title: D0-3

source_name: microglia isolated from PLX treated mice (PLX5622, 1200 mg/kg, 14 days)


title: Hacha root control [15_S16]

status: Public on May 09 2020

type: SRA

city: Dusseldorf

first: Hans-Joerg

last: Mai

address: Universitaetsstrasse 1

department: Institute of Botany

country: Germany

institute: Heinrich Heine University

library_source: transcriptomic

data_processing:
Basecalls were performed and demultiplexed using bcl2fastq2.
Sequenced reads were trimmed for adapter sequence and masked for low-complexity or low-quality sequence, then mapped to the IRGSP 1.0 reference transcriptome using kallisto.
TSV files with TPM (transcripts per million) values were generated using kallisto.
Average insert length information was extracted from the command line output of kallisto.
Genome_build: IRGSP 1.0
Supplementary_files_format_and_content: TSV files were generated using kallisto. Besides normalized TPM values they contain counts and length information.

molecule: total RNA

organism: Oryza sativa

source_name: Roots of 11-day old Hacha rice plants that were previously grown under control conditions for 2 days

growth_protocol: Plant growth was conducted in a controlled growth chamber, with a 16-hour light/ 8-hour dark cycle, 70 % humidity, a light intensity of 220 µmol*m-2*s-1, a day/night temperature of 26 °C. Rice seeds were disinfected using 1 % sodium hypochlorite for 15 min. Subsequently, seeds were soaked in water for one day at 4 °C and transferred for three days in the dark to 30 °C for germination. Homogenously grown seedlings were transplanted into 1 l pots filled with half-strength modified Hoagland solution for two days. Then, half-strength nutrient solution was replaced with a full-strength solution containing 1 mM calcium nitrate, 2.5 mM potassium nitrate, 2.86 mM ammonium nitrate, 1 mM potassium dihydrogen phosphate, 1 mM magnesium sulfate, 0.045 μM boric acid, 0.009 µM manganese chloride, 0.666 μM zinc sulfate, 0.4 μM copper sulfate, and 0.0176 μM sodium molybdate and 50 µM Fe sodium EDTA, pH 6.2, which also represented the control treatment condition. The nutrient solutions were renewed every second day.

extract_protocol:
RNA was isolated from 100 mg plant material using the RNeasy plant mini kit (Qiagen) according to the manufacturer‘s instructions.
Libraries were constructed with the TruSeq RNA Sample Prep Kit v2 (Illumina Technologies). Double-stranded cDNA was purified for end repair, adaptor ligation, and DNA fragment enrichment.

treatment_protocol: 9-days old plants were treated for two days with Fe stress with full-strength Hoagland medium plus 15 mM Fe sulfate at pH 5.2 was applied or plants were exposed to control conditions (50 µM Fe).

tag: line

value: Hacha (derived from a cross of CRM 53 X IR 64)

tag: age

value: 11 days

tag: tissue

value: whole root


title: C30-22-2: unstressed progeny of C30 (2nd generation) rep2

city: shanghai

first: junzhong

last: Liu

state: shanghai

address: 300 Feng Lin Road

department: National Key Laboratory of Plant Molecular Genetics

country: China

institute: Institute of Plant Physiology and Ecology, SIBS, CAS

data_processing:
Sequenced reads were trimmed for adaptor sequence, and get rid of ribosome RNA reads and low-quality sequence, then mapped to TAIR10 using Hisat2 (version 2.0.4)
The number of mapped reads of each gene were calculated using Stringtie (version:1.3.0), and normalized by TMM (trimmed mean of M values), and then the FPKM (Fragments Per Kilobase of exon model per Million mapped reads) for each gene were calculated.
Genome_build: TAIR10
Supplementary_files_format_and_content: A single excel include RPKM values and counts for all samples

molecule: polyA RNA

organism: Arabidopsis thaliana

growth_protocol: The seeds were plated on 1/2 Murashige and Skoog (MS) agar medium and placed at 4°C in darkness for 3 d, and then moved to a growth chamber and incubated at 22°C. One week later, the seedlings were transplanted to the soil and retained at 22°C or transferred to 30°C for heat treatment under long-day conditions (16-h light/8-h dark)

extract_protocol:
Total RNA was extracted using TRIZOL Reagent (Cat#15596-018，Life technologies, Carlsbad, CA, US)following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNAClean XP Kit (Cat A63987, Beckman Coulter,Inc.Kraemer Boulevard Brea, CA,USA)and RNase-Free DNase Set  (Cat#79254, QIAGEN, GmBH, Germany).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Total RNA was isolated from 4-week-old 22ºC or 30ºC-grown plants.

tag: genotype

value: the fifth true leaves


title: Lachit root control [20_S21]

source_name: Roots of 11-day old Lachit rice plants that were previously grown under control conditions for 2 days

value: Lachit (derived from a cross between CRM 13-3241 and Kalinga 2)


title: Anther, rep 1

city: St. Louis

first: Blake

middle: C.

last: Meyers

state: MO

address: 975 N Warson Road

country: USA

institute: Donald Danforth Plant Science Center

data_processing:
The adapter sequences were trimmed from raw sequence reads, and then the RNA sequences were trimmed to the lengths between 18 and 50 nucleotides.
The reads were mapped to the Soy genome (version JGI version2 genome). We used Trimmomatic version for the removal of the adapter sequences.
Genome_build: SoyGenome (version JGI version2)
Supplementary_files_format_and_content: Text containing distinct smallRNAs with their raw abundance after removing the adapter sequences

organism: Glycine max

source_name: Anther

extract_protocol:
RNA-seq library constructed from soybean.
The RNA-seq library was constructed with Illumina TruSeq RNA preparation kit (not stranded)

value: Anther


title: C30-2: Col-0 grown at 30℃ (1st generation) rep2


title: Hacha root control [14_S15]


title: C30-22-1: unstressed progeny of C30 (2nd generation) rep1


title: D0-1

city: New York

first: Li

last: Gan

state: NY

address: 413 East 69th Street, 9th Floor BB904

department: Helen and Robert Appel Alzheimer’s Disease Research Institute

institute: Weill Cornell Medicine

data_processing:
The Illumina BCL output files were processed by the Cell Ranger software (3.1.0, 10x Genomics)
Genome_build: mm10
Supplementary_files_format_and_content: barcodes.tsv, features.tsv and matrix.mtx files were generated by Cell Ranger count.

organism: Mus musculus

extract_protocol:
Whole brain was dissected, with the cerebellum removed, and homogenized. The homogenates were then processed for myelin depletion using myelin removal beads. The myelin-depleted fraction was incubated with a Cd11b antibody and then Sytox-blue live/dead stain. Live Cd11b+ fraction was sorted using FACS and used to make scRNAseq library.
Single-cell expression libraries were prepared using the 10x genomics Chromium single cell 3′ library and gel bead kit v3 reagents (10x Genomics, PN-1000075)

treatment_protocol: Six C57BL/6 mice (2 brains/sample) were treated with PLX diet (1200 mg/kg) for 14 days (D0). An additional six mice (2 brains/sample) were switched to a control diet for 2 days after PLX treatment (D2). Three age-matched non-treated mice were used as control (Ctrl).

tag: strain

tag: treatment


title: nodule

source_name: nodule

value: nodule


title: Hacha root control [13_S14]


title: C30-1: Col-0 grown at 30℃ (1st generation) rep1


title: pod shell 14DAF

source_name: pod shell

value: pod shell


title: Ctrl-3

source_name: microglia isolated from naïve mice

value: naïve


title: Lachit leaf excess Fe [12_S13]

source_name: L2 leaves of 11-day old Lachit rice plants that were previously grown on excess Fe media for 2 days

value: L2 leaves


title: C22-2: WT rep2


title: pod shell 10DAF


title: Ctrl-2


title: Ctrl-1


title: one cm pod

source_name: pod

value: pod


title: C22-1: WT rep1


title: Lachit leaf excess Fe [11_S12]


title: Seed cotyledon stage

source_name: Seed

value: Seed


title: GNC

city: Wuhan

first: Miusi

last: Shi

state: Hubei

address: No.237 in Luoyu Road

department: School of Stomatology

institute: The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei MOST)

data_processing:
Base-calling using Bcl2fastq (v2.17.1.14)
Filtering using Cutadapt（version 1.9.1）
Clean data were aligned to the mm10 genome via software Hisat2(v2.0.1)
Estimate gene and isoform expression levels from the pair-end clean data using  HTSeq (v0.6.1)
Differential expression analysis used the DESeq Bioconductor package,P value <0.05
GO-TermFinder was used identifying Gene Ontology (GO) terms that annotate a list of enriched genes with a significant p-value less than 0.05;use scripts in house to enrich significant differential expression gene in KEGG pathways.
Novel transcripts can be predicted via results of  Cuffcompare
Alternative splicing analysis using  Asprofile v1.0
Samtools v0.1.18 with command mpileup and Bcftools v0.1.19 were used to do SNV calling
Usage of exons caused by the experimental condition(DEU) was analysed by Bioconductor package DEXSeq (V 1.21.1).
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file includes FPKM values for each Sample

source_name: Abelson murine leukemia virus-induced tumor

growth_protocol: The murine-derived macrophage cell line RAW 264.7 cells (China Center for Type Culture Collection, CCTCC) was used. RAW 264.7 cells cultured in Dulbecco’s modified Eagle Medium (DMEM) containing 10% fetal bovine serum (FBS, Gibco, Life Technologies Corporation) and 1% penicillin/streptomycin (P/S, HyClone, Thermo Fisher Scientific Inc).  All cultures were performed at 37℃ in a humidified 5% CO2 atmosphere.

extract_protocol:
Total RNA was extracted using RNAiso Plus (TaKaRa Bio Inc., Japan) following the manufacturer’s protocol.
Library preparations were constructed according to the manufacturer’s protocol (NEBNext® UltraTM RNA Library Prep Kit for Illumina®)

treatment_protocol: RAW 264.7 cells were treated with 0.5mM hydroxyurea (HU, H8627, Sigma Aldrich) and gold nanoparticles at same time, then cultured for 12 hours.

value: ascites

tag: cell line

tag: passages

value: hydroxyurea + gold nanocages (at same time)


title: Lachit root excess Fe [8_S9]

source_name: Roots of 11-day old Lachit rice plants that were previously grown on excess Fe media for 2 days


title: Lachit root excess Fe [9_S10]


title: root

source_name: root

value: root


title: Con

value: control


title: Seed early maturity stage 1


title: Seed early maturity stage 2


title: Young leaf

source_name: leaf

value: leaf


title: Hacha leaf excess Fe [6_S7]

source_name: L2 leaves of 11-day old Hacha rice plants that were previously grown on excess Fe media for 2 days

value: Hacha (derived from a cross of CRM 53 X IR 64)


title: Hacha leaf excess Fe [5_S6]

value: 11 days


title: Lachit leaf excess Fe [10_S11]


title: 480_KD3: SCN5A knockdown SW480 cells-3

city: Guangzhou

first: Qiaoqi

last: Sui

address: Dongfeng East Road 651

institute: Sun Yat-sen University Cancer Center

description: SCN5A knockdown SW480 cells-3

data_processing:
The purified l library products were evaluated using the Agilent 2200 TapeStation and Qubit®2.0(Life Technologies, USA) and then diluted to 10 pM for cluster generation in situ on the pair-end flow cell followed by sequencing (2×150 bp) on Illumina HiSeq3000.
The clean reads were obtained after removal of reads containing adapter, ploy-N and at low quality from raw data. HISAT2 was used to align the clean reads to the human reference genome hg19 with default parameters.
HTSeq was subsequently employed to convert aligned short reads into read counts for each gene model. Differential expression was assessed by DE sequencing read counts as input.
The Benjamini–Hochberg multiple test correction method was enabled. Differentially expressed genes were chosen according to the criteria of adjusted p-value < 0.05.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

organism: Homo sapiens

source_name: colorectal carcinoma

growth_protocol: SW480 (Human colorectal cancer cells) were cultured at 37°C in complete media (RMPI1640 supplemented with 100 µg/ml streptomycin, 100 IU/ml penicillin, and 10% FBS).

extract_protocol:
Cells were collected, and RNA was isolated and purified with the Trizol (Invitrogen).then RNA was isolated and purified with the Trizol (Invitrogen). RNA purity was assessed using the ND-1000 Nanodrop. Each RNA sample had an A260:A280 ratio above 1.8 and A260:A230 ratio above 2.0. RNA integrity was evaluated using the Agilent 2200 TapeStation (Agilent Technologies, USA) and each sample had the RIN above 7.0. Briefly, rRNAs were removed from Total RNA using EpicentreRibo-Zero rRNA Removal Kit (illumina, USA) and fragmented to approximately 200bp. Subsequently, the purified RNAs were subjected to first strand and second strand cDNA synthesis following by adaptor ligation and enrichment with a low-cycle according to instructions of NEBNext® Ultra™ RNA Library Prep Kit for Illumina (NEB, USA).(Vazyme, Nanjing, China) to enrich mRNA, and RNA library was performed by using VAHTS mRNA-seq v2 Library Prep Kit from Illumina.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were cultured at 37°C in fresh complete media for 24 hours before RNA was isolated.

value: colorectal carcinoma

tag: cell type

value: colorectal cancer


title: 480_KD1: SCN5A knockdown SW480 cells-1

description: SCN5A knockdown SW480 cells-1


title: Lachit root excess Fe [7_S8]

value: Lachit (derived from a cross between CRM 13-3241 and Kalinga 2)

value: whole root


title: Hacha leaf excess Fe [4_S5]


title: 480_KD2: SCN5A knockdown SW480 cells-2

description: SCN5A knockdown SW480 cells-2


title: ucd65bone scRNA-seq

city: Aurora

first: Peter

last: Kabos

state: CO

address: 12801 E. 17th Avenue

department: Division of Medical Oncology

institute: University of Colorado School of Medicine

data_processing:
UMI count matrices were generated using the 10x genomics CellRanger count (2.1.1) pipeline with default parameters.
The count matrices were combined and normalized using Seurat.
The combined matrix was then further filtered to exclude cells not passing the following QC measures: at least 500 genes detected (UMI > 0) and proportion of UMIs derived from mitochondia less than 7.5% (UCD46) or 15% (UCD4 and UCD65). Cell barcodes identified as murine cells or human-murine doublets after alignment to the mm10 genome were also, discarded, as were cell barcodes with more than 9000 (UCD46) or 8000 genes (UCD4 and UCD65) detected (likely human doublets).
After filtering, this matrix was normalized and used for tSNE projection and graph based clustering. Following cell-embeddings and clustering, the original UMI data was used for all analyses and are provided as per-model count_matrix.tsv.gz tables.
Genome_build: GRCh38
Supplementary_files_format_and_content: Count matrix with UMI counts per gene per cell.

source_name: UCD65 PDX Bone Metastasis

growth_protocol: Breast cancer PDX were derived in female NOD/SCID/ILIIrg−/− (NSG) mice. PDX were transduced with luciferase-gfp lentivirus, regrown into tumors, and processed into single cell suspensions. 1x10^6 viable cells suspended in 0.1 mL PBS were injected into the aorta of female NSG mice to model late stage metastases. For subcutaneous (primary) tumors, cells were placed into mammary fat pads suspended in 50% DMEM/50% Cultrex. Animals were monitored by IVIS imaging biweekly starting at 10 weeks post-injection, and sacrificed at 2-3 months post-injection or when moribund.

extract_protocol:
Single cell suspensions were prepared as described for viral transduction. Human PDX cells were enriched using a mouse cell depletion kit (Miltenyi Biotech). Isolated cells were loaded onto a 10x genomics (San Francisco, CA) controller per manufacturer instructions to generate barcoded single cell GEMs using the 10x genomics 3’ kit.
10x Genomics 3' end library kit

treatment_protocol: All animals were supplemented with subcutaneous silastic pellets containing 17β-estradiol.

tag: metastatic site

value: Bone

value: Human breast tumor


title: HU

value: hydroxyurea


title: ucd4tumor scRNA-seq

source_name: UCD4 PDX Primary Tumor

value: Primary Tumor


title: 480_NC2: control SW480 cells-2

description: control SW480 cells-2


title: ucd4liver scRNA-seq

source_name: UCD4 PDX Liver Metastasis

value: Liver


title: Control-2

type: RNA

city: Baltimore

first: Gabsang

last: Lee

state: MD

address: 733 North Broadway

department: School of Medicine

institute: The Johns Hopkins University

description: D2325 hiPSC-derived myoblasts treated DMSO(control)-rep2

hyb_protocol: 17 hours at 45° C with rotation (60rpm) as described by Affymetrix in their GeneChip Expression Analysis Technical Manual.

scan_protocol: Using Affymetrix’ GeneChip Scanner 3000 7G and default parameters described by the manufacturer in their GeneChip Expression Analysis Technical Manual.

data_processing: Affymetrix CEL files were extracted with the Partek GS 6.6 platform and their data RMA and quantile-normalized to create log2 transcript signal values, which were used in subsequent ANOVA analysis.

label: biotin

source_name: hiPSC-derived DMD patient myoblasts

label_protocol: RNA was labeled with the Affymetrix GeneChip WT PLUS Reagent Kit using the manufacturer's protocol.

growth_protocol: The DMD(D2325) hiPSC-derived myoblasts which carries mutation c.457 C->T were differentiated using the CHIR-DAPT protocol . Briefly, hiPSCs were plated as single cells on Geltrex (Gibco) treated dishes, at a density of 1.5 x 105 cells per well of a 24-well plate, in the presence of MEF-conditioned N2 media containing 10 ng/ml of FGF-2 (PeproTech) and 10 μM of Y-27632 (Cayman). The cells were induced to differentiate into myoblasts by adding CHIR99021 (3μM) in N2 medium for 4 days and by DAPT (10 μM) for the following 8 days. Afterwards cells continue to differentiate and mature in N2 medium for the next 13 days. Myoblasts were collected by FACS with the selection marker NCAM+/HNK1-. The NCAM+/HNK1- myoblasts were maintained in a humidified incubator containing 5% CO2 at 37°C, and grown in N2 media supplemented with 10% fetal bovine serum (FBS). To induce myotube formation, expanded NCAM+/HNK1- myoblasts were plated to confluence, and switched to N2 media without serum.

extract_protocol: RNA was extracted from Trizol-suspended cells with the QIAGEN RNeasy Mini Kit according to manufacturer's protocol.

treatment_protocol: Triplicate samples were used in microarray analysis. D2 hiPSC-derived myoblasts were treated with ginsenoside (5μM), fenofibrate (8μM) and DMSO for 24h in the differentiation medium.

value: hiPSC-derived DMD patient myoblasts

value: DMSO treated for 24 hours


title: Hacha root excess Fe [2_S3]

source_name: Roots of 11-day old Hacha rice plants that were previously grown on excess Fe media for 2 days


title: Hacha root excess Fe [1_S2]


title: 480_NC1: control SW480 cells-1

description: control SW480 cells-1


title: Gin-3

description: D2325 hiPSC-derived myoblasts treated with ginsenoside Rd-rep3

value: ginsenoside Rd(5 micromolar) treated for 24 hours


title: Control-3

description: D2325 hiPSC-derived myoblasts treated DMSO(control)-rep3


title: D0-2

source_name: microglia isolated from PLX treated mice (PLX5622, 1200 mg/kg, 14 days)


title: Flower

source_name: Flower

value: Flower


title: Control-1

description: D2325 hiPSC-derived myoblasts treated DMSO(control)-rep1


title: Gin-2

description: D2325 hiPSC-derived myoblasts treated with ginsenoside Rd-rep2


title: Fen-3

description: D2325 hiPSC-derived myoblasts treated with fenofibrated-rep3

value: fenofibrate(8 micromolar) treated for 24 hours


title: Gin-1

description: D2325 hiPSC-derived myoblasts treated with ginsenoside Rd-rep1


title: Fen-1

description: D2325 hiPSC-derived myoblasts treated with fenofibrated-rep1


title: Fen-2

description: D2325 hiPSC-derived myoblasts treated with fenofibrated-rep2


title: PANC-32: Control 32

status: Public on May 08 2020

city: Montreal

first: Francois

last: Lefebvre

state: QC

address: 845 Sherbrooke St W

department: Human Genetics

country: Canada

institute: McGill University

description: Control 32

hyb_protocol: RNA samples were hybridized on Affymetrix Human Gene ST 2.0 microarrays (Santa Clara, CA, USA)

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix)

data_processing: Expression values were obtained by applying the Robust Multi-array Average (RMA) method as implemented in the oligo Bioconductor package and filtering for feature categories main,rescue,reporter. CEL files for sperm and embryo data were separately read into R (version 3.1.0), where the Bioconductor package oligo was used to calculate transcript-cluster level expression values with the RMA (Robust Multi-array Average) algorithm. Differential expression analysis between the experimental groups was conducted using the limma package

source_name: Whole blood

label_protocol: Double-stranded cDNA was generated from the amplified cRNA with the SensationPlus WT kit (Affymetrix) and labelled according to manufacturer's instructions.

extract_protocol: Whole blood RNA was extracted using the PaxGene Blood RNA kit (Qiagen, Valencia, CA, USA), according to the manufacturer's instructions.

treatment_protocol: Blood samples were obtained from antecubital vein into PAXgene RNA tubes (Qiagen, Valencia, CA, USA)

tag: disease state

value: normolipemic control

value: Whole blood

tag: batch

tag: Sex

value: M

tag: tg pheno

value: NORM

tag: pancreatitis

value: Control


title: PANC-29: Control 29

description: Control 29

value: F


title: PANC-23: Control 23

description: Control 23


title: PANC-66: MCM Patient 66

description: MCM Patient 66

value: multifactorial chylomicronemia (MCS)

value: MCS


title: PANC-24: Control 24

description: Control 24


title: PANC-28: Control 28

description: Control 28


title: PANC-25: Control 25

description: Control 25


title: PANC-26: Control 26

description: Control 26


title: PANC-31: Control 31

description: Control 31


title: PANC-21: Control 21

description: Control 21


title: PANC-62: MCM Patient 62

description: MCM Patient 62


title: PANC-54: MCM Patient 54

description: MCM Patient 54


title: PANC-53: MCM Patient 53

description: MCM Patient 53

value: 1 to 3


title: PANC-18: Control 18

description: Control 18


title: PANC-57: MCM Patient 57

description: MCM Patient 57


title: PANC-61: MCM Patient 61

description: MCM Patient 61


title: PANC-63: MCM Patient 63

description: MCM Patient 63


title: 480_NC3: control SW480 cells-3

description: control SW480 cells-3

value: colorectal carcinoma

value: colorectal cancer


title: PANC-30: Control 30

description: Control 30


title: PANC-59: MCM Patient 59

description: MCM Patient 59


title: PANC-22: Control 22

description: Control 22


title: PANC-27: Control 27

description: Control 27


title: PANC-20: Control 20

description: Control 20


title: PANC-19: Control 19

description: Control 19


title: PANC-58: MCM Patient 58

description: MCM Patient 58


title: PANC-55: MCM Patient 55

description: MCM Patient 55


title: PANC-56: MCM Patient 56

description: MCM Patient 56


title: PANC-52: MCM Patient 52

description: MCM Patient 52


title: PANC-65: MCM Patient 65

description: MCM Patient 65


title: PANC-64: MCM Patient 64

description: MCM Patient 64


title: PANC-47: MCM Patient 47

description: MCM Patient 47


title: PANC-50: MCM Patient 50

description: MCM Patient 50


title: PANC-17: MCM Patient 17

description: MCM Patient 17


title: PANC-10: MCM Patient 10

description: MCM Patient 10


title: PANC-13: MCM Patient 13

description: MCM Patient 13

value: 4 or more


title: PANC-15: MCM Patient 15

description: MCM Patient 15


title: PANC-16: MCM Patient 16

description: MCM Patient 16


title: PANC-09: MCM Patient 09

description: MCM Patient 09


title: PANC-08: MCM Patient 08

description: MCM Patient 08


title: PANC-41: FCS Patient 41

description: FCS Patient 41

value: familial chylomicronemia (FCS)

value: FCS


title: PANC-46: FCS Patient 46

description: FCS Patient 46


title: PANC-38: FCS Patient 38

description: FCS Patient 38


title: PANC-05: FCS Patient 05

description: FCS Patient 05


title: PANC-45: FCS Patient 45

description: FCS Patient 45


title: PANC-42: FCS Patient 42

description: FCS Patient 42


title: PANC-35: FCS Patient 35

description: FCS Patient 35


title: PANC-43: FCS Patient 43

description: FCS Patient 43


title: PANC-07: MCM Patient 07

description: MCM Patient 07


title: PANC-40: FCS Patient 40

description: FCS Patient 40


title: PANC-39: FCS Patient 39

description: FCS Patient 39


title: PANC-33: FCS Patient 33

description: FCS Patient 33


title: HGADFN169

city: Heidelberg

first: Guenter

last: Raddatz

address: Im Neuenheimer Feld 580

institute: German Center for Cancer Research

data_processing:
Illumina Casava1.8.1 software used for basecalling.
Preprocessing, read trimming and quality filtering: Trimmomatic 0.39
Transcriptome mapping: Tophat 2.0.6
computation of count data: htseq.py
Genome_build: hg19
Supplementary_files_format_and_content: count table containing the count values for all genes in all samples

source_name: skin

extract_protocol:
RNA was isolated using TRIzol (Invitrogen) and following the manufacturer’s instructions. Total RNA was then purified with the RNA Clean & Concentrator-5 kit (Zymo Research) and reverse-transcribed using SuperScript III reverse transcriptase (Invitrogen), again following the manufacturer’s instructions.
Sequencing libraries were prepared using 1µg of DNAse-treated total RNA in the first step of the TruSeq RNA Sample Preparation v2 protocol (Illumina, Part# 15026495 Rev. A) as recommended by the manufacturer.

value: fibroblasts

tag: disease status

value: HGPS


title: HGADFN167


title: PANC-04: FCS Patient 04

description: FCS Patient 04


title: PANC-34: FCS Patient 34

description: FCS Patient 34


title: PANC-36: FCS Patient 36

description: FCS Patient 36


title: HGADFN143


title: HGADFN164


title: HGADFN155


title: GM00969

value: control


title: HGFDFN168


title: HGMDFN090


title: PANC-02: FCS Patient 02

description: FCS Patient 02


title: HGADFN188


title: PANC-01: FCS Patient 01

description: FCS Patient 01


title: PANC-37: FCS Patient 37

description: FCS Patient 37


title: 15724-T

city: Indianapolis

first: Jiali

last: Han

state: Indiana

address: 1050 Wishard Blvd.Health Sciences Building, RG 5112

department: Department of Epidemiology

institute: Indiana University School of Public Health

description:
SCC-9T
processed data file: S35_log2GE.txt

data_processing:
Base calling and quality scoring were performed in Illumina HiSeq.
The reads were mapped to the human genome using Tophat by The Broad Institute.
Htseq-count (HTSeq version 0.6.0) was used to count those sorted alignment files to gtf files (“Homo_sapiens.GRCh37.73.gtf” downloaded from Ensembl).
Raw counts were normalized by total reads in each sample and multiplied by one million. The final gene expression was evaluated as log2(C+1), where C is normalized counts.
Paired t-test was used to perform differential analysis.
Genome_build: GRCh37
Supplementary_files_format_and_content: S35_log2GE.txt: Tab-delimited text file includes log of expression.

source_name: Skin

growth_protocol: Surgically removed tissues.

extract_protocol:
TRI Reagent® Protocol.
Library Construction RNA polyA+.

treatment_protocol: No prior treatment.

value: Squamous cell carcinoma (SCC)

value: Tumor

tag: patient id


title: 16059-T

description:
SCC-10T
processed data file: S35_log2GE.txt


title: 16059-N

description:
SCC-10N
processed data file: S35_log2GE.txt

value: Normal adjacent tissue


title: PANC-51: MCM Patient 51

description: MCM Patient 51

value: Whole blood


title: HeLa.1.1_PCHiC

city: Moscow

first: Arkadiy

last: Golov

address: Vavilova, 34/5

country: Russia

institute: Institute of Gene Biology, RAS

library_source: genomic

data_processing:
Library strategy: PCHi-C
Standard Illumina Sequencing Pipeline
Hi-C Processing: HiCUP v0.6.1 (Wingett et al. 2015 HiCUP: pipeline for mapping and processing Hi-C data, F1000Res., Nov 20;4:1310) with Bowtie v2.2.3 as the aligner.
CHiCAGO input files were generated from  HICUP output bam files with bam2chicago script (https://bitbucket.org/chicagoTeam/chicago/src/master/chicagoTools/). Tab-separated files ‘Golov_design.rmap’ and ‘Golov_design.baitmap’ (in which hg19 binning layout and coordinatesCHiCAGO input files.of bins with probed promoter are indicated) were used to obtain CHiCAGO input files.
Genome_build: hg19
Supplementary_files_format_and_content: CHiCAGO input (chinput) files for each sample. Tab delimited (txt) design files contain three columns representing hg19 genomic coordinates (<chr> <start> <end>) of bins (Golov_design.rmap) and bait regions (Golov_design.baitmap). Fourth columns in both files stand for bin numeric IDs. ‘Golov_design.baitmap’ file has an additional column, in which names of baited promoters are indicated.

molecule: genomic DNA

source_name: cervical carcinoma

growth_protocol: HeLa cells were cultured in a DMEM medium supplemented with 10% FBS, 100 U/ml penicillin and 100 U/ml streptomycin at 37°C in 5% CO2 in a humidified atmosphere.

extract_protocol: 3C-seq libraries for two samples (HeLa.1.1_PCHiC  and HeLa.1.2_PCHiC) were prepared according to Golov et al. (Golov et al., 2020 C-TALE, a new cost-effective method for targeted enrichment of Hi-C/3C-seq libraries, Methods, Jan 1;170:48-60). A DpnII restriction enzyme was used for chromatin digestion. Precusors of hybridization probes for 867 human promoters were obtained with a semiconductor-based electrochemical synthesis service, provided by CustomArray, Inc (USA). For probe preparation, the synthesised pool of oligonucleotides was PCR-amplified with KAPA HiFi HotStart polymerase (Roche, cat.# 07958897001) and 5’-biotinylated primers. Two rounds of hybridization were performed according to Golov et al. (Golov et al., 2020 C-TALE, a new cost-effective method for targeted enrichment of Hi-C/3C-seq libraries, Methods, Jan 1;170:48-60) with the following minor modifications: 1) Per hybridization reaction, one combined mix (instead of two) was prepared in a PCR tube before DNA melting. Each mix contained 1 ug of sheared salmon DNA (Sigma-Aldrich, cat. #D1626), 10 pmol of Illumina Uni oligo (5′ AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCTC 3′), 10 pmol of Illumina PE 2.0 primer (5′ CAAGCAGAAGACGGCATACGA 3′), 1 ug of 3C-seq library and 500 ng of probes in a total volume of 60 ul. 2) After DNA melting at 95°C, the hybridization mix was cooled to 70°C, then an equal volume of pre-warmed 2x hybridization buffer (10x SSPE buffer, 10x Denhardt’s solution, 10mM EDTA, 0.2% SDS) was added to each reaction. Tubes were incubated at 70°C for an additional 45 minutes, then the temperature was lowered to 65°C and hybridization took place for 20-30 hours. We also made two biological replicates using a slightly modified protocol (samples HeLa.2.1_PCHiC  and HeLa.2.2_PCHiC). Several changes introduced in this protocol include: 1) A 2% formaldehyde solution was used for chromatin fixation instead of 1.5%. 2) Hybridization reactions were conducted at 60°C instead of 65°C. 3) Streptavidin beads were washed with an HS washing buffer (0.1x SSC buffer, 0.1% SDS) at 55°C instead of 65°C.

value: HeLa

tag: protocol

value: alternative PCHi-C protocol (see 'Extraction protocol' for details)


title: 15685-T

description:
SCC-8T
processed data file: S35_log2GE.txt


title: HeLa.2.1_PCHiC


title: 15554-T

description:
SCC-6T
processed data file: S35_log2GE.txt


title: 15554-N

description:
SCC-6N
processed data file: S35_log2GE.txt


title: 15678-T

description:
SCC-7T
processed data file: S35_log2GE.txt


title: 15551-T

description:
SCC-5T
processed data file: S35_log2GE.txt


title: HeLa.1.2_PCHiC


title: 15551-N

description:
SCC-5N
processed data file: S35_log2GE.txt


title: 15685-N

description:
SCC-8N
processed data file: S35_log2GE.txt


title: 15179-N

description:
SCC-3N
processed data file: S35_log2GE.txt


title: 15336-T

description:
SCC-4T
processed data file: S35_log2GE.txt


title: 14672-N

description:
SCC-2N
processed data file: S35_log2GE.txt


title: 14672-T

description:
SCC-2T
processed data file: S35_log2GE.txt


title: 15179-T

description:
SCC-3T
processed data file: S35_log2GE.txt


title: HeLa.2.2_PCHiC


title: 15724-N

description:
SCC-9N
processed data file: S35_log2GE.txt


title: 15678-N

description:
SCC-7N
processed data file: S35_log2GE.txt


title: 14478-N

description:
SCC-1N
processed data file: S35_log2GE.txt


title: 16037-T

description:
BCC-23T
processed data file: S35_log2GE.txt

value: Basal cell carcinoma (BCC)


title: 16111-N

description:
BCC-25N
processed data file: S35_log2GE.txt


title: 16072-T

description:
BCC-24T
processed data file: S35_log2GE.txt


title: 16072-N

description:
BCC-24N
processed data file: S35_log2GE.txt


title: 15797-T

description:
BCC-22T
processed data file: S35_log2GE.txt


title: PANC-12: MCM Patient 12

description: MCM Patient 12

value: multifactorial chylomicronemia (MCS)

value: F

value: MCS


title: 15715-T

description:
BCC-21T
processed data file: S35_log2GE.txt


title: 15797-N

description:
BCC-22N
processed data file: S35_log2GE.txt


title: 14478-T

description:
SCC-1T
processed data file: S35_log2GE.txt


title: 15715-N

description:
BCC-21N
processed data file: S35_log2GE.txt


title: 16111-T

description:
BCC-25T
processed data file: S35_log2GE.txt


title: 15484-N

description:
BCC-17N
processed data file: S35_log2GE.txt


title: 15484-T

description:
BCC-17T
processed data file: S35_log2GE.txt


title: 15706-T

description:
BCC-19T
processed data file: S35_log2GE.txt


title: 15514-N

description:
BCC-18N
processed data file: S35_log2GE.txt


title: 15472-N

description:
BCC-16N
processed data file: S35_log2GE.txt


title: 15416-N

description:
BCC-15N
processed data file: S35_log2GE.txt


title: 15706-N

description:
BCC-19N
processed data file: S35_log2GE.txt


title: 15714-N

description:
BCC-20N
processed data file: S35_log2GE.txt


title: 15409-T

description:
BCC-14T
processed data file: S35_log2GE.txt


title: 15472-T

description:
BCC-16T
processed data file: S35_log2GE.txt


title: 15514-T

description:
BCC-18T
processed data file: S35_log2GE.txt


title: 15409-N

description:
BCC-14N
processed data file: S35_log2GE.txt


title: 15392-T

description:
BCC-13T
processed data file: S35_log2GE.txt


title: 16037-N

description:
BCC-23N
processed data file: S35_log2GE.txt


title: 15392-N

description:
BCC-13N
processed data file: S35_log2GE.txt


title: 15372-N

description:
BCC-12N
processed data file: S35_log2GE.txt


title: 15416-T

description:
BCC-15T
processed data file: S35_log2GE.txt


title: 15714-T

description:
BCC-20T
processed data file: S35_log2GE.txt


title: 15360-N

description:
BCC-11N
processed data file: S35_log2GE.txt


title: 15360-T

description:
BCC-11T
processed data file: S35_log2GE.txt


title: 15318-T

description:
BCC-10T
processed data file: S35_log2GE.txt


title: 15318-N

description:
BCC-10N
processed data file: S35_log2GE.txt


title: 15047-T

description:
BCC-9T
processed data file: S35_log2GE.txt


title: 15047-N

description:
BCC-9N
processed data file: S35_log2GE.txt


title: 14666-N

description:
BCC-7N
processed data file: S35_log2GE.txt


title: 14688-N

description:
BCC-8N
processed data file: S35_log2GE.txt


title: 14666-T

description:
BCC-7T
processed data file: S35_log2GE.txt


title: 14644-N

description:
BCC-6N
processed data file: S35_log2GE.txt


title: 14644-T

description:
BCC-6T
processed data file: S35_log2GE.txt


title: 14476-T

description:
BCC-2T
processed data file: S35_log2GE.txt


title: 14630-N

description:
BCC-5N
processed data file: S35_log2GE.txt


title: 14630-T

description:
BCC-5T
processed data file: S35_log2GE.txt


title: 14487-T

description:
BCC-3T
processed data file: S35_log2GE.txt


title: 14522-N

description:
BCC-4N
processed data file: S35_log2GE.txt


title: 14522-T

description:
BCC-4T
processed data file: S35_log2GE.txt


title: 14473-T

description:
BCC-1T
processed data file: S35_log2GE.txt


title: 14476-N

description:
BCC-2N
processed data file: S35_log2GE.txt


title: 14473-N

description:
BCC-1N
processed data file: S35_log2GE.txt


title: PANC-44: FCS Patient 44

description: FCS Patient 44


title: PANC-11: MCM Patient 11

description: MCM Patient 11

value: M

value: 1 to 3


title: MAT_GRAN_MM_16540

city: Cosenza

first: Cirino

last: Botta

address: Via Migliori

department: Hematology Unit

country: Italy

institute: "Annunziata" Hospital of Cosenza

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to HG19 by using, sequentially bcl2fastq2 v2.19.1.403; cutadapt v1.13-gcc-6.4.0-2dfskgp; star v2.5.3a-gcc-4.9.4-vojlnhd. Raw table containing gene counts was obtained by using quant3p
Genome_build: HG19
Supplementary_files_format_and_content: counts

source_name: Bone marrow (CD11b+CD16+ cells)

extract_protocol:
Purification of RNA from sorted cells using Dynabeads mRNA DIRECT Purification Kit
We barcoded RNA from each sample in a retrotranscription (RT) reaction with AffinityScript Multiple Temperature Reverse Transcriptase (Agilent, Santa Clara, CA) and different RT primers. After qPCR, cDNA with similar Ct values were pooled together. cDNA was purified with SPRIselect 1.2X (Beckman Coulter –BC-, Brea, CA) and amplified using the T7 promotor as template previously introduced in the RT reaction. T7 polimerase (NEB) was added for 16 hours at 37ºC. RNA molecules were fragmented with 2µL of 10X Zn2+ fragmentation buffer (Ambion™, ThermoFisher) for 1 min at 70ºC and purified with SPRIselect 2X. Afterwards, a ssRNA adaptor (Illumina, San Diego, CA) was ligated to the 3’-end of the RNA fragments in presence of DMSO, 100 mM ATP, 50% PEG and T4 RNA ligase I (NEB) for 2 hours at 22ºC. A second RT reaction was performed with AffinityScript Multiple Temperature Reverse Transcriptase and resulting cDNA was purified with SPRIselect 1.5X. Finally, cDNA was amplified with 12.5µL Kappa Hifi ready mix + 1µL 25 µM primer mix per sample and purified with SPRIselect 0.7X. Qubit, TapeStation and qPCR analysis were done as quality controls.

value: bone marrow


title: MAT_GRAN_MM_17089


title: MAT_GRAN_MM_20674


title: MAT_GRAN_MM_20795


title: 14688-T

description:
BCC-8T
processed data file: S35_log2GE.txt


title: MAT_GRAN_MM_20610


title: MAT_GRAN_MM_17090


title: MAT_GRAN_MM_15733


title: MAT_GRAN_H_S3


title: MAT_GRAN_H_DS2


title: 14487-N

description:
BCC-3N
processed data file: S35_log2GE.txt


title: MAT_GRAN_H_17260


title: MAT_GRAN_H_17240


title: MAT_GRAN_H_17078


title: INT_GRAN_MM_20795

source_name: Bone marrow (CD11b-CD16+ cells)


title: MAT_GRAN_H_16830


title: PANC-48: MCM Patient 48

description: MCM Patient 48


title: MAT_GRAN_MM_15879


title: INT_GRAN_MM_20674


title: MAT_GRAN_H_S2


title: INT_GRAN_MM_17089


title: INT_GRAN_MM_20610


title: inf_cDC2_virus_2

city: Zwijnaarde

first: Liesbet

last: Martens

address: Technologiepark 927

department: VIB Inflammation Research Center

country: Belgium

institute: VIB-University of Ghent

description:
CD172+MAR1+ cDC2 in virus (flu) condition
CD172+MAR1+ cDC2 in virus (flu) condition

hyb_protocol: All Methods listed in Bosteels et al.  Inflammatory Type 2 cDCs Acquire Features of cDC1s and Macrophages to Orchestrate Immunity to Respiratory Virus Infection. Immunity. 2020.

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing: Data were processed using limma Bioconductor. Normalisation was done by RMA.

source_name: Lung


title: INT_GRAN_H_S3


title: MAT_GRAN_H_S1


title: INT_GRAN_MM_15733


title: PANC-03: FCS Patient 03

description: FCS Patient 03

value: familial chylomicronemia (FCS)

value: FCS

value: 4 or more


title: inf_cDC2_virus_3

label_protocol: All Methods listed in Bosteels et al.  Inflammatory Type 2 cDCs Acquire Features of cDC1s and Macrophages to Orchestrate Immunity to Respiratory Virus Infection. Immunity. 2020.


title: INT_GRAN_MM_16540


title: INT_GRAN_H_S2


title: INT_GRAN_H_17260


title: INT_GRAN_H_S1


title: INT_GRAN_H_DS2


title: 15372-T

description:
BCC-12T
processed data file: S35_log2GE.txt


title: cDC2_virus_3

description:
CD172+MAR1- cDC2 in virus (flu) condition
CD172+MAR1- cDC2 in virus (flu) condition

growth_protocol: All Methods listed in Bosteels et al.  Inflammatory Type 2 cDCs Acquire Features of cDC1s and Macrophages to Orchestrate Immunity to Respiratory Virus Infection. Immunity. 2020.


title: MC_virus_1

description:
CD64+ monocyte-derived cell in virus (flu) condition
CD64+ monocyte-derived cell in virus (flu) condition

extract_protocol: All Methods listed in Bosteels et al. Inflammatory Type 2 cDCs Acquire Features of cDC1s and Macrophages to Orchestrate Immunity to Respiratory Virus Infection. Immunity. 2020.


title: cDC1_virus_1

description:
XCR1+MAR1- cDC1 in virus (flu) condition
XCR1+MAR1- cDC1 in virus (flu) condition

treatment_protocol: All Methods listed in Bosteels et al.  Inflammatory Type 2 cDCs Acquire Features of cDC1s and Macrophages to Orchestrate Immunity to Respiratory Virus Infection. Immunity. 2020.


title: inf_cDC2_virus_1


title: MC_virus_2


title: INT_GRAN_H_17240


title: INT_GRAN_MM_17090


title: cDC2_virus_2


title: cDC1_virus_3


title: cDC1_virus_2


title: MC_mock_1

description:
CD64+ monocyte-derived cell in mock condition
CD64+ monocyte-derived cell in mock condition


title: MC_mock_2


title: MC_mock_3


title: cDC2_virus_1


title: cDC1_mock_5

description:
XCR1+MAR1- cDC1 in mock condition
XCR1+MAR1- cDC1 in mock condition


title: INT_GRAN_H_17078


title: IMM_GRAN_MM_17090

source_name: Bone marrow (CD11b+CD16- cells)


title: cDC1_mock_3


title: IMM_GRAN_MM_17089


title: IMM_GRAN_MM_20674


title: IMM_GRAN_MM_20795


title: IMM_GRAN_MM_15733


title: IMM_GRAN_MM_16540


title: INT_GRAN_H_16830


title: cDC1_mock_2


title: cDC1_mock_1


title: cDC2_mock_5

description:
CD172+MAR1- cDC2 in mock condition
CD172+MAR1- cDC2 in mock condition


title: cDC1_mock_4


title: IMM_GRAN_H_S1


title: IMM_GRAN_H_S3


title: cDC2_mock_4


title: IMM_GRAN_H_S2


title: Wild-type replicate 9

city: Dallas

first: Thomas

last: Carroll

address: 6000 Harry Hines Blvd.

institute: UT Southwestern

data_processing:
Base calling was performed using bcl2fastq version 2.17.1.14.
Transcript abundance was estimated without aligning reads using Salmon against an index of coding sequences from the Ensembl GRCm38 assembly.
Transcript-level abundance was imported and count and offset matrices generated using the tximport R/Bioconductor package.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text file including FPKM values for each sample.

source_name: Wild-type mouse kidneys

extract_protocol:
Dissected kidneys stored in RNA later solution (Invitrogen, Cat. AM7020). RNA was extracted with the QIAGEN's RNeasy Micro Kit (QIAGEN Cat. 74004).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: developmental stage

value: mixed

value: Wild-type


title: cDC2_mock_3


title: Wild-type replicate 7


title: Wild-type replicate 8


title: IMM_GRAN_H_DS2

tag: tissue


title: cDC2_mock_1


title: cDC2_mock_2


title: IMM_GRAN_H_17260


title: IMM_GRAN_H_17240


title: IMM_GRAN_MM_20610


title: 15336-N

description:
SCC-4N
processed data file: S35_log2GE.txt

value: Squamous cell carcinoma (SCC)


title: IMM_GRAN_H_16830


title: IMM_GRAN_H_17078


title: MM_26619_MO_C2_500nM

source_name: Bone marrow CD11+CD16+ neutrophils

treatment_protocol: We treated whole BM samples from MM patients (N = 3) with a selective and reversible inhibitor of histone methyltransferase G9a and DNA-methyltransferase 24 (CM-272), testing two different drug concentrations (250 and 500 nM). Approximately 3x106 cells were seeded per well in a 24-well plate and left in culture for 48 hours. Cells were treated at time 0 and +24 hours. After incubation at 37ºC, cells were labelled with SYTOX™ Blue, CD15-FITC, CD13-PE, CD45-PerCP-Cy5.5, CD16-PE-Cy7 and CD11b-APC to isolate neutrophil subsets for RNAseq analysis.


title: MM_26619_MO


title: Ctnnb1-delta3 c/+;Six2 replicate 2

source_name: Ctnnb1-delta3 c/+;Six2 mouse kidneys

tag: genotype

value: Ctnnb1-delta3 c/+;Six2


title: MM_26615_MO_C2_500nM


title: Ctnnb1-delta3 c/+;Six2 replicate 3

tag: strain


title: MM_26619_MO_C2_250nM

tag: treatment


title: Ctnnb1-delta3 c/+;Six2 replicate 1


title: MM_26615_MO


title: MM_26615_MO_C2_250nM


title: MM_26511_MO_C2_250nM


title: MM_26511_MO_C2_500nM


title: SP3_control

source_name: Peripheral blood neutrophils

treatment_protocol: We exposed whole PB from HA (N = 3) to 1ng/mL of TGF-β for 48 hours. After incubation at 37ºC, cells were labelled with SYTOX™ Blue (Thermo Fisher Scientific, MA, USA), CD15-FITC, CD13-PE, CD45-PerCP-Cy5.5, CD16-PE-Cy7 and CD11b-APC and mature  neutrophils were stored in Lysis/Binding Buffer (Invitrogen™, CA, USA) for RNAseq

value: peripheral blood

tag: drug concentration

tag: units

value: ng/mL


title: SP3_1


title: SP2_control


title: SP2_1


title: 6_L2HGDH2-3

city: Birmingham

first: Sunil

last: Sudarshan

state: AL

address: FOT 1120 -  510 20th Street South

institute: University of Alabama at Birmingham

description: L2HGDH2 replicate 3

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with GenomeStudio version2011.1

source_name: Human Cell Line

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up  with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

tag: cell line

tag: vector


title: 3_Control Vector-3

description: CV replicate 3

value: control


title: 5_L2HGDH2-2

description: L2HGDH2 replicate 2


title: 1_Control Vector-1

description: CV replicate 1


title: SP1_control


title: SP1_1


title: MM20610

data_processing:
ATACseq reads were aligned to the hg19 genome build using bowtie2 with default parameters (except commands adapted for these specific data such as --very-sensitive and --non-deterministic options that improve accuracy and results when there are many identical reads) and filtered based on mapping score (MAPQ ≥ 30) by Samtools version 1.3.159. The MACS2 version 2.1.0 was used to identify peaks for each sample with default settings. ChiPQC package was used for quality control and blacklisted peaks removal. ChipSeeker was used to assess overlap of differential peaks and relate peaks to annotated transcription start sites using default options.
Genome_build: HG19
Supplementary_files_format_and_content: .narrowPeak, containing peaks localization

source_name: Bone marrow CD11b+CD16+ neutrophils

extract_protocol:
FACSorting of neutrophils from total BM samples of MM patients and HA
Approximately 20,000 cells of various neutrophils subsets were FACSorted from total BM samples of HA (N = 3) or MM patients (N = 3), and placed in a PCR tube with 100µL of PBS+BSA 0.05%. After centrifugation (500g, 4ºC, 10 min), the pellet was suspended in 25µL of the transposase reaction mixture (15µL of Buffer TD2x (Illumina), 1µL of TDE1 enzyme (Illumina), 0.25µL of 5%digitonin (Promega) and 8.75µL of nuclease-free water). The resulting mix was incubated at 37ºC for 30 min at 450 rpm. Afterwards, the transposase reaction was stopped on ice and 5µL of clean up buffer, 2µL of 5% SDS and 2µL of Proteinase K (New England Biolabs) were added to the previous mix and incubated for 30 min at 40ºC. Transposase-reaction products were cleaned up with AMPure magnetic beads 2X (BC). Finally, the DNA fragments were amplified with 22µL Kappa Hifi ready mix + 4µL of primer 1 i5 and 2 i7 mix per sample. Library was purified with AMPure magnetic beads 2X. Quality control was performed with Qubit and TapeStation

tag: condition

value: MM patient


title: MM20674


title: HD3

value: Healthy subject


title: MM20795


title: 4_L2HGDH2-1

description: L2HGDH2 replicate 1


title: 2_Control Vector-2

description: CV replicate 2


title: HD2


title: WT Rep1 PROSeq

city: Ithaca

first: Rachel

middle: Leigh

last: Cosby

address: 218 Biotechnology Bldg, 526 Campus Rd

department: Molecular Biology and Genetics

institute: Cornell University

description: nascent RNA

data_processing:
The pipeline used to process PRO-seq data is available at https://github.com/JAJ256/PROseq_alignment.sh.
Preprocessing: UMIs extracted and adapter sequences trimmed using fastp (Chen, et al. 2018). Ribosomal reads removed by mapping to one copy of human rDNA repeat using bowtie2 (Langmead and Salzer 2012), retaining unmapped reads.
Mapping: Reads were mapped to Myoluc2.0 reference assembly with wild-type KRABINER transgene spiked in as an additional contig (bowtie2) and PCR duplicates were removed with UMI-tools using the directional method (Smith, et al. 2017)
bigWig score tracks for visualization and downstream analysis were generated using deepTools bamCoverage (Ramirez, et al. 2014)
Identifying transcribed regulatory elements (TREs): non-normalized bigWig tracks were used to identify transcribed regulatory elements for each sample using dREG (Wang, et al. 2019) and then merged (bedtools merge; Quinlan and Hall 2010) to generate a comprehensive set of transcribed regulatory elements for Myotis velifer embyronic fibroblasts
Quantification of gene body and TRE expression: Read counts for gene bodies (defined as trasncription start site [TSS] plus 500bp to transcription end site [TES] and TSS minus 500bp TES for + and - strand Myoluc2 ENSEMBL genes respectively [GCA_000147115.1]) and TREs were calculated by generating single nucleotide resolution bedGraph files using a custom script and bedtools map (Quinlan and Hall, 2010)
Differential transcription analysis of gene bodies and TREs: PROSeq read counts from each sample were combined to generate a single counts matrix, and differential expression analysis was performed for gene bodies and TREs separetly using DESeq2 (Love, et al. 2014). Three comparisons were performed: KRABINER KO vs WT, WT/mutDBD/mutKRAB KRABINER rescue vs KO, and WT/mutDBD/mutKRAB over-expression vs rescue. Over-expression vs rescue comparisons were performed individually, controlling for clonal identity.
Genome_build: Myoluc2
Supplementary_files_format_and_content: bigWig files were generated with deeptools bamCoverage; normalized bigWigs were generated in the same manner as non-normalized bigWigs except with scale factors based on library size normalization; TRE annotation files were generated using dREG (Wang, et al. 2019) and bedtools merge (Quinlan and Hall 2010); Expression values for genes and TREs for each comparison were generated using DESeq2 (Love, et al. 2014)

organism: Myotis velifer

source_name: Embryonic fibroblasts

growth_protocol: Myotis velifer embryonic fibroblast cells of various genotypes were cultured at 37C, 5% CO2, with DMEM + 20% FBS, with passaging at ~80% confluency

extract_protocol:
PRO-seq libraries were prepared as previously described (Judd, et al. 2020; Mahat, et al. 2016; Kwak, et al. 2013). In brief, cells were grown to approximately 80% confluency and were chilled on ice, washed twice with ice cold PBS, incubated in PBS with 1 mM EDTA for 5 minutes, and harvested by scraping. Cells were permeabilized by incubating on ice for 5 minutes in permeabilization buffer (10 mM Tris-Cl pH 7.5, 10 mM KCl, 250 mM Sucrose, 5 mM MgCl2, 1 mM EGTA, 0.5 mM DTT, 0.05% Tween-20, 4 U/mL SUPERase-In [Thermo Fisher], 1X EDTA Free Pierce Protease Inhibitors [Thermo Fisher], and 0.1% NP-40). Permeabilization was verified using Trypan blue staining followed by visual inspection. Cells were washed once with permeabilization buffer and flash frozen in LN2 in storage buffer (50 mM Tris-Cl pH 8.0, 40% v/v Glycerol, 5 mM MgCl2 0.1 mM EDTA, and 0.5 mM DTT).
Nuclear Run-On was performed for 5 minutes at 37˚C by mixing equal volumes of permeabilized cells in storage buffer with 2X Run-On buffer (10 mM Tris-Cl pH 8.0, 5 mM MgCl2, 1 mM DTT, 300 mM KCl, 40 µM ATP, 40 µM GTP, 40 µM Biotin-11-CTP [Perkin Elmer], 40 µM Biotin-11-UTP [Perkin Elmer], 2 U/mL SUPERase-In [Thermo Fisher], and 1% Sarkosyl). RNA was isolated by TRIzol [Thermo Fisher] extraction and was fragmented by base hydrolysis in 0.2 N NaOH on ice for 5 min. Following neutralization with pH 6.8 Tris-Cl, RNA was passed through an RNase free Bio-Gel P-30 column [Bio-Rad]. The 3’ and 5’ adapters used were identical to those in (Mahat, et al. 2016) except 6 random nucleotides were added at the ligation junction as a unique molecular identifier (UMI) to facilitate computational removal of PCR duplicates. The 3’ adapter was ligated to the total RNA pool (containing both nascent and non-nascent RNAs) for 1 h at 25 ˚C using 30 U T4 RNA ligase 1 [NEB] in 10% PEG8000. Nascent RNA was then captured using Dynabeads MyOne C1 Streptavidin beads [Thermo Fisher] and washed once with high salt wash buffer and once with low salt wash buffer as described in (Mahat, et al. 2016). RNA was 5’ phosphorylated while attached to the beads using T4 PNK [NEB] and then 5’ uncapped using RppH [NEB] while attached to the beads. RNA was then eluted from the beads using TRIzol, the 5’ adapter was ligated using 10 U T4 RNA Ligase 1 for 1 h at 25 ˚C. RNA was again isolated using Dynabeads MyOne C1 Streptavidin beads, and reverse transcription was performed on the beads using Maxima H- RT [Thermo Fisher]. cDNA was eluted from the beads by heating, and final libraries were amplified for 11 PCR cycles using Q5 High Fidelity DNA Polymerase [NEB]. Libraries were sequenced on an Illumina NextSeq 500 platform using paired end 37 by 37-bp chemistry.
library strategy: PRO-Seq

tag: cell type

value: Embryonic fibroblasts

value: WT

tag: transgene

tag: clone


title: WT Rep2 PROSeq

description: nascent RNA


title: SFMSC_IL-1β treated_rep2

city: guang zhou

first: Yangpeng

last: Sun

state: guang dong

address: 56 Lingyuan West Road, Guangzhou, Guangdong

institute: Guangdong Provincial Key Laboratory of Stomatology, Stomatology Hospital of Sun Yat-sen University

hyb_protocol: The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000. 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60°C for 30 min, finally 25 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the LncRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2505C).

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v12.1 software package (Agilent Technologies). After quantile normalization of the raw data, LncRNAs and mRNAs that at least 3 out of 6 samples have flags in Present or Marginal (“All Targets Value”) were chosen for further data analysis. Differentially expressed LncRNAs and mRNAs with statistical significance between the two groups were identified through P-value/FDR filtering. Differentially expressed LncRNAs and mRNAs between the two samples were identified through Fold Change filtering. Hierarchical Clustering and combined analysis were performed using homemade scripts.

source_name: human temporomandibular joint SFMSCs treated with  IL-1β for 2 hours

label_protocol: Sample labeling and array hybridization were performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology) with minor modifications. Briefly, mRNA was purified from total RNA after removal of rRNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre). Then, each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3' bias utilizing a mixture of oligo(dT) and random primers (Arraystar Flash RNA Labeling Kit, Arraystar).

growth_protocol: SFMSC were plated on culture dishes (Corning) with complete culture medium [α‑minimum essential medium (α‑MEM)] supplemented with 10% fetal bovine serum (FBS) and 1X GlutaMAX (Gibco, USA) at 37˚C in 5% CO2.

extract_protocol: Total RNA were extracted using Trizol. The RNA quantity and quality were measured by NanoDrop ND-1000. RNA integrity was assessed by standard denaturing agarose gel electrophoresis.

treatment_protocol: The treated groups were treated with 10 ng/ml IL-1β for 2 h,and the control groups were treated without IL-1β

value: human temporomandibular joint synovial fluid derived mesenchymal stem cell (SFMSC)

value: IL-1β for 2 hours


title: HEK293 B23 treated rep 2

city: Singapore

first: Pierre-alexis

last: Goy

state: Singapore

address: 60 Biopolis Street

country: Singapore

institute: Genome Institute of Singapore (GIS-ASTAR)

data_processing:
Raw reads from fastq files were aligned to the hg38 genome using STAR 2.6.1d (using options --sjdbGTFfile gencode.v29.annotation.gtf --sjdbOverhang 75 --outSAMtype BAM   Unsorted --outSAMstrandField intronMotif  --twopassMode Basic).
Bam files were sorted with samtools sort and indexed with samtools index.
The number of reads mapping to each gene was quantified with htseq-count (using options --format=bam --order=pos --stranded=reverse  --idattr=gene_name --nonunique=all) on features from the gtf file gencode.v29.annotation.gtf.
The raw counts of reads were then imported into EdgeR in R to perform the differential expression analyses.
Genome_build: hg38
Supplementary_files_format_and_content: Counts per million (CPM) from EgdeR in excel format

source_name: human embryonic kidney cells

growth_protocol: HEK 293 (CRL-1573TM) cells were cultured in RPMI (Roswell Park Memorial Institute) media supplemented with 10% (v/v) FBS. All cells were grown at 37°C in an atmosphere of 5% CO2.

extract_protocol:
RNA was isolated from the cells after compound treatment using Quick-RNA Miniprep kit (Zymo Research)
Total RNA, 2.5μg, was used for RNASequencing library preparation with the TruSeq Stranded mRNA Library Prep kit (Illumina) largely according to manufacturer’s instructions.

treatment_protocol: HEK 293 were treated with the B23 compound

value: human embryonic kidney cells

value: Quinolinol B23


title: SFMSC_Control_rep3

source_name: untreated human temporomandibular joint SFMSCs

value: none; untreated control


title: HEK293 B23 treated rep 3


title: MM_26511_MO

value: bone marrow


title: SFMSC_Control_rep1


title: SFMSC_IL-1β treated_rep1


title: SFMSC_Control_rep2


title: SFMSC_IL-1β treated_rep3


title: HEK293 B23 treated rep 1


title: WT OE Rep4 PROSeq

description: nascent RNA

value: KRABINER KO

value: WT KRABINER

value: doxycycline (induced)


title: KKO Rep1 PROSeq

description: nascent RNA


title: WT OE Rep5 PROSeq

description: nascent RNA


title: HD1


title: HGADFN188

data_processing:
Illumina Casava1.8.1 software used for basecalling.
Preprocessing, read trimming and quality filtering: Trimmomatic 0.39
Read mapping: Bowtie2
Peak calling: MACS2
Genome_build: hg19
Supplementary_files_format_and_content: output of MACS2 peak calling

source_name: skin

extract_protocol:
50,000 cells were washed with ice cold 1x PBS and resuspended in 50 μl lysis buffer (10 mM TRIS-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630). The lysis reaction was carried out while spinning down the samples at 500 g for 10 minutes at 4°C. Samples were then resuspended in transposition buffer (25 μl 2x TD buffer (Illumina), 2.5 μl TDEI (Tagment DNA Enzyme, Illumina) and 22.5 μl ddH2O) and incubated for 30 minutes at 37°C.
Samples were purified using the MinElute PCR Purification kit (Qiagen). Final libraries were then PCR-amplified, purified once again with the same kit and subjected to paired-end sequencing on a HiSeq 4000 platform (Illumina).

value: fibroblasts

tag: patient status

value: young


title: WT OE Rep3 PROSeq

description: nascent RNA


title: KKO Rep2 PROSeq

description: nascent RNA


title: Non-arthritic mouse 3 [methylation]

type: genomic

city: Chicago

first: Tibor

middle: T

last: Glant

state: IL

address: 1735 West Harrison

department: Orthopedic Surgery

institute: Rush University Medical Center

description:
Control 3
The  processed data is also provided as native .gff files

hyb_protocol: According to NimbleGen kit

scan_protocol: Following NimbleScan's default using Agilent Scanner

data_processing: Loes normalisation was applied excluding top 5% probes with the largest original Cy5/Cy3 log2 ratio

source_name: methylated DNA fraction by MIRA

label_protocol: According to the standard NimbleGen protocol

extract_protocol: Genomic DNA was purified from naive and arthritic B cells by standard procedures by using proteinase K digestion, phenol chloroform extraction, and ethanol precipitation. Genomic DNA was fragmented by sonication and enrichment of methylated DNA fractions was conducted by MIRA method

value: BALB/c

tag: gender

value: female

value: control (non-arthritic) B cells

source_name: Input

tag: sample type

value: input


title: Arthritic mouse 2 [methylation]

description:
PGIA 2
The  processed data is also provided as native .gff files

value: arthritic B cell


title: WT OE Rep6 PROSeq

description: nascent RNA

value: Embryonic fibroblasts


title: Arthritic mouse 3 [methylation]

description:
PGIA 3
The  processed data is also provided as native .gff files


title: Non-arthritic mouse 2 [methylation]

description:
Control 2
The  processed data is also provided as native .gff files


title: HEK293 control rep 3

value: DMSO-control


title: WT resc Rep6 PROSeq

description: nascent RNA

value: untreated (non-induced)


title: WT OE Rep1 PROSeq

description: nascent RNA


title: HGADFN271


title: HGFDFN168

value: control


title: HEK293 control rep 2

value: human embryonic kidney cells


title: HEK293 control rep 1


title: WT resc Rep4 PROSeq

description: nascent RNA


title: HGADFN155


title: WT OE Rep2 PROSeq

description: nascent RNA


title: HGADFN169

value: old


title: Wild-type replicate 5

value: mixed

value: Wild-type


title: WT resc Rep3 PROSeq

description: nascent RNA

value: KRABINER KO

value: WT KRABINER


title: HGADFN167

value: fibroblasts


title: mutKRAB OE Rep3 PROSeq

description: nascent RNA

value: mutKRAB KRABINER

value: doxycycline (induced)


title: Wild-type replicate 6


title: WT resc Rep2 PROSeq

description: nascent RNA


title: Arthritic mouse 1 [methylation]

description:
PGIA 1
The  processed data is also provided as native .gff files

value: BALB/c

value: female


title: HGADFN143


title: mutKRAB OE Rep2 PROSeq

description: nascent RNA


title: WT resc Rep5 PROSeq

description: nascent RNA


title: Non-arthritic mouse 4 [methylation]

description:
Control 4
The  processed data is also provided as native .gff files

value: control (non-arthritic) B cells

value: input


title: WT resc Rep1 PROSeq

description: nascent RNA

value: Embryonic fibroblasts


title: Wild-type replicate 4


title: mutKRAB OE Rep1 PROSeq

description: nascent RNA


title: mutKRAB resc Rep3 PROSeq

description: nascent RNA


title: Wild-type replicate 3


title: HGMDFN090


title: Wild-type replicate 2


title: mutDBD OE Rep3 PROSeq

description: nascent RNA

value: mutDBD KRABINER


title: GR WT Dex rep2 ChIP-Seq

city: Freising

first: Franziska

last: Greulich

address: Gregor-Mendel-Str. 2

department: Metabolic Programming

institute: TU München

data_processing:
Reads were aligned to the mouse mm10 reference genome using BWA-MEM version 0.7.13 with default parameter settings.
PCR duplicates were removed using Picard Tools version 1.119.
Due to high variation of peaks called between replicates, replicates were merged before mapping, downsampled to 64mio reads per genotype and one peak file generated from the merged replicates.
Peaks  were  called  using  MACS2 version  2.1.0 in paired-end mode with a FDR threshold of 0.05.
Blacklisted regions (http://mitra.stanford.edu/kundaje/akundaje/release/blacklists/mm10-mouse/mm10.blacklist.bed.gz) and peaks detected in GRKO MEFs were removed from the called peaks.
Peaks were annotated to the closest TSS using the ChiPpeakAnno R package. (doi: 10.1186/1471-2105-11-237)
Genome_build: mm10
Supplementary_files_format_and_content: The .txt or .tab files contain annotated peaks called with MACS2 version 2.1.0 and cleared from blacklisted regions and peaks called in GRKO MEFs. The .bedGraph files contain tracks for visualization.

source_name: mouse embryonic fibroblasts (MEFs)

growth_protocol: MEFs generation: C57BL/6 male mouse embryos from either wild-type, GR Zn/Zn or GRKO were harvested at 13.5 days after vaginal plug formation. Internal organs (mainly heart and liver) and head were removed and embryos were minced and digested with Trypsin 10-15min at 37°C. MEFs were cultured for 7 days in high glucose DMEM incl. 10% FBS and 1% Pen/Strep.

extract_protocol:
ChIP was performed as previously described (Uhlenhaut et al., 2013) with the addition of a chromatin pre-clearing step. Briefly, cells were fixed with 30min DSG and 10min 1% formaldehyde. Crosslink was quenced with 0.2M glycine for 5min. Cells were lysed with Fast IP buffer (150mM NaCl, 5mM EDTA, 5mM Tris, 1% Triton X-100 and 0.5% NP40). Chromatin was sheared in shearing buffer (1% SDS, 10µM EDTA and 0.05% Tris) until majority of chromatin fragments were between 200-500bp. Chromatin pre-clearing was done by incubation with Dynabeads at 4°C rotating before IP set-up overnight. Next day, Dynabeads were added to IPs and 6h incubated at 4°C rotating. IPs were washed 6 times with Fast IP buffer. DNA was eluted with ChIP elution buffer (100mM NaHCO3 and 1%SDS).
Library preperation was performed from 2 ng of ChIP DNA using the Kapa Hyper Prep Kit with PCR library amplification (#KK8504, KapaBiosystems) according to the manufactur's protocol. Shortly, ChIP DNA was end-repaired and A-tailed before adapter ligation. After adapter ligation, the ChIP DNA was purified with Agencourt AMPure XP beads (#A63880, Beckman Coulter) and size-selected for 360-600 bp using the Pippin Prep System from Saga Science. The size-selected library is amplified by PCR using the Kapa Hyper Prep Kit (#KK8504,KapaBiosystems) and purified terminally with Agencourt AMPure XP beads (#A63880, Beckman Coulter).

treatment_protocol: 16h 1uM Dex in EtOH + 3h 100ng/ul LPS (Dex+LPS) or only 16h 1uM Dex in EtOH

tag: antibody

value: Glucocorticoid Receptor - Proteintech 24050-1-AP

tag: Sex

value: male

value: GR wt / wt

value: 16h 1µM Dex in EtOH


title: mutKRAB resc Rep1 PROSeq

description: nascent RNA

value: untreated (non-induced)


title: mutDBD OE Rep1 PROSeq

description: nascent RNA


title: Ctnnb1-delta3 c/+;Foxd1 replicate 5

source_name: Ctnnb1-delta3 c/+;Foxd1 mouse kidneys

tag: developmental stage

value: mixed

value: Ctnnb1-delta3 c/+;Foxd1


title: IPFSC_4

city: Morgantown

first: Gangqing

last: Hu

state: West Virginia

address: 64 Medical Center Drive

department: MicroBiology, Immunology, and Cell Biology

institute: West Virginia University

data_processing:
We mapped the pair-end RNA-Seq reads to the reference genome of Oryctolagus cuniculus (OryCun2.0) using the Subread aligner (PMC3664803). The number of read counts corresponding to gene transcripts annotated by Ensembl (OryCun2.0.98) were summarized by the featureCounts function from the Rsubread package (PMC6486549). Gene expression levels were quantified by Reads Per Kilobase of transcript, per Million mapped reads (RPKM; PMID: 18516045) with in-house script. We applied Edger3 (PMC3378882) to call differentially expressed genes with the following criteria: FC > 2, FDR < 0.05, and an average expression (RPKM) higher than one in at least one condition.
Genome_build: OryCun2.0
Supplementary_files_format_and_content: XLS file, from left to right represent "Ensemb_gene_id", "Gene_sumbol", "log2FC (IPFSC/SCASC)", "FDR", "logCPM", "Pvalue", RPKMs for four SCASC samples, and RPKM for four IPFSC samples. Columns "log2FC (IPFSC/SCASC)", "FDR", "logCPM", and "Pvalue" are output from EdgeR 3.

organism: Oryctolagus cuniculus

source_name: stem cells isolated from tissue

extract_protocol:
RNA from expanded stem cells was isolated using Trizol (Invitrogen, Carlsbad, CA).
The WVU Genomics Core Facility used the Stranded mRNA kit from Kapa Biosystems Inc. (Wilmington, MA) following manufacturer’s recommended protocol when starting with 1 ug of total RNA. Upon completion of the libraries, a final QC check was initiated, which involved Qubit quantification and size estimation on the Agilent Bioanalyzer using a High Sensitivity DNA chip.

tag: tissue

value: infrapatellar fat pad

value: IPFSC


title: GR MUT Dex rep1 ChIP-Seq

tag: strain

tag: genotype

value: GR Zn / Zn


title: mutDBD resc Rep3 PROSeq

description: nascent RNA

value: KRABINER KO

tag: treatment


title: mutKRAB resc Rep2 PROSeq

description: nascent RNA

value: mutKRAB KRABINER


title: IPFSC_3


title: Ctnnb1-delta3 c/+;Foxd1 replicate 4


title: IPFSC_2


title: Wild-type replicate 1

value: Wild-type


title: 6334

city: Houston

first: Yuan

last: Qi

state: TX

address: 1400 Pressler St

department: Bioinformatics & Computational Biology

institute: University of Texas M.D. Anderson Cancer Center

data_processing:
alignment and gene count by STAR (version 2.6.0b)
gene annotation used GENCODE M19 (Ensembl 94)
differential expression analysis carried out in R (3.5.1) using Bioconductor package DESeq2
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-deliminated data matrix of normalized gene counts

source_name: pancreas

extract_protocol:
Flash frozen tissue was pulverized and homogenized in TRIzol RNA isolation reagent (Invitrogen). RNA was then purified based on manufacturer protocol.
Barcoded, Illumina compatible, strand-specific total RNA libraries were prepared using the TruSeq Stranded Total RNA Sample Preparation Kit (Illumina).

value: pancreas

value: Daxxfl/flPdx1-CreTg (DC)

tag: age

value: six week old


title: Ctnnb1-delta3 c/+;Foxd1 replicate 3


title: Non-arthritic mouse 1 [methylation]

description:
Control 1
The  processed data is also provided as native .gff files

value: BALB/c

value: female

value: control (non-arthritic) B cells

value: input


title: mutDBD resc Rep1 PROSeq

description: nascent RNA

value: Embryonic fibroblasts

value: mutDBD KRABINER


title: 6336


title: mutDBD OE Rep2 PROSeq

description: nascent RNA

value: doxycycline (induced)


title: IPFSC_1


title: Arthritic mouse 4 [methylation]

description:
PGIA 4
The  processed data is also provided as native .gff files

value: arthritic B cell


title: Ctnnb1-delta3 c/+;Foxd1 replicate 2

value: mixed

value: Ctnnb1-delta3 c/+;Foxd1


title: SCASC_4

value: subcutaneous adipose tissue

value: SCASC


title: GR WT Dex rep1 ChIP-Seq

value: Glucocorticoid Receptor - Proteintech 24050-1-AP

value: male

value: GR wt / wt

value: 16h 1µM Dex in EtOH


title: mutDBD resc Rep2 PROSeq

description: nascent RNA

value: KRABINER KO

value: untreated (non-induced)


title: 6332

value: pancreas

value: Daxxfl/flPdx1-CreTg (DC)

value: six week old


title: SCASC_3


title: Ctnnb1-delta3 c/+;Foxd1 replicate 1


title: 6324


title: 6328

value: wild type (WT)


title: SCASC_2


title: SCASC_1


title: 6326


title: fp_ltm_24hr_1

city: Rehovot

first: Noam

last: Stern-Ginossar

address: 234 herzel

department: Molecular Genetics

country: Israel

institute: Weizmann Institute

data_processing:
The reads of the ribo-seq libraries was trimmed to remove the linker CTGTAGGCACCATCAAT by using cutadapt.
Reads aligned to hg19 based rRNA and tRNA reference were removed. Then reads were aligned to combined reference of the host and the virus.
Reads that failed to align to genome, were aligned to the host transcriptome and to the viral breaking points according to strong break point at Kim et. al, plus few breakpoints from our our STAR runs.
The alignments above was made with Bowtie1. In the ribo-seq libraries the p-site was calculated as an offset (adjusted to the read length) from the read start site.
The STAR alignment was made with the flags recommended by Kim et. al. to get all the breakpoints.
Genome_build: Host : Chlorosebus sabaeus genome and annotation ENSEMBL release 99. Virus Genebank NC_045512.2 with 3 changes to match the used strain, 241:C->T, 3037:C->T, 23403:A->G.
Supplementary_files_format_and_content: Wiggle files of the p site for each read of the ribo-seq samples, and the read p prime for the rna-seq samples. A tab delimited file of breakpoints from the STAR run on the rna-seq samples and the ribo-seq chx samples that appear in at least 2 different samples.

organism:
Chlorocebus aethiops aethiops
Severe acute respiratory syndrome coronavirus 2

extract_protocol:
For RNA-seq, cells were harvested with Tri-Reagent (Sigma-Aldrich), total RNA was extracted, and poly-A selection was performed using Dynabeads mRNA DIRECT Purification Kit (Invitrogen). For ribosome profiling, medium was aspirated from dishes, which were immediately placed on ice and rinsed with 10 ml ice-cold PBS supplemented with drugs used in pretreatment of the cells. PBS was aspirated and 800 μl ice-cold lysis buffer (20 mM Tris, pH 7.4, 250 mM NaCl, 15 mM MgCl2, 1 mM dithiothreito, 0.5% Triton X-100 and 24 U / ml Turbo DNase (Ambion, AM2239), along with any drugs used for sample treatment) was dripped onto dishes. Cells were scraped and the lysate was removed and incubated 10 min on ice. The lysate was then clarified by centrifugation for 10 min at 20,000 × g, 4°C and ∼1.1 ml supernatant was recovered.
RNA-seq: mRNA samplewas subjected to DNAseI treatment and 3’ dephpsphorylation using FastAP Thermosensitive Alkaline Phosphatase (Thermo Scientific) and T4 PNK (NEB) followed by 3’ adaptor ligation using T4 ligase (NEB). The ligated products used for reverse transcription with SSIII (Invitrogen) for first strand cDNA synthesis. The cDNA products were 3’ ligated with a second adaptor using T4 ligase and amplified for 8 cycles in a PCR for final library products of 200-300bp. Ribo-seq:
RNAseq and ribosome profiling

treatment_protocol: Cells were infected for 5 or 24 hours before treatment. For Ribo-seq libraries, cells were treated with either 50μM lactimidomycin(LTM) for 30 minutes or 2μg/mL Harringtonine (Harr) for 5 minutes, for translation initiation libraries (LTM and Harr libraries correspondingly), or left untreated for the translation elongation libraries (cycloheximide [CHX] library). All three samples were subsequently treated with 100μg/mL CHX for 1 minute. Cells were placed on ice immediately after treatment, washed twice with PBS containing 100μg/mL CHX.

tag: virus strain

tag: cell line

value: Vero cells, ATCC, CCL-81

tag: hours post infection


title: fp_harr_24hr_1


title: fp_ltm_24hr_2


title: fp_chx_24hr_2

description: STAR.SJ.tab


title: mrna_24hr_2

description: STAR.SJ.tab


title: fp_harr_24hr_2


title: 6325


title: PCF cells, 8d_4

city: Mainz

first: Falk

last: Butter

state: Germany

address: Ackermannweg 4

department: Quantitative Proteomics

institute: Institute of Molecular Biology gGmbH

data_processing:
Spliced-leader sequences (CAATATAGTACAGAAACTGTTCTAATAATAGCGTTAGTT) were removed from the reads using cutadapt (DOI:10.14806/ej.17.1.200)
Single reads were mapped to the T. brucei 11 megabase chromosomes (TriTrypDB version 36) using STAR version 2.5.2b (https://doi.org/10.1093/bioinformatics/bts635), allowing up to 2 mismatches, a minimum intron length of 21 and keeping only uniquely aligned reads (on average 75.1 % of all reads).
No. of reads per gene were counted using featureCounts (https://doi.org/10.1093/bioinformatics/btt656) from the subread package version 1.5.1 with default parameters and using the gene models provided by TriTrypDB version 36.
For the differential expression analysis, we used R version 3.4.3 (http://www.R-project.org/) and DESeq2 version 1.18.1 (https://doi.org/10.1186/s13059-014- 525 0550-8) to normalize, transform, and model the data. The counts were fitted to a Negative Binomial generalized linear model (GLM) and the Wald significance test was used to determine the differentially expressed genes between control and knockdown samples.
Genome_build: T. brucei TriTrypDB version 36
Supplementary_files_format_and_content: .txt raw count per gene files

organism: Trypanosoma brucei

source_name: whole animals

growth_protocol: T. brucei PCF cells strains 29.13, transgenic for T7 RNA polymerase and the tetracycline repressor, were grown in vitro at 27°C in SDM-80 media containing hemin (7.5 mg/ml) and 10% FBS. The pLew100v5 vector for RBP6 expression was linearized with NotI enzyme and  transfected into the cell line as described previously (Wirtz, 1999). RBP6OE cells were grown in SDM-80 medium containing no glucose, further supplemented with 50 mM N-acetyl glucose amine to block uptake of residual glucose molecules from 10% FBS.

extract_protocol:
Total RNA was isolated from T. brucei at different stages (1 × 10e8 cells/replicate) using the miRNeasy Kit (Qiagen) according to the manufacturer's protocol. An additional DNase1 digestion step was performed to ensure that the samples were not contaminated with genomic DNA.
NGS library prep was performed with TruSeq Strand-Specific mRNA Library Prep with PolyA Selection following Illumina standard protocol.
Libraries were sequenced on an Illumina NextSeq 500. The RNA-Seq measurement yielded on average 11.1 M single reads of 75 nt per sample.

treatment_protocol: The induction of ectopically expressed RBP6 protein was triggered by the addition of 10 μg/ml of tetracycline into the media.

tag: cell type

value: PCF cells

tag: timepoint

value: 8 days after induction of ectopically expressed RBP6 protein

tag: replicate


title: mrna_24hr_1

description: STAR.SJ.tab


title: fp_chx_24hr_1

description: STAR.SJ.tab


title: snRNA-seq_Tibialis

city: Paris

first: Matthieu

last: Dos Santos

state: Paris

address: 24 rue du Faubourg Saint Jacques

country: France

institute: Institut Cochin

data_processing:
For snATAC-Seq samples: cellranger-atac count --id=[sample ID as in fastq name] --fastqs=[path/to/fastqs/rep] --sample=[sample ID for output files] --reference=cellranger-atac-mm10-1.1.0  (available on 10X website)
For snRNA-Seq samples: cellranger count --id=[sample ID as in fastq name] --fastqs=[path/to/fastqs/rep] --sample=[sample ID for output files] –transcriptome=/home/genomic/refdata-cellranger-mm10-3.0.0_premrna  (available on 10X website)
Genome_build: mm10

source_name: Adult skeletal muscle

growth_protocol: adult 2 months old female mouse

extract_protocol:
For snRNA-seq : Muscles were dissected and pulled in cold PBS with 0,2U/μl RNase inhibitor. PBS was removed and muscles were minced in 1ml cold lysis buffer (10mM Tris-HCl pH7.5, 10mM NaCl, 3mM MgCl2, and 0.1% NonidetTM P40 in Nuclease-Free Water) with scissors. After 2min, 4ml of cold lysis buffer were added and muscles were lysed for 3 min at +4°C. 9ml of cold wash buffer (PBS, BSA 2% and 0.2U/μl RNase inhibitor from Roche) was added and the lysate was dounced with 10 strokes of loose pestle avoiding too much pressure and air bubbles. The homogenate was filtered with 70μm and 40μm cell strainers. Nuclei were pelleted by centrifugation for 5min at 500g at +4°C. Nuclei were washed to remove ambient RNAsin 1ml of cold wash buffer, transferred in a 1.5ml Eppendorf tube and centrifuged 5min at 500g at +4°C. The pellet was resuspended in 250 μl of wash buffer and stained during 15 min in the dark at +4°C with DAPI (10 μg/mL). Then the nuclei were washed with 1ml of wash buffer, centrifuged 5min at 500g at +4°C, resuspended in 300μl of wash buffer and filtered with 30μm cell strainers. Nuclei were then FACS sorted to exclude debris with a BD FACSAria III and the BD FACSDIVA software. For snATAc-seq : We  usedthe  10X  genomic  nuclei  Isolation  for  Single  Cell  ATAC  Sequencing  protocol (CG000169 | Rev B) with some changes. 12 quadriceps and 12 soleus were dissected and pulled in cold PBS.PBS was removed and muscles were minced 2 minutes in 1 ml of cold ATAC-lysisbuffer (10mM Tris-HCl pH7.4, 10mM NaCl, 3mM MgCl2, 1% BSA and 0.1% Tween-20 in Nuclease-Free Water). 6mlof cold ATAC-lysis buffer were added and muscles were lysed on ice. After 3 minutes the lysate was dounced with 10 strokes of loose pestle avoiding too much  pressure  and  air  bubbles.  After  douncing, 8  ml  of  wash  buffer  were  added  and  the homogenate was filtered with 70μm, 40μm and 20μm cell strainers. Nuclei were pelleted by centrifugation for 5min at 500g at +4°C.
For snRNA-seq : We used the Single Cell 3’ Reagent Kit v3 according to the manufacturer’s protocol. GEM-RT was performed in a thermal cycler: 53°C for 45 min, 85°C for 5 min. Post GEM-RT  Cleanup  using  DynaBeads  MyOne  Silane  Beads  was  followed  by  cDNA amplification (98°C for 3 min, cycled 12 x 98°C for 15 s, 67°C for 20s, 72°C for 1 min). After a cleanup with SPRIselect Reagent Kit and fragment size estimation with High SensitivityTM HS  DNA  kit  runned  on  2100  Bioanalyzer  (Agilent),  the  libraries  were  constructed  by performing  the  following  steps:  fragmentation,  end-repair,  A-tailing,  SPRIselect  cleanup, adaptor ligation, SPRIselect cleanup, sample index PCR, and SPRIselect size selection. The fragment size estimation of the resulting libraries was assessed with High SensitivityTM HS DNA kit runned on 2100 Bioanalyzer (Agilent) and quantified using the QubitTM dsDNA High Sensitivity HS assay (ThermoFisher Scientific). Libraries were then sequenced by pair with a HighOutput flowcel using an Illumina Nextseq 500with the following mode:26base-pairs (bp) (10X Index + UMI), 8bp (i7 Index) and 57bp (Read 2).  For snATAC-seq : GEM incubation and amplification were performed in a thermal cycler: 72°C for 5 min, 98°C for 30 sec and 12 repeated cycles of 98°C for 10 sec, 59°C for 30 sec and 72°C for 1 min. Post GEM Cleanup using DynaBeads MyOne Silane Beads was followed by library construction (98°C for 45 sec, cycled 12 x 98°C for 20 sec, 67°C for 30 sec, 72°C for1 min).The libraries were constructed by adding sample index PCR, and SPRIselect size selection. The fragment size estimation of the resulting libraries was assessed with High SensitivityTM HS DNA kit runned  on  2100  Bioanalyzer  (Agilent)  and  quantified  using  the  QubitTM  dsDNA  High Sensitivity HS assay (ThermoFisher Scientific). Libraries were then sequenced by pair with a HighOutput flowcel using an Illumina Nextseq 500.

value: Tibialis

value: 2 months

value: female


title: snATAC-seq_Soleuis_quadriceps_1

value: Soleus+Quadriceps


title: snRNA-seq_Mix


title: snATAC-seq_Soleuis_quadriceps_2


title: snRNA-seq_Soleus

value: Soleus


title: snRNA-seq_Quadriceps

value: Quadriceps


title: PCF cells, 8d_3


title: 6327


title: PCF cells, 8d_2


title: FAE.epi4.WT

city: Boston

first: Adam

last: Haber

state: Massachusetts

address: 665 Huntington Ave, HSPH Building 1, Room 305

institute: Harvard T. H. Chan School of Public Health

description: 3' polyA RNA-seq. The expression levels for each gene (rows) in each single cell (column) in UMI counts as calculated using the CellRanger pipeline. Each column header provides the sequencing batch id, the cell barcode, and the cell type as identified by cluster analysis. Each ID is seperated by '_'

data_processing:
3' polyA RNA-seq; BAM file of 3' RNAseq reads aligned to mm10
CellRanger 1.0
PCA (prcomp in R)
kNN-based graph clustering (R code)
Genome_build: mm10
Supplementary_files_format_and_content: UMI count expression values for each gene (rows) in each cell (columns)

source_name: WT Mouse intestinal epithelial cells

extract_protocol:
3' polyA RNA seq
10X Genomics Chromium Prep

value: Wild type

value: intestinal epithelial cells


title: fp_harr_05hr_2


title: fp_harr_05hr_1


title: 7071

data_processing:
cut adapter by trim_galore (0.4.5)
aligment by bowtie2 (2.3.4.2)
remove duplicates by PICARD (2.9.0)
peak calling by MACS2 (2.1.2)
differential open region by csaw (1.16.1)
Genome_build: GRCm38
Supplementary_files_format_and_content: bed file of open regions

extract_protocol:
Flash frozen tissue was pulverized and ATAC-seq was performed as described in Corces et al., Nature Methods 14, 959-962(2017), with 50,000 nuclei used in each reaction
Library prepartion followed the protocols in Corces et al., Nature Methods 14, 959-962(2017)

treatment_protocol: Adult mice (6-10 weeks old) were admisistered 4 hourly intraperitoneal injections of caerulein (individual dose: 50 ug/kg), 3 times a week for 3 consecutive weeks. Mice were sacrificed and tissue collected 5 days following the final treatment.

value: Daxxfl/flMen1fl/flPdx1-CreTg (DMC)


title: 6959


title: FAE.epi3.WT


title: PCF cells, 8d_1


title: 6962


title: fp_ltm_05hr_1


title: 6995

value: Men1fl/flPdx1-CreTg (MC)


title: fp_chx_05hr_2

description: STAR.SJ.tab


title: fp_ltm_05hr_2


title: PCF cells, 6d_3

value: 6 days after induction of ectopically expressed RBP6 protein


title: 6999

value: pancreas


title: fp_chx_05hr_1

description: STAR.SJ.tab


title: 7078


title: 7000


title: mrna_05hr_2

description: STAR.SJ.tab


title: PCF cells, 6d_4


title: 6997


title: AB2841 LCMV spleen

first: Ido

last: Amit

address: 234 Herzl st.

department: Immunology

institute: Weizmann Institute of Science

data_processing:
bcl2fastq/2.15.0.4
Sequences with RMT of low quality (defined as RMT with minimum Phred score of less than 27) were filtered out.
Pool-barcode and well-barcode-RMT were extracted from the first and second end of the read (respectively) and concatenated to the fastq header, delimited by a underscore i.e. POOL_BARCODE_WELL_BARCODE_RMT while "NNNNNN" was used as a place holders if plate barcode was not used.
Reads were separated by POOL_BARCODE_WELL_BARCODE header data, allowing 1 sequencing error. This process created a single fastq file for each source well.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include mRNA molecule count values for each Sample

source_name: LCMV spleen

growth_protocol: All mice were maintained under specific pathogen-free conditions

extract_protocol:
Mice were perfused with 5 ml PBS via the left ventricle and spinal cord samples were harvested from individual mice. CNS tissues were cut into small pieces and homogenized through a 100mm mesh filter without tissue digestion. After washing, the cell pellet was resuspended in 40% Percoll and the myelin fraction was separated from mononuclear cells by density centrifugation (2200rpm, 20 min at 14ºC with low acceleration and no brake).
Samples were flow sorted either using AriaII, AriaIII or Aria-Fusion (BD Biosciences, BD Diva Software) cell sorter.
3' end mRNA libraries were prepared for sequencing using MARS-seq (Jaitin et al, Science 2014)

treatment_protocol: Mice were immunized subcutaneously with 200μg of MOG35-55 peptide emulsified in CFA containing 1mg of Mycobacterium tuberculosis as described previously. Mice received intraperitonal injections of 250ng pertussis toxin at the time of immunization and 48 hours later.

tag: organ

value: Spleen

tag: selection marker

value: GFP+ cells

value: 72h post LCMV-GFP infection

tag: mouse age

value: 6-8 weeks


title: AB2840 LCMV spleen


title: AB2842 LCMV spleen


title: AB2036 LCMV Lymph node

source_name: LCMV Lymph node

value: Lymph node

value: 24h post LCMV infection


title: AB2037 LCMV Lymph node


title: mrna_05hr_1

description: STAR.SJ.tab

value: Vero cells, ATCC, CCL-81


title: CD45.2 WT derived cells from WT:WT chimeric mice

description: CD45.2 WT derived cells from WT:WT chimeras

data_processing:
Raw data bcl files were first demultiplexed using Cell Ranger 2.0.0 and 2.0.2 mkfastq
Demultiplexed data was then processed using the Cell Ranger 2.0.0 and 2.0.2 count pipeline
Genome_build: mm10
Supplementary_files_format_and_content: h5 files including raw counts (output CellRanger Count) for each sample

source_name: Lung

extract_protocol:
All Methods listed in Bosteels et al.  Inflammatory Type 2 cDCs Acquire Features of cDC1s and Macrophages to Orchestrate Immunity to Respiratory Virus Infection. Immunity. 2020.
All Methods listed in Bosteels et al.  Inflammatory Type 2 cDCs Acquire Features of cDC1s and Macrophages to Orchestrate Immunity to Respiratory Virus Infection. Immunity. 2020.

tag: platform

value: 10x Genomics – v2

tag: number of cells


title: AB2035 LCMV Lymph node


title: CD45.1 WT derived cells from WT:WT chimeric mice

description: CD45.1 WT derived cells from WT:WT chimeras


title: PCF cells, 4d_4

value: PCF cells

value: 4 days after induction of ectopically expressed RBP6 protein


title: PCF cells, 6d_2


title: PCF cells, 6d_1


title: lps3

city: Guangzhou

first: Jinhuan

last: Song

state: Guangdong

address: Jinan University, No.601, West Huangpu Avenue

institute: Jinan University

description: processed data file: exp_detail_20191018_220549.txt

data_processing:
Illumina platform converts sequenced image signals into text signals through CASAVA base recognition, and stores them in fastq format as raw data.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence.
The expression levels of genes and transcripts were quantitatively analyzed by software in order to analyze the differential expression of genes/transcripts between different samples in the future, and the regulation mechanism of genes could be revealed by combining sequence function information.
Genome_build: http://www.ensembl.org/Gallus_gallus/Info/Index
Supplementary_files_format_and_content: exp_detail_20191018_220549.txt: Tab-delimited text file includes FPKM values.

organism: Gallus gallus

source_name: embryos

growth_protocol: Fertilized Leghorn eggs were obtained from the Avian Farm of the South China Agriculture University (Guangzhou, China), and incubated until reaching to the required developmental stage (Hamburger and Hamilton) (Misske et al., 2007) in a humidified incubator.

extract_protocol:
Total RNA was extracted from the chicken embryos using a Trizol kit (Invitrogen, USA). First-strand cDNA was synthesized to a final volume of 20μL using a SuperScript RIII first-strand kit.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: For the LPS-treated early stage embryos, the HH0 chicken embryos in EC culture were treated with 10 μg/ml LPS (Sigma–Aldrich, St. Louis, MO) or PBS (control) until the experimentally required developmental stage.

tag: breed

value: Leghorn

value: Embryo

value: LPS


title: PCF cells, 4d_3


title: PCF cells, 4d_1


title: PCF cells, 4d_2


title: CD45.2 Irf8 fl/fl Itgax-cre derived cells from WT:Irf8 fl/fl Itgax-cre chimeric mice

description: CD45.2 Irf8 fl/fl Itgax-cre derived cells from WT:KO chimeras


title: PCF cells, 3d_4

value: 3 days after induction of ectopically expressed RBP6 protein


title: AB2033 VSV Lymph node

source_name: VSV Lymph node

value: 24h post VSV infection


title: lps1

tag: tissue


title: PCF cells, 3d_3


title: control3

value: PBS


title: control2


title: lps2


title: IV-1

city: Iowa City

first: Isaac

middle: J

last: Jensen

state: IA

institute: University of Iowa

description: replicate 1

data_processing:
The sequencing quality of RNA-Seq libraries was assessed by FastQC v0.11.3 (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/ )
STAR (v 2.7.1a) with reference genome were used for sequence alignment.
Gene expressions were calculated with featureCounts (v1.6.0)
Differential expression analysis done using DE-Seq2 (v1.22.2)
Genome_build: mm10
Supplementary_files_format_and_content: Excel file includes DESeq2 values for each sample.

source_name: OT-I CD8 T cells

extract_protocol:
OT-I CD8 T cells were sort purified and total RNA extracted via NucleoSpin® RNA II Columns
RNA-seq libraries were constructed using NEBNext Single Cell/Low Input RNA Library Prep Kit for Illumina

tag: strain

value: Brain

tag: cell phenotype

tag: file #


title: IV+2

description: replicate 2


title: IV-2

description: replicate 2


title: AB2034 VSV Lymph node

tag: treatment


title: IV+1

description: replicate 1


title: 4TLI_S16_L004

city: Portland

first: Kevin

last: Burfeind

state: OR

address: 3181 SW Sam Jackson Park Rd

institute: Oregon Health & Science University

data_processing:
Raw reads were normalized and analyzed using the Bioconductor package DESeq2 (Love, Huber and Anders, 2014).  Only those genes that were expressed in at least one sample were included in differential expression analysis (28,762 out of 51,916 genes).
Genes were normalized taking into account the sample’s library size, which is the total number of reads mapping to a gene.  Raw p-values were adjusted for multiple comparisons using the Benjamani-Hochberg method (Benjamini and Hochberg, 1995)
Prior to performing Differential Expression Analysis, we performed Exploratory Data Analysis (EDA) to identify any issues with samples that would affect downstream analysis.  Issues such as samples not clustering with replicates or outlier samples could affect our ability to detect differentially expressed genes.
We defined down-regulated genes using the following criteria: statistical significance (Adjusted P-value < 0.05) and effect size (log2 Fold Change (log2fc) less than/equal to -2 ). Similarly, up-regulated genes were defined using same statistical significance and  effect size of log2fc greater than/equal to 2.  Independent filtering was performed to select a set of genes which will result in the most genes with adjusted p-values.  Tumor Brain was used as baseline for all Tumor related analyses (Tumor Blood vs Tumor Brain, Tumor Liver vs Tumor Brain, Tumor Tumor vs Tumor Brain).
We perform two enrichment analysis, Pathway (using Reactome) and Gene Ontology, using the Goseq Bioconductor R package (Young et al 2010), which takes into account gene length when performing enrichment analysis. Longer genes are more likely to be detected in sequencing and would therefore bias enrichment analysis.
Genome_build: mm10
Supplementary_files_format_and_content: see .xlsx files for processed and normalized reads

source_name: Neutrophils from Liver

extract_protocol:
Total RNA was isolated from FACS-sorted CD11bhighLy6Ghigh neutrophils using an RNAeasy Plus Micro kit (Qiagen). RNA integrity was verified by a Bioanalyzer (Agilent).
Sample cDNAs were prepared using the SMART-Seq v4 Ultra Low Input kit (Takara) using 250 pg of input total RNA followed by library preparation using a TruSeq DNA Nano kit (Illumina). Libraries were verified by Tapestation (Agilent). Library concentrations were determined by real-time PCR with a StepOnePlus Real Time PCR System (Thermo Fisher) and a Kapa Library Quantification Kit (Kapa Biosystems / Roche). Libraries were sequenced with a 100 cycle single read protocol on a Illumina HiSeq 2500 (Illumina) with four libraries per lane. Fastq files were assembled using Bcl2Fastq2 (Illumina).

tag: disease state

value: Tumor

value: Neutrophils

value: Liver

tag: chip antibody


title: SP2

description: replicate 2

value: Spleen


title: 1SBL_S15_L004

source_name: Neutrophils from Blood

value: Sham

value: Blood


title: SP1

description: replicate 1


title: CD45.1 WT derived cells from WT:Irf8 fl/fl Itgax-cre chimeric mice

city: Zwijnaarde

first: Liesbet

last: Martens

address: Technologiepark 927

institute: VIB-University of Ghent

description: CD45.1 WT derived cells from WT:KO chimeras


title: 3TBL_S14_L004


title: GR MUT Dex rep2 ChIP-Seq

tag: antibody

value: Glucocorticoid Receptor - Proteintech 24050-1-AP

tag: Sex

value: male

tag: genotype

value: GR Zn / Zn

value: 16h 1µM Dex in EtOH


title: control1

value: Leghorn

tag: age


title: 2TTU_S17_L005

source_name: Neutrophils from Tumor

tag: cell type


title: PCF cells, 3d_2

value: PCF cells

tag: timepoint

tag: replicate


title: PCF cells, 2d_4

value: 2 days after induction of ectopically expressed RBP6 protein


title: PCF cells, 0d_4

value: control

value: before induction of ectopically expressed RBP6 protein


title: PCF cells, 2d_1


title: PCF cells, 3d_1

value: 3 days after induction of ectopically expressed RBP6 protein


title: 4TBR_S12_L003

source_name: Neutrophils from Brain

value: Brain


title: PCF cells, 0d_2


title: PCF cells, 2d_2


title: PCF cells, 2d_3


title: PCF cells, 0d_1


title: 3SBL_S10_L003


title: PCF cells, 0d_3


title: 1TBL_S13_L004

value: Tumor


title: MF3

city: Anyang

first: Jianyong

last: Wu

address: Huanghe Dadao 38#

institute: Institute of Cotton Research, CAAS

description: At the start of squaring stage

data_processing:
Using the Illumina paired-end RNA-seq approach
we aligned reads of  all samples to the reference genome using HISAT package
StringTie and Ballgown was used to estimate the expression levels of all transcripts. StringTie was used to perform expression level for mRNAs by calculating FPKM
The differentially expressed mRNAs and genes were selected with log2 (fold change) >1 or log2 (fold change) <-1 and with statistical significance (p value < 0.05) by R package – Ballgown.
Supplementary_files_format_and_content: xls include FPKM values for each Sample

organism: Gossypium hirsutum

source_name: Flower buds

growth_protocol: Field experiments

extract_protocol:
T.RNA with Sigma Spectrum Plant Total RNA kit (Sigma-  448 Aldrich, USA)
Accordance with the protocol for the mRNA-Seq sample preparation kit (Illumina, San Diego, USA)

value: Flower buds

tag: developmental stage

value: Squaring stage


title: MF1

description: At the start of squaring stage


title: MF2

description: At the start of squaring stage


title: DPAM2

description: At the start of squaring stage

source_name: 1 day post anthesis ovule

value: 1 day post anthesis ovule


title: DPAM1

description: At the start of squaring stage


title: MRL3

description: At the start of squaring stage

source_name: Leaf

value: Leaf


title: DPAM3

description: At the start of squaring stage


title: DPAL3

description: At the start of squaring stage


title: 5TBR_S11_L003

value: Neutrophils


title: 1TTU_S9_L003