 1099_T1

value: Whole Blood


title: 1108_T4


title: 1036_T3


title: 1051_T2


title: Total Stranded RNA-sequencing_9wk_Rnaseh2b_CB_2

description:
AA12_G1_9wk_Rnaseh2b_CB_2
processed data file: 9wk_log2CPM.txt
processed data file: 9wk_FPKM.txt

value: RnaseH2B Nes-cre


title: MM150_S34_L007_R1_001

value: PAD (bortezomib + doxorubicin + dexamethasone) 2, VCD (bortezomib + cyclophosphamide + dexamethasone) 2


title: 1138_T3


title: 1118_T3


title: 1107_T3


title: MM148_S16_L006_R1_001

value: male

value: PAD (bortezomib + doxorubicin + dexamethasone) 6


title: 1062_T3


title: MM147_S14_L004_R1_001

value: VCD (bortezomib + cyclophosphamide + dexamethasone) 6


title: 1149_T4

value: Female

value: T4 (three months after meditation)


title: 1022_T4


title: 1149_T3


title: MM146_S32_L007_R1_001

value: VCD (bortezomib + cyclophosphamide + dexamethasone) 12


title: 1149_T1

value: T1 (baseline)


title: 1149_T2

value: T2 (before meditation)


title: Pl9_Male_SPF_Micr_1

city: Freiburg

first: Roman

last: Sankowski

address: Breisacher Str. 64

department: Institute of Neuropathology

institute: University of Freiburg Medical Center

description: library of 192

data_processing:
For image aquisition, intensity extraction and basecalling HiSeq Control Software 2.0.2, RTA 2.4.11 / Recipe Fragment 2.0.0.2
Paired end reads were aligned to the transcriptome using bwa (version 0.6.2-r126) with default parameters. The transcriptome contained all gene models based on the mouse ENCODE VM9 release downloaded from the UCSC genome browser comprising 57,207 isoforms derived from 57,207 gene loci with 57,114 isoforms mapping to fully annotated chromosomes (1 to 19, X, Y, M). All isoforms of the same gene were merged to a single gene locus. Furthermore, gene loci overlapping by >75% were merged to larger gene groups. This procedure resulted in 34,111 gene groups.
The right mate of each read pair was mapped to the ensemble of all gene loci and to the set of 92 ERCC spike-ins in sense direction. Reads mapping to multiple loci were discarded. The left read contains the barcode information: the first six bases correspond to the cell specific barcode followed by six bases representing the unique molecular identifier (UMI). The remainder of the left read contains a poly(T) stretch. The left read was not used for quantification. For each cell barcode, the number of UMIs per transcript was counted and aggregated across all transcripts derived from the same gene locus.
Based on binomial statistics, the number of observed UMIs was converted into transcript counts (Gruen et al., 2014).
Genome_build: ENCODE VM9
Supplementary_files_format_and_content: CSV files, columns represent each cell barcode (total barcodes used = 192), rows represent the geneid and the values in the file are the quantified number of transcripts.
Supplementary_files_format_and_content: prdata.RData: concatenated counts file of all cells
Supplementary_files_format_and_content: seurat_all_without_doublets.RData: seurat object of all cells
Supplementary_files_format_and_content: seurat_cp.RData: seurat object of choroid plexus cells
Supplementary_files_format_and_content: seurat_men.RData: seurat object of leptomeningeal cells
Supplementary_files_format_and_content: seurat_micr.RData: seurat object of parenchymal cells
Supplementary_files_format_and_content: seurat_pvm.RData: seurat object of perivascular space cells
Supplementary_files_format_and_content: all_cell_metadata.csv: metadata of all cells
Supplementary_files_format_and_content: cp_cell_metadata.csv: metadata of choroid plexus cells
Supplementary_files_format_and_content: men_cell_metadata.csv: metadata of leptomeningeal cells
Supplementary_files_format_and_content: micr_cell_metadata.csv: metadata of parenchymal microglia cells
Supplementary_files_format_and_content: pvm_cell_metadata.csv: metadata of perivascular space cells

source_name: Cortex

growth_protocol: SPF mouse facility

extract_protocol:
Leptomeninges were dissected from brains to obtain separate samples of the leptomeninges, parenchyma and perivascular space. All choroid plexuses were removed from the ventricles. Myelin was removed from the homogenized parenchyma and perivascular space using a 37 % Percoll gradient (Sigma-Aldrich) at 800 g (4°C for 30 min). Cell suspensions from the choroid plexuses and leptomeninges were obtained through mechanical dissociation through a 70-μm cell strainer. Cell suspensions were stained using the Fixable Viability Dye eFluor 780 (1:1000, eBioscience, San Diego, USA) followed by incubation with Fc receptor blocking antibody CD16/CD32 (BD Bioscience, Heidelberg, Germany). Afterwards, cells were incubated with primary antibodies directed against CD11b (M1/70), CD45 (30-F11; eBioscience, San Diego, USA), CD206 (C068C2), B220 (RA3-6B2; BioLegend), CD3 (ASP34-2), Ly6C (AL-21) and Ly6G (1A8; BD Bioscience, Heidelberg, Germany) at a dilution of 1:200 at 4°C for 30 min. Viable single cells from n ≥ 5 animals per condition were pooled and sorted with a MoFlo Astrios (Beckman Coulter, Krefeld, Germany) into 384-well plates and further processed.
As described in mCEL-Seq2 protocol (Hashimshony et al. 2016 and Herman et al. 2018)
Adapted from TruSeq Small RNA Library Preparation Protocol

treatment_protocol: Mice housed under Specific pathogen-free and Germ-free conditions

value: Parenchyma - microglia


title: Pl9_Male_GF_Micr_2

description: library of 192


title: MM145_S10_L007_R1_001

value: multiple myeloma

value: VCD (bortezomib + cyclophosphamide + dexamethasone) 8


title: 1148_T4


title: Pl8_Male_Micr_SPF_3

description: library of 192

value: Male


title: MM144_S13_L004_R1_001

value: female

value: VCD (bortezomib + cyclophosphamide + dexamethasone) 7


title: 1148_T2

value: Whole Blood


title: Total Stranded RNA-sequencing_9wk_Rnaseh2b_CB_3

description:
AA13_G1_9wk_Rnaseh2b_CB_3
processed data file: 9wk_log2CPM.txt
processed data file: 9wk_FPKM.txt

value: Cerebellum

value: 9 weeks

value: RnaseH2B Nes-cre

value: Total RNA seq


title: 1148_T1


title: 1147_T4


title: Pl8_Male_Micr_GF_4

description: library of 192


title: Pl6_Fem_SPF_Men_7

description: library of 192

value: Leptomeninges


title: 1147_T3

value: T3 (after meditation)


title: MM141_S12_L004_R1_001

value: male

value: VCD (bortezomib + cyclophosphamide + dexamethasone) 2, PAD (bortezomib + doxorubicin + dexamethasone) 2


title: Total Stranded RNA-sequencing_9wk_RnaseH2B_CB_1

description:
AA11_G1_9wk_Rnaseh2b_CB_1
processed data file: 9wk_log2CPM.txt
processed data file: 9wk_FPKM.txt


title: 1147_T2


title: 1147_T1

value: T1 (baseline)


title: MM140_S31_L007_R1_001

value: PAD (bortezomib + doxorubicin + dexamethasone) 2, VCD (bortezomib + cyclophosphamide + dexamethasone) 3


title: MM139_S11_L004_R1_001

value: VCD (bortezomib + cyclophosphamide + dexamethasone) 2, PAD (bortezomib + doxorubicin + dexamethasone) 1


title: 1145_T4

value: Female

value: T4 (three months after meditation)


title: Pl5_Fem_SPF_Men_5

description: library of 192


title: MM138_S30_L006_R1_001

value: multiple myeloma

value: PAD (bortezomib + doxorubicin + dexamethasone) 4, VCD (bortezomib + cyclophosphamide + dexamethasone) 3


title: 1145_T2

value: T2 (before meditation)


title: 1145_T1

value: Whole Blood


title: 1145_T3


title: MM137_S29_L006_R1_001

value: female

value: PAD (bortezomib + doxorubicin + dexamethasone) 2, VCD (bortezomib + cyclophosphamide + dexamethasone) 6


title: 1141_T4

value: Male


title: 1141_T3


title: 1141_T2


title: Pl5_Fem_GF_Men_6

description: library of 192


title: Pl6_Fem_GF_Men_8

description: library of 192


title: MM136_S28_L006_R1_001

value: PAD (bortezomib + doxorubicin + dexamethasone) 4


title: 1148_T3


title: 1141_T1


title: Pl4_Fem_PVM_SPF_5

description: library of 192

value: Parenchyma - perivascular space


title: Pl4_Fem_PVM_GF_6

description: library of 192


title: 1140_T4


title: 1140_T3

value: T3 (after meditation)


title: Pl3_Fem_SPF_PVM

description: library of 192


title: MM134_S15_L006_R1_001

value: PAD (bortezomib + doxorubicin + dexamethasone) 5


title: MM135_S10_L003_R1_001

value: male

value: VCD (bortezomib + cyclophosphamide + dexamethasone) 8


title: Pl3_Fem_GF_PVM

description: library of 192


title: 1140_T1

value: T1 (baseline)


title: Pl2_Fem_Micr_SPF

description: library of 192

value: Parenchyma - microglia


title: 1137_T4


title: 1137_T3


title: 1139_T1

value: Female


title: Pl2_Fem_Micr_GF_2

description: library of 192


title: MM132_S26_L006_R1_001

value: PAD (bortezomib + doxorubicin + dexamethasone) 4, VCD (bortezomib + cyclophosphamide + dexamethasone) 1


title: MM131_S46_L008_R1_001

value: multiple myeloma

value: VCD (bortezomib + cyclophosphamide + dexamethasone) 7


title: 1137_T2

value: T2 (before meditation)


title: 1135_T4

value: T4 (three months after meditation)

value: Whole Blood


title: 1135_T3


title: MM129_S14_L006_R1_001


title: 1137_T1


title: Pl14_Male_SPF_CP

description: library of 192

source_name: lateral 3rd and 4th ventricle

value: Choroid plexus


title: MM130_S25_L006_R1_001


title: MM128_S24_L006_R1_001

value: female

value: VCD (bortezomib + cyclophosphamide + dexamethasone) 5


title: Pl13_Male_SPF_Men_5

description: library of 192

value: Leptomeninges

value: Male


title: 1135_T2


title: MM126_S23_L006_R1_001

value: VCD (bortezomib + cyclophosphamide + dexamethasone) 6


title: Pl14_Male_GF_CP_8

description: library of 192


title: 1134_T3

value: T3 (after meditation)


title: 1140_T2


title: 1134_T4


title: 1135_T1


title: Pl13_Male_GF_Men_6

description: library of 192


title: 1133_T3


title: 1134_T2


title: Pl11_Male_SPF_PVM_3

description: library of 192

value: Parenchyma - perivascular space


title: MM122_S22_L006_R1_001

value: VCD (bortezomib + cyclophosphamide + dexamethasone) 4


title: 1133_T2


title: 1133_T1

value: T1 (baseline)


title: MM121_2_S19_L004_R1_001

value: male

value: VCD (bortezomib + cyclophosphamide + dexamethasone) 3


title: 1131_T4


title: 1131_T2


title: Pl10_Male_PVM_SPF

description: library of 192


title: 1127_T4

value: Female


title: MM120_S9_L007_R1_001

value: multiple myeloma


title: Pl10_Male_PVM_GF

description: library of 192


title: MM118_S8_L007_R1_001

value: PAD (bortezomib + doxorubicin + dexamethasone) 4


title: 1127_T3


title: MM117_S50_L008_R1_001

value: PAD (bortezomib + doxorubicin + dexamethasone) 4, VCD (bortezomib + cyclophosphamide + dexamethasone) 8


title: 1133_T4

value: T4 (three months after meditation)

value: Whole Blood


title: MM123_S9_L003_R1_001

value: female

value: VCD (bortezomib + cyclophosphamide + dexamethasone) 10


title: 1127_T2

value: T2 (before meditation)


title: Pl1_Fem_GF_Micr

description: library of 192

value: Parenchyma - microglia


title: 1131_T3

value: Male


title: MM116_S7_L003_R1_001

value: VCD (bortezomib + cyclophosphamide + dexamethasone) 2, PAD (bortezomib + doxorubicin + dexamethasone) 4


title: 1127_T1


title: 1124_T3

value: T3 (after meditation)


title: MM115_S13_L006_R1_001

value: PAD (bortezomib + doxorubicin + dexamethasone) 4, VCD (bortezomib + cyclophosphamide + dexamethasone) 2


title: Male_CP_SPF

description: library of 192

value: Choroid plexus


title: Male_CP_GF

description: library of 192


title: 1124_T4


title: 1124_T2


title: Pl11_Male_GF_PVM_4

description: library of 192

value: Parenchyma - perivascular space


title: 1123_T4


title: MM111_S21_L006_R1_001

value: male


title: Female_CP_SPF

description: library of 192

value: Female


title: 1123_T3


title: Female_CP_GF

description: library of 192


title: 1131_T1

value: T1 (baseline)


title: 1123_T2


title: Pl1_Fem_SPF_Micr

description: library of 192


title: 1122_T2


title: 1122_T3


title: MM108_S1_L001_R1_001

value: multiple myeloma

value: PAD (bortezomib + doxorubicin + dexamethasone) 3, VCD (bortezomib + cyclophosphamide + dexamethasone) 1; then supportive treatment - VCD  (bortezomib + cyclophosphamide + dexamethasone) 8


title: MM109_S20_L005_R1_001


title: 1121_T4

value: T4 (three months after meditation)


title: MM107_S19_L005_R1_001

value: PAD (bortezomib + doxorubicin + dexamethasone) 3, VCD (bortezomib + cyclophosphamide + dexamethasone) 1


title: 1123_T1

value: Whole Blood


title: 1121_T3


title: 1124_T1


title: 1121_T1


title: 1120_T3


title: 1121_T2


title: MM104_2_S18_L004_R1_001

value: female

value: PAD (bortezomib + doxorubicin + dexamethasone) 4,  VCD (bortezomib + cyclophosphamide + dexamethasone) 1


title: 1120_T1


title: all 0h-3

city: Hangzhou

first: Haiwen

last: Lu

address: zhejiang A&F university, Lin 'an District, Hangzhou City, Zhejiang Province, China

institute: zhejiang A&F university

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data(clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30, GC-content and sequence duplication level of the clean data were  calculated. All the downstream analyses were based on clean data with high quality.
The adaptor sequences and low-quality sequence reads were removed from the data sets. Raw sequences were transformed into clean reads after data processing. These clean reads were then mapped to the reference genome sequence. Only reads with a perfect match or one mismatch were further analyzed and annotated based on the  reference genome. Hisat2 tools soft were used to map with reference genome.
Gene function was annotated based on the following databases:Nr (NCBI non-redundant protein sequences)；Nt (NCBI non-redundant nucleotide sequences)；Pfam (Protein family)；KOG/COG (Clusters of Orthologous Groups of proteins)；Swiss-Prot (A manually annotated and reviewed protein sequence database)；KO (KEGG Ortholog database)；GO(Gene Ontology).
we investigated the global gene expression depending on the different time points in the same stress treatment and sequencing reads were analysed with DESeq2 R package24 (the significantly differential expression threshold was set as FDR≥0.01 FC≥|2|).
Genome_build: Bamboo genome (Version 2)
Supplementary_files_format_and_content: Matrix table with FPKM values for each Sample
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Phyllostachys edulis

source_name: leaves

growth_protocol: The moso bamboo seedlings culture in the nutrient solution 1/4 Hoagland(25±2 °C, 70±10% relative humidity and natural photoperiods).

extract_protocol:
Total RNA of Moso bamboo was extracted using RNAprep Pure Plant Plus Kit (No. DP441; Polysaccharides & Polyphenolics-rich; Tiangen Co. Ltd, Beijing, China; http://www.tiangen.com/).
A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations. Library construction was prepared using the TruSeq NEBNext UltraTM RNA Library Prep Kit, Illumina (NEB, USA). The mRNA was purified from total RNA using poly-T oligo-attached magnetic beads and mRNA was fragmented using divalent cations in higher temperature in NEBNext First Strand Synthesis Reaction Buffer (5X). Using the random hexamer primer and M-MuLV Reverse Transcriptase, the first-strand cDNA was synthesized. Second strand cDNA synthesis was subsequently synthesized using DNA Polymerase I and RNase H. overhangs were converted into blunt ends using exonuclease activity. The NEBNext Adaptor containing a hairpin loop structure were ligated to prepare for hybridization. Further, the library fragments were purified with the AMPure XP system (Beckman Coulter, Beverly, USA) to select the cDNA fragments of 240 bp in length. Then 3 μl USER Enzyme (NEB, USA) was added to the adaptor-ligated, size-selected cDNA and incubated at 37°C for 15 min followed by denaturation 95°C for 5 min before PCR. Using Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer, PCR was performed. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

treatment_protocol: We used a nutrient solution containing 200 mM NaCl and 25% PEG for salinity and drought stress, respectively. Further, we used a nutrient solution containing SA and ABA with 1 mM and 1 μM concentrations for SA and ABA treatments, respectively.

value: leaves

tag: agent

value: all

tag: time point


title: all 0h-2


title: 1120_T2

value: T2 (before meditation)


title: WT_ScrAB_B

city: Athens

first: Ronan

middle: Kevin

last: Carroll

state: OHIO

address: 107 Irvine Hall

department: Biological Sciences

institute: Ohio University

description: total RNA, rRNA-depleted

data_processing:
Raw data files (.fastq) were imported into the CLC Genomics Workbench software platform for analysis
Reads corresponding to ribosomal RNA were filtered out and removed
Expression values were caculated using the "RNA-Seq Analysis" function in CLC Genomics Workbench
Replicate data sets were grouped and normalized using "quantile normalization"
Normalized expression values were exported into excel files
Genome_build: The reference genome used for the analysis was based on NC_007793 and included annotations for sRNA genes (https://dx.doi.org/10.6084/m9.figshare.2061132.v1)
Supplementary_files_format_and_content: Expression values for each gene were initially calculated as RPKM values. The RPKM values were then normalized and the "Normalized expression values" are presented in the excel files

organism: Staphylococcus aureus

source_name: Bacterial cells, pelleted

growth_protocol: Strains were grown in TSB medium at 37°C with shaking

extract_protocol:
Total bacterial RNA was isolated utilizing the Qiagen RNeasy mini kit and contaminating DNA was removed by treatment with Ambion DNA-free
Library construction was performed using the Illumina TruSeq Stranded mRNA Sample Prep Kit

treatment_protocol: Samples were stored at -80°C prior to RNA extraction

value: wild-type

tag: plasmid

tag: growth medium

value: TSB

tag: temperature


title: ABA 24h-3

value: ABA


title: WT_ScrAB_A

description: total RNA, rRNA-depleted


title: ABA 24h-2


title: all 0h-4


title: 1119_T1

tag: treatment


title: 1119_T3

value: T3 (after meditation)


title: 1119_T2


title: ABA 24h-1


title: WT_EV_C

description: total RNA, rRNA-depleted

tag: genotype


title: WT_EV_B

description: total RNA, rRNA-depleted


title: all 0h-1

tag: tissue


title: ABA 3h-3


title: ABA 3h-2


title: 1116_T4


title: 1117_T3


title: 1117_T1


title: 1117_T2


title: WT_EV_A

description: total RNA, rRNA-depleted


title: 1115_T4


title: 1116_T2


title: SA 24h-3

value: SA


title: 1115_T3

value: Female


title: CD11c+_3

city: Kodaira

first: Kimitoshi

last: Kimura

state: Tokyo

address: 4-1-1 Ogawahigashi

department: Department of Immunology, National Institute of Neuroscience

institute: National Center of Neurology and Psychiatry

hyb_protocol: According to Nanostring protocol

scan_protocol: According to Nanostring protocol

data_processing: The data were analyzed with advanced analysis function in nSolver software. Ncount of each RNA was normalized using the geometric mean of 11 housekeeping genes, EEF1G, RPL19, TBP, SDHA, POLR2A, PPIA, OAZ1, G6PD, ABCF1, TUBB, and POLR1B, which were selected by nCounter algorhythm. The genes, which were detected above the low count threshold level for less than 25% of the samples, were excluded from the analysis. Next, the normalized data were used for further analysis with iDEP software.

label: biotin

source_name: CD11c+CD27- B cells, patient 3

label_protocol: According to Nanostring protocol

extract_protocol: B cell populations were sorted for nCounter analysis with GX Human Immunology V2 kit (NanoString Technologies). Cell lysate was prepared with RLT buffer (QIAGEN), and used as input material according to the manufacturer’s protocol.

value: multiple sclerosis

tag: gender

value: male

tag: source tissue

value: peripheral blood


title: 1115_T2


title: CD11c+_2

source_name: CD11c+CD27- B cells, patient 2


title: 1116_T3


title: CD11c+_1

source_name: CD11c+CD27- B cells, patient 1


title: 1114_T4

value: T4 (three months after meditation)


title: 1114_T2


title: SA 24h-1


title: DP_3

source_name: CD11c+CD27+ B cells, patient 3


title: 1114_T1

value: T1 (baseline)


title: 1119_T4

value: Whole Blood


title: 1114_T3


title: ABA 3h-1


title: 1113_T4


title: SA 3h-2


title: SA 3h-3


title: 1113_T2


title: SA 24h-2


title: 1113_T3


title: 1113_T1


title: SA 3h-1


title: DP_2

source_name: CD11c+CD27+ B cells, patient 2

value: female


title: 1115_T1


title: DP_1

source_name: CD11c+CD27+ B cells, patient 1


title: 1117_T4


title: 1112_T3

value: Male


title: CD27+_2

source_name: CD11c-CD27+ B cells, patient 2


title: NaCl 24h-2

value: leaves

value: NaCl


title: NaCl 24h-3


title: 1109_T3


title: 1112_T1


title: 1109_T2

source_name: T2 (before meditation)_whole blood

value: T2 (before meditation)


title: CD27+_1

source_name: CD11c-CD27+ B cells, patient 1


title: NaCl 3h-3


title: 1109_T1

source_name: T1 (baseline)_whole blood


title: DN_3

source_name: CD11c-CD27- B cells, patient 3


title: 1106_T4

source_name: T4 (three months after meditation)_whole blood


title: 1106_T3

source_name: T3 (after meditation) _whole blood


title: DN_2

source_name: CD11c-CD27- B cells, patient 2


title: 1112_T4


title: CD27+_3

source_name: CD11c-CD27+ B cells, patient 3


title: 1106_T2


title: NaCl 3h-2

source_name: leaves


title: DN_1

source_name: CD11c-CD27- B cells, patient 1


title: 1106_T1


title: 1105_T3


title: NaCl 3h-1


title: 1112_T2


title: NaCl 24h-1


title: 1105_T2


title: 1104_T2


title: peg 24h-2

value: peg


title: 1104_T4


title: 1104_T1


title: 1104_T3


title: 1102_T3


title: peg 24h-1


title: 1102_T2


title: 1100_T4


title: peg 24h-3


title: 1100_T3


title: peg 3h-2


title: 1100_T1


title: 1097_T4


title: peg 3h-1


title: 1097_T3


title: 1097_T2


title: 1097_T1


title: 1100_T2


title: CK 24h-3

value: CK


title: atg5_T30_C1_HN

city: Versailles

first: Celine

last: Masclaux-Daubresse

address: Route de Saint Cyr

country: France

institute: IJPB INRAE

description: Gene expression data from atg5 rosette, in high nitrate at 60 days after sowing

hyb_protocol: Microarray hybridations were performed at RIKEN Plant Science Center (Yokohama Japan) using ATH1 microarrays according to manufacturer's instructions.

scan_protocol: standard Affymetrix protocol

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: atg5 60 days growth under HN culture 1

label_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

growth_protocol: Plants were grown under low nitrate (2 mM) or high nitrate (10 mM) for 30 and 60 days after sowing in short days (160 micromol.m-2.s-1; 8 h light, 16 h dark) (www.plantcell.org/cgi/doi/10.1105/tpc.114.124677)

value: atg5 mutant

tag: organ

value: whole rosette

tag: nutrition

value: high nitrate


title: CK 24h-2


title: 1095_T4

tag: Sex


title: 1095_T2


title: CK 24h-1


title: Col-0_T30_C2_HN

description: Gene expression data from wild type rosette, in high nitrate at 60 days after sowing

source_name: Col-0 60 days growth under HN culture 2

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

value: Col-0 wild type


title: peg 3h-3


title: Col-0_T30_C1_HN

source_name: Col-0 60 days growth under HN culture 1


title: atg5_T60_C2_LN

description: Gene expression data from atg5 rosette, in low nitrate at 60 days after sowing

source_name: atg5 60 days growth under LN culture 2

value: low nitrate


title: 1093_T3

value: T3 (after meditation)


title: 1095_T1


title: CK 3h-3


title: 1092_T4

value: Female


title: atg5_T30_C2_HN

source_name: atg5 60 days growth under HN culture 2


title: atg9_T60_C2_LN

description: Gene expression data from atg9 rosette, in low nitrate at 60 days after sowing

source_name: atg9 60 days growth under LN culture 2

value: atg9 mutant


title: 1092_T3


title: Col-0_T60_C2_LN

description: Gene expression data from wild type rosette, in low nitrate at 60 days after sowing

source_name: Col-0 60 days growth under LN culture 2


title: 1095_T3


title: 1092_T2

source_name: T2 (before meditation)_whole blood


title: Col-0_T30_C2_LN

description: Gene expression data from wild type rosette, in low nitrate at 30 days after sowing

source_name: Col-0 30 days growth under LN culture 2


title: S12_120min_3

city: Guangzhou

first: Yun

last: Fang

state: Guangzhou

address: 100 Central Xianlie Road

institute: Guangdong Institute of Microbiology

data_processing:
After sequencing, four steps were taken to get a clean reads dataset with high quality. (1) Remove the reads with excess of "N"; (2) eliminate the reads caused by adapter contamination; (3) get rid of the reads that have more than 36 bases with low quality (quality score < 20); (4) Wipe away the duplicated reads generated by PCR amplification.
The clean data were mapped on the annotated genomic objects identified in the genome of S. decolorationis S12 using Tophat 2.0.11 and samtools 0.1.18.0, yielding BAM files (Trapnell et al., 2012; Li et al., 2009).
Sorted and indexed BAM files were analyzed by Cufflinks 2.0.0 (Trapnell et al., 2010) to calculate the number of fragments per kilobase of transcript permillion mapped reads (FPKM) for all genes and thereby detect differentially expressed genes.
Based on the calculations made by Cuffdiff, genes with |log2 fold changes (filamentous verse normal cell)| > 1 and FDR-p value < 0.05 were marked as significant.
Genome_build: AXZL01000000 (Shewanella decolorationis S12)
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Shewanella decolorationis

growth_protocol: Shewanella decolorationis S12  was grown to a defined medium (pH 7.0) containing 7.64 g/L Na2HPO4, 3.00 g/L KH2PO4, 0.50 g/L NH4Cl, 1.00 g/L NaCl, 5.00 mmol/L sodium lactate, 0.5 g/L yeast extract, 1 mmol/L amaranth and statically cultivated at 30°C in anaerobic workstation (BugBox, Ruskinn Technologies).

extract_protocol:
Total RNA from the cell pellet was isolated using a TRIzol Reagent kit (Invitrogen, Carlsbad, USA) following the manufacturer’s instructions. RNA samples were treated with RNase-free DNaseI (QIAGEN, Carlsbad, USA) to digest residual genomic DNA and then purified by an RNeasy kit (Qiagen, Valencia, USA). Ribosomal RNA was removed by a RiboZero™ rRNA Removal kit (Epicenter, Madison, USA) following the manufacturer’s protocols (Bhagwat et al., 2014).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Fe0 (60 mM) was added into the defined medium inoculated with the S12 cells. Cell samples were collected from three independent experiments grown with Fe0 condition and without Fe0 condition for 10, 30, 60, 120 min, respectively, and centrifuged at 80,000×g for 10 min at 4°C

tag: strain

tag: taxonomy

value: Gammaproteobacteria

value: untreated

tag: treatment duration

value: 120 min


title: 1092_T1

source_name: T1 (baseline)_whole blood

tag: age

value: T1 (baseline)

value: Whole Blood


title: atg5_T30_C2_LN

description: Gene expression data from atg5 rosette, in low nitrate at 30 days after sowing

source_name: atg5 30 days growth under LN culture 2


title: atg9_T60_C1_LN

source_name: atg9 60 days growth under LN culture 1


title: atg9_T30_C2_LN

description: Gene expression data from atg9 rosette, in low nitrate at 30 days after sowing

source_name: atg9 30 days growth under LN culture 2


title: Col-0_T60_C1

source_name: Col-0 60 days growth under LN culture 1


title: atg5_T60_C1_LN

source_name: atg5 60 days growth under LN culture 1


title: 1090_T4

source_name: T4 (three months after meditation)_whole blood

value: Male

value: T4 (three months after meditation)


title: atg9_T30_C1_LN

source_name: atg9 30 days growth under LN culture 1


title: 1090_T3

source_name: T3 (after meditation) _whole blood


title: 1093_T1


title: S12_120min_2


title: CK 3h-2

source_name: leaves

value: leaves

tag: agent


title: 1093_T2

value: T2 (before meditation)


title: S12_120min_1


title: 1090_T1


title: 1090_T2


title: 1088_T2


title: S12_60min_3

value: 60 min


title: atg5_T30_C1_LN

source_name: atg5 30 days growth under LN culture 1

value: atg5 mutant

value: whole rosette


title: 1088_T4


title: CK 3h-1

value: CK

tag: time point


title: 1088_T3


title: 1085_T4


title: S12_60min_2


title: S12_60min_1


title: 1088_T1


title: Col-0_T30_C1_LN

source_name: Col-0 30 days growth under LN culture 1

value: Col-0 wild type

value: low nitrate


title: S12_30min_3

value: 30 min


title: 1085_T3

value: Female

value: T3 (after meditation)


title: 1085_T2


title: 1085_T1


title: 1084_T4


title: 1084_T3


title: S12_30min_1

value: Gammaproteobacteria

value: untreated


title: S12_30min_2


title: 1084_T2


title: 1084_T1

value: T1 (baseline)


title: 1083_T3

value: Data not available

value: Whole Blood


title: WT_ScrAB_C

description: total RNA, rRNA-depleted

source_name: Bacterial cells, pelleted

value: wild-type

tag: plasmid

value: TSB


title: S12_10min_2

value: 10 min


title: 1080_T4

value: T4 (three months after meditation)


title: 1083_T1


title: S12_10min_1


title: 1080_T3


title: 1080_T1


title: 1078_T3


title: S12_Fe0_120min_3

value: 120 min


title: S12_10min_3


title: 1078_T2

value: T2 (before meditation)


title: CNP-KO_12M_Rep1wm_White Matter

city: Munich

first: Moritz

last: Rossner

address: Nussbaumstr. 7

department: Psychiatry

hyb_protocol: At least 5 μg of labeled cRNA was fragmented by heating the sample to 95°C for 35 min in a volume of 20 μl containing 40 mM Tris acetate, pH 8.1, 100 mM KOAc, and 30 mM MgOAc. Fragmentation was checked by alkaline agarose electrophoresis. Hybridization, washing, staining, and scanning were performed under standard conditions as described by the manufacturer. Mouse430A 2.0 genechips were used that contain over 22,600 probe sets representing transcripts and variants from over 14,000 well-characterized mouse genes.

scan_protocol: Affymetrix Scanner 3000 7G; Gene chip operating software

data_processing: Microarray raw data (.cel files) were exported using Gene chip operating software (gcos) (Affymetrix). Normalization and higher-level analysis were done in R environment employing affy, simpleaffy, limma and several other packages downloaded from Bioconductor (detailed list see section 5.1.1.2). Data normalization, filtering and determination of significance cut-offs were performed following rigorous standards, optimized to achieve a minimum of false positive discoveries. Briefly, normalization was carried out using the Robust Multichip Average (RMA) model implemented in the R package Affy, using default settings.

source_name: LCM Whtie Matter track Corpus Callosum

label_protocol: Total RNA of pooled single cells or micro-regions was resuspended with pretested T7- tagged dT21V oligonucleotides. Two-round T7-RNA polymerase-mediated linear amplification was performed according to optimized protocols for low-input RNA amounts (see Small Sample Target Labeling Assay Version II; Affymetrix). Biotinlabeled second-round aRNA was generated with a NTP-mix containing Biotin-11-CTP and Biotin-16-UTP (PerkinElmer, Boston, MA) (2 mM f.c.). Biotin-labeled amplified RNA (aRNA) size distribution and quantity was analyzed with the Agilent 2100 Bioanalyser using the RNA 6000 Nano LabChip kit (Agilent Technologies, Boeblingen, Germany). Samples with lower size compressed RNA products were discarded.

growth_protocol: For this study 1, 3, 6 and 12 month old male Cnp1-/-, Plp1-/Y and age-matched control mice (n = 3/genotype) were sacrificed by cervical dislocation. To reduce biological variation, all mice were processed between 9 and 10 h after light onset. Brains were removed from the skull and bisected along the midline using a razorblade. One half was frozen on dry ice, sealed with parafilm and stored at –80°C until further use and the other half was post immersion fixed in 4% paraformaldehyd (PFA) for 48 hours and paraffin embedded.

extract_protocol: ‘RNeasy mini preps’ (Qiagen) were used to purify the total RNA from e.g. FACS-sorted microglia, glial precursor cells and oligodendroytes as well as for brain lysates. Total RNA was purified following the manufacturer’s instructions. In brief, cells or tissue were lysed in RLT buffer and kept at -20°C until further use. The samples were thawed quickly by incubating them at 37°C in a water bath and further homogenized by vigorous vortexing for 1 min. 100% EtOH was added to provide the appropriate binding conditions, and the homogenates were applied to RNeasy mini columns where the total RNA binds to the membrane and the contaminants are efficiently washed away. The RNAs were eluted from the column with 100 μl of RNase-free ddH2O.

treatment_protocol: Serial coronal brain sections at the level of the striatum (bregma 1 mm to 0.5 mm), were prepared using a cryostat (Leica) at –18°C and were mounted on Starfrost glass slides (Sigma Aldrich) for single cell isolation (8 μm thick sections) and for micro region isolation (20 μm thick sections) on PEN-membrane slides (Molecular Devices). Once the first section had been mounted, the slide was kept inside the cryochamber (-18°C) while the next section was cut. Eight to twelve sections were mounted in this way on each slide. Cutting and mounting was performed as quickly as possible to ensure that all sections adhered properly to the membrane. Two slides were prepared at a time and processed in parallel. After sectioning, the slides were stored on dry ice until dehydration and staining. Sections mounted on PEN slides (for micro region isolation) were stained prior to dehydration. Slides were fixed in 70% EtOH for 30 sec, rehydrated in H2O for 10 sec stained in 2% thionin staining solution (Sigma) washed two times in fresh H2O. For dehydration sections were subsequently fixed in 70% EtOH for 30 sec, followed by a dehydration series in 95% EtOH for 30 sec, two times ‘freshly’ pured 100% EtOH for one min. and two times Xylene for two min. After dehydration slides were air dried, transported and kept in a box with desiccant. Sections for single cell isolation were only subjected to dehydration procedure. We used only precooled RNAse free plasticware and solutions;  The EYFP+ cells were microdissected from the motor and somatosensory cortex from 10 slides in total; we used the HS Transfer Caps (Molecular Devices) to capture between 100 and 300 neurons per cap, for a total sample size between 700 and 800 microdissected neurons. The corresponding CC-WM microregions were microdissected from 10 adjacent slides and were also pooled. For the microdissection, we used the Arcturus Veritas microdissection system with fluorescence package (Molecular Devices). The isolation of EYFP+ cells was done by identifying single bright fluorescent cells in the fluorescence mode. Cells were only collected if no adjacent nuclei were detected in close proximity. Successful cutting and collection steps were subsequently validated in bright-field and fluorescent mode on the quality control slot of the device. Microdissected samples were lysed in 100 μl of RNA lysis buffer (Qiagen, Hilden, Germany) byvigorous vortexing for 30 sec and stored at -80°C until further use. All procedures were done under RNAse-free conditions.

value: Male

value: CNP-KO


title: CNP-KO_12M_Rep2wm_White Matter


title: S12_Fe0_120min_2


title: CNP-KO_12M_Rep3wm_White Matter


title: PLP-KO_12M_Rep3wm_White Matter

value: PLP-KO


title: PLP-KO_12M_Rep2wm_White Matter


title: PLP-KO_12M_Rep1wm_White Matter


title: 1083_T2


title: 1077_T3


title: S12_Fe0_120min_1


title: CNP-KO_6M_Rep3wm_White Matter


title: 1078_T1


title: 1080_T2


title: WT_12M_Rep2wm_White Matter

value: WT


title: 1077_T1


title: 1077_T2


title: WT_12M_Rep3wm_White Matter


title: CNP-KO_6M_Rep2wm_White Matter


title: 1076_T3


title: 1076_T4


title: S12_Fe0_60min_2

value: 60 min


title: 1076_T2


title: WT_12M_Rep1wm_White Matter


title: S12_Fe0_60min_3


title: 1076_T1


title: 1072_T4

value: Female


title: S12_Fe0_60min_1

value: Gammaproteobacteria


title: CNP-KO_6M_Rep1wm_White Matter


title: 1072_T3

value: T3 (after meditation)


title: 1068_T4


title: S12_Fe0_30min_2

value: 30 min


title: PLP-KO_6M_Rep2wm_White Matter


title: S12_Fe0_30min_3


title: S12_Fe0_30min_1


title: PLP-KO_6M_Rep1wm_White Matter


title: 1068_T2


title: WT_6M_Rep2wm_White Matter


title: 1072_T1

value: T1 (baseline)


title: 1072_T2

value: Whole Blood


title: CNP-KO_3M_Rep3wm_White Matter


title: WT_6M_Rep3wm_White Matter


title: 1067_T1


title: 1068_T3


title: 1066_T4


title: 1068_T1


title: S12_Fe0_10min_3


title: 1067_T3


title: 1067_T4


title: 1066_T3


title: PLP-KO_6M_Rep3wm_White Matter


title: 1067_T2


title: 1066_T1


title: 1066_T2


title: S12_Fe0_10min_2


title: CNP-KO_3M_Rep2wm_White Matter


title: WT_6M_Rep1wm_White Matter


title: 1065_T4


title: S12_Fe0_10min_1


title: 1065_T2


title: 1065_T3


title: 1064_T3


title: WT_3M_Rep1wm_White Matter


title: 1064_T2


title: 1065_T1


title: 1064_T1


title: PLP-KO_3M_Rep2wm_White Matter


title: PLP-KO_3M_Rep1wm_White Matter


title: FEC + oHSV-1, subcutaneous [6RR-F+O-s]

city: Hamilton

first: Karen

last: Mossman

state: Ontario

address: 1280 Main St West

department: Department of Medicine

country: Canada

institute: McMaster University

description: Gene expression data from tumours

hyb_protocol: Fragmented sample was hybridized to Affymetrix Clariom S human arrays at 45 °C overnight

scan_protocol: Arrays were imaged using GeneChip Scanner 3000 7G (Affymetrix)  value and linear value were calculated for all probe sets

data_processing: Data was analyzed using the Transcriptome Analysis Console software, Thermo Fischer. Data was processed using RMA, Quantile Normalization, HDF5 output

source_name: tumour

label_protocol: RNA was normalized to an input amount of 100 ng and underwent reverse transcription. sscDNA was purified using magnetic beads and fragmented using UDG

growth_protocol: 5x10^6 E0771 cells were implanted subcutaneously on the left flank OR 1x10^5 E0771 cells were implanted orthoptopically in the mammary fat pad

extract_protocol: 5 days after the start of treatment mice were sacrificed and tumours harvested. Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Once palpable tumours arose (~12 days) mice were treated with either PBS or FEC (20 mg/kg 5-fluorouracil, 3 mg/kg epirubicin, 20 mg/kg cyclophosphamide; i.p.) + 3 doses of oHSV-1 (2x10^7 pfu; i.t. 24 hr apart)

tag: group

value: Mouse RR notch

value: FEC + oHSV-1, subcutaneous


title: FEC + oHSV-1, subcutaneous [6o-F+O-s]

description: Gene expression data from tumours

value: Mouse no notch


title: CNP-KO_1M_Rep2wm_White Matter


title: FEC + oHSV-1, subcutaneous [6LL-F+O-s]

description: Gene expression data from tumours

value: Mouse LL notch


title: FEC + oHSV-1, subcutaneous [6L-F+O-s]

description: Gene expression data from tumours

value: Mouse L notch


title: CNP-KO_3M_Rep1wm_White Matter


title: FEC + oHSV-1, subcutaneous [6R-F+O-s]

description: Gene expression data from tumours

value: Mouse R notch


title: 1060_T3


title: CNP-KO_1M_Rep3wm_White Matter

value: Male


title: FEC + oHSV-1, subcutaneous [5RR-F+O-s]

description: Gene expression data from tumours


title: FEC + oHSV-1, subcutaneous [5LL-F+O-s]

description: Gene expression data from tumours


title: PLP-KO_3M_Rep3wm_White Matter


title: FEC + oHSV-1, subcutaneous [5L-F+O-s]

description: Gene expression data from tumours


title: CNP-KO_1M_Rep1wm_White Matter

value: CNP-KO


title: PLP-KO_1M_Rep2wm_White Matter

value: PLP-KO


title: 1060_T1


title: 1060_T2

source_name: T2 (before meditation)_whole blood

value: T2 (before meditation)


title: 1058_T4

value: T4 (three months after meditation)


title: PLP-KO_1M_Rep3wm_White Matter


title: PLP-KO_1M_Rep1wm_White Matter


title: 1058_T1


title: 1058_T2


title: WT_1M_Rep2wm_White Matter

value: WT


title: FEC + oHSV-1, subcutaneous [5o-F+O-s]

description: Gene expression data from tumours


title: PBS, subcutaneous [4LL-P-s]

description: Gene expression data from tumours

value: PBS, subcutaneous


title: 1057_T4

value: Female


title: CNP-KO_12M_Rep2_Neuron

source_name: LCM Neurons Layer V Cx


title: CNP-KO_12M_Rep3_Neuron


title: PBS, subcutaneous [4L-P-s]

description: Gene expression data from tumours


title: CNP-KO_12M_Rep1_Neuron


title: PLP-KO_12M_Rep3_Neuron


title: WT_1M_Rep1wm_White Matter


title: FEC + oHSV-1, subcutaneous [5R-F+O-s]

description: Gene expression data from tumours


title: 1058_T3

value: T3 (after meditation)


title: 1057_T3


title: PLP-KO_12M_Rep2_Neuron


title: 1057_T2


title: PBS, subcutaneous [4RR-P-s]

description: Gene expression data from tumours


title: PBS, subcutaneous [4R-P-s]

description: Gene expression data from tumours


title: FEC + oHSV-1, orthotopic [3LL-F+O-o]

description: Gene expression data from tumours

value: FEC + oHSV-1, orthotopic


title: PBS, subcutaneous [4o-P-s]

description: Gene expression data from tumours


title: 1057_T1

source_name: T1 (baseline)_whole blood

value: T1 (baseline)

value: Whole Blood


title: 1055_T3


title: PLP-KO_12M_Rep1_Neuron


title: FEC + oHSV-1, orthotopic [3RR-F+O-o]

description: Gene expression data from tumours

value: Mouse RR notch


title: WT_12M_Rep2_Neuron


title: 1055_T1


title: 1055_T2


title: 1052_T3


title: 1052_T4


title: FEC + oHSV-1, orthotopic [3o-F+O-o]

description: Gene expression data from tumours

value: Mouse no notch


title: FEC + oHSV-1, orthotopic [2RR-F+O-o]

description: Gene expression data from tumours


title: FEC + oHSV-1, orthotopic [3R-F+O-o]

description: Gene expression data from tumours


title: FEC + oHSV-1, orthotopic [3L-F+O-o]

description: Gene expression data from tumours


title: FEC + oHSV-1, orthotopic [2LL-F+O-o]

description: Gene expression data from tumours

value: Mouse LL notch


title: WT_12M_Rep3_Neuron


title: CNP-KO_6M_Rep2_Neuron


title: WT_12M_Rep1_Neuron


title: PLP-KO_6M_Rep3_Neuron


title: 1052_T1


title: 1052_T2


title: PBS, orthotopic [1LL-P-o]

description: Gene expression data from tumours

value: PBS, orthotopic


title: 1049_T3


title: FEC + oHSV-1, orthotopic [2R-F+O-o]

description: Gene expression data from tumours

value: Mouse R notch


title: PLP-KO_6M_Rep2_Neuron

value: Male


title: PLP-KO_6M_Rep1_Neuron


title: CNP-KO_6M_Rep1_Neuron

value: CNP-KO


title: CNP-KO_6M_Rep3_Neuron


title: 1049_T1


title: WT_6M_Rep3_Neuron


title: 1049_T2


title: 1047_T4


title: PBS, orthotopic [1R-P-o]

description: Gene expression data from tumours


title: 1047_T3


title: PBS, orthotopic [1RR-P-o]

description: Gene expression data from tumours


title: FEC + oHSV-1, orthotopic [2L-F+O-o]

description: Gene expression data from tumours

value: Mouse L notch


title: FEC + oHSV-1, orthotopic [2o-F+O-o]

description: Gene expression data from tumours


title: 1047_T2

value: T2 (before meditation)


title: PBS, orthotopic [1L-P-o]

description: Gene expression data from tumours


title: 1047_T1


title: WT_6M_Rep2_Neuron


title: 1046_T3


title: WT_6M_Rep1_Neuron


title: 1042_T2

value: Data not available


title: 1046_T2


title: PLP-KO_3M_Rep3_Neuron

value: PLP-KO


title: PBS, orthotopic [1o-P-o]

description: Gene expression data from tumours


title: CNP-KO_3M_Rep1_Neuron


title: 1041_T4

value: T4 (three months after meditation)


title: cre, epididymal fat pad, batch 2, biological rep10

city: Columbia

first: Diego

last: Altomare

state: SC

address: 715 Sumter Street, Room 617

department: Department of Drug Discovery and Biomedical Sciences

institute: University of South Carolina

description: macrophage-derived TNF-α deficient, epididymal fat pad total RNA

hyb_protocol: Amplified/labeled samples were hybridized to Clariom S, Mouse Arrays for 16 h at 45°C using a GeneChip Hybridization Oven 645 and the GeneChip™ Hybridization, Wash, and Stain Kit (Thermo Fisher Scientific). Hybridized arrays were washed and stained using the kit just mentioned and a GeneChip Fluidics Stations 450 (Thermo Fisher Scientific).

scan_protocol: Arrays were scanned with a GeneChip Scanner 3000 7G system using Affymetrix GeneChip Command Console Scan Control 4.0 software.

data_processing:
The resulting probe cell intensity (CEL) files were imported into Transcriptome Analysis Console 4.0.2.15 and processed at the gene-level using Clariom_S_Mouse.r1.na36.mm10.a1.transcript.csv annotation file and the Signal Space Transformation - Robust Multichip Analysis (SST-RMA) algorithm to generate CHP files.
Clariom_S_Mouse.r1.na36.mm10.a1.transcript.csv

label_protocol: Total RNA samples were amplified and biotinylated using GeneChip WT PLUS Reagent Kit (Thermo Fisher Scientific), according to the manufacturer's recommendations.

growth_protocol: Male offspring were on a normal chow diet until 10 weeks of age.

extract_protocol: RNeasy Lipid Tissue Mini Kit (Qiagen) was used to isolate total RNA from epididymal adipose tissue according to the manufacturer's recommendations. RNA quality was assessed with a NanoDrop 2000 (Thermo Scientific) and an Agilent 2100 Bioanalizer.

treatment_protocol: At 10 weeks of age, mice were fed ad libitum during 18 weeks with a custom-made purified high-fat diet (4.57 kcal/g) comprised of 47%, 40%, and 13% of total calories from carbohydrate, fat, and protein, respectively, with saturated fat making up 12% of total calories .

value: male

value: 28 weeks

value: epididymal fat pad

value: TNF-αFlox/FLox, LyzMcre+/- , C57BL/6 (cre)

tag: litter

value: littermate


title: CNP-KO_3M_Rep3_Neuron


title: DroshaKO_miR-320a_antagomir_BR2

first: Christopher

middle: James

last: Fields

state: Florida

address: 2033 Mowry Road

department: Biochemistry and Molecular Biology

data_processing:
Adapter sequences were removed with Cutadapt.
Trimmed reads were aligned to the genome with Hisat2. Output sam files were converted to sorted bam files using samtools.
Transcripts were assembled using StringTie.
Differential Gene Expression was determined using Ballgown.
processed data files format and content: .txt file containing gene counts
Genome_build: hg38

source_name: HCT116 Drosha KO

growth_protocol: HCT116 cells were cultured in McCoy's 5A media supplemented with 10% FBS and 1% penicillin/Streptomycin

extract_protocol:
Total RNA was extracted from cells using TRIzol (Invitrogen) and treated with RQ1 Dnase (Promega).
mRNA is isolated using oligo(dT) beads, fragmented randomly in fragmentation buffer, and reverse-transcribed with mRNA template and random heximer primer. Following second strand synthesis is a series of terminal repair, sequencing adapter ligation, size selection, and PCR enrichment.

tag: cell line

value: Drosha KO

tag: treatment


title: PLP-KO_3M_Rep2_Neuron

tag: genotype


title: cre, epididymal fat pad, batch 1, biological rep7

source_name: macrophage-derived TNF-α deficient, epididymal fat pad

tag: tissue


title: cre, epididymal fat pad, batch 2, biological rep8


title: cre, epididymal fat pad, batch 2, biological rep6


title: CNP-KO_3M_Rep2_Neuron


title: DroshaKO_miR-320a_antagomir_BR1


title: WT_3M_Rep3wm_White Matter

value: WT


title: cre, epididymal fat pad, batch 1, biological rep9


title: 1041_T3

value: Female

value: T3 (after meditation)

value: Whole Blood


title: PLP-KO_3M_Rep1_Neuron

value: Male


title: WT_3M_Rep3_Neuron


title: 1041_T2


title: cre, epididymal fat pad, batch 2, biological rep4


title: cre, epididymal fat pad, batch 2, biological rep2


title: cre, epididymal fat pad, batch 1, biological rep3


title: DroshaKO_ctrl_antagomir_BR3


title: cre, epididymal fat pad, batch 1, biological rep1


title: 1041_T1

value: T1 (baseline)


title: WT_3M_Rep2_Neuron


title: WT_3M_Rep1_Neuron


title: DroshaKO_miR-320a_antagomir_BR3


title: DroshaKO_ctrl_antagomir_BR2


title: cre, epididymal fat pad, batch 1, biological rep5


title: 1038_T4


title: DroshaKO_ctrl_antagomir_BR1


title: wt, epididymal fat pad, batch 2, biological rep10

description: wild-type, epididymal fat pad total RNA

source_name: wild-type, epididymal fat pad

value: TNF-αFlox/FLox, LyzMcre-/- , C57BL/6  (wt)


title: 1038_T3


title: CNP-KO_1M_Rep2_Neuron

value: CNP-KO


title: CNP-KO_1M_Rep3_Neuron


title: CNP-KO_1M_Rep1_Neuron


title: wt, epididymal fat pad, batch 2, biological rep8

description: wild-type, epididymal fat pad total RNA


title: wt, epididymal fat pad, batch 1, biological rep9

description: wild-type, epididymal fat pad total RNA


title: 1038_T2

value: T2 (before meditation)


title: 1038_T1


title: D8_VO

first: Noah

last: Shroyer

address: One Baylor Plaza, Room N710

department: Medicine Section of Gastroenterology and Hepatology

institute: Baylor College of Medicine

description:
Duodenal Enteroids Norovirus Infected
Line - D8

data_processing:
Pseudosalignment was performed using Kallisto (https://pachterlab.github.io/kallisto/) and raw gene counts were output as tsv files
Genome_build: hg38
Supplementary_files_format_and_content: Tab-delimited files with raw gene counts for every gene and every sample

source_name: Intestine

growth_protocol: Enteroids were mainted in IntestiCult Proliferation and differentiated in IntestiCult Differentiation

extract_protocol:
Total RNA was extracted using a Qiagen RNeasy kit
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Enteroids were treated with vehicle or BCM 16-16 norovirus in IntestiCult Differentiation

tag: segment

value: Duodenum

tag: format

value: Monolayer

tag: substrate

value: Collagen IV


title: D109_VO

description:
Duodenal Enteroids Norovirus Infected
Line - D109


title: PLP-KO_1M_Rep3_Neuron

tag: Sex

value: PLP-KO


title: wt, epididymal fat pad, batch 1, biological rep7

description: wild-type, epididymal fat pad total RNA

value: male

value: 28 weeks

value: epididymal fat pad


title: D4_VO

description:
Duodenal Enteroids Norovirus Infected
Line - D4


title: PLP-KO_1M_Rep1_Neuron


title: WT_1M_Rep3_Neuron


title: D109_MO

description:
Duodenal Enteroids Mock Infected
Line - D109


title: PLP-KO_1M_Rep2_Neuron


title: wt, epididymal fat pad, batch 2, biological rep6

description: wild-type, epididymal fat pad total RNA

value: littermate


title: D104_VO

description:
Duodenal Enteroids Norovirus Infected
Line - D104


title: S. pneumoniae degust [37]

city: Brisbane

first: David

middle: Manuel Pereira

last: De Oliveira

state: QLD

address: St Lucia

department: School of Chemistry and Molecular Biosciences

country: Australia

institute: The University of Queensland

data_processing:
HiSeq 2500 ultra-high-throughput sequencing system was used for base-calling
Samples were uploaded to the Galaxy web platform (public server at usegalaxy.org), trimmed and mapped to the reference genome (S. pneumoniae ATCC 700669 accession number: NC_011900) using bowtie2 with default parameters
Read counts were determined using featureCounts and differential gene expression was analyzed with edgeR with the CPM threshold set at 1.0
Genome_build: NC_011900
Supplementary_files_format_and_content: Read counts and CPM

organism: Streptococcus pneumoniae

source_name: Bacteria

growth_protocol: Bacteria were grown in cation-adjusted Mueller-Hinton broth (CA-MHB) as per CLSI guidelines at 37°C under aerobic conditions.

extract_protocol:
RNA was isolated using the RNeasy Plus Kit (Qiagen). Briefly, bacteria were grown to OD600 of 0.5 in CA-MHB in the presence or absence of PBT2 + ZnSO4. Two volumes of RNAprotect (Qiagen) were added to the cultures and the samples were then centrifuged at 5,000 x g for 25 min at 4°C to pellet cells. RNA was isolated from the dry pellet as per the manufacturer’s instructions. To ensure complete removal of DNA, the RNA was then further purified using the TURBO DNA-free kit (Thermo Fisher Scientific) according to the manufacturer’s instructions.
RNASeq analysis was performed at the Australian Genome Research Facility. The cDNA library was prepared using a Ribo-zero stranded protocol. In brief, rRNA was depleted with Ribo Zero, RNA was fragmented (heat and divalent cations) and 1st strand cDNA synthesis was done with SuperScript II Reverse Transcriptase (Invitrogen). For the 2nd strand cDNA synthesis, the strand was “marked” with dUTP.  A 3’ adenylation of DNA fragments was performed followed by sequencing adapter ligation (utilizing T-A pairing of adapter and DNA fragments). The library was amplified by PCR (amplification of “unmarked” 1st strand only). Libraries were assessed using either Agilent’s Bioanalyzer DNA 1000 chip or TapeStation D1K TapeScreen system. qPCR was used to quantify individual libraries before normalizing (2 nM) and pooling. Libraries were pooled and clustered through the Illumina cBot system using TruSeq PE Cluster Kit v3 reagents followed by sequencing on the Illumina HiSeq 2500 system with TruSeq SBS Kit v3 reagents with 110 (101 read 1, 9 cycles index read). Libraries were sequenced with a HiSeq 2500 ultra-high-throughput sequencing system (Illumina) to produce 50-base-single end reads. An average of 30 million reads per sample were generated, uploaded to the Galaxy web platform (public server at usegalaxy.org), and mapped to the reference genome (S. pneumoniae ATCC 700669 accession number: NC_011900) using bowtie2 with default parameters. Read counts were determined using featureCounts and differential gene expression was analyzed with edgeR with the CPM threshold set at 1.0. Figures were generated using ggplot2 and ggpubr packages in R-studio

treatment_protocol: Bacteria were grown to  OD600 of 0.5 in CA-MHB in the presence or absence of PBT2 (32 µM) and ZnSO4 (8 µM).

tag: strain

value: Strain 23F

value: CAMHB + 32 µM PBT2 + 8 µM ZnSO4


title: 1029_T4

source_name: T4 (three months after meditation)_whole blood

value: Female

value: T4 (three months after meditation)


title: 1030_T4

value: Male

value: Whole Blood


title: D4_MO

description:
Duodenal Enteroids Mock Infected
Line - D4


title: 1030_T3

value: T3 (after meditation)


title: WT_1M_Rep1_Neuron

value: WT


title: wt, epididymal fat pad, batch 1, biological rep5

description: wild-type, epididymal fat pad total RNA

value: TNF-αFlox/FLox, LyzMcre-/- , C57BL/6  (wt)


title: D104_MO

description:
Duodenal Enteroids Mock Infected
Line - D104

value: Duodenum


title: 1030_T2

value: T2 (before meditation)


title: S. pneumoniae degust [39]


title: 1029_T3


title: S. pneumoniae degust [38]


title: 1029_T2


title: 1030_T1

value: T1 (baseline)


title: S. pneumoniae degust [35]

value: Treatment with CA-MHB (reference sample)


title: S. pneumoniae degust [36]


title: skin stromal cells, Hu_EF01

city: San Francisco

first: Ian

middle: Chen

last: Boothby

state: CA

address: 513 Parnassus Ave, HSW-1201B

institute: University of California San Francisco

data_processing:
Alignment, generation of gene-barcode matrices, and filtering were performed using the cellranger count function in Cellranger 2.1 with default parameters
Genome_build: mm10 (mouse); GrCh38 (human)
Supplementary_files_format_and_content: h5 files for each sample containing raw gene count-barcode matrices

source_name: Skin stromal cells, eosinophilic fasciitis patient

extract_protocol:
10X Chromium 3'-v3 chemistry
cDNA libraries were prepared for sequencing using standard Illumina protocols
single cell RNAseq (10X Chromium 3')

treatment_protocol: skin was finely minced and digested in collagenase IV and Dnase overnight at 37C; then filtered, washed in media, and run on a FACS Aria to sort stromal cells

value: 52 years

value: F

value: skin

tag: site

value: forearm

tag: cell type

value: live CD45- CD31- Ecadherin- CD235a- stromal cells

tag: disease state

value: Eosinophilic fasciitis


title: skin stromal cells, Hu_HC03

source_name: Skin stromal cells, healthy control

tag: age

value: 64 years

value: M

value: leg

value: Healthy


title: 1029_T1

first: VIJAYENDRAN

last: CHANDRAN

address: Assistant Professor, Department of Pediatrics,  University of Florida, School of Medicine, 1600 SW Archer Road, Box 100296

data_processing:
Bluebee’s genomics analysis platform
Sequencing targeted mean three million 65-nt single-stranded reads per sample, which were mapped to the human transcriptome and quantified as transcripts per million mapped reads using the STAR aligner. Briefly, all sequencing data were uploaded to Illumina’s BaseSpace in real-time for downstream analysis of quality control. Raw Illumina (fastq.gz) sequencing files were downloaded from BaseSpace, and uploaded to Bluebee’s genomics analysis platform (https://www.bluebee.com) to align reads against the human genome and to obtain raw read counts.
Supplementary_files_format_and_content: Three csv file contains: (1) raw read counts, (2) normalized read counts with batch correction, and (3) normalized read counts with batch correction and cell type correction for every gene and every sample.

extract_protocol:
The human blood samples collected into PAXgene Blood RNA Tubes were removed from the -80°C freezer and incubated overnight at room temperature before RNA extraction. RNA was harvested using the RNeasy Tissue Mini Kit (Qiagen), according to manufacturer’s instructions. RNA was reverse transcribed to complementary DNA (Lexogen QuantSeq 3′ FWD), and sequenced on a HiSeq 4000 instrument (Illumina).
RNA libraries were prepared for sequencing using  manufacturer’s instructions  (Lexogen QuantSeq 3′ FWD)

value: Female

value: Whole Blood


title: skin stromal cells, Hu_HC02

value: 67 years

value: forehead


title: wt, epididymal fat pad, batch 2, biological rep2

description: wild-type, epididymal fat pad total RNA

value: male

value: 28 weeks

value: epididymal fat pad

value: TNF-αFlox/FLox, LyzMcre-/- , C57BL/6  (wt)

value: littermate


title: 1028_T2

value: Male

value: T2 (before meditation)


title: WT_1M_Rep2_Neuron

value: WT


title: wt, epididymal fat pad, batch 1, biological rep1

description: wild-type, epididymal fat pad total RNA


title: S. pneumoniae degust [34]

value: Strain 23F

tag: agent

value: Treatment with CA-MHB (reference sample)


title: thymus_TBI_day0_rep3

city: Seattle

first: Kirsten

last: Cooper

address: 1100 Fairview Ave. N, Rm S3-208

institute: Fred Hutchinson Cancer Research Center

description: Gene expression from CD45- thymic stromal cells

hyb_protocol: 10 ug of cDNA was hybridized for 16 hr to the Affymetrix array as described in the Expression Analysis Technical Manual. GeneChips were washed and stained in the Affymetrix Fluidics Station FS450.

scan_protocol: Affymetrix GeneArray scanner 7G

data_processing: Feature intensity was extracted by Affymetrix GeneChip Command Console as CEL files. Used Bioconductor Affy for normalization (GC-RMA) and gene annotation

source_name: Untreated mouse thymus

label_protocol: 500 ng total RNA converted to cRNA using Affymetrix GeneChip®3' IVT Kit and in vitro transcription resulting into biotin-labeled cRNA, fragmented prior to hybridization (Affymetrix Expression Analysis Technical Manual, as described).

extract_protocol: RNA extraction plus kit was used to isolate RNA, and cDNA was made with Invitrogen Superscriptase.

treatment_protocol: Cells were first isolated using CD45 MACS cell depletion, then endothelial cells were FACS purified (CD45- EpCAM- VE-Cad+). To obtain sufficient RNA for every timepoint, thymic ECs of several mice were pooled.

tag: gender

value: female

value: untreated

value: thymus

value: thymic endothelial cells


title: 1027_T3

source_name: T3 (after meditation) _whole blood

value: Female

value: T3 (after meditation)

value: Whole Blood


title: wt, epididymal fat pad, batch 1, biological rep3

description: wild-type, epididymal fat pad total RNA

value: male


title: thymus_TBI_day0_rep2


title: wt, epididymal fat pad, batch 2, biological rep4

description: wild-type, epididymal fat pad total RNA

value: 28 weeks


title: skin stromal cells, Hu_HC01

value: 66 years

value: M

value: skin

value: cheek

value: live CD45- CD31- Ecadherin- CD235a- stromal cells

value: Healthy


title: 1027_T2

value: T2 (before meditation)


title: 1027_T1

value: T1 (baseline)