title: HUCPVC-male-P9-biological rep2

source_name: male HUCPVCs at end of P9

tag: donor population name


title: HUCPVC-male-P8-biological rep2

status: Public on Sep 03 2019

type: RNA

city: Medicine Hat

first: Lorena

last: Braid

state: Alberta

address: PO Box 21053, Crescent Heights PO

country: Canada

institute: Aurora BioSolutions Inc.

hyb_protocol: The total amount of cRNA for the hybridization reaction was 20 µg. Arrays were hybridized for 16 hours at 45°C, 60 RPM in a GeneChip™ Hybridization Oven 640 (Affymetrix, Waltham, MA).

scan_protocol: Chips were scanned using a GeneChip™ 3000 7G Scanner (Affymetrix, Waltham, MA) and the resulting probe array images subjected to grid alignment and fluorescence intensity review in AGCC Viewer. fluidics protocol: Program FS450_0002 was used with GeneChip™ Fluidics Station 450 (Affymetrix, Waltham, MA).

data_processing: The data were analyzed using R/Bioconductor packages, including simpleaffy for .CEL file upload and Affymetrix-recommended quality assessment, and gcrma for GCRMA pre-processing.

label: 3' IVT Biotin

molecule: total RNA

organism: Homo sapiens

source_name: male HUCPVCs at end of P8

label_protocol: RNA was amplified and labeled using GeneChip™ 3’ IVT Plus kits (Affymetrix, Waltham, MA) following the manufacturer’s instructions with the following modification: 200 ng of RNA was used for the cDNA synthesis.

growth_protocol:
cell culture protocol: HUCPVCs were thawed according to TRT’s proprietary standard operating procedures and expanded in Mesenchymal Stem Cell Growth Media – Chemically Defined™ (MSCGM-CD™; Lonza, Walkersville, MD). Culture vessels were coated with fibronectin (Corning, Corning, NY) at 0.75 µg/cm2 diluted in 0.133 ml/cm2 in Dulbecco’s phosphate buffered saline without calcium or magnesium (DPBS -/-, ThermoFisher Scientific, Waltham, MA) prior to cell seeding into a culture vessel at a density of 1333 cells/cm2. At 70-80% confluence, culture media was removed and cells were washed with DPBS. DPBS wash was removed, and cells enzymatically detached using TrypLE™ Select (ThermoFisher Scientific, Waltham, MA). Once cells were dissociated, an equal volume of MSCGM-CD was added to the suspension and cells were counted with a Millipore Scepter cell counter using 60 µm probes (Millipore, Billerica, MA). Cells were centrifuged at 149 x g for 5 minutes. Supernatant was removed, and the cell pellet was suspended in fresh MSCGM-CD™. An appropriate volume of cells was seeded into new culture vessels at a density of 1333 cells/cm2.
population doubling level calculation: PDL = 3.32 (logXe – logXb) + S  where Xe is the final cell count, Xb is the initial cell count, and S is the PDL at the start of the culture incubation

extract_protocol:
RNA sample collection protocol: The cell suspension was pelleted by centrifugation at 149 x g for 5 minutes. Supernatant was removed, and the cells suspended in 0.5 ml of RNAprotect® Cell reagent (Qiagen, Germantown, MD) and stored at -80⁰C.
Qiagen RNeasy® Plus Mini Kits (Qiagen, Germantown, MD) were used to extract RNA according to manufacturer’s recommendations.  20 µl of 2 M dithiothreitol (DTT) was added per ml of kit buffer (RLT buffer) and 600 µl RLT buffer was used for each sample.  RNA quality (260/280 absorption ratio of 1.8-2.1) and concentration was assessed in 96 well plates using a BioTek Synergy HT microplate reader (BioTek Instruments Inc., Winooski, VT) and  Gen5 2.05 software accounting for path length correction.

tag: donor sex

value: M

tag: passage number

tag: experimental start date batch

tag: chip run batch

tag: overall batch

tag: population doubling level


title: LB10-0205L

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

country: France

institute: IPMC/CNRS

description: RNA extracted from Lung Adenocarcinoma (LUAD) patient

hyb_protocol: Agilent : 200.0 ng at 65 degree_C during 17 hours

scan_protocol: Arrays were scanned using the Agilent SureScan High Resolution Scanner.

data_processing: Feature extraction data processing. Quantile normalization and differential analysis using Limma package in R / Bioconductor.

label_protocol: Agilent - Low RNA input QuickAmp

extract_protocol: Total RNAs were extracted using TRIzol reagent (Invitrogen)

tag: tissue

value: Lung

tag: histology

value: LUAD

tag: gender

value: Male

tag: age

tag: sample type

value: Tumor

tag: tumor stage

value: IIB

tag: recurrence

value: No

tag: vital status

value: Alive


title: LB10-0205S

description: RNA extracted from normal lung tissue of patient

value: Normal


title: LB10-0281L

value: Female

value: yes


title: LB10-0167S


title: 5-621-1-BBN963-cdTu-RNA-RNS_GAGATTC-TAATCTT

type: SRA

city: Chapel Hill

first: Benjamin

middle: Garrett

last: Vincent

state: NC

address: Lineberger Comprehensive Cancer Center, CB# 7295 125 Mason Farm Rd. Room 5230E Marsico Hall

department: Department of Microbiology and Immunology UNC-Chapel Hill Immunology Division of Hematology/Oncology

country: USA

institute: University of North Carolina at Chapel Hill

library_source: transcriptomic

data_processing:
Illumina bcl2fastq used to convert BCL to FASTQ format
Tumor mutations were called from WES tumor versus match-normal samples using UNCeqR (https://lbc.unc.edu/~mwilkers/unceqr_dist/). RNA-seq files were  used to quantify read coverage, with filter set for >5x coverage for a predicted mutation to be considered for downstream antigen calling.  As such, RNA-seq data was not run through a quantifier (i.e. RSEM) and expression matrix data were not generated or considered for the analysis.  Matched-normal samples for T11 tumor (BALB/c) have been previously deposited at https://www.ncbi.nlm.nih.gov/sra/?term=SRR3502701.
Translated 8-11mer (class I) or 15mer (class II) peptides were derived across all open reading frames, and then predicted for MHC binding affinity using NetMHCPan2.8 (MHC I; http://www.cbs.dtu.dk/services/NetMHCpan-2.8/) and NetMHCIIPan3.0 (MHC II; http://www.cbs.dtu.dk/services/NetMHCIIpan-3.0/).  Class I minor mismatch antigens were predicted similarly in the P815 model against the BALB/c histocompatible donor.
Predicted binders were filtered by binding affinity <500 nM, generally accepted cutoff for immunogenicity as previously noted, with top epitopes screened for immunogenicity using a vaccine/ELISpot approach.
Genome_build: mm9
Supplementary_files_format_and_content: Excel .xlsx file containing top predicted binding affinity MHC I and II tumor-specific antigens from all models represented in the fastq files.

organism: Mus musculus

growth_protocol: P815 tumor samples were collected directly from cell line culture (10e5 cells per sample).  For remaining tumors, mice were injected with tumors and monitored until size reached 100mm3 by caliper measurement. Matched normal samples were collected from tail clippings or liver.

extract_protocol:
RNA was extracted from single cell suspension of tumors using Qiagen RNeasy Mini kit (cat. # 74104), and DNA was extracted from single cell suspensions of tumors and matched-normal tail clippings or livers using Qiagen DNeasy kit (cat. # 69504), all according to manufacturer protocol.
Whole exome and transcriptome library preparation was performed using Agilent SureSelect XT All Exon and Illumina TruSeq Stranded mRNA library preparation kits, respectively.

tag: injected cell line


title: LB10-0167L


title: HUCPVC-male-P7-biological rep2

source_name: male HUCPVCs at end of P7


title: Ouabain36hPlusC_Rep3

city: London

first: Gopuraja

last: Dharmalingam

address: Faculty of Medicine, Imperial College, Hammersmith Hospital Campus

department: Epigenetics section

country: United Kingdom

institute: MRC London Institute of Medical Sciences

description:
mRNA expression profile of senescent IMR90 ER:RAS treated with Ouabain 36h and Caspase inhibitor
GeneCounts.xlsx

data_processing:
RNA-Seq sequencing reads were aligned to hg19 genome using Tophat v2.0.11 using parameters "--library-type fr-firststrand" and using known transcripts annotation from ensembl gene verion 72
Number of reads counts on exons were summarised using featureCounts function available in rsubread R package.
Genome_build: hg19
Supplementary_files_format_and_content: reads counts on genes

source_name: +4OHT + Ouabain 36h + Casp. Inh O/N

growth_protocol: IMR90 ER:RAS cells were grown in DMEM, 10% FBS, for 6 days and media change was performed at day 3

extract_protocol:
Cells were scraped and homogenised in TRIzol® RNA isolation reagent, mixed with Chloroform in a 5:1 ratio, centrifuged at 15,000 rpm for 30 min and after successful phase separation, the top clear RNA-containing phase was purified using the RNAeasy® Mini Kit (Qiagen)
Libraries were prepared according to Illumina's kit instructions (mRNA stranded library prep kit)

treatment_protocol: To induce RAS expression and senescence, cells were treated with 100nM 4OHT

tag: cell line

value: IMR90 ER:RAS

tag: imr90 passage

tag: days after 4oht induction

value: 6 + treatment time


title: 15-AW-05-LI-DNA_WES_1st_2ndPrep_GAATCTG

library_source: genomic

data_processing:
Library strategy: DNA-seq
Illumina bcl2fastq used to convert BCL to FASTQ format
Tumor mutations were called from WES tumor versus match-normal samples using UNCeqR (https://lbc.unc.edu/~mwilkers/unceqr_dist/). RNA-seq files were  used to quantify read coverage, with filter set for >5x coverage for a predicted mutation to be considered for downstream antigen calling.  As such, RNA-seq data was not run through a quantifier (i.e. RSEM) and expression matrix data were not generated or considered for the analysis.  Matched-normal samples for T11 tumor (BALB/c) have been previously deposited at https://www.ncbi.nlm.nih.gov/sra/?term=SRR3502701.
Translated 8-11mer (class I) or 15mer (class II) peptides were derived across all open reading frames, and then predicted for MHC binding affinity using NetMHCPan2.8 (MHC I; http://www.cbs.dtu.dk/services/NetMHCpan-2.8/) and NetMHCIIPan3.0 (MHC II; http://www.cbs.dtu.dk/services/NetMHCIIpan-3.0/).  Class I minor mismatch antigens were predicted similarly in the P815 model against the BALB/c histocompatible donor.
Predicted binders were filtered by binding affinity <500 nM, generally accepted cutoff for immunogenicity as previously noted, with top epitopes screened for immunogenicity using a vaccine/ELISpot approach.
Genome_build: mm9
Supplementary_files_format_and_content: Excel .xlsx file containing top predicted binding affinity MHC I and II tumor-specific antigens from all models represented in the fastq files.

molecule: genomic DNA

value: Matched-normal

value: Liver and tail


title: WT1 Nx

description: RNA extracted from parental A549 cells cultured in normoxia (replicate 1)

source_name: WT1 Nx

tag: rin number

tag: genotype/variation

value: wild type

tag: culture conditions

value: normoxia


title: Ouabain36hPlusC_Rep2


title: LB09-0538S


title: Ouabain36hPlusC_Rep1


title: 14-AW-04-LI-DNA_WES_1st_2ndPrep_ATGCCTA


title: HUCPVC-male-P4-biological rep2

source_name: male HUCPVCs at end of P4

tag: donor population name

tag: donor sex

value: M

tag: passage number

tag: experimental start date batch

tag: chip run batch

tag: overall batch


title: Ouabain16h_Rep3

description:
mRNA expression profile of senescent IMR90 ER:RAS treated with Ouabain 16h
GeneCounts.xlsx

source_name: +4OHT + Ouabain 16h


title: 13-AW-03-LI-DNA_WES_1st_2ndPrep_GACAGTG

tag: sample type

tag: tissue


title: HUCPVC-male-P3-biological rep2

source_name: male HUCPVCs at end of P3

tag: population doubling level


title: 12-AW-02-LI-DNA_WES_1st_2ndPrep_AAGGACA


title: Ouabain16h_Rep2


title: HUCPVC-male-P5-biological rep2

source_name: male HUCPVCs at end of P5


title: 11-AW-01-LI-DNA_WES_1st_2ndPrep_GATAGAC


title: HUCPVC-male-P2-biological rep2

source_name: male HUCPVCs at end of P2


title: Ouabain16h_Rep1


title: LB09-0122L

value: Lung

tag: histology

tag: gender

tag: age

tag: tumor stage

value: IA

tag: recurrence

value: Yes

tag: vital status


title: Minus36h_Rep3

description:
mRNA expression profile of proliferating IMR90 ER:RAS treated with vehicle 36h
GeneCounts.xlsx

source_name: -4OHT + Vehicle 36h

tag: cell line

tag: imr90 passage

tag: days after 4oht induction


title: HUCPVC-female-P16-biological rep1

source_name: female HUCPVCs at end of P16, replicate of F2 population

tag: donor population name

tag: donor sex

value: F


title: 9-AW-04-Tu-DNA-WES_1st_2ndPrep_GAGTTAG

value: Tumor

tag: injected cell line


title: LB08-0713L

value: LUAD

value: Dead


title: LB08-0650L

value: Male

value: IIB


title: 8-AW-03-Tu-DNA-WES_1st_2ndPrep_AAACATC


title: Minus36h_Rep2


title: HUCPVC-female-P14-biological rep1

source_name: female HUCPVCs at end of P14, replicate of F2 population

tag: passage number

tag: experimental start date batch

tag: chip run batch


title: LB06-0453L

tag: tissue

tag: sample type

value: IIA

value: No

value: Alive


title: HUCPVC-female-P15-biological rep1

source_name: female HUCPVCs at end of P15, replicate of F2 population

tag: overall batch

tag: population doubling level


title: LB06-0486L

tag: histology

tag: gender

value: Female

tag: age


title: LB06-0356L

tag: tumor stage

value: IB

tag: recurrence

tag: vital status


title: LB06-0424L


title: LB06-0452L


title: HUCPVC-female-P13-biological rep2

source_name: female HUCPVCs at end of P13, replicate of F2 population


title: 7-AW-02-Tu-DNA-WES_1st_2ndPrep_GAGCTGA


title: Minus36hPlusC_Rep3

description:
mRNA expression profile of proliferating IMR90 ER:RAS treated with vehicle 36h and Caspase inhibitor
GeneCounts.xlsx

source_name: -4OHT + Vehicle 36h + Casp. Inh O/N

tag: cell line

value: IMR90 ER:RAS

tag: imr90 passage

tag: days after 4oht induction

value: 6 + treatment time


title: 10-AW-05-Tu-DNA-WES_1st_2ndPrep_CGAACTT

tag: injected cell line


title: Minus36hPlusC_Rep2


title: HUCPVC-female-P11-biological rep2, technical rep2

source_name: female HUCPVCs at end of P11, replicate of F2 population

tag: donor population name

tag: donor sex

tag: passage number


title: Minus36hPlusC_Rep1


title: 5-AW-05-Tu-RNA-RNS_S61

tag: tissue


title: 4-AW-04-Tu-RNA-RNS_S60

tag: sample type


title: Minus16h_Rep3

description:
mRNA expression profile of proliferating IMR90 ER:RAS treated with vehicle 16h
GeneCounts.xlsx

source_name: -4OHT + Vehicle 16h


title: 3-AW-03-Tu-RNA-RNS_S59


title: Minus36h_Rep1


title: 6-AW-01-Tu-DNA-WES_1st_2ndPrep_AGCAGGA


title: LB06-0337L


title: HUCPVC-female-P12-biological rep2

source_name: female HUCPVCs at end of P12, replicate of F2 population

tag: experimental start date batch

tag: chip run batch

tag: overall batch


title: HUCPVC-female-P8-biological rep2, technical rep2

source_name: female HUCPVCs at end of P8, replicate of F2 population

tag: population doubling level


title: HUCPVC-female-P9-biological rep2, technical rep2

source_name: female HUCPVCs at end of P9, replicate of F2 population


title: HUCPVC-male-P6-biological rep2

source_name: male HUCPVCs at end of P6

value: M


title: LB06-0258L

value: Lung

tag: histology

tag: gender

tag: age


title: HUCPVC-female-P7-biological rep2, technical rep2

source_name: female HUCPVCs at end of P7, replicate of F2 population


title: Minus16h_Rep1


title: 1-AW-01-Tu-RNA-RNS_S57


title: HUCPVC-female-P5-biological rep2, technical rep2

source_name: female HUCPVCs at end of P5, replicate of F2 population


title: LB05-0450L

tag: tumor stage

tag: recurrence

tag: vital status


title: Digoxin36h_Rep3

description:
mRNA expression profile of senescent IMR90 ER:RAS treated with Digoxin 36h
GeneCounts.xlsx

source_name: +4OHT + Digoxin 36h

tag: cell line

tag: imr90 passage

tag: days after 4oht induction


title: ATAC_FOSminus_NE1h_rep1

city: Sant Joan d'Alacant

first: Angel

last: Barco

state: Alicante

address: Av. Santiago Ramón y Cajal

country: Spain

institute: Instituto de Neurociencias (UMH-CSIC)

description:
Paired-end
processed data file:
ATAC_FOSminus_NE1h.bw

data_processing:
All sequenced datasets adapters were trimmed using cutadapt v1.18 (Martin, 2011) and aligned to mm10. Only reads with mapq > 30 and mapping to nuclear chromosomes were used for the posterior analysis. Data was processed with the extensive use of custom scripts, and Samtools (v1.9) (Li et al., 2009), bedtools v2.26.0 (Quinlan and Hall, 2010) and DeepTools v3.1.0 (Ramirez et al., 2016). RNA-seq data: Reads were aligned with HISAT2 v2.1.0 (Kim et al., 2015). ATAC-seq data: Reads were aligned with bowtie2 v2.2.6 (Langmead and Salzberg, 2012). Duplicated reads were removed with Picardtools and only paired reads were used for the posterior analysis. ChIP-seq data: Reads were aligned with bowtie2 v2.2.6 (Langmead and Salzberg, 2012). HiC data: Hi-C datasets were processed using the Juicer pipeline (Durand et al., 2016) to align reads, filter duplicates, perform matrix normalizations, and obtain the eigenvector. Reads with a mapping quality >= 30 and binned at 25 kb were used in all downstream analyses.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files from whole genome alignments normalized to RPM (read per million sequenced reads).

source_name: Hippocampal excitatory neurons

growth_protocol: Mice were maintained and bred under standard conditions, consistent with Spanish and European regulations and approved by the Institutional Animal Care and Use Committee.

extract_protocol:
Hippocampi were micro-dissected after cervical dislocation, washed in ice-cold PBS and pooled together, when fixation was needed 1% FA was used. TRAP immunoprecipitation followed the original protocol by (Heiman et al., 2014) with small changes. Nuclei were isolated using our improved FANS protocol for SUN1-GFP+ cells, in case NE condition nuclei were stained against FOS. Extensive description of protocols indicated in Supplemental Experimental Procedures.
For riboRNA and nuRNA, extraction was re-suspended in RLT buffer for purification with RNeasy Micro kit (Qiagen 74004). Truseq libraries were prepared from ribo-depleted total RNA in the case of nuRNA-seq and from polyA-selected mRNA in the case of riboRNA-seq. ATAC-seq experiments were conducted as the original protocol (Buenrostro et al., 2013), libraries were purified with MinElute PCR purification kit (Qiagen 28004). ChIP-seq was conducted as previously described (Lopez-Atalaya et al., 2013) using the anti-H3K4me3 (Millipore 07-473), anti-CBP (sc583x) and anti-RNAPII (sc901x). In situ Hi-C were conducted as the original protocol (Rao et al., 2014), libraries were prepared with TruSeq.

treatment_protocol: Mice received intragastric administration of tamoxifen when they were ~2 month-old, and we wait 4 weeks before experimentation. For the induction of SE by Kainic Acid (KA), 25 mg/kg was injected intraperitoneally. For the blocking of transcription by Triptolide (TPL) a concentration of 0.8 mg/kg was injected intraperitoneally per mice 2 h before the injection of KA or Saline. For novelty exposure (NE), individually housed mice received 3-4 days of 5 min handling before exposing them to a novel environment during 1h.

tag: strain

value: Adult Forebrain (hippocampus)

value: 3-6 month

value: male


title: HUCPVC-female-P11-biological rep2, technical rep1

source_name: female HUCPVCs at end of P11

tag: donor population name

tag: donor sex

value: F

tag: passage number


title: LB06-0226L

tag: tissue

value: LUAD

tag: sample type

value: Tumor

value: IA

value: Yes


title: Digoxin36h_Rep2


title: LB10-0489L

value: Male


title: LB10-0570L

value: IIB


title: Minus16h_Rep2


title: Digoxin36h_Rep1


title: HUCPVC-female-P10-biological rep2

source_name: female HUCPVCs at end of P10

tag: experimental start date batch

tag: chip run batch

tag: overall batch


title: ATAC_FOSplus_NE1h_rep1

description:
Paired-end
processed data file:
ATAC_FOSplus_NE1h.bw

tag: gender


title: ATAC_DMSO2h_Sal1h_rep1

description:
Paired-end
processed data file:
ATAC_DMSO2h_Sal.bw

tag: age


title: HUCPVC-female-P6-biological rep2, technical rep2

source_name: female HUCPVCs at end of P6, replicate of F2 population

tag: population doubling level


title: Digoxin36hPlusC_Rep3

description:
mRNA expression profile of senescent IMR90 ER:RAS treated with Digoxin 36h and Caspase inhibitor
GeneCounts.xlsx

source_name: +4OHT + Digoxin 36h + Casp. Inh O/N


title: LB09-0471L

tag: histology

tag: tumor stage

tag: recurrence

value: Dead


title: Digoxin36hPlusC_Rep2

tag: cell line

tag: imr90 passage


title: HUCPVC-female-P7-biological rep2, technical rep1

source_name: female HUCPVCs at end of P7


title: LB09-0538L

value: No

tag: vital status


title: HUCPVC-female-P8-biological rep2, technical rep1

source_name: female HUCPVCs at end of P8

tag: donor population name


title: ATAC_TPL2h_KA1h_rep1

description:
Paired-end
processed data file:
ATAC_TPL2h_KA1h.bw

tag: strain


title: HUCPVC-female-P9-biological rep2, technical rep1

source_name: female HUCPVCs at end of P9

tag: donor sex

tag: passage number


title: ATAC_TPL2h_Sal_rep1

description:
Paired-end
processed data file:
ATAC_TPL2h_Sal.bw

tag: tissue


title: Ouabain36h_Rep2

description:
mRNA expression profile of senescent IMR90 ER:RAS treated with Ouabain 36h
GeneCounts.xlsx

source_name: +4OHT + Ouabain 36h

tag: days after 4oht induction


title: LB06-0637L

tag: sample type

value: IIA


title: LB09-0471S

value: Normal


title: HUCPVC-female-P6-biological rep2, technical rep1

source_name: female HUCPVCs at end of P6

tag: experimental start date batch

tag: chip run batch

tag: overall batch


title: HUCPVC-female-P5-biological rep2, technical rep1

source_name: female HUCPVCs at end of P5

tag: population doubling level


title: Digoxin36hPlusC_Rep1

value: IMR90 ER:RAS

value: 6 + treatment time


title: LB05-0404L

value: Lung

tag: histology

tag: gender

tag: age

value: Alive


title: Digoxin16h_Rep3

description:
mRNA expression profile of senescent IMR90 ER:RAS treated with Digoxin 16h
GeneCounts.xlsx

source_name: +4OHT + Digoxin 16h

tag: cell line


title: ATAC_KA48h_rep1

description:
Paired-end
processed data file:
ATAC_KA48h.bw

value: Adult Forebrain (hippocampus)

value: 3-6 month


title: ATAC_KA48h_rep2

value: male


title: Digoxin16h_Rep2

tag: imr90 passage


title: ATAC_KA6h_rep2

description:
Paired-end
processed data file:
ATAC_KA6h.bw


title: HUCPVC-female-P4-biological rep2

source_name: female HUCPVCs at end of P4

value: F


title: Digoxin16h_Rep1


title: ATAC_KA6h_rep1


title: siDDX5 rep3

city: Huddinge

first: Karin

last: Dahlman-Wright

address: Blickagången 16

department: Department of Biosciences and Nutrition

country: Sweden

institute: Karolinska Institutet

data_processing:
Clustering was done by 'cBot' and samples were sequenced on HiSeq2500 (HiSeq Control Software 2.2.58/RTA 1.18.64) with a 2x126 setup using 'HiSeq SBS Kit v4' chemistry.
The Bcl to FastQ conversion was performed using bcl2fastq-v2.17.1.14 from the CASAVA software suite.
The quality scale used is Sanger / phred33 / Illumina 1.8+. Raw sequencing data is demultiplexed and converted to FastQ
To ensure of data quality and quantity, a number of standardised bioinformatics quality control checks are performed which includes checking the yield, sequence read quality and cross-sample contamination.
FPKMs for genes and transcripts were generated using cufflinks/2.1.1.
Genome_build: Human (Homo sapiens, GRCh37)
Supplementary_files_format_and_content: FPKM values generated by cufflinks/2.1.1

growth_protocol: Cells  were maintained in RPMI 1640 supplemented with 10% FBS.

extract_protocol:
Total RNA was extracted using RNeasy Mini Kit (Qiagen, Valencia, CA).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: No treatment

tag: cell type

value: ERalpha-negtive breast cancer cells

tag: genotype/variation

value: DDX5 knockdown


title: siDDX5 rep2


title: siDDX5 rep1


title: ATAC_KA1h_rep1

description:
Paired-end
processed data file:
ATAC_KA1h.bw

tag: strain


title: ATAC_Sal_rep2

description:
Paired-end
processed data file:
ATAC_Sal.bw


title: ATAC_KA1h_rep2


title: siFra-1 rep3

value: Fra-1 knockdown


title: ATAC_Sal_rep1


title: LB10-0031L

description: RNA extracted from Lung Adenocarcinoma (LUAD) patient

value: LUAD

value: Male

value: Tumor

tag: tumor stage

tag: recurrence

value: Yes

tag: vital status


title: siFra-1 rep2


title: LB05-0039L

tag: tissue

value: Female

value: IIA

value: Dead


title: siControl rep2

value: control


title: LB06-0210L

value: Lung

tag: sample type

value: IB

value: No


title: siFra-1 rep1


title: siControl rep3


title: ChIP_CBP_KA1h_rep2

description:
Single-end
processed data file:
ChIP_CBP_KA1h.bw

source_name: Hippocampal tissue

value: Adult Forebrain (hippocampus)

value: 3-6 month


title: ChIP_CBP_KA1h_rep1

value: male


title: ChIP_CBP_Sal

description:
Single-end
processed data file:
ChIP_CBP_Sal.bw


title: HUCPVC-female-P2-biological rep2

source_name: female HUCPVCs at end of P2

tag: donor population name

tag: donor sex

value: F

tag: passage number

tag: experimental start date batch


title: LB10-0498L

tag: histology


title: HUCPVC-female-P11-biological rep1

tag: chip run batch

tag: overall batch

tag: population doubling level


title: HUCPVC-female-P10-biological rep1


title: HUCPVC-female-P1-biological rep1

source_name: female HUCPVCs at end of P1


title: HUCPVC-female-P9-biological rep1


title: HUCPVC-female-P13-biological rep1

source_name: female HUCPVCs at end of P13


title: HUCPVC-female-P12-biological rep1

source_name: female HUCPVCs at end of P12


title: HUCPVC-female-P6-biological rep1


title: LB07-0134L

tag: gender

tag: age

value: Alive


title: siControl rep1

tag: cell line

tag: cell type

value: ERalpha-negtive breast cancer cells

tag: genotype/variation


title: HUCPVC-female-P7-biological rep1


title: LB07-0134S

description: RNA extracted from normal lung tissue of patient

value: LUAD

value: Normal

tag: tumor stage

tag: recurrence


title: LB06-0200S

tag: tissue

tag: vital status


title: LB04-0138L

tag: sample type

value: Tumor

value: IIB


title: HUCPVC-female-P3-biological rep2

source_name: female HUCPVCs at end of P3

tag: donor population name

tag: donor sex


title: LB04-0087S

value: Male


title: LB05-0140S


title: HUCPVC-female-P8-biological rep1

tag: passage number

tag: experimental start date batch


title: LB06-0196L

tag: histology


title: ChIP_Pol2_KA1h

description:
Single-end
processed data file:
ChIP_Pol2_KA1h.bw

tag: strain


title: LB06-0141L

value: Female

value: IIA

value: Yes


title: HUCPVC-female-P5-biological rep1

tag: chip run batch

tag: overall batch

tag: population doubling level


title: GM3: LNCaP_siGATA2_MDV

city: Durham

first: Zhong

last: Chen

address: 905 S. LaSalle Street

department: Pathology

institute: Duke University

data_processing:
RNA-seq process: The RNA-seq data was aligned by TopHat 2.0. Reads were mapped to the reference genome build (hg19). Read counts were calculated with Partek. The reads count in exon regions was used to estimate the expression level of the genes.
Genome_build: hg19
Supplementary_files_format_and_content: For RNA-seq, tab-delimited text files include read counts of all genes for each Sample.

molecule: polyA RNA

source_name: prostate cancer cells

growth_protocol: The prostate cancer cell line LNCaP was cultured in the RPMI complete medium (10% FBS).

extract_protocol:
For RNA-seq, total RNA was isolated using an RNeasy kit (QIAGEN). Next, mRNA was enriched using NEBNext Poly(A) mRNA Magnetic Isolation Module. After two rounds of processes, the  mRNA was recovered for library generation.
For RNA-seq, the library preparation was performed with NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina following the manufacturer’s instructions. The cDNA molecules were amplified by 8 cycles of PCR. Non-size selection libraries were then sequenced for using Illumina HiSeq 4000 at the Duke sequencing core.

treatment_protocol: For all experiments, cells transfected with either non-targeting control siRNA or siGATA2 were maintained in phenol red-free RPMI medium with 5-10% charcoal-stripped FBS for 3 days before treatment. Then cells were treated with vehicle, DHT and MDV for indicated time.

tag: cell line

value: LNCaP

value: Prostate adenocarcinoma

tag: sirna

tag: treatment

value: Enzalutamide

tag: replicate

value: Biological replicate 3


title: 2-AW-02-Tu-RNA-RNS_S58

tag: injected cell line


title: ChIP_H3K27ac_Sal_rep1

description:
Single-end
processed data file:
ChIP_H3K27ac_Sal.bw

tag: tissue

value: Adult Forebrain (hippocampus)

tag: age

value: 3-6 month

tag: gender


title: ChIP_Pol2_Sal

description:
Single-end
processed data file:
ChIP_Pol2_Sal.bw

value: male


title: LB10-0524L

value: Lung

tag: sample type

tag: tumor stage

value: IA

tag: recurrence

value: No

tag: vital status

value: Alive


title: ChIP_H3K27ac_Sal_rep2


title: LB06-0200L

tag: histology

value: LUAD

value: Tumor

value: IB


title: HUCPVC-female-P3-biological rep1

tag: donor population name

tag: donor sex

value: F

tag: passage number

tag: experimental start date batch


title: nuRNA_KA48h_rep1

description:
total nuclearRNA
Single-end
processed data file:
nuRNA_KA48h.bw

source_name: Hippocampal excitatory neurons

tag: strain


title: HUCPVC-female-P4-biological rep1

tag: chip run batch

tag: overall batch

tag: population doubling level


title: GM2: LNCaP_siGATA2_MDV

tag: cell line

tag: sirna

tag: treatment

tag: replicate

value: Biological replicate 2


title: nuRNA_KA6h_rep2

description:
total nuclearRNA
Single-end
processed data file:
nuRNA_KA6h.bw

tag: tissue

tag: age

tag: gender


title: GV2: LNCaP_siGATA2_Vehicle

value: Vehicle


title: LB05-0354L

value: Male

tag: sample type

tag: tumor stage

tag: recurrence

value: Yes

tag: vital status

value: Dead


title: GV1: LNCaP_siGATA2_Vehicle

value: LNCaP

value: Prostate adenocarcinoma

value: Biological replicate 1


title: nuRNA_KA6h_rep1

value: Adult Forebrain (hippocampus)

value: 3-6 month

value: male


title: GM1: LNCaP_siGATA2_MDV

value: Enzalutamide


title: nuRNA_KA1h_rep2

description:
total nuclearRNA
Single-end
processed data file:
nuRNA_KA1h.bw


title: HUCPVC-female-P2-biological rep1

tag: donor population name

tag: donor sex

tag: passage number


title: GV3: LNCaP_siGATA2_Vehicle

value: Biological replicate 3


title: LB08-0507L

value: Lung

tag: histology

value: LUAD

value: IIA

value: Alive


title: CM2: LNCaP_sicontrol_MDV

value: Biological replicate 2


title: CM3: LNCaP_sicontrol_MDV


title: LB08-0680L

value: Tumor

value: IA


title: nuRNA_KA1h_rep1

tag: strain


title: LB08-0800L

value: Male

value: Yes


title: HUCPVC-male-P11-biological rep1

source_name: male HUCPVCs at end of P11

value: M

tag: experimental start date batch

tag: chip run batch

tag: overall batch

tag: population doubling level


title: HUCPVC-male-P12-biological rep1

source_name: male HUCPVCs at end of P12


title: CM1: LNCaP_sicontrol_MDV

tag: cell line

value: LNCaP

value: Prostate adenocarcinoma

tag: sirna

tag: treatment

tag: replicate


title: nuRNA_Sal_rep2

description:
total nuclearRNA
Single-end
processed data file:
nuRNA_Sal.bw

tag: tissue

value: Adult Forebrain (hippocampus)

tag: age

tag: gender


title: CV3: LNCaP_sicontrol_Vehicle

value: Vehicle


title: LB07-0293L

tag: sample type

tag: tumor stage

value: IB

tag: recurrence

tag: vital status

value: Dead


title: nuRNA_Sal_rep1

value: 3-6 month

value: male


title: CV2: LNCaP_sicontrol_Vehicle


title: HUCPVC-male-P8-biological rep1

source_name: male HUCPVCs at end of P8

tag: donor population name

tag: donor sex

tag: passage number


title: LB04-0097L

value: Lung

tag: histology

value: LUAD

value: IIB


title: LB07-0328L


title: LB05-0360L


title: HUCPVC-male-P7-biological rep1

source_name: male HUCPVCs at end of P7

tag: experimental start date batch

tag: chip run batch

tag: overall batch


title: HUCPVC-male-P9-biological rep1

source_name: male HUCPVCs at end of P9

tag: population doubling level


title: riboRNA_KA1h_rep3

description:
polyA riboRNA
Single-end
processed data file:
riboRNA_KA1h.bw

data_processing:
Library strategy: ribo-seq
All sequenced datasets adapters were trimmed using cutadapt v1.18 (Martin, 2011) and aligned to mm10. Only reads with mapq > 30 and mapping to nuclear chromosomes were used for the posterior analysis. Data was processed with the extensive use of custom scripts, and Samtools (v1.9) (Li et al., 2009), bedtools v2.26.0 (Quinlan and Hall, 2010) and DeepTools v3.1.0 (Ramirez et al., 2016). RNA-seq data: Reads were aligned with HISAT2 v2.1.0 (Kim et al., 2015). ATAC-seq data: Reads were aligned with bowtie2 v2.2.6 (Langmead and Salzberg, 2012). Duplicated reads were removed with Picardtools and only paired reads were used for the posterior analysis. ChIP-seq data: Reads were aligned with bowtie2 v2.2.6 (Langmead and Salzberg, 2012). HiC data: Hi-C datasets were processed using the Juicer pipeline (Durand et al., 2016) to align reads, filter duplicates, perform matrix normalizations, and obtain the eigenvector. Reads with a mapping quality >= 30 and binned at 25 kb were used in all downstream analyses.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files from whole genome alignments normalized to RPM (read per million sequenced reads).

tag: strain


title: NSD2_Low_2_Hi-C

city: New York

first: Priscillia

last: Lhoumaud

state: NY

address: 550 first avenue Smilow 307

institute: NYU Langone Health

description:
Hi-C in NSD2 Low cells replicate 2 of 2
NSD2_LOW_arima.hic, NSD2_LOW_compartments.bedGraph, NSD2_LOW_domains.k=001.bed, NSD2_LOW_filtered_Acompartments.bed, NSD2_LOW_filtered_Bcompartments.bed

data_processing:
Reads were trimmed using trim-galore/0.4.4
Reads were aligned to the hg38 assembly of mouse genome using bowtie2
Reads with quality < 30 and duplicates were removed using Samtools/1.3 for ATAC-seq and ChIP-seq
Peaks were called using Macs/1.4
rwas counts were obtained using Htseq in genes for RNAseq or peaks for ChIP-seq
Bigwigs were generated from bam files with RPKM (Reads Per Kilobase per Megabase) normalization using Deeptools. For H3K36me2 spiked-in, Bigwigs were created after normalization with the   spike-in Drosophila read counts.
Genome_build: hg38
Supplementary_files_format_and_content: bigwigs and peak files were generated from bam files for data visualization.

source_name: TKO

growth_protocol: Cells were grown in RPMI 1640 supplemented with 10% FBS and 1% Pen/Strep.

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit from Qiagen (Cat. No. 74104) in accordance with the prescribed protocol provided with the kit.
For ATAC-seq,ChIP-seq and HiChIP, sequencing libraries were constructed using the Illumina Nextera DNA Sample prep kit. RNA libraries were prepared for sequencing using standard Illumina protocols. Hi-C libraries were prepared as per the Arima kit guidelines.
RNAseq, ChIP-seq, ATAC-seq, Hi-C, HiChIP, 4C

tag: parental cell line

tag: cell type

value: multiple myeloma cell line

tag: genotype/variation

value: overexpressed NSD2 allele inactivated

tag: kit

value: Arima


title: riboRNA_KA1h_rep2

tag: tissue

tag: age

tag: gender


title: HUCPVC-male-P10-biological rep1

source_name: male HUCPVCs at end of P10


title: NSD2_Low_1_Hi-C

description:
Hi-C in NSD2 Low cells replicate 1 of 2
NSD2_LOW_arima.hic, NSD2_LOW_compartments.bedGraph, NSD2_LOW_domains.k=001.bed, NSD2_LOW_filtered_Acompartments.bed, NSD2_LOW_filtered_Bcompartments.bed


title: LB04-0115L

value: Male

tag: sample type

value: Tumor

tag: tumor stage

value: IIA

tag: recurrence

tag: vital status


title: LB05-0361L

tag: histology

value: No

value: Alive


title: HUCPVC-male-P6-biological rep1

source_name: male HUCPVCs at end of P6

tag: donor population name

tag: donor sex

value: M

tag: passage number

tag: experimental start date batch


title: LB10-0174L

value: Female

value: IA


title: NSD2_High_2_Hi-C

description:
Hi-C in NSD2 High cells replicate 2 of 2
NSD2_HIGH_arima.hic, NSD2_HIGH_compartments.bedGraph, NSD2_HIGH_domains.k=001.bed, NSD2_HIGH_filtered_Acompartments.bed, NSD2_HIGH_filtered_Bcompartments.bed

source_name: NTKO

value: wild type NSD2 allele inactivated


title: CV1: LNCaP_sicontrol_Vehicle

tag: cell line

value: LNCaP

value: Prostate adenocarcinoma

tag: sirna

tag: treatment

value: Vehicle

tag: replicate

value: Biological replicate 1


title: HUCPVC-male-P5-biological rep1

source_name: male HUCPVCs at end of P5

tag: chip run batch

tag: overall batch

tag: population doubling level


title: riboRNA_Sal_rep2

description:
polyA riboRNA
Single-end
processed data file:
riboRNA_Sal.bw

tag: strain

tag: tissue

value: Adult Forebrain (hippocampus)

tag: age

value: 3-6 month

tag: gender

value: male


title: LB10-0298L

value: Lung

value: LUAD

tag: sample type

tag: tumor stage

value: IIB

tag: recurrence

value: Yes

tag: vital status


title: riboRNA_KA1h_rep1


title: T5

city: Shanghai

first: Lin

last: Wang

address: 180 Fenglin Rd.

department: Department of thoracic surgery

country: China

institute: Zhongshan Hospital, Fudan University

data_processing:
Reads filtering under criteria removing reads with 20% of the base quality lower than 13
HISAT2 mapping to reference genome
count counting
Genome_build: GRCh38
Supplementary_files_format_and_content: TXT file contain counts for each sample

source_name: Esophageal squamous cell carcinoma

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

value: Esophageal squamous cell carcinoma

value: Male

tag: Stage

value: III


title: riboRNA_Sal_rep1


title: 48hours_rep3

city: Philadelphia

first: Boris

last: Striepen

state: PA

address: 380 S University Ave

department: Department of Pathobiology

institute: University of Pennsylvania

data_processing:
fastq files were pseudoaligned to the Cryptosporidium parvum reference transcriptome (ASM16534v1) using kallisto v0.44.0
transcripts were collapsed to gene symbols in R using Bioconductor tximport and a transcript-to-gene key generated from the C. parvum Iowa II TSV file available for download from EnsemblProtists (ASM15634v1.37)
Expression data was normalized using the VOOM function in the Limma package in R
Differentially expressed genes (³ 2-fold and p-value £ 0.01) were identified by linear modeling and Bayesian statistics using the Limma package
Genome_build: Cryptosporidium parvum reference transcriptome Iowa II (ASM16534v1)
Supplementary_files_format_and_content: tab-delimited text files include log2 counts per million (CPM) values for each Sample ...

organism: Cryptosporidium parvum

source_name: Cryptosporidium parvum infected HCT8 cells

growth_protocol: 80% confluent monolayers of HCT-8 cells in 24-well plates were infected with 100,000 oocysts per well for 48 hours at 5% CO2 and 37 ℃

extract_protocol:
For sorted cells RNA was isolated using the RNeasy Micro Kit (Qiagen) and processed as per manufacturer’s instructions. For bulk infections, RNA was isolated using the RNeasy Mini Kit (Qiagen) and processed as per manufacturer's instructions.
cDNA was generated using the SMART-Seq v4 Ultra Low Input RNA Kit (Takara Bio USA Inc) for the sorted cells, and all libraries were prepared using the Nextera XT DNA Library Preparation Kit (Illumina), according to the manufacturer’s instructions.

treatment_protocol: For sorted cells, infected cells were sorted directly into RLT buffer from the RNeasy Micro Kit (Qiagen)

tag: oocyst source

value: Sterling Farms, University of Arizona

tag: parasite strain

value: wildtype

tag: in vitro/in vivo

value: in vitro

tag: host

value: Human cell line HCT8


title: 48hours_rep2


title: Young_Rep6

description: GeneCounts.xlsx

data_processing:
RNA-Seq sequencing reads were aligned to mm9 genome using Tophat v2.0.11 using parameters "--library-type fr-firststrand" and using known transcripts annotation from ensembl gene verion 67
Number of reads counts on exons were summarised using featureCounts function available in rsubread R package.
Genome_build: mm9
Supplementary_files_format_and_content: reads counts on genes

source_name: Liver of young mice

extract_protocol:
Livers were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Liver

value: 7 weeks old

tag: Sex

value: Female

tag: treatment


title: T4


title: riboRNA_Sal_rep3

value: Adult Forebrain (hippocampus)


title: LB05-0306L

tag: histology

value: Tumor

value: IB

value: Dead


title: HUCPVC-male-P3-biological rep1

source_name: male HUCPVCs at end of P3

tag: donor population name

tag: donor sex

value: M

tag: passage number

tag: experimental start date batch

tag: chip run batch

tag: overall batch

tag: population doubling level


title: HUCPVC-male-P1-biological rep1

source_name: male HUCPVCs at end of P1


title: HUCPVC-male-P2-biological rep1

source_name: male HUCPVCs at end of P2


title: LB09-0052L

tag: tissue

value: Lung

value: LUAD

tag: gender

tag: age

tag: sample type

tag: tumor stage

tag: recurrence


title: LB05-0241L

value: IA

value: Yes

tag: vital status


title: LB05-0140L

value: Male

value: No

value: Alive


title: HUCPVC-male-P4-biological rep1

source_name: male HUCPVCs at end of P4


title: T1

value: Esophageal squamous cell carcinoma

tag: Stage

value: IIA


title: T9

value: III


title: 24hours_rep2

growth_protocol: 80% confluent monolayers of HCT-8 cells in 24-well plates were infected with 1,000,000 oocysts per well for 24 hours at 5% CO2 and 37 ℃

tag: oocyst source

value: Sterling Farms, University of Arizona

tag: parasite strain

value: wildtype

tag: in vitro/in vivo

value: in vitro

tag: host

value: Human cell line HCT8


title: N9

source_name: Normal esophagus

value: Normal esophagus


title: N5


title: 48hours_rep1


title: Young_Rep3

description: GeneCounts.xlsx

value: Liver

value: 7 weeks old

tag: Sex

value: Female

tag: treatment


title: Young_Rep4

description: GeneCounts.xlsx


title: sporozoites_rep3

source_name: excysted Cryptosporidium parvum oocysts

growth_protocol: Oocysts were incubated in 0.8% sodium deoxytaurocholate and incubated at 37℃ for 2 hours.

value: Isolated from cow feces


title: N4

value: IIB


title: LB05-0097L

value: Lung

tag: histology

value: LUAD

value: Tumor

value: IB

value: Yes


title: Young_Rep1

description: GeneCounts.xlsx


title: sporozoites_rep2


title: Old_Vehicle_Rep6

description: GeneCounts.xlsx

source_name: Liver of old mice treated with Vehicle

value: 24 months old

value: Saline


title: 24hours_rep1

value: Sterling Farms, University of Arizona


title: sporozoites_rep1

value: wildtype


title: Young_Rep2

description: GeneCounts.xlsx


title: LB05-0198S

value: Male

value: Normal


title: LB05-0035L

value: IIA

value: No

value: Alive


title: Old_Vehicle_Rep4

description: GeneCounts.xlsx

value: Liver

value: Female


title: Young_Rep5

description: GeneCounts.xlsx

value: 7 weeks old


title: Old_Vehicle_Rep3

description: GeneCounts.xlsx


title: LB05-0132L

value: Lung


title: wt4

city: Melbourne

first: Enzo

last: Porrello

state: Victoria

address: c/o Royal Children’s Hospital

department: Cell Biology

country: Australia

institute: Murdoch Children's Research Institute

data_processing:
Trimming using the Skewer (version 0.2.2).
Aligned to the zebrafish genome (GRCz11.95) using STAR (version 2.5.2a).
Mapped reads were counted with featureCounts (v1.5.0).
Genes were filtered if the sums of reads across all samples was less than 10.
Genome_build: GRCz11.95
Supplementary_files_format_and_content: Filtered raw counts of sequencing reads.

organism: Danio rerio

source_name: zebrafish ventricle

extract_protocol:
RNA extraction was performed from fresh tissue using Direct-zol™ RNA Miniprep kit (Zymo/ Integrated Science, R2051).
Libraries were generated using TruSeq Stranded mRNA Library Prep Kit (#20020595, Illumina).

value: heart

tag: chamber

value: ventricle

tag: genotype


title: wt5

tag: tissue


title: wt3


title: LB04-0087L

value: LUAD

tag: gender

value: Tumor

value: IB

value: Dead


title: LB04-0075S

tag: age


title: LB05-0067L

tag: sample type

value: IIB


title: 24hours_rep3

value: Sterling Farms, University of Arizona

value: wildtype

value: in vitro

value: Human cell line HCT8


title: LB04-0073L

value: Male

tag: tumor stage

value: IIA

value: Yes


title: N1

value: Normal esophagus

value: Female


title: LB04-0034L

value: Lung

tag: recurrence

value: No

value: Alive


title: WC8

data_processing:
Trimming using the Skewer (version 0.2.2).
Aligned to the zebrafish genome (GRCz11.95) using Burrows Wheeler Aligner (BWA, version 0.7.17).
Mapped reads were counted with featureCounts (v1.5.0).
Genes were filtered if the sums of reads across all samples was less than 10.
Genome_build: GRCz11.95
Supplementary_files_format_and_content: Filtered raw counts of sequencing reads.

source_name: zebrafish ventricle_with cryoinjury

extract_protocol:
RNA extraction was performed from PFA-fixed (4% PFA) and Tissue-Tek® O.C.T. compound (ProSciTech)-embedded heart cryosections (8μm). A scalpel was used to collect 12 sections of the ventricle per sample. Sections were transferred to a tube on ice containing 100μl of TRIzol® Reagent (15596018, Invitrogen) and then processed with Direct-zol™ RNA Microprep kit (Zymo/ Integrated Science, R2061).
Ribosomal RNA was depleted from total RNA using NEBNext rRNA Depletion Kit (Human/Mouse/Rat) (E6310, New England Biolabs) followed by library generation using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (E7760, New England Biolabs) to select library fragment sizes of 200-400bp.

value: heart

value: ventricle


title: LB04-0025L

value: LUAD

value: Tumor

value: IA

tag: vital status


title: Old_Vehicle_Rep2

description: GeneCounts.xlsx

value: Liver

value: 24 months old

value: Saline


title: R02_W55

city: Urbana

first: Lila

middle: O.

last: Vodkin

state: IL

address: 1201 W. Gregory Dr.

department: Crop Sciences

institute: University of Illinois

description: Raw data not available for this record.

data_processing:
Standard Illumina pipeline including CASSAVA
Sequenced reads were aligned to 56,044 gene models, build Wm82.a2.v1 DNA soybean cDNA gene models determined by the Soybean Genome Project (Schmutz et al. 2010) using Bowtie (Langmead et al. 2009). Bowtie parameters allowed up to three mismatches and up to 25 alignments per read.
Reads per kilobase of gene model per million mapped reads (RPKM) were calculated according to Mortazavi et al. (2008).
Genome_build: Wm82.a2.v1
Supplementary_files_format_and_content: Excel file includes RPKM values for each Sample

organism: Glycine max

source_name: seed coat dissected from 25-50 mg immature seed

growth_protocol: Plants were grown in optimal greenhouse conditions. Tissues were harvested at stated mg fresh weight, length (for leaves), or days after planting (for roots), or at maturity. Whole seeds were dissected by hand into cotyledons,  seed coats, and embryo axis for some samples.

extract_protocol:
Total RNA was extracted from freeze-dried tissues using phenol:chloroform and a lithium chloride precipitation (Gonzalez and Vodkin 2007). Sequencing was performed by the Keck Center (University of Illinois) using an Illumina Genome Analyzer II or an Illumina HiSeq 2000.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cultivar/genotype

value: Williams 55, i mutation, PI547881

value: immature seed coat

tag: Stage


title: Old_Vehicle_Rep1

description: GeneCounts.xlsx


title: WC7


title: R15_RT1

source_name: 1-1.5 inch rolled (furled) trifoliates from adult plants

value: Williams (PI548631)

value: leaves

value: Adult


title: Old_Ouabain_Rep6

description: GeneCounts.xlsx

source_name: Liver of old mice treated with Ouabain

value: Female

value: Ouabain


title: wt1


title: LB05-0017L

value: Lung

value: Male

value: IB

value: No

value: Dead


title: WC6

value: heart

value: ventricle


title: WC5


title: Old_Ouabain_Rep5

description: GeneCounts.xlsx

value: Liver


title: female_sort_invivo4

source_name: sorted Cryptosporidium parvum infected mouse intestinal epithelial cells

growth_protocol: IFNg-/- mice were infected with 200,000 oocysts per mouse for 2 days

tag: oocyst source

value: Sterling Farms, University of Arizona

tag: parasite strain

value: COWP1 tdTomato

value: in vivo

value: Mus musculus intestinal epithelial cells


title: mut8

value: vegfc(hy-/-);vegfd(-/-)


title: R01_W43

description: Raw data not available for this record.

value: Williams (PI548631)

value: immature seed coat


title: WC4


title: Old_Ouabain_Rep4

description: GeneCounts.xlsx

value: 24 months old

value: Female


title: WC3


title: Il1a-/- DCa1

city: Seattle

first: James

middle: William

last: MacDonald

state: WA

address: 4225 Roosevelt Way NE

department: Environmental and Occupational Health Sciences

institute: University of Washington

description: myeloid dendritic cells

hyb_protocol: The standard hybridization protocol was used as recommended by Affymterix.

scan_protocol: GeneChips were scanned using the Affymetrix GeneArray Scanner 3000 through the University of Washington Functional Genomics Laboratory in the Center for Ecogenetics and Environmental Health (http://depts.washington.edu/ceeh/ServiceCores/FC1/FC1.html).

data_processing: Bioconductor software, RMA normalization log2

label: biotin

source_name: Mouse lung mononuclear cells

label_protocol: For microarray hybridization, RNA was processed for hybridization to Affymetrix Mouse Gene 1.0 ST Array through a core facility in the Functional Genomics Laboratory in the Center for Ecogenetics and Environmental Health at the University of Washington according to the manufacturer's instructions.

extract_protocol: Total RNA was extracted from myeloid dendritic cells with TriZol reagent (Invitrogen) according to a standard protocol.  RNA integrity of individual samples was confirmed with an Agilent 2100 Bioanalyzer.   CD11c+ cells were purified to 97% purify from lung mononuclear cells by two consecutive rounds of magnetic cell separation using CD11c-antibody-labled magnetic beads and LS columns for positive cell selection as per manufacturer’s protocol (Miltenyi Biotech). The purity of CD11c+ cells was verified by flow cytometry prior to pooling CD11c+ cells from three mice for total RNA isolation. Two pools of CD11c+ cells from three mice each were prepared for WT and Il1a-/- experimental groups.

value: wild-type

value: CDC11c+ lung mononuclear cells

tag: genetic background


title: Wild-type DCwt1

description: myeloid dendritic cells


title: Wild-type DCwt2

description: myeloid dendritic cells


title: female_sort_invivo3

tag: in vitro/in vivo

tag: host


title: Il1a-/- DCa2

description: myeloid dendritic cells


title: Old_Ouabain_Rep3

description: GeneCounts.xlsx

tag: Sex

tag: treatment

value: Ouabain


title: female_sort_invivo2


title: mut6

tag: chamber

tag: genotype


title: WC1

tag: tissue


title: wt2


title: MC6


title: HK_DOX_WCE_1

city: Houston

first: Charles

middle: Yang

last: Lin

state: TX

address: 1 Baylor Plaza

department: Molecular and Human Genetics

institute: Baylor College of Medicine

description: Whole cell extract input control in cells in cells treated with doxycycline (see treatment)

data_processing:
All single-end ChIPmentation datasets were aligned using Bowtie2 (version 2.2.8) to build version NCBI37/HG19.
Alignments were performed using all default parameters. We used the MACS version 1.4.2 (Model based analysis of ChIP-seq) (Zhang et al., 2008) peak finding algorithm to identify regions of ChIP-seq enrichment over background. A p-value threshold of enrichment of 1e-9 was used for all datasets.
Genome_build: hg19
Supplementary_files_format_and_content: Processed ChIP-Seq data files are in wiggle format from MACS output

source_name: Human primary keratinocytes

growth_protocol: All human cells were purchased from approved commercial suppliers who has obtained the necessary patient consent for skin donation for research purposes. The cells were obtained and handled in compliance with the Swiss Human Research Act. Normal human neonatal epidermal keratinocyte progenitor cells (nHPEKs, Lot #EB1110044 (pooled)) and adult normal human epidermal keratinocyte progenitor cells (aHPEKs Lots #ES1303277, and #MC1511045 (both abdominal)) were purchased from CELLnTEC (Bern, Switzerland) at Passage 2 (P2). HPEKs were expanded until Passage 4 (P4) and pellets of 1x106 cells were cryopreserved in liquid nitrogen for later use. HPEKs were cultured from P4 by seeding at an initial density of 5.3x104 cells/cm² using CnT-Prime media (CELLnTEC, #CnT-PR). When cells reached 70-85% confluency, they were detached from the cell culture dish using Accutase Cell Detachment Solution (CELLnTEC). For serial passaging experiments, aHPEKs were grown and passaged about 13 times. aHPEKs were collected for various assays and were considered as “HSCP-HKs” when fast-dividing (between Passages 7-9) whereas aHPEKs that were slow-dividing (Passages 15-17) were considered as “LSCP-HKs”.

extract_protocol:
Chromatin immunoprecipitations were performed using the ChIPmentation protocol as described (Schmidl et al., 2015) with minor changes. The cells were trypsinized and 1 million cells were used for each replicate. Cells were fixed by adding formaldehyde to a final concentration of 0.8% in a crosslinking buffer (0.1M NaCl, 1mM EDTA, 0.5mM EGTA, 50mM Hepes, ph8.0) and incubated for 5 min on a rocker at 4°C. The fixation was terminated by incubating with 2.5 M Glycine for 5 min on a rocker at RT for 5 min. The cells were washed in ice cold PBS and resuspended in Hypotonic buffer (20mM Tris-HCl, 10mM NaCl, 3mM MgCl2) supplemented with Protease Inhibitors and 0.5mM PMSF and incubated on ice for 10 min. NP-40 (final 0.5%) was added to the mixture and vortexed for 20 sec. The nuclei were pelleted by centrifugation at 14000 rpm for 30 sec at 4°C. The pellet was resuspended in 1ml of 1X Wash Buffer C (truChIP Chromatin Shearing Kit) and incubated at 4°C for 10 min in a rocker. The nuclei were pelleted by centrifugation at 1700g for 5 min at 4°C and subsequently resuspended in shearing buffer D3 (truChIP Chromatin Shearing Kit) with Protease Inhibitors and 0.5mM PMSF, vortexed thrice and incubated at 4°C for 15 min in a rocker. Nuclear pellets  were collected by centrifugation at 2000g for 5 mins at 4°C and resuspended in 130µl of TE (10mM Tris and 1mM EDTA) with 0.1% SDS and DNA was sheared at 4°C using a covaris LE220 sonicator (Covaris, Woburn, MA) for 4 minutes with 200 cycles per burst, 15% duty factor and a peak incident power of 300. Sonicated lysates were supplemented with salts and detergents to a final concentration of 1% Triton X-100, 150mM NaCl and 0.1% Na-deoxycholate. The chromatin was then cleared by centrifugation at 10,000g for 10 min and incubated with 5ul of Dynabeads™ Protein A (Thermo Fisher Scientific, Waltham, MA) for one hour to preclear the lysate. After collecting the input, the supernatant was incubated with end-over-end rotation overnight at 4°C with Dynabeads™ Protein A magnetic beads prebound with antibody. The antibody was bound to the beads by incubating the beads with the antibody in 200µl of bead binding buffer (TE, 0.2% Igepal) in a rotor at 4°C for 2 hours. Beads were washed once with low salt wash buffer (250mM NaCl, 10mM Tris-HCl, 1mM EDTA, 0.1% SDS, 0.1% Na-deoxycholate, 0.1% Triton X-100), once with wash buffer containing 500mM NaCl, once  with LiCl wash buffer (20mM Tris pH 8.0, 1mM EDTA, 250mM LiCl, 0.5% NP-40, 0.5% Na-deoxycholate), once with TE,0.1% Triton X-100 and twice with ice cold 10mM Tris-HCl. The beads and the input were then incubated at 37°C for 12 min with the Tagment DNA enzyme (Illumina, San Diego, CA), following tagmentation, the beads were washed twice with the low salt wash buffer and DNA was eluted TE Buffer, 250mM NaCl and 0.3% SDS. Cross-links were reversed by incubation first at 55°C and continued with protein digestion with the addition of Proteinase K for 10 hours at 64°C. DNA was purified using DNA Clean & Concentrator-5 (Zymo Research, Irvine, CA).
Library preparations were performed as described with minor changes (Buenrostro et al., 2015). The amplified libraries were cleaned, and size selected using AMPure XP (Beckman Coulter, Indianapolis, IN).
The libraries were sequenced using NextSeq® 500/550 High Output Kit v2 (75 cycles) (Illumina) in a NextSeq 550 (Illumina).

treatment_protocol: For doxycycline treated cells, cells were grown as above and treated with 1μg/ml Doxycycline for 3 days plus 2 days with 2μg/ml Doxycycline to induce the HA tagged-IRF2 overexpression

tag: cell type

value: Human primary keratinocytes engineered with stable IRF2 shRNA knockdown and a doxycyline inducible IRF2-3xHA allele

tag: input

value: Cells were treated with 1μg/ml Doxycycline for 3 days plus 2 days with 2μg/ml Doxycycline

tag: barcode

value: GTGTGGTG

tag: antibody

tag: antibody maker

tag: antibody catalog number


title: female_sort_invitro3

source_name: sorted Cryptosporidium parvum infected HCT8 cells

growth_protocol: 80% confluent monolayers of HCT-8 cells in 6-well plates were infected with 300,000 oocysts per well for 48 hours at 5% CO2 and 37 ℃

value: in vitro

value: Human cell line HCT8


title: female_sort_invitro2

value: Sterling Farms, University of Arizona


title: Old_Vehicle_Rep5

description: GeneCounts.xlsx

value: Liver

tag: age

value: Saline


title: 7_WTB2_ChIP_S87_Oct30

city: Toronto

first: Alejandro

last: Saettone

state: Ontario

address: 686 Bay Street

department: Genetics & Genome Biology

institute: The Hospital for Sick Children

description:
FINAL.table.8_WT2_Input_S88_R1_001-7_WTB2_ChIP_S87_R1_001--SORTED
tableIGR--FINAL.table.8_WT2_Input_S88_R1_001-7_WTB2_ChIP_S87_R1_001_INPUTs-IPs_20190119-200459

data_processing:
ChIP-seq reads were assessed for quality using fastqc
ChIP-Seq reads were aligned using BWA and SAMtools
RACS: Reads calling from the genetic and intergenic regions were respectively counted and extracted
Genome_build: T_thermophila_June2014_assembly.fasta (http://ciliate.org/index.php/home/downloads)
Supplementary_files_format_and_content: csv files containing reads were generated using RACS

organism: Tetrahymena thermophila

source_name: Cells grown in SPP liquid media

growth_protocol: 30C; 100rpm; SPP liquid media

extract_protocol:
Lysates were clarified from sonicated nuclei and incubated with ANTI-FLAG® M2 Affinity Gel (Sigma)
Illumina's  TruSeq ChIP Sample Preparation Kit (cat# IP-202-1012)

tag: strain

tag: developmental stage

value: vegetative growth

tag: chip antibody

value: ANTI-FLAG M2 Affinity Gel (Sigma) A2220


title: 8_WT2_Input_S88_Oct30


title: MC5

value: heart

value: ventricle

value: vegfc(hy-/-);vegfd(-/-)


title: female_sort_invivo1

tag: oocyst source

tag: parasite strain

value: COWP1 tdTomato

tag: in vitro/in vivo

value: in vivo

value: Mus musculus intestinal epithelial cells


title: MC4


title: MC3


title: 6_WT1_Input_S86_Oct30

description:
FINAL.table.6_WT1_Input_S86_R1_001-5_WTB1_ChIP_S85_R1_001--SORTED
tableIGR--FINAL.table.6_WT1_Input_S86_R1_001-5_WTB1_ChIP_S85_R1_001_INPUTs-IPs_20190119-200453


title: HK_DOX_WCE_2

tag: treatment

value: TGGGTTTC


title: 5_WTB1_ChIP_S85_Oct30


title: HK_DOX_HA_1

description: HA ChIPmentation in cells treated with doxycyline (see treatment)

value: Human primary keratinocytes engineered with stable IRF2 shRNA knockdown and a doxycyline inducible IRF2-3xHA allele

value: ACCACTGT

value: anti-HA

value: cell signaling


title: female_sort_invitro4

value: in vitro

tag: host

value: Human cell line HCT8


title: female_sort_invitro1

value: Sterling Farms, University of Arizona


title: MC2

tag: chamber

tag: genotype


title: asexual_sort_invitro4

growth_protocol: 80% confluent monolayers of HCT-8 cells in 6-well plates were infected with 300,000 oocysts per well for 24 hours at 5% CO2 and 37 ℃

value: Bunchgrass Farms

value: eno tdNeon


title: 8_WT2_Input_S8_Nov09

description:
FINAL.table.8_WT2_Input_S8_R1_001-7_WTB2_ChIP_S7_R1_001--SORTED
tableIGR--FINAL.table.8_WT2_Input_S8_R1_001-7_WTB2_ChIP_S7_R1_001_INPUTs-IPs_20190119-200501

value: vegetative growth


title: 7_WTB2_ChIP_S7_Nov09

value: ANTI-FLAG M2 Affinity Gel (Sigma) A2220


title: HK_CTL_WCE_2

description: Whole cell extract input control in cells in cells without doxycycline

tag: cell type

value: no treatment

value: GAGGGGTT


title: asexual_sort_invitro2


title: asexual_sort_invitro1


title: Old_Ouabain_Rep2

description: GeneCounts.xlsx

tag: tissue

value: Liver

value: 24 months old

tag: Sex

value: Female

value: Ouabain


title: mRNA 24h-M3

city: Athens

first: Robert

middle: J

last: Schmitz

state: GA

address: B416 Davison Life Sciences

department: Genetics

institute: University of Georgia

data_processing:
RNA-seq: was performed using TopHat v2.1.0 and Cufflinks v2.2.1
Genome_build: https://www.ncbi.nlm.nih.gov/assembly/GCA_000004515.4
Supplementary_files_format_and_content: FPKM

source_name: root hair cells_288 hrs after sowing

growth_protocol: The soybean plants were growth with an ultrasound aeroponic system (Qiao et al., 2013) under controlled conditions.

extract_protocol: Truseq RNA-seq v2 (Illumina)

value: willam 82

value: 288 hours after sowing

value: root hair cells


title: mut9

value: heart

value: ventricle

value: vegfc(hy-/-);vegfd(-/-)


title: 6_WT1_Input_S6_Nov09

description:
FINAL.table.6_WT1_Input_S6_R1_001-5_WTB1_ChIP_S5_R1_001--SORTED
tableIGR--FINAL.table.6_WT1_Input_S6_R1_001-5_WTB1_ChIP_S5_R1_001_INPUTs-IPs_20190119-200456


title: mRNA 12h-M3

source_name: root hair cells_276 hrs after sowing

value: 276 hours after sowing


title: HK_CTL_HA_2

description: HA ChIPmentation

value: Human primary keratinocytes engineered with stable IRF2 shRNA knockdown and a doxycyline inducible IRF2-3xHA allele

tag: input

tag: barcode

value: GTAGAGGA

tag: antibody

value: anti-HA

value: cell signaling


title: HK_CTL_WCE_1

value: no treatment

value: TGCTGGGT

tag: antibody maker

tag: antibody catalog number


title: young_CD31_2

status: Public on Sep 02 2019

city: Ulm

first: Johannes

last: Pospiech

address: Albert-Einstein Allee 11

country: Germany

institute: Ulm University

data_processing:
Read filtering, alignment, barcode counting and UMI counting was performed using the Cellranger pipeline of 10X Genomics (version 2.1.1; cellranger count with default settings).
Single cell data were filtered based on total number of UMIs (>= 1000), total number of detected genes (>= 1000, at least one read) and percentage of mitochondrial reads (< 10%) using the scater toolkit (version 1.10.1, R 3.5.2).
Counts were normalized using the calcNormFunction of the edgeR package (version 3.24.3, R 3.5.2) using the "upperquartile" method. Highly variable genes were selected from log-transformed and normalized data using the M3Drop package (version 1.8.1, R 3.5.2).
Differential expression analysis was performed on hypervariable genes using DESeq2 (version 1.22.2, R 3.5.2). The analysis was performed on raw counts and the likelihood ratio test with the experimental batches as covariables was used. Dispersions were estimated using a local fit and size factors were estimated using the “poscounts” setting. "minmu" was set to "1e-6" and "minReplicatesForReplace" was set to "Inf".
Genome_build: mm10
Supplementary_files_format_and_content: Tab delimited txt files contain raw feature counts for all detected barcodes and all genes as obtained by the Cellranger pipeline. Row names show ENSEMBL gene IDs, column names show barcodes.

source_name: BM CD45-CD31+ endothelial cells_young

extract_protocol:
Young and aged bone marrow CD45- CD31 endothelial cells were sorted from endosteal preparations and frozen in IMDM + 20% FCS + 10% DMSO.
Endothelial cells were thawed, washed once in warm PBS, and subjected immediately to encapsulation in oil droplets using the Chromium system by 10X Genomics. cDNA synthesis and library preparation were done according to the manufacturer’s instructions for 3’ end counting. PCR cycles for both cDNA synthesis and amplification were adjusted for each sample individually to the number of cells loaded cDNA yield respectively.

tag: strain

value: Nes-GFP

tag: sample group

value: young

tag: age

value: 10-12 weeks

value: BM CD45-CD31+ endothelial cells

tag: replicate


title: young_CD31_3


title: 5_WTB1_ChIP_S5_Nov09

tag: developmental stage

value: vegetative growth

tag: chip antibody

value: ANTI-FLAG M2 Affinity Gel (Sigma) A2220


title: young_CD31_1


title: aged_CD31_2

source_name: BM CD45-CD31+ endothelial cells_aged

value: aged

value: > 20 months


title: HK_CTL_HA_1

description: HA ChIPmentation in cells without doxycyline

tag: treatment

value: AAGAGGCA


title: Vehi_wounded_4 [s14]

city: Bethesda

first: Maria

middle: Irene

last: Morasso

state: Maryland

address: Bldg 50

institute: NIAMS NIH

data_processing:
BCL Conversion and Demultiplex bcl2fastq
Map to mm10 using Tophat 2.1.0
Calculate RPKM using Partek GS 6.6
ANOVA comparison using Partek GS 6.6
Genome_build: mm10
Supplementary_files_format_and_content: Excel, RPKM and ANOVA results

source_name: Veh wounded_Skin

extract_protocol:
Skin tissue was removed and added in RNA-later solution, and RNA was harvested using Trizol reagent and Rnesay Mini Kit (QIAGEN).
cDNA libraries were generated using NEBnext and NuGen kits. Sequencing was performed on the HiSeq3000

treatment_protocol: 5 mg/ml of tamoxifen dissolved in ethanol 200 µul or same volume of ethanol (as a control) was topically applied

tag: genotype/variation

value: Skin

tag: wound

value: Wounded

value: Vehicle


title: Vehi_wounded_2 [s10]


title: Vehi_wounded_1 [s08]


title: Vehi_wounded_3 [s12]


title: Tam_wounded_4 [s15]

source_name: Tam wounded_Skin

value: Tamoxifen


title: Tam_wounded_3 [s06]


title: aged_CD31_3

tag: cell type


title: Tam_wounded_2 [s04]

tag: tissue


title: Vehi_unwounded_4 [s13]

source_name: Veh unwounded_Skin

value: Unwounded


title: Vehi_unwounded_1 [s07]


title: Vehi_unwounded_3 [s11]


title: Tam_unwounded_4 [s05]

source_name: Tam unwounded_Skin


title: Tam_unwounded_3 [s03]


title: cDC2_CD5-CD163+CD14+_Systemic sclerosis_R6861

city: Singapore

first: Vipin

last: Narang

address: Immunos #04-01, 8A Biomedical Grove, Singapore-138648

country: Singapore

institute: Singapore Immunology Network (SIgN)

data_processing:
Paired-end reads obtained from RNA sequencing were mapped to human transcript sequences obtained from Gencode version 28 (PMID: 22955987) using Salmon version 0.9.1 (PMID: 28263959).
Transcript abundances quantified by Salmon were summarized to gene-level counts and normalized gene-level abundances in transcript per million (TPM) units using the tximport R/Bioconductor package (version 1.2.0).
Genome_build: GRCh38
Supplementary_files_format_and_content: The processed data files are in in tab delimited text format and contain (i) a matrix of gene-level counts, and (ii) a matrix of normalized gene-level abundances in transcript per million (TPM) units.

source_name: FACS sorted from PBMC

extract_protocol:
PBMCs were isolated from healthy subjects and patients with autoimmune disease and cDC2 subsets were defined by FACS.
cDNA libraries were prepared from 100 cells using the SMARTSeq v2 protocol (Picelli et al., 2014) with the following modifications: (i) 1 mg/mL BSA Lysis buffer (Ambion Thermo Fisher Scientific, Waltham, MA, USA); (ii) addition of 20 mM TSO; and (iii) 200 pg cDNA with 1/5 reaction of Illumina Nextera XT kit (Illumina, San Diego, CA, USA). The length distribution of the cDNA libraries was monitored using a DNA High Sensitivity Reagent Kit on the Perkin Elmer Labchip (Perkin Elmer, Waltham, MA, USA). All samples were subjected to an indexed paired-end sequencing run of 2x151 cycles on an Illumina HiSeq 4000 system (Illumina, San Diego, CA, USA), with 23- 24 samples/lane.

tag: disease state

value: Systemic sclerosis


title: cDC2_CD5-CD163+CD14+_Systemic sclerosis_R6853


title: cDC2_CD5-CD163+CD14+_SLE_R6797

value: SLE


title: cDC2_CD5-CD163+CD14+_SLE_R6789


title: cDC2_CD5-CD163+CD14-_Systemic sclerosis_R6886


title: cDC2_CD5-CD163+CD14-_Systemic sclerosis_R6878


title: cDC2_CD5-CD163+CD14-_Systemic sclerosis_R6870


title: 4C-seq, rep1

city: Los Angeles

first: Wange

last: Lu

state: CA

address: 1425 San Pablo Street, BCC 409

institute: University of Southern California

data_processing:
RIP-seq reads were aligned to the mm9 genome assembly using TopHat2 version 2.1.0. Duplicates were removed using Picard MarkDuplicates version 1.141. HTSeq version 0.6.0 was used to quantitate the filtered reads mapped to each gene. Read counts were further normalized and compared between conditions using DESeq2 version 1.14.1.
4C-seq reads were aligned to the mm9 genome assembly using BWA version 0.7.15.
Adaptor sequences were trimmed off from raw reads using Trim Galore version 0.4.2. Read pairs with central overlap were reconstructed into single reads using FLASH version 1.2.11. In silico resctriction enzyme digestion was performed to identify junctions formed by distally interacting sub-fragment and "viewpoint" sub-fragment. Sub-fragments were aligned to the mm9 genome assembly using bowtie2 version 2.2.9.
RNA-seq reads were aligned to the mm9 genome assembly using TopHat2 version 2.1.0. HTSeq version 0.6.0 was used to quantitate the filtered reads mapped to each gene. Read counts were further normalized and compared between conditions using DESeq2 version 1.14.1.
Genome_build: mm9
Supplementary_files_format_and_content: For RIP-seq and capture-C, bedgraph files were generated with the score in the 4th column representing intensity. For 4C-seq, bed files were generated including significant interacting regions for each replicate. For RNA-seq, txt files were generated including regularized log transformed counts over the gene*sample matrix.

source_name: ESC

growth_protocol: Mouse ESCs were cultured in growth medium consisting of 85% GMEM (Gibico), 15% FBS (Hyclone), 2 mM L-glutamine, 5000 units/ml penicillin and streptomycin, 0.1 mM non-essential amino acids (Invitrogen), 0.1 mM 2-mercaptoethanol (Sigma), 1 mM Sodium Pyruvate (Thermo), and 1000 units/ml LIF (ESGRO).

extract_protocol:
RIP-seq: RIP library was constructed with EZ-Magna Nuclear RIP™ (Cross-Linked) Nuclear RNA-Binding Protein Immunoprecipitation KitMillipore Kit (Millipore), using antibodies of Klf4 (R&D) and FLAG(Sigma). Libraries were then constructed and indexed with NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® (NEB). The size and concentration of library was examined with the DNA bioanalyzer.  4C-seq: 10e7 cells were resuspended and fixed in 2% formaldehyde in culture medium for 10 min at room temperature and then quenched by 0.125M ice-cold glycine. Cells were centrifuged for 8 min at 320 g at 4°C and washed once in 10 ml of cold PBS. All the supernatant was removed and then the cell pellet was resuspended in 5 ml cold lysis buffer (10 mM Tris, 10 mM NaCl, 5 mM MgCl2, 0.1 mM EGTA, 1×protease inhibitors, 0.2% NP-40) and incubated for 10 min on ice. Cells were centrifuged for 5 min at 600 g at 4°C and the supernatant was removed. The cell pellet was resuspended once with 10 ml of cold PBS. After centrifugation for 5 min at 600g at 4°C, the supernatant was discarded. The cell pellet was resuspended in 440 μl Milli-Q, 60 μl of 10*RE buffer and 7.5 μl of 20% SDS and incubated for 1 h at 37°C while shaking at 900 RPM. 50 μl of 20% Triton X-100 was added followed by incubation for 1 h at 37°C while shaking at 900 RPM. 400 U restriction enzyme HindIII (NEB) was added followed by incubation o/n at 37°C while shaking at 900 RPM. Another 200 U DpnII was added followed by incubation for 6 hours at 37°C while shaking at 900 RPM. Then 40 μl of 20% SDS was added followed by incubation for 20 min at 65°C to inactivate the enzyme. The samples were transferred (~600 μl) to a 50-ml Falcon tube with addition of 700 μl of 10×ligation buffer and 5.7 ml Milli-Q to 7 ml. 375 μl of 20% Triton X-100 was added followed by incubation for 1 h at 37°C while shaking gently. 100U T4 ligase (Clontech) was added followed by incubation o/n at 4°C. 15 μl Prot K (20 mg/ml, 300 μg) was added and samples were de-crosslinked o/n at 65°C. 30 μl RNase A (10 mg/ml, 300μg) was added followed by incubation for 45 min at 37°C. DNA was then extracted with phenol–chloroform and 3C library was quantified by NanoDrop. Then the 3C library was digested in 500 μl reaction with 50 U DpnII followed by incubation o/n at 37°C. Then the library was ligated in 14 ml reaction with 100 U Ligase at 16 C o/n followed by purification with phenol-chloroform. The samples were purified with the QIAquick PCR purification kit (Qiagen) and quantified with NanoDrop. 3.2 μg 4C templates were pre-mixed with 160 μl of 5×PCR buffer, 40 μl dNTP (10 mM), 19.2 μl forward primer (50 uM), 19.2 μl Reverse primer (50 uM), 11.2 μl Expand Long Template Polymerase (Roche), and ddH2O to 800 μl in total. The library was separated into 16 reactions of 50 μl for each. Then PCR was conducted with the program: 2 min 94°C, 10 sec 94°C, 1 min 55°C, 3 min 68°C, 29 repeats, 5 min 68°C, and 4°C forever. The samples were purified with QIAquick PCR purification kit and run on Agarose-gel (2%) for 10 min. The gel excision (150 bp-800 bp) and extraction were performed with QIAquick Gel Extraction Kit (Qiagen). Then the 4C library was purified with QIAquick PCR purification kit. The quality and concentration of 4C library were examined with bio-analyzer.   capture-C: 10e7 cells were resuspended and fixed in 2% formaldehyde in culture medium for 10 min at room temperature and then quenched by 0.125M ice-cold glycine. Cells were centrifuged for 8 min at 320 g at 4°C and washed once in 10 ml of cold PBS. All the supernatant was removed and then the cell pellet was resuspended in 5 ml cold lysis buffer (10 mM Tris, 10 mM NaCl, 5 mM MgCl2, 0.1 mM EGTA, 1×protease inhibitors, 0.2% NP-40) and incubated for 10 min on ice. Cells were centrifuged for 5 min at 600 g at 4°C and the supernatant was removed. The cell pellet was resuspended once with 10 ml of cold PBS. After centrifugation for 5 min at 600g at 4°C, the supernatant was discarded. The cell pellet was resuspended in 440 μl Milli-Q, 60 μl of 10*RE buffer and 7.5 μl of 20% SDS and incubated for 1 h at 37°C while shaking at 900 RPM. 50 μl of 20% Triton X-100 was added followed by incubation for 1 h at 37°C while shaking at 900 RPM. 400 U restriction enzyme DpnII (NEB) was added followed by incubation o/n at 37°C while shaking at 900 RPM. Another 200 U DpnII was added followed by incubation for 6 hours at 37°C while shaking at 900 RPM. Then 40 μl of 20% SDS was added followed by incubation for 20 min at 65°C to inactivate the enzyme. The samples were transferred (~600 μl) to a 50-ml Falcon tube with addition of 700 μl of 10×ligation buffer and 5.7 ml Milli-Q to 7 ml. 375 μl of 20% Triton X-100 was added followed by incubation for 1 h at 37°C while shaking gently. 100U T4 ligase (Clontech) was added followed by incubation o/n at 4°C. 15 μl Prot K (20 mg/ml, 300 μg) was added and samples were de-crosslinked o/n at 65°C. 30 μl RNase A (10 mg/ml, 300μg) was added followed by incubation for 45 min at 37°C. DNA was then extracted with phenol–chloroform and 3C library was quantified by NanoDrop. The 3C library was then sonicated to 100-300bp. The library was constructed and indexed with NEBNext DNA Library Prep Master Mix Set for Illumina (NEB). Then 1 μg from each indexed library was pooled together and then captured with two biotin-labeled probes using the SeqCap EZ Hybridization and Wash Kit (Roche). After amplification with P5&P7 primers, a second capture step was performed with the same probes. Then Capture-C library was amplified with P5&P7 primers followed by the purification with AMPure XP system (Beckman). The size and concentration of library were examined with DNA bio-analyzer.  RNA-seq: RNA library was constructed with the TruSeq Stranded Total RNA with Ribo-Zero Human/Mouse/Rat (Illumina).
RIP-seq, 4C-seq, capture-C, RNA-seq


title: cDC2_CD5-CD163+CD14-_Systemic sclerosis_R6862


title: Vehi_unwounded_2 [s09]


title: Tam_wounded_1 [s02]


title: nuRNA_KA48h_rep2

description:
total nuclearRNA
Single-end
processed data file:
nuRNA_KA48h.bw

data_processing:
All sequenced datasets adapters were trimmed using cutadapt v1.18 (Martin, 2011) and aligned to mm10. Only reads with mapq > 30 and mapping to nuclear chromosomes were used for the posterior analysis. Data was processed with the extensive use of custom scripts, and Samtools (v1.9) (Li et al., 2009), bedtools v2.26.0 (Quinlan and Hall, 2010) and DeepTools v3.1.0 (Ramirez et al., 2016). RNA-seq data: Reads were aligned with HISAT2 v2.1.0 (Kim et al., 2015). ATAC-seq data: Reads were aligned with bowtie2 v2.2.6 (Langmead and Salzberg, 2012). Duplicated reads were removed with Picardtools and only paired reads were used for the posterior analysis. ChIP-seq data: Reads were aligned with bowtie2 v2.2.6 (Langmead and Salzberg, 2012). HiC data: Hi-C datasets were processed using the Juicer pipeline (Durand et al., 2016) to align reads, filter duplicates, perform matrix normalizations, and obtain the eigenvector. Reads with a mapping quality >= 30 and binned at 25 kb were used in all downstream analyses.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files from whole genome alignments normalized to RPM (read per million sequenced reads).

source_name: Hippocampal excitatory neurons

extract_protocol:
Hippocampi were micro-dissected after cervical dislocation, washed in ice-cold PBS and pooled together, when fixation was needed 1% FA was used. TRAP immunoprecipitation followed the original protocol by (Heiman et al., 2014) with small changes. Nuclei were isolated using our improved FANS protocol for SUN1-GFP+ cells, in case NE condition nuclei were stained against FOS. Extensive description of protocols indicated in Supplemental Experimental Procedures.
For riboRNA and nuRNA, extraction was re-suspended in RLT buffer for purification with RNeasy Micro kit (Qiagen 74004). Truseq libraries were prepared from ribo-depleted total RNA in the case of nuRNA-seq and from polyA-selected mRNA in the case of riboRNA-seq. ATAC-seq experiments were conducted as the original protocol (Buenrostro et al., 2013), libraries were purified with MinElute PCR purification kit (Qiagen 28004). ChIP-seq was conducted as previously described (Lopez-Atalaya et al., 2013) using the anti-H3K4me3 (Millipore 07-473), anti-CBP (sc583x) and anti-RNAPII (sc901x). In situ Hi-C were conducted as the original protocol (Rao et al., 2014), libraries were prepared with TruSeq.

value: Adult Forebrain (hippocampus)

value: 3-6 month

tag: gender

value: male


title: cDC2_CD5-CD163+CD14-_SLE_R6798


title: Tam_unwounded_2 [s01]


title: 4C-seq, rep2


title: cDC2_CD5-CD163+CD14-_SLE_R6790


title: cDC2_CD5-CD163+CD14-_SLE_R6750


title: cDC2_CD5-CD163+CD14-_NA_R6822


title: cDC2_CD5-CD163+CD14-_SLE_R6758


title: cDC2_CD5-CD163+CD14-_NA_R6838


title: cDC2_CD5-CD163+CD14-_SLE_R6782


title: cDC2_CD5-CD163+CD14-_SLE_R6774


title: cDC2_CD5-CD163+CD14-_SLE_R6766


title: cDC2_CD5-CD163+CD14-_NA_R6814


title: cDC2_CD5-CD163+CD14-_Control_R6742

value: Healthy


title: cDC2_CD5-CD163+CD14-_Control_R6718


title: cDC2_CD5-CD163+CD14-_Control_R6726


title: cDC2_CD5-CD163+CD14-_Systemic sclerosis_R6854


title: cDC2_CD5-CD163+CD14+_NA_R6837


title: cDC2_CD5-CD163+CD14-_Control_R6710


title: cDC2_CD5-CD163-_SLE_R6754


title: cDC2_CD5-CD163-_Control_R6714


title: cDC2_CD5+_Systemic sclerosis_R6879


title: cDC2_CD5+_Systemic sclerosis_R6863


title: cDC2_CD5-CD163-_Control_R6706


title: cDC2_CD5+_Systemic sclerosis_R6887


title: cDC2_CD5+_Systemic sclerosis_R6855


title: cDC2_CD5+_SLE_R6791


title: cDC2_CD5+_SLE_R6799


title: cDC2_CD5-CD163+CD14-_Control_R6734


title: cDC2_CD5+_SLE_R6775


title: cDC2_CD5+_SLE_R6783


title: cDC2_CD5+_NA_R6839


title: cDC2_CD5+_NA_R6831


title: cDC2_CD5+_SLE_R6751


title: cDC2_CD5+_SLE_R6759


title: cDC2_CD5+_SLE_R6767


title: cDC2_CD5+_NA_R6823


title: cDC2_CD5+_Control_R6743


title: Old_Ouabain_Rep1

city: London

first: Gopuraja

last: Dharmalingam

address: Faculty of Medicine, Imperial College, Hammersmith Hospital Campus

institute: MRC London Institute of Medical Sciences

description: GeneCounts.xlsx

source_name: Liver of old mice treated with Ouabain

value: Liver

value: 24 months old

tag: Sex

value: Female

value: Ouabain


title: cDC2_CD5+_NA_R6815


title: cDC2_CD5+_Control_R6735


title: WT-vein-2

first: Hailing

last: Zi

address: Chenhua road3888

institute: Shanghai center for plant stress biology

data_processing:
Illumina Casava1.7 software used for basecalling.
Raw reads were first subject to 3’ adapter removal and quality filtering (Q > 17 and length >= 25 bp). Clean reads were mapped to the Cucumber genome sequence (http://cucumber.genomics.org.cn, v2i) using TopHat. Read counts of each gene were summarized by the HTSeq-count. Lowly expressed genes were removed and only genes with an expression level of at least 1 RPM (readss per million) in at least two samples were kept for further analysis.
Please note that [1] the identifiers in the processed data file is searchable at: http://www.icugi.org/cgi-bin/ICuGI/genome/home.cgi?ver=2&organism=cucumber&cultivar=Chinese-long [2] the "M" is changed to "G", and the isoform information has been deleted. For example,  the "Csa3G002400"  correponds to "Csa3M002400.1" in the website.
Genome_build: v2i (http://cucumber.genomics.org.cn)
Supplementary_files_format_and_content: Tab-delimited text file include RPM(Reads per Million) values for 8 Samples .

organism: Cucumis sativus

source_name: WT-vein

growth_protocol: Cucumber (Cucumis stativus L.) inbred line R1461, a northern China type cucumber with dark green fruits similar to the sequenced Chinese Long 9930, was used in this study. The cucumber seeds were germinated in 28℃ in dark, and grown in a growth chamber under 16h/8h and 25ºC/18ºC in day/night until two true-leaf stage, then the cucumber seedlings were transferred to a greenhouse under standard conditions in the experimental field of China Agricultural University in Beijing. Water management and pest control were performed according to standard protocols. The Arabidopsis seeds of ind-2 mutant were obtained from Lars Østergaard (Girin et al., 2011). The Arabidopsis thaliana Columbia (Col) ecotype and ind-2 plants were grown in soil in a growth chamber under 16h light/8h dark at 22℃.

extract_protocol:
Leaf veins and fruits four days before anthesis of WT and transgenic cucumber plants were collected for RNA-seq analysis. Total RNAs were extracted using the RNA extraction kit (Huayueyang, Beijing, China), and RNA quality check were performed as previously described (Sun et al., 2016). Two biological replicates were performed for each tissue sample. RNA-seq library construction was performed using the NEBNext Ultra Directional RNA Library Prep Kit for Illumina (NEB, Ispawich, USA) according to the manufacturer’s instructions and four index codes were added to attribute sequences to different samples(Wang et al., 2009).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: genotype background

value: inbred line 1461

value: wild type

value: leaf vein


title: cDC2_CD5+_Control_R6727


title: cDC2_CD5+_Control_R6711


title: WT-fruit-1

source_name: WT-fruit

value: fruit


title: CsIND-vein-1

source_name: CsIND-vein

value: CsIND-RNAi transgenic


title: CsIND-vein-2


title: WT-vein-1


title: WT-fruit-2


title: CsIND-fruit-2

source_name: CsIND-fruit


title: HK_DOX_HA_2

source_name: Human primary keratinocytes

value: Human primary keratinocytes engineered with stable IRF2 shRNA knockdown and a doxycyline inducible IRF2-3xHA allele

tag: input

value: Cells were treated with 1μg/ml Doxycycline for 3 days plus 2 days with 2μg/ml Doxycycline

tag: barcode

value: TGGATCTG

tag: antibody

value: anti-HA

tag: antibody maker

value: cell signaling


title: CsIND-fruit-1


title: mycelia 3

city: Kitakami

first: Yuichi

last: Sakamoto

state: Iwate

department: Department of Bioresource

country: Japan

institute: Iwate Biotechnology Research Center

description: T. matsutake 6 months cultured mycelia on agar plate

data_processing:
Data processing is carried out using clc genomics workbench v11.
Supplementary_files_format_and_content: .csv tab-delimited text files include RPKM values for each Sample

organism: Tricholoma matsutake

source_name: mycelia

growth_protocol:
Mycorrhizal synthesis was carried out using 500mL polycarbonate bottle (Agri pot, TGK Co. Ltd., Tokyo) containing 100 mL of vermiculite: sphagnum moss (80:1 w/w) moisturized with MYPG liquid media. The bottles were autoclaved at 121°C for 20 minutes, cooled to room temperature, then inoculated with T. matsutake colony grown on MYPG plate as described below. Rim of fungal colony was cut into 1cm cubic blocks, and three blocks were inserted into the substrate of each bottle. After inoculation of T. matsutake mycelium blocks, these bottles were placed in an incubator at 23°C for 1 month without light. Consequently, one aseptic seedling was transplanted into the substrate, and bottles were placed in a growth chamber at 23°C with light condition until use.
T. matsutake mycelia was inoculated on MYPG agar plate for 6 months at 25˚C in the dark
fruiting body of T. matsutake collected in wild, Iwate prefecture, 39°56’ N, 141°14’ E
Pine seedlings were cultured using 500mL polycarbonate bottle (Agri pot, TGK Co. Ltd., Tokyo) containing 100 mL of vermiculite: sphagnum moss (80:1 w/w) moisturized with MYPG liquid media. The bottles were autoclaved at 121°C for 20 minutes. Consequently, one aseptic seedling was transplanted into the substrate, and bottles were placed in a growth chamber at 23°C with light condition until use.

extract_protocol:
RNA from mycorrhiza and pine root werer extracted by modified CTAB method reported by chang et al. 1993. RNA from mycelia and fruiting body were extracted by RNeasy plant kit (Qiagen)
library was constracted by Truseq RNA-seq kit (illumina) following manifacture's protocol.

value: mycelia

tag: passages

value: cultured 6 months on agar plate

tag: strain

value: T. matsutake strain IS01


title: fruiting body 2

description: fruiting body collected in wild

source_name: fruiting body

value: fruiting body

value: collected in wild

value: wild strain


title: pine root (without T. matsutake) 1

description: pine root cultured without T. matsutake

organism: Pinus densiflora

source_name: pine root

value: root

value: cultured 6 months without T. matsutake

value: T. matsutake strain IS01, Pinus densiflora in Iwate


title: fruiting body 1

description: fruiting body collected in wild


title: fruiting body 3

description: fruiting body collected in wild


title: mycelia 1


title: mycelia 2


title: pine root (without T. matsutake) 2

description: pine root cultured without T. matsutake


title: mycorrhiza 3

description: mycorrhiza co-cultured with pine root for 6 months

organism:
Tricholoma matsutake
Pinus densiflora

source_name: mycorrhiza

value: mycorrhiza

value: co-clutred 6 months


title: mycorrhiza 1


title: mut7

source_name: zebrafish ventricle

value: heart

tag: chamber

value: ventricle

tag: genotype

value: vegfc(hy-/-);vegfd(-/-)


title: hiHeps (hHPLCs-2 P28)

city: Beijing

first: Bingqing

last: Xie

address: Peking University, No.5 Yiheyuan Road Haidian District, Beijing, P.R.China

institute: Peking University

data_processing:
The transcriptome reads were mapped using STAR.
The read counts for each gene were calculated using featureCounts. For microRNA, clean fasta format sequencing reads generated from the sequencer mapped against the human genome build hg19 and calculated read counts by miRDeep2.
Gene expression was normalized by DESeq2, and low expression genes with total counts across all samples less than 1 were excluded.
Genome_build: hg19 for human
Supplementary_files_format_and_content: CSV files include the expression values for each sample

source_name: human induced hepatocytes

extract_protocol:
Total RNA from each sample was isolated using Direct-zol RNA Miniprep kit (ZYMO RESEARCH) or TRNzol Universal (TIANGEN).
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 and index codes were added to attribute sequences to each sample. Briefly, mRNA was 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 (RNaseH-). 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 Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 150~200bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 μl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95 °C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.For microRNAs, RNA sequencing libraries were prepared using the NEB Next® Multiplex Small RNA Library Prep Set for Illumina (NEB, USA) following the manufacturer’s recommendations.

treatment_protocol: hHPLCs  were cultured in HEM and collected from RNA extraction at indicated passages. hiHeps derived from hHPLCs of different passages were cultured in 2C medium for 10 days and then collected from RNA extraction. Primary huaman hepatocytes were fresh isolated.

tag: batch number

value: batch 3

tag: treatment

value: 2C medium

value: human induced hepatocytes


title: MC1

source_name: zebrafish ventricle_with cryoinjury


title: hiHeps (hHPLCs-2 P6)


title: capture-C-seq, hom, rep2


title: hHPLCs-2 P5

source_name: human hepatic progenitor-like cells

value: HEM

value: human hepatic progenitor-like cells


title: hHPLCs-2 P28


title: capture-C-seq, hom, rep1


title: Sham

city: Cincinnati

first: Nathan

last: Salomonis

state: OH

address: 3333 Burnet Avenue

department: Biomedical Informatics

institute: Cincinnati Children's Hospital

data_processing:
Count matrices were filtered to cells having a minimum of 200 genes expressed, proportion of mitochondrial genes < 0.25 and >= 400 UMIs (Sham n=13,858; MI n=11,240). Standard Seurat processing was conducted, including log-normalization, regressing out nUMI, mitochondrial proportion and cell cycle indicators (proportion of histone and Seurat G2/M transcripts), and scaling. Predicted cell doublet profiles were excluded from each dataset after selecting the union of doublet predictions from the softwares DoubletDecon and Scrublet (DePasquale, et al., 2018; Wolock, et al.).  The application of the Seurat 3 integration procedure began with these objects. For the evaluation of cellHarmony, the Seurat cellHarmony processing script (http://altanalyze.org/cellHarmony/) was used to convert the Sham sample expression matrix, cell-state marker genes and cellular barcode clusters to an AltAnalyze compatible heatmap.
Genome_build: mm10
Supplementary_files_format_and_content: tab delimited text

extract_protocol:
Acute myocardial infarction (MI) was modeled in C57BL6/J wild type (WT) 8-10-week-old male mice (The Jackson Laboratories and confirmed via echocardiographic analysis, similar to previously described (Duan, et al., 2017). A left thoracotomy was performed via the fourth intercostal space and the lungs retracted to expose the heart. After opening the pericardium, the left anterior descending coronary artery was ligated with 7-0 silk suture approximately 2 mm below the edge of the left atrial appendage. Ligation was considered successful when the anterior wall of the left ventricle turned pale. The lungs were inflated by increasing positive end-expiratory pressure and the thoracotomy site closed in layers with 6-0 suture. Animals were maintained on a 37 °C heating pad until recovery and for 2 h after surgery. Another group of mice underwent sham ligation, with a similar surgical procedure without tightening the suture around the coronary artery. Mice with an estimated pressure gradient across the aortic constriction below 40 mmHg were not included in the experiments. Hearts were collected at 14 days post-Sham surgery (n=4, pooled) or MI (n=1), perfused with ice-cold PBS to remove red blood cells followed by perfusion with 50 mM KCl to arrest the heart in diastole and then fixed for 4 hours in freshly prepared 4% PFA at 4 °C, rinsed with PBS and cryoprotected in 30% sucrose/PBS overnight before embedding in OCT (Tissue-Tek). DropSeq was performed as previously described (Macosko, et al., 2015). The quantity and quality of cDNA was measured using an Agilent Bioanalyzer hsDNA chip. To generate a library cDNA was fragmented and amplified (12 cycles) using the Nextera XT DNA Sample prep kit with three separate reactions of 600, 1,200 and 1,800 pg input cDNA.
The quantity and quality of cDNA was measured using an Agilent Bioanalyzer hsDNA chip. To generate a library cDNA was fragmented and amplified (12 cycles) using the Nextera XT DNA Sample prep kit with three separate reactions of 600, 1,200 and 1,800 pg input cDNA. The libraries were pooled and purified twice using 0.7X volume of SPRIselect beads. The purified libraries were quantified using an hsDNA chip and were sequenced on an Illumina HiSeq 2500 using the sequencing parameters described in the DropSeq protocol.
DropSeq was performed as previously described (Macosko et al., 2015).

value: sham treatment

value: male


title: MI

value: Acute myocardial infarction


title: pine root (without T. matsutake) 3

description: pine root cultured without T. matsutake


title: mycorrhiza 2


title: KO : AOMDSS : V29_7

city: Salt Lake City

first: Jordan

middle: A

last: Berg

state: UT

address: 15 N Medical Drive East, Rm 5520

department: Biochemistry

institute: University of Utah

description: Loss of the mitochondrial pyruvate carrier promotes stem cell gene expression in AOMDSS colon adenomas, though loss of Apc promotes a more unified pehnotype.

hyb_protocol: RNA was hybridized to probes and detection probes using the NanoString nCounter system according to the manufacturer's protocol (below). Probes were based on manufacturer's  fourescent barcode system.

scan_protocol: Scanning was carried out on the NanoString Elements platform according to manufacturer's protocols at the University of Utah Molecular Diagnostics Core.

data_processing: We scaled the raw data by generating a geometric mean scaling factor per sample to normalize the dataset. This was performed using NanoString nSolver 4

label: Manufacturer designed probes with flourescent tag barcodes

source_name: colon adenoma

extract_protocol: if tumors, at least 8-10 section of 8um thick sections were stained with aniline blue and microdissected for tumors over normal crypts or microdissected upon animal sacrifice and snap frozen. if crypts, crypts were isolated from the colon (Schell et al 2017), washed and snap frozen. Whole crypt RNA was extracted using the QIAGEN RNeasy kit. Tumor tissue RNA was extracted using the QIAGEN FFPE RNeasy kit or the QIAGEN RNeasy kit (please refer to associated manuscript for full details).

treatment_protocol: colon epithelial tumors were induced spontaneously in mice by either chemical treatment (AOMDSS) or genetic recombination (loss of Apc).

value: colon adenoma

tag: genetic mouse model

value: AOMDSS

tag: sample prep

value: FFPE

tag: days post tamoxifen

value: Female

tag: grade

value: high grade


title: capture-C-seq, het, rep1

source_name: ESC


title: anlr-hsc_28

data_processing:
Barcodes and adaptors were trimmed from raw reads.
Alignment to mm10 with UCSC annotations using a proprietary Burrow-Wheeler Transform alignment (COBWeb). Reads that aligned to more than one location or exhibited an alignment quality of <30 were removed.
Generation of FPKM counts using an EM algorithm. Normalization using the DESeq algorithm and baselining to the median of all samples.
Differential expression analysis was performed using a moderated t-test with significance set at p<0.05 and FC>3.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files contain DESeq-normalized and baselined log(FPKM) counts for each sample. Row names show ENTREZ gene IDs, column names indicate samples.

source_name: Non Label retaining LT-HSCs

extract_protocol:
Bone marrow was flushed from femora and tibiae of SCL-TAxH2B-GFP double heterozygous mice. Hematopoietic mononuclear cells were isolated by low-density centrifugation and depleted of lineage cells using magnetic separation. Lineage depleted cells were sorted as single LT-HSCs (LSK CD34-/low Flk2- CD48- CD150+) based on GFP expression (positive and negative). Cells were cultured overnight without growth factors at 3% O2 and washed twice with PBS before processing. RNA was isolated using Clontech's SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing. Amplified cDNA was purified using Beckman Coulter's Agencourt AMPure XP beads.
Libraries were manually prepared using Illumina's Nextera XT DNA Library preparation kit. Manual library normalization was performed after quantification using Agilent's Bioanalyzer.

tag: age

value: > 20 months

tag: tissue

value: Bone marrow (flushed from femora and tibiae)

tag: cell type

value: Hematopoietic mononuclear cells

tag: replicate

tag: gfp expression


title: KO : AOMDSS : V32_5

label_protocol: Manufacturer designed probes with flourescent tag barcodes

tag: Sex


title: KO : AOMDSS : V29_1

value: low grade


title: KO : AOMDSS : V29_2


title: HepG2 cells

source_name: human hepatocarcinoma

value: batch 2

value: HEF medium

value: human hepatocarcinoma


title: hFLCs-1

source_name: human fetal liver cells

value: HEM

value: human fetal liver cells


title: KO : AOMDSS : V32_4