title: HCI002_262_H_LU_78


title: HCI002_262_H_LU_66

status: Public on Feb 20 2020

type: SRA

city: Irvine

first: Devon

middle: A

last: Lawson

state: CA

address: 839 Health Science Road, Sprague Hall 114

department: Physiology and Biophysics

country: USA

institute: UC Irvine

library_source: transcriptomic

data_processing:
Files from the HiSeq2500 were demultiplexed and converted to FASTQ files. Paired-end 100bp reads were aligned to the hg21 human transcriptome using Bowtie2 and quantified using RSEM with the following parameters: rsem-calculate-expression -p $CORES --bowtie2 --paired-end READ1 READ2 gencodehg21. Expression values were log-transformed into log(TPM+1) matrices and loaded into the Seurat analysis package with the following parameters: p10 <- CreateSeuratObject(raw.data = p10.mat, min.cells = 8, min.genes = 1000,  project = "HCI010").
Genome_build: hg21
Supplementary_files_format_and_content: genes.results.FPKM.txt

molecule: total RNA

organism: Homo sapiens

source_name: Patient Derived Xenograft Single Cells

extract_protocol:
Animals at endpoint were euthanized by asphyxiation with CO2 followed by cervical dislocation and perfusion with 10mM EDTA in D-PBS.  Prior to perfusion, Evan’s Blue (Sigma-Aldrich, Cat. No. E2129-10G) was injected into the footpads and ears of anesthetized mice to aid in lymph node visualization. Solid tissues from the mice, which includes the primary tumour, lung, and lymph nodes were processed for flow cytometry by mechanically chopping with blades, followed by Collagenase IV digest (Sigma-Aldrich Cat. No. C5138-1G) in media (DMEM/F12 with 5% FBS, 5µg/mL insulin, and 1% Penstrep/Ampho B) for 45 min at 37°C. Cell suspensions were washed with 2 µg/mL DNAseI for 5 min and further dissociated with 0.05% Trypsin for 10 min. Following a wash with HBBS/2% FBS, cells were passed through a 70µm filter. Lung and primary tumour cells were treated with 1X RBC lysis buffer, followed by resuspension in DMEM/F12 with 10% FBS for FACS. We used the human-specific antibody CD298 (PE, BioLegend, Cat. No. 341704) and the mouse-specific antibody MHCI (APC, ThermoFisher, Scientific Cat. No. 17-5957-80). Flow cytometry was performed using the BD FACSAria Fusion cell sorter. Cell viability was determined by negative staining for SYTOX Blue (ThermoFisher Scientific Cat. No. S34857). Forward scatter area by forward scatter width (FSC W x FSC A) and side scatter area by side scatter width (SSC W x SSC A) was used to discriminate single cells from doublet and multiplet cells. Mouse cells were excluded by gating out CD298-MHCI+. Human primary tumour cells and metastatic cells were selected by gating on Sytox-CD298+MHC-I-.
Single cells were sorted directly into each well of a skirted 96-well PCR plate (Fisher Scientific, Eppendorf, Cat. No. E951020443) containing lysis buffer (0.2% Triton X-100, 2 U/µL RNAseOUT, 10µM oligo-dT30VN, and 10µM dNTPs). The plates were snap frozen on dry ice and stored at -80°C until further processing. Total RNA was converted into cDNA using the SmartSeq2 protocol and prepared for Illumina sequencing with the Nextera XT DNA Library Preparation Kit (Illumina, Cat No. FC-131-1096). Cells were sequenced at a depth of 1 million reads/cell on the HiSeq2500.

tag: patient id

tag: status

value: Metastasis

tag: tissue source

value: Lung

tag: mouse


title: HCI002_262_H_LU_65


title: HCI002_262_H_LU_64


title: HCI002_262_H_LU_62


title: HCI002_262_H_LU_63


title: HCI002_262_H_LU_59


title: HCI002_262_H_LU_60


title: HCI002_262_H_LU_61


title: HCI002_262_H_LU_55


title: HCI002_262_H_LU_56


title: HCI002_262_H_LU_53


title: HCI002_262_H_LU_58


title: HCI002_262_H_LU_57


title: HCI002_262_H_LU_52


title: HCI002_262_H_LU_54


title: HCI002_262_H_LU_51


title: HCI002_262_H_LU_50


title: HCI002_262_H_LU_48


title: HCI002_262_H_LU_46


title: HCI002_262_H_LU_47


title: HCI002_262_H_LU_44


title: HCI002_262_H_LU_43


title: HCI002_262_H_LU_45


title: HCI002_262_H_LU_42


title: HCI002_262_H_LU_41


title: HCI002_262_H_LU_40


title: HCI002_262_H_LU_36


title: HCI002_262_H_LU_37


title: HCI002_262_H_LU_35


title: HCI002_262_H_LU_38


title: HCI002_262_H_LU_34


title: HCI002_262_H_LU_39


title: HCI002_262_H_LU_30


title: HCI002_262_H_LU_31


title: HCI002_262_H_LU_49


title: HCI002_262_H_LU_32


title: HCI002_262_H_LU_33


title: HCI002_262_H_LU_26


title: HCI002_262_H_LU_23


title: HCI002_262_H_LU_28


title: HCI002_262_H_LU_24


title: HCI002_262_H_LU_25


title: HCI002_262_H_LU_21


title: HCI002_262_H_LU_27


title: HCI002_262_H_LU_22


title: HCI002_262_H_LU_20


title: HCI002_262_H_LU_16


title: HCI002_262_H_LU_18


title: HCI002_262_H_LU_19


title: HCI002_262_H_LU_14


title: HCI002_262_H_LU_17


title: HCI002_262_H_LU_15


title: HCI002_262_H_LU_13


title: HCI002_262_H_LU_29


title: HCI002_262_H_LU_10


title: HCI002_262_H_LU_11


title: HCI002_262_H_LU_7


title: HCI002_262_H_LU_8


title: HCI002_262_H_LU_9


title: HCI002_262_H_LU_6


title: HCI002_262_H_LU_3


title: HCI002_241_T_PT_163

value: Tumor

value: Primary Tumor


title: HCI002_241_T_PT_164


title: HCI002_262_H_LU_1


title: HCI002_241_T_PT_165


title: HCI002_262_H_LU_5


title: HCI002_241_T_PT_162


title: HCI002_241_T_PT_161


title: HCI002_241_T_PT_160


title: HCI002_241_T_PT_154


title: HCI002_241_T_PT_155


title: HCI002_241_T_PT_156


title: HCI002_262_H_LU_12


title: HCI002_241_T_PT_158


title: HCI002_241_T_PT_157


title: HCI002_241_T_PT_153


title: HCI002_262_H_LU_4


title: HCI002_241_T_PT_159


title: HCI002_241_T_PT_146


title: HCI002_241_T_PT_139


title: HCI002_241_T_PT_150


title: HCI002_241_T_PT_148


title: HCI002_241_T_PT_149


title: HCI002_241_T_PT_151


title: HCI002_241_T_PT_141


title: HCI002_241_T_PT_140


title: HCI002_241_T_PT_147


title: HCI002_241_T_PT_145


title: HCI002_241_T_PT_137


title: HCI002_241_T_PT_135


title: HCI002_241_T_PT_143


title: HCI002_241_T_PT_142


title: HCI002_241_T_PT_132


title: HCI002_241_T_PT_131


title: HCI002_241_T_PT_134


title: HCI002_241_T_PT_136


title: HCI002_241_T_PT_133


title: HCI002_241_T_PT_127


title: HCI002_241_T_PT_152


title: HCI002_241_T_PT_144


title: HCI002_241_T_PT_128


title: HCI002_241_T_PT_130


title: HCI002_241_T_PT_129


title: HCI002_241_T_PT_138


title: HCI002_241_T_PT_125


title: HCI002_262_H_LU_2


title: HCI002_241_T_PT_126


title: HCI002_241_T_PT_124


title: HCI002_241_T_PT_122


title: HCI002_241_T_PT_123


title: HCI002_241_T_PT_121


title: HCI002_241_T_PT_117


title: HCI002_241_T_PT_110


title: HCI002_241_T_PT_115


title: HCI002_241_T_PT_113


title: HCI002_241_T_PT_118


title: HCI002_241_T_PT_111


title: HCI002_241_T_PT_108


title: HCI002_241_T_PT_120


title: HCI002_241_T_PT_106


title: HCI002_241_T_PT_116


title: HCI002_241_T_PT_109


title: HCI002_241_T_PT_112


title: HCI002_241_T_PT_104


title: HCI002_241_T_PT_119


title: HCI002_241_T_PT_103


title: HCI002_241_T_PT_101


title: HCI002_241_T_PT_105


title: HCI002_241_T_PT_98


title: HCI002_241_T_PT_107


title: HCI002_241_T_PT_100


title: HCI002_241_T_PT_99


title: HCI002_241_T_PT_97


title: HCI002_241_T_PT_94


title: HCI002_241_T_PT_96


title: HCI002_241_T_PT_95


title: HCI002_241_T_PT_102


title: HCI002_241_T_PT_114


title: HCI002_241_T_PT_86


title: HCI002_241_T_PT_85


title: HCI002_241_T_PT_92


title: HCI002_241_T_PT_89


title: HCI002_241_T_PT_88


title: HCI002_241_T_PT_93


title: HCI002_241_T_PT_87


title: HCI002_241_T_PT_84


title: HCI002_241_T_PT_80


title: HCI002_241_T_PT_91


title: HCI002_241_T_PT_79


title: HCI002_241_T_PT_81


title: HCI002_241_T_PT_82


title: HCI002_241_T_PT_76


title: HCI002_241_T_PT_77


title: HCI002_241_T_PT_78


title: HCI002_241_T_PT_73


title: HCI002_241_T_PT_74


title: HCI002_241_T_PT_83


title: HCI002_241_T_PT_71


title: HCI002_241_T_PT_72


title: HCI002_241_T_PT_70


title: HCI002_241_T_PT_90


title: HCI002_241_T_PT_69


title: HCI002_241_T_PT_67


title: HCI002_241_T_PT_66


title: HCI002_241_T_PT_65


title: HCI002_241_T_PT_64


title: HCI002_241_T_PT_75


title: HCI002_241_T_PT_62


title: HCI002_241_T_PT_63


title: HCI002_241_T_PT_60


title: HCI002_241_T_PT_59


title: HCI002_241_T_PT_58


title: HCI002_241_T_PT_61


title: HCI002_241_T_PT_55


title: HCI002_241_T_PT_56


title: HCI002_241_T_PT_53


title: HCI002_241_T_PT_50


title: HCI002_241_T_PT_54


title: HCI002_241_T_PT_49


title: HCI002_241_T_PT_51


title: HCI002_241_T_PT_46


title: HCI002_241_T_PT_47


title: HCI002_241_T_PT_48


title: HCI002_241_T_PT_44


title: HCI002_241_T_PT_42


title: HCI002_241_T_PT_40


title: HCI002_241_T_PT_45


title: HCI002_241_T_PT_41


title: HCI002_241_T_PT_43


title: HCI002_241_T_PT_39


title: HCI002_241_T_PT_37


title: HCI002_241_T_PT_38


title: HCI002_241_T_PT_36


title: HCI002_241_T_PT_35


title: HCI002_241_T_PT_34


title: HCI002_241_T_PT_52


title: HCI002_241_T_PT_57


title: HCI002_241_T_PT_33


title: HCI002_241_T_PT_32


title: HCI002_241_T_PT_29


title: HCI002_241_T_PT_30


title: HCI002_241_T_PT_28


title: HCI002_241_T_PT_27


title: HCI002_241_T_PT_25


title: HCI002_241_T_PT_22


title: HCI002_241_T_PT_24


title: HCI002_241_T_PT_20


title: HCI002_241_T_PT_16


title: HCI002_241_T_PT_17


title: HCI002_241_T_PT_18


title: HCI002_241_T_PT_15


title: HCI002_241_T_PT_14


title: HCI002_241_T_PT_13


title: HCI002_241_T_PT_11


title: HCI002_241_T_PT_12


title: HCI002_241_T_PT_68


title: HCI002_241_T_PT_31


title: HCI002_241_T_PT_10


title: HCI002_241_T_PT_8


title: HCI002_241_T_PT_9


title: HCI002_241_T_PT_7


title: HCI002_241_T_PT_5


title: HCI002_241_T_PT_23


title: HCI002_241_T_PT_6


title: HCI002_241_T_PT_26


title: HCI002_241_T_PT_21


title: HCI002_241_L_LU_25


title: HCI002_241_T_PT_19


title: HCI002_241_L_LU_22


title: HCI002_241_L_LU_20


title: HCI002_241_L_LU_21


title: HCI002_241_L_LU_17


title: HCI002_241_L_LU_18


title: HCI002_241_L_LU_23


title: HCI002_241_L_LU_15


title: HCI002_241_L_LU_13


title: HCI002_241_L_LU_14


title: HCI002_241_T_PT_3


title: HCI002_241_T_PT_2


title: HCI002_241_L_LU_12


title: HCI002_241_L_LU_10


title: HCI002_241_T_PT_1


title: HCI002_241_T_PT_4


title: HCI002_241_L_LU_9


title: HCI002_241_L_LU_7


title: HCI002_241_L_LU_8


title: HCI002_241_L_LU_27


title: HCI002_241_L_LU_26


title: HCI002_241_L_LU_4


title: HCI002_241_L_LU_24


title: HCI002_241_L_LU_5


title: HCI002_241_L_LU_6


title: HCI002_241_L_LU_3


title: HCI002_241_L_LU_19


title: HCI002_241_L_LU_2


title: HCI002_241_L_LU_16


title: HCI002_241_L_LU_1


title: HCI002_241_L_LU_11


title: HCI002_242_T_PT_131


title: HCI002_242_T_PT_128


title: HCI002_242_T_PT_125


title: HCI002_242_T_PT_124


title: HCI002_242_T_PT_129


title: HCI002_242_T_PT_127


title: HCI002_242_T_PT_126


title: HCI002_242_T_PT_122


title: HCI002_242_T_PT_130


title: HCI002_242_T_PT_121


title: HCI002_242_T_PT_123


title: HCI002_242_T_PT_118


title: HCI002_242_T_PT_119


title: HCI002_242_T_PT_120


title: HCI002_242_T_PT_116


title: HCI002_242_T_PT_113


title: HCI002_242_T_PT_115


title: HCI002_242_T_PT_117


title: HCI002_242_T_PT_110


title: HCI002_242_T_PT_112


title: HCI002_242_T_PT_111


title: HCI002_242_T_PT_109


title: HCI002_242_T_PT_114


title: HCI002_242_T_PT_108


title: HCI002_242_T_PT_106


title: HCI002_242_T_PT_132


title: HCI002_242_T_PT_107


title: HCI002_242_T_PT_104


title: HCI002_242_T_PT_105


title: HCI002_242_T_PT_103


title: HCI002_242_T_PT_100


title: HCI002_242_T_PT_102


title: HCI002_242_T_PT_101


title: Drought_2 (Degradome)

city: Nanjing

first: Rong

last: Zhou

address: 50 Zhongling Street

country: China

institute: Jiangsu Academy of Agricultural Sciences

description: Degradome sequencing

data_processing:
Degradome-Seq: Raw sequencing reads were obtained using Illumina’s software to remove adaptors and low quality reads.
Degradome-Seq: The extracted sequencing reads were then used to identify potentially cleaved targets by the CleaveLand pipeline.
Degradome-Seq: The degradome reads were mapped to the mRNA database. Only the perfect matching alignment(s) for the given read would be kept for degradation analysis.
Degradome-Seq: All resulting reads (t-signature) were reverse- complemented and aligned to the miRNA identified in our study. No more than four alignment scores were allowed. Alignments where the degradome sequence position coincident with the tenth or eleventh nucleotide of miRNA were retained and scored. The target was selected and categorized as 0, 1, 2，3，or 4. category 0—over one raw read at the position, abundance at the position is equal to the maximum on the transcript, and there is only one maximum on the transcript; category 1—over one raw read at theposition, abundance at the position is equal to the maximum on the transcript, and there is more than one maximum position on the transcript; category 2—over one raw read at the position, abundance at position is less than the maximum but higher than the median for the transcript; category 3—over one raw read at the position, abundance at the position is equal to or less than the median for the transcript; and category 4—only one raw read at the position.
Genome_build: mRNA database (ftp://ftp.solgenomics.net/tomato_genome/assembly/build_3.00/ITAG3.2_cDNA.fasta)
Supplementary_files_format_and_content: normalized counts

organism: Solanum lycopersicum

source_name: Drought, plants leaves

growth_protocol: Single seeds were sown in a plug tray and then cultured in climate chambers (RDN-560E-4, Dongnan Instrument Co, Ltd, Ningbo, China). The air temperature was 26/18°C (14 h/10 h, 6:00-20:00/20:00-6:00, day/night) with a light intensity of 300 μmol m–2 s–1 photosynthetic photon flux density (PPFD) (LED light source, Dongnan Instrument Co, Ltd, Ningbo, China) and 50-60% relative humidity (RH). The seedlings were irrigated by water every five days. Then, the 15-day-old seedlings were irrigated by nutrient solution according to the Japanese Garden test formula [Ca(NO3)2.4H2O, 945mg/L; KNO3, 809 mg/L; NH4H2PO4, 153 mg/L; MgSO4.7H2O, 493 mg/L; FeSO4.7H2O, 13.9 mg/L; Na2-EDTA, 18.6 mg/L; H3BO3, 2.86 mg/L; MnSO4.4H2O, 2.13 mg/L; ZnSO4.7H2O, 0.22 mg/L; CuSO4.5H2O, 0.08 mg/L; (NH4)6Mo7O24.4H2O, 0.02 mg/L] every three days. The 21-day-old healthy and uniform seedlings were transferred to plastic plots (11 cm diameter, 9 cm height) and then cultured in the climate chambers under the same conditions.

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure
The libraries were sequenced by Illumina Hiseq 2500/Hiseq 4000 at the LC-BIO following the vendor’s recommended protocol.

treatment_protocol: The 24-day-old seedlings were divided into two groups with one group irrigated by water and another group without irrigation. After three days, half of the seedlings from the group with/without irrigation were treated at a normal temperature (26°C, 48 h, day) as a control and drought stress treatment. The rest half of the seedlings from the group with/without irrigation were treated at high temperature (38°C, 48 h, day) as a heat and combined stress treatment. The 24-day-old and 27-day-old seedlings at control and heat stress treatment were subjected to two additional irrigations with water as compared to that at drought and combined stress.

tag: genotype

value: wild type

tag: treatment

value: Drought

tag: tissue

value: plants leaves


title: Heat_2 (Degradome)

description: Degradome sequencing

source_name: Heat, plants leaves

value: Heat


title: Drought_1 (Degradome)

description: Degradome sequencing


title: Heat_1 (Degradome)

description: Degradome sequencing


title: HCI002_242_T_PT_98


title: HCI002_242_T_PT_99


title: Control_3 (Degradome)

description: Degradome sequencing

source_name: Control, plants leaves

value: Control


title: Control_2 (Degradome)

description: Degradome sequencing


title: HCI002_242_T_PT_95


title: HCI002_242_T_PT_97


title: Combination_3 (miRNA)

description: miRNA sequencing

data_processing:
miRNA-Seq: Unique sequences with length in 18~25 nucleotide were mapped to specific species precursors in miRBase 21.0 by BLAST search to identify known miRNAs and novel 3p- and 5p- derived miRNAs.
miRNA-Seq: Length variation at both 3' and 5' ends and one mismatch inside of the sequence were allowed in the alignment.
miRNA-Seq: The unique sequences mapping to specific species mature miRNAs in hairpin arms were identified as known miRNAs. The unique sequences mapping to the other arm of known specific species precursor hairpin opposite to the annotated mature miRNA-containing arm were considered to be novel 5p- or 3pderived miRNA candidates.
miRNA-Seq: The remaining sequences were mapped to other selected species precursors (with the exclusion of specific species) in miRBase by BLAST search, and the mapped pre-miRNAs were further BLASTed against the specific species genomes to determine their genomic locations.
miRNA-Seq: The above two we defined as known miRNAs. The unmapped sequences were BLASTed against the specific genomes, and the hairpin RNA structures containing sequences were predicated from the flank 80 nt sequences using RNAfold software (http://rna.tbi.univie.ac. at/cgi-bin/RNAfold.cgi). The criteria for secondary structure prediction were: (1) number of nucleotides in one bulge in stem (≤12) (2) number of base pairs in the stem region of the predicted hairpin (≥16) (3) cutoff of free energy (kCal/mol ≤-15) (4) length of hairpin (up and down stems + terminal loop ≥50) (5) length of hairpin loop (≤20). (6) number of nucleotides in one bulge in mature region (≤8) (7) number of biased errors in one bulge in mature region (≤4) (8) number of biased bulges in mature region (≤2) (9) number of errors in mature region (≤7) (10) number of base pairs in the mature region of the predicted hairpin (≥12) (11) percent of mature in stem (≥80).
Genome_build: miRBase 21.0
Supplementary_files_format_and_content: normalized counts

source_name: Combination, plants leaves

value: Combination


title: HCI002_242_T_PT_92


title: HCI002_242_T_PT_96


title: HCI002_242_T_PT_93


title: Heat_3 (miRNA)

description: miRNA sequencing


title: Combination_2 (miRNA)

description: miRNA sequencing


title: Control_1 (Degradome)

description: Degradome sequencing


title: Combination_1 (miRNA)

description: miRNA sequencing


title: HCI002_242_T_PT_91


title: HCI002_242_T_PT_89


title: Heat_2 (miRNA)

description: miRNA sequencing


title: HCI002_242_T_PT_88


title: Drought_3 (Degradome)

description: Degradome sequencing


title: Heat_1 (miRNA)

description: miRNA sequencing


title: Drought_2 (miRNA)

description: miRNA sequencing


title: Drought_3 (miRNA)

description: miRNA sequencing


title: HCI002_242_T_PT_86


title: HCI002_242_T_PT_87


title: Control_3 (miRNA)

description: miRNA sequencing


title: HCI002_242_T_PT_85


title: HCI002_242_T_PT_84


title: HCI002_242_T_PT_94


title: Drought_1 (miRNA)

description: miRNA sequencing


title: Control_2 (miRNA)

description: miRNA sequencing


title: HCI002_242_T_PT_83


title: HCI002_242_T_PT_82


title: Sm22_CA_SMC_Exp3

city: Aurora

first: Mary

last: Weiser-Evans

state: CO

address: 12700 East 19th Avenue, C281

department: Renal Diseases & Hypertension

data_processing:
Basecalls were performed using bcl2fastq_v1.8.4
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using hisat2 version 2.1.0 with default parameters
For the RNA-seq experiments comparing AdvSca1-SM, AdvSca1-MA, and SMCs, Cufflinks 2.2.1 was employed to assemble the transcript from the aligned sequencing data and generate fragments per kilobase of exon per million fragments mapped (FPKM) data.
For carotid artery injury experiments, raw gene counts were generated with HTSeq 0.10.0 for subsequent analysis and EdgeR 3.10 was used to filter out low expression genes (CPM>=4 in at least 2 samples), perform paired comparison and generate Normalized counts per million (CPM) data.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM or CPM values for each Sample

organism: Mus musculus

source_name: Smooth muscle cells

extract_protocol:
Harvested descending aortas and combined aortic arch plus left and right carotid arteries were digested to single cells at 37°C for 1 hour. For flow sorting, single cell suspensions were suspended in 100 μl PBS + 0.1% CS and incubated with a rat anti-mouse monoclonal anti-Sca1 antibody; live cells were sorted based on Sca1-APC and endogenous YFP expression. Total RNA was extracted from flow cytometry-sorted cells using QIAshredders and an RNeasy Plus Micro kit (Qiagen). RNA quality and quantity were analyzed using a NanoDrop and Bioanalyzer.
RNA-Seq library preparation and sequencing were conducted at the Genomics and Microarray Core at the University of Colorado Anschutz Medical Campus. Libraries were constructed using a SMARTer Stranded Total RNA-Seq kit (Clontech) customized with mouse specific oligos for rRNA removal.

tag: strain

tag: cell type

value: Smooth muscle cells

value: Carotid arteries

tag: age

value: 8 weeks

value: no treatment


title: Control_1 (miRNA)

description: miRNA sequencing


title: HCI002_242_T_PT_80


title: HCI002_242_T_PT_90


title: Sm22_CA_SMC_Exp1

institute: University of Colorado Anschutz Medical Campus


title: HCI002_242_T_PT_79


title: HCI002_242_T_PT_78


title: HCI002_242_T_PT_81


title: Sm22_CA_AdvSca1-SM_Exp1

source_name: AdvSca1-SM cells

value: AdvSca1-SM cells


title: Sm22_CA_SMC_Exp2


title: Sm22_CA_AdvSca1-SM_Exp2


title: HCI002_242_T_PT_76


title: Sm22_CA_AdvSca1-MA_Exp2

source_name: AdvSca1-MA cells

value: AdvSca1-MA cells


title: HCI002_242_T_PT_77


title: Sm22_AO_SMC_Exp3

value: Aortae


title: Sm22_AO_SMC_Exp2


title: HCI002_242_T_PT_75


title: Sm22_CA_AdvSca1-MA_Exp1


title: HCI002_242_T_PT_73


title: HCI002_242_T_PT_74


title: HCI002_242_T_PT_72


title: Sm22_AO_SMC_Exp1


title: Sm22_AO_AdvSca1-SM_Exp2


title: HCI002_242_T_PT_71


title: Sm22_AO_AdvSca1-SM_Exp1


title: Sm22_AO_AdvSca1-MA_Exp2


title: HCI002_242_T_PT_70


title: HCI002_242_T_PT_69


title: Sm22_AO_AdvSca1-MA_Exp1


title: HCI002_242_T_PT_68


title: HCI002_242_T_PT_67


title: HCI002_242_T_PT_66


title: HCI002_242_T_PT_65


title: HCI002_242_T_PT_62


title: HCI002_242_T_PT_61


title: HCI002_242_T_PT_63


title: HFD21-1

city: Genève

first: Jordi

last: Altirriba

address: Rue Michel-Servet 1

department: Dpts de Médecine Interne et de Physiologie cellulaire et Métabolisme

country: Switzerland

institute: Centre Médical Universitaire de Genève

data_processing:
Samples passed the quality controls stablished in the FastQC software
Were mapped to mouse reference genome mm10 with TopHat v2.0.13
Its alignment was checked with Picard Tools v1.80
Gene expression counts were obtained with the HTSeq software v.0.6.1
Normalized counts (CPM) were obtained by edgeR library v.3.10.5 in R
Genome_build: Mouse reference genome mm10
Supplementary_files_format_and_content: txt file containing all the gene expressions for all the samples. Each column is a sample. Each row is a gene.

source_name: POMC neurons from POMC RiboTag mouse

growth_protocol: Mice were maintained on a 12h-light/12h-dark cycle with free access to water and food

extract_protocol:
Mediobasal hypothalamic were ice-cold homogenized and incubated with HA antibody to specifically select Pomc-RiboTag active translatome. Antibody-tissue homogenates were mixed with Dynabeads for Immunoprecipitation of RNA-HA complexes. Total RNA was purified using a RNeasy Micro Kit (Qiagen) and quantified using a Quant-iT™ RiboGreen™ RNA assay kit (Invitrogen). RNA integrity was assessed on a 2100 Bioanalyzer device (Agilent Technologies) using the RNA 6000 Pico kit (Agilent Technologies).
Sequencing libraries were prepared with the NexteraXT kit (Illumina, San Diego, CA, USA) and were sequenced in a HiSeq 2500 (Illumina) obtaining 50 base single read fragments

treatment_protocol: Six-week-old POMCRiboTag females were divided into two dietary groups: Standard chow (Envigo – Teklad Global Diet 2014) or high fat diet (45% HFD, Research Diets - D12451). After 4 weeks, mice were mated and continued with the same diet until the weaning of the offspring or 21 days post-natal.

value: POMC neurons

tag: post-natal day

tag: type of food administered

value: High fat diet

tag: biological replicate

tag: molecule subtype

value: Translating RNA from ribosomes


title: HFD0-5


title: HFD0-3


title: HFD21-2


title: HFD21-4


title: HFD0-4


title: HFD0-2


title: HFD21-3


title: HFD0-1


title: HCI002_242_T_PT_58

value: Tumor

value: Primary Tumor


title: HCI002_242_T_PT_59


title: CD21-2

value: Chow diet


title: HCI002_242_T_PT_57


title: CD21-3


title: HCI002_242_T_PT_64


title: CD21-1


title: HCI002_242_T_PT_55


title: CD0-4


title: HCI002_242_T_PT_53


title: CD0-3


title: CD0-2


title: HCI002_242_T_PT_52


title: HCI002_242_T_PT_60


title: HCI002_242_T_PT_51


title: KO_LPS3

city: Hangzhou

first: He

last: Jia

address: 866 Yuhangtang Rd

institute: Zhejiang university

data_processing:
Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
Clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text file includes counts and fpkms

source_name: Bone marrow

growth_protocol: BMDMs were generated from the bone marrow of 6- to 8-week-old mice. Bone marrow cells were collected from the femurs and tibias of mice, and macrophages were cultured in 1640 supplemented with 10% FCS, 20% conditioned media collected from L929 cells and 1% PenStrep at 37˚C in 5% CO2 for 6d

extract_protocol:
RNA degradation and contamination was monitored on 1% agarose gels. RNA purity was checked using the NanoPhotometer® spectrophotometer (IMPLEN, CA, USA) . RNA concentration was measured using Qubit® RNA Assay Kit in Qubit®2.0 Flurometer (Life Technologies, CA, USA). RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM 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.
Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.
The library preparations were sequenced on an Illumina Hiseq platform and 125 bp/150 bp paired-end reads were generated.

treatment_protocol: In experiment group, WT and KO BMDM were treated with LPS for 3 hours.

value: LysM-cre FBXW7f/f

value: LPS


title: CD0-1


title: HCI002_242_T_PT_50


title: WT_LPS3


title: KO

value: control


title: HCI002_242_T_PT_49


title: CD0-5


title: HCI002_242_L_LN_11

value: Metastasis

value: Lymph Node


title: HCI002_242_L_LN_10


title: HCI002_242_L_LN_12


title: HCI002_242_L_LN_9


title: WT


title: HCI002_242_T_PT_56


title: HCI002_242_T_PT_54


title: HCI002_242_L_LN_8


title: HCI002_242_L_LN_5


title: HCI002_242_L_LN_7


title: HCI002_242_L_LN_6


title: HCI002_242_L_LN_4


title: HCI002_242_L_LN_3


title: HCI002_242_L_LN_2


title: HCI002_242_T_PT_48


title: HCI002_242_L_LN_1


title: C4-2-siR2-2

city: New York

first: Bic

last: MSKCC

state: NY

address: 1275 York Ave.

institute: Memorial SLoan-Kettering Cancer Center

description: RRM2_siRNA cell_2

data_processing:
Dara processing were performed with Partek Flow according to Manufactures Instruction
Supplementary_files_format_and_content: Excel File contain the gene list

growth_protocol: Cell are cultured in standard condition according to ATCC

extract_protocol:
Total RNA was extracted using the Direct-Zol RNA kit  (Zymo Research, Irvine, CA)
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell line

value: Human Prostate cancer Cell

tag: cell  type

value: Transformed  cell

tag: source

value: ATCC


title: C4-2-NS2

description: Scrambled Control Cell_2


title: C4-2-siR2-1

description: RRM2_siRNA cell_1


title: C4-2-NS1

description: Scrambled Control Cell_1


title: HCI002_242_T_PT_47

tag: patient id


title: HCI002_242_T_PT_44

tag: status


title: ASTROCYTE-rep2

type: RNA

city: Nagoya

first: Keisuke

last: Katsushima

address: 1 Kawasumi, Mizuho-cho, Mizuho-ku

department: Department of Epigenomics

country: Japan

institute: Nagoya City University Graduate School of Medical Sciences

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to SurePrint G3 Mouse GE 8×60K array slides (G4858A, Agilent Technologies) at 65 °C with rotation at 10 rpm for 17 hours in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent Technologies) and 1 minute with 37°C GE Wash buffer 2 (Agilent Technologies), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent Microarray Scanner (G2565BA, Agilent Technologies) using one color scan setting for 8x60k array slides.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 039494_D_F_20150612) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: ASTROCYTE

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 200 ng RNA using Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technologies) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN). Dye incorporation and cRNA yield were checked with the NanoDrop 2000 Spectrophotometer.

extract_protocol: Total RNA was isolated using TRIzol (Life Technologies) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-2000.

tag: strain background

tag: genotype/variation

value: normal, wild type

value: brain

value: Astrocyte cells


title: HCI002_242_T_PT_43

tag: tissue source

tag: mouse


title: HCI002_242_T_PT_46


title: NSC-rep2

source_name: NSC

tag: tissue

value: neural stem cell (NSC)


title: NSC-rep1


title: TP53-KO-ASTROCYTE-rep2

value: TP53 knocked-out mice


title: MADM-CELL-rep2

source_name: MADM-glioma cells

value: Mosaic Analysis with Double Markers (MADM) mouse [PMID:21737130]

value: brain tumor

value: glioma cells


title: TP53-KO-ASTROCYTE-rep1


title: ASTROCYTE-rep1


title: HCI002_242_T_PT_45

value: Tumor

value: Primary Tumor


title: HCI002_242_T_PT_41


title: HCI002_242_T_PT_42


title: HCI002_242_T_PT_40


title: LNCaP-RRM2-2

description: RRM2 cell_2

source_name: LNCaP

value: transformed  cell


title: MADM-CELL-rep1


title: EZH2-KO-MADM-rep3

source_name: EZH2-KO-MADM_glioma tissue

value: EZH2 knocked-out


title: HCI002_242_T_PT_38


title: HCI002_242_T_PT_39


title: EZH2-KO-MADM-rep1


title: EZH2-KO-MADM-rep2


title: LNCaP-EV2

description: empty vector Cell_2


title: HCI002_242_T_PT_36


title: HCI002_242_T_PT_37


title: HCI002_242_T_PT_35


title: LNCaP-EV1

description: empty vector Cell_1


title: C42-COH20-2

description: COH29_20uM_ cell_2

data_processing:
Data processing were performed with Partek Flow according to Manufactures Instruction
Supplementary_files_format_and_content: Excel File contain the gene list

value: drug treated  cell


title: C42-COH10-2

description: COH29_10uM_ cell_2


title: C42-COH20-1

description: COH29_20uM_ cell_1


title: HCI002_242_T_PT_34


title: LNCaP-RRM2-1

description: RRM2 cell_1


title: HCI002_242_T_PT_29


title: HCI002_242_T_PT_33


title: C42-NT1

description: DMSO treated cell_1


title: C42-NT2

description: DMSO treated cell_2


title: C42-COH10-1

description: COH29_10uM_ cell_1


title: HCI002_242_T_PT_26


title: HCI002_242_T_PT_27


title: HCI002_242_T_PT_25


title: HCI002_242_T_PT_32


title: HCI002_242_T_PT_30


title: HCI002_242_T_PT_23


title: HCI002_242_T_PT_22


title: HCI002_242_T_PT_31


title: HCI002_242_T_PT_21


title: HCI002_242_T_PT_20


title: HCI002_242_T_PT_28


title: HCI002_242_T_PT_18


title: HCI002_242_T_PT_19


title: HCI002_242_T_PT_24


title: C57BL6_SPL_WT2_BN NPC WT

city: Scottsdale

first: Marta

last: Chesi

state: AZ

address: 13400 E Shea Blvd

institute: Mayo Clinic

description: Gene expression data

hyb_protocol: Following fragmentation, cRNA were hybridized for 16 hr at 45C on Affymetrix Mouse 430 2.0 GeneChip.

scan_protocol: GeneChips were scanned using the Affymetrix Genechip Scanner 3000.

data_processing: RMA normalization method.

label: Biotin

source_name: SPL

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 50ng total RNA.

extract_protocol: Total RNA extraction was performed using the Rneasy Micro Kit according to the manufacturer's instructions (Qiagen).

tag: strain

tag: donor/recipient

tag: tumor

tag: bortezomib

value: BN

tag: diagnosis

value: NPC

tag: cell of origin

value: PC

tag: Sex

value: M

tag: genotype

value: WT


title: HCI002_242_T_PT_17


title: HCI002_242_T_PT_16


title: XRPC24_ASC_CL_BN PCT WT

description: Gene expression data

source_name: ASC

value: Balb/c

value: CL

value: PCT


title: HCI002_242_T_PT_15

source_name: Patient Derived Xenograft Single Cells


title: C57BL6_BM_WT2_BN NPC WT

description: Gene expression data

source_name: BM

value: F


title: LS136_ASC_CL_BN PCT WT

description: Gene expression data


title: 9857_TM_CL_BN BL MYC+

description: Gene expression data

source_name: TM

value: BL

value: B

value: MYC+


title: C57BL6_BM_WT3_BN NPC WT

description: Gene expression data


title: HCI002_242_T_PT_14

value: Tumor


title: 9996_TM_CL_BN BL MYC+

description: Gene expression data


title: HCI002_242_T_PT_13

value: Primary Tumor


title: HCI002_242_T_PT_12


title: C57BL6_SPL_WT1_BN NPC WT

description: Gene expression data


title: 9855_BM_OT_BN MM MYC+

description: Gene expression data

value: OT

value: MM


title: HCI002_242_T_PT_9


title: HCI002_242_T_PT_8


title: 25703_TM_OT_BN EMM MYC+MIRhet

description: Gene expression data

value: EMM

value: MYC+MIRhet


title: HCI002_242_T_PT_10


title: 9384_TM_CL_BN BL MYC+

description: Gene expression data

value: BN


title: 25214_TM_OT_BN EMM MYC+MIRnull

description: Gene expression data

value: PC

value: MYC+MIRnull


title: C57BL6_BM_WT1_BN NPC WT

description: Gene expression data

value: NPC

value: WT


title: 25283_TM_OT_BN EMM MYC+MDRhet

description: Gene expression data

value: M

value: MYC+MDRhet


title: 25183_SPL_OT_BN EMM MYC+MIRnull

description: Gene expression data


title: 25410_TM_OT_BN EMM MYC+MIRnull

description: Gene expression data

value: F


title: HCI002_242_T_PT_7


title: 23589_TM_OT_BN EMM MYC+MIRnull

description: Gene expression data


title: HCI002_242_T_PT_6


title: 24095_SPL_OT_BN EMM MYC+MDRhet

description: Gene expression data


title: HCI002_242_T_PT_5


title: 23117_SPL_OT_BN EMM MYC+MIRnull

description: Gene expression data


title: HCI002_242_T_PT_4


title: HCI002_242_T_PT_11


title: 22428_TM_OT_BN EMM MYC+MIRhet

description: Gene expression data


title: HCI002_242_T_PT_3


title: HCI002_242_T_PT_2


title: 25039_SPL_OT_BN EMM MYC+MIRnull

description: Gene expression data


title: HCI002_242_T_PT_1


title: 22633_TM_OT_BN EMM MYC+MDRnull

description: Gene expression data

value: MYC+MDRnull


title: HCI002_242_L_LU_47

value: Metastasis

value: Lung


title: 22304_TM_OT_BN EMM MYC+MIRnull

description: Gene expression data


title: 24094_SPL_OT_BN EMM MYC+MDRhet

description: Gene expression data


title: 21787_SPL_OT_BN EMM MYC+MDRnull

description: Gene expression data


title: HCI002_242_L_LU_48


title: 22182_SPL_OT_BN EMM MYC+MIRnull

description: Gene expression data


title: HCI002_242_L_LU_46


title: HCI002_242_L_LU_44


title: HCI002_242_L_LU_45


title: HCI002_242_L_LU_39


title: HCI002_242_L_LU_40


title: HCI002_242_L_LU_38


title: HCI002_242_L_LU_43


title: HCI002_242_L_LU_42


title: HCI002_242_L_LU_36


title: 16804_SPL_OT_BN EMM MYC+CCND1+

description: Gene expression data


title: 21598_LV_OT_BN EMM MYC+MDRnull

description: Gene expression data

source_name: LV


title: 17122_SPL_OT_BN EMM MYC+BCL2+

description: Gene expression data


title: 18318_TM_OT_BN EMM MYC+MIRhet

description: Gene expression data


title: HCI002_242_L_LU_35


title: HCI002_242_L_LU_34


title: 15166_BM_OT_BN MM MYC+

description: Gene expression data

value: MYC+


title: HCI002_242_L_LU_33


title: 14774_SPL_OT_BN EMM MYC+CCND1+

description: Gene expression data


title: 16711_SPL_OT_BN EMM MYC+CCND1+

description: Gene expression data


title: 14787_SPL_OT_BN EMM MYC+CCND1+

description: Gene expression data


title: HCI002_242_L_LU_32


title: 15002_SPL_OT_BN EMM MYC+BCL2+

description: Gene expression data


title: 16606_SPL_OT_BN EMM MYC+BCL2+

description: Gene expression data


title: 14383_TM_OT_BN EMM MYC+

description: Gene expression data


title: 14660_SPL_OT_BN EMM MYC+

description: Gene expression data


title: 14451_TM_OT_BN EMM MYC+

description: Gene expression data


title: 14660_TM_OT_BN EMM MYC+

description: Gene expression data


title: 14699_SPL_OT_BN EMM MYC+

description: Gene expression data


title: 14963_TM_OT_BR EMM MYC+FGFR3_expression unknown

description: Gene expression data

value: BR

value: MYC+FGFR3_expression unknown


title: 14258_BM_OT_BN EMM MYC+BCL6+

description: Gene expression data

value: OT


title: HCI002_242_L_LU_31


title: HCI002_242_L_LU_37


title: HCI002_242_L_LU_29


title: HCI002_242_L_LU_30


title: HCI002_242_L_LU_28


title: HCI002_242_L_LU_26


title: HCI002_242_L_LU_25


title: HCI002_242_L_LU_41


title: HCI002_242_L_LU_23


title: HCI002_242_L_LU_24


title: 18042_SPL_OT_BN EMM MYC+MIRhet

description: Gene expression data

value: EMM


title: 14154_BM_R1_BN MM MYC+

description: Gene expression data

value: MM


title: 14246_BMSPL_OT_BN EMM MYC+BCL6+

description: Gene expression data

source_name: BMSPL

value: BN


title: 14153_SPL_R_BN EMM MYC+

description: Gene expression data

value: R

value: PC


title: 14153_SPL_OT_BN EMM MYC+

description: Gene expression data


title: 13834_BM_OT_BN MM MYC+FGFR3+

description: Gene expression data


title: HCI002_242_L_LU_22


title: 13855_SPL_OT_BN EMM MYC+

description: Gene expression data


title: 14118_SPL_R_BN EMM MYC+FGFR3+

description: Gene expression data


title: HCI002_242_L_LU_20


title: HCI002_242_L_LU_21


title: HCI002_242_L_LU_27


title: HCI002_242_L_LU_17


title: 13794_BM_OT_BN EMM MYC+

description: Gene expression data


title: 13801_TM_OT_BN EMM MYC+

description: Gene expression data


title: 14118_TM_OT_BN EMM MYC+FGFR3+

description: Gene expression data


title: HCI002_242_L_LU_19


title: 13826_SPL_OT_BN EMM MYC+

description: Gene expression data


title: HCI002_242_L_LU_14


title: HCI002_242_L_LU_15


title: HCI002_242_L_LU_18


title: HCI002_242_L_LU_13


title: 13756_SPL_OT_BR EMM MYC+

description: Gene expression data


title: 13768_BM_OT_BN MM MYC+

description: Gene expression data


title: HCI002_242_L_LU_12


title: 13808_BM_OT_BN EMM MYC+

description: Gene expression data


title: HCI002_242_L_LU_11


title: 13769_BM_OT_BN MM MYC+FGFR3+

description: Gene expression data


title: HCI002_242_L_LU_10


title: 13742_SPL_OT_BN EMM MYC+

description: Gene expression data


title: 13764_BM_OT_BR EMM MYC+

description: Gene expression data


title: 13457_TM_OT_BN EMM MYC+

description: Gene expression data


title: 13457_BM_OT_BN EMM MYC+

description: Gene expression data


title: HCI002_242_L_LU_16


title: 13410_TM_OT_BN EMM MYC+

description: Gene expression data


title: HCI002_242_L_LU_9


title: HCI002_242_L_LU_8


title: HCI002_242_L_LU_7


title: HCI002_242_L_LU_6


title: HCI002_242_L_LU_4


title: HCI002_242_L_LU_3


title: HCI002_242_L_LU_2


title: HCI002_242_L_LU_1


title: 13325_BM_OT_BN MM MYC+FGFR3_expression unknown

description: Gene expression data


title: 13044_BM_R_BN MM MYC+

description: Gene expression data


title: 13045_SPL_R_BN EMM MYC+

description: Gene expression data


title: 13051_SPL_R_BN EMM MYC+

description: Gene expression data


title: 13429_BM_OT_BN MM MYC+

description: Gene expression data


title: HCI001_257_T_PT_96

value: Tumor

value: Primary Tumor


title: HCI001_257_T_PT_94


title: 12996_SPL_OT_BN EMM MYC+

description: Gene expression data

value: M


title: 12869_BM_R_BN EMM MYC+

description: Gene expression data


title: 13038_BM_OT_BN MM MYC+FGFR3+

description: Gene expression data


title: 12854_BM_OT_BN EMM MYC+FGFR3+

description: Gene expression data


title: HCI001_257_T_PT_92


title: HCI001_257_T_PT_93


title: 13034_BM_OT_BN EMM MYC+

description: Gene expression data


title: HCI002_242_L_LU_5


title: HCI001_257_T_PT_91


title: HCI001_257_T_PT_90


title: HCI001_257_T_PT_95


title: HCI001_257_T_PT_89


title: HCI001_257_T_PT_88


title: HCI001_257_T_PT_87


title: 12811_BM_OT_BN EMM MYC+

description: Gene expression data


title: 12803_BM_OT_BN EMM MYC+

description: Gene expression data


title: 12811_SPL_OT_BN EMM MYC+

description: Gene expression data


title: 12741_SPL_R_BN EMM MYC+

description: Gene expression data


title: 12803_SPL_OT_BN EMM MYC+

description: Gene expression data


title: HCI001_257_T_PT_82


title: HCI001_257_T_PT_83


title: HCI001_257_T_PT_84


title: 12916_BM_OT_BN MM MYC+

description: Gene expression data


title: 12653_SPL_R1_BR EMM MYC+

description: Gene expression data


title: 12625_BM_R1_BN MM MYC+

description: Gene expression data


title: 12653_SPL_R2_BR EMM MYC+

description: Gene expression data


title: 12653_SPL_R3_BN EMM MYC+

description: Gene expression data


title: HCI001_257_T_PT_86


title: 12724_BM_OT_BN MM MYC+

description: Gene expression data


title: HCI001_257_T_PT_80


title: HCI001_257_T_PT_79


title: HCI001_257_T_PT_81


title: 12598_SPL_R2_BR EMM MYC+

description: Gene expression data


title: 12625_SPL_R2_BN EMM MYC+

description: Gene expression data


title: 12728_BM_OT_BN MM MYC+

description: Gene expression data


title: 12598_BM_R1_BR EMM MYC+

description: Gene expression data


title: 12574_TM_CL_BN BL MYC+

description: Gene expression data

value: CL

value: BL

value: B


title: 12598_SPL_R1_BR EMM MYC+

description: Gene expression data


title: HCI001_257_T_PT_85


title: HCI001_257_T_PT_78


title: HCI001_257_T_PT_76


title: 12498_BM_OT_BN MM MYC+

description: Gene expression data


title: HCI001_257_T_PT_75


title: HCI001_257_T_PT_74


title: HCI001_257_T_PT_71


title: HCI001_257_T_PT_72


title: HCI001_257_T_PT_70


title: HCI001_257_T_PT_77


title: HCI001_257_T_PT_68


title: HCI001_257_T_PT_69


title: HCI001_257_T_PT_67


title: HCI001_257_T_PT_66


title: HCI001_257_T_PT_73


title: 12452_BM_R_BN EMM MYC+

description: Gene expression data


title: HCI001_257_T_PT_65


title: 13575_ASC_OT_BN EMM MYC+

description: Gene expression data


title: 11935_BM_OT_BN MM MYC+

description: Gene expression data


title: 12183_BM_OT_BN EMM MYC+

description: Gene expression data


title: HCI001_257_T_PT_64


title: 13402_BM_OT_BN MM MYC+

description: Gene expression data

value: F


title: 12161_BM_OT_BN MM MYC+

description: Gene expression data


title: 12439_BM_OT_BN MM MYC+

description: Gene expression data


title: 12251_BM_OT_BN MM MYC+

description: Gene expression data


title: 12135_BM_OT_BN MM MYC+

description: Gene expression data


title: 11900_BM_OT_BN MM MYC+

description: Gene expression data


title: 12150_BM_OT_BN EMM MYC+

description: Gene expression data


title: HCI001_257_T_PT_63


title: 12422_TM_CL_BN BL MYC+BCL2+

description: Gene expression data


title: 10907_BM_OT_BN EMM MYC+BCL2+

description: Gene expression data


title: HCI001_257_T_PT_60


title: 11597_BM_OT_BN MM MYC+

description: Gene expression data


title: HCI001_257_T_PT_59


title: 10753_BM_OT_BN EMM MYC+

description: Gene expression data


title: HCI001_257_T_PT_58


title: 10551_BM_OT_BN EMM MYC+BCL2+

description: Gene expression data


title: HCI001_257_T_PT_57


title: 12598_BM_OT_BR EMM MYC+

description: Gene expression data


title: HCI001_257_T_PT_56


title: HCI001_257_T_PT_55


title: HCI001_257_T_PT_54


title: 12372_BM_OT_BN MM MYC+

description: Gene expression data


title: HCI001_257_T_PT_53


title: HCI001_257_T_PT_61


title: HCI001_257_T_PT_50


title: HCI001_257_T_PT_62


title: HCI001_257_T_PT_49


title: HCI001_257_T_PT_51


title: HCI001_257_T_PT_47


title: HCI001_257_T_PT_46


title: HCI001_257_T_PT_45


title: HCI001_257_T_PT_44


title: WT_ChIP

city: West Lafayette

first: Jian-Kang

last: Zhu

state: IN

address: 625 Agriculture Mall Dr.

department: Department of Horticulture and Landscape Architecture

institute: Purdue University

library_source: genomic

data_processing:
The quality of the sequencing data were first checked with FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/). The first 10 bp and last 80 bp of each read were trimmed. Clean paired-end reads were mapped to the TAIR10 A. thaliana genome using Bowtie2 with “--very-sensitive --no-unal --no-mixed --no-discordant -k 10” and only uniquely aligned reads were kept. Duplicated reads were removed using the SAMtools “markdup” command
Genome_build: TAIR10
Supplementary_files_format_and_content: The bedGraph files were generated using genomeCoverageBed from bedtools with parameter  -bg -pc

molecule: genomic DNA

organism: Arabidopsis thaliana

source_name: seedlings

growth_protocol: 10-day-old WT and 35S::GFP-ICE1 transgenic plants grown on solid Murashige and Skoog media under a 16 h light/8 h dark light cycle were collected for ChIP-Seq analysis

extract_protocol:
Briefly, tissues were cross-linked using 1% formaldehyde and quenched with glycine. To isolate the nuclei or chromatin, approximately 0.5 g of samples were ground in liquid nitrogen into fine powder and resuspended in 30 ml of EB1 buffer (0.4 M sucrose, 10 mM Tris–HCl, 5 mM b-mercaptoethanol, and 1 mM PMSF). The mixture was filtered through Miracloth (Millipore, cat. No. 475855-1R), and the filtrate was centrifuged at 1,800 × g for 10 min at 4 °C. The pellet was washed three times in 1.5 ml of EB2 buffer (0.25 M sucrose, 10 mM Tris–HCl, 5 mM b-mercaptoethanol, 10 mM MgCl2, 1% Triton X-100, and 1 mM PMSF) and centrifuged at 2,000 × g for 10 min at 4 °C. Next, the pellet was washed in 0.5 ml of EB3 buffer (1.7 M sucrose, 10 mM Tris–HCl, 5 mM b-mercaptoethanol, 2 mM MgCl2, 0.15% Triton X-100, and 1 mM PMSF) and centrifuged at 2,000 × g for 1 h at 4 °C. The final pellet was resuspended in 0.25 ml of NLB buffer, and the chromatin was fragmented into 200–500 bp by sonication in a Bioruptor (Diagenode). The chromatin sample was then centrifuged at 2,000 × g for 10 min at 4 °C, and the supernatant was used for IP. ChIP was performed using anti-GFP antibodies (ChromoTek, gtma-20).
After washing the bead-IP complexes, ChIP DNA purification, library preparation was prepared using an NEBNext® Ultra™ II DNA library prep kit for Illumina® sequencing (New England BioLabs, E7645). Finally, the DNA library was sequenced using an Illumina HiSeq X Ten system.

value: WT


title: GFP-ICE1_ChIP


title: 12571_BM_OT_BN EMM MYC+

description: Gene expression data

value: MYC+


title: HCI001_257_T_PT_42


title: HCI001_257_T_PT_52


title: HCI001_257_T_PT_41


title: HCI001_257_T_PT_38


title: HCI001_257_T_PT_43


title: HCI001_257_T_PT_48


title: HCI001_257_T_PT_37


title: HCI001_257_T_PT_39


title: HCI001_257_T_PT_34


title: HCI001_257_T_PT_35


title: HCI001_257_T_PT_32


title: HCI001_257_T_PT_33


title: HCI001_257_T_PT_31


title: VASCULAR SURGERY T1 [N049]

city: Gainesville

first: Azra

last: Bihorac

state: FL

address: 1600 SW Archer Road

department: Medicine

institute: University of Florida

description: VASCULAR SURGERY DAY 1

hyb_protocol: Labeled cDNA was hybridized to GeneChip™ Human Transcriptome 2.0 arrays according to ThermoFisher Scientific instructions, 16 hours at 45C at 60 rpm.

scan_protocol: Arrays were scanned GeneChip Scanner 3000 7G using AGCC software

data_processing: Background Correction, Normalization and Summarization were done by RMA using Transcriptome Analysis Console (TAC) software provided by Affymetrix. Statistical comparison was done using empirical Bayes method in Linear Models for Microarray Analysis (LIMMA) using TAC. Significance threshold was adjusted for multiple testing using Benjamini-Hochberg false discovery rate (FDR).

label: biotin

source_name: URINE

label_protocol: cDNA was amplified using GeneChip™ WT PLUS Reagent Kit, from ThermoFisher Scientific following manufacturers instructions.Amplified cDNA was fragmented with UDG and APE1 enzymes according to ThermoFisher Scientific instructions. Labeling was performed with TdT with biotin reagent followed by streptavidin/phycoerythrin.

extract_protocol: total RNA was extracted from the urine of patients using Qiagen RNeasy mini kit (250) Catalog Number - 74106 according the manufacturer's protocol.

treatment_protocol: Approximately 50mL Urine was spun down at 1500g for 30 min at 4 degrees Celsius. Pellet was collected, lysed using 1mL RLT lysis buffer with 10uL β-mercaptoethanol from the kit and processed according the manufacturer's protocol.

tag: gender

value: Male

tag: age


title: HCI001_257_T_PT_40

tag: patient id


title: VASCULAR SURGERY T1 [N091]

description: VASCULAR SURGERY DAY 1


title: VASCULAR SURGERY T1 [N059]

description: VASCULAR SURGERY DAY 1


title: HCI001_257_T_PT_36

tag: status


title: HCI001_257_T_PT_30


title: HCI001_257_T_PT_29


title: SEPTIC T1 [P0432]

description: SEPTIC DAY 1

value: Female


title: VASCULAR SURGERY T1 [N058]

description: VASCULAR SURGERY DAY 1


title: VASCULAR SURGERY T1 [N052]

description: VASCULAR SURGERY DAY 1


title: SEPTIC T1 [P0428]

description: SEPTIC DAY 1


title: VASCULAR SURGERY T1 [N090]

description: VASCULAR SURGERY DAY 1


title: VASCULAR SURGERY T1 [N047]

description: VASCULAR SURGERY DAY 1


title: VASCULAR SURGERY T1 [N056]

description: VASCULAR SURGERY DAY 1


title: VASCULAR SURGERY T1 [N094]

description: VASCULAR SURGERY DAY 1


title: VASCULAR SURGERY T1 [N089]

description: VASCULAR SURGERY DAY 1


title: HCI001_257_T_PT_28


title: VASCULAR SURGERY T1 [N044]

description: VASCULAR SURGERY DAY 1


title: HCI001_257_T_PT_26


title: HCI001_257_T_PT_27


title: HCI001_257_T_PT_25


title: HCI001_257_T_PT_24


title: HCI001_257_T_PT_23


title: VASCULAR SURGERY T1 [N093]

description: VASCULAR SURGERY DAY 1


title: HCI001_257_T_PT_22


title: HCI001_257_T_PT_20


title: HCI001_257_T_PT_19


title: HCI001_257_T_PT_18


title: VASCULAR SURGERY T1 [N092]

description: VASCULAR SURGERY DAY 1


title: HCI001_257_T_PT_17


title: HCI001_257_T_PT_16


title: VASCULAR SURGERY T1 [N054]

description: VASCULAR SURGERY DAY 1


title: VASCULAR SURGERY T1 [N088]

description: VASCULAR SURGERY DAY 1


title: VASCULAR SURGERY T1 [N055]

description: VASCULAR SURGERY DAY 1


title: HCI001_257_T_PT_14


title: VASCULAR SURGERY T1 [N077]

description: VASCULAR SURGERY DAY 1


title: HCI001_257_T_PT_15


title: VASCULAR SURGERY T1 [N073]

description: VASCULAR SURGERY DAY 1


title: HCI001_257_T_PT_21


title: HCI001_257_T_PT_13


title: VASCULAR SURGERY T1 [N082]

description: VASCULAR SURGERY DAY 1


title: VASCULAR SURGERY T1 [N085]

description: VASCULAR SURGERY DAY 1


title: VASCULAR SURGERY T1 [N080]

description: VASCULAR SURGERY DAY 1


title: VASCULAR SURGERY T1 [N079]

description: VASCULAR SURGERY DAY 1


title: VASCULAR SURGERY T1 [N078]

description: VASCULAR SURGERY DAY 1


title: VASCULAR SURGERY T1 [N083]

description: VASCULAR SURGERY DAY 1


title: HCI001_257_T_PT_12


title: VASCULAR SURGERY T1 [N076]

description: VASCULAR SURGERY DAY 1


title: VASCULAR SURGERY T1 [N075]

description: VASCULAR SURGERY DAY 1


title: VASCULAR SURGERY T1 [N074]

description: VASCULAR SURGERY DAY 1


title: VASCULAR SURGERY T1 [N072]

description: VASCULAR SURGERY DAY 1


title: HCI001_257_T_PT_11


title: VASCULAR SURGERY T1 [N070]

description: VASCULAR SURGERY DAY 1


title: HCI001_257_T_PT_10


title: VASCULAR SURGERY T1 [N071]

description: VASCULAR SURGERY DAY 1


title: VASCULAR SURGERY T1 [N069]

description: VASCULAR SURGERY DAY 1


title: HCI001_257_T_PT_8


title: HCI001_257_T_PT_9


title: VASCULAR SURGERY T1 [N068]

description: VASCULAR SURGERY DAY 1


title: HCI001_257_T_PT_7


title: HCI001_257_T_PT_6


title: HCI001_257_T_PT_5


title: HCI001_257_T_PT_4


title: HCI001_257_T_PT_3


title: HCI001_257_T_PT_1


title: HCI001_257_I_LU_96

value: Metastasis

value: Lung


title: HCI001_257_I_LU_95


title: HCI001_257_I_LU_94


title: SEPTIC T1 [P0438]

description: VASCULAR SURGERY DAY 1


title: HCI001_257_I_LU_93


title: SEPTIC T1 [P0419]

description: SEPTIC DAY 1


title: SEPTIC T1 [P0440]

description: VASCULAR SURGERY DAY 1


title: SEPTIC T1 [P0443]

description: VASCULAR SURGERY DAY 1


title: SEPTIC T1 [P0420]

description: SEPTIC DAY 1


title: SEPTIC T1 [P0418]

description: SEPTIC DAY 1


title: SEPTIC T1 [P0404]

description: SEPTIC DAY 1


title: HCI001_257_I_LU_92


title: SEPTIC T1 [P0435]

description: SEPTIC DAY 1


title: SEPTIC T1 [P0417]

description: SEPTIC DAY 1


title: SEPTIC T1 [P0441]

description: VASCULAR SURGERY DAY 1


title: SEPTIC T1 [P0403]

description: SEPTIC DAY 1


title: SEPTIC T1 [P0436]

description: SEPTIC DAY 1


title: HCI001_257_T_PT_2


title: SEPTIC T1 [P0425]

description: SEPTIC DAY 1


title: HCI001_257_I_LU_90


title: SEPTIC T1 [P0434]

description: SEPTIC DAY 1


title: HCI001_257_I_LU_89


title: SEPTIC T1 [P0401]

description: SEPTIC DAY 1


title: HCI001_257_I_LU_88


title: HCI001_257_I_LU_87


title: HCI001_257_I_LU_85


title: HCI001_257_I_LU_86


title: HCI001_257_I_LU_83


title: HCI001_257_I_LU_84


title: HCI001_257_I_LU_82


title: SEPTIC T1 [P0392]

description: SEPTIC DAY 1


title: HCI001_257_I_LU_77


title: HCI001_257_I_LU_78


title: HCI001_257_I_LU_79


title: HCI001_257_I_LU_80


title: HCI001_257_I_LU_81


title: SEPTIC T1 [P0385]

description: SEPTIC DAY 1


title: HCI001_257_I_LU_76


title: SEPTIC T1 [P0396]

description: SEPTIC DAY 1


title: SEPTIC T1 [P0390]

description: SEPTIC DAY 1


title: SEPTIC T1 [P0402]

description: SEPTIC DAY 1


title: HCI001_257_I_LU_75


title: HCI001_257_I_LU_74


title: HCI001_257_I_LU_72


title: HCI001_257_I_LU_73


title: SEPTIC T1 [P0382]

description: SEPTIC DAY 1


title: SEPTIC T1 [P0387]

description: SEPTIC DAY 1


title: HCI001_257_I_LU_71


title: SEPTIC T1 [P0375]

description: SEPTIC DAY 1


title: SEPTIC T1 [P0398]

description: SEPTIC DAY 1


title: SEPTIC T1 [P0380]

description: SEPTIC DAY 1


title: HCI001_257_I_LU_70


title: SEPTIC T1 [P0359]

description: SEPTIC DAY 1


title: SEPTIC T1 [P0362]

description: SEPTIC DAY 1


title: HCI001_257_I_LU_68


title: HCI001_257_I_LU_69


title: SEPTIC T1 [P0364]

description: SEPTIC DAY 1


title: SEPTIC T1 [P0381]

description: SEPTIC DAY 1


title: SEPTIC T1 [P0389]

description: SEPTIC DAY 1


title: SEPTIC T1 [P0341]

description: SEPTIC DAY 1


title: HCI001_257_I_LU_66


title: HCI001_257_I_LU_67


title: HCI001_257_I_LU_65


title: SEPTIC T1 [P0383]

description: SEPTIC DAY 1


title: SEPTIC T1 [P0357]

description: SEPTIC DAY 1


title: SEPTIC T1 [P0353]

description: SEPTIC DAY 1


title: SEPTIC T1 [P0352]

description: SEPTIC DAY 1


title: SEPTIC T1 [P0348]

description: SEPTIC DAY 1


title: SEPTIC T1 [P0343]

description: SEPTIC DAY 1


title: HCI001_257_I_LU_64


title: HCI001_257_I_LU_62


title: HCI001_257_I_LU_61


title: HCI001_257_I_LU_60


title: SEPTIC T1 [P0344]

description: SEPTIC DAY 1


title: HCI001_257_I_LU_59


title: HCI001_257_I_LU_58


title: VASCULAR SURGERY T1_N045

description: cDNA prepared from urine cellular mRNA

value: URINE

tag: sample type

value: VASCULAR SURGERY DAY 1


title: SEPTIC T1 [P0347]

description: SEPTIC DAY 1


title: HCI001_257_I_LU_56


title: HCI001_257_I_LU_57


title: VASCULAR SURGERY T1_N053

description: cDNA prepared from urine cellular mRNA


title: VASCULAR SURGERY T1_N048

description: cDNA prepared from urine cellular mRNA


title: HCI001_257_I_LU_55


title: VASCULAR SURGERY T1_N046

description: cDNA prepared from urine cellular mRNA


title: VASCULAR SURGERY T1_N043

description: cDNA prepared from urine cellular mRNA


title: HCI001_257_I_LU_63


title: HCI001_257_I_LU_54


title: VASCULAR SURGERY T1_N051

description: cDNA prepared from urine cellular mRNA


title: VASCULAR SURGERY T1_N041

description: cDNA prepared from urine cellular mRNA


title: VASCULAR SURGERY T1_N040

description: cDNA prepared from urine cellular mRNA


title: VASCULAR SURGERY T1_N039

description: cDNA prepared from urine cellular mRNA


title: VASCULAR SURGERY T1_N042

description: cDNA prepared from urine cellular mRNA


title: SEPTIC T1_P0332

description: cDNA prepared from urine cellular mRNA

value: SEPTIC DAY 1


title: HCI001_257_I_LU_53


title: HCI001_257_I_LU_51


title: HCI001_257_I_LU_47


title: HCI001_257_I_LU_52


title: HCI001_257_I_LU_45


title: SEPTIC T1_P0323

description: cDNA prepared from urine cellular mRNA


title: SEPTIC T1_P0324

description: cDNA prepared from urine cellular mRNA


title: SEPTIC T1_P0320

description: cDNA prepared from urine cellular mRNA


title: VASCULAR SURGERY T1_N037

description: cDNA prepared from urine cellular mRNA


title: SEPTIC T1_P0322

description: cDNA prepared from urine cellular mRNA


title: HCI001_257_I_LU_43


title: HCI001_257_I_LU_42


title: HCI001_257_I_LU_41


title: HCI001_257_I_LU_49


title: HCI001_257_I_LU_40


title: HCI001_257_I_LU_48


title: SEPTIC T1_P0315

description: cDNA prepared from urine cellular mRNA


title: HCI001_257_I_LU_46


title: SEPTIC T1_P0314

description: cDNA prepared from urine cellular mRNA


title: HCI001_257_I_LU_50


title: SEPTIC T1_P0304

description: cDNA prepared from urine cellular mRNA


title: SEPTIC T1_P0310

description: cDNA prepared from urine cellular mRNA


title: SEPTIC T1_P0318

description: cDNA prepared from urine cellular mRNA


title: SEPTIC T1_P0308

description: cDNA prepared from urine cellular mRNA


title: HCI001_257_I_LU_39


title: SEPTIC T1_P0300

description: cDNA prepared from urine cellular mRNA


title: SEPTIC T1_P0298

description: cDNA prepared from urine cellular mRNA


title: SEPTIC T1_P0302

description: cDNA prepared from urine cellular mRNA


title: SEPTIC T1_P0327

description: cDNA prepared from urine cellular mRNA


title: SEPTIC T1_P0309

description: cDNA prepared from urine cellular mRNA


title: SEPTIC T1_P0296

description: cDNA prepared from urine cellular mRNA


title: HCI001_257_I_LU_44


title: SEPTIC T1_P0292

description: cDNA prepared from urine cellular mRNA


title: HCI001_257_I_LU_91


title: HCI001_257_I_LU_37


title: HCI001_257_I_LU_38


title: HCI001_257_I_LU_36


title: HCI001_257_I_LU_33


title: HCI001_257_I_LU_35


title: HCI001_257_I_LU_34


title: SEPTIC T1_P0287

description: cDNA prepared from urine cellular mRNA


title: HCI001_257_I_LU_32


title: HCI001_257_I_LU_31


title: HCI001_257_I_LU_28


title: HCI010_469_L_LU_91


title: SEPTIC T1_P0279

description: cDNA prepared from urine cellular mRNA


title: HCI010_469_L_LU_89


title: SEPTIC T1_P0282

description: cDNA prepared from urine cellular mRNA


title: HCI010_469_L_LU_88


title: HCI010_469_L_LU_92


title: HCI010_469_L_LU_90


title: SEPTIC T1_P0283

description: cDNA prepared from urine cellular mRNA


title: SEPTIC T1_P0284

description: cDNA prepared from urine cellular mRNA


title: HCI001_257_I_LU_30


title: SEPTIC T1_P0255

description: cDNA prepared from urine cellular mRNA


title: SEPTIC T1_P0264

description: cDNA prepared from urine cellular mRNA


title: SEPTIC T1_P0253

description: cDNA prepared from urine cellular mRNA


title: HCI001_257_I_LU_29


title: SEPTIC T1_P0271

description: cDNA prepared from urine cellular mRNA


title: SEPTIC T1_P0254

description: cDNA prepared from urine cellular mRNA


title: HCI010_469_L_LU_87


title: HCI010_469_L_LU_86


title: HCI010_469_L_LU_85


title: SEPTIC T1_P0270

description: cDNA prepared from urine cellular mRNA


title: SEPTIC T1_P0245

description: cDNA prepared from urine cellular mRNA


title: SEPTIC T1_P0273

description: cDNA prepared from urine cellular mRNA


title: SEPTIC T1_P0251

description: cDNA prepared from urine cellular mRNA


title: SEPTIC T1_P0276

description: cDNA prepared from urine cellular mRNA


title: SEPTIC T1_P0272

description: cDNA prepared from urine cellular mRNA


title: HCI010_469_L_LU_84


title: SEPTIC T1_P0246

description: cDNA prepared from urine cellular mRNA


title: HCI010_469_L_LU_83


title: HCI010_469_L_LU_82


title: HCI010_469_L_LU_81


title: SEPTIC T1_P0244

description: cDNA prepared from urine cellular mRNA


title: HCI010_469_L_LU_80


title: HCI010_469_L_LU_79


title: HCI010_469_L_LU_78


title: HCI010_469_L_LU_77


title: HCI010_469_L_LU_76


title: SEPTIC T1_P0247

description: cDNA prepared from urine cellular mRNA


title: HCI010_469_L_LU_75


title: HCI010_469_L_LU_74


title: HCI010_469_L_LU_73


title: SEPTIC T1_P0095

description: cDNA prepared from urine cellular mRNA


title: HCI010_469_L_LU_72


title: HCI010_469_L_LU_71


title: SEPTIC T1_P0237

description: cDNA prepared from urine cellular mRNA


title: HCI010_469_L_LU_70


title: HCI010_469_L_LU_69


title: HCI010_469_L_LU_68


title: SEPTIC T1_P0235

description: cDNA prepared from urine cellular mRNA


title: SEPTIC T1_P0240

description: cDNA prepared from urine cellular mRNA


title: HCI010_469_L_LU_67


title: SEPTIC T1_P0068

description: cDNA prepared from urine cellular mRNA


title: HCI010_469_L_LU_65


title: SEPTIC T1_P0236

description: cDNA prepared from urine cellular mRNA


title: SEPTIC T1_P0232

description: cDNA prepared from urine cellular mRNA


title: SEPTIC T1_P0228

description: cDNA prepared from urine cellular mRNA


title: SEPTIC T1_P0225

description: cDNA prepared from urine cellular mRNA


title: HCI010_469_L_LU_66


title: SEPTIC T1_P0233

description: cDNA prepared from urine cellular mRNA


title: SEPTIC T1_P0222

description: cDNA prepared from urine cellular mRNA


title: SEPTIC T1_P0229

description: cDNA prepared from urine cellular mRNA


title: HCI010_469_L_LU_64


title: HCI010_469_L_LU_63


title: SEPTIC T1_P0230

description: cDNA prepared from urine cellular mRNA


title: HCI010_469_L_LU_62


title: SEPTIC T1_P0218

description: cDNA prepared from urine cellular mRNA


title: HCI010_469_L_LU_61


title: SEPTIC T1_P0224

description: cDNA prepared from urine cellular mRNA


title: HCI010_469_L_LU_60


title: SEPTIC T1_P0216

description: cDNA prepared from urine cellular mRNA


title: SEPTIC T1_P0220

description: cDNA prepared from urine cellular mRNA


title: SEPTIC T1_P0217

description: cDNA prepared from urine cellular mRNA


title: HCI010_469_L_LU_59


title: HCI010_469_L_LU_57


title: HCI010_469_L_LU_58


title: SEPTIC T1_P0214

description: cDNA prepared from urine cellular mRNA


title: HCI010_469_L_LU_55


title: HCI010_469_L_LU_56


title: HCI010_469_L_LU_54


title: HCI010_469_L_LU_53


title: SEPTIC T1_P0213

description: cDNA prepared from urine cellular mRNA


title: HCI010_469_L_LU_52


title: SEPTIC T1_P0211

description: cDNA prepared from urine cellular mRNA


title: SEPTIC T1_P0210

description: cDNA prepared from urine cellular mRNA


title: HCI010_469_L_LU_51


title: HCI010_469_L_LU_50


title: SEPTIC T1_P0208

description: cDNA prepared from urine cellular mRNA


title: HCI010_469_L_LU_49


title: HCI010_469_L_LU_48


title: HCI010_469_L_LU_47


title: SEPTIC T1_P0205

description: cDNA prepared from urine cellular mRNA


title: SEPTIC T1_P0207

description: cDNA prepared from urine cellular mRNA


title: HCI010_469_L_LU_46


title: HCI010_469_L_LU_45


title: HCI010_469_L_LU_43


title: SEPTIC T1_P0190

description: cDNA prepared from urine cellular mRNA


title: SEPTIC T1_P0242

description: cDNA prepared from urine cellular mRNA


title: SEPTIC T1_P0186

description: cDNA prepared from urine cellular mRNA


title: SEPTIC T1_P0202

description: cDNA prepared from urine cellular mRNA


title: SEPTIC T1_P0197

description: cDNA prepared from urine cellular mRNA


title: SEPTIC T1_P0176

description: cDNA prepared from urine cellular mRNA


title: SEPTIC T1_P0168

description: cDNA prepared from urine cellular mRNA


title: SEPTIC T1_P0188

description: cDNA prepared from urine cellular mRNA


title: SEPTIC T1_P0200

description: cDNA prepared from urine cellular mRNA


title: SEPTIC T1_P0174

description: cDNA prepared from urine cellular mRNA


title: SEPTIC T1_P0175

description: cDNA prepared from urine cellular mRNA


title: SEPTIC T1_P0189

description: cDNA prepared from urine cellular mRNA


title: SEPTIC T1_P0187

description: cDNA prepared from urine cellular mRNA


title: SEPTIC T1_P0203

description: cDNA prepared from urine cellular mRNA


title: SEPTIC T1_P0204

description: cDNA prepared from urine cellular mRNA


title: HCI010_469_L_LU_40


title: SEPTIC T1_P0184

description: cDNA prepared from urine cellular mRNA


title: HCI010_469_L_LU_42


title: HCI010_469_L_LU_44


title: HCI010_469_L_LU_41


title: HCI010_469_L_LU_36


title: HCI010_469_L_LU_34


title: HCI010_469_L_LU_39


title: HCI010_469_L_LU_32


title: HCI010_469_L_LU_33


title: HCI010_469_L_LU_38


title: HCI010_469_L_LU_37


title: HCI010_469_L_LU_30


title: HCI010_469_L_LU_28


title: SEPTIC T1_P0159

description: cDNA prepared from urine cellular mRNA


title: HCI010_469_L_LU_27


title: SEPTIC T1_P0158

description: cDNA prepared from urine cellular mRNA


title: HCI010_469_L_LU_35


title: HCI010_469_L_LU_31


title: SEPTIC T1_P0167

description: cDNA prepared from urine cellular mRNA


title: SEPTIC T1_P0177

description: cDNA prepared from urine cellular mRNA


title: SEPTIC T1_P0162

description: cDNA prepared from urine cellular mRNA


title: SEPTIC T1_P0156

description: cDNA prepared from urine cellular mRNA


title: SEPTIC T1_P0149

description: cDNA prepared from urine cellular mRNA


title: HCI010_469_L_LU_26


title: SEPTIC T1_P0157

description: cDNA prepared from urine cellular mRNA


title: SEPTIC T1_P0142

description: cDNA prepared from urine cellular mRNA


title: SEPTIC T1_P0141

description: cDNA prepared from urine cellular mRNA


title: SEPTIC T1_P0147

description: cDNA prepared from urine cellular mRNA


title: SEPTIC T1_P0152

description: cDNA prepared from urine cellular mRNA


title: HCI010_469_L_LU_23


title: HCI010_469_L_LU_29


title: SEPTIC T1_P0140

description: cDNA prepared from urine cellular mRNA


title: SEPTIC T1_P0135

description: cDNA prepared from urine cellular mRNA


title: SEPTIC T1_P0134

description: cDNA prepared from urine cellular mRNA


title: SEPTIC T1_P0133

description: cDNA prepared from urine cellular mRNA


title: HCI010_469_L_LU_22


title: HCI010_469_L_LU_24


title: HCI010_469_L_LU_25


title: SEPTIC T1_P0129

description: cDNA prepared from urine cellular mRNA


title: HCI010_469_L_LU_20


title: HCI010_469_L_LU_21


title: HCI010_469_L_LU_19


title: SEPTIC T1_P0121

description: cDNA prepared from urine cellular mRNA


title: HCI010_469_L_LU_17


title: SEPTIC T1_P0120

description: cDNA prepared from urine cellular mRNA


title: HCI010_469_L_LU_16


title: SEPTIC T1_P0125

description: cDNA prepared from urine cellular mRNA


title: SEPTIC T1_P0111

description: cDNA prepared from urine cellular mRNA


title: HCI010_469_L_LU_14


title: HCI010_469_L_LU_13


title: HCI010_469_L_LU_11


title: HCI010_469_L_LU_12


title: HCI010_469_L_LU_10


title: SEPTIC T1_P0116

description: cDNA prepared from urine cellular mRNA


title: HCI010_469_L_LU_18


title: SEPTIC T1_P0166

description: cDNA prepared from urine cellular mRNA


title: SEPTIC T1_P0107

description: cDNA prepared from urine cellular mRNA


title: HCI010_469_L_LU_8


title: HCI010_469_L_LU_9


title: HCI010_469_L_LU_15


title: HCI010_469_L_LU_7


title: SEPTIC T1_P0104

description: cDNA prepared from urine cellular mRNA


title: SEPTIC T1_P0102

description: cDNA prepared from urine cellular mRNA


title: HCI010_469_L_LU_6


title: VASCULAR SURGERY T1_N031

description: cDNA prepared from urine cellular mRNA


title: HCI010_469_L_LU_4


title: VASCULAR SURGERY T1_N016

description: cDNA prepared from urine cellular mRNA


title: VASCULAR SURGERY T1_N028

description: cDNA prepared from urine cellular mRNA


title: HCI010_469_L_LU_2


title: HCI010_469_L_LU_3


title: VASCULAR SURGERY T1_N024

description: cDNA prepared from urine cellular mRNA


title: HCI010_469_L_LU_1


title: VASCULAR SURGERY T1_N004

description: cDNA prepared from urine cellular mRNA


title: HCI010_470_T_PT_95


title: HCI010_470_T_PT_96


title: HCI010_470_T_PT_94


title: VASCULAR SURGERY T1_N036

description: cDNA prepared from urine cellular mRNA


title: VASCULAR SURGERY T1_N027

description: cDNA prepared from urine cellular mRNA


title: VASCULAR SURGERY T1_N006

description: cDNA prepared from urine cellular mRNA


title: VASCULAR SURGERY T1_N019

description: cDNA prepared from urine cellular mRNA


title: SEPTIC T1_P0053

description: cDNA prepared from urine cellular mRNA


title: VASCULAR SURGERY T1_N014

description: cDNA prepared from urine cellular mRNA


title: HCI010_470_T_PT_93


title: VASCULAR SURGERY T1_N018

description: cDNA prepared from urine cellular mRNA


title: HCI010_469_L_LU_5


title: VASCULAR SURGERY T1_N034

description: cDNA prepared from urine cellular mRNA


title: HCI010_470_T_PT_92


title: HCI010_470_T_PT_91


title: VASCULAR SURGERY T1_N023

description: cDNA prepared from urine cellular mRNA


title: VASCULAR SURGERY T1_N011

description: cDNA prepared from urine cellular mRNA


title: VASCULAR SURGERY T1_N021

description: cDNA prepared from urine cellular mRNA


title: VASCULAR SURGERY T1_N020

description: cDNA prepared from urine cellular mRNA


title: HCI010_470_T_PT_90


title: HCI010_470_T_PT_89


title: VASCULAR SURGERY T1_N032

description: cDNA prepared from urine cellular mRNA


title: VASCULAR SURGERY T1_N033

description: cDNA prepared from urine cellular mRNA


title: VASCULAR SURGERY T1_N025

description: cDNA prepared from urine cellular mRNA


title: VASCULAR SURGERY T1_N022

description: cDNA prepared from urine cellular mRNA


title: HCI010_470_T_PT_88


title: HCI010_470_T_PT_87


title: HCI010_470_T_PT_86


title: VASCULAR SURGERY T1_N001

description: cDNA prepared from urine cellular mRNA


title: HCI010_470_T_PT_85


title: HCI010_470_T_PT_84


title: SEPTIC T1_P0076

description: cDNA prepared from urine cellular mRNA


title: HCI010_470_T_PT_83


title: HCI010_470_T_PT_82


title: HCI010_470_T_PT_80


title: HCI010_470_T_PT_79


title: HCI010_470_T_PT_81


title: SEPTIC T1_P0056

description: cDNA prepared from urine cellular mRNA


title: SEPTIC T1_P0062

description: cDNA prepared from urine cellular mRNA


title: SEPTIC T1_P0073

description: cDNA prepared from urine cellular mRNA


title: HCI010_470_T_PT_78


title: SEPTIC T1_P0072

description: cDNA prepared from urine cellular mRNA


title: HCI010_470_T_PT_76


title: SEPTIC T1_P0074

description: cDNA prepared from urine cellular mRNA


title: SEPTIC T1_P0066

description: cDNA prepared from urine cellular mRNA


title: HCI010_470_T_PT_74


title: HCI010_470_T_PT_73


title: HCI010_470_T_PT_75


title: SEPTIC T1_P0089

description: cDNA prepared from urine cellular mRNA


title: SEPTIC T1_P0100

description: cDNA prepared from urine cellular mRNA


title: SEPTIC T1_P0094

description: cDNA prepared from urine cellular mRNA


title: SEPTIC T1_P0091

description: cDNA prepared from urine cellular mRNA


title: SEPTIC T1_P0101

description: cDNA prepared from urine cellular mRNA


title: SEPTIC T1_P0078

description: cDNA prepared from urine cellular mRNA


title: SEPTIC T1_P0087

description: cDNA prepared from urine cellular mRNA


title: SEPTIC T1_P0049

description: cDNA prepared from urine cellular mRNA


title: HCI010_470_T_PT_77


title: HCI010_470_T_PT_72


title: HCI010_470_T_PT_71


title: HCI010_470_T_PT_70


title: SEPTIC T1_P0052

description: cDNA prepared from urine cellular mRNA


title: SEPTIC T1_P0046

description: cDNA prepared from urine cellular mRNA


title: SEPTIC T1_P0077

description: cDNA prepared from urine cellular mRNA


title: HCI010_470_T_PT_67


title: HCI010_470_T_PT_69


title: SEPTIC T1_P0085

description: cDNA prepared from urine cellular mRNA


title: HCI010_470_T_PT_66


title: SEPTIC T1_P0045

description: cDNA prepared from urine cellular mRNA


title: SEPTIC T1_P0044

description: cDNA prepared from urine cellular mRNA


title: HCI010_470_T_PT_65


title: HCI010_470_T_PT_64


title: HCI010_470_T_PT_63


title: HCI010_470_T_PT_68


title: HCI010_470_T_PT_61


title: SEPTIC T1_P0029

description: cDNA prepared from urine cellular mRNA


title: HCI010_470_T_PT_60


title: HCI010_470_T_PT_59


title: HCI010_470_T_PT_58


title: HCI010_470_T_PT_57


title: SEPTIC T1_P0032

description: cDNA prepared from urine cellular mRNA


title: SEPTIC T1_P0031

description: cDNA prepared from urine cellular mRNA


title: HCI010_470_T_PT_62


title: SEPTIC T1_P0042

description: cDNA prepared from urine cellular mRNA


title: SEPTIC T1_P0025

description: cDNA prepared from urine cellular mRNA


title: SEPTIC T1_P0023

description: cDNA prepared from urine cellular mRNA


title: SEPTIC T1_P0017

description: cDNA prepared from urine cellular mRNA


title: SEPTIC T1_P0027

description: cDNA prepared from urine cellular mRNA


title: HCI010_470_T_PT_54


title: SEPTIC T1_P0020

description: cDNA prepared from urine cellular mRNA


title: HCI010_470_T_PT_53


title: SEPTIC T1_P0019

description: cDNA prepared from urine cellular mRNA


title: SEPTIC T1_P0024

description: cDNA prepared from urine cellular mRNA


title: HCI010_470_T_PT_50


title: HCI010_470_T_PT_51


title: SEPTIC T1_P0015

description: cDNA prepared from urine cellular mRNA


title: HCI010_470_T_PT_52


title: SEPTIC T1_P0011

description: cDNA prepared from urine cellular mRNA


title: HCI010_470_T_PT_56


title: SEPTIC T1_P0004

description: cDNA prepared from urine cellular mRNA


title: SEPTIC T1_P0006

description: cDNA prepared from urine cellular mRNA


title: HCI010_470_T_PT_55


title: HCI010_470_T_PT_49


title: HCI010_470_T_PT_48


title: HCI010_470_T_PT_47


title: HCI010_470_T_PT_46


title: HCI010_470_T_PT_44


title: IPF009-14non-in

city: Los angeles

first: Xue

last: Liu

address: AHSP A9404, 127 S. San Vicente Blvd

institute: Cedars-Sinai Medical Center

data_processing:
We used Cell Ranger version 1.3.1 (10x Genomics) to process raw sequencing data and Cell Ranger R kit version 3.0.0 and Seurat suite version 3.0.0 for downstream analysis.
For clustering, principal-component analysis was performed for dimension reduction.
Top 10 principal components (PCs) were selected by using a permutationbased test implemented in Seurat and passed to t-SNE for clustering visualization. sSeq version 1.0.0 integrated in the Cell Ranger R kit was used for modeling the gene expression with negative binomial distribution to identify genes whose expression was enriched in specific clusters. The Benjamini-Hochberg procedure was used for correcting errors of multiple testing.

source_name: Primary lung fibroblasts

growth_protocol: Human lung fibroblasts were isolated from surgical lung biopsies or lung transplant explants obtained from patients with IPF. The diagnosis of IPF was arrived at by standard accepted American Thoracic Society recommendations (ATS/ERS, 2000). The tissues were minced, digested, and cultured in DMEM supplemented with 15% FBS and Antibiotic-Antimycotic.

extract_protocol:
After 24 hours culture, cells passed through the matrigel layer and clung to the bottom of the insert membrane were determined as invasive fibroblasts. Cells remaining on the upper chamber were defined as non-invasive fibroblasts.
scRNA-seq libraries were prepared per the Single Cell 30 Reagent Kit User Guide v2 (10x Genomics). Cellular suspensions were loaded on a Chromium Controller instrument (10x Genomics) to generate single-cell gel bead-inemulsions (GEMs). GEM-reverse transcriptions (GEM-RTs) were performed in a Veriti 96-well thermal cycler (Thermo Fisher Scientific). After RT, GEMs were harvested and the cDNAs were amplified and cleaned up with the SPRIselect Reagent Kit (Beckman Coulter). Indexed sequencing libraries were constructed using the Chromium Single-Cell 30 Library Kit (10x Genomics) for enzymatic fragmentation, end-repair, A-tailing, adaptor ligation, ligation cleanup, sample index PCR, and PCR cleanup. The barcoded sequencing libraries were quantified by quantitative PCR using the KAPA Library Quantification Kit (KAPA Biosystems).

treatment_protocol: Fibroblasts were loaded into the top chamber of cell culture insert with 8.0 μm pore (for migration) or BioCoat Matrigel Invasion Chamber (for invasion). PDGF-BB (10 ng/ml, Peprotech) was used as a chemoattractant in the bottom chamber.

tag: lung fibroblasts

value: Non-invasive lung fibroblasts

tag: passages

tag: assay

value: scRNA-sequencing


title: IPF007-14in

value: Invasive lung fibroblasts


title: IPF009-14in


title: IPF007-14non-in


title: HCI010_470_T_PT_45

value: Tumor

tag: tissue source

value: Primary Tumor

tag: mouse


title: SEPTIC T1_P0008

description: cDNA prepared from urine cellular mRNA

tag: tissue


title: SEPTIC T1_P0002

description: cDNA prepared from urine cellular mRNA


title: HCI010_470_T_PT_43


title: HCI010_470_T_PT_42


title: HCI010_470_T_PT_41


title: T24 shCTL, biological rep2

first: Xiaojing

last: Huang

address: Xue Fu Road 12

institute: Model Animal Research Center of Nanjing University

hyb_protocol: Array hybridization and washing was performed using GeneChip® Hybridization, Wash and Stain Kit (Cat#900720, Affymetrix, Santa Clara, CA, US)in a Hybridization Oven 645 (Cat#00-0331-220V, Affymetrix, Santa Clara, CA, US)and a Fluidics Station 450 (Cat#00-0079, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions.

scan_protocol: Arrays were scanned by Affymetrix GeneChip® Scanner 3000 (Cat#00-00213, Affymetrix, Santa Clara, CA, US). Command Console Software (Affymetrix, Santa Clara, CA, US) was used to control the scanner and summarize probe cell intensity data (CEL file generation) with default settings. Then raw data were normalized by Expression Console.

source_name: bladder cancer cell line

label_protocol: Total RNA was amplified, labeled and purified by Affymetrix  WT PLUS Reagent Kit(Cat#902280， Affymetrix, Santa Clara, CA, US) according to the manufacturer’s instructions to obtain biotin labeled cDNA.

growth_protocol: T24 cell lines were cultured with RPMI 1640 medium (Life Technologies) with supplemented with 10% FBS.

extract_protocol: Total RNA was extracted using TRIZOL Reagent (Cat#15596-018，Life technologies, Carlsbad, CA, US)following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNeasy micro kit (Cat#74004, QIAGEN, GmBH, Germany) and RNase-Free DNase Set (Cat#79254, QIAGEN, GmBH, Germany).

tag: cell line

tag: genotype/variation

value: shCTL control


title: SEPTIC T1_P0010

description: cDNA prepared from urine cellular mRNA


title: CC008-15in


title: CC007-15in


title: T24 sh1, biological rep2

data_processing: Command Console Software (Affymetrix, Santa Clara, CA, US) was used to control the scanner and summarize probe cell intensity data (CEL file generation) with default settings. Then raw data were normalized by Expression Console.

value: HP1gamma knock down


title: HCI010_470_T_PT_40


title: T24 sh1, biological rep1


title: T24 shCTL, biological rep1


title: RNA-seq_K562_dCas9-cBio-sgSE_rep2

city: Memphis

first: Jian

last: Xu

state: Tennessee

address: 262 Danny Thomas Place, MS 345

department: Pathology

institute: St. Jude Children's Research Hospital

data_processing:
Sequencing reads were aligned to human genome assembly hg19 or mm10 by STAR.
The number of reads aligned to RefSeq annotated genes' exons were counted and further normalized to be of unit RPKM (number of reads per kilo base pair per million total reads).
Genome_build: hg19, mm10
Supplementary_files_format_and_content: text file of gene FPKM values

source_name: Human K562 cells

growth_protocol: Human K562 cells were cultured in IMDM supplemented with 10% heat-inactivated fetal bovine serum (FBS).  G1E-ER4 cells were cultured in IMDM medium containing 15% FBS, 50 ng/mL recombinant SCF, and 2 U/ml recombinant human erythropoietin (EPO).

extract_protocol: For RNA-seq analysis using the illumina NextSeq500, 200ng of total RNA was processed for library generation using the NEBNext Ultra RNA Library Prep Kit for Illumina (New England Biolabs) following the manufacturer’s protocol.

treatment_protocol: G1E-ER4 cells were treated with 10-7 M β-estradiol to induce erythroid differentiation.

value: K562 cells


title: RNA-seq_K562_dCas9-cBio-sgLCR-HS1-5_rep2


title: CC008-15non-in


title: HCI010_470_T_PT_36


title: HCI010_470_T_PT_38


title: RNA-seq_K562_WT_rep2


title: CAPTURE-ChIP-seq_K562_dCas9-Cbio-sgGAL4_rep4

data_processing:
Raw reads were aligned to human (hg19)  genome assembly using Bowtie2 59  with default parameters.
Peak detection was performed with the Model-based Analysis of ChIP-Seq (MACS) algorithm (http://liulab.dfci.harvard.edu/MACS/).
The wig files were generated by a moving window of size 200bp. The tag count in the windown was further normalized by total read count for ChIP-seq data generated by NextSeq500.
Genome_build: hg19
Supplementary_files_format_and_content: wig file, peak bed file

growth_protocol: Human K562 cells were cultured in IMDM supplemented with 10% heat-inactivated fetal bovine serum (FBS) and 2% penicillin-streptomycin.

extract_protocol: For ChIP-seq analysis using the Illumina NextSeq500, 10-20 ng of ChIP DNA was processed for library generation using the NEBNext ChIP-seq Library Prep Master Mix following the manufacturer’s protocol (New England Biolabs).

value: Human K562 cells

tag: streptavidin dynabeads

value: ThermoFisher 65602


title: CC007-15non-in


title: CAPTURE-ChIP-seq_K562_dCas9-Cbio-sgGAL4_rep3


title: HCI010_470_T_PT_37


title: HCI010_470_T_PT_34


title: HCI010_470_T_PT_39


title: HCI010_470_T_PT_35


title: RNA-seq_K562_dCas9-cBio-sgSE_rep1


title: HCI010_470_T_PT_32


title: RNA-seq_K562_WT_rep1


title: HCI010_470_T_PT_31


title: CAPTURE-ChIP-seq_K562_dCas9-Cbio-sgGAL4_rep2


title: RNA-seq_K562_dCas9-cBio-sgLCR-HS1-5_rep1


title: CAPTURE-ChIP-seq_K562_dCas9-Cbio-sgSE_rep2


title: HCI010_470_T_PT_29


title: CAPTURE-ChIP-seq_K562_dCas9-Cbio-sgLCR_HS1-5_rep2


title: CAPTURE-ChIP-seq_K562_dCas9-Cbio-sgSE_rep1


title: HCI010_470_T_PT_27


title: HCI010_470_T_PT_26


title: CAPTURE-ChIP-seq_K562_dCas9-Cbio-sgLCR_HS1-5_rep1


title: HCI010_470_T_PT_25


title: HCI010_470_T_PT_33


title: CAPTURE-3C-seq_K562_sgSE-combined

description: CAPTURE-3C-seq_K562_sgSE_combined_interaction

data_processing:
Library strategy: 3C-seq
Sequencing reads were aligned to human genome assembly hg19  or mm10 using Bowtie2 v2.2.8 with default parameters. The reads with low mapping qualit and duplicate reads were removed after the aligment with the Picard command-line tools.
After preprocessing and filtering, we generated the list of count numbers of read pairs from the bait region to any chromosomal regions. A pair of reads that located within two different regions is considered an interaction between them.
The interaction significance between the bait region and another chromosomal region was calculated by a Bayesian-Mixture Model. The PETs from bait region to any chromosomal regions were reported in Pairwise interaction format (http://wiki.wubrowse.org/Long-range).
Genome_build: hg19, mm10
Supplementary_files_format_and_content: Pairwise Interaction Format

extract_protocol: For 3C-seq analysis using the Illumina NextSeq500, 10 ng of 3C DNA was processed for library generation using the NEBNext ChIP-seq Library Prep Master Mix following the manufacturer’s protocol (New England Biolabs). Raw reads that aligned to exactly one location in the reference human genome (hg19) were retained for downstream data analysis.


title: CAPTURE-3C-seq_K562_sgSE_rep1


title: CAPTURE-3C-seq_K562_sgSE_rep2


title: HCI010_470_T_PT_23

data_processing:
Files from the HiSeq2500 were demultiplexed and converted to FASTQ files. Paired-end 100bp reads were aligned to the hg21 human transcriptome using Bowtie2 and quantified using RSEM with the following parameters: rsem-calculate-expression -p $CORES --bowtie2 --paired-end READ1 READ2 gencodehg21. Expression values were log-transformed into log(TPM+1) matrices and loaded into the Seurat analysis package with the following parameters: p10 <- CreateSeuratObject(raw.data = p10.mat, min.cells = 8, min.genes = 1000,  project = "HCI010").
Genome_build: hg21
Supplementary_files_format_and_content: genes.results.FPKM.txt


title: HCI010_470_T_PT_24


title: HCI010_470_T_PT_28


title: CAPTURE-3C-seq_K562_sgHS1-5-combined

description: CAPTURE-3C-seq_K562_sgHS1-5_combined_interaction


title: CAPTURE-3C-seq_K562_sgHS1-5_rep2


title: CAPTURE-3C-seq_K562_sgHS1-5_rep1


title: HCI010_470_T_PT_22


title: P_US_3

city: Newcastle upon Tyne

first: Andrew

middle: James

last: Skelton

state: Tyne and Wear

address: Framlington Place

department: Bioinformatics

country: United Kingdom

institute: Newcastle University

description: Patient Unstimulated

data_processing:
Transcript Level Quantification Using Kallisto
Aggregated gene level quantification using DESeq2
Normalisation using DESeq2
Genome_build: GRCh38
Supplementary_files_format_and_content: Gene Level Counts, Tab Delimited Text (Raw, Normalised)

source_name: primary dermal fibroblasts from patient with Behçet’s-like autoinflammatory disease

growth_protocol: DMEM with 10% FBS, 1% penicillin-streptomycin

extract_protocol:
Extracted with ReliaPrep RNA isolation kit according to manufacturers protocol
Truseq stranded mRNA library preparation

treatment_protocol: Recombinant TNF-alpha (10ng/mL) or media only (mock)

value: primary dermal fibroblasts

tag: treatment

value: Media only (mock)


title: HCI010_470_T_PT_30


title: HCI010_470_T_PT_20


title: HCI010_470_T_PT_21


title: CAPTURE-ChIP-seq_K562_dCas9-Cbio-sgGAL4_rep1


title: HCI010_470_T_PT_19


title: P_US_2

description: Patient Unstimulated


title: SEPTIC T1_P0060

description: cDNA prepared from urine cellular mRNA

value: Male


title: P_US_1

description: Patient Unstimulated


title: P_STIM_3

description: Patient TNF Stimulated

value: TNF stimulated


title: HCI010_470_T_PT_16


title: P_STIM_2

description: Patient TNF Stimulated


title: HCI010_470_T_PT_17


title: P_STIM_1

description: Patient TNF Stimulated


title: HCI010_470_T_PT_15


title: HCI010_470_T_PT_14


title: HCI010_470_T_PT_13


title: C_US_3

description: Control Unstimulated

source_name: primary dermal fibroblasts from healthy (control) patient


title: C_US_2

description: Control Unstimulated


title: HCI010_470_T_PT_12


title: C_US_1

description: Control Unstimulated


title: C_STIM_2

description: Control TNF Stimulated


title: HCI010_470_T_PT_11


title: HCI010_470_T_PT_10


title: HCI010_470_T_PT_18


title: HCI010_470_T_PT_9


title: C_STIM_1

description: Control TNF Stimulated


title: RNA-seq_G1E-ER4_24hr_rep2

source_name: Mouse G1E-ER4

value: G1E-ER4 cells


title: HCI010_470_T_PT_6


title: HCI010_470_T_PT_8


title: HCI010_470_T_PT_5


title: HCI010_470_T_PT_7


title: RNA-seq_G1E-ER4_12hr_rep2


title: RNA-seq_G1E-ER4_24hr_rep1


title: HCI010_470_T_PT_3


title: ChIP-seq_G1E-ER4_24hr_CTCF

description: ChIP DNA

data_processing:
Raw reads were aligned to mouse (mm10) genome assembly using Bowtie2 with default parameters.
Peak detection was performed with the Model-based Analysis of ChIP-Seq (MACS) algorithm.
The wig files were generated by a moving window of size 200bp. The tag count in the window was further normalized by total read count for ChIP-seq data generated by NextSeq500.
Genome_build: mm10
Supplementary_files_format_and_content: bigWig file and peak bed file

source_name: mouse G1E-ER4 cells

growth_protocol: G1E-ER4 cells were cultured in IMDM medium containing 15% FBS, 50 ng/mL recombinant SCF, and 2 U/ml recombinant human erythropoietin (EPO).

extract_protocol: For ChIP-seq analysis using the Illumina NextSeq500, 5 ng of ChIP DNA was processed for library generation using the NEBNext ChIP-seq Library Prep Master Mix following the manufacturer’s protocol (New England Biolabs). Raw reads that aligned to exactly one location in the reference human genome (hg19) were retained for downstream data analysis.

treatment_protocol: Cells were treated with 10-7 M β-estradiol to induce erythroid differentiation.

value: Mouse G1E-ER4 cells

tag: chip antibody

value: CTCF, Millipore, 07-729


title: HCI010_470_T_PT_1

extract_protocol:
Animals at endpoint were euthanized by asphyxiation with CO2 followed by cervical dislocation and perfusion with 10mM EDTA in D-PBS.  Prior to perfusion, Evan’s Blue (Sigma-Aldrich, Cat. No. E2129-10G) was injected into the footpads and ears of anesthetized mice to aid in lymph node visualization. Solid tissues from the mice, which includes the primary tumour, lung, and lymph nodes were processed for flow cytometry by mechanically chopping with blades, followed by Collagenase IV digest (Sigma-Aldrich Cat. No. C5138-1G) in media (DMEM/F12 with 5% FBS, 5µg/mL insulin, and 1% Penstrep/Ampho B) for 45 min at 37°C. Cell suspensions were washed with 2 µg/mL DNAseI for 5 min and further dissociated with 0.05% Trypsin for 10 min. Following a wash with HBBS/2% FBS, cells were passed through a 70µm filter. Lung and primary tumour cells were treated with 1X RBC lysis buffer, followed by resuspension in DMEM/F12 with 10% FBS for FACS. We used the human-specific antibody CD298 (PE, BioLegend, Cat. No. 341704) and the mouse-specific antibody MHCI (APC, ThermoFisher, Scientific Cat. No. 17-5957-80). Flow cytometry was performed using the BD FACSAria Fusion cell sorter. Cell viability was determined by negative staining for SYTOX Blue (ThermoFisher Scientific Cat. No. S34857). Forward scatter area by forward scatter width (FSC W x FSC A) and side scatter area by side scatter width (SSC W x SSC A) was used to discriminate single cells from doublet and multiplet cells. Mouse cells were excluded by gating out CD298-MHCI+. Human primary tumour cells and metastatic cells were selected by gating on Sytox-CD298+MHC-I-.
Single cells were sorted directly into each well of a skirted 96-well PCR plate (Fisher Scientific, Eppendorf, Cat. No. E951020443) containing lysis buffer (0.2% Triton X-100, 2 U/µL RNAseOUT, 10µM oligo-dT30VN, and 10µM dNTPs). The plates were snap frozen on dry ice and stored at -80°C until further processing. Total RNA was converted into cDNA using the SmartSeq2 protocol and prepared for Illumina sequencing with the Nextera XT DNA Library Preparation Kit (Illumina, Cat No. FC-131-1096). Cells were sequenced at a depth of 1 million reads/cell on the HiSeq2500.


title: RNA-seq_G1E-ER4_6hr_rep2


title: RNA-seq_G1E-ER4_12hr_rep1


title: ChIP-seq_G1E-ER4_0hr_CTCF

description: ChIP DNA


title: HCI010_470_T_PT_2


title: RNA-seq_G1E-ER4_6hr_rep1


title: HCI010_470_H_LU_96

value: Metastasis

value: Lung


title: RNA-seq_G1E-ER4_2hr_rep2


title: RNA-seq_G1E-ER4_2hr_rep1


title: HCI010_470_H_LU_95


title: RNA-seq_G1E-ER4_0hr_rep2


title: C_STIM_3

description: Control TNF Stimulated


title: HCI010_470_H_LU_94


title: HCI010_470_H_LU_93


title: HCI010_470_H_LU_92


title: RNA-seq_G1E-ER4_dCas9-cBIO_sgRep_24hr_rep3


title: RNA-seq_G1E-ER4_0hr_rep1


title: RNA-seq_G1E-ER4_dCas9-cBIO_sgRep_24hr_rep2


title: HCI010_470_T_PT_4


title: RNA-seq_G1E-ER4_dCas9-cBIO_sgRep_24hr_rep1


title: HCI010_470_H_LU_90


title: HCI010_470_H_LU_88


title: HCI010_470_H_LU_91


title: HCI010_470_H_LU_89


title: RNA-seq_G1E-ER4_dCas9-cBIO_sgAct_24hr_rep3


title: HCI010_470_H_LU_87


title: RNA-seq_G1E-ER4_dCas9-cBIO_sgRep_0hr_rep1


title: HCI010_470_H_LU_85


title: RNA-seq_G1E-ER4_dCas9-cBIO_sgRep_0hr_rep3


title: RNA-seq_G1E-ER4_dCas9-cBIO_sgRep_0hr_rep2


title: RNA-seq_G1E-ER4_dCas9-cBIO_sgAct_24hr_rep2


title: HCI010_470_H_LU_83


title: HCI010_470_H_LU_84


title: RNA-seq_G1E-ER4_dCas9-cBIO_sgAct_0hr_rep3


title: HCI010_470_H_LU_82


title: RNA-seq_G1E-ER4_dCas9-cBIO_sgAct_0hr_rep2


title: HCI010_470_H_LU_81


title: RNA-seq_G1E-ER4_dCas9-cBIO_sgAct_0hr_rep1


title: RNA-seq_G1E-ER4_dCas9-sgGAL4_24hr_rep3


title: HCI010_470_H_LU_79


title: RNA-seq_G1E-ER4_dCas9-sgGAL4_24hr_rep2


title: HCI010_470_H_LU_80


title: HCI010_470_H_LU_77


title: HCI010_470_H_LU_78


title: RNA-seq_G1E-ER4_dCas9-sgGAL4_24hr_rep1


title: RNA-seq_G1E-ER4_dCas9-sgGAL4_0hr_rep3


title: HCI010_470_H_LU_76


title: HCI010_470_H_LU_75


title: RNA-seq_G1E-ER4_dCas9-sgGAL4_0hr_rep1


title: CAPTURE-3C-seq_G1E-ER4_sgPromoter_24hr-combined

description: 3C DNA

data_processing:
Sequencing reads were aligned to human genome assembly hg19  or mm10 using Bowtie2 v2.2.8 with default parameters. The reads with low mapping qualit and duplicate reads were removed after the aligment with the Picard command-line tools.
After preprocessing and filtering, we generated the list of count numbers of read pairs from the bait region to any chromosomal regions. A pair of reads that located within two different regions is considered an interaction between them.
The interaction significance between the bait region and another chromosomal region was calculated by a Bayesian-Mixture Model. The PETs from bait region to any chromosomal regions were reported in Pairwise interaction format (http://wiki.wubrowse.org/Long-range).
Genome_build: hg19, mm10
Supplementary_files_format_and_content: Pairwise Interaction Format

source_name: Mouse G1E-ER4 cells

extract_protocol:
For 3C-seq analysis using the Illumina NextSeq500, 10 ng of 3C DNA was processed for library generation using the NEBNext ChIP-seq Library Prep Master Mix following the manufacturer’s protocol (New England Biolabs). Raw reads that aligned to exactly one location in the reference human genome (hg19) were retained for downstream data analysis.
3C-seq


title: RNA-seq_G1E-ER4_dCas9-cBIO_sgAct_24hr_rep1


title: HCI010_470_H_LU_86


title: HCI010_470_H_LU_74


title: HCI010_470_H_LU_72


title: CAPTURE-3C-seq_G1E-ER4_sgPromoter_24hr_rep4

description: 3C DNA


title: CAPTURE-3C-seq_G1E-ER4_sgPromoter_12hr-combined

description: 3C DNA


title: CAPTURE-3C-seq_G1E-ER4_sgPromoter_12hr_rep4

description: 3C DNA


title: HCI010_470_H_LU_73


title: HCI010_470_H_LU_70


title: CAPTURE-3C-seq_G1E-ER4_sgPromoter_6hr-combined

description: 3C DNA


title: CAPTURE-3C-seq_G1E-ER4_sgPromoter_6hr_rep4

description: 3C DNA


title: HCI010_470_H_LU_69


title: RNA-seq_G1E-ER4_dCas9-sgGAL4_0hr_rep2


title: CAPTURE-3C-seq_G1E-ER4_sgPromoter_2hr_rep4

description: 3C DNA


title: CAPTURE-3C-seq_G1E-ER4_sgPromoter_0hr_rep4

description: 3C DNA


title: CAPTURE-3C-seq_G1E-ER4_sgPromoter_0hr-combined

description: 3C DNA


title: HCI010_470_H_LU_67


title: HCI010_470_H_LU_71


title: G12.3_NAA50amiRNA 12 Hr

city: Bloomington

first: Roger

last: Innes

address: Myers Hall 302

department: Biology

institute: Indiana University

data_processing:
Trimmomatic (1; version 0.33; non-default parameters = ILLUMINACLIP<adapter_file>:2:20:6 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:20 MINLEN:35) was used to trim reads of adapter and low-quality bases
Reads were mapped to the Arabidopsis thaliana genome using STAR with the final parameters (4; version 2.5.2a; --outSAMattributes All --outSAMunmapped Within --outReadsUnmapped Fastx --outFilterMultimapNmax 1 --seedSearchStartLmax 25 --chimSegmentMin 20 --quantMode GeneCounts --twopassMode Basic --outWigType wiggle --outWigStrand Unstranded --outWigNorm None --sjdbGTFtagExonParentTranscript Parent --sjdbGTFtagExonParentGene ID --outSAMtype BAM SortedByCoordinate).
Read counts were determined using a custom perl script.
Differential expression comparisons of all features with 5 or more reads (in total across all samples) were carried out with DESeq2 (2; R package version 3.4.0) along with the IHW (3) package to adjust for multiple testing procedures.
Genome_build: TAIR10
Supplementary_files_format_and_content: Processed data files are tab-delimited files indicating the number of reads associated with a gene

source_name: Arabidopsis thaliana rosette

growth_protocol: 8/16 hr day/night cycle.

extract_protocol:
For each sample,  0.4 g leaf tissue was taken from the 4th leaf of 4 unique plants. RNA was extracted from 4-week-old Arabidopsis leaves using the Spectrum plant total RNA kit (Sigma-Aldritch) according to manufacturer’s instructions.
Total RNA was prepared into equimolar pools for each sample submitted to Indiana University’s Center for Genomics and Bioinformatics for cDNA library construction using a TruSeq Stranded mRNA LT Sample Prep Kit (Illumina) following the standard manufacturing protocol.

treatment_protocol: Samples were sprayed with 50 μM dexamethasone.

tag: genotype

value: leaf

tag: time (hours)


title: G0.2_NAA50amiRNA 0 Hr


title: G24.3_NAA50amiRNA 24 Hr


title: G12.1_NAA50amiRNA 12 Hr


title: G12.2_NAA50amiRNA 12 Hr


title: G0.3_NAA50amiRNA 0 Hr


title: G24.1_NAA50amiRNA 24 Hr


title: HCI010_470_H_LU_65


title: G0.1_NAA50amiRNA 0 Hr


title: HCI010_470_H_LU_66


title: HCI010_470_H_LU_64


title: HCI010_470_H_LU_68


title: S24.3_ScrambledamiRNA 24 Hr

value: ScrambledamiRNA


title: HCI010_470_H_LU_63


title: CAPTURE-3C-seq_G1E-ER4_sgPromoter_2hr-combined

description: 3C DNA