title: P_AgP25-1

status: Public on Oct 18 2020

type: SRA

city: Brisbane

first: Jianhua

last: Guo

address: Research Road, Level 4 Gehrmann Building

department: Australian Centre for Water and Environmental Biotechnology

country: Australia

institute: University of Queensland

library_source: transcriptomic

data_processing:
base calling through an integrated primary analysis software called RTA (Real Time Analysis. v1.18).
The NGS QC toolkit (version 2.3.3) was used to treat the raw sequence reads to trim the 3’-end residual adaptors and primers, and the ambiguous characters in the reads were removed. Then, the sequence reads consisting of at least 85% bases were progressively trimmed at the 3’-ends until a quality value ≥ 20 were kept. Downstream analyses were performed using the generated clean reads of no shorter than 75 bp.
The clean reads of each sample were aligned to the E. coli reference genome (NC_000913) using SeqAlto (version 0.5). Cufflinks (version 2.2.1) was used to calculate the strand-specific coverage for each gene, and to analyze the differential expression in triplicate bacterial cell cultures. The statistical analyses and visualization were conducted using CummeRbund package in R (http://compbio.mit.edu/cummeRbund/).
Gene expression was calculated as fragments per kilobase of a gene per million mapped reads (FPKM, a normalized value generated from the frequency of detection and the length of a given gene.
Genome_build: NC_000913.3
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

molecule: total RNA

organism: Pseudomonas aeruginosa PAO1

source_name: Pseudomonas aeruginosa PAO1 bacteria

growth_protocol: liquid M9 culture at 30 °C

extract_protocol:
Bacterial cells were then harvested by centrifugation at 8000 × g for 10 min. Total RNA was extracted from the mutants using the QIAGEN miRNeasy Mini Kit (QIAGEN, Germany) manufacturer’s protocol with one extra bead-beating step to completely lyse the bacterial cells.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Pseudomonas aeruginosa PAO1 was cultured in 10 mLM9 media containing 0, 1, 20 and 25 mg/L AgNPs or 0, 1,30 and 300 mg/L AgNRs for 2 h, at 30 °C, with shaking

tag: strain

tag: tissue

value: liquid M9 culture


title: P_AgP20


title: P_AgP25-2


title: P_AgP1


title: P_AgR30


title: P_AgR300


title: P_AgR1


title: P_Control


title: EZH1-0hour-R1

status: Public on Oct 17 2020

city: Minhang

first: bing

last: zhang

state: Shanghai

address: 800 Dong Chuan Road

department: Shanghai Center for Systems Biomedicine

country: China

institute: Shanghai Jiao Tong University

library_source: genomic

data_processing:
ChIP-seq reads were aligned to the hg19 human genome assembly using bowtie2 with the following configurations: -p 1
Mapped reads were selected for further analysis using SAMTools.
ngsplot was used for visualization, IGVTools was used to make TDF files.
Genome_build: hg19
Supplementary_files_format_and_content: TDF files.

molecule: genomic DNA

organism: Homo sapiens

source_name: HUVEC

growth_protocol: Primary HUVEC cells purchased from Lonza within 3-6 passages were grown in EBM2+1% FBS or EGM2 medium (Lonza)

extract_protocol:
ChIP-seq: Chromatin DNA was extracted from sonicated nuclei and further selectively accumulated by ChiP-specific antibody. RNA-seq: total RNA were purified by Qiagen RNeasy column.
Novaseq

treatment_protocol: 50ng/ml VEGFa was used to treat serum-starved HUVEC cells. For modified RNA experiments, 0.5ug/ml modified RNA expressing GFP and ETS1 was used. For siRNA experiment, 10ng/ml siRNA was used.

tag: cell type

value: HUVEC

tag: antibody

tag: time point


title: Input-R1

value: input


title: H3K27me1-0hour-R1


title: H3K27me1-12hour-R1


title: H3K27me1-4hour-R1


title: EZH1-12hour-R1


title: H3K27me1-1hour-R1


title: EZH1-1hour-R1


title: EZH1-4hour-R1


title: sample_12_6: Ad_preF

status: Public on Oct 16 2020

city: Oxford

first: Dylan

last: Sheerin

address: Churchill Hospital, Old Road

country: United Kingdom

institute: University of Oxford

data_processing:
RNA was sequenced (75 bp, paired end) using an Illumina HISeq 4000
Raw fastq files were analysed for sequence quality using fastqc software
Reads were aligned to the Mus musculus reference genome (GRCm38) and genes were quantified using STAR with the --quantMode GeneCounts function
Resultant count matrices were filtered to include only genes with counts per million of greater than 1 million in 5 or more samples (smallest group size)
Count matrices were analysed for differential gene expression using the limma/voom pipeline
Genome_build: GRCm38, release 95
Supplementary_files_format_and_content: Tab-delimited files (.tab) were generated using STAR –quantMode GeneCounts and each value represent the number of reads incident to a gene in a given sample

organism: Mus musculus

source_name: Whole blood

extract_protocol:
RNA was extracted from mouse whole blood samples using a Mouse RiboPure(TM)-Blood RNA Isolation Kit (Life Technologies) and depleted for glibin mRNA using a GLOBINclear(TM) mouse/rat Kit (Life Technologies)
Polyadenylated transcripts were oligo (dT) bead-selected, reverse transcribed, amplified and labelled with an Illumina TotalPrep(TM)-96 RNA Amplification Kit (Life Technologies)
Sample fragments were 75 bp size-selected and multiplexed

treatment_protocol: Groups of 3-6 female C57BL/6 mice (6-8 weeks old) were immunised intramuscularly with 1/5 of the human dose (1e7 viral particles of MVA or 1e9 viral particles of adenovirus) of one of the listed vaccines. Mice were given a second dose of vaccine 3 weeks later (8 weeks for viral vectored vaccines) and cardiac bled to obtain whole blood 24h ours after this second dose.

value: Whole blood

tag: Sex

value: Female

tag: batch

tag: condition

value: Test

tag: vaccine/antigen

value: Adenovirus expressing prefusion F


title: sample_12_3: Ad_preF


title: sample_12_5: Ad_preF


title: sample_12_4: Ad_preF


title: sample_12_2: Ad_preF


title: sample_11_4: Tru.Tru

value: 2nd dose MenB-fHbp


title: sample_12_1: Ad_preF


title: sample_11_3: Tru.Tru


title: sample_11_2: Tru.Tru


title: sample_11_5: Tru.Tru


title: sample_10_6: Trumenba

value: 1st dose MenB-fHbp


title: sample_10_5: Trumenba


title: sample_9_5: Ad_empty

value: Empty adenovirus vector


title: sample_9_4: Ad_empty


title: sample_10_2: Trumenba


title: sample_10_1: Trumenba


title: sample_10_4: Trumenba


title: sample_11_1: Tru.Tru


title: sample_10_3: Trumenba


title: sample_9_6: Ad_empty


title: sample_9_2: Ad_empty


title: sample_8_6: Ad.MVA

value: Adenovirus prime, MVA boost


title: sample_8_2: Ad.MVA


title: sample_9_1: Ad_empty


title: sample_8_3: Ad.MVA


title: sample_8_1: Ad.MVA


title: sample_7_3: None

value: Control

value: Naïve


title: sample_7_1: None


title: sample_6_3: None


title: sample_6_2: None


title: sample_6_1: None


title: sample_5_5: MVA.Ad

value: MVA prime, adenovirus boost


title: sample_5_6: MVA.Ad


title: sample_5_3: MVA.Ad


title: sample_5_1: MVA.Ad


title: sample_9_3: Ad_empty


title: sample_4_6: Bex.Bex

value: 2nd dose 4CMenB


title: sample_3_6: Bexsero

value: 1st dose 4CMenB


title: sample_4_5: Bex.Bex


title: sample_4_4: Bex.Bex


title: sample_5_2: MVA.Ad


title: sample_3_5: Bexsero


title: sample_3_4: Bexsero


title: sample_4_1: Bex.Bex


title: sample_4_3: Bex.Bex


title: sample_8_5: Ad.MVA


title: sample_7_2: None


title: sample_3_3: Bexsero


title: sample_4_2: Bex.Bex


title: sample_3_2: Bexsero


title: sample_2_5: MVA_fHbp

value: MVA expressing fHbo


title: sample_2_4: MVA_fHbp


title: sample_3_1: Bexsero


title: sample_8_4: Ad.MVA


title: sample_2_3: MVA_fHbp


title: sample_2_2: MVA_fHbp


title: sample_2_1: MVA_fHbp


title: sample_1_6: Ad_fHbp

value: Adenovirus expressing fHbp


title: sample_1_5: Ad_fHbp


title: sample_1_4: Ad_fHbp


title: sample_1_3: Ad_fHbp


title: sample_1_2: Ad_fHbp


title: sample_1_1: Ad_fHbp


title: Gills, HSFinput

city: Qingdao

first: Youli

last: Liu

address: Nanhai Road No. 7

institute: Institute of Oceanology

data_processing:
raw data of fastq format were processed through in house perl scripts. In this step, clean data were obtained by removed adapter, low-quality reads (Q<20) and the sequence less than 50bp
ChIP-seq reads were aligned to the Crassostrea gigas genome assembly using BWA0.7.10
peak calling used the MACS2,model fold = [5, 50], qvalue cutoff = 5.00e-02, Range for calculating regional lambda is: 1000 bps and 10000 bps,
Genome_build: Crassostrea gigas 24.0
Supplementary_files_format_and_content: bed file was generated by MACS2

organism: Magallana gigas

source_name: gills

extract_protocol:
Lysates were clarified from sonicated nuclei and HSF1-DNA complexes were isolated with antibody.
The sample concentration was measured using the Qubit Fluorometer, and the fragment size and distribution were detected using the Agilent 2000. The 3'–5' exonuclease and polymerase were used to repair DNA fragments with overhangs. The 3' end of each DNA fragment was ligated to the single base A to ensure the complementary pairing of the DNA fragment with the linker. The tagged linker and DNA fragment were linked with a ligase. The linker was removed and the DNA fragment was evaluated by gel purification. A DNA fragment with a linker at both ends was selectively enriched by PCR, and a DNA library was generated. To evaluate library quality, Pico green was used for quantification and Agilent 2000 was used to detect the fragment size and distribution of the sample DNA. The library was diluted to 4–5 pmol/L and then sequenced using the Illumina HiSeq 2500 platform.

treatment_protocol: 35℃heated 0.5h

value: gills

tag: treatment

value: 35C-heated, 0.5h

tag: chip antibody


title: Gills, HSFchip

value: HSF1 monoclonal antibody, custom-made (BGI, China)


title: sample_2_6: MVA_fHbp

value: Whole blood

value: Female


title: treat 2(15)_RNA-Seq

status: Public on Oct 15 2020

city: Shanghai

first: Tong

last: Li

address: No.  910 Hengshan Rd

institute: International Peace Maternity & Child Health Hospital

data_processing:
Raw sequence reads were initially processed by FASTQC for quality control, and then adapter sequences and poor quality reads were removed by using CUTADAPT
Quality filtered reads were then mapped to hg19 using STAR
Read counts were calculated by using htseq-count
Genome_build: hg19
Supplementary_files_format_and_content: Differential gene expression analysis was done using R package DESeq2. DEGs are defined as having a Benjamini and Hochberg false discovery rate of < 0.05 %

source_name: treat_dNK cells

extract_protocol:
Total RNA was extracted from purified decidual NK cells using TRIzol reagent  (Invitrogen, USA) in accordance with the manufacturer’s protocol. RNA purity was checked using the NanoPhotometer® spectrophotometer (IMPLEN, CA, USA), concentration was measured using Qubit® RNA Assay Kit in Qubit® 2.0Flurometer (Life Technologies, CA, USA) and integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
A total amount of 3 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations. Briefly, mRNAs and lncRNAs with poly A-tails were purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer (5x). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext adaptors with hairpin loop structure were ligated to prepare for hybridization. The library fragments were purified with AMPure XP system (Beckman Coulter, USA). Then 3 μL USER Enzyme (NEB, USA) was added with size-selected, adaptor-ligated cDNA before PCR, which was performed with Phusion High-Fidelity DNA polymerase, universal PCR primers and Index primers. At last, PCR products were purified with AMPure XP system and library quality was assessed on the Agilent Bioanalyzer 2100 system.

treatment_protocol: Non-enzymatic isolation of decidual mononuclear leukocytes was performed as previously described. In brief, fresh decidua samples were rinsed extensively in sterile PBS and were then minced repeatedly until into <1 mm3 pieces using ocular scissors. The suspensions were strained through a 74-μm nylon mesh to obtain single-cell suspensions, which were then gently loaded on the density gradient media Lymphoprep™ (Axis-Shield, Alere Technologies AS, Norway). Decidual mononuclear cells containing monocytes and lymphocytes were then isolated and purified by density gradient centrifugation. Surface staining of the isolated decidual mononuclear cell suspensions was realized by incubating cells directly with the fluorochrome-conjugated anti-human CD56 and CD3 monoclonal antibodys in 500 uL PBS containing 3% FBS at 4℃ for 1 hour. The decidual NK cells were then purified based on the surface expression of CD56 and CD3 markers (CD56+CD3-) using a standard FACSAriaII flow cytometer (BD Biosciences, USA). The data were analyzed via FlowJo 7.6.1 software (TreeStar, San Carlos, Calif). Anti-CD56 APC (clone: B159), anti-CD3 FITC (HIT3a), anti-CD45 PE (HI30) and anti-CD16 BV421 (3G8) antibodies were purchased from BD Bioscience.

tag: subject status

value: patient with missed abortion

value: decidua

tag: cell type source

value: decidual NK cells

value: FACS-sorted primary cells

tag: molecule subtype

value: mRNA and lncRNA with poly-A tail


title: treat 3(A8-NK)_RNA-Seq


title: treat 1(dNK12)_RNA-Seq


title: control 3(NK-4)_RNA-Seq

source_name: control_dNK cells

value: healthy control women undergoing elective abortions


title: control 2(2A-3NK)_RNA-Seq


title: control 1(A2-NK)_RNA-Seq


title: WT rep3

type: RNA

city: Tokyo

first: Fumika

middle: Clara

last: Kubo

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

department: School of Science, Department of Biological Sciences

country: Japan

institute: The University of Tokyo

description: WT shoot apices

hyb_protocol: Hybridization, washing, and staining procedures were run on Fluidics Station 450 (Thermo Fisher Scientific) with GeneChip Hybridization, Wash, and Stain Kit (Thermo Fisher Scientific).

scan_protocol: GeneChips were scanned with GeneChip Scanner 3000 7G (Thermo Fisher Scientific).

data_processing: Normalization was performed by using the standard settings for GeneChip Gene 1.0 ST arrays on Expression Console Version 1.3 (Thermo Fisher Scientific).

label: biotin

organism: Oryza sativa

source_name: shoot apices

label_protocol: The sense-strand DNA target was prepared by using a WT Expression Kit (Thermo Fisher Scientific) and a GeneChip WT Terminal Labeling and Controls Kit (Thermo Fisher Scientific) in accordance with the manufacturers’ instructions.

growth_protocol: Plants were grown in plastic containers holding soil.

extract_protocol: Total RNA was extracted using TRIsure (BIOLINE).

treatment_protocol: The shoot apices of each strain were dissected under microscope and frozen in liquid nitrogen for the subsequent RNA extraction.

tag: genotype

value: WT


title: Natural_1

status: Public on Oct 31 2019

city: London

first: Kelly

last: Marno

address: 4 Newark Street

department: Centre for Immunology and Infectious Disease

institute: Blizard Institute, Barts and the London SMD, Queen Mary University of London

description:
5W1
replicate 1

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalized using quantile normalization with GenomeStudio software.

source_name: MDM, natural IFN treated

label_protocol: Samples were labelled with the Illumina TotalPrep RNA Amplification Kit according to the manufacturer's instructions.

growth_protocol: Monocytes were isolated from PBMC by adherence. Cells were then plated at 2×106 cells/ml and left to differentiate for 7-14 days in RPMI 1640/20% autologous human serum and 20ng/ml macrophage colony stimulating factor (M-CSF).

extract_protocol: Total RNA was extracted with QIAGEN RNeasy Plant Mini Kit according to the manufacturer's protocol. Quality control was performed by Agilent Bioanalyzer.

treatment_protocol: MDM were treated with 500IU/ml IFNα (recombinant; Sigma #I4401-100KU, natural; Wellferon® GlaxoSmithKline) for 24hr prior to RNA extraction, or left untreated.

value: primary human monocyte-derived macrophages (MDMs)

value: natural IFNα


title: Natural_2

description:
5W2
replicate 2


title: dsl1 rep3

description: dsl1 shoot apices


title: WT rep2

description: WT shoot apices


title: wt_24h [E14_24h_3]

city: Madrid

first: Manuel

middle: J

last: Gomez

state: Madrid

address: Melchor Fernández Almagro, 3

country: Spain

institute: CNIC

data_processing:
Fastq files containing reads for each library were extracted and demultiplexed using Casava v1.8.2.
Sequencing adaptor contaminations were removed from reads using Cutadapt v1.3.
Preprocessed reads were mapped and quantified on the transcriptome using RSEM v1.2.3.
Genome_build: GRCm38 assembly, Ensembl genebuild 76
Supplementary_files_format_and_content: matrix_table.xls file contains ENSEMBL gene Ids and TMM-Normalized counts per million for each sample.

molecule: polyA RNA

growth_protocol: ESCs were maintained in serum-free conditions with Knock out serum replacement (Thermo Fisher), LIF (produced in-house), and 2i (CHIR-99021, Selleckchem; and PD0325901, Axon) over inactive mouse embryonic fibroblast (MEFs). The NanogKO (BT12) and their parental wild-type control (E14Tg2a) ES cells were kindly provided by Ian Chambers and Austin Smith (Chambers et al., 2007).

extract_protocol:
RNA from single embryos was isolated using the Arcturus PicoPure RNA Isolation Kit (Applied Biosystems)
New England Biolabs Nest Ultra RNA library prep Kit
single read Next generation sequencing (Illumina HiSeq 2500)

treatment_protocol: RNA from NanogKO ES cells and their parental line was extracted using the RNeasy Mini Kit (Qiagen)

value: E14Tg2a Embryonic stem cell


title: dsl1 rep2

description: dsl1 shoot apices


title: No IFN_3

description:
5-3
replicate 3

source_name: MDM, untreated

value: untreated


title: Natural_3

description:
5W3
replicate 3


title: wt_12h [E14_12h_2]


title: wt_12h [E14_12h_3]


title: Recombinant_1

description:
5S1
replicate 1

source_name: MDM, recombinant IFN treated

value: recombinant IFNα


title: wt_24h [E14_24h_2]


title: wt_24h [E14_24h_1]


title: wt_12h [E14_12h_1]


title: wt_0h [E14_0h_3]


title: NanogKO_24h [BT12_24h_3]

value: BT12 Embryonic stem cell

value: Nanog KO


title: wt_0h [E14_0h_2]


title: NanogKO_24h [BT12_24h_2]


title: No IFN_1

description:
5-1
replicate 1


title: NanogKO_24h [BT12_24h_1]


title: dsl1 rep1

description: dsl1 shoot apices


title: NanogKO_12h [BT12_12h_3]


title: NanogKO_12h [BT12_12h_2]


title: NanogKO_12h [BT12_12h_1]


title: NanogKO_0h [BT12_0h_3]


title: Recombinant_2

description:
5S2
replicate 2


title: NanogKO_0h [BT12_0h_2]


title: NanogKO_0h [BT12_0h_1]


title: Gata6 flox/flox;Pdx1-Cre 4

city: Seville

first: Anabel

last: Rojas

state: Seville

address: Avda. Américo Vespucio

department: Stem Cell

institute: CABIMER

hyb_protocol: Following fragmentation, 5.5 ug of single-stranded cDNA were hybridized for 16 hr at 45C on GeneChip® Mouse Gene 2.0 ST Array. GeneChips were washed and stained in the GeneChip® Fluidics Station 450 according to GeneChip® Expression AnalysisTechnical Manual, Affymetrix, 2004.

scan_protocol: Microarrays were scanned using GeneChip® Scanner 3000 7G

data_processing: The .CEL files were generated using Affymetrix AGCC software and further processed into expression values using Robust Multiarray Average (RMA) method by Irrizarry et al. The following statistical data analysis (ANOVA unpaired one-way) were performed using the TAC software (Transcriptome Analysis Console) developed by Affymetrix.

source_name: G6KO, primary isolated islets

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 250 ng total RNA Labeling Protocol (The Ambion WT Expression kit for Affymetrix GeneChip® Whole Transcript Expression Arrays, Life Technologies Corporation, 2009).

growth_protocol: Mice were maintained in SPF animal house  on a light/dark (12/12 hours) cycle at 24oC, receiving food and water ad libitum.

extract_protocol: Islets were isolated used by collagenase digestion. Total RNA was extracted using RNA extraction kit (Qiagen).

treatment_protocol: Mice were sacrified by cervical dislocation prior to islets isolation.

value: pancreatic islets

tag: genotype/variation

value: Gata6 KO


title: Gata6 flox/flox 3

source_name: Ctrl, primary isolated islets

value: control


title: WT rep1

description: WT shoot apices


title: Gata6 flox/flox;Pdx1-Cre 1


title: 478_HIP

first: Dervis

middle: A

last: Salih

address: Gower St

department: Dementia Research Institute

institute: University College London

data_processing:
Adaptors and low quality base pairs were removed from FASTQ files using Trim Galore (Babraham Bioinformatics).
Transcripts were quantified with Salmon (Patro et al., 2017), using gene annotation from ENSEMBL GRCm38.
To obtain gene level quantification from the transcripts, and correct for average transcript length and library size, expressed as transcripts per million (TPM), the tximport R package was used (Soneson et al., 2015).
Genome_build: GRCm38
Supplementary_files_format_and_content: xls file includes TPM values for each sample.

source_name: Hippocampus

extract_protocol:
Total RNA was isolated from flash frozen hippocampi using the miRNeasy 96 kit (Qiagen).
RNA strand-specific libraries were created using commercially available kits according to the manufacturer’s instructions (TruSeq Stranded mRNA Library Preparation Kit, Illumina). In brief, poly(A)-RNA was extracted from total RNA using an oligo(dT)-bead based method. After fragmentation of the mRNA, first-strand and dUTP-based second strand synthesis was carried out, followed by end-repair, A-tailing, ligation of the indexed Illumina adapter and digestion of the dUTP-strand. Size selection was performed using a bead-based method. After PCR amplification, the resulting fragments were purified, pooled, quantified and used for cluster generation. For sequencing, pooled libraries were loaded on the cBot (Illumina) and cluster generation was performed according the manufacturer’s instructions. Paired-end sequencing using 100 bp read length (multiplex 12 samples per lane - 28M reads) was performed on a HiSeq2500 (HiSeq Control Software 2.2.58) using HiSeq Flow Cell v4 and TruSeq SBS Kit v4.

treatment_protocol: Five transgenic lines: TAS10-mice, TPM-mice, HET-TASTPM-mice, HO-TASTPM-mice and Tau-mice. Control line: C57Bl/6J wild-type mice. Four ages: 2, 4, 8 and 18 months.

tag: age (months)


title: 2187_HIP

tag: strain


title: 2314_HIP

value: TPM


title: 969_HIP


title: Gata6 flox/flox;Pdx1-Cre 3

tag: tissue


title: Gata6 flox/flox 2


title: No IFN_2

description:
5-2
replicate 2

tag: cell type


title: 2438_HIP

value: WILD


title: Recombinant_3

description:
5S3
replicate 3


title: Gata6 flox/flox 1


title: GFPNeg_TB_2

city: New York

first: Joan

last: Massague

state: NY

address: 417 E 68th St

department: Cancer Biology and Genetics

country: USA

institute: Memorial Sloan Kettering Cancer Center

description:
RNASeq
P5867F_Id1GFP_normalized_counts.csv
4-GFPnTb

data_processing:
QC: FastQC v0.11.5
Alignment: STAR2.5.2b for RNASeq, Bowtie2 for ChIPseq
RNAseq annotation: HTSeq v0.6.1p1
RNAseq normalization: DESeq2 v3.4
ChIPseq sorting, normalization, and visualization: Sam Tools & HOMER
Genome_build: mm10, hg19
Supplementary_files_format_and_content: RNASeq: Normalized Counts in .csv; ChIPSeq/ATACSeq: genome browser tracks in .tdf

source_name: pancreatic ductal adenocarcinoma

growth_protocol: High glucose DMEM + 10% FBS

extract_protocol:
Total RNA was collected using Qiagen's Rneasy Mini Kit (74106) and assessed for RNA integrity number >9.5. For ChIP-seq, cells were fixed, quenched, sonicated to ~250 bp in 1% SDS lysis buffer, and incubated with Protein A Dynabeads (Novex 10008) and 5 µg of the indicated antibody. 2% pre-cleared chromatin prior to primary antibody addition was kept as input DNA. After wash, treatment with RNAse A and Proteinase K, DNA was eluted and purified with Qiagen's PCR purification kit (28106).For ATACSeq, cell nuclei were prepared from 5x104 cells and incubated with 2.5 μL transposase (Illumina) in a 50 μL reaction for 30 minutes at 37°C.
For RNASeq, library construction was performed using TruSeq RNA Sample Prep Kit v2 (Illumina) following manufacturer’s instructions. For ChIPSeq, DNA quality was checked using Agilent Technologies 2200 TapeStation and quantified using PicoGreen. Library construction was performed using the NEBNext ChIP-seq Library Prep Master Mix Set for Illumina  according to manufacturer's conditions. Samples were pooled and submitted to New York Genome Center for SE50 sequencing. For ATACSeq, following purification of transposase-fragmented DNA, the library was amplified  by PCR and subjected to PE50 high-throughput sequencing.

treatment_protocol: Cells were plated at 300k per 15 cm plate in 2.5 µM MK2206 (ChemieTek CT-MK2206) 12h prior to treatment with 2.5 µM SB505124 (Sigma S4696) or 100 pM TGFβ (R&D 101-B1). Where indicated, doxycycline at 1 µg/mL at plating.

tag: cell line

tag: timepoint

value: TGFβ


title: GFPNeg_TB_1

description:
RNASeq
P5867F_Id1GFP_normalized_counts.csv
3-GFPnTb


title: D10F_SB12h_1

description:
RNASeq
P5867_AKT_normalized_counts.csv
D10F-SB-12h


title: Akt_Tb2h_2

description:
RNASeq
P5867_AKT_normalized_counts.csv
Akti-Tb-2h


title: GFPPos_TB_2

description:
RNASeq
P5867F_Id1GFP_normalized_counts.csv
8-GFPpTb


title: GFPPos_TB_1

description:
RNASeq
P5867F_Id1GFP_normalized_counts.csv
7-GFPpTb


title: Akt_Tb2h_1


title: D10F_Tb12h_2

description:
RNASeq
P5867_AKT_normalized_counts.csv
D10F-Tb-12h


title: D10F_Tb12h_1


title: D10F_SB12h_2


title: 2398_HIP


title: 2434_HIP


title: Gata6 flox/flox;Pdx1-Cre 2


title: 2155_HIP


title: 2418_HIP


title: 2393A_HIP


title: 2417_HIP


title: 1108_HIP


title: 812_HIP


title: 510_HIP


title: 1826_HIP

value: TAU


title: 2376_HIP


title: 2392_HIP


title: 2416_HIP


title: 154_HIP


title: 2153_HIP


title: 811_HIP


title: 1819_HIP


title: 2152_HIP


title: 2360_HIP


title: 835_HIP


title: 454_HIP


title: 2440_HIP


title: 1825_HIP


title: 2337_HIP


title: 476_HIP


title: 2375_HIP


title: 2351_HIP


title: 1494_HIP


title: 2344_HIP


title: 2342_HIP


title: 2154_HIP


title: 2423_HIP


title: 2350_HIP


title: 1824_HIP


title: 1474_HIP


title: 2338_HIP


title: 1107_HIP


title: 2098_HIP


title: 810_HIP


title: 2439_HIP


title: 1811_HIP


title: 2374_133_2_HIP


title: 2443_HIP


title: 2330_HIP


title: 1463_HIP


title: 2306_HIP


title: sample_5_4: MVA.Ad

value: Whole blood

tag: Sex

value: Female

value: Test

value: MVA prime, adenovirus boost


title: 2442_HIP


title: 475_HIP


title: 1106_HIP


title: 968_HIP


title: 1839_HIP


title: 1818_HIP


title: 2339_HIP


title: 1161_HIP


title: 1150_HIP


title: 493_HIP


title: 452_HIP


title: 113_HIP


title: 509_HIP


title: 2425_HIP


title: 2431_HIP


title: 1817_HIP


title: 1473_HIP


title: 2334_HIP


title: 1472_HIP


title: 2336_HIP


title: 834_HIP


title: 2424_HIP


title: 451_HIP


title: 967_HIP


title: 2335_HIP


title: 1461_HIP


title: 1809_HIP


title: 833_HIP


title: 453_HIP


title: 1808_HIP


title: 2125_HIP


title: 2415_HIP


title: 1105_HIP


title: 832_HIP


title: 809_HIP


title: 2099_HIP


title: 97_HIP


title: 2391_HIP


title: 1810_HIP


title: 966_HIP


title: 460_HIP


title: 1816_HIP


title: 1149_HIP


title: 2357_HIP


title: 1151_HIP


title: 2297_HIP


title: 1462_HIP


title: 1838_HIP


title: KOWT95

city: Toronto

first: Michael

middle: W

last: Salter

state: Ontario

address: 686 Bay Street

department: Neurosciences & Mental Health

country: Canada

institute: Hospital for Sick Children

description:
RNA-Seq poly A**
processed data file: rawCountMatrix.tsv
processed data file: matrixRPKM.tsv

data_processing:
Base calling was done using bcl2fastq2 v2.17.
Alignment was carried out using STAR ver. 2.5.0c.
RPKM was calculated using Cufflinks ver2.2.1.
RNAseq data were with the RNAseq pipeline in GenPipes ver 2.2.0 (https://bitbucket.org/mugqic/genpipes).
Genome_build: GRCm38
Supplementary_files_format_and_content: rawCountMatrix.tsv: Tab-separated text file includes raw counts.
Supplementary_files_format_and_content: matrixRPKM.tsv: Tab-separated text file includes RPKM values.

source_name: cortical brain

extract_protocol:
Mouse brain cortexes were harvested from Wild-type, Grin1-exon5 knockout and Grin1-exon5 constitutive genotypes and put into RNAlater solution (Ambion). The brain tissues were homogenized in Qiazol using the Tissue Shredder (Qiagen) and total RNA was isolated from using RNeasy Lipid Tissue Mini Kit (Qiagen). Purified RNAs were quantified with a Nanodrop 1000 (Thermo Scientific) and the quality of the RNA assessed using an Agilent Bioanalyzer (Agilent). All RNA used had an RNA Integrity Number > 8.0. RNAs from each mouse contains at least 300 ng of RNA.
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: strain/background

tag: mutation

value: Knock-out wt

value: Wild type

value: Cortical brain

tag: age

value: Adult


title: KOWT93


title: 492_HIP


title: KO360

value: Knock-out


title: KIWT350

value: Knock-in wt


title: KIWT345


title: 2319_HIP


title: KI346

value: Knock-in


title: KI347


title: KIWT358


title: KI341


title: WTNoGlucose Rep2

city: Newark

first: Jean-Pierre

last: Etchegaray

state: NJ

address: 225 University Ave

department: Biological Sciences

institute: Rutgers University

data_processing:
RNA-Seq data for WT and SIRT6 KO ESCs were aligned to mouse mm9 transcriptome using tophat2 version 2.0.10
gene counts were found using htseq version 0.6.1, and finally differentially expressed genes were found using the Bioconductor package DESeq2
Genes were called differentially regulated if they had an adjusted p-value less than 0.1
Authors state "We didn't perform genome wide analysis in the other 3 samples (WT-NoGlucose), they're just used for comparison of a handful of genes in genome browser."
Genome_build: mm9
Supplementary_files_format_and_content: raw counts

source_name: mouse embryonic stem cells

growth_protocol: ESCs were grown under standard conditions in DMEM supplemented with 10% fetal bovine serum, LIF, glutamine, pen-strep, and beta-mercaptoethanol.

extract_protocol: RNA libraries were prepared for sequencing using standard Illumina protocols

value: Embryonic stem cells

tag: treatment

value: Wild-type Glucose deprivation

tag: passages

value: Passage 21

value: 129 SvJae F1


title: WTNoGlucose Rep3


title: WTNoGlucose Rep1


title: 2359_HIP

value: TPM


title: Sirt6-KO Rep3

value: SIRT6-Knock Out


title: KOWT366


title: Sirt6-KO Rep2


title: 1145_HIP

value: WILD


title: WT Rep2

value: Wild-type


title: KO368


title: Sirt6-KO Rep1


title: WT Rep3


title: WT Rep1


title: clear cell from corpus 2

city: Boston

first: Maria

middle: Agustina

last: Battistone

state: Massachusetts

department: Program in Membrane Biology, Center for Systems Biology and Nephrology Division, Department of Medicine

institute: Massachusetts General Hospital. Harvard Medical Scholl

data_processing:
RNA-seq libraries were prepared using the Clontech SMARTER Kit v4, followed by sequencing on an Illumina HiSeq2500 instrument.
Transcriptome mapping was performed with STAR (PMID:23104886) using the Ensembl annotation of mm9 reference genome. Read counts for individual genes were produced using HTSeq (PMID:25260700).
Read counts for individual genes were produced using HTSeq (PMID:25260700). Differential expression analysis was performed using the EdgeR package (PMID:19910308) after normalizing read counts and including only those genes with CPM > 1 for at least one out of all samples.
Genome_build: mm9
Supplementary_files_format_and_content: Read counts for individual genes

source_name: clear cell from corpus 2

growth_protocol: EGFP+ clear cells were isolated by double cell sorting from the caput, corpus and cauda epididymal regions of B1 V ATPase - EGFP transgenic mice that specifically express EGFP in clear cells.  Eac sample  sample was obtained using 12 epididymides.

extract_protocol:
The RNA was isolated using PicoRNA KIT (Thermo Fisher Scientific)
RNA-seq libraries were prepared using the Clontech SMARTER Kit v4, followed by sequencing on an Illumina HiSeq2500 instrument.

treatment_protocol: no treatment

value: Transgenic mice that express EGFP under the control of the ATP6V1B1 gene promoter

value: 12 weeks

value: epididymis

tag: tissue region

value: corpus

value: clear cell


title: KO101

value: Cortical brain

value: Adult


title: clear cell from cauda 2

source_name: clear cell from cauda 2

value: cauda


title: clear cell from cauda 1

source_name: clear cell from cauda 1


title: H3 Sirt6-KO

data_processing:
Reads were aligned to mm9 using BWA 0.7.4, and PCR duplicates were removed by samtools.
bigWig files were generated by bamCoverage in Deeptools.
Genome_build: mm9

extract_protocol:
For H3K36me3, H3K79me2 and Pol II ChIP-seq experiments: approximately 5x10^7 formaldehyde-crosslinked ESCs were lysed with IP-Star (Diagenode) buffer. Chromatin was sonicated on the Bioruptor (Diagenode) to an average size of 0.2-1 kb. ChIP was performed on chromatin from approximately 5 million cells with 3 μg of antibody (above) using the IP-Star Automated System (Diagenode), and 2.5% of chromatin was used for each whole cell extract (WCE). Following reversal of crosslinks, sample and WCE DNA was purified. ChIP DNA was dissolved in water and placed on the SPRI-TE (Beckman Coulter) for Illumina sample preparation. For H3K9ac, H3K56ac and LEO1 ChIP-seq experiements: approximately 5x10^7 formaldehyde-crosslinked ESCs were lysed and prepared for ChIP-seq according to the protocol described by Black et al., (2013) (PMID: 23871696).
For H3K9ac, H3K56ac and LEO1 ChIP-seq experiments: libraries were constructued according to the protocol described by TruSeq ChIP Sample ptreparation from Illumina Part# 15023092 Rev.B, Cat# IP-202-9001DOC.

value: Mouse strain:129 SvJae F1

tag: chip antibody


title: clear cell from corpus 1

source_name: clear cell from corpus 1


title: H3 WT

value: Embryonic stem cells


title: clear cell from caput 2

source_name: clear cell from caput 2

value: caput


title: Irf1KO_D26_3

city: MONTREAL

first: Philippe

last: Gros

state: QC

address: 3649 Sir William Osler Street, Rm 370, Rm 370

institute: McGill University

data_processing:
Quality of sequence reads was assessed using BVATools and sequence reads were mapped against the UCSC mm9 reference genome using TopHat v2.0.9 in conjunction with Bowtie v1.0.0  (Langmead et al., 2009; Trapnell et al., 2009; Kim et al., 2013)
Gene expression was quantified using featureCounts for UCSC reference genes using default parameters (Liao et al., 2014).
Batch normalization was performed for all samples with the Bioconductor package RUVSeq (Risso et al., 2014)
Differential gene analysis was done using the Bioconductor edgeR package (Robinson and Oshlack, 2010), where genes that had a minimum expression level of 5 counts per million reads (CPM) in at least 3 samples were retained.
Genes were considered significantly differentially expressed if fold change was ≥ 1.5 or ≤ -1.5 and false discovery rate < 0.01
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include batch normalized CPM values for each sample

source_name: colon

extract_protocol:
Distal colons were collected and frozen in liquid nitrogen. RNA was isolated from homogenized tissue with TRIzol reagent (Life Technologies) and then purified using an RNeasy Mini Kit (Qiagen)
Following ribosomal RNA depletion, libraries were prepared using Kapa stranded RNA-seq kit and sequenced on an Illumina HiSeq 2500 to acquire 50 bp paired-end reads.

value: d26 after 1 AOMxDSS treatment


title: clear cell from caput 1

source_name: clear cell from caput 1


title: B6_D26_1

value: wildtype


title: Irf1KO_CTL_2

description: B6CTL_vs_Irf1CTL.txt, Irf1CTL_vs_Irf1D26.txt

value: untreated


title: Irf1KO_CTL_3


title: B6_D26_2


title: Irf1KO_CTL_1


title: B6_CTL_2_3


title: B6_CTL_2_2


title: IPEC-J2 cells, Lv20NC_3

first: Yong

last: Zhao

state: Shandong

address: 700 Changcheng Road

department: College of Life Sciences

institute: Qingdao Agricultural University

description:
The group information is prefixed with  Lv20NC_3 in the column of processed data file
IPECJ2gene_expression.txt

data_processing:
The reads were mapped to reference gene using SOAPaligner (Version 2.20) with a maximum of two nucleotide mismatch allowed at the parameters of “-m 0 -x 1000 -s 40 -l 35 -v 3 -r 2”. The read number of each gene was transformed into RPKM (Reads Per Kilo bases per Million reads), and then differently expressed genes were identified by the DEGseq package using the MARS (MA-plot-based method with Random Sampling model) method. The threshold was set as FDR≤ 0.001 and an absolute value of log2Ratio≥1 to judge the significance of gene expression difference.
Genome_build: Sscrofa11.1
Supplementary_files_format_and_content: FPKMs

organism: Sus scrofa

source_name: Lv20NC_3_IPEC-J2 cells

extract_protocol:
IPEC-J2 cells samples were isolated for RNA. Then RNA samples were sequenced.
Total RNA was used for the library.

value: IPEC-J2 intestinal epithelial cell line


title: IPEC-J2 cells, Lv143_1

description:
The group information is prefixed with  Lv143_1 in the column of processed data file
IPECJ2ALLFPKM.csv

source_name: Lv143_1_IPEC-J2 cells


title: IPEC-J2 cells, Lv143_2

description:
The group information is prefixed with  Lv143_2 in the column of processed data file
IPECJ2ALLFPKM.csv

source_name: Lv143_2_IPEC-J2 cells


title: IPEC-J2 cells, Lv20NC_1

description:
The group information is prefixed with  Lv20NC_1 in the column of processed data file
IPECJ2gene_expression.txt

source_name: Lv20NC_1_IPEC-J2 cells


title: IPEC-J2 cells, OV143_3

description:
The group information is prefixed with  OV143_3  in the column of processed data file
IPECJ2gene_expression.txt

source_name: OV143_3_IPEC-J2 cells


title: IPEC-J2 cells, Lv143_3

description:
The group information is prefixed with  Lv143_3 in the column of processed data file
IPECJ2ALLFPKM.csv

source_name: Lv143_3_IPEC-J2 cells


title: IPEC-J2 cells, Lv133_3

description:
The group information is prefixed with Lv133_3 in the column of processed data file
IPECJ2ALLFPKM.csv

source_name: Lv133_3_IPEC-J2 cells


title: Irf1KO_D26_2


title: IPEC-J2 cells, Lv20NC_2

description:
The group information is prefixed with  Lv20NC_2 in the column of processed data file
IPECJ2gene_expression.txt

source_name: Lv20NC_2_IPEC-J2 cells


title: Akt_Tb12h_1

description:
RNASeq
P5867_AKT_normalized_counts.csv

source_name: pancreatic ductal adenocarcinoma

value: TGFbeta


title: Irf1KO_D26_1


title: B6_CTL_1_2


title: IPEC-J2 cells, Lv3NC_2

description:
The group information is prefixed with  Lv3NC_2 in the column of processed data file
IPECJ2ALLFPKM.csv

source_name: Lv3NC_2_IPEC-J2 cells


title: IPEC-J2 cells, Lv133_1

description:
The group information is prefixed with  Lv133_1 in the column of processed data file
IPECJ2ALLFPKM.csv

source_name: Lv133_1_IPEC-J2 cells


title: IPEC-J2 cells, Lv3NC_3

description:
The group information is prefixed with  Lv3NC_3 in the column of processed data file
IPECJ2ALLFPKM.csv

source_name: Lv3NC_3_IPEC-J2 cells


title: B6_D26_3


title: IPEC-J2 cells, Lv3NC_1

description:
The group information is prefixed with Lv3NC_-1 in the column of processed data file
IPECJ2ALLFPKM.csv

source_name: Lv3NC_1_IPEC-J2 cells


title: B6_CTL_1_1


title: IPEC-J2 cells, OV143_1

description:
The group information is prefixed with  OV143_1 in the column of processed data file
IPECJ2gene_expression.txt

source_name: OV143_1_IPEC-J2 cells


title: IPEC-J2 cells, Lv133_2

description:
The group information is prefixed with Lv133_2 in the column of processed data file
IPECJ2ALLFPKM.csv

source_name: Lv133_2_IPEC-J2 cells


title: IPEC-J2 cells, OV143_2

description:
The group information is prefixed with   OV143_2  in the column of processed data file
IPECJ2gene_expression.txt

source_name: OV143_2_IPEC-J2 cells


title: B6_CTL_2_1

source_name: colon


title: Bam1_RIP

city: Cologne

first: Andreas

last: Wodarz

address: Kerpener Str. 62, Building 37

department: Anatomy

country: Germany

institute: Uniklinik Cologne

description: immunoprecipitated RNA

data_processing:
Illumina RTA v2.7.7 was used for basecalling and demultiplexing  was performed using Illumina bcl2fastq2-v2.20.0.422
Quality control on the resulting reads was performed with FastQC (v0.11.7). Reads were mapped to the Drosophila genome (FlyBase 6.05) with STAR (v2.4.0). The resulting SAM files were converted to BAM files with SAMtools (v0.1.19)
Sorted BAM files were then used to call counts using Htseq (v0.11.0). Further processing of counts was done using Bioconductor (v3.7) in R (v3.5). Count data was fitted using an inverse beta binomial distribution for paired sample testing in R (Pham et al. (2012). Bioinformatics. i596-i602) for calculating transcript enrichment with respect to control.
Genome_build: Flybase 6.05
Supplementary_files_format_and_content: csv file containing p-values and log(fold changes) arising out of inverse beta binomial algorithm

organism: Drosophila melanogaster

source_name: ovary

extract_protocol:
RNA was isolated using TRIzol™ purification after GFP-trap bead immunoprecipitation.
Libraries were prepared using standard Illumina protocols based on the Illumina TruSeq RNA kit.

value: ovary

value: Bam-fTRG-GFP


title: WT1_RIP

description: immunoprecipitated RNA

value: Bam-Gal4 ::UASp-GFP


title: Bam3_RIP

description: immunoprecipitated RNA


title: ATAC_S4_Tb

description:
ATACSeq
Sample_Chr2431-806S4-Tb-AT-A11-CGTACTAG.tdf


title: Akt_SB12h_1

description:
RNASeq
P5867_AKT_normalized_counts.csv


title: GFPNeg_SB_2

description:
RNASeq
P5867F_Id1GFP_normalized_counts.csv


title: WT3_RIP

description: immunoprecipitated RNA


title: Bam2_RIP

description: immunoprecipitated RNA


title: ATAC_S4_SB

description:
ATACSeq
Sample_Chr2430-806S4-SB-AT-A11-TAAGGCGA.tdf


title: GFPPos_SB_2


title: GFPNeg_SB_1


title: Akt_SB12h_2

description:
RNASeq
P5867_AKT_normalized_counts.csv


title: WT2_RIP

description: immunoprecipitated RNA


title: S4.1_Tb_1

description:
RNASeq
P5867F_S4_S4.1_normalized_counts.csv


title: S4.1_SB_2


title: S4.1_SB_1


title: S4_Tb_1


title: S4_SB_2


title: S4_Tb_2


title: S4.1_Tb_2


title: TOId1_PlusDox_Tb_2

description:
RNASeq
P5867B_Id1_normalized_counts.csv


title: S4_SB_1


title: TOId1_NoDox_Tb_1

description:
RNASeq
P5867B_Id1_normalized_counts.csv


title: TOId1_NoDox_Tb_2

description:
RNASeq
P5867B_Id1_normalized_counts.csv


title: TOId1_NoDox_SB_2

description:
RNASeq
P5867B_Id1_normalized_counts.csv


title: TOId1_NoDox_SB_1

description:
RNASeq
P5867B_Id1_normalized_counts.csv


title: Pol2_S4.1_SB

description:
ChIP with Mouse mAb Anti-Anti-RNA polymerase II CTD repeat YSPTSPS (8WG16), ab821
Sample_A1-SB-Pol2-TS10-A12.tdf


title: Pol2_S4.1_Tb

description:
ChIP with Mouse mAb Anti-Anti-RNA polymerase II CTD repeat YSPTSPS (8WG16), ab822
Sample_A1-Tb-Pol2-TS11-A12.tdf


title: Pol2_S4.1_Input

description:
ChIP with Mouse mAb Anti-Anti-RNA polymerase II CTD repeat YSPTSPS (8WG16), ab820
Sample_A1-SB-Input-TS13-A12.tdf


title: TOId1_PlusDox_SB_2

description:
RNASeq
P5867B_Id1_normalized_counts.csv


title: 13876_PBMC EDTA replicate 2

city: Silver Spring

first: Aarti

last: Gautam

state: MD

address: 503 Robert Grant Avenue

department: Medical Readiness Systems Biology

institute: WRAIR

description: 13876_PBMC EDTA 2

hyb_protocol: cRNA was hybridized to SurePrint G3 Human GE v2 8x60K microarrays (Agilent Technologies) following manufacturer's instructions

scan_protocol: Slides were scanned on a Agilent Technologies Scanner G2600D Images were quantified using Agilent Feature Extraction Software

data_processing: Agilent Feature Extraction Software (v 11.5.1.1) was used for background subtraction and R script v3.3 software was used to conduct the preliminary data filtration and statistical analysis.

source_name: Agilent's Universal Human Reference RNA composed of pooled total RNA from ten cell lines representing different human tissues

label_protocol: Total RNA (200ng) was used as starting material, which was amplified using the Low Input Quick Amp Two-Color Kit (Agilent Technologies).The labelled cRNA was purified using an RNeasy Mini Kit (Qiagen, Hilden, Germany), and eluted, labelled cRNA was quantified using a NanoDrop ND-2000 spectrophotometer (Thermo Fisher Scientific Inc, Waltham, MA, USA).

growth_protocol: growth protocol is not applicable

extract_protocol: RNA purchased from vendor.

tag: reference

value: Agilent's Universal Human Reference RNA

source_name: Whole blood

extract_protocol:
[Collection protocol] Blood was collected and preserved in five tubes, namely, PAXgene™ RNA tubes, RNAgard® Blood Tubes, BD Vacutainer™ tubes with ACD-A and K2EDTA and CPT (LeukoLOCK) tubes from five healthy volunteers. In parallel, PBMCs were isolated from EDTA, CPT and ACD-A tubes following the manufacturer’s instructions.
[Extract protocol] See 'extraction methodology' in the Channel 2 Characteristics section above. All extractions were performed following manufacturer's instructions.

tag: biological replicate

value: 2 of 3

tag: blood storage

value: Whole Blood collected in EDTA tube

tag: extraction methodology

value: PBMCs isolated from whole Blood. RNA extracted using TRIzol reagent from PBMCs.

tag: blood component

value: PBMC

tag: individual

value: donor 13876

tag: disease state

value: healthy


title: 13876_RNAgard replicate 2

description: 13876_RNAgard 2

value: Whole Blood collected in RNAgard tube

value: RNA extracted using Biomaxi/Paxgene blood miRNA kit

value: whole blood


title: 13876_RNAgard replicate 1

description: 13876_RNAgard 1

value: 1 of 3


title: 13876_PBMC CPT replicate 2

description: 13876_PBMC CPT 2

value: Whole Blood collected in CPT tube


title: 13876_PBMC ACD-A_magbead replicate 3

description: 13876_PBMC ACD-A_magbead 3

value: 3 of 3

value: Whole Blood collected in ACD-A tube

value: PBMCs isolated using magnetic beads from whole Blood. RNA extracted using TRIzol reagent from PBMCs.


title: 13876_PBMC EDTA replicate 3

description: 13876_PBMC EDTA 3


title: TOId1_PlusDox_Tb_1

description:
RNASeq
P5867B_Id1_normalized_counts.csv

tag: cell line

value: TGFbeta


title: 13876_PBMC ACD-A_magbead replicate 2

description: 13876_PBMC ACD-A_magbead 2


title: Pol2_S4_Tb

description:
ChIP with Mouse mAb Anti-Anti-RNA polymerase II CTD repeat YSPTSPS (8WG16), ab819
Sample_806S4-Tb-Pol2-TS9-A12.tdf

tag: timepoint


title: 13876_PBMC ACD-A_magbead replicate 1

description: 13876_PBMC ACD-A_magbead 1


title: 13876_PBMC CPT replicate 1

description: 13876_PBMC CPT 1


title: 13876_paxgene replicate 3

description: 13876_paxgene 3

value: Whole Blood collected in PAXgene RNA tube

value: RNA extracted using Paxgene Blood miRNA kit


title: 13876_PBMC CPT replicate 3

description: 13876_PBMC CPT 3

value: Agilent's Universal Human Reference RNA


title: KO liver 780

city: Chicago

first: Jennie

last: Lin

address: 303 E Superior

institute: Northwestern University

description: KO 780

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using STAR
Differential expression was determined using Cuffdiff2 and DESeq2 using standard settings per their online manuals.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include read counts for each sample

source_name: Liver

extract_protocol:
Livers were removed, flash frozen on dry ice, and RNA was harvested using the miRNeasy kit by Qiagen. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

tag: tissue

value: Liver

value: 6-8 weeks old

tag: genotype


title: KO liver 588

description: KO 588

tag: age


title: KO liver 591

description: KO 591


title: Pol2_S4_SB

description:
ChIP with Mouse mAb Anti-Anti-RNA polymerase II CTD repeat YSPTSPS (8WG16), ab818
Sample_806S4-SB-Pol2-TS8-A12.tdf

tag: treatment


title: Pol2_S4_Input

description:
ChIP with Mouse mAb Anti-Anti-RNA polymerase II CTD repeat YSPTSPS (8WG16), ab817
Sample_806S4-SB-Input-TS12-A12.tdf


title: 13876_paxgene replicate 2

description: 13876_paxgene 2

value: 2 of 3


title: KO liver 574

description: KO 574


title: KO liver 602

description: KO 602


title: WT liver 778

description: WT  778

value: Wild-type


title: WT liver 776

description: WT  776


title: KO liver 584

description: KO 584


title: WT liver 777

description: WT  777


title: WT liver 601

description: WT  601


title: WT liver 590

description: WT  590


title: WT liver 573

description: WT  573


title: 13876_leukoLOCK replicate 2

description: 13876_leukoLOCK 2

value: Whole Blood collected in EDTA tube passed through LeukoLOCK™ filter system

value: RNA extracted using TRIzol reagent

value: donor 13876

value: healthy


title: 13876_paxgene replicate 1

description: 13876_paxgene 1

value: 1 of 3

value: whole blood


title: TOId1_PlusDox_SB_1

description:
RNASeq
P5867B_Id1_normalized_counts.csv


title: 13876_RNAgard replicate 3

description: 13876_RNAgard 3

value: 3 of 3

value: Whole Blood collected in RNAgard tube

value: RNA extracted using Biomaxi/Paxgene blood miRNA kit


title: B6_CTL_1_3

value: wildtype

value: untreated


title: 13876_EDTA_ACK lysing replicate 2

description: 13876_EDTA_ACK lysing 2

value: Whole Blood collected in EDTA tube

value: RNA extracted using ACK lysing buffer/miRNeasy Mini kit


title: 13876_EDTA_ACK lysing replicate 3

description: 13876_EDTA_ACK lysing 3

value: Agilent's Universal Human Reference RNA


title: 13876_EDTA_ACK lysing replicate 1

description: 13876_EDTA_ACK lysing 1


title: Liver_30 mg Casodex/kg b.w./day_rep_2

city: Wageningen

first: Peter

last: Hendriksen

address: Akkermaalsbos 2

department: RIKILT

country: Netherlands

institute: Wageningen University & Research

description:
Male Wistar rats (PND23 at start of treatment)
individual RNA liver sample

hyb_protocol: 1 µg of each sample was hybridized to 4x44K whole genome rat oligo microarrays (Agilent) according to the manufacturer's instructions (Two-color microarray based gene expression analysis, Agilent). After a 17-h incubation period, slides were washed using various dilutions of SSPE (sodium chloride, sodium phosphate, EDTA) buffer according to the protocol provided by Agilent.

scan_protocol: Arrays were scanned using an Agilent microarray scanner (G2565B). The fluorescent readings from the scanner were converted to quantitative files using Feature Extraction 9.1 software (Agilent Technologies).

data_processing: Quality check of the arrays was performed using software package LimmaGUI in R version 2.3.1. Data were normalized in GeneMaths XT 1.5 (Applied Maths, St. MartensLatem, Belgium) as described before (Pellis et al. 2003, Physiol Genomics 16, 99-106). 2log ratios were calculated for individual liver samples vs. the pool of all liver samples.

organism: Rattus norvegicus

source_name: Liver_30 mg Casodex/kg b.w./day_rep_2

label_protocol: 1 μg of each RNA sample was amplified using a low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies, Amstelveen, the Netherlands). The individual RNA liver samples were labeled with Cy5. A pool of all liver samples was used as common reference and was labeled with Cy3. The labeled cRNAs were purified with (QIAquick spin columns, Qiagen)

extract_protocol: For RNA isolation, liver tissue was homogenized in liquid nitrogen using a cooled mortar and pestle. Total RNA was isolated using TRIzol reagent (Invitrogen, Breda, the Netherlands) followed by purification using RNeasy columns (Qiagen, Venlo, the Netherlands) according to manufacturer’s instructions. RNA concentration and purity were measured using the nanodrop system (IsoGen Life Science, Maarssen, the Netherlands). Where RNA samples did not reach quality standards (ratio OD260/OD230 and OD260/OD280 both >1.8), the samples were purified again using RNeasy columns. RNA integrity was checked on the Experion (Bio-Rad, Veenendaal, the Netherlands) using Experion StdSense chips (Bio-Rad)

value: Wistar

tag: gender

value: Male

value: 30 mg Casodex/kg b.w./day

tag: pool of all liver samples as common reference

value: Pool of all liver samples as common reference

source_name: 30 mg Casodex/kg b.w./day

value: The processus papillaris part of the caudal liver lobe


title: Liver_30 mg Casodex/kg b.w./day_rep_3

source_name: Liver_30 mg Casodex/kg b.w./day_rep_3


title: Liver_30 mg Casodex/kg b.w./day_rep_1

source_name: Liver_30 mg Casodex/kg b.w./day_rep_1


title: 13876_EDTA TRIzol LS replicate 3

description: 13876_EDTA TRIzol LS 3

value: RNA extracted using TRIzol LS reagent

value: donor 13876


title: Liver_30 mg Casodex/kg b.w./day_rep_6

source_name: Liver_30 mg Casodex/kg b.w./day_rep_6


title: 13876_EDTA TRIzol LS replicate 1

description: 13876_EDTA TRIzol LS 1

value: 1 of 3

value: healthy


title: Liver_30 mg Casodex/kg b.w./day_rep_4

source_name: Liver_30 mg Casodex/kg b.w./day_rep_4


title: 13876_EDTA TRIzol LS replicate 2

description: 13876_EDTA TRIzol LS 2

value: 2 of 3

value: whole blood


title: Liver_30 mg Casodex/kg b.w./day_rep_5

source_name: Liver_30 mg Casodex/kg b.w./day_rep_5


title: 13876_leukoLOCK replicate 1

description: 13876_leukoLOCK 1

value: Whole Blood collected in EDTA tube passed through LeukoLOCK™ filter system

value: RNA extracted using TRIzol reagent


title: Liver_50 mg flutamide/kg b.w./day_rep_5

source_name: Liver_50 mg flutamide/kg b.w./day_rep_5

value: 50 mg flutamide/kg b.w./day

source_name: 50 mg flutamide/kg b.w./day


title: Liver_50 mg flutamide/kg b.w./day_rep_3

source_name: Liver_50 mg flutamide/kg b.w./day_rep_3


title: Liver_50 mg flutamide/kg b.w./day_rep_2

source_name: Liver_50 mg flutamide/kg b.w./day_rep_2


title: 13876_ACD-A TRIzol LS replicate 2

description: 13876_ACD-A TRIzol LS 2

value: Whole Blood collected in ACD-A tube


title: 13876_ACD-A TRIzol LS replicate 3

description: 13876_ACD-A TRIzol LS 3

value: 3 of 3


title: Liver_50 mg flutamide/kg b.w./day_rep_4

source_name: Liver_50 mg flutamide/kg b.w./day_rep_4


title: 13876_leukoLOCK replicate 3

description: 13876_leukoLOCK 3

value: Agilent's Universal Human Reference RNA


title: 13876_ACD-A TRIzol LS replicate 1

description: 13876_ACD-A TRIzol LS 1


title: GFPPos_SB_1

source_name: pancreatic ductal adenocarcinoma


title: Liver_50 ng TCDD/kg b.w./day_rep_5

source_name: Liver_50 ng TCDD/kg b.w./day_rep_5

value: Wistar

value: 50 ng TCDD/kg b.w./day

source_name: 50 ng TCDD/kg b.w./day


title: Akt_Tb12h_2

description:
RNASeq
P5867_AKT_normalized_counts.csv

value: TGFbeta


title: Liver_50 ng TCDD/kg b.w./day_rep_6

source_name: Liver_50 ng TCDD/kg b.w./day_rep_6

value: Male

value: Pool of all liver samples as common reference


title: Liver_50 mg flutamide/kg b.w./day_rep_6

source_name: Liver_50 mg flutamide/kg b.w./day_rep_6

value: The processus papillaris part of the caudal liver lobe


title: 13876_ACD-A _ACK lysing replicate 3

description: 13876_ACD-A _ACK lysing 3

source_name: Agilent's Universal Human Reference RNA composed of pooled total RNA from ten cell lines representing different human tissues

source_name: Whole blood

value: RNA extracted using ACK lysing buffer/miRNeasy Mini kit

value: donor 13876


title: 13876_ACD-A _ACK lysing replicate 2

description: 13876_ACD-A _ACK lysing 2

value: healthy


title: Liver_50 mg flutamide/kg b.w./day_rep_1

source_name: Liver_50 mg flutamide/kg b.w./day_rep_1


title: Liver_50 ng TCDD/kg b.w./day_rep_4

source_name: Liver_50 ng TCDD/kg b.w./day_rep_4


title: Liver_50 ng TCDD/kg b.w./day_rep_1

source_name: Liver_50 ng TCDD/kg b.w./day_rep_1


title: Liver_50 ng TCDD/kg b.w./day_rep_3

source_name: Liver_50 ng TCDD/kg b.w./day_rep_3


title: Liver_50 ng TCDD/kg b.w./day_rep_2

source_name: Liver_50 ng TCDD/kg b.w./day_rep_2


title: Liver_500mg 2-ITX/kg b.w./day_rep_6

source_name: Liver_500mg 2-ITX/kg b.w./day_rep_6

value: 500mg 2-ITX/kg b.w./day

source_name: 500mg 2-ITX/kg b.w./day


title: Liver_500mg 2-ITX/kg b.w./day_rep_5

source_name: Liver_500mg 2-ITX/kg b.w./day_rep_5


title: 13876_ACD-A _ACK lysing replicate 1

description: 13876_ACD-A _ACK lysing 1

value: 1 of 3

value: whole blood


title: 13875_RNAgard replicate 2

description: 13875_RNAgard 2

value: 2 of 3

value: Whole Blood collected in RNAgard tube

value: RNA extracted using Biomaxi/Paxgene blood miRNA kit

value: donor 13875


title: 13875_RNAgard replicate 3

description: 13875_RNAgard 3

value: Agilent's Universal Human Reference RNA

value: 3 of 3


title: 13876_PBMC EDTA replicate 1

description: 13876_PBMC EDTA 1

value: Whole Blood collected in EDTA tube

value: PBMCs isolated from whole Blood. RNA extracted using TRIzol reagent from PBMCs.

value: PBMC


title: Liver_500mg 2-ITX/kg b.w./day_rep_4

source_name: Liver_500mg 2-ITX/kg b.w./day_rep_4

value: Wistar

value: Male

value: Pool of all liver samples as common reference


title: 13875_RNAgard replicate 1

description: 13875_RNAgard 1


title: Liver_150mg 2-ITX/kg b.w./day_rep_6

source_name: Liver_150mg 2-ITX/kg b.w./day_rep_6

value: 150mg 2-ITX/kg b.w./day

source_name: 150mg 2-ITX/kg b.w./day

value: The processus papillaris part of the caudal liver lobe


title: Liver_500mg 2-ITX/kg b.w./day_rep_1

source_name: Liver_500mg 2-ITX/kg b.w./day_rep_1

value: 500mg 2-ITX/kg b.w./day


title: Liver_150mg 2-ITX/kg b.w./day_rep_5

source_name: Liver_150mg 2-ITX/kg b.w./day_rep_5


title: 13875_PBMC EDTA replicate 3

description: 13875_PBMC EDTA 3

value: healthy


title: Liver_150mg 2-ITX/kg b.w./day_rep_3

source_name: Liver_150mg 2-ITX/kg b.w./day_rep_3


title: Liver_500mg 2-ITX/kg b.w./day_rep_3

source_name: Liver_500mg 2-ITX/kg b.w./day_rep_3


title: Liver_50mg 2-ITX/kg b.w./day_rep_3

source_name: Liver_50mg 2-ITX/kg b.w./day_rep_3

value: 50mg 2-ITX/kg b.w./day

source_name: 50mg 2-ITX/kg b.w./day


title: 13875_PBMC EDTA replicate 1

description: 13875_PBMC EDTA 1

source_name: Agilent's Universal Human Reference RNA composed of pooled total RNA from ten cell lines representing different human tissues

source_name: Whole blood

value: 1 of 3


title: Liver_150mg 2-ITX/kg b.w./day_rep_4

source_name: Liver_150mg 2-ITX/kg b.w./day_rep_4


title: Liver_150mg 2-ITX/kg b.w./day_rep_1

source_name: Liver_150mg 2-ITX/kg b.w./day_rep_1


title: 13875_PBMC EDTA replicate 2

description: 13875_PBMC EDTA 2

value: 2 of 3


title: Liver_150mg 2-ITX/kg b.w./day_rep_2

source_name: Liver_150mg 2-ITX/kg b.w./day_rep_2


title: Liver_50mg 2-ITX/kg b.w./day_rep_5

source_name: Liver_50mg 2-ITX/kg b.w./day_rep_5


title: 13875_PBMC CPT replicate 3

description: 13875_PBMC CPT 3

value: Whole Blood collected in CPT tube


title: 13875_PBMC ACD-A_magbead replicate 3

description: 13875_PBMC ACD-A_magbead 3

value: Whole Blood collected in ACD-A tube

value: PBMCs isolated using magnetic beads from whole Blood. RNA extracted using TRIzol reagent from PBMCs.

value: donor 13875


title: Liver_50mg 2-ITX/kg b.w./day_rep_4

source_name: Liver_50mg 2-ITX/kg b.w./day_rep_4


title: Liver_vehicle_Control_rep_8

value: vehicle control (corn oil alone (0.5 ml per 100 g b.w.)


title: Liver_vehicle_Control_rep_7

source_name: vehicle control (corn oil alone (0.5 ml per 100 g b.w.)


title: Liver_50mg 2-ITX/kg b.w./day_rep_1

source_name: Liver_50mg 2-ITX/kg b.w./day_rep_1


title: Liver_50mg 2-ITX/kg b.w./day_rep_2

source_name: Liver_50mg 2-ITX/kg b.w./day_rep_2


title: Liver_vehicle_Control_rep_5


title: 13875_PBMC CPT replicate 2

description: 13875_PBMC CPT 2

value: Agilent's Universal Human Reference RNA

value: PBMCs isolated from whole Blood. RNA extracted using TRIzol reagent from PBMCs.


title: Liver_vehicle_Control_rep_6

value: Wistar


title: 13875_PBMC CPT replicate 1

description: 13875_PBMC CPT 1

value: PBMC


title: Liver_vehicle_Control_rep_3

value: Male

value: Pool of all liver samples as common reference


title: Liver_vehicle_Control_rep_4

value: The processus papillaris part of the caudal liver lobe


title: 13875_PBMC ACD-A_magbead replicate 2

description: 13875_PBMC ACD-A_magbead 2


title: Liver_500mg 2-ITX/kg b.w./day_rep_2

source_name: Liver_500mg 2-ITX/kg b.w./day_rep_2

value: 500mg 2-ITX/kg b.w./day

source_name: 500mg 2-ITX/kg b.w./day


title: jmj17-1_7days _long day_R1

city: Taipei

first: Wan-Sheng

last: Lo

state: Taiwan

address: 128 Academia Road, Section 2, Nankang

department: IPMB

country: Taiwan

institute: Academia Sinica

data_processing:
The prepared library was pooled for single-end sequencing using Illumina HiSeq 2500 at YOURGENE BIOSCIENCE Co. (New Taipei City, Taiwan) with 100bp single-ended sequence read.
Reads from RNA-seq were mapped to TAIR10 genome using BLAT (http://genome.ucsc.edu/cgi-bin/hgBlat).
RPKM computation and comparison (Z score) were made using RackJ (http://rackj.sourceforge.net/).
Supplementary_files_format_and_content: tab-delimited excel files include RPKM values for each Sample

organism: Arabidopsis thaliana

source_name: Whole seedling

growth_protocol: Seeds of each genotypes were grown in 1/2MS without sucrose media containing plates for 7 days in long day condition (16h light/8h dark)

extract_protocol:
Total RNA from 7day-old light grown (16h light/8h dark) and 4d dark grown Col-0 and jmj17-1 seedling was isolated using RNeasy Plant Mini Kit (QIAGEN), Cat. No. 74904
Libraries for RNA-seq were prepared using Illumina TruSeq RNA library Prep Kit (RS-122-2001, Illumina) according to the manufacturer’s protocol.

treatment_protocol: Long day(16h light/8h dark)

tag: ecotype

value: Col-0 background

value: jmj17-1 (mutant)

value: Whole seedling


title: 13875_PBMC ACD-A_magbead replicate 1

description: 13875_PBMC ACD-A_magbead 1

tag: reference

value: 1 of 3

value: healthy


title: 13875_leukoLOCK replicate 3

description: 13875_leukoLOCK 3

tag: biological replicate

value: 3 of 3

value: Whole Blood collected in EDTA tube passed through LeukoLOCK™ filter system

value: RNA extracted using TRIzol reagent

value: whole blood


title: 13875_EDTA_ACK lysing replicate 1

description: 13875_EDTA_ACK lysing 1

value: Agilent's Universal Human Reference RNA

tag: blood storage

value: Whole Blood collected in EDTA tube

value: RNA extracted using ACK lysing buffer/miRNeasy Mini kit

value: donor 13875


title: 13875_paxgene replicate 2

description: 13875_paxgene 2

value: 2 of 3

value: Whole Blood collected in PAXgene RNA tube

tag: extraction methodology

value: RNA extracted using Paxgene Blood miRNA kit


title: 13875_paxgene replicate 1

description: 13875_paxgene 1

tag: blood component


title: 13875_EDTA TRIzol LS replicate 3

description: 13875_EDTA TRIzol LS 3

value: RNA extracted using TRIzol LS reagent

tag: individual


title: Liver_vehicle_Control_rep_2

value: Wistar

value: Male

value: vehicle control (corn oil alone (0.5 ml per 100 g b.w.)

value: Pool of all liver samples as common reference

value: The processus papillaris part of the caudal liver lobe


title: 13875_EDTA_ACK lysing replicate 2

description: 13875_EDTA_ACK lysing 2

tag: disease state

value: healthy


title: 13875_leukoLOCK replicate 2

description: 13875_leukoLOCK 2

value: Whole Blood collected in EDTA tube passed through LeukoLOCK™ filter system


title: 13875_ACD-A TRIzol LS replicate 1

description: 13875_ACD-A TRIzol LS 1

value: 1 of 3

value: Whole Blood collected in ACD-A tube


title: 13875_ACD-A TRIzol LS replicate 3

description: 13875_ACD-A TRIzol LS 3

value: Agilent's Universal Human Reference RNA

value: 3 of 3

value: whole blood


title: 13875_EDTA_ACK lysing replicate 3

description: 13875_EDTA_ACK lysing 3

value: Whole Blood collected in EDTA tube

value: RNA extracted using ACK lysing buffer/miRNeasy Mini kit

value: donor 13875


title: 13875_leukoLOCK replicate 1

description: 13875_leukoLOCK 1

value: RNA extracted using TRIzol reagent


title: 13875_EDTA TRIzol LS replicate 2

description: 13875_EDTA TRIzol LS 2

value: 2 of 3

value: RNA extracted using TRIzol LS reagent


title: 13875_ACD-A TRIzol LS replicate 2

description: 13875_ACD-A TRIzol LS 2


title: 13874_RNAgard replicate 1

description: 13874_RNAgard 1

value: Whole Blood collected in RNAgard tube

value: RNA extracted using Biomaxi/Paxgene blood miRNA kit

value: donor 13874


title: 13875_EDTA TRIzol LS replicate 1

description: 13875_EDTA TRIzol LS 1


title: 13875_ACD-A _ACK lysing replicate 1

description: 13875_ACD-A _ACK lysing 1


title: 13874_RNAgard replicate 3

description: 13874_RNAgard 3


title: 13875_paxgene replicate 3

description: 13875_paxgene 3

value: Whole Blood collected in PAXgene RNA tube

value: RNA extracted using Paxgene Blood miRNA kit


title: 13874_RNAgard replicate 2

description: 13874_RNAgard 2

value: healthy


title: 13875_ACD-A _ACK lysing replicate 2

description: 13875_ACD-A _ACK lysing 2


title: Liver_vehicle_Control_rep_1

value: Wistar

value: Male

value: vehicle control (corn oil alone (0.5 ml per 100 g b.w.)

value: Pool of all liver samples as common reference

value: The processus papillaris part of the caudal liver lobe


title: 13874_PBMC EDTA replicate 3

description: 13874_PBMC EDTA 3

value: Agilent's Universal Human Reference RNA

value: 3 of 3

value: Whole Blood collected in EDTA tube

value: PBMCs isolated from whole Blood. RNA extracted using TRIzol reagent from PBMCs.

value: PBMC


title: 13875_ACD-A _ACK lysing replicate 3

description: 13875_ACD-A _ACK lysing 3

value: Whole Blood collected in ACD-A tube

value: RNA extracted using ACK lysing buffer/miRNeasy Mini kit

value: whole blood

value: donor 13875


title: 13874_PBMC CPT replicate 2

description: 13874_PBMC CPT 2

value: 2 of 3

value: Whole Blood collected in CPT tube

value: donor 13874


title: 13874_PBMC CPT replicate 3

description: 13874_PBMC CPT 3

value: healthy


title: 13874_PBMC EDTA replicate 2

description: 13874_PBMC EDTA 2


title: 13874_PBMC CPT replicate 1

description: 13874_PBMC CPT 1

value: 1 of 3


title: 13874_PBMC EDTA replicate 1

description: 13874_PBMC EDTA 1


title: 13874_paxgene replicate 3

description: 13874_paxgene 3

value: Whole Blood collected in PAXgene RNA tube

value: RNA extracted using Paxgene Blood miRNA kit


title: K562_dCas9-KRAB_NC_sgNC-1_3

city: Dallas

first: Gary

last: Hon

state: TX

address: 5323 Harry Hines Blvd, J7.125, Hon Lab

institute: UT Southwestern Medical Center

data_processing:
Basecalls performed bcl2fastq v2.17.1.14.
RNA-seq reads were aligned using the STAR aligner v2.4.2a with default parameters to the hg38 genome assembly augmented with a sequence representing the sgRNA-containing plasmid.
Mapped reads were filtered for mapping quality >= 10, and PCR duplicates were removed with Picard v1.117.
Read counts were tabulated with featureCounts v1.5.0. For gene annotation, we use Gencode V29.
Genome_build: hg38
Supplementary_files_format_and_content: read counts for all genes

source_name: K562 cells

growth_protocol: K562 were cultured in IMDM plus 10% FBS and pen/strep at 37C and 5% CO2.

extract_protocol:
total RNA was extracted from cells using Trizol Reagent (Thermo), and were subjected to enrichment of polyA+ RNA using the NEBNext Poly(A) kit (NEB).
Strand-specific polyA+ RNA-Seq was performed using the LM-Seq method, as described previously. Briefly, PolyA+ RNA was fragmented at 85°C in SmartScribe first-strand buffer (CloneTech) supplemented with a 3’ sequencing adapter containing a random hexamer sequence.  The fragmented RNA were subjected to first strand cDNA synthesis, followed by RNase A/H treatment.  The remaining single-stranded DNA were ligated to a 5’ sequencing adapter.  The libraries were then amplified by PCR using Illumina TruSeq-compatible primers and purified using SPRI purification beads.

treatment_protocol: HEK293T cells were cultured in DMEM with 10% FBS and pen/strep. For lentiviral packaging, 3X106 293T cells were seeded in a 6 cm dish one day before transfection. The indicated viral plasmid(s) were co-transfected with lentivirus packaging plasmids pMD2.G and psPAX2 (Addgene ID 12259 and 12260) with 4:2:3 ratio by using Lipofectamine 3000 (Thermo Fisher) according to the manufacturer's protocol. Twelve hours after transfection, media was changed to fresh DMEM with 10% FBS plus Pen/Strep. Seventy-two hours after transfection, virus-containing media was collected, passed through a 45 um filter, and aliquoted into 1.5ml tubes. Viruses were stored in -80°C before infection or titration. For virus infection, 2X105 K562 cells were seeded in 24 well plate per well with 500 µl complete medium plus 1µg/ml polybrene. Virus aliquot(s) were thawed to room temperature and added to the plates. The plate was then centrifuged at 1000xg at 36 °C and returned to the incubator. The following day, the media was changed to fresh complete medium with antibiotics to screen for infected cells. Cells were kept at ~30% confluence during antibiotic selection.

tag: cell line

tag: sgrna id

tag: target region

value: NC


title: K562_dCas9-KRAB_ARL15-enh_sgRNA-5_2


title: K562_dCas9-KRAB_ARL15-enh_sgRNA-5_1


title: K562_dCas9-KRAB_NC_sgNC-3_2


title: K562_dCas9-KRAB_NC_sgNC-1_1


title: 13874_PBMC ACD-A_magbead replicate 1

description: 13874_PBMC ACD-A_magbead 1

value: Agilent's Universal Human Reference RNA

value: PBMCs isolated using magnetic beads from whole Blood. RNA extracted using TRIzol reagent from PBMCs.


title: K562_dCas9-KRAB_NC_sgNC-1_2


title: 13874_paxgene replicate 2

description: 13874_paxgene 2


title: 13874_EDTA_ACK lysing replicate 3

description: 13874_EDTA_ACK lysing 3

value: 3 of 3

value: Whole Blood collected in EDTA tube


title: 13874_EDTA TRIzol LS replicate 2

description: 13874_EDTA TRIzol LS 2

value: RNA extracted using TRIzol LS reagent


title: 13874_EDTA_ACK lysing replicate 1

description: 13874_EDTA_ACK lysing 1


title: 13874_PBMC ACD-A_magbead replicate 2

description: 13874_PBMC ACD-A_magbead 2

value: Whole Blood collected in ACD-A tube

value: PBMC


title: 13874_EDTA TRIzol LS replicate 1

description: 13874_EDTA TRIzol LS 1

value: whole blood


title: 13874_EDTA_ACK lysing replicate 2

description: 13874_EDTA_ACK lysing 2

value: RNA extracted using ACK lysing buffer/miRNeasy Mini kit


title: 13874_EDTA TRIzol LS replicate 3

description: 13874_EDTA TRIzol LS 3


title: Liver_50mg 2-ITX/kg b.w./day_rep_6

source_name: Liver_50mg 2-ITX/kg b.w./day_rep_6

tag: strain

value: Wistar

value: Male

value: 50mg 2-ITX/kg b.w./day

value: Pool of all liver samples as common reference

tag: tissue

value: The processus papillaris part of the caudal liver lobe


title: 13874_leukoLOCK replicate 2

description: 13874_leukoLOCK 2

value: 2 of 3

value: Whole Blood collected in EDTA tube passed through LeukoLOCK™ filter system

value: RNA extracted using TRIzol reagent

value: donor 13874

value: healthy


title: 13874_leukoLOCK replicate 3

description: 13874_leukoLOCK 3

value: Agilent's Universal Human Reference RNA

value: 3 of 3


title: 13874_paxgene replicate 1

description: 13874_paxgene 1

value: 1 of 3

value: Whole Blood collected in PAXgene RNA tube

value: RNA extracted using Paxgene Blood miRNA kit


title: K562_dCas9-KRAB_ARL15-enh_sgRNA-10_2


title: 13874_leukoLOCK replicate 1

description: 13874_leukoLOCK 1

value: whole blood


title: 13874_ACD-A TRIzol LS replicate 3

description: 13874_ACD-A TRIzol LS 3

value: Whole Blood collected in ACD-A tube

value: RNA extracted using TRIzol LS reagent


title: K562_dCas9-KRAB_ARL15-enh_sgRNA-9_2


title: 13874_ACD-A TRIzol LS replicate 2

description: 13874_ACD-A TRIzol LS 2


title: 13874_PBMC ACD-A_magbead replicate 3

description: 13874_PBMC ACD-A_magbead 3

value: PBMCs isolated using magnetic beads from whole Blood. RNA extracted using TRIzol reagent from PBMCs.

value: PBMC


title: K562_dCas9-KRAB_ARL15-enh_sgRNA-8_2


title: 13874_ACD-A TRIzol LS replicate 1

description: 13874_ACD-A TRIzol LS 1


title: K562_dCas9-KRAB_ARL15-enh_sgRNA-7_2


title: K562_dCas9-KRAB_ARL15-enh_sgRNA-6_2


title: K562_dCas9-KRAB_ARL15-enh_sgRNA-4_2


title: K562_dCas9-KRAB_ARL15-enh_sgRNA-3_2


title: K562_dCas9-KRAB_ARL15-enh_sgRNA-2_2


title: K562_dCas9-KRAB_ARL15-enh_sgRNA-1_2


title: K562_dCas9-KRAB_ARL15-enh_sgRNA-4_1


title: K562_dCas9-KRAB_ARL15-enh_sgRNA-8_1


title: K562_dCas9-KRAB_ARL15-enh_sgRNA-1_1


title: K562_dCas9-KRAB_ARL15-enh_sgRNA-9_1


title: K562_dCas9-KRAB_ARL15-enh_sgRNA-6_1


title: K562_dCas9-KRAB_ARL15-enh_sgRNA-10_1


title: K562_dCas9-KRAB_ARL15-enh_sgRNA-7_1


title: K562_dCas9-KRAB_ARL15-enh_sgRNA-3_1


title: K562_dCas9-KRAB_NC_sgNC-3_1

value: NC


title: K562_dCas9-KRAB_ARL15-enh_sgRNA-2_1


title: 13873_RNAgard replicate 3

description: 13873_RNAgard 3

value: Whole Blood collected in RNAgard tube

value: RNA extracted using Biomaxi/Paxgene blood miRNA kit

value: donor 13873


title: 13874_ACD-A _ACK lysing replicate 1

description: 13874_ACD-A _ACK lysing 1

value: RNA extracted using ACK lysing buffer/miRNeasy Mini kit


title: 13873_RNAgard replicate 1

description: 13873_RNAgard 1


title: 13873_PBMC EDTA replicate 3

description: 13873_PBMC EDTA 3

value: Whole Blood collected in EDTA tube

value: PBMCs isolated from whole Blood. RNA extracted using TRIzol reagent from PBMCs.


title: 13873_PBMC CPT replicate 3

description: 13873_PBMC CPT 3

value: Agilent's Universal Human Reference RNA

value: Whole Blood collected in CPT tube

value: healthy


title: 13873_RNAgard replicate 2

description: 13873_RNAgard 2

value: 2 of 3


title: 13874_ACD-A _ACK lysing replicate 3

description: 13874_ACD-A _ACK lysing 3

value: 3 of 3

value: donor 13874


title: 13874_ACD-A _ACK lysing replicate 2

description: 13874_ACD-A _ACK lysing 2

value: Whole Blood collected in ACD-A tube

value: whole blood


title: 13873_PBMC EDTA replicate 2

description: 13873_PBMC EDTA 2


title: 13873_PBMC EDTA replicate 1

description: 13873_PBMC EDTA 1

value: 1 of 3


title: K562-dCas9-KRAB_NC_sgNC-1_2


title: K562-dCas9-KRAB_NC_sgNC-3_1


title: K562-dCas9-KRAB_MYB-enh-3_sgRNA-8_2


title: K562-dCas9-KRAB_MYB-enh-3_sgRNA-10_1


title: K562-dCas9-KRAB_MYB-enh-3_sgRNA-8_1


title: K562-dCas9-KRAB_MYB-enh-3_sgRNA-6_1


title: K562-dCas9-KRAB_NC_sgNC-3_2


title: K562-dCas9-KRAB_MYB-enh-3_sgRNA-10_2


title: K562-dCas9-KRAB_MYB-enh-3_sgRNA-7_1


title: 13873_PBMC CPT replicate 2

description: 13873_PBMC CPT 2

value: PBMC


title: K562-dCas9-KRAB_NC_sgNC-1_1

value: NC


title: 13873_PBMC CPT replicate 1

description: 13873_PBMC CPT 1


title: K562-dCas9-KRAB_MYB-enh-3_sgRNA-6_2


title: K562-dCas9-KRAB_MYB-enh-3_sgRNA-9_1


title: K562-dCas9-KRAB_MYB-enh-3_sgRNA-5_1


title: K562-dCas9-KRAB_MYB-enh-3_sgRNA-4_2


title: K562-dCas9-KRAB_MYB-enh-3_sgRNA-3_2


title: K562-dCas9-KRAB_MYB-enh-3_sgRNA-9_2


title: 13873_PBMC ACD-A_magbead replicate 1

description: 13873_PBMC ACD-A_magbead 1

value: PBMCs isolated using magnetic beads from whole Blood. RNA extracted using TRIzol reagent from PBMCs.


title: 13873_paxgene replicate 3

description: 13873_paxgene 3

value: Whole Blood collected in PAXgene RNA tube

value: RNA extracted using Paxgene Blood miRNA kit


title: 13873_PBMC ACD-A_magbead replicate 3

description: 13873_PBMC ACD-A_magbead 3

value: donor 13873


title: 13873_leukoLOCK replicate 3

description: 13873_leukoLOCK 3

value: Whole Blood collected in EDTA tube passed through LeukoLOCK™ filter system

value: RNA extracted using TRIzol reagent


title: 13873_PBMC ACD-A_magbead replicate 2

description: 13873_PBMC ACD-A_magbead 2

value: Agilent's Universal Human Reference RNA


title: K562-dCas9-KRAB_MYB-enh-3_sgRNA-7_2


title: 13873_paxgene replicate 2

description: 13873_paxgene 2


title: 13873_paxgene replicate 1

description: 13873_paxgene 1


title: K562-dCas9-KRAB_MYB-enh-3_sgRNA-1_1


title: sip300_3

city: Jerusalem

first: Maayan

last: Salton

address: Ein-Kerem Canpus

country: Israel

institute: Hebrew University

description:
DESeq2_final.xls
A3SS_final_p.xlsx
A5SS_final_p.xlsx
MXE_final_p.xlsx
RI_final_p.xlsx
SE_final_p.xlsx

data_processing:
Illumina bcl2fastq, v2.17.1.14, was used for transforming basecalls to fastq files, using default parameters, for both sequencing runs.
Expression processing: Raw reads were quality trimmed at both ends with PHRED score threshold of 32, adapter sequences were trimmed with cutadapt, v1.12, leaving only reads of length 15 and above after trimming, and filtered for low-quality reads with the FASTX package, v0.0.14, with parameters -p 90 and -q 20. The remaining reads were then paired again to produce proper paired R1 and R2 files and a single file for single-reads. Alignment was done with TopHat, v2.0.14, with parameters -N 3 --read-gap-length 5 --read-edit-dist 8 --segment-length 20 --read-realign-edit-dist 3 --no-coverage-search --library-type fr-firststrand, given the Ensembl release 84 GTF file (-G), the GRCh38 genome index and the paired- and single-reads as input. Counts were calculated for each sequencing run with htseq-count, version 0.6.0, using parameters -s reverse and a GTF file masked for genes of type IG, TR, Mt, rRNA, tRNA, miRNA, misc_RNA, scRNA, snRNA, snoRNA, sRNA, scaRNA, piRNA, vaultRNA, ribozyme, artifact and LRG_gene. The counts from both runs were summed to give the final counts per gene per sample. Differential expression was done with DESeq2, v1.12.4, using default parameters, except for a more stringent significance threshold of padj<0.05. The design included the siRNA factor, as well as a batch factor for the day of preparation.
Alternative splicing processing: Reads of the longer sequencing run were processed as for expression analysis, but only reads of length at least 70 were kept, then trimmed to length 70 with the FASTX package. Only paired-reads were used for alignment, with the same parameters as for the expression analysis. Uniquely mapped reads, where both reads of the pair mapped to the same chromosome were taken for further analysis. Alternative splicing was calculated with rMATS, v3.2.5, using parameters -t paired -len 70 -c 0.05 -analysis P -libType fr-firststrand -novelSS 1, and giving the Ensembl release 84 GTF file (-gtf). In addition, reads from the short sequencing run were processed similarly, leaving reads of length 38, then aligned with similar parameters except for --segment-length 18. The BAM files of that alignment were merged with an alignment result for the reads of the long sequencing run, after trimming those also to a length of 38 nucleotides, and the merged BAM files were used as input for rMATS. New alternative splicing events from this analysis were added to the results obtained for the reads of the long sequencing run alone.
Genome_build: GRCh38
Supplementary_files_format_and_content: An Excel file for the expression analysis, with general gene details, raw counts, normalized counts, the DESeq2 results, a column indicating significance (padj<0.05) and a column indicating significance and an absolute log2-fold-change greater than 0.6. An Excel file for the alternative splicing analysis, a file for each splicing event type, containing general gene details, the rMATS results, and columns for indicating significance in the junction-and-exon analysis (JnR) and junction-only analysis (JO), where significance is taken as padj<0.05 and a minimal average counts (>10 for JnR and >3 for JO). Multiple data is separated by semicolon. Missing data is represented by a question mark.

source_name: MCF7 cell line

growth_protocol: MCF7 (ATCC Number: HTB-22) cells were grown in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% fetal bovine serum; cell lines were maintained at 37°C and 5% CO2 atmosphere.

extract_protocol:
RNA was isolated from cells using the GENEzol TriRNA Pure Kit (GeneAid).
RNA ScreenTape kit (catalog #5067-5576; Agilent Technologies, Santa Clara, CA), D1000 ScreenTape kit (catalog #5067-5582; Agilent Technologies), Qubit® RNA HS Assay kit (catalog # Q32852; Invitrogen, Carlsbad, CA) and Qubit® DNA HS Assay kit (catalog #32854; Invitrogen) were used for each specific step for quality control and quantity determination of RNA and library preparation. For mRNA library preparation: TruSeq RNA Library Prep Kit v2 was used (Illumina). In brief, 1 g was used for the library construction; library was eluted in 20 l of elution buffer. Libraries were adjusted to 10 mM, then 10 l (50%) from each sample was collected and pooled in one tube. Multiplex sample pool (1.5 pM including PhiX 1.5%) was loaded in NextSeq 500/550 High Output v2 kit (75 cycles cartridge and 150 cycles cartridge; Illumina, San Diego, CA). Run conditions were in paired end (43X43bp and 80X80 bp, respectively) and loaded on NextSeq 500 System machine (Illumina).

treatment_protocol: Cells were transfected with TransIT-X2 Transfection Reagent (Roche) following the manufacturer’s instructions. After 72 h in culture, RNA was extracted from siRNA transfected cells.

tag: condition

value: Experiment

tag: transfection


title: siNT_2

value: Control

value: siNT


title: K562-dCas9-KRAB_MYB-enh-3_sgRNA-3_1


title: siNT_1


title: 13873_leukoLOCK replicate 2

description: 13873_leukoLOCK 2

value: 2 of 3

value: healthy


title: K562-dCas9-KRAB_MYB-enh-3_sgRNA-2_2


title: K562-dCas9-KRAB_MYB-enh-3_sgRNA-1_2


title: K562-dCas9-KRAB_MYB-enh-3_sgRNA-5_2


title: sip300_2


title: sip300_1


title: K562-dCas9-KRAB_MYB-enh-3_sgRNA-4_1


title: 13873_EDTA_ACK lysing replicate 3

description: 13873_EDTA_ACK lysing 3

value: 3 of 3

value: Whole Blood collected in EDTA tube

value: RNA extracted using ACK lysing buffer/miRNeasy Mini kit


title: siNT_3


title: Cell82_LNinnervating

city: Cambridge

first: Alex

last: Shalek

state: MA

address: 77 Massachusetts Ave

department: Chemistry

institute: Massachusetts Institute of Technology

data_processing:
Pooled libraries were demultiplexed using bcl2fastq (v2.17.1.14) with default settings, and aligned using STAR  to the mouse UCSC genome reference (version mm10), and a gene expression matrix was generated using RSEM (v1.2.3) in paired-end mode. Read counts were normalized to transcripts-per-million (TPM). Single-cell libraries with fewer than 3,000 unique genes and fewer than 17% of reads mapping to transcriptomic regions were excluded from subsequent analysis, resulting in a final dataset of 52 LN-innervating neurons collected from 8 mice, and 31 skin-innervating neurons collected from 4 mice.
Genome_build: mm10
Supplementary_files_format_and_content: Processed data is a tab delimited text file containing a TPM-corrected gene expression matrix with the number of TPM for each gene (rows) and cell (columns). The 2-8th row represent metadata defined in column 1, including mouse number, cell collection date, innervation target, sequencing batch, and reads, gene count, and % transcriptomic alignment per library

source_name: Dorsal root ganglion single neuron

growth_protocol: All of the animals were handled according to approved institutional animal care and use committee (IACUC) protocols of Harvard Medical School.

extract_protocol:
Single-cell libraries were generated according to the Smart-Seq2 protocol (Picelli et al. Nature Methods 2014 and Trombetta et al. Current Protocols in Molecular Biology 2014). Each fluorescent cell was pipetted up and down the micropipette three times to remove unwanted contamination before being ejected into 10 μl of cold RLT Buffer (Qiagen) supplemented with 1% β-mercaptoethanol in a 96-well plate, and snap-frozen on dry ice and stored at -80ºC. RNA from single-cell lysates was purified using AMPure RNA Clean Spri beads (Beckman Coulter) at a 2.2x volume ratio.
Following AMPure Bead cleanup, RNA was eluted in water and mixed with oligo-dT primer (SmartSeq2 3’ Oligo-dT Primer), dNTPs, and RNase inhibitor at 72ºC for 3 minutes on a thermal cycler to anneal the 3’ primer to polyadenylated mRNA. Reverse transcription was carried out in a master mix of Maxima RNaseH-minus RT enzyme and buffer, MgCl2, Betaine, RNase inhibitor, and a 5’ template switch oligonucleotide using the following protocol: 42ºC for 90 minutes, followed by 10 cycles of 50ºC for 2 minutes, 42ºC for 2 minutes, and followed by inactivation at 70ºC for 15 minutes. Whole transcriptome amplification was achieved by addition of KAPA HiFi HotStart ReadyMix and IS PCR primerto the reverse transcription product and amplification on a thermal cycler using the following protocol: 98ºC for 3 minutes, followed by 21 cycles of 98ºC for 15 seconds, 67ºC for 20 seconds, 72ºC for 6 minutes, followed by a final 5-minute extension at 72ºC. Libraries were purified using AMPure XP SPRI beads at a volume ratio of 0.8x followed by 0.9x. Library size was assessed using a High-Sensitivity DNA chip (Agilent Bioanalyzer), confirming the expected size distribution of ~1000-2000 bp. Tagmentation reactions were carried out with the Nextera XT DNA Sample Preparation Kit (Illumina) using 250 pg of cDNA per single cell as input, with modified manufacturer’s instructions as described. Libraries were purified twice with AMPure XP SPRI beads at a volume ratio of 0.9x, size distribution assessed using a High Sensitivity DNA chip (Agilent Bioanalyzer) and Qubit High-Sensitivity DNA kit. Libraries were pooled and sequenced using NextSeq500/550 High Output v2 kits (75 cycles, Illumina) using 30-30 paired end sequencing with 8-mer dual indexing

tag: innervation target

value: LN

tag: genotype

tag: mouse number


title: Cell75_LNinnervating


title: K562-dCas9-KRAB_MYB-enh-3_sgRNA-2_1


title: Cell80_LNinnervating


title: Cell76_LNinnervating


title: Cell73_LNinnervating


title: 13873_EDTA_ACK lysing replicate 2

description: 13873_EDTA_ACK lysing 2

source_name: Agilent's Universal Human Reference RNA composed of pooled total RNA from ten cell lines representing different human tissues

tag: reference

value: whole blood


title: 13873_leukoLOCK replicate 1

description: 13873_leukoLOCK 1

source_name: Whole blood

tag: biological replicate

value: 1 of 3


title: 13873_EDTA TRIzol LS replicate 1

description: 13873_EDTA TRIzol LS 1

tag: blood storage

value: RNA extracted using TRIzol LS reagent


title: 13873_EDTA_ACK lysing replicate 1

description: 13873_EDTA_ACK lysing 1

tag: extraction methodology


title: Cell81_LNinnervating


title: Cell79_LNinnervating


title: 13873_EDTA TRIzol LS replicate 2

description: 13873_EDTA TRIzol LS 2

tag: blood component


title: 13873_EDTA TRIzol LS replicate 3

description: 13873_EDTA TRIzol LS 3

tag: individual


title: Cell78_LNinnervating


title: Cell77_LNinnervating


title: Cell67_LNinnervating


title: Cell68_LNinnervating


title: Cell66_LNinnervating


title: Cell72_LNinnervating


title: Cell83_LNinnervating


title: Cell71_LNinnervating


title: Cell70_LNinnervating


title: 13873_ACD-A TRIzol LS replicate 3

description: 13873_ACD-A TRIzol LS 3

value: Whole Blood collected in ACD-A tube

tag: disease state


title: Cell69_LNinnervating


title: Cell74_LNinnervating


title: 13873_ACD-A _ACK lysing replicate 2

description: 13873_ACD-A _ACK lysing 2

value: donor 13873


title: Cell64_LNinnervating


title: 13873_ACD-A TRIzol LS replicate 2

description: 13873_ACD-A TRIzol LS 2


title: 13873_ACD-A _ACK lysing replicate 3

description: 13873_ACD-A _ACK lysing 3


title: Cell58_Skininnervating

value: Skin


title: Cell60_Skininnervating


title: Cell59_LNinnervating


title: 13873_ACD-A _ACK lysing replicate 1

description: 13873_ACD-A _ACK lysing 1


title: 13872_RNAgard replicate 3

description: 13872_RNAgard 3

value: Whole Blood collected in RNAgard tube

value: RNA extracted using Biomaxi/Paxgene blood miRNA kit

value: donor 13872


title: 13873_ACD-A TRIzol LS replicate 1

description: 13873_ACD-A TRIzol LS 1

value: Agilent's Universal Human Reference RNA


title: Cell65_LNinnervating


title: Cell63_LNinnervating


title: Cell62_LNinnervating


title: Cell61_LNinnervating


title: Cell55_Skininnervating


title: Cell57_Skininnervating


title: Cell56_Skininnervating


title: Cell54_Skininnervating


title: Cell50_Skininnervating


title: Cell53_Skininnervating


title: 13872_PBMC EDTA replicate 2

description: 13872_PBMC EDTA 2

value: PBMCs isolated from whole Blood. RNA extracted using TRIzol reagent from PBMCs.

value: PBMC


title: 13872_RNAgard replicate 1

description: 13872_RNAgard 1

value: healthy


title: Cell52_Skininnervating


title: Cell49_Skininnervating


title: 13872_PBMC CPT replicate 2

description: 13872_PBMC CPT 2

value: 2 of 3

value: Whole Blood collected in CPT tube


title: Side population cells of myeloma bone marrow_rep_6

city: Iowa City

first: Fenghuang

last: Zhan

state: IA

address: Newton rd. CBRB 3269

department: Department of Internal Medicine

institute: University of Iowa

description: Gene expression data from SP/LP or CD138+ populations in multiple myeloma patients

hyb_protocol: The RNA was then converted to cDNA and they were hybridized to the Human Genome U133Plus 2.0 GeneChip microarrays (Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: The microarrays were scanned using the GeneChip® Scanner 3000 7G.

data_processing: All data used in these analyses were derived with the  Affymetrix expression console version1.1 software.

source_name: Side population cells in myeloma patient 024

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA.

growth_protocol: bone marrow were taken out from multiple myeloma patients

extract_protocol: The total RNA was isolated from these populations using the RNeasy RNA isolation kit (Qiagen).

treatment_protocol: Side populations and CD138+ from MM patients were isolated by flow cytometry using Hoechst 33342 and CD138 antibody.

value: bone marrow

tag: cell population

value: Side population cells

tag: subject id

tag: diagnosis

value: myeloma


title: Side population cells of myeloma bone marrow_rep_4

source_name: Side population cells in myeloma patient 020


title: Side population cells of myeloma bone marrow_rep_5

source_name: Side population cells in myeloma patient 021


title: Side population cells of myeloma bone marrow_rep_3

source_name: Side population cells in myeloma patient 018


title: 13872_PBMC CPT replicate 3

description: 13872_PBMC CPT 3

value: 3 of 3


title: 13872_RNAgard replicate 2

description: 13872_RNAgard 2

value: whole blood


title: 13872_PBMC ACD-A_magbead replicate 3

description: 13872_PBMC ACD-A_magbead 3

value: Whole Blood collected in ACD-A tube

value: PBMCs isolated using magnetic beads from whole Blood. RNA extracted using TRIzol reagent from PBMCs.


title: 13872_PBMC EDTA replicate 1

description: 13872_PBMC EDTA 1

value: 1 of 3

value: Whole Blood collected in EDTA tube


title: Side population cells of myeloma bone marrow_rep_1

source_name: Side population cells in myeloma patient 006


title: Side population cells of myeloma bone marrow_rep_7

source_name: Side population cells in myeloma patient 029


title: Main population CD138+ cells of myeloma bone marrow_rep_7

source_name: Main population CD138+ cells in myeloma patient 029

value: main population CD138+


title: 13872_PBMC CPT replicate 1

description: 13872_PBMC CPT 1

value: donor 13872


title: 13872_PBMC EDTA replicate 3

description: 13872_PBMC EDTA 3

value: Agilent's Universal Human Reference RNA


title: Main population CD138+ cells of myeloma bone marrow_rep_6

source_name: Main population CD138+ cells in myeloma patient 024


title: 13872_paxgene replicate 2

description: 13872_paxgene 2

value: Whole Blood collected in PAXgene RNA tube

value: RNA extracted using Paxgene Blood miRNA kit


title: Main population CD138+ cells of myeloma bone marrow_rep_5

source_name: Main population CD138+ cells in myeloma patient 021


title: Cell47_Skininnervating

value: Skin


title: 13872_PBMC ACD-A_magbead replicate 2

description: 13872_PBMC ACD-A_magbead 2

value: 2 of 3

value: PBMC

value: healthy


title: Cell48_Skininnervating


title: 13872_PBMC ACD-A_magbead replicate 1

description: 13872_PBMC ACD-A_magbead 1


title: 13872_paxgene replicate 1

description: 13872_paxgene 1


title: WT3

data_processing:
Illumina Casava v1.8.2 was used for basecalling
Quality control on the resulting reads was performed with FastQC (v0.11.7). Reads were mapped to the Drosophila genome (FlyBase 6.05) with STAR (v2.4.0). The resulting SAM files were converted to BAM files with SAMtools (v0.1.19)
Sorted BAM files were used to call counts using Htseq (v0.11.0). Further processing of counts was done using Bioconductor (v3.7) in R (v3.5). Counts were normalized and differential expression was calculated using DESeq2 (v1.14.0).
Genome_build: Flybase 6.05
Supplementary_files_format_and_content: normalization parameters arising out of DESeq2

source_name: ovary

extract_protocol:
RNA was isolated using TRIzol™ purification from single-cell suspensions of GFP+ FACS-sorted cells of respective genotypes.
Libraries were prepared using standard Illumina protocols based on the Illumina TruSeq RNA kit.

value: ovary

tag: strain

value: vas-GFP


title: Cell51_Skininnervating


title: Cell46_Skininnervating


title: Cell42_Skininnervating


title: Cell43_Skininnervating


title: 13872_leukoLOCK replicate 2

description: 13872_leukoLOCK 2

value: Whole Blood collected in EDTA tube passed through LeukoLOCK™ filter system

value: RNA extracted using TRIzol reagent


title: 13872_paxgene replicate 3

description: 13872_paxgene 3

value: 3 of 3

value: whole blood


title: Side population cells of myeloma bone marrow_rep_2

source_name: Side population cells in myeloma patient 015

tag: tissue

value: bone marrow

value: Side population cells

value: myeloma


title: Main population CD138+ cells of myeloma bone marrow_rep_2

source_name: Main population CD138+ cells in myeloma patient 015

value: main population CD138+


title: Cell45_Skininnervating


title: Cell41_Skininnervating


title: 13872_leukoLOCK replicate 3

description: 13872_leukoLOCK 3

value: Agilent's Universal Human Reference RNA

value: donor 13872


title: WT2


title: Main population CD138+ cells of myeloma bone marrow_rep_4

source_name: Main population CD138+ cells in myeloma patient 020


title: Cell44_Skininnervating


title: Main population CD138+ cells of myeloma bone marrow_rep_3

source_name: Main population CD138+ cells in myeloma patient 018


title: Bam1

value: vas-GFP; bam_delta86/bam_delta86


title: 13872_EDTA_ACK lysing replicate 2

description: 13872_EDTA_ACK lysing 2

value: Whole Blood collected in EDTA tube

value: RNA extracted using ACK lysing buffer/miRNeasy Mini kit


title: Main population CD138+ cells of myeloma bone marrow_rep_1

source_name: Main population CD138+ cells in myeloma patient 006


title: WT1


title: Bam2


title: Bam3


title: 13872_leukoLOCK replicate 1

description: 13872_leukoLOCK 1

source_name: Agilent's Universal Human Reference RNA composed of pooled total RNA from ten cell lines representing different human tissues

value: 1 of 3


title: 13872_EDTA_ACK lysing replicate 3

description: 13872_EDTA_ACK lysing 3

source_name: Whole blood

value: healthy


title: 13872_EDTA TRIzol LS replicate 2

description: 13872_EDTA TRIzol LS 2

value: 2 of 3

value: RNA extracted using TRIzol LS reagent


title: 13872_EDTA_ACK lysing replicate 1

description: 13872_EDTA_ACK lysing 1


title: Cortical brain, B3684

city: Jacksonville

first: Yingxue

last: Ren

state: FL

address: 4500 San Pablo Rd S

institute: Mayo Clinic

data_processing:
Reads were mapped to the mouse genome mm10 using the STAR aligner version 2.5.2b
Raw gene read counts, along with sequencing quality control, were generated using the Mayo Clinic RNA-sequencing analytic pipeline, MAP-RSeq Version 2.1.1 (Kalari et al., 2014)
In order to correct for GC bias and gene length differences and obtain similar quantile-by-quantile distributions of gene expression levels across samples, we performed conditional quantile normalization (CQN) on the raw gene counts (Hansen et al., 2012). According to the bimodal distribution of the CQN-normalized and log2-transformed reads per kb per million (RPKM) gene expression values, genes with average log2 RPKM of 2 or more in at least one group were considered expressed above detection threshold.
Genome_build: mm10
Supplementary_files_format_and_content: tab-separated text file including raw counts for all samples

source_name: brain

extract_protocol:
Mouse cortical samples were treated with TRIzol RNA Isolation Reagents (Thermo Fisher Scientific, 15596026), and total RNAs were subsequently extracted from samples using DNase (QIAGEN, 79254) and an RNeasy mini kit (QIAGEN, 74104).
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: age

value: 55 days

value: control

tag: stimulus

value: brain


title: Cell35_Skininnervating

source_name: Dorsal root ganglion single neuron

tag: innervation target

value: Skin


title: 13872_EDTA TRIzol LS replicate 3

description: 13872_EDTA TRIzol LS 3

value: 3 of 3

value: whole blood


title: Cell38_Skininnervating

tag: genotype


title: Cortical brain, B3679


title: Cell33_LNinnervating

value: LN

tag: mouse number


title: Cell39_Skininnervating


title: Cortical brain, B3677

value: LPS


title: 13872_ACD-A TRIzol LS replicate 1

description: 13872_ACD-A TRIzol LS 1

tag: reference

value: Agilent's Universal Human Reference RNA

value: Whole Blood collected in ACD-A tube


title: Cell40_Skininnervating