title: differentiated_LaminB1-Dam_Tmem120a/b-knockdown

description:
differentiated LaminB1-Dam - Tmem120a/b knockdown
DamID profile for visualisation (differentiated adipocytes with Tmem120a/b knock-down, samples DB10/DB9)

library_source: genomic

data_processing:
Library strategy: DamID
Basecalls and quality filtering performed by BGI according to their standard procedures
Clean reads were aligned to the mouse mm9 genome using the Burrows-Wheeler aligner bwa mem. Mitochondrial sequences (a common contaminant in these experiments) and unaligned reads were filtered out.
Reads were counted per DpnI fragment (genomic sequence flanked by GATC motifs), and log2(ratio LaminB1/dam) measurements were obtained for undifferentiated and differentiated samples. The log2 ratios were then normalised using quantile normalisation (Bioconductor Limma package) and converted to bigwig format for visualisation purposes.
To identify LADs, we used a circular binary segmentation algorithm (CBS) from the R/Bioconductor package 'DNAcopy' (Venkatraman E. Seshan and Adam Olshen (). DNAcopy: DNA copy number data analysis. R package version 1.44.0) using default parameters. Positive signal segments identified by the CBS algorithm were merged if closer than 5Kb, and then any regions smaller than 15Kb were removed.
Regions that change peripheral association between conditions (PI regions represent loss of peripheral association after activation, and IP regions represent a gain) were then identified by comparing the LAD regions between the two conditions. Regions smaller than 15Kb were discarded.
Genome_build: mm9
Supplementary_files_format_and_content: LADs_U_15cut_sm0_X.bed -  LAD peaks (BED format) for undifferenciated preadipocytes
Supplementary_files_format_and_content: LADs_D_15cut_sm0_X.bed -  LAD peaks (BED format) for differenciated adipocytes
Supplementary_files_format_and_content: LADs_kdA_15cut_sm0_X.bed -  LAD peaks (BED format) for differenciated adipocytes under Tmem120a knock-down
Supplementary_files_format_and_content: LADs_kdA_15cut_sm0_X.bed -  LAD peaks (BED format) for differenciated adipocytes under Tmem120a/b knock-down
Supplementary_files_format_and_content: DR1_U_08.bed - contains coordinates for differential regions (DR) that appear more associated with the nuclear envelope in the undifferentiated state (PI regions)
Supplementary_files_format_and_content: DR1_D_08.bed - contains coordinates for differential regions (DR) that appear more associated with the nuclear envelope in the undifferentiated state (IP regions)
Supplementary_files_format_and_content: sq07_U.bw - contains DamID profiles for undifferentiated 3T3L1 preadipocytes as log2(LaminB1/Dam-control), for visualisation purposes
Supplementary_files_format_and_content: sq07_D.bw - contains DamID profiles for differentiated 3T3L1 preadipocytes as log2(LaminB1/Dam-control), for visualisation purposes
Supplementary_files_format_and_content: sq07_kdA.bw - contains DamID profiles for differentiated 3T3L1 Tmem120a kock-down preadipocytes as log2(LaminB1/Dam-control), for visualisation purposes
Supplementary_files_format_and_content: sq07_kdAB.bw - contains DamID profiles for undifferentiated 3T3L1 preadipocytes as log2(LaminB1/Dam-control), for visualisation purposes

source_name: adipocyte

growth_protocol: 3T3-L1 cells were maintained in high glucose DMEM (SIGMA) supplemented with 10% fetal bovine serum (FBS), MEM non-essential amino acids, 1 mM Sodium Pyruvate, 100 µg/µl penicillin and 100 µg/µl streptomycin sulfate. Cells were plated at ~10% confluency and always split by 60% confluency to maintain differentiation capacity

extract_protocol:
Lentivirus encoding the control Dam, or LaminB1-Dam fusion, was used to transduce untreated preadipocytes or differentiating adipocytes at day 6 post-induction. Transduction was allowed for 36h. At day 9 post-induction genomic DNA was extracted.
Genomic DNA was extracted using Qiagen DNA-Easy kit, following manufacturer's instructions.
Dam-methylated genomic DNA was enriched using the standard protocol as described by Vogel et al. (2007) Nature Protocols 2:1467-1478. It involves digesting gDNA with DpnI enzyme, which cuts at non-Adenine-methylated GATC motifs.
Libraries were prepared by Beijing Genomics Institute (BGI) to Illumina's specifications

treatment_protocol: Adipogenesis was induced two days post-confluency by replacing growth medium with induction medium containing 0.5 μM insulin, 1 µM dexamethasone, 0.5 mM 3-isobutyl-1-methylxanthine (IBMX), and 1 μM rosiglitazone. Induction medium was replaced after two days with maintenance medium containing growth medium supplemented with insulin and rosiglitazone only, which was replaced every 48h, up to day 9 post-induction.

value: differentiated day9

tag: damid

tag: condition

value: Tmem120a/b shRNA


title: Sample 115_TENA2560_P05_R4

status: Public on Nov 18 2021

type: SRA

city: Basel

first: DBM Bioinformatics

last: Core Facility

state: BS

address: Hebelstrasse 20

department: Departement of Biomedicine

country: Switzerland

institute: University of Basel

description: BSSE_QGF_140481_HLLWMDRXX_1_TENA2560_P5_CGTACAGGAA_TAGGTTCTCT_S115_L001

library_source: transcriptomic

data_processing:
Paired-end reads were aligned to the mouse genome (UCSC version mm10 analysis set) with STAR with default parameters except for allowing up 10 hits to genome (outFilterMultimapNmax 10), reporting only one location for hits with equal score (outSAMmultNmax 1), and for filtering reads without evidence in spliced junction table (outFilterType "BySJout").
The output was sorted and indexed with samtools. Read and alignment quality was evaluated using the qQCReport function of the Bioconductor package QuasR.
The featureCounts function from Bioconductor package subread was used to count the number of read (5'ends) overlapping with the exons of each gene assuming an exon union model (with used gene model provided by ensembl v96).
Processing of the read count matrix for genes was done according to the steps illustrated in Bioconductor Single Cell Analysis workflow (Amezquita et al., 2020).
Genome_build: mm10
Supplementary_files_format_and_content: TXT file (with tab separated values) with raw counts for Ensembl Genes, 1.column is Ensembl Gene ID, 2. and remaining columns contain raw counts

molecule: total RNA

organism: Mus musculus

source_name: Murine mammary tumor cell lines derived from tumors of lineage-traced MMTV-PyMT transgenic mice

growth_protocol: Cells were directly sorted from tumors of mice

extract_protocol:
FACS-sorted cells were collected as 5-cell pools in 2.5µl of 0.2% TX-100 and 2U/μl RNase inhibitor (TakaraBio, 2313B) in PBS into 96-well plates (Thermo Fisher Scientific, 4346906) and kept in -80°C prior to use. RNAseq libraries were prepared according to the Smart-seq2 method (Picelli, 2014).
5-cell RNA-seq: RNA/cDNA preamplification and Nextera XT library preparation reactions were set up with a Mosquito HV system (SPT Labtech). After reverse transcription and amplification, the concentration of cDNA generated from each sample was measured using PicoGreen (Thermo Fisher Scientific). cDNA was normalized to 0.1-0.15ng/µl and 0.75 µl were used for library preparation with the Nextera XT DNA library preparation kit (Illumina). Multiplexed library pools were then pooled and PE 2x51 sequenced with an Illumina NovaSeq 6000 system, v1 reagents.

treatment_protocol: Each mouse was treated with 2mg of Tamoxifen twice per week starting at 9 weeks of age and continuing until sacrifice (around 13 to 14 weeks of age)

tag: system

value: TENA

tag: mouse

tag: population

tag: egfp

value: neg

tag: mcherry

value: high

tag: epcam

tag: passedqc

value: TRUE


title: Total Blood Bmem 1

city: Melbourne

first: Hyon Xhi

last: Tan

state: Victoria

address: 792 Elizabeth St

department: Department of Microbiology and Immunology

country: Australia

institute: The University of Melbourne, at the Peter Doherty Institute for Infection and Immunity

data_processing:
RNAseq analysis was performed using the web-based Galaxy platform maintained by Melbourne Bioinformatics.
Reads were mapped to the Mus musculus reference genome (mm10) using HISAT2 and reads were quantified using HTSeq.
Count matrices were generated and inputted into Degust (http://degust.erc.monash.edu) for final data analysis and visualization. The Degust Voom/Limma method was selected for data processing.
Genome_build: mm10
Supplementary_files_format_and_content: Normalized abundance measurements - Degust output
Supplementary_files_format_and_content: Raw counts -- HTseq

source_name: Murine blood

extract_protocol:
RNA was isolated from sorted cells using a QIAGEN RNeasy Plus Micro Kit, as per manufacturer's protocol.
Illumina Truseq Stranded mRNA kit was use for library construction. RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tissues

value: Blood

tag: cell type

value: B220+ IgD- CD38hi GL7- CD45.2IV+

tag: treatment

value: Post-intranasal influenza virus infection


title: HSB179_4_DG

city: New haven

first: Nenad

last: Sestan

state: CT

address: 333 Cedar street

department: Neuroscience

country: USA

institute: Yale University

description:
nuclear RNA
Human_cell_meta.txt.gz
Human_counts.mtx.gz
Human_genes.txt.gz

data_processing:
Cell Raner (v3.0.2) were used for reads alignment, filtering, UMI and barcode counting
Seurat (v3) was used for quality control, batch correction, dimension reduction and cell clustering
Please refer STAR methods for more details
Genome_build: hg38; Mmul10; susScr11
Supplementary_files_format_and_content: tab-delimited text files including meta annotation for each cell; tab-delimited text files including UMI counts; tab-delimited text files for gene symbols

organism: Homo sapiens

source_name: Human HIP-EC

extract_protocol:
The brain cell nuclei were isolated according to our previous protocol (Li et al., 2018; Zhu et al., 2018) with some modifications. Hippocampal regions (DG, CA1, CA2-4, Sub) and adjacent entorhinal cortex were dissected from three frozen adult human brains (Table S1). In order to avoid experimental bias and evenly dissociate the tissue for cell nuclei isolation, whole tissue was finely pulverized to powder in liquid nitrogen with mortar and pestle (Coorstek #60316, #60317). All buffers were ice cold and all reagents used for consequent nuclear isolation were molecular biology grade unless stated otherwise. 5 - 10 mg of pulverized tissue was added into 5 ml of ice-cold lysis buffer consisting of 320 mM sucrose (Sigma #S0389), 5 mM CaCl2 (Sigma #21115), 3 mM Mg(Ace)2 (Sigma #63052), 10mM Tris-HCl (pH 8) (AmericanBio #AB14043), protease inhibitors w/o EDTA (Roche #11836170001), 0.1 mM EDTA (AmericanBio #AB00502), RNAse inhibitor (80U/ml) (Roche #03335402001), 1mM DTT (Sigma #43186), and  0.1% TX-100 (v/v) (Sigma#T8787). DTT, RNAse Protector, protease inhibitors, and TX-100 were added immediately before use. The suspension was transferred to Dounce tissue grinder (15ml volume, Wheaton #357544; autoclaved, RNAse free, ice-cold) and homogenized with loose and tight pestles, 30 cycles each, with constant pressure and without introduction of air. The homogenate was strained through 40 um tube top cell strainer (Corning #352340) which was pre-wetted with 1ml wash buffer: (250 mM sucrose (Sigma #S0389), 25 mM KCl (Sigma #60142), 5mM MgCl2 (Sigma #M1028), 20mM Tris-HCl (pH 7.5) (AmericanBio #AB14043; Sigma #T2413), protease inhibitors w/o EDTA (Roche #11836170001), RNAse inhibitor (80U/ml) (Roche #03335402001), 1mM DTT (Sigma #43186)). Additional 4 ml of wash buffer was added to wash the strainer. Final 10 ml of solution was mixed with 10 ml of 50% Optiprep (Axis-Shield# 1114542) solution (50% iodixanol (v/v), 250 mM sucrose (Sigma #S0389), 25 mM KCl (Sigma #60142), 5mM MgCl2 (Sigma #M1028), 20mM Tris-HCl (pH 7.5) (AmericanBio #AB14043; Sigma #T2413), protease inhibitors w/o EDTA (Roche #11836170001), RNAse inhibitor (80U/ml) (Roche #03335402001), 1mM DTT (Sigma #43186)) by inverting the tube 10x and carefully pipetted into 2 centrifuge tubes (Corning #430791). The tubes were centrifuged at 1000g, for 30 min at 4 ˚C on centrifuge (Eppendorf #5804R) and rotor (Eppendorf #S-4-72). Upon end of centrifugation, the supernatant was carefully and completely removed and total of 5 ml of resuspension buffer (250 mM sucrose (Sigma #S0389), 25 mM KCl (Sigma #60142), 5mM MgCl2 (Sigma #M1028), 20mM Tris-HCl (pH 7.5) (AmericanBio #AB14043; Sigma #T2413), protease inhibitors w/o EDTA (Roche #11836170001), RNAse inhibitor (80U/ml) (Roche #03335402001), 1mM DTT (Sigma #43186)) was added carefully on the pellets in tubes and centrifuged at 1000g, for 10 min at 4 ˚C on the same centrifuge and rotor. Supernatants were then carefully and completely removed, pellets were gently dissolved by adding 100 ul of resuspension buffer (see above) and pipetting 30x with 1ml pipette tip, pooled and filtered through 35 um tube top cell strainer (Corning #352340). Finally, nuclei were counted on hemocytometer and diluted to 1 million/ml with sample-run buffer: 0.1% BSA (Gemini Bio-Products #700-106P), RNAse inhibitor (80U/ml) (Roche#03335402001), 1mM DTT (Sigma #43186) in DPBS (Gibco #14190).
10X Chromium Single Cell 3ʹ v3

tag: tissue

value: Dentate gyrus

tag: age

tag: Sex

value: Male


title: Sample 114_TENA2560_P17_R4

description: BSSE_QGF_140480_HLLWMDRXX_1_TENA2560_P17_GATATTGTGT_ACCACACGGT_S114_L001

value: FALSE


title: differentiated_Dam_Tmem120a/b-knockdown

city: Edinburgh

first: Jose

middle: Ignacio

last: de las Heras

address: Max Born Crescent

department: Wellcome Trust Centre

country: United Kingdom

institute: University of Edinburgh

description: differentiated Dam control - Tmem120a/b knockdown

molecule: genomic DNA

value: Dam


title: HSB179_5_DG


title: day0, undifferentiated preadipocyte, rep2

type: RNA

description: replicate 2

scan_protocol: Standard Protocols (Clinical Research Facility Edinburgh), Scanner: HiScan H166

data_processing: Data were log2 transformed and quantile normalised using the BioConductor package Limma.

label: biotin

source_name: 3T3L1 preadipocyte cell line

label_protocol: Ambion Illumina TotalPrep kit

growth_protocol: 3T3-L1 cells were maintained in high glucose DMEM (SIGMA) supplemented with 10% fetal bovine serum (FBS), MEM non-essential amino acids, 1 mM Sodium Pyruvate, 100 µg/µl penicillin and 100 µg/µl streptomycin sulfate. Cells were plated at ~10% confluency and always split by 60% confluency to maintain differentiation capacity.

extract_protocol: total RNA extraction was performed using Trizol reagent (Invitrogen) according to the manufacturer's instructions

treatment_protocol:
Adipogenesis was induced two days post-confluency by replacing growth medium with induction medium containing 0.5 μM insulin, 1 µM dexamethasone, 0.5 mM 3-isobutyl-1-methylxanthine (IBMX), and 1 μM rosiglitazone. Induction medium was replaced after two days with maintenance medium containing growth medium supplemented with insulin and rosiglitazone only, which was replaced every 48h, up to day 9 post-induction.
Control and Tmem120a/b knock-downs were generated by transduction of non-target (control) or Tmem120a/b-specific shRNA-encoding lentiviruses as described in Batrakou et al. (2015) PLoS ONE 10(05): e0127712.

tag: time

value: day 0

value: undifferentiated

tag: genotype/variation

value: non-target shRNA control


title: day9, differentiated adipocyte, rep2

description: replicate 2

hyb_protocol: Standard Protocols (Clinical Research Facility Edinburgh)

value: day 9

value: differentiation


title: Sample 113_TENA2560_P18_R4

description: BSSE_QGF_140479_HLLWMDRXX_1_TENA2560_P18_AGAGAACCTA_GGTTATGCTA_S113_L001


title: day9, differentiated adipocyte, rep1

description: replicate 1


title: Sample 112_TENA2560_P22_R3

description: BSSE_QGF_140478_HLLWMDRXX_1_TENA2560_P22_AGGACAGGCC_CATTCCAGCT_S112_L001


title: Total Spleen Bmem 3

source_name: Murine spleen

value: Spleen

value: B220+ IgD- CD38hi GL7-


title: HSB179_3_DG


title: Total Spleen Bmem 2


title: Sample 119_TENA2560_P18_R5

description: BSSE_QGF_140485_HLLWMDRXX_1_TENA2560_P18_TCTAGGCGCG_CGAAGGTTAA_S119_L001

value: TENA

value: neg


title: differentiated_LaminB1-Dam_Tmem120a-knockdown

description:
differentiated LaminB1-Dam - Tmem120a knockdown
DamID profile for visualisation (differentiated adipocytes with Tmem120a knock-down, samples DB8/DB7)

value: differentiated day9

tag: damid

value: Tmem120a shRNA


title: UCSF EWSR1-BEND2 glioma #3

type: genomic

city: Stanford

first: David

middle: A.

last: Solomon

state: CA

address: 300 Pasteur Dr, Lane L216

department: Pathology

institute: Stanford University School of Medicine

description: EWSR1-BEND2 glioma

hyb_protocol: bisulfite converted DNA was amplified, fragmented, and hybridized to Illumina Infinium EPIC 850k Human DNA Methylation Beadchips using standard Illumina protocol

scan_protocol: Arrays were imaged using the Illumina iScan instrument following standard recommended Illumina scanner setting

data_processing: Methylation data were preprocessed using the minfi package (v.1.30.0) in R. The detection p-value for each sample was computed. Functional normalization with NOOB background correction and dye-bias normalization was performed.

label: Cy5 and Cy3

source_name: glioma tumor tissue

label_protocol: standard Illumina protocol

growth_protocol: Primary human tumor tissue was used as the source of genomic DNA for all patients.  No ex vivo culture or xenografting was performed.

extract_protocol: Tumor tissue was selectively punched from formalin-fixed, paraffin-embedded tissue blocks using using 2.0 mm disposable biopsy punches (Integra Miltex Instruments, cat# 33-31-P/25) or selectively scraped from unstained sections cut from formalin-fixed, paraffin-embedded tissue blocks.  Genomic DNA was extracted using the QIAamp DNA FFPE Tissue Kit (Qiagen) according to the manufacturer’s protocol.

treatment_protocol: Primary human tumor tissue was used as the source of genomic DNA for all patients in the absence of any radiation or chemotherapy administration.  No ex vivo culture or xenografting was performed.

tag: patient sex

value: Female

tag: patient age at dx (yrs)

tag: fusion type

value: EWSR1-BEND2 fusion


title: Total Spleen Bmem 1

value: Post-intranasal influenza virus infection


title: Sample 111_TENA2560_P09_R3

description: BSSE_QGF_140477_HLLWMDRXX_1_TENA2560_P9_TCCGCCAATT_CTCCGTGCTG_S111_L001

tag: system

tag: mouse

tag: population

value: high

value: med

value: TRUE


title: Total MLN Bmem 1

source_name: Murine mediastinal lymph node

value: Mediastinal lymph node


title: differentiated_Dam_Tmem120a-knockdown

description: differentiated Dam control - Tmem120a knockdown

value: Dam

tag: condition


title: HSB179_1_DG

value: Dentate gyrus

value: Male


title: day0, undifferentiated preadipocyte, rep1

description: replicate 1

value: day 0

value: undifferentiated

value: non-target shRNA control


title: differentiated_LaminB1-Dam

description:
differentiated LaminB1-Dam - normal
DamID profile for visualisation (differentiated adipocytes, samples DB4/DB3)

value: control non-target shRNA


title: Sample 110_TENA2560_P16_R3

description: BSSE_QGF_140476_HLLWMDRXX_1_TENA2560_P16_ATACTTGTTC_TAACCGCCGA_S110_L001

value: TENA

tag: egfp

tag: mcherry

value: neg

tag: epcam

tag: passedqc

value: FALSE


title: differentiated_Dam

description: differentiated Dam control - normal

tag: treatment

value: differentiated day9


title: HSB628_DG

tag: tissue

tag: age

value: Female


title: CTXDTA_VDJ_rep1,rep2,rep3,rep4,rep5

city: New York

first: Bic

last: MSKCC

state: NY

address: 1275 York Ave.

institute: Memorial SLoan-Kettering Cancer Center

description: 10x VDJ

data_processing:
Filtered gene expression matrices were generated using 10X CellRanger (version 3.1.0).
Paired single-cell VDJ sequences and annotations were generated using 10X Cellranger VDJ (version 3.1.0) and high confidence sequences were mapped to gene expression barcodes.
Feature barcode matrices were generated for each sample with five mouse using antibody barcode patterns from TotalSeq.
Mouse specific barcodes were demultiplexed by HTO using Seurat (version 3.2.3).
Genome_build: Ensembl mm10
Supplementary_files_format_and_content: Hirschhorn_Gene_counts.csv Raw gene count matrix
Supplementary_files_format_and_content: Hirschhorn_annotations.txt Annotation data, cell barcode to mouse by HTO, barcoded VDJ sequences
Supplementary_files_format_and_content: contig_annotations.csv

extract_protocol:
N/A (10X Genomics)
Chromium Single Cell 5' Reagent Kit
Chromium Single Cell V(D)J Enrichment Kit Mouse T Cell
Chromium Single Cell 5' Feature Barcode Library Kit

treatment_protocol: Cohorts of 5 mice were injected with B16. On day 8, CTX was injected. The next day,  mice were injected with anti-GITR antibody or IgG. Additional cohorts of mice were  injected with B16 on day 8, on day 15 mice were injected with DTA or IgG. After 1 week,  all cohorts of mice were sacrificed, and single cell suspensions were prepared.  Asynchronous B16 challenge was needed for the CTX groups a week apart given the  lack of immune infiltrates caused by chemotherapy treatment. Single cell suspensions  were simultaneously stained with anti-CD5-PE (BD Bioscience) and TotalSeq™- antimouse  hashtag antibodies (C0301, C0302, C0303, C0304, C0305; Biolegend). The cells  were FACS sorted based on CD5+ and next next-generation TCR coupled with 10X  sequencing was performed.

tag: cell type

value: Tumor infiltrating T cells

tag: strain

value: CTX + anti-GITR


title: Sample 109_TENA2560_P15_R3

description: BSSE_QGF_140475_HLLWMDRXX_1_TENA2560_P15_ATCGGCGAAG_TCCAAGAATT_S109_L001

value: high


title: undifferentiated_LaminB1-Dam

description:
undifferentiated LaminB1-Dam
DamID profile for visualisation (undifferentiated adipocytes, samples DB2/DB1)

source_name: preadipocyte

value: undifferentiated day0

tag: damid

value: untreated


title: HSB628_CA2-4

tag: Sex


title: Sample 108_TENA2560_P05_R3

description: BSSE_QGF_140474_HLLWMDRXX_1_TENA2560_P5_AGGCAGCTCT_CGGCTAACGT_S108_L001


title: DTA_VDJ_rep1,rep2,rep3,rep4,rep5

description: 10x VDJ

value: anti-GITR


title: Sample 129_TENA2560_P17_R7

description: BSSE_QGF_140495_HLLWMDRXX_1_TENA2560_P17_CGCAGCAATT_ATTCCGCTAT_S129_L001


title: undifferentiated_Dam

description: undifferentiated Dam control

value: Dam


title: HSB628_CA1


title: HSB179_2_DG

value: Dentate gyrus

value: Male


title: Sample 107_TENA2560_P17_R3

description: BSSE_QGF_140473_HLLWMDRXX_1_TENA2560_P17_TAGAATTGGA_GTTAATCTGA_S107_L001


title: HSB628_SUB

value: Subiculum


title: RMB3_2_DG

description: <= 1h PMI

data_processing:
Cell Raner (v3.0.2) were used for reads alignment, filtering, UMI and barcode counting
Seurat (v3) was used for quality control, batch correction, dimension reduction and cell clustering
Please refer STAR methods for more details
Genome_build: Mmul10; susScr11
Supplementary_files_format_and_content: tab-delimited text files including meta annotation for each cell; tab-delimited text files including UMI counts; tab-delimited text files for gene symbols

organism: Macaca mulatta

source_name: Macaque dentate gyrus

tag: molecule subtype

value: nuclear RNA


title: IgG_VDJ_rep1,rep2,rep3,rep4,rep5

description: 10x VDJ

value: IgG


title: RMB3_1_DG

description: <= 1h PMI


title: HSB628_EC

value: Entorhinal cortex


title: Sample 105_TENA2560_P22_R2

description: BSSE_QGF_140471_HLLWMDRXX_1_TENA2560_P22_TGATGGCTAC_CCAACAACAT_S105_L001

value: TENA

value: TRUE


title: RMB2_1_DG

description: <= 1h PMI


title: 618 (KO) Treg Thym

city: Berlin

first: Pawel

last: Durek

address: Charitéplatz 1

country: Germany

institute: Deutsches Rheuma-Forschungszentrum

data_processing:
Sequence alignment and clone assembly were performed by MiXCR v2.1.3 (MiXCR.CLNS.V05) (67) on Mus Musculus (-s mnu) CDR3 Vβ genes (-c TRB) in default parameter settings.
Genome_build: mm10
Supplementary_files_format_and_content: tsv: tab-seperated values including clonal counts, fractions, the VDJ-Gene annotation and the nucleotide and aminoacid sequence of the CDR3 region

extract_protocol:
Total RNA was isolated from T cells of thymus, spleen and lung sorted directly into RNA lysis buffer (RNeasy, Qiagen). RNA quality was controlled by Bioanalyzer (Agilent Technologies) RNA 6000 Pico kit (Agilent Technologies) regarding RIN > 9.
First strand cDNA synthesis, library construction and indexing was performed according to manufacturer’s guidelines (SMARTer Mouse TCR a/b Profiling Kit, Takara).

value: thymus

tag: mouse id

tag: genotype

value: Foxn1Cre x NIKfl/fl


title: HSB237_SUB

description:
nuclear RNA
Human_cell_meta.txt.gz
Human_counts.mtx.gz
Human_genes.txt.gz


title: 617 (KO) Treg Thym


title: CTX_VDJ_rep1,rep2,rep3,rep4,rep5

description: 10x VDJ

value: Tumor infiltrating T cells

value: CTX


title: 597 (KO) Treg Thym


title: HSB237_EC


title: Sample 103_TENA2560_P16_R2

description: BSSE_QGF_140469_HLLWMDRXX_1_TENA2560_P16_TAATTAGCGT_TGGTTAAGAA_S103_L001

tag: system

tag: mouse

value: high

value: neg

value: med

value: FALSE


title: 615 (WT) Treg Thym

value: Foxn1Cre x NIKfl/wt


title: HSB237_DG

value: Dentate gyrus


title: Sample 102_TENA2560_P15_R2

description: BSSE_QGF_140468_HLLWMDRXX_1_TENA2560_P15_AGTACTCATG_ATGTCGTGGT_S102_L001

tag: population


title: 614 (WT) Treg Thym


title: HSB237_CA2-4

value: Male


title: Sample 101_TENA2560_P05_R2

description: BSSE_QGF_140467_HLLWMDRXX_1_TENA2560_P5_GAACGCAATA_ATCTTACTGT_S101_L001

tag: egfp


title: 613 (WT) Treg Thym


title: HSB237_CA1


title: Sample 106_TENA2560_P18_R3

description: BSSE_QGF_140472_HLLWMDRXX_1_TENA2560_P18_GAATTACAAG_ACCGGCTCAG_S106_L001

tag: mcherry


title: Z_1

city: Shanghai

first: Kailin

last: Li

address: Tian Ping

department: Shanghai Institute of Nutrtion and Health

country: China

institute: Chinese Academy of Sciences

description: two paired-end sequencing

data_processing:
Illumina HiSeq X Ten (2×150bp) sequencer with two paired-end was used for sequencing
Sequenced reads were trimmed for adaptor sequence, mapped with reference genome Triticum aestivum (Taxonomy ID 4565) and Fusarium graminearum (Taxonomy ID 5518)
Software RSEM was used to quantitatively analyze gene expression levels respectively
Genome_build: Triticum aestivum (Taxonomy ID 4565) and Fusarium graminearum (Taxonomy ID 5518)
Supplementary_files_format_and_content: tab-delimited text files include TPM values for every gene and every sample

organism:
Triticum aestivum
Fusarium graminearum

source_name: Fusarium graminearum-infected wheat grains

growth_protocol: Two 5 mm-diameter colonies taken from the edge of F. graminearum strains that were cultivated on PDA medium at 25 ℃ for 5 days.

extract_protocol:
Total RNA was extracted using RNAiso Plus Kits (Takara, China) according to the manufacturer’s recommendation. To eliminate genomic DNA contamination, the DNase I (TaKara, China) was used.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: One portion for every 25 g of Sumai 3, Zhongmai 66B and Annong 0711 wheat grains was plated into a 100 mL sterile conical flask, and the initial aw of the wheat kernel was 0.572, which was confirmed by using a Novasina Labmaster-Neo water activity meter (Novasina, Inc., WA, Swit). Then, sterile distilled water was added to rehydrate to aw: 0.99. The incubation process was carried out in 20 ℃ and humidity (50%) incubator.

value: wheat grains

tag: infection status

value: infected with Fusarium graminearum

tag: cultivar

value: Zhongmai 66B


title: 618 (KO) CD8 Thym


title: HSB231_CA2-4

value: Female


title: 617 (KO) CD8 Thym


title: A_3

description: two paired-end sequencing

value: Annong 0711


title: Sample 104_TENA2560_P09_R2

description: BSSE_QGF_140470_HLLWMDRXX_1_TENA2560_P9_ATTAACAAGG_TGTTGTTCGT_S104_L001

value: TENA

tag: epcam

tag: passedqc

value: TRUE


title: A_2

description: two paired-end sequencing

tag: tissue


title: Sample 99_TENA2560_P18_R2

description: BSSE_QGF_140465_HLLWMDRXX_1_TENA2560_P18_CAGCAATCGT_TGTGATGTAT_S99_L001


title: HSB231_CA1

tag: age


title: Sample 98_TENA2560_P22_R1

description: BSSE_QGF_140464_HLLWMDRXX_1_TENA2560_P22_GGTCTATTAA_CCACGACACG_S98_L001


title: RMB1_1_DG

description: <= 1h PMI

value: nuclear RNA


title: 597 (KO) CD8 Thym

value: thymus

value: Foxn1Cre x NIKfl/fl


title: HSB231_DG


title: A_1

description: two paired-end sequencing


title: 615 (WT) CD8 Thym


title: Z_3

description: two paired-end sequencing


title: HSB231_SUB

value: Subiculum


title: S_3

description: two paired-end sequencing

value: Sumai 3


title: Sample 96_TENA2560_P16_R1

description: BSSE_QGF_140462_HLLWMDRXX_1_TENA2560_P16_ATGGCGCCTG_TCCACGGCCT_S96_L001

value: high

value: neg

value: med


title: Sample 100_TENA2560_P17_R2

description: BSSE_QGF_140466_HLLWMDRXX_1_TENA2560_P17_TTCTGTAGAA_GAGCGCAATA_S100_L001

value: FALSE


title: HSB231_EC

value: Entorhinal cortex


title: 614 (WT) CD8 Thym

value: Foxn1Cre x NIKfl/wt


title: Sample 95_TENA2560_P10_R1

description: BSSE_QGF_140461_HLLWMDRXX_1_TENA2560_P10_ATATGCATGT_TGGTGCCTGG_S95_L001

value: low


title: 613 (WT) CD8 Thym


title: rdd 4acC IP rep-2

city: Fuzhou

first: mao

last: fei

state: Fujian

address: Shangxiadianlu NO.15

department: National Engineering Research Center of JUNCAO

institute: Fujian Agriculture and Forestry University

data_processing:
Bowtie2 was used to match reads to Arabidopsis genome TAIR10. After mapping, only unique reads were used to analysis in the next step. 4acC peaks were called by MASC2 with the cutoffs false discovery rate (FDR) <0.05  Clean reads were aligned to TAIR10 using TopHat v2.0.9. Cufflinks v2.1.1 was used to calculate FPKMs of coding genes.
Genome_build: TAIR10
Supplementary_files_format_and_content: Processed data were stored in bigWigl files and xlsx files.

organism: Arabidopsis thaliana

source_name: leaves

extract_protocol: TIANGEN genomic DNA extraction kit (DP350) and Trizol reagent were used to extract genomic DNA and Total RNA, respectively.  NEBNext Ultra II DNA and RNA Library Prep Kit (E7645S and E7770S) were used to construct sequencing libraries according to standard instructions.Libraries were sequenced on the Illumina NovaSeq6000 platform with 150-bp paired-end reads following the manufacturer's protocols.

value: 3 weeks

tag: strain

tag: chip antibody

value: 4acC (Abcam, ab252215)


title: Sample 130_TENA2560_P05_R7

description: BSSE_QGF_140496_HLLWMDRXX_1_TENA2560_P5_ACGTTCCTTA_GACCGCTGTG_S130_L001


title: 618 (KO) CD4 Thym


title: A27-LV-3

city: Jinan

first: dan

middle: zhen

last: Zhao

state: Shandong Province

address: 107 Wenhua West Road

department: Department of Gynecology and Obstetrics

institute: Shandong University

data_processing:
Basecalls performed using CASAVA version 1.8
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using FASTX-Toolkit  version 0.0.13 and Perl version 5.8.8
mRNA-seq reads were aligned to the mm10 genome assembly using Tophat version 2.0.6 with parameters: -r 100 -I 50000  --max-segment-intron 50000 -a 10 -g 10
Gene abundance measurements were generationed and normalized  using Cufflink version 2.0.2.Linux_x86_64 ; The normalized standard were Fragments Per Kilobase of exon per Megabase of library size (FPKM)
Differential expression were analysed  using DEGseq function package in R program version 2.10.0
Genome_build: GRCh38.91
Supplementary_files_format_and_content: tab-delimited text files include normalized FPKM values and raw fragment counts for each Sample

source_name: human ovarian cancer cell line

extract_protocol:
Total RNA was isolated using RNeasy mini kit (Qiagen, Germany).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: the control group (A27-NC) was tranfected by blank lentivirus, the overexpress group (A27-LV) was transfected by lentivirus overexpressing EPDR1

tag: cell line

tag: treatment

value: EPDR1 overexpressed


title: met1 4acC IP rep-2


title: A27-LV-1


title: A27-LV-2


title: 617 (KO) CD4 Thym

tag: mouse id


title: rdd 4acC IP rep-1


title: A27-NC-3

value: untreated


title: 597 (KO) CD4 Thym

tag: genotype


title: Sample 93_TENA2560_P05_R1

description: BSSE_QGF_140459_HLLWMDRXX_1_TENA2560_P5_TCTCACACGC_CGGACAGTGA_S93_L001

tag: system

value: TENA


title: WT mRNA-seq rep-2

data_processing:
Bowtie2 was used to match reads to Arabidopsis genome TAIR10. After mapping, only unique reads were used to analysis in the next step. 4acC peaks were called by MASC2 with the cutoffs false discovery rate (FDR) <0.05
Clean reads were aligned to TAIR10 using TopHat v2.0.9. Cufflinks v2.1.1 was used to calculate FPKMs of coding genes.
Genome_build: Arabidopsis genome TAIR10
Supplementary_files_format_and_content: Processed data were stored in bigWigl files and xlsx files.

molecule: polyA RNA

growth_protocol: Col-0 plants were grown at 22℃ for 3 weeks.

extract_protocol:
TIANGEN genomic DNA extraction kit (DP350) and Trizol reagent were used to extract  genomic DNA and Total RNA, respectively.
NEBNext Ultra II DNA and RNA Library Prep Kit (E7645S and E7770S) were used to construct sequencing libraries according to standard instructions.Libraries were sequenced on the Illumina NovaSeq6000 platform with 150-bp paired-end reads following the manufacturer's protocols.

treatment_protocol: Extracted genomic DNA is treated with 100 mM NH2OH for 2 h at 60 ℃.

value: leaves


title: S_1

description: two paired-end sequencing

value: wheat grains

value: infected with Fusarium graminearum


title: Sample 91_TENA2560_P18_R1

description: BSSE_QGF_140457_HLLWMDRXX_1_TENA2560_P18_TGCCGGTCAG_CCTGATACAA_S91_L001

tag: mouse

value: TRUE


title: 615 (WT) CD4 Thym

value: thymus


title: met1 4acC IP rep-1


title: Sample 90_TENA2517_P05_R12

description: BSSE_QGF_140456_HLLWMDRXX_1_TENA2517_P5_CCTCCGTCCA_CACATCGGTG_S90_L001

tag: population

value: high


title: 614 (WT) CD4 Thym


title: A27-NC-2


title: WT mRNA-seq rep-1


title: Sample 88_TENA2517_P09_R12

description: BSSE_QGF_140454_HLLWMDRXX_1_TENA2517_P9_TCATAGATTG_GATTAAGGTG_S88_L001

tag: egfp

value: neg


title: 618 (KO) CD8 lung

value: lung

value: Foxn1Cre x NIKfl/fl


title: Sample 89_TENA2517_P22_R12

description: BSSE_QGF_140455_HLLWMDRXX_1_TENA2517_P22_GTATTCCACC_ATGTAGACAA_S89_L001

tag: mcherry

value: FALSE


title: A27-NC-1


title: Sample 94_TENA2560_P15_R1

description: BSSE_QGF_140460_HLLWMDRXX_1_TENA2560_P15_TCAATGGAGA_GCACTACAAC_S94_L001


title: 617 (KO) CD8 lung


title: Sample 87_TENA2517_P16_R12

description: BSSE_QGF_140453_HLLWMDRXX_1_TENA2517_P16_ACATATCCAG_TATGTGCAAT_S87_L001

value: med


title: WT NH2OH 4acC IP rep-2

value: genomic DNA is treated with 100 mM NH2OH for 2 h at 60 C


title: Sample 86_TENA2517_P10_R12

description: BSSE_QGF_140452_HLLWMDRXX_1_TENA2517_P10_GCGTTGGTAT_ACATACTTCC_S86_L001

value: low


title: WT NH2OH 4acC IP rep-1

value: 3 weeks

value: 4acC (Abcam, ab252215)


title: WT 4acC IP rep-2


title: 597 (KO) CD8 lung


title: 615 (WT) CD8 lung

value: Foxn1Cre x NIKfl/wt


title: WT 4acC IP rep-1


title: Total Lung Bmem IV+ 1

source_name: Murine lungs

tag: tissues

value: Lungs

tag: cell type

value: B220+ IgD- CD38hi GL7- CD45.2IV+

value: Post-intranasal influenza virus infection


title: Sample 83_TENA2517_P05_R11

description: BSSE_QGF_140449_HLLWMDRXX_1_TENA2517_P5_GGAGCGTGTA_ATCCGTAAGT_S83_L001

value: TENA

tag: epcam


title: pZT14_4

city: Irvine

first: Kim

last: Green

address: 3208 Biological Sciences 3

department: Neurobiology and Behavior

institute: University of California, Irvine

data_processing:
Illumina HiSeq4000 was used to produce 50bp single-end reads.
Sequenced reads mapped to mm10 whole genome using STAR aligner.
featureCounts were calculated using function of the Rsubread package in R.
After filtering out low-count genes, count distributions were scaled using the calcNormFactors function of the edgeR package.
plotMDS function of the limma package in R was used to perform principal component analysis. Reads Per Kilobase of exon per Megabase of library size (RPKM)  were prepared and fitted to linear models using the voom and lmfit functions.
Genome_build: mm10
Supplementary_files_format_and_content: Excel Workbook file includes RPKM values for all Samples.

source_name: Cortex

extract_protocol:
Brains were removed, flash frozen on dry ice, and cortex was microdissected. RNA was extracted using Rneasy Mini Kit (Qiagen). cDNA synthesis, amplification, library construction and sequencing were performed by Novogene Inc. using Illumina NovaSeq and HiSeq platforms with paired-end 150 bp (PE 150) sequencing strategy.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: 10 day PLX5622 Diet

tag: brain region

value: Cortex


title: pZT14_3


title: 613 (WT) CD8 lung

tag: tissue


title: 613 (WT) CD4 Thym

value: thymus


title: WT input

value: leaves

tag: age


title: Sample 84_TENA2517_P18_R12

description: BSSE_QGF_140450_HLLWMDRXX_1_TENA2517_P18_GTCCGTAAGC_CGTGTATCTT_S84_L001

value: neg

value: high

tag: passedqc


title: Sample 85_TENA2517_P17_R12

description: BSSE_QGF_140451_HLLWMDRXX_1_TENA2517_P17_ACTTCAAGCG_GAACCATGAA_S85_L001

value: FALSE


title: Sample 82_TENA2517_P22_R11

description: BSSE_QGF_140448_HLLWMDRXX_1_TENA2517_P22_CCTCTACATG_GATACCTCCT_S82_L001


title: Sample 81_TENA2517_P09_R11

description: BSSE_QGF_140447_HLLWMDRXX_1_TENA2517_P9_TTGGAATTCC_ACGTCAATAC_S81_L001

value: med


title: 614 (WT) CD8 lung

value: lung


title: 618 (KO) CD4 lung

value: Foxn1Cre x NIKfl/fl


title: 617 (KO) CD4 lung


title: Sample 80_TENA2517_P16_R11

description: BSSE_QGF_140446_HLLWMDRXX_1_TENA2517_P16_TGGTACCTAA_CATGAGTACT_S80_L001


title: 597 (KO) CD4 lung


title: pZT10_4

tag: strain


title: pZT14_1


title: Sample 79_TENA2517_P10_R11

description: BSSE_QGF_140445_HLLWMDRXX_1_TENA2517_P10_ACAAGTGGAC_GCGCGATGTT_S79_L001

value: low


title: 615 (WT) CD4 lung


title: pZT10_3


title: Sample 92_TENA2560_P17_R1

description: BSSE_QGF_140458_HLLWMDRXX_1_TENA2560_P17_CACTCAATTC_TTAAGTTGTG_S92_L001


title: pZT14_2


title: Sample 76_TENA2517_P05_R10

description: BSSE_QGF_140442_HLLWMDRXX_1_TENA2517_P5_GGCAAGCCAG_CAAGCATCCG_S76_L001


title: pZT10_2


title: 618 (KO) CD8 spl

value: spleen


title: pZT6_3


title: 614 (WT) CD4 lung

value: Foxn1Cre x NIKfl/wt


title: 615 (WT) CD8 spl


title: 613 (WT) CD4 lung


title: pZT2_4


title: 614 (WT) CD8 spl


title: pZT2_3


title: pZT10_1


title: pZT2_2


title: pZT6_1


title: Sample 77_TENA2517_P18_R11

description: BSSE_QGF_140443_HLLWMDRXX_1_TENA2517_P18_TGTCGCTGGT_TCGTCTGACT_S77_L001


title: 617 (KO) CD8 spl


title: Sample 75_TENA2517_P22_R10

description: BSSE_QGF_140441_HLLWMDRXX_1_TENA2517_P22_ACGGTCAGGA_CGGCCTCGTT_S75_L001


title: Sample 70_TENA2517_P18_R10

description: BSSE_QGF_140436_HLLWMDRXX_1_TENA2517_P18_CCTGCGGAAC_ATCATAGGCT_S70_L001


title: Sample 74_TENA2517_P09_R10

description: BSSE_QGF_140440_HLLWMDRXX_1_TENA2517_P9_CATTAGTGCG_TGACTACATA_S74_L001


title: pZT6_4


title: Sample 72_TENA2517_P10_R10

description: BSSE_QGF_140438_HLLWMDRXX_1_TENA2517_P10_CTGACTCTAC_ACGGCCGTCA_S72_L001


title: 613 (WT) CD8 spl


title: 618 (KO) CD4 spl


title: Sample 69_TENA2517_P05_R9

description: BSSE_QGF_140435_HLLWMDRXX_1_TENA2517_P5_ACACAGGTGG_TGAGCGTTGT_S69_L001


title: Sample 78_TENA2517_P17_R11

description: BSSE_QGF_140444_HLLWMDRXX_1_TENA2517_P17_ACCGTTACAA_CTCATAGCGA_S78_L001


title: Sample 73_TENA2517_P16_R10

description: BSSE_QGF_140439_HLLWMDRXX_1_TENA2517_P16_TCTGGTATCC_CGTTGCTTAC_S73_L001


title: 597 (KO) CD8 Spl


title: Sample 71_TENA2517_P17_R10

description: BSSE_QGF_140437_HLLWMDRXX_1_TENA2517_P17_TTCATAAGGT_TGTTAGAAGG_S71_L001


title: pZT2_1


title: Sample 68_TENA2517_P22_R9

description: BSSE_QGF_140434_HLLWMDRXX_1_TENA2517_P22_CTTGTACACC_AAGCGCGCTT_S68_L001


title: 597 (KO) CD4 Spl


title: Sample 67_TENA2517_P09_R9

description: BSSE_QGF_140433_HLLWMDRXX_1_TENA2517_P9_GTATTGACGT_GGAATTCCAA_S67_L001


title: 617 (KO) CD4 spl


title: 615 (WT) CD4 spl


title: pZT22_3


title: pZT6_2


title: pZT22_2


title: pZT22_4


title: Sample 65_TENA2517_P10_R9

description: BSSE_QGF_140431_HLLWMDRXX_1_TENA2517_P10_CACGGAACAA_AACCTAGCAC_S65_L001


title: 613 (WT) CD4 spl


title: Sample 64_TENA2517_P17_R9

description: BSSE_QGF_140430_HLLWMDRXX_1_TENA2517_P17_ATACCAACGC_AATTGCTGCG_S64_L001


title: Sample 66_TENA2517_P16_R9

description: BSSE_QGF_140432_HLLWMDRXX_1_TENA2517_P16_TGGAGTACTT_TCTGTGTGGA_S66_L001


title: pZT18_4


title: pZT18_3


title: Sample 62_TENA2517_P05_R8

description: BSSE_QGF_140428_HLLWMDRXX_1_TENA2517_P5_TGGCGCGAAC_AACTGATACT_S62_L001


title: pZT22_1


title: Sample 63_TENA2517_P18_R9

description: BSSE_QGF_140429_HLLWMDRXX_1_TENA2517_P18_TAATGTGTCT_GTAAGGCATA_S63_L001


title: pZT18_2


title: RNAseq Hnf4a 0.05 induced rep2

city: St. Louis

first: Barak

last: Cohen

state: MO

address: 4515 McKinley Ave

department: Genetics

institute: Washington University in St. Louis

data_processing:
We aligned transcripts using Salmon (Patro et al. 2017) with default parameters.
We filtered out any transcripts with fewer than 10 reads.
We called differentially expressed transcripts with DeSeq2 (Love et al. 2014).
Genome_build: hg19
Supplementary_files_format_and_content: Transcript count files from Salmon are in .tar.gz format.

source_name: RNAseq Hnf4a 0.05 induced

growth_protocol: We derived clonal FoxA1, Hnf4a, and FoxA1-Hnf4a lines by transducing K562 lymphoblast cells (ATCC CCL-243) with lentiviral constructs. We then cultured lines in IMDM supplemented with 10% FBS, 1% penicillin-streptomycin, and 1% non-essential amino acids at 37C.

extract_protocol:
We extracted RNA from 1e6 cells/sample using the PureLink RNA Mini column extraction kit (Invitrogen #12183020) and completed on-column DNA digestion with PureLink DNase (Invitrogen #12185010).
We generated libraries by following the NEBNext Ultra II Directional RNA Library Prep Kit (NEB #E7765S) and then size selected the libraries with AmpureXP beads.

treatment_protocol: We induced transgene expression by treating cells for 24 hours with 0.05µg/ml doxycycline.

tag: cell line background

value: Immortalized lymphoblast

value: Hnf4a doxycycline-inducible clonal line

value: 0.05µg/ml doxycycline for 24 hours


title: RNAseq Hnf4a 0.05 induced rep1

tag: treatment


title: RNAseq FoxA1 0.05 induced rep3

source_name: RNAseq FoxA1 0.05 induced

value: FoxA1 doxycycline-inducible clonal line


title: RNAseq Hnf4a 0.05 induced rep3


title: Sample 61_TENA2517_P22_R8

description: BSSE_QGF_140427_HLLWMDRXX_1_TENA2517_P22_ATTGCGCGGT_TTGGCTCCGC_S61_L001

value: TENA


title: Sample 60_TENA2517_P09_R8

description: BSSE_QGF_140426_HLLWMDRXX_1_TENA2517_P9_AACACTGTTA_GCAAGTCTCA_S60_L001

value: TRUE


title: pZT18_1

value: 10 day PLX5622 Diet

value: Cortex


title: Sample 97_TENA2560_P09_R1

description: BSSE_QGF_140463_HLLWMDRXX_1_TENA2560_P9_TCCGTTATGT_TTGTAGTGTA_S97_L001

value: neg


title: RNAseq FoxA1 0.05 induced rep2


title: 614 (WT) CD4 spl

tag: mouse id


title: cZT14_3

value: Control Diet


title: cZT14_2


title: Sample 58_TENA2517_P10_R8

description: BSSE_QGF_140424_HLLWMDRXX_1_TENA2517_P10_TTACCTGGAA_ACAGTTCCAG_S58_L001

value: high

value: FALSE


title: Sample 59_TENA2517_P16_R8

description: BSSE_QGF_140425_HLLWMDRXX_1_TENA2517_P16_TGGCTAATCA_AGGCATGTAG_S59_L001

value: med


title: Sample 57_TENA2517_P17_R8

description: BSSE_QGF_140423_HLLWMDRXX_1_TENA2517_P17_CTCGCTTCGG_TACTAGTCAA_S57_L001


title: CUTTag Hnf4a 0.05 induced +Hnf4a ab rep2

data_processing:
Library strategy: CUT&Tag
We aligned transcripts with bowtie2 using recommended parameters (Kaya-Okur et al. 2020): --very-sensitive --end-to-end --no-mixed --no-discordant -I 10 -X700.
We used DeepTools bamCoverage (Ramirez et al. 2016) to generate RPKM normalized bigwig coverage files.
We called peaks with macs2 with p=1e-5.
We combined overlapping peaks from replicate samples with bedtools intersect.
Genome_build: hg19
Supplementary_files_format_and_content: Peak files from macs2 are in .narrowPeak format.

source_name: CUTTag Hnf4a 0.05 induced

extract_protocol:
We isolated 1e5 cells/sample and then followed the CUTANA Direct-to-PCR CUT&Tag protocol (Epicypher).
We generated libraries by following the CUTANA Direct-to-PCR CUT&Tag protocol (Epicypher) and then size selected the libraries with AmpureXP beads.

tag: genotype

tag: primary antibody

value: Mouse anti-human Hnf4a monoclonal (Invitrogen #MA1-199)

tag: secondary antibody

value: Goat anti-mouse (Epicypher #13-0048)


title: cZT10_3


title: cZT14_1


title: RNAseq FoxA1 0.05 induced rep1


title: CUTTag FoxA1 0.05 induced +FoxA1 ab rep2

source_name: CUTTag FoxA1 0.05 induced

value: Rabbit anti-human FoxA1 monoclonal (Cell Signaling #53528)

value: Goat anti-rabbit (Epicypher #13-0047)


title: Sample 55_TENA2517_P05_R7

description: BSSE_QGF_140421_HLLWMDRXX_1_TENA2517_P5_AACGCACGAG_GCCTCGGATA_S55_L001

source_name: Murine mammary tumor cell lines derived from tumors of lineage-traced MMTV-PyMT transgenic mice

tag: system

tag: mouse

tag: population


title: CUTTag Hnf4a 0.05 induced +Hnf4a ab rep1

value: Immortalized lymphoblast


title: CUTTag FoxA1 0.05 induced +FoxA1 ab rep1


title: cZT10_4


title: Sample 54_TENA2517_P22_R7

description: BSSE_QGF_140420_HLLWMDRXX_1_TENA2517_P22_CTGAGGAATA_CTTAACCACT_S54_L001

tag: egfp

tag: mcherry


title: cZT10_2


title: cZT10_1


title: Sample 52_TENA2517_P16_R7

description: BSSE_QGF_140418_HLLWMDRXX_1_TENA2517_P16_GGAATTGTAA_AGCACATCCT_S52_L001

tag: epcam


title: Sample 51_TENA2517_P10_R7

description: BSSE_QGF_140417_HLLWMDRXX_1_TENA2517_P10_TGATGTAAGA_GTGCGTCCTT_S51_L001

value: low


title: MDA_231_SILENCED_INF__EXP2

city: Kuwait City

first: Rashed

last: Alhammad

address: Safat 13110 - Kuwait

department: Department of Pharmacology & Toxicology, Faculty of Medicine, Health Sciences Centre

country: Kuwait

institute: Kuwait University

description:
Final Gene List.xlsx
MDA_231_without_dups_INF__standard_analysis_sig_Deseq2.csv

data_processing:
Initial alignment of RNA transcript counts, sequence short reads, and normalization has been carried out at the Next Generation Sequencing facility (University of Leeds, United Kingdom).
Genome_build: Human (hg38) genome reference sequences, obtained from UCSC database
Supplementary_files_format_and_content: Final Gene List.xlsx:  Final Gene List (showing the final up/downregulated genes in eight groups: MCF7 IFN upregulated; MCF7 IFN downregulated; MCF7 ETOP upregulated; MCF7 ETOP downregulated; MDA-MB-231 IFN upregulated; MDA-MB-231 IFN downregulated; MDA-MB-231 ETOP upregulated; and MDA-MB-231 ETOP downregulated). Here, up/downregulated does not mean relative to untreated cells; it means up/downregulated following P4HB/PDIA1 silencing compared to scramble (but 'control' and the 'treated' were treated with the drug (ETOP/IFN)
Supplementary_files_format_and_content: Deseq2.csv files:  Statistically significantly differentially expressed genes (padj < 0.01) for each cell line (MCF-7 or MDA-MB-231) with ETOP or IFN with scramble compared to ETOP or IFN with siRNA against P4HB / PDIA1.

growth_protocol: Cells were grown in Dulbecco’s modified Eagle’s medium (Sigma-Aldrich, UK) supplemented with 10% fetal bovine serum (Gibco) and 1% penicillin/streptomycin (Lonza) at 37°C in a humidified atmosphere containing 5% CO2 until they reached 70% confluency.

extract_protocol:
MCF-7 and MDA-MB-231 breast cancer cell lines were seeded in 6-well plate at a concentration of 3x10^5 cells per well for 24 hr after treatment. RNA was extracted according to the RNeasy Mini Kit supplier instructions (Qiagen, UK). After collecting RNA, the samples were kept at -80°C before sequencing carried out by the Next Generation Sequencing Facility (University of Leeds, United Kingdom). In addition, initial alignment of RNA transcript counts, sequence short reads, and normalization has been carried out at the Next Generation Sequencing facility (University of Leeds, United Kingdom).
Handled at the Next Generation Sequencing facility (University of Leeds, United Kingdom)

treatment_protocol:
Where indicated cells were treated with 10 ng/ml interferon-γ (IFN-γ) (Sigma-Aldrich) for 24 h or 10 μM etoposide (ETO) for 24 h (Sigma-Aldrich).
Concentration of 5µM of the siGENOME PDIA1 siRNA and 5µM of the siGENOME non-targeting siRNA pool was added to each well containing 2x10^5 cells in DMEM and  incubated for 72h according to the suppliers’ instructions (Dharmacon, UK).

tag: cell line

tag: cell type

value: Human Breast Cancer Cell

tag: erα status

value: Negative

tag: tp53 status

value: Mutated (R280K)

tag: drug treatment

value: 10 ng/ml interferon-γ (IFN-γ) for 24 h

tag: sirna status

value: siRNA P4HB/PDIA1


title: MDA_231_SILENCED_ETOP_EXP3

description:
Final Gene List.xlsx
MDA_231_without_dups_ETOP__standard_analysis_sig_Deseq2.csv

value: 10 μM etoposide (ETO) for 24 h


title: MDA_231_SILENCED_INF_EXP1


title: cZT6_2

tag: strain

tag: treatment

tag: brain region

value: Cortex


title: MDA_231_SILENCED_ETOP_EXP2


title: cZT6_1

value: Control Diet


title: Sample 48_TENA2517_P05_R6

description: BSSE_QGF_140414_HLLWMDRXX_1_TENA2517_P5_CAGTGGCACT_TAACAATAGG_S48_L001

value: TENA

value: neg

value: high

tag: passedqc

value: TRUE


title: MDA_231_SILENCED_ETOP_EXP1


title: cZT2_4


title: cZT2_3


title: MDA_231_CNTRL_INF_EXP3

value: Scramble


title: Sample 50_TENA2517_P17_R7

description: BSSE_QGF_140416_HLLWMDRXX_1_TENA2517_P17_GACACCATGT_TCAACGTGTA_S50_L001


title: Sample 49_TENA2517_P18_R7

description: BSSE_QGF_140415_HLLWMDRXX_1_TENA2517_P18_AGTGTTGCAC_CTGGTACACG_S49_L001


title: Sample 47_TENA2517_P22_R6

description: BSSE_QGF_140413_HLLWMDRXX_1_TENA2517_P22_GTCCTGGATA_CGGTGGCGAA_S47_L001


title: MDA_231_CNTRL_INF_EXP2


title: MDA_231_CNTRL_INF_EXP1


title: cZT2_2


title: cZT6_3


title: MDA_231_CNTRL_ETOP_EXP3


title: Sample 45_TENA2517_P16_R6

description: BSSE_QGF_140411_HLLWMDRXX_1_TENA2517_P16_CGTTATTCTA_CCATAAGGTT_S45_L001

value: med

value: FALSE


title: Sample 46_TENA2517_P09_R6

description: BSSE_QGF_140412_HLLWMDRXX_1_TENA2517_P9_AGATCCATTA_ATCTCTACCA_S46_L001


title: cZT22_4


title: Sample 44_TENA2517_P10_R6

description: BSSE_QGF_140410_HLLWMDRXX_1_TENA2517_P10_CTGCGAGCCA_AATCCGGCCA_S44_L001


title: cZT22_3


title: Sample 43_TENA2517_P15_R6

description: BSSE_QGF_140409_HLLWMDRXX_1_TENA2517_P15_CCATCTCGCC_TTCTATGGTT_S43_L001


title: cZT22_2


title: MDA_231_CNTRL_ETOP_EXP1


title: MDA_231_CNTRL_ETOP_EXP2


title: MCF_7_SILENCED_INF__EXP3

description:
Final Gene List.xlsx
MCF_7_without_dups_INF__standard_analysis_sig_Deseq2.csv

value: Positive

value: Wild-type


title: cZT22_1


title: Sample 53_TENA2517_P09_R7

description: BSSE_QGF_140419_HLLWMDRXX_1_TENA2517_P9_GCATAAGCTT_TTCCGTCGCA_S53_L001


title: MDA_231_SILENCED_INF__EXP3

value: Human Breast Cancer Cell


title: cZT6_4


title: Sample 41_TENA2517_P18_R6

description: BSSE_QGF_140407_HLLWMDRXX_1_TENA2517_P18_ACTCGGCAAT_GACAACTGAA_S41_L001


title: MCF_7_SILENCED_INF__EXP2


title: cZT18_4


title: MCF_7_SILENCED_INF_EXP1


title: cZT18_3


title: MCF_7_SILENCED_ETOP_EXP3

description:
Final Gene List.xlsx
MCF_7_without_dups_ETOP__standard_analysis_sig_Deseq2.csv


title: Sample 39_TENA2517_P22_R5

description: BSSE_QGF_140405_HLLWMDRXX_1_TENA2517_P22_CAATCGGCTG_GCTGTAGGAA_S39_L001


title: cZT2_1


title: cZT18_2


title: Sample 38_TENA2517_P09_R5

description: BSSE_QGF_140404_HLLWMDRXX_1_TENA2517_P9_GTGCAGACAG_TACCATCCGT_S38_L001


title: MCF_7_SILENCED_ETOP_EXP2


title: cZT18_1


title: MCF_7_SILENCED_ETOP_EXP1


title: Sample 37_TENA2517_P16_R5

description: BSSE_QGF_140403_HLLWMDRXX_1_TENA2517_P16_TGTAATCGAC_GATCACCGCG_S37_L001


title: MCF_7_CNTRL_INF_EXP3


title: Sample 36_TENA2517_P10_R5

description: BSSE_QGF_140402_HLLWMDRXX_1_TENA2517_P10_ACCGGCCGTA_TGGCAATATT_S36_L001

value: low


title: Sample_87881

city: Ann Arbor

first: Maria Luisa

last: Varela

state: Michigan

address: 1150 West Medical Center Drive

department: Neurosurgery

institute: University of Michigan

data_processing:
We checked the quality of the raw reads data for each sample using FastQC (version v0.11.3)
Tuxedo Suite software package for alignment, differential expression analysis, and post-analysis diagnostics
We aligned reads to the reference genome including both mRNAs and Ensembl lncRNAs (UCSC mm10)  using TopHat (version 2.0.13) and Bowtie2 (version 2.2.1.).
We used FastQC for a second round of quality control (post-alignment), to ensure that only high quality data would be input to expression quantitation and differential expression analysis.
We ran the following technique for differential expression analysis: Cufflinks/CuffDiff using UCSC mm10.fa as the reference genome sequence. Cufflinks/Cuffdiff (version 2.1.1):
Genome_build: mm10
Supplementary_files_format_and_content: For expression quantitation, normalization, and differential expression analysis, we used parameter settings: “--multi-read-correct” to adjust expression calculations for reads that map in more than one locus, as well as “--compatible-hits-norm” and “--upper-quartile–norm” for normalization of expression values. We generated diagnostic plots using the CummeRbund R package.

source_name: Streams

extract_protocol:
Glioma bearing mice prefused with sucrose, brains were removed, cryopreserved in OCT and  cryosectioned at 10 µm thickness. Tumor sections were fixed in ethanol and stained with 4% Cresyl violet and 0.5% eosin. Oncostream areas from 3 independent mouse glioma samples were dissected from surrounding glioma tissue using a LMD7000 Leica laser capture microdissection. RNA was isolated for laser microdissected tissues using the RNeasy Plus Micro Kit following the manufacturer recommendations (Qiagen). sequenced on the Illumina HiSeq 4000, as paired-end 50 nt reads with 10% PhiX spike-in, according to manufacturer's recommended protocols.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tissue

value: Tumor (glioma)

tag: age

value: 6 weeks


title: Sample 42_TENA2517_P17_R6

description: BSSE_QGF_140408_HLLWMDRXX_1_TENA2517_P17_GTCTAATGGC_AGTGGTCAGG_S42_L001

data_processing:
Paired-end reads were aligned to the mouse genome (UCSC version mm10 analysis set) with STAR with default parameters except for allowing up 10 hits to genome (outFilterMultimapNmax 10), reporting only one location for hits with equal score (outSAMmultNmax 1), and for filtering reads without evidence in spliced junction table (outFilterType "BySJout").
The output was sorted and indexed with samtools. Read and alignment quality was evaluated using the qQCReport function of the Bioconductor package QuasR.
The featureCounts function from Bioconductor package subread was used to count the number of read (5'ends) overlapping with the exons of each gene assuming an exon union model (with used gene model provided by ensembl v96).
Processing of the read count matrix for genes was done according to the steps illustrated in Bioconductor Single Cell Analysis workflow (Amezquita et al., 2020).
Genome_build: mm10
Supplementary_files_format_and_content: TXT file (with tab separated values) with raw counts for Ensembl Genes, 1.column is Ensembl Gene ID, 2. and remaining columns contain raw counts

tag: system

tag: mouse


title: Sample_87882


title: Sample 35_TENA2517_P15_R5

description: BSSE_QGF_140401_HLLWMDRXX_1_TENA2517_P15_GGTAACTCGC_AAGTTGGTGA_S35_L001

tag: population

tag: egfp


title: Sample_87880


title: Sample 34_TENA2517_P17_R5

description: BSSE_QGF_140400_HLLWMDRXX_1_TENA2517_P17_CAGCCGCGTA_ACTAGCCGTG_S34_L001

tag: mcherry

tag: epcam


title: MCF7_CNTRL_INF_EXP1

tag: cell line

tag: cell type

value: 10 ng/ml interferon-γ (IFN-γ) for 24 h


title: MCF_7_CNTRL_INF_EXP2

tag: erα status

tag: tp53 status


title: Sample 40_TENA2517_P05_R5

description: BSSE_QGF_140406_HLLWMDRXX_1_TENA2517_P5_TATGTAGTCA_CGCACTAATG_S40_L001


title: MCF_7_CNTRL_ETOP_EXP3

tag: drug treatment

value: 10 μM etoposide (ETO) for 24 h

tag: sirna status


title: Sample_87879

source_name: NoStreams

tag: strain


title: Sample 32_TENA2517_P05_R4

description: BSSE_QGF_140398_HLLWMDRXX_1_TENA2517_P5_ACAGTGTATG_GAACATACGG_S32_L001


title: Sample_87878


title: MCF_7_CNTRL_ETOP_EXP2


title: Sample 31_TENA2517_P22_R4

description: BSSE_QGF_140397_HLLWMDRXX_1_TENA2517_P22_GTGACACGCA_GCTTACGGAC_S31_L001


title: Sample_87877


title: Sample 30_TENA2517_P09_R4

description: BSSE_QGF_140396_HLLWMDRXX_1_TENA2517_P9_CCACCAGGCA_CTTATGGAAT_S30_L001


title: CTXDTA_HTO_rep1,rep2,rep3,rep4,rep5

description: 10x HTO

value: Tumor infiltrating T cells

tag: treatment

value: CTX + anti-GITR


title: CTX_HTO_rep1,rep2,rep3,rep4,rep5

description: 10x HTO

value: CTX


title: MCF_7_CNTRL_ETOP_EXP1


title: Sample 29_TENA2517_P16_R4

description: BSSE_QGF_140395_HLLWMDRXX_1_TENA2517_P16_GCCGCACTCT_TCCGACCTCG_S29_L001

value: TENA

value: neg

tag: passedqc


title: MDA-βs1_2

city: Richardson

first: Nikki

last: Delk

address: 800 West Campbell Road

department: Biological Sciences

institute: University of Texas at Dallas

description: cell line derived from MDA-PCa-2b treated with 0.5 ng/ml IL-1 alpha for 4 months

data_processing:
Raw data were de-multiplexed and converted to fastq files using bcl2fastq (v2.17)
The fastq files were checked for quality using fastqc (v0.11.2) and fastq_screen (v0.4.4)
Sequencing reads were mapped to hg19 reference genome (from igenomes) using STAR (v2.5.3a), counted using featureCounts (subread/v1.6.0)
Genome_build: hg19
Supplementary_files_format_and_content: tab delimited text file with raw read counts calculated using igenomes gtf file

extract_protocol:
RNA was extracted from cells treated with cytokines using GeneJET RNA Purification kit (Thermo Fisher Scientific, Waltham, MA; K0732) as per manufacturer’s instructions. Genomic DNA contamination was removed by treating 1 ug of RNA with 1 U of DNase-I (Thermo scientific, Waltham, MA; EN0521) following manufacturer’s instructions.
RNA-seq was performed by the Genome Center at tThe University of Texas at Dallas (Richardson, TX). Total RNA library was prepared using Illumina Truseq Stranded Total RNA prep Gold kit (Illumina). The prepared libraries were sequenced on an Illumina NextSeq 500 platform (San Diego, CA) with 75bp single-end reads.

treatment_protocol: MDA-PCa-2b cells were chronically cultured in 0.5 ng/ml IL-1 alpha or IL-1 beta (in HPC1 + 20% FBS) for 4 months. IL-1 is cytotoxic/static, so the viable, proliferating colonies that emerged after 4 months in IL-1 alpha or IL-1 beta were expanded to generate the IL-1a subline (MDA-αs1) and the IL-1b subline (MDA-βs1). MDA-PCa-2b parental cells were cultured in vehicle (0.1% BSA in 1xPBS) in HPC1 + 20% FBS. For RNA sequencing, MDA-PCa-2b parental, MDA-αs1 and MDA-βs1 cells were plated and cultured in HPC1 + 20% FBS for 3 days and the MDA-PCa-2b parental cells were also treated with 25 ng/ml IL-1a or IL-1b for 3 days.  Total RNA was isolated from 3 biological replicates for RNA sequencing.

tag: tissue

value: prostate cancer

tag: treated

value: 0.5 ng/ml IL-1 beta for 4 months


title: Sample 56_TENA2517_P18_R8

description: BSSE_QGF_140422_HLLWMDRXX_1_TENA2517_P18_TCTATCCTAA_CGTCGACTGG_S56_L001

extract_protocol:
FACS-sorted cells were collected as 5-cell pools in 2.5µl of 0.2% TX-100 and 2U/μl RNase inhibitor (TakaraBio, 2313B) in PBS into 96-well plates (Thermo Fisher Scientific, 4346906) and kept in -80°C prior to use. RNAseq libraries were prepared according to the Smart-seq2 method (Picelli, 2014).
5-cell RNA-seq: RNA/cDNA preamplification and Nextera XT library preparation reactions were set up with a Mosquito HV system (SPT Labtech). After reverse transcription and amplification, the concentration of cDNA generated from each sample was measured using PicoGreen (Thermo Fisher Scientific). cDNA was normalized to 0.1-0.15ng/µl and 0.75 µl were used for library preparation with the Nextera XT DNA library preparation kit (Illumina). Multiplexed library pools were then pooled and PE 2x51 sequenced with an Illumina NovaSeq 6000 system, v1 reagents.

tag: system

value: high

value: TRUE


title: Sample 28_TENA2517_P10_R4

description: BSSE_QGF_140394_HLLWMDRXX_1_TENA2517_P10_ACCACGACAT_TCGTATGCGG_S28_L001

tag: mouse

value: FALSE


title: DTA_HTO_rep1,rep2,rep3,rep4,rep5

description: 10x HTO

value: anti-GITR


title: MDA-βs1_3


title: IgG_HTO_rep1,rep2,rep3,rep4,rep5

description: 10x HTO

value: IgG


title: Lung MBC 4

data_processing:
RNAseq analysis was performed using the web-based Galaxy platform maintained by Australian Galaxy Team (https://usegalaxy.org.au/).
Reads were mapped to the Homo sapiens reference genome (hg38) using HISAT2 and reads were quantified using HTSeq.
Count matrices were generated and inputted into Degust (http://degust.erc.monash.edu) for final data analysis and visualization. The Degust Voom/Limma method was selected for data processing.
Genome_build: hg38
Supplementary_files_format_and_content: CSV/tab-delimited text files include raw counts or CPM values

source_name: Lung

extract_protocol:
RNA was isolated from sorted cells using a Zymo Research Direct-zol RNA Microprep Kit, as per manufacturer's protocol.
Ribosomal RNA depletion was performed using Nugen Ovation SoLo RNA-Seq system. Nugen Ovation SoLo library construction chemistry kit was use for library construction. RNA libraries were prepared for sequencing using standard manufacturer's protocols.

value: Lung

value: Live-dead negative, CD14-, CD8-, CD16-, CD10-, Streptavidin-, CD20+ CD19+ IgD- IgG+


title: Sample 27_TENA2517_P15_R4

description: BSSE_QGF_140393_HLLWMDRXX_1_TENA2517_P15_TAAGCATCCA_TCAATCCATT_S27_L001

tag: population


title: MDA-αs1_3

description: cell line derived from MDA-PCa-2b treated with 0.5 ng/ml IL-1 beta for 4 months


title: MDA-αs1_2


title: Lung MBC 3


title: Sample 33_TENA2517_P18_R5

description: BSSE_QGF_140399_HLLWMDRXX_1_TENA2517_P18_TGATTATACG_GTCGATTACA_S33_L001

tag: egfp


title: MDA-αs1_1


title: Lung MBC 2


title: Sample 25_TENA2517_P18_R4

description: BSSE_QGF_140391_HLLWMDRXX_1_TENA2517_P18_AACCATAGAA_GGCGAGATGG_S25_L001

tag: mcherry


title: MDA-PCa-2b_acute_IL-1b_3

description: parental cell line treated with 25 ng/ml IL-1b for 3 days

value: 25 ng/ml IL-1a for 3 days


title: Lung MBC 1


title: MDA-PCa-2b_acute_IL-1b_2


title: Sample 23_TENA2517_P22_R3

description: BSSE_QGF_140389_HLLWMDRXX_1_TENA2517_P22_ACGCCTTGTT_TAAGGAACGT_S23_L001

tag: epcam


title: Sample 22_TENA2517_P09_R3

description: BSSE_QGF_140388_HLLWMDRXX_1_TENA2517_P9_TATTGCGCTC_CTGTGTTAGG_S22_L001

value: med


title: Sample 24_TENA2517_P05_R3

description: BSSE_QGF_140390_HLLWMDRXX_1_TENA2517_P5_TTCTACATAC_CTAACTGTAA_S24_L001


title: Lung lymph node MBC 4

source_name: Lung lymph node

value: Lung lymph node


title: MDA-PCa-2b_acute_IL-1b_1

tag: cell line


title: Sample 21_TENA2517_P16_R3

description: BSSE_QGF_140387_HLLWMDRXX_1_TENA2517_P16_ATGGTTGACT_GGCCTGTCCT_S21_L001


title: Lung lymph node MBC 2

tag: cell type


title: MDA-PCa-2b_acute_IL-1a_3

description: parental cell line treated with 25 ng/ml IL-1a for 3 days


title: MDA-βs1_1


title: MDA-PCa-2b_acute_IL-1a_2


title: Sample 26_TENA2517_P17_R4

description: BSSE_QGF_140392_HLLWMDRXX_1_TENA2517_P17_GGTTGCGAGG_AATAGAGCAA_S26_L001


title: Sample 20_TENA2517_P10_R3

description: BSSE_QGF_140386_HLLWMDRXX_1_TENA2517_P10_GATAGGCCGA_CGCACATGGC_S20_L001

value: low


title: Sample 19_TENA2517_P15_R3

description: BSSE_QGF_140385_HLLWMDRXX_1_TENA2517_P15_CCATCATTAG_GGTTGCCTCT_S19_L001


title: MDA-PCa-2b_acute_IL-1a_1


title: MDA-PCa-2b_3

description: parental cell line


title: Waldenstrom Patient 6 CITE

city: Decatur

first: Akhilesh

last: Kaushal

state: GA

address: 1760 Haygood street

institute: Emory University

data_processing:
Library strategy: CITE-Seq
Reads were aligned to human reference sequence GRCh38/hg38, filtered, deduplicated and converted into a feature barcode matrix using Cell Ranger 4.0
Data were filtered using the following specifications…
Cells with fewer than 200 unique sequenced genes, more than 10% mitochondrial gene and more than 70,000 sequenced features were filtered to exclude dead cells and doublets
Seurat V3 pipeline for multi-modal data was used for analysis. Batch correction was performed using CCA method in Seurat.
Genome_build: GRCh38/hg38
Supplementary_files_format_and_content: BAM files

source_name: Bone Marrow Mononuclear cells

extract_protocol:
Cells were fixed, permeabilized and washed in accordance with the fluidigm`s cell surface and nuclear staining protocol as described.
Gene expression and cell surface libraries were prepared according to the protocol from 10X Genomics

value: Bone Marrow Mononuclear cells

tag: disease state

value: Waldenstrom


title: PBMC MBC 4

source_name: PBMC

value: PBMC


title: Sample 17_TENA2517_P18_R3

description: BSSE_QGF_140383_HLLWMDRXX_1_TENA2517_P18_GAGAATGGTT_TCGGCAGCAA_S17_L001

value: TENA

value: neg


title: Sample 16_TENA2517_P05_R2

description: BSSE_QGF_140382_HLLWMDRXX_1_TENA2517_P5_CGGTTACGGC_AAGACTATAG_S16_L001


title: MDA-PCa-2b_2

description: parental cell line

value: prostate cancer


title: Lung lymph node MBC 3


title: Waldenstrom Patient 5 CITE


title: Lung lymph node MBC 1


title: Sample 14_TENA2517_P09_R2

description: BSSE_QGF_140380_HLLWMDRXX_1_TENA2517_P9_GAAGCGGCAC_CGGCTCTACT_S14_L001

value: high


title: Sample 15_TENA2517_P22_R2

description: BSSE_QGF_140381_HLLWMDRXX_1_TENA2517_P22_TCCATTGCCG_GAATGCACGA_S15_L001

value: TRUE


title: Waldenstrom Patient 3 CITE


title: Waldenstrom Patient 2 CITE


title: PBMC MBC 2


title: Sample 13_TENA2517_P16_R2

description: BSSE_QGF_140379_HLLWMDRXX_1_TENA2517_P16_CTTGCCATTA_ATCACGAAGG_S13_L001


title: MMV675968 rep 3

city: Calgary

first: Haeun

last: Kim

state: AB

address: 3330 Hospital Drive N.W.  HSC-B045

country: Canada

institute: University of Calgary

data_processing:
Using FastQC (39), each of the raw reads were checked for their per base sequence quality and overrepresented sequences for any adaptor sequence recognition. Following parameters were used with Trimmomatic on Galaxy platform to improve the quality of the sequences including removing any of the recognized adapters: 1) initial ILLUMINACLIP with customized adapter sequences, 2) filtering out poor quality sequences using pre-set parameters of sliding window, leading, and trailing functions, and 3) heading cropping sequences improving per base sequence content.
The quality checked sequences for each sample were mapped against the genomic sequence of V. cholerae O1 biovar El Tor str. N16961 which were calculated for expression levels and normalized using the Geneious software version 10.1.3 (Geneious does not separately provide count data when reads are processed). DESeq2 was used to calculate the differential expression between DMSO control and each of the compound-treated samples. For MMV687807-treated reads, genes with differential expression log2 value greater than 2 were considered upregulated whereas genes with differential expression log2 value less than -2 were considered downregulated. On the other hand, genes from MMV675968-treated samples had log2 value greater than 1 and less than -1 as its cutoffs.  Both sets of genes were considered statistically significant if the adjusted p-value was <0.05. The biological pathways of each upregulated or downregulated gene were identified using KEGG pathway mapper and UniProtKB.
Genome_build: V. cholerae O1 biovar El Tor str. N16961 (NC_002505.1, NC_002506.1)
Supplementary_files_format_and_content: Excel files of information on genes with adjusted p <0.05 that passed the cutoff described above. It also has pathways each gene was categorized to.

organism: Vibrio cholerae

source_name: Bacteria

growth_protocol: V. cholerae El Tor strain C6706 was aerobically grown at 37 oC in LB (w/v 1% tryptone, 0.5% yeast extract, 0.5% NaCl) shaking at 225 rpm to an OD600 of 0.4

extract_protocol:
700 µl of cells were incubated with 100 µl of 8x lysis buffer (0.8% SDS and 16 mM EDTA) and an equal volume of acidic phenol and incubated at 65 oC for 5 minutes, followed by incubation on ice for 10 minutes.  After phase separation by centrifugation for 2 minutes at 13,000 x g, the aqueous phase was isolated and combined with an equal volume of anhydrous ethanol.  RNA was purified using the Direct-zolTM RNA miniprep kit (Zymo Research) with an in-column DNaseI digest to remove contaminating DNA.  After quantification of RNA, the ribosomal RNA was removed with the RiboZero kit from Illumina.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were then incubated with sub-inhibitory concentrations of MMV687807 (2.5 mM), MMV675968 (10 nM) or DMSO control (0.2 %) in triplicate

value: El Tor strain C6706


title: PBMC MBC 5


title: MMV675968 rep 1


title: PBMC MBC 1


title: MMV675968 rep 2


title: MMV687807 rep 3


title: Waldenstrom Patient 1 CITE


title: Sample 12_TENA2517_P10_R2

city: Basel

first: DBM Bioinformatics

last: Core Facility

address: Hebelstrasse 20

institute: University of Basel

description: BSSE_QGF_140378_HLLWMDRXX_1_TENA2517_P10_GAGTCATAGG_GTGTGGCGCT_S12_L001


title: Sample 18_TENA2517_P17_R3

description: BSSE_QGF_140384_HLLWMDRXX_1_TENA2517_P17_AGAGGCAACC_CTAATGATGG_S18_L001

value: FALSE


title: MGUS Patient 7 CITE

value: MGUS


title: T4WT_CDMN_Exp_5_20210119

city: Baltimore

first: Suvarna

last: Nadendla

state: MD

address: 670 W.Baltimore Street

department: Institute for Genome Sciences

institute: University of Maryland School of Medicine

data_processing:
Illumina reads were mapped using Bowtie to the genome of Streptococcus pneumoniae TIGR4. Gene expression counts for all samples were then estimated using HTseq. Counts were then tabularized for analysis then imported into Rstudio for analyses and normalized Variance Stabilized Transformation (VST) counts were acquired using the DESeq2 R package. We then estimated differentially expressed (DE) genes using the DESeq2 R package and filtered using an FDR cutoff of 0.05 and an absolute log2 fold change of 1.
Genome_build: Streptococcus pneumoniae TIGR4 (NC_003028.3)

organism: Streptococcus pneumoniae TIGR4

source_name: Chemically defined medium mimicking nasopharynx

growth_protocol: To model growth in human nasopharynx and human blood, bacteria were grown to exponential phase in chemically defined medium (CDM) containing carbohydrates at levels present in the nasopharynx (CDMN: 0.6 g/L galactose and 0.3 g/L sialic acid) and bloodstream (CDMB: 1 g/L glucose and 0.6 g/L sialic acid).

extract_protocol:
Samples were stored in RNAprotect Bacteria Reagent (Qiagen), and stored at −80C. On the day of RNA extractions, samples were thawed and spun down to discard the supernatant. Pellets were then incubated in 100 μL of lysis buffer (10 μL of mutanolysin, 20 μL of proteinase K,30 μL of lysozyme, 40 μL of TE buffer) for 10 minutes. Pellets were mechanically disrupted in 600 μL RLT buffer (RNeasy Mini Kit, Qiagen) containing 1% b-mercaptoethanol, using a motorized pestle for 30 seconds. Samples were then spun through a Qiashredder followed by the addition of 590 μL of 80% ethanol, and RNA was captured on the RNeasy Mini Kit columns with DNase treatment on column (Qiagen protocol), followed by additional DNase treatment in solution. Extracted RNA was quantitated using a Bioanalyzer (Agilent). Ribosomal RNA was depleted using the NEBNext rRNA Depletion Kit Bacteria (Catalog #: E7850S) for Gram-positive + Gram-negative species.
300 bp-insert RNA-seq Illumina libraries were constructed using 0.01 – 2.0 μg of enriched mRNA that was fragmented then used for synthesis of strand-specific cDNA using the NEBNext Ultra II Directional RNA Library Prep Kit (NEB #E7103). The cDNA was purified between enzymatic reactions and the size selection of the library performed with AMPure SpriSelect Beads (Beckman Coulter Genomics). The titer and size of the libraries were assessed on the LabChip GX (Perkin Elmer) and with the Library Quantification Kit (Kapa Biosciences).

tag: genotype

value: wildtype


title: Sample 11_TENA2517_P15_R2

description: BSSE_QGF_140377_HLLWMDRXX_1_TENA2517_P15_CCGTATGTTC_CATACACTGT_S11_L001


title: Waldenstrom Patient 7 CITE


title: PBMC MBC 3

city: Melbourne

first: Hyon Xhi

last: Tan

address: 792 Elizabeth St

institute: The University of Melbourne, at the Peter Doherty Institute for Infection and Immunity

value: Live-dead negative, CD14-, CD8-, CD16-, CD10-, Streptavidin-, CD20+ CD19+ IgD- IgG+


title: Waldenstrom Patient 4 CITE


title: Sample 10_TENA2517_P17_R2

description: BSSE_QGF_140376_HLLWMDRXX_1_TENA2517_P17_AGTCAGACGA_ACCAGCGACA_S10_L001


title: T4WT_CDMN_Exp_4_20210119


title: MMV687807 rep 2


title: MMV687807 rep 1


title: MGUS Patient 5 CITE


title: Sample 9_TENA2517_P18_R2

description: BSSE_QGF_140375_HLLWMDRXX_1_TENA2517_P18_GACTGAGTAG_GTTGATAGTG_S9_L001


title: T4WT_CDMB_Exp_5_20210119

source_name: Chemically defined medium mimicking blood


title: DMSO rep 3

description:
used as control to compare treatments to
Processed_Data_1.xlsx
Processed_Data_2.xlsx

value: 0.2% DMSO


title: T4WT_CDMB_Exp_4_20210119


title: T4delta_ccpA_CDMN_Exp_2_20210119

value: delta ccpA


title: Sample 8_TENA2517_P05_R1

description: BSSE_QGF_140374_HLLWMDRXX_1_TENA2517_P5_GATCAAGGCA_CCTTGTTAAT_S8_L001


title: MGUS Patient 3 CITE


title: MGUS Patient 4 CITE


title: MGUS Patient 2 CITE


title: Sample 7_TENA2517_P22_R1

description: BSSE_QGF_140373_HLLWMDRXX_1_TENA2517_P22_CTAGTGCTCT_TGGAACAGTA_S7_L001


title: MGUS Patient 6 CITE


title: T4delta_ccpA_CDMB_Exp_3_20210119


title: Sample 6_TENA2517_P09_R1

description: BSSE_QGF_140372_HLLWMDRXX_1_TENA2517_P9_AACATCGCGC_GTCCACTTGT_S6_L001

value: med


title: HAEC-CoCl2_H3K27ac

city: Tokyo

first: Naoko

last: Hattori

address: 5-1-1 Tsukiji, Chuo-ku

department: Research Institute

country: Japan

institute: National Cancer Center

data_processing:
Fastp (version 0.20.0) was used for sequencing QC and adapter trimming.
All reads were aligned to the human genome GRCh38/hg38 using the short-read aligner Bowtie 2 (version 2.4.2) with default parameters.
The resultant SAM file was converted into a BAM file, duplicates were removed using SAMtools (version 1.11), and blacklisted regions were filtered.
Peak calling was performed with the input control using MACS2 (version 2.1.0) with default parameters
Genome_build: hg38
Supplementary_files_format_and_content: Peak files were obtained from MACS2 in bed format

source_name: human aortic endothelial cells

growth_protocol: Human aortic EC (HAEC; Lonza, CC-2535) was grown in EGMTM-2 BulletKitTM supplemented with 2% (v/v) fetal bovine serum and growth factors. These ECs were used between passage 6 and 10.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Sequencing library was prepared with GenNext NGS Library Prep Kit (Toyobo, LPK-101) from 5 ng for a final sequencing depth of 20 million reads per sample.

treatment_protocol: Stock solution (10 mM) of CoCl2 was prepared in sterile distilled water and further diluted in medium in order to obtain the final desired concentrations. HAEC was cultured in medium with 100 μM of CoCl2, and incubated for 48 hours (h) in standard CO2 incubator.

tag: chip antibody

value: H3K27ac (ab4729, Abcam)

value: 100 microM CoCl2


title: MGUS Patient 1 CITE

value: Bone Marrow Mononuclear cells


title: T4delta_ccpA_CDMB_Exp_2_20210119


title: HAEC-CoCl2_Input


title: Sample 5_TENA2517_P16_R1

description: BSSE_QGF_140371_HLLWMDRXX_1_TENA2517_P16_GACGAGATTA_ACATTATCCT_S5_L001


title: Healthy Donor4 CITE

value: healthy donor


title: T4delta_ccpA_CDMB_Exp_1_20210119


title: HAEC-CTRL_H3K27ac

value: Control


title: Sample 4_TENA2517_P10_R1

description: BSSE_QGF_140370_HLLWMDRXX_1_TENA2517_P10_ATTCCATAAG_TGCCTGGTGG_S4_L001

value: TENA

value: neg

value: low


title: conB_3

description: two paired-end sequencing

organism: Triticum aestivum

source_name: non-infected wheat grains

value: wheat grains

tag: infection status

value: not infected

tag: cultivar

value: Sumai 3


title: Healthy Donor3 CITE


title: T4delta_ccpA_CDMN_Exp_3_20210119

tag: strain


title: HAEC-CTRL_Input

tag: treatment


title: DMSO rep 1

value: El Tor strain C6706


title: T4delta_ccpA_CDMN_Exp_1_20210119


title: Sample 3_TENA2517_P15_R1

description: BSSE_QGF_140369_HLLWMDRXX_1_TENA2517_P15_CGTCTCATAT_TATAGTAGCT_S3_L001

value: high

tag: passedqc

value: TRUE


title: Healthy Donor2 CITE


title: Healthy Donor1 CITE


title: conB_2

description: two paired-end sequencing

tag: tissue


title: Sample 1_TENA2517_P18_R1

description: BSSE_QGF_140367_HLLWMDRXX_1_TENA2517_P18_GAACTGAGCG_TCGTGGAGCG_S1_L001

tag: system


title: Sample 2_TENA2517_P17_R1

description: BSSE_QGF_140368_HLLWMDRXX_1_TENA2517_P17_AGGTCAGATA_CTACAAGATA_S2_L001

tag: mouse

value: FALSE


title: DMSO rep 2

value: 0.2% DMSO


title: conB_1

description: two paired-end sequencing


title: plasmid PB1 Library #1

status: Public on Nov 17 2021

city: San Diego

first: Alistair

middle: Brian

last: Russell

address: 9500 Gilman Dr,

institute: University of California, San Diego

description: barcode

data_processing:
Data were processed with a custom pipeline described at https://github.com/a5russell/Defective_Library_Mendes_Russell
grch38
Supplementary_files_format_and_content: tab-delineated files with raw count data for transcripts or barcodes

organism: Influenza A virus (A/WSN/1933(H1N1))

source_name: plasmid

extract_protocol:
RNA was extracted using column-based miniprep kits, either from Qiagen or NEB.
SMART-Seq for mRNA samples, amplicon sequencing for others

tag: library treatment

value: plasmid

tag: library identity


title: minigenome(-PB2) PB1 Library #2

description:
barcode
293t cells were transfected with indicated libraries and plasmids expressing PB1, PA, and NP but not PB2. Harvested at 24h.

source_name: 293t cells


title: plasmid HA Library #3

description: barcode

value: HA


title: plasmid HA Library #2

description: barcode


title: minigenome(-PB2) PB1 Library #3


title: plasmid HA Library #1

description: barcode


title: plasmid PB1 Library #2

description: barcode


title: supernatant HA Library #1

description: barcode

source_name: 293t and MDCK-SIAT1 cells

value: supernatant


title: supernatant PB1 Library #3

description: barcode


title: supernatant PB1 Library #1

description: barcode


title: supernatant HA Library #3

description: barcode


title: supernatant PB1 Library #2

description: barcode


title: supernatant HA Library #2

description: barcode


title: minigenome(-PB2) PB1 Library #1


title: minigenome(-PB2) HA Library #3


title: B73 4acC IP

data_processing:
Bowtie2 was used to match reads to Arabidopsis genome TAIR10 or B73 genome Zea_mays_AGPv4. After mapping, only unique reads were used to analysis in the next step. 4acC peaks were called by MASC2 with the cutoffs false discovery rate (FDR) <0.05. Bowtie2 was used to match reads to B73 genome Zm-B73-APvp4
Clean reads were aligned to TAIR10 using TopHat v2.0.9. Cufflinks v2.1.1 was used to calculate FPKMs of coding genes.
Genome_build: Arabidopsis genome TAIR10,B73 genome Zea_mays_AGPv4
Supplementary_files_format_and_content: Processed data were stored in bigWigl files and xlsx files.

organism: Zea mays

source_name: leaves

extract_protocol:
TIANGEN genomic DNA extraction kit (DP350) and Trizol reagent were used to extract genomic DNA and Total RNA, respectively.
NEBNext Ultra II DNA and RNA Library Prep Kit (E7645S and E7770S) were used to construct sequencing libraries according to standard instructions.Libraries were sequenced on the Illumina NovaSeq6000 platform with 150-bp paired-end reads following the manufacturer's protocols.

tag: tag

value: 2 weeks

tag: antibody

value: 4acC (Abcam, ab252215)


title: minigenome(-PB2) HA Library #2


title: minigenome(-PB2) HA Library #1


title: minigenome HA Library #2

description:
barcode
293t cells were transfected with indicated libraries and plasmids expressing PB2, PB1, PA, and NP. Harvested at 24h.

value: minigenome


title: IFNL1-depleted PB1 Library #3

description:
barcode
A549 cells infected with the indicated library at an MOI of 0.05 were sorted on an IFNL1 reporter at 14h post-infection

source_name: A549 cells

value: IFNL1 MACS-depleted


title: minigenome PB1 Library #1


title: minigenome HA Library #3


title: minigenome PB1 Library #2


title: minigenome HA Library #1


title: IFNL1-depleted PB1 Library #2


title: plasmid PB1 Library #3

description: barcode


title: minigenome PB1 Library #3


title: IFNL1-depleted PB1 Library #1


title: IFNL1-depleted HA Library #3


title: MDA-PCa-2b_1

description: parental cell line

value: prostate cancer

tag: cell line


title: IFNL1-depleted HA Library #2


title: IFNL1-depleted HA Library #1


title: IFNL1-enriched HA Library #1

value: IFNL1 MACS-enriched


title: IFNL1-enriched PB1 Library #2


title: IFNL1-enriched HA Library #2


title: IFNL1-enriched PB1 Library #1


title: IFNL1-enriched HA Library #3


title: Junction Sequencing HA and PB1 Library #2

description:
barcode and junctions
initial sequencing of plasmid libraries from BtgZI digest

value: junction assembly

value: HA and PB1


title: Junction Sequencing HA and PB1 Library #1


title: seed_Ver3

city: Shenyang

first: Zhiyong

last: Liu

state: Liaoning Province

address: Dongling Road 120

institute: Shenyang Agriculral University

data_processing:
Illumina Casava1.8 software used for basecalling.
Prior to assembly, the low quality reads(1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20) were removed.
We aligned reads of samples to the reference genome using HISAT2 package.
The mapped reads of each sample were assembled using StringTie, all transcriptomes were merged to reconstruct a comprehensive transcriptome.
Unmapped reads were still mapped to genome using tophat-fusion. CIRCExplorer2 and CIRI2 were used to identify circRNAs.
Genome_build: BRAD：Brassica_rapa_v3.0
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each isoforms

organism: Brassica rapa subsp. pekinensis

source_name: seeds that were vernalized at 4℃ for 25 days

growth_protocol: The seeds germinated and grew in a wet filter paper culture dish at room temperature.

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer’s procedure. The total RNA quantity and purity were analysis of Aglient 2100 Bioanalyzer and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0.
Approximately 10 ug of total RNA was used to deplete ribosomal RNA according to the manuscript of the Ribo-Zero™ rRNA removal kit (Illumina, San Diego, USA).Then the left RNA was fragmented into small pieces using divalent cations under elevated temperature. The cleaved RNA fragments were reverse-transcribed to create the final cDNA library in accordance with the protocol for the Truseq Stranded Total RNA HT Sample Prep Kit (Illumina, San Diego, USA).

treatment_protocol: After germination, the seeds were divided into two groups. One group was vernalized. The germinated seeds were placed in a refrigerator at 4 ℃ and treated at low temperature for 25 days under dark conditions, which was called ‘Ver’. The other group, without low-temperature vernalization, was placed at room temperature (about 48 hours), which was called ‘Nor’.

value: seeds


title: Junction Sequencing HA and PB1 Library #3


title: seed_Nor3

source_name: seeds germinated about 48 hours at room temperature


title: seed_Nor1

value: seeds germinated about 48 hours at room temperature


title: seed_Nor2


title: seed_Ver1

value: seeds that were vernalized at 4℃ for 25 days


title: ZD8, rep

city: Ynagling

first: Shiduo

last: Sun

address: Xinong Rd #22

institute: Northwest A&F University

data_processing:
We applied the reads filtering towards the raw reads after sequencing to achieve the clean data following the criteria: a) a)10% base quality <15 b) 13% base quality <20 c) 15bp < read length < 33bp.
Utilizing the BWA software, we mapped the clean data to miRBase 22.0 Sus scrofa miRNA database and sscrofa11.1 genome.
TPM counting
Genome_build: sscrofa11.1
Supplementary_files_format_and_content: TXT file contain TPM for each sample

organism: Sus scrofa

source_name: ovary

growth_protocol: The ovaries in our study were collected from sows 4 days post the 4th delivery picked from a commercial sow piggery in Hanshiwei Food Ltd., Co., (Dahua, Guangxi, China), which is negative for PRRSV (porcine reproductive and respiratory syndrome virus) and PCV (porcine circovirus). All sows were slaughtered in a standard slaughterhouse in Xinyouxian Livestock Ltd., Co., (Xining, Guangxi, China), and the left ovaries were quickly taken and frozen in liquid nitrogen.

extract_protocol:
Total RNA was extracted from cell or animal tissue by Trizol reagent (Invitrogen) separately. The RNA quality was checked by Bioanalyzer 2200 (Aligent) and kept at -80℃.The RNA with RIN >8.0 is right for cDNA library construction.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: group

value: large litter size (LLS)


title: ZD7, rep


title: ZD12, rep

value: small litter size (SLS)


title: ZD3, rep


title: ZD5, rep


title: ZD2, rep


title: IFNL1-enriched PB1 Library #3


title: seed_Ver2


title: seed_Ver1_miRNA

description: Small RNA

data_processing:
Raw reads were subjected to an in-house program, ACGT101-miR (LC Sciences, Houston, Texas, USA) to remove adapter dimers, junk, low complexity, common RNA families (rRNA, tRNA, snRNA, snoRNA) and repeats
Subsequently, unique sequences with length in 18~26 nucleotide were mapped to specific species precursors in miRBase 22.0 by BLAST search to identify known miRNAs and novel 3p- and 5p- derived miRNAs.
Length variation at both 3' and 5' ends and one mismatch inside of the sequence were allowed in the alignment.
The unique sequences mapping to specific species mature miRNAs in hairpin arms were identified as known miRNAs. The unique sequences mapping to the other arm of known specific species precursor hairpin opposite to the annotated mature miRNA-containing arm were considered to be novel 5p- or 3p-derived miRNA candidates.
The remaining sequences were mapped to other selected species precursors (with the exclusion of specific species) in miRBase 22.0 by BLAST search, and the mapped pre-miRNAs were further BLASTed against the specific species genomes to determine their genomic locations.
The above two we defined as known miRNAs. The unmapped sequences were BLASTed against the genomes, and the hairpin RNA structures containing sequences were predicated from the flank 120 nt sequences using RNAfold software (http://rna.tbi.univie.ac. at/cgi-bin/RNAfold.cgi). The criteria for secondary structure prediction were: (1) number of nucleotides in one bulge in stem (≤12) (2) number of base pairs in the stem region of the predicted hairpin (≥16) (3) cutoff of free energy (kCal/mol ≤-15) (4) length of hairpin (up and down stems + terminal loop ≥50) (5) length of hairpin loop (≤200). (6) number of nucleotides in one bulge in mature region (≤4) (7) number of biased errors in one bulge in mature region (≤2) (8) number of biased bulges in mature region (≤2) (9) number of errors in mature region (≤4) (10) number of base pairs in the mature region of the predicted hairpin (≥12) (11) percent of mature in stem (≥80).
Genome_build: BRAD：Brassica_rapa_v3.0
Supplementary_files_format_and_content: tab-delimited text files include sequence and expression of all miRNAs

source_name: seed

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer’s procedure. The total RNA quantity and purity were analysis of Aglient 2100 Bioanalyzer and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0.
Approximately 5 µg of total RNA were used to prepare nine small RNA librariesaccording to the protocol of TruSeq Small RNA Sample Prep Kits (Illumina, San Diego, CA, USA).


title: seed_Nor1_miRNA

description: Small RNA


title: seed_Ver2_miRNA

description: Small RNA


title: seed_Ver3_miRNA

description: Small RNA


title: seed_Nor3_miRNA

description: Small RNA


title: 7M_KO_M7_AF_L

city: Philadelphia

first: Makarand

last: Risbud

address: 1025 Walnut Street

institute: Thomas Jefferson University

description: Total RNA from ABCC6 KO AF tissue; sst-rma normalization; DABG p<0.05; p<0.01; FC 1.75

hyb_protocol: Affymetrix Gene chips, Mouse Clariom S, were hybridized with 2.5 μg fragmented and biotin-labeled cDNA in 100 μl of hybridization cocktail.

scan_protocol: Array scanning was performed on an Affymetrix GeneChip Scanner 3000 7G using Command Console Software (Affymetrix).

data_processing: Raw data were processed and .CHP files were generated by sst-rma normalization from Affymetrix .CEL files, and quality control of the experiment was performed in Transcriptome Analysis Console (TAC) v4.0.2 (Affymetrix). The experimental group was compared to the control group in the TAC, including all probe sets where at least 50% of the samples had a DABG (detected above background) p < 0.05. Inclusion cutoffs were defined at a 1.75-fold change and p-value < 0.05.

source_name: AF KO

label_protocol: Single-stranded cDNA was generated, then fragmented and biotin-labeled using the GeneChip WT Plus kit according to ABI protocol (Thermo Fisher Scientific).

growth_protocol: ABCC6WT and ABCC6KO mice were obtained from the lab of Koen Van de Wetering at Thomas Jefferson University. All mice were aged to 7 months. Genotypes were confirmed by PCR.

extract_protocol: AF tissue was micro-dissected from lumbar intervertebral discs of 4 ABCC6 WT and 4 ABCC6 knock-out animals and immediately placed in RNAlater® Reagent (INVITROGEN). Tissues were homogenized with a Pellet Pestle Motor (Sigma Aldrich, Z359971) and RNA was extracted from tissue lysates using RNeasy Mini Kit (Qiagen), according to the manufacturer's instructions.

value: AF

tag: Sex

value: female


title: seed_Nor2_miRNA

description: Small RNA


title: 7M_WT_M1_AF_L

description: Total RNA from ABCC6 WT AF tissue; sst-rma normalization; DABG p<0.05; p<0.01; FC 1.75

source_name: AF WT


title: 7M_WT_M5_AF_L


title: 7M_KO_M8_AF_L


title: 7M_KO_M9_AF_L


title: 7M_WT_M2_AF_L


title: 7M_WT_M3_AF_L


title: 7M_KO_M6_AF_L


title: Donor 2 Infected Chip 2

city: Cambridge

first: Vincent

middle: Nevan

last: Miao

state: Massachusetts

address: 400 Main St.

institute: MIT

data_processing:
Demultiplex w/ bcl2fastq v2.2 implemented on Cumulus (snapshot 4)
Align w/ STAR implemented on Cumulus (snapshot 9)
Genome_build: Custom human/pseudovirus based on hg38
Supplementary_files_format_and_content: Text file w/ cells x genes digital gene expression (UMIs)

source_name: Primary Human Intestine

growth_protocol: See manuscript

extract_protocol: Seq-Well S3 according to https://doi.org/10.1016/j.immuni.2020.09.015

treatment_protocol: See manuscript

tag: donor

tag: infected

value: TRUE

tag: disease state

value: NL63 coronavirus

tag: num. arrays

value: Primary Human Intestine


title: PBMCs_TB patient_sample 10

city: Beijng

first: Fang

last: Xu

state: Beijing

address: 56 Nanlishi Road, Xicheng District

department: Beijing Pediatric Research Institute

institute: Beijing Children’s Hospital, Capital Medical University

hyb_protocol: Each slide was hybridized with 1.65μg Cy3-labeled cRNA using Gene Expression Hybridization Kit (Cat.# 5188-5242, Agilent technologies, Santa Clara, CA, US) in Hybridization Oven (Cat.# G2545A, Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes (Cat.# 121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(Cat.# 5188-5327, Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions.

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent technologies, Santa Clara, CA, US) with default settings, Dye channel: Green, Scan resolution=3μm, PMT 100%, 20bit. Data were extracted with Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US). Raw data were normalized by Quantile algorithm, limma packages in R.

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: peripheral blood

label_protocol: Total RNA was amplified and labeled by Low Input Quick Amp WT Labeling Kit (Cat.# 5190-2943, Agilent technologies, Santa Clara, CA, US), following the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (Cat.# 74106, QIAGEN, GmBH, Germany).

extract_protocol: Total RNA was extracted and purified using miRNeasy Mini Kit（Cat#217004，QIAGEN, GmBH, Germany) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).

value: peripheral blood mononuclear cell(PBMC)

tag: patient diagnosis

value: TB


title: PBMCs_TB patient_sample 6


title: EV_GL261_1

city: Gifu

first: Hiroyuki

last: Tomita

address: 1-1 Yanagido

institute: Gifu University

description: transplanted glioma cells to mouse brain and then extraqcted RNA

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent-028005 SurePrint G3 Mouse GE 8x60K Microarray for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

source_name: obtained from B6(EV) male brain

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was extracted using a RNeasy kit (Qiagen, TX, USA) according to the manufacturer’s protocol. cDNAs were synthesized using a SuperScript III First-Strand Synthesis Kit (Life Technologies, Inc., MD, USA).

treatment_protocol: All the GL261 gloma cells were transplanted to mouse brains of WT(wild type) and EV(Ext1 flox/flox; VE-Cre) mice. Brain tumors were removed from the mice 14 to 21 days later and then extraced RNA.

tag: genotype

value: glioma transplanted to  Ext1 flox/flox; VE-Cre

tag: cell type

value: glioma (GL261) cells

value: brain


title: PBMCs_TB patient_sample 9

tag: tissue


title: PBMCs_TB patient_sample 2


title: Donor 2 Infected Chip 1


title: PBMCs_TB patient_sample 3


title: WT_GL261_1

source_name: obtained from B6(WT) male brain

value: glioma transplanted to WT


title: PBMCs_Healthy Control_sample 4

value: healthy


title: EV_GL261_4


title: PBMCs_TB patient_sample 1


title: EV_GL261_3


title: PBMCs_Healthy Control_sample 9


title: PBMCs_Healthy Control_sample 1


title: WT_GL261_3


title: PBMCs_Healthy Control_sample 5


title: PBMCs_TB patient_sample 8


title: WT_GL261_4


title: PBMCs_Healthy Control_sample 2


title: PBMCs_Healthy Control_sample 7


title: PBMCs_TB patient_sample 5


title: EV_GL261_2


title: Donor 1 Uninfected Chip 2

value: FALSE

value: uninfected


title: PBMCs_TB patient_sample 7


title: PBMCs_Healthy Control_sample 6


title: PBMCs_TB patient_sample 4


title: PBMCs_Healthy Control_sample 8


title: PBMCs_Healthy Control_sample 3


title: PBMCs_Healthy Control_sample 10


title: Donor 2 Uninfected Chip 2


title: WT_GL261_2


title: 25NHV

city: Wien

first: Andreas

middle: B

last: Diendorfer

address: Leberstraße 20

country: Austria

institute: TAmiRNA GmbH

data_processing:
fastQC (v0.11.8) quality control
cutadapt (v2.3) adapter trimming and filtering
bowtie (v1.2.2) genome alignment
miRDeep2 (v2.0.1.2) miRNA quantification
edgeR (v3.28) differential expression
Genome_build: GRCh38.p12
Supplementary_files_format_and_content: miRNA RPM matrix

source_name: Plasma

extract_protocol:
Maxwell RSC miRNA Tissue kit (Promega, AS1460)
RealSeq-Biofluids Plasma/Serum miRNA Library kit for Illumina sequencing (RealSeq Biosciences, 600-00048; protocol 20181220_RealSeq-BF_CL)

value: NHV


title: 67non-severe

value: COVID

value: Non-severe


title: Donor 1 Uninfected Chip 1


title: 68non-severe


title: Donor 2 Uninfected Chip 1


title: 5NHV


title: 60NHV


title: 66non-severe


title: 63non-severe


title: 52non-severe


title: 39non-severe


title: 50non-severe


title: 61non-severe


title: 2non-severe


title: 45non-severe


title: 46non-severe


title: 31non-severe


title: 8NHV


title: 64non-severe


title: 22non-severe


title: 75NHV


title: 39NHV


title: 11non-severe


title: 62severe

value: Severe


title: 15NHV


title: 57severe


title: 13non-severe


title: 59severe


title: 37non-severe


title: 56severe


title: 54severe


title: 65NHV


title: 38non-severe


title: 49severe


title: 47severe


title: 60severe


title: 51severe


title: 35severe


title: 44severe


title: 28severe


title: 8severe


title: 19severe


title: 30severe


title: 24severe


title: 51NHV


title: 26severe


title: 19NHV


title: 25severe