title: MOCK-GY9613-rep1

city: Gif sur Yvette

first: Fabrice

last: Confalonieri

address: Avenue de la Terrasse

department: Genome Biology

country: France

institute: Institute for Integrative Biology of the Cell (I2BC)

description: WT

data_processing:
The quality score was verified with FASTQC software and Illumina adaptor sequences were removed with Cutadapt software
For RNA-seq samples: Read sequences were mapped with BWA mem [v. 0.7.9a-r786] using default settings
For RNA-seq samples: coverage values of all genomic features were computed with the bedtools “coverage” command [v2.17.0]
For RNA-seq samples: RNA differential gene expression analysis was performed with the DESeq R-package [v. 1.39.0]
For ChIP-seq samples : Sequence alignments on the genomic sequence were performed with Bowtie2 software (default parameters)
For ChIP-seq samples : Output SAM files were converted and indexed into BAM files, using the Samtools software
For ChIP-seq samples: They were used for additional conversion into BED files with Bedtools software providing the input file format required by bPeaks programs to perform peak calling (bPeaks parameters: 2,2,0.5,0.9)
Genome_build: PRJNA684478

organism: Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539

growth_protocol: D. radiodurans cells were grown at 30°C in TGY2X (1% tryptone, 0.2% dextrose, 0.6% yeast extract)

extract_protocol: For ChIP seq samples: cells were cross-linked with 1% formaldehyde in TGY2X medium for 25 min at 30°C with continuous shaking. Crosslinking reactions were quenched by the addition of 125 mM glycine for 15 min. Cells were harvested by centrifugation (4000 rpm, 10min, 4°C), washed twice with cold Tris Buffer Solution (TBS) and then resuspended in 3 mL of lysis buffer [160 nM NaCl, 20 mM, Tris-HCl pH7.5, 1 mM EDTA, protease inhibitor cocktail (Roche)]. Cells were disrupted and DNA sheared using a One Shot Cell Disruptor (CellD SARL) to an average size of 100-300 bp (2 rounds of 2.4kbar). Insoluble material was removed by centrifugation at 15,000 rpm for 10 min at 4°C and the supernatant was collected in a sterile microcentrifuge tube. Then, 500 µL of supernatant fluid was added to 25 µL of pre-incubated protein G magnetic beads (ChIP-Adembeads ChIP-Adem-Kit, Ademtech SA) with 5 µg of anti-V5 rabbit polyclonal antibody (ab9116, Abcam) in IP buffer [50 mM HEPES-KOH pH 7.5, 150 mM NaCl, 1 mM EDTA, 1% Triton 100, protease inhibitor cocktail (Roche)]. After overnight incubation at 4°C with rotation, the immunoprecipitates were washed 5 times with washing buffers (ChIP-Adembeads ChIP-Adem-Kit, Ademtech SA).   Immune complexes were eluted in 200 µL of elution buffer. 20 µL The eluted samples (20µL) were saved for control Western blots, and the remainder was incubated for 2 h at 37°C with shaking with 100 µg/mL Proteinase K. Then, the supernatant was incubated overnight at 65°C to reverse cross-linking with 100 µg/mL RNAse A. The DNA was purified using the PCR Clean-up kit (Macherey-Nagel).

treatment_protocol: For RNAseq samples : cells were grown at 37°C at indicated times for each samples

value: WT

tag: treatment


title: Low Arsenic exposed subject  KP161

status: Public on Oct 27 2021

type: genomic

city: Maastricht

first: Danyel

last: Jennen

address: Universiteitssingel 40

department: Toxicogenomics

country: Netherlands

institute: Maastricht University

hyb_protocol: For analysis of DNA methylation levels, the Human DNA Methylation 2.1M Deluxe Promoter Array (Roche NimbleGen) was used. This array has a density of 2.1 million probes (50-75 oligonucleotides long, median probe spacing 100 bp) that represent all annotated human promoters (~ 26,210), 27,867 CpG islands, and 750 miRNA promoters per slide. The promoters and CpG islands largely overlap with transcription start sites of well characterized RefSeq genes, covering, on average, 8 kb upstream and 3 kb downstream. Labeling and hybridization of arrays was performed according to the manufactures’ protocol. In brief, 1 µg of Input DNA and 1 µg of MeDIP DNA were labeled with Cy3 and Cy5 respectively by random priming using the Dual Color DNA labeling kit (Roche NimbleGen). The labeled samples were precipitated using isopropanol and quantified spectrophotometrically using the NanoDrop 1000. 34 µg of Cy3 Input and 34 µg of Cy5 MeDIP DNA were pooled and completely dried by using a speed vac. The pellet was dissolved in hybridization solution using the NimbleGen Hybridization kit. After denaturing, the probe was hybridized overnight on the 2.1M Deluxe Promoter Arrays using the HX1 mixers and the NimbleGen Hybridization system 4. Slides were washed using the NimbleGen wash buffer kit and scanned using the 2 µm high resolution NimbleGen MS 200 micro array scanner.

scan_protocol: Slides were scanned using the 2 µm high resolution NimbleGen MS 200 micro array scanner per manufacturer's protocol.

data_processing:
Signal intensity data was extracted from the scanned images of each array using NimbleScan v2.6 software and quantile normalized on a per channel basis. Log2 ratios of the intensities were computed (ratio of MeDIP signal / Input signal) and for each array, centering was performed by subtracting the global array bi-weight mean of the log2 ratios such that the computed log2 ratios were centered around 0. Identiﬁcation of methylated regions was performed using the Probe Sliding Window-ANOVA algorithm (PSW-ANOVA). PSW-ANOVA was implemented in the R statistical programming environment (v2.15.3) (http://www.r-project.org) as a custom script and was provided by Roche NimbleGen. PSW-ANOVA (sliding window of 750 bp comprising 7 probes without selection of a cutoff p-value) was used to identify methylated regions.  Peaks were identified in the methylated regions by searching for regions containing at least 8 consecutive probes.   Peaks were mapped to promoter regions (from 3 kb upstream to 1 kb downstream of the transcription start site (20) and CpG islands of genes using the NimbleScan v2.6 software.
[CpG_sites_arsenic_Pakistan.txt]  Scaled, log2 (medip/Input) ratio for demethylated regions

molecule: genomic DNA

organism: Homo sapiens

source_name: input DNA from human buffy coat

label_protocol: Genomic DNA was sonicated to obtain fragments ranging from 200 bp to 600 bp. MeDIP was performed using the MagMeDIP kit (Diagenode, Liège, Belgium) according to the manufacturer’s protocol. In brief, IP incubation mix (containing magbuffer A, magbuffer B, 1.5 µg methylated DNA positive control, 1.5 µg non-methylated DNA negative control) was added to 10 µg of sonicated sample and denatured at 95 °C. 10% of this was kept aside as Input sample and stored at 4°C. Beads were washed 3 times with ice-cold diluted magbuffer A and collected in 20 µl of diluted magbuffer A. The remaining sample was immunoprecipitated using 5µl of antibodymix (containing an antibody against 5’-methylcytidine (provided in the kit) magbuffer A and magbuffer C) and 20 µl of magnetic beads solution. Immunoprecipitation was performed overnight at 4 °C on a rotating wheel. The following day, magnetic beads were washed twice with wash buffer 1 and once with wash buffer 2 and kept on ice. Next, DNA elution was performed using the IPure kit (Diagenode, Liège, Belgium). 50 µl of elution buffer was added to the MeDIP-bead pellet and 92.5 µl to the Input sample and incubated for 15 min at room temperature on a rotating wheel. Supernatant was transferred to a new Eppendorf tube using a magnetic rack at room temperature. Samples were subsequently incubated with 2 µl of glycogen carrier, 100 µl of 100% isopropanol and 15 µl of magnetic beads and incubated for 1 hour at room temperature on a rotating wheel. Magnetic beads were washed using wash buffer 1 and wash buffer 2 for 5 minutes. The DNA was eluted twice by using 75 µl of buffer C and incubated for 15 min at room temperature on a rotating wheel. All the samples were precipitated with sodium acetate and ethanol with glycogen as a carrier for 30 min at -80 °C and centrifuged at max speed for 30 min at 4°C. The cell pellet was washed using 70% ethanol and after air drying suspended in 20µl MQ. 20 ng of both Input and MeDIP samples were used for amplification by whole genome amplification (WGA) using the WGA2 and WGA3 kit (Sigma Aldrich) following the manufacturer’s instruction, without performing the fragmentation step. WGA reactions were cleaned up using silica columns (Sigma Aldrich) and eluted in water. Methylation enrichment in the paired samples MeDIP/Input was derived from qPCR data by calculating the ratio positive control/negative control, applying the ΔΔCq method using the primers included in the kit.

extract_protocol: DNA used for MeDIP-Chip analyses was isolated from buffy coats using standard phenol-chloroform method. The total amount was at least 10 µg DNA, the 260/280 ratio ranged between 1.7-1.9, and the 260/230 ratio appeared higher than 1.6. A total of 57 DNA samples were prepared for the MeDIP-Chip experiments.

tag: exposure

value: Low Arsenic exposed

tag: tissue

value: buffy coat

tag: chip antibody

source_name: medip DNA from human buffy coat

value: monoclonal antibody against 5’-methylcytidine


title: cell line LXFE_66

type: RNA

city: Freiburg

first: Vincent

last: Vuaroqueaux

address: Am Flughafen 14

department: Bioinformatics

country: Germany

institute: 4HF Biotec

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix protocol

data_processing: RMA preprocessing

label: biotin

molecule: total RNA

source_name: cell line

label_protocol: Standard Affymetrix protocol

growth_protocol: Patient-derived xenografts were passaged from mouse to mouse until RNA extraction. Cell lines were used at low passages and checked by STR analysis to confirm their identity before preparing stock cryovials.

extract_protocol: RNA were extracted either from cells cultured in Petri dishes (in vitro cell culture) or from pieces of snap frozen tumor xenografts from four individual tumors of the same tumor model in the same or different passages using the mirVana kit (Ambion) according to the manufacturer’s instructions. A DNAse digest was performed. Each RNA preparation was subjected to quality control using NanoDrop 2000 to control for purity and Bioanalyzer (Agilent) to control for RNA integrity. Only  the RNA samples with an integrity number (RIN)  between 6.5 and 10  and a ratio between 28s and 18 sRNA between 1.0 and 2.0, and the RNA was pure (260/280 nm and 260/230 nm close to 2.0), were used for the microarray analysis.

tag: cell line


title: cell line LXFA_629


title: Low Arsenic exposed subject  KM51


title: INPUT-GY18220-rep1

type: SRA

library_source: genomic

tag: strain

tag: genotype


title: BREC1

city: Blacksburg

first: Honglin

last: Jiang

state: VA

address: 3130 Litton Reaves Hall

department: Animal and Poultry Sciences

country: USA

institute: Virginia Polytechnic Institute and State University

description: cattle

library_source: transcriptomic

data_processing:
Raw reads were processed to generate clean reads through in-house perl scripts. Clean reads were mapped to the bovine genome (Bos_taurus UMD3.1.79) using Tophat2/Bowtie2. Gene expression level was quantified as counts.
Genome_build: Bos_taurus UMD3.1.79
Supplementary_files_format_and_content: BREC1_gene_counts.xlsx: Excel file for gene counts.

organism: Bos taurus

source_name: rumen epithelium

growth_protocol: Cells were cultured in growth medium consisting of DMEM and 10% FBS and 1% antibiotics.

extract_protocol:
Total RNA was extracted using TRIzol.
RNA-seq library was constructed using the NEBNext Ultra RNA Library Prep Kit for Illumina.

tag: cell type

value: rumen epithelium cell

tag: age

value: adult


title: cell line LXFA_737


title: cell line LXFE_2478


title: IP-GY18220-rep3


title: cell line LXFA_586


title: sgRc3h1_1

city: Beijing

first: Hanfei

last: Zhao

state: Beijing

address: Haidian District

department: School of Medicine

country: China

institute: Tsinghua University

data_processing:
Basecalls performed using Zebracall version 1.2.1
Data were filtered using SOAPnuke v1.5.2 with parameters -l 15 -q 0.5 -n 0.1
Sequenced reads were aligned to the GCF_000001635.25_GRCm38.p genome using Bowtie2 v2.2.5 with parameters -q --phred64 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -p 16 -k 200
Genome_build: GCF_000001635.25_GRCm38.p (NCBI)
Supplementary_files_format_and_content: Tab-delimited text file include reads and normalized expression for every gene and every sample

organism: Mus musculus

source_name: OT-I T cells

extract_protocol:
Cas9-expressing OT-I cells expressing indicated sgRNAs were injected into wild-type mice via tail vein. At 7 days post-activation, Thy1.1+ cells from spleen were sorted using a S3e cell sorter. Total RNA was extracted with RNAprep pure Cell Kit (TIANGEN BIOTECH Cat# DP430) according to manufacturer’s protocol.
mRNAs were purified from total RNA using oligo(dT) attached magnetic beads and fragmented into small pieces using fragmentation reagent. cDNAs were generated by reverse transcription and PCR to produce libraries for sequencing.

value: T cells


title: sgControl_2


title: sgRc3h1_2


title: sgControl_1


title: cell line LXFA_923


title: cell line LXFA_623


title: cell line LXFA_677


title: IP-GY18220-rep1


title: IP-GY18220-rep2


title: cell line LXFA_526


title: cell line LP-1


title: cell line LOVO

value: LOVO


title: cell line LXFA_1647


title: 17357_16H-rep2

description: ΔddrO/ p:repU::ddrO+

extract_protocol:
For RNAseq samples : total RNA was isolated using the Fast RNA Pro Blue Kit (MP Biomedicals) and the FastPrep-24 instrument, according to the manufacturer’s protocols. Extracted RNA was rigorously treated with TURBO DNA-free (Invitrogen).
The rRNA depletion and Illumina libraries were made following the Illumina protocol (Script-Seq)

value: deltaddrO/ p:repU::ddrO+

tag: time point


title: 17357_24H-rep2

description: ΔddrO/ p:repU::ddrO+


title: 17357_24H-rep1

description: ΔddrO/ p:repU::ddrO+


title: Low Arsenic exposed subject  GR124


title: 17357_16H-rep3

description: ΔddrO/ p:repU::ddrO+


title: 17357_16H-rep1

description: ΔddrO/ p:repU::ddrO+


title: cell line LXFA_289


title: Low Arsenic exposed subject  SM16


title: Low Arsenic exposed subject  SM18


title: 17357_8H-rep3

description: ΔddrO/ p:repU::ddrO+


title: Low Arsenic exposed subject  SM19


title: cell line LOU-NH91


title: 17357_6H-rep3

description: ΔddrO/ p:repU::ddrO+


title: 17357_8H-rep1

description: ΔddrO/ p:repU::ddrO+


title: Neu-WT-3b_S15 [q5]

city: San Diego

first: Ezra

last: Wiater

state: CA

address: 10010 N Torrey Pines Rd

department: PBL

institute: Salk Institute For Biological Studies

data_processing:
MiSeq Generation of fastq files
tophat2 alignment
cuffdiff alignment
Genome_build: mm10
Supplementary_files_format_and_content: .diff file from cuffdiff comparing all four samples

molecule: polyA RNA

source_name: Neu CXCL1/2_WT_epididymal WAT

growth_protocol: Mouse Diet

extract_protocol:
total RNA extracted by RNA isolation kit from Zymo Research
polyA RNA isolated and library prepared with NEBnext Ultra kit

treatment_protocol: Tissue Extraction

tag: genotype/strain

value: WT-mice

tag: diet

value: high fat (9weeks)

value: a-CXCL1/2 Ab injected

value: epididymal WAT


title: 17357_24H-rep3

description: ΔddrO/ p:repU::ddrO+


title: 17357_8H-rep2

description: ΔddrO/ p:repU::ddrO+


title: 17357_6H-rep2

description: ΔddrO/ p:repU::ddrO+


title: Neu-WT-2b_S14 [q5]


title: cell line KYSE-70


title: 17357_4H-rep3

description: ΔddrO/ p:repU::ddrO+


title: patient-derived tumor xenograft LEXFAM_2531

source_name: patient-derived tumor xenograft


title: cell line LN-229


title: Neu-WT-1b_S13 [q5]


title: 17357_4H-rep1

description: ΔddrO/ p:repU::ddrO+


title: 17357_4H-rep2

description: ΔddrO/ p:repU::ddrO+


title: cell line L-363


title: con-AKO-3b_S12 [q4]

source_name: CON_dAKO_epididymal WAT

value: CRTC2/3 dAKO mice

value: IgG injected


title: con-AKO-2b_S11 [q4]


title: 17370_24H-rep3

description: ΔddrO/ p:repUts::ddrO+

value: deltaddrO/ p:repUts::ddrO+


title: 17357_1H-rep3

description: ΔddrO/ p:repU::ddrO+


title: cell line KYSE-520


title: 17357_1H-rep2

description: ΔddrO/ p:repU::ddrO+


title: 17357_6H-rep1

description: ΔddrO/ p:repU::ddrO+


title: 17357_1H-rep1

description: ΔddrO/ p:repU::ddrO+


title: 17370_24H-rep2

description: ΔddrO/ p:repUts::ddrO+


title: con-AKO-1b_S10 [q4]


title: 17370_16H-rep3

description: ΔddrO/ p:repUts::ddrO+


title: con-wt-3b_S9 [q3]

source_name: CON_WT_epididymal WAT

value: WT mice


title: 17370_16H-rep2

description: ΔddrO/ p:repUts::ddrO+


title: cell line KYSE-180


title: 17370_8H-rep3

description: ΔddrO/ p:repUts::ddrO+


title: cell line KM-H2


title: 17370_24H-rep1

description: ΔddrO/ p:repUts::ddrO+


title: con-wt-2b_S8 [q3]


title: cell line KYSE-150


title: cell line KM12


title: cell line KLE

value: KLE


title: 17370_16H-rep1

description: ΔddrO/ p:repUts::ddrO+


title: 17370_6H-rep3

description: ΔddrO/ p:repUts::ddrO+


title: Low Arsenic exposed subject  KM52

value: Low Arsenic exposed


title: cell line KU-19-19


title: cell line KG-1


title: con-wt-1b_S7 [q3]


title: 17370_4H-rep3

description: ΔddrO/ p:repUts::ddrO+


title: cell line MEXF_1792


title: 17370_8H-rep2

description: ΔddrO/ p:repUts::ddrO+


title: 17370_6H-rep2

description: ΔddrO/ p:repUts::ddrO+


title: 17370_6H-rep1

description: ΔddrO/ p:repUts::ddrO+


title: NCD-3b_S3 [q1]

source_name: NCD_epididymal WAT

value: Normal Chow Diet (NCD)


title: HFD-3b_S6 [q2]

source_name: HFD_epididymal WAT

value: 15weeks High Fat Diet (HFD)


title: 17370_4H-rep1

description: ΔddrO/ p:repUts::ddrO+


title: 17370_1H-rep2

description: ΔddrO/ p:repUts::ddrO+


title: 17370_8H-rep1

description: ΔddrO/ p:repUts::ddrO+


title: HFD-2b_S5 [q2]


title: U-937

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.

data_processing:
Affymetrix Genome wide SNP6.0 CEL files were loaded into the Affymetrix Genotyping Console 4.1 Software (Affymetrix). After scanning, arrays were checked for quality using the Affymetrix Genotyping Console. In accordance with Affymetrix guidelines, SNP6.0 arrays with a Contrast QC value above 0.4 and MAPD below 0.35 were excluded from further analysis. Copy number variations were calculated using Affymetrix GTC v4.1 and PICNIC software provided by the Cancer Genome Project from the Welcome Trust Sanger Institute.   The PICNIC algorithm  (PICNIC - Predicting Integral Copy Numbers In Cancer) includes improved normalisation of the data together with determination of underlying copy numbers for each segment by genome wide analysis of allele ratio and signal strength data. The data was subsequently rescaled and plotted onto its predicted underlying integer value and segmentation was applied. This data analysis procedure also allowed for assignment of a genotype to each SNP. The PICNIC segment files were further compiled to generate a simplified gene matrix. A gene was assigned a deletion (CNV=0) if a deletion segment overlaps with the gene, otherwise the copy number of the most amplified segment overlapping with the gene was assigned.    Article reference PICNIC algorithm: Greenman CD, Bignell G, Butler A, et al. PICNIC: an algorithm to predict absolute allelic copy number variation with microarray cancer data. Biostatistics 2010; 11: 164—75
PICNIC integer copy number score (0 is considered as a gene deletion, values of 1 and between 3-7 are considered as a moderate gene copy number alteration, values equal or greater than 8 are considered as a gene amplification)

label_protocol: As per manufacturer (Affymetrix)

growth_protocol: Cells lines were cultured following growth recommendations from the cell line source vendors. Cells were incubated at 37 ºC at 5% CO2 until 70% confluency was reached. Pellets were harvested 48 hours post media change, flash frozen, and stored at -80 ºC until nucleic acid extraction.

extract_protocol: DNA was extracted from snap frozen material. DNA was extracted with a mix of phenol:chloroform:isoamylalcohol and precipitated with ethanol. DNA pellets were washed and resuspended in Tris-EDTA buffer. Each DNA preparation was subjected to quality control using a 1.3% agarose gel and using NanoDrop 2000 to control for purity. Only DNA samples with no sign of degradation (a clearly defined high molecular weight band on the agarose gel) and the DNA was pure (260/280 nm and 260/230 nm close to 2.0), were used for the microarray analysis.


title: U-251MG


title: cell line JURL-MK1


title: cell line JURKAT

value: JURKAT


title: cell line KCL-22


title: SXFO_678


title: 17370_4H-rep2

description: ΔddrO/ p:repUts::ddrO+


title: 17370_1H-rep3

description: ΔddrO/ p:repUts::ddrO+


title: SW756


title: SW620

value: CRC


title: cell line K-562


title: cell line IM95


title: cell line JHH-4


title: NCD-1b_S1 [q1]


title: THP-1


title: UXF_1138


title: NCD-2b_S2 [q1]


title: 17370_1H-rep1

description: ΔddrO/ p:repUts::ddrO+


title: T47D

value: Breast


title: SXFS_1301

value: SA_soft t


title: U-2-OS


title: Passage_1_kidney_rep_3

city: Liverpool

first: Kim

last: Clarke

address: Crown Street

country: United Kingdom

institute: University of Liverpool

description: P1 K3

hyb_protocol: Samples were hybridised to Agilent Mouse Whole Genome 60K arrays according to the manufacturers instructions.

scan_protocol: Samples were scanned using an Agilent SureScan scanner.

data_processing: Data were filtered and processed using the R software. Data was log2 transformed and quantile normalised.

source_name: primary tumour after implantation onto kidney

label_protocol: Samples were labelled using Agilent Low-Input Quick Amp Labelling Kits according to the manufacturers instructions. Samples were labelled with Cy5.

growth_protocol: Tumors were implanted by sub-capsular injections of 1 × 10^5 Renca cells into the left kidney of wild type BALB/c mice. For the intravenous injections, 5 × 10^5 Renca cells were injected into the caudal vein of wild type BALB/c mice.

extract_protocol: Samples were homogenised using a QIAGEN TissueRuptor. RNA was extracted using QIAgen RNeasy columns according to the manufacturers instructions.

tag: passage

tag: experiment

value: kidney


title: cell line IGROV-1


title: cell line JIMT-1


title: cell line JHH-6


title: Passage_5_kidney_rep_5

description: P5 K5


title: Passage_5_lung_rep_3

description: P5 L3

source_name: lung mets formed after tumour implantation onto kidney

value: lung


title: SF268


title: SN12C

value: Kidney


title: SNB-75


title: RXF_393


title: SNU-398


title: RXF_2516


title: RXF_486


title: SK-OV-3

value: Ovary


title: RXF_1781


title: cell line HUP-T3


title: Passage_3_lung_rep_4

description: P3 L4


title: cell line IM-9


title: RT112

value: Bladder


title: RXF_1183


title: RPMI-8226


title: Passage_3_kidney_rep_1

description: P3 K1


title: cell line HT-1080


title: RPMI-2650

value: HNSC


title: RKO

source_name: RKO

value: RKO


title: Passage_0_parental_rep_1

description: P0 P1

source_name: parental RENCA cell line

value: parental


title: Passage_4_tail_rep_4

description: P4 T4

source_name: lung mets formed after tumour cell injection via tail

value: tail


title: RXF_2282


title: cell line HT-29


title: Passage_1_tail_rep_4

description: P1 T4


title: cell line HUT-78


title: cell line Hs 729


title: PXF_698

value: Mesothelioma


title: RAJI

source_name: RAJI

value: RAJI


title: PXF_1752


title: PXF_1118


title: cell line HNXF_1859


title: cell line HPAF-II

value: HPAF-II


title: PL-21


title: Passage_5_tail_rep_5

description: P5 T5


title: cell line HPAC

value: HPAC


title: Passage_5_kidney_rep_2

description: P5 K2


title: Passage_6_kidney_rep_2

description: P6 K2


title: PC-3M

value: Prostate


title: Passage_4_tail_rep_1

description: P4 T1


title: PAXF_546

value: Pancreas


title: RXF_1220


title: Passage_3_lung_rep_1

description: P3 L1


title: PAXF_2035


title: PAXF_1998


title: PAXF_1997


title: PAXF_2059


title: PAXF_2005


title: HFD-1b_S4 [q2]

value: 15weeks High Fat Diet (HFD)

value: epididymal WAT


title: OVXF_899


title: PAXF_1986


title: PAXF_1657


title: OVXF_1023


title: OVCAR-5


title: cell line HL-60


title: Passage_1_tail_rep_3

description: P1 T3


title: OCUM-1

value: Stomach


title: Passage_6_kidney_rep_1

description: P6 K1

value: kidney


title: Passage_2_tail_rep_3

description: P2 T3


title: cell line Hep-G2


title: cell line HH

value: HH


title: PANC-1


title: Passage_6_tail_rep_4

description: P6 T4


title: cell line HLE

value: HLE


title: cell line HNXF_1853


title: cell line HeLa

value: HeLa


title: cell line HCT-15


title: Passage_5_kidney_rep_1

description: P5 K1


title: NUGC-4


title: NOMO-1


title: OCI-AML2


title: NCI-H82

value: SCLC


title: Passage_5_tail_rep_4

description: P5 T4


title: cell line HEC-1-A


title: Passage_3_tail_rep_5

description: P3 T5


title: NCI-H69


title: NCI-H460


title: cell line HCT116


title: NCI-H345


title: MOLT-4


title: MV4-11


title: Passage_4_kidney_rep_5

description: P4 K5


title: MKN45


title: cell line HCC2998


title: MIA-PaCa-2


title: MKN1


title: Passage_2_kidney_rep_2

description: P2 K2


title: MEXF_535

value: Melanoma


title: MEXF_622


title: NCI-H727


title: Passage_6_tail_rep_3

description: P6 T3


title: cell line HCC33


title: Passage_1_tail_rep_2

description: P1 T2


title: MEXF_520


title: cell line HCC1937


title: MEXF_394


title: cell line H69AR


title: Passage_5_lung_rep_6

description: P5 L6

value: lung


title: MEXF_2090


title: cell line GXF_251


title: Passage_5_tail_rep_3

description: P5 T3

value: tail


title: cell line GXF_23132


title: cell line GXA_3067


title: cell line GXF_1172


title: Passage_4_lung_rep_5

description: P4 L5


title: cell line GXA_3023


title: Passage_3_tail_rep_3

description: P3 T3


title: Passage_6_kidney_rep_5

description: P6 K5


title: Passage_4_kidney_rep_3

description: P4 K3


title: MEXF_462


title: MEXF_276


title: MDA-MB-231

value: Breast


title: MDA-MB-468


title: MEXF_1792


title: MEXF_1829


title: MEG-01


title: MAXF_401


title: Passage_6_tail_rep_2

description: P6 T2


title: Passage_2_kidney_rep_1

description: P2 K1


title: cell line FADU

value: FADU


title: LXFL_529


title: cell line GXA_3011


title: cell line GXA_3013


title: MEXF_1341


title: Passage_5_lung_rep_5

description: P5 L5


title: Passage_1_kidney_rep_5

description: P1 K5


title: MCF7


title: cell line FU97


title: LXFL_1674


title: cell line EM-2


title: LXFE_66


title: LXFL_430


title: LXFA_983


title: cell line EJM

value: EJM


title: LXFL_1121


title: LXFL_1072


title: LXFE_2478


title: cell line EFO-27


title: Passage_3_tail_rep_2

description: P3 T2


title: LXFA_923


title: cell line EVSA-T

value: EVSA-T


title: Passage_5_tail_rep_2

description: P5 T2


title: Passage_4_lung_rep_3

description: P4 L3


title: Passage_1_LOT1

description: P1 LOT1


title: LXFA_677


title: cell line EFO-21


title: LXFA_629


title: LXFA_586


title: LXFA_623


title: LXFA_526


title: LXFA_737


title: LXFA_1647


title: Passage_1_kidney_rep_4

description: P1 K4


title: cell line EFE-184


title: KG-1


title: cell line DU-4475


title: Passage_5_tail_rep_1

description: P5 T1


title: Passage_4_kidney_rep_1

description: P4 K1


title: cell line DMS-273


title: cell line DoTc2-4510


title: Passage_6_tail_rep_1

description: P6 T1


title: L-363


title: Passage_4_lung_rep_1

description: P4 L1


title: KM12

value: CRC


title: JURL-MK1


title: LXFA_289


title: LP-1


title: KCL-22


title: JURKAT

source_name: JURKAT

value: JURKAT


title: LEXFAM_2531


title: K-562


title: Passage_3_kidney_rep_2

description: P3 K2


title: Passage_3_lung_rep_5

description: P3 L5


title: HUT-78


title: cell line DIFI

value: DIFI


title: HT-29


title: cell line DAUDI

value: DAUDI


title: cell line DETROIT562


title: cell line DU-145


title: HL-60


title: Passage_6_kidney_rep_4_batch2

description: P6 K4 B2


title: Passage_0_parental_rep_2

description: P0 P2

value: parental


title: cell line CXF_280


title: Passage_6_kidney_rep_2_batch2

description: P6 K2 B2

value: kidney


title: cell line CXF_94


title: patient-derived tumor xenograft CXF_260

value: patient-derived tumor xenograft CXF_260


title: Passage_6_kidney_rep_1_batch2

description: P6 K1 B2


title: HNXF_1853

value: HNSC


title: IM-9


title: HCT116


title: HNXF_1859


title: Hep-G2


title: HeLa

source_name: HeLa

value: HeLa


title: Passage_6_lung_rep_2

description: P6 L2


title: IM95

value: Stomach


title: Passage_0_parental_rep_2_batch2

description: P0 P2 B2


title: Passage_6_lung_rep_3

description: P6 L3


title: HCT-15


title: cell line CXF_1103

source_name: cell line


title: GXA_3023


title: Passage_1_lung_rep_3

description: P1 L3


title: Passage_1_kidney_rep_2

description: P1 K2


title: cell line COLO-205


title: cell line COLO-320


title: Passage_0_parental_rep_1_batch2

description: P0 P1 B2


title: GXA_3013


title: GXA_3011


title: cell line CCRF-CEM

value: CCRF-CEM


title: HCC2998


title: H69AR

value: SCLC


title: GXF_1172


title: cell line CNXF_498


title: GXF_251


title: Passage_6_lung_rep_1

description: P6 L1

value: lung


title: DoTc2-4510


title: DIFI

source_name: DIFI


title: GXF_23132


title: CXF_94


title: cell line Calu-1


title: FU97


title: GXA_3067


title: EM-2


title: cell line BXF_1352


title: cell line CAL-51


title: Passage_6_kidney_rep_4

description: P6 K4


title: Passage_5_lung_rep_2

description: P5 L2


title: CXF_260


title: cell line CAKI-1


title: CXF_1103


title: DU-145

value: Prostate


title: DAUDI

source_name: DAUDI


title: cell line CAL-27


title: DMS-273


title: Passage_1_tail_rep_5

description: P1 T5

value: tail


title: Passage_5_kidney_rep_4

description: P5 K4


title: COLO-205


title: CCRF-CEM

source_name: CCRF-CEM


title: Passage_4_tail_rep_3

description: P4 T3


title: Passage_1_kidney_rep_1

description: P1 K1


title: CXF_280


title: BXF_1036

value: Bladder


title: A-431

value: Vulva


title: Passage_3_lung_rep_3

description: P3 L3


title: CNXF_498


title: 22RV1


title: Passage_2_lung_rep_1

description: P2 L1


title: cell line CAL-33


title: Passage_5_tail_rep_6

description: P5 T6


title: patient-derived tumor xenograft BXF_1228

source_name: patient-derived tumor xenograft


title: cell line BT-549


title: cell line A-431


title: cell line A498


title: BXF_1352


title: CAKI-1

value: Kidney


title: cell line BT-474


title: Passage_6_kidney_rep_3

description: P6 K3


title: Passage_5_kidney_rep_3

description: P5 K3


title: Passage_3_lung_rep_2

description: P3 L2


title: cell line ACHN

value: ACHN


title: BXF_1228


title: LAP preB-ALL 2 (BLNK1)

city: Tokyo

first: Takuro

last: Nakamura

address: 3-8-31 Ariake, Koto-ku

department: The Cancer Institute

country: Japan

institute: Japanese Foundation for Cancer Research

description: Gene expression data from mouse ALL

hyb_protocol: Following fragmentation, 7.5 ug of aRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome 430 PM Array. GeneChips were washed and stained in the Affymetrix GeneAtlas Fluidics Station.

scan_protocol: GeneChips were scanned using the Affymetrix GeneAtlas Imaging Station.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: preB-ALL tumor developed in Cebpb LAP transgenic mice

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: BKO408 cells were grown in RPMI1640 culture medium supplemented with 10% fetal bovine serum, and 5 ng/ml IL-7. Mouse ALL developed in Blnk homozygous knock-out, Cebpb LAP transgenic, or Blnk KO/LAP tg mice.

extract_protocol: Total RNA was purified using RNA Easy kit (QIAGEN) according to the manufacturer's protocol

treatment_protocol: No treatment was provided.

value: preB-ALL tumor

tag: developed in

value: Cebpb LAP transgenic mice


title: LAP preB-ALL 1 (BLNK1)

description: Gene expression data from mouse ALL


title: LAP preB-ALL 3 (BLNK1)

description: Gene expression data from mouse ALL


title: 293 CU1ENU rep 1

city: El Paso

first: Shrikanth

last: Gadad

state: TX

address: 5001 El Paso Drive

department: Department of Molecular and Translational Medicine

institute: Texas Tech University Health Sciences Center El Paso

data_processing:
Reads were aligned to GRCh38.p13 using the hisat2 aligner
Read counts were generated using feature counts with Ensembl version 101 and GENCODE v35 as reference with "-t exon, -g gene_id or -g exon_id, and -a annotation.gtf" as options.
Differential gene expression was determined using the DeSeq2 package in R
Genome_build: GRCh38.p13
Supplementary_files_format_and_content: tab delimited txt file with raw read counts for each sample

growth_protocol: HEK-293 cells (CRL-1573, ATCC) were grown in Eagle’s Minimum Essential Medium (30-2003, ATCC) supplemented with 10% FBS and 1% Pen/Strep

extract_protocol:
Total RNA extraction from the transfected HEK-293 cells was performed with EZ-10 DNAaway RNA Miniprep Kit (BS88136, Bio Basic Inc.), following manufacturer’s protocol.
Only samples with RIN values of >9 in agilent tapestation were included in subsequent analysis. Libraries were prepared by Novogene Corporation.
Strand-Specific (dUTP-based) paired end libraries

treatment_protocol: HEK-293 cells were transfected with 5 µg of LINC01016 isoforms plasmids (cloned in pcDNA3.0 vector) using Lipofectamine 3000 transfection reagent (L3000015, Thermo Fisher Scientific). Cells were seeded in 60mm plates. Transfected cells were collected 48h post-transfection for RNA extraction.

value: Embryonic kidney

tag: morphology

value: Epithelial


title: 293 CU1ENU rep 2


title: cell line A2780


title: 293 CU1ENC rep 2


title: 293 CU1ENC rep 1


title: cell line A-253


title: Passage_4_tail_rep_2

description: P4 T2


title: LAP preB-ALL 4 (BLNK1)

description: Gene expression data from mouse ALL


title: Blnk preB-ALL 5 (BLNK1)

description: Gene expression data from mouse ALL

source_name: preB-ALL tumor developed in Blnk KO mice

value: Blnk KO mice


title: cell line A172


title: cell line A204


title: 293 CU2 rep 1


title: Passage_2_tail_rep_4

description: P2 T4


title: 293 CU2 rep 2


title: cell line 22RV1


title: cell line BXF_1036


title: LAP/Blnk preB-ALL 1 (BLNK1)

description: Gene expression data from mouse ALL

source_name: preB-ALL tumor developed in Blnk KO/LAP tg mice

value: Blnk KO/LAP tg mice


title: LAP B-ALL 2 (BLNK1)

description: Gene expression data from mouse ALL

source_name: B-ALL tumor devevloped in Cebpb LAP transgenic mice

value: B-ALL tumor


title: LAP B-ALL 1 (BLNK1)

description: Gene expression data from mouse ALL


title: LAP B-ALL 3 (BLNK1)

description: Gene expression data from mouse ALL


title: cell line 786-O


title: Input_D13

city: Aachen

first: Ivan

last: Costa

address: Pauwelsstraße 19

institute: Unikilink RWTH Aachen

description: used as control for correction of CG bias and size of open chromatin regions.

data_processing:
HiSeq 4000 System (Illumina®) with single-end reads of 50bp
Reads were trimmed with skewer and aligned with Bowtie2(2.3.4.1) to the human hg19 genome.
MACS2(2.1.1.20160309) peakcalling between “TF” and “Input”. P-value under 1-e8.  condition specific peaks using corresponding input DNA.
Input_D10 and Input_D05 corresponds to input DNA sequences of Day 5 and Day 10 of our cultures. These sequences are given as controls (for correction of CG bias and size of open chromatin regions) together with ChIP-seq data of the corresponding day for peak calling algorithms
Genome_build: hg19
Supplementary_files_format_and_content: We provide predicted peaks (bed files) and genomic signals (bw files) from all ChIP libraries.

growth_protocol: CyT49 hESC were subjected to pancreatic differentiation according to Wang et al. (Cell Stem Cell, 2015; DOI:https://doi.org/10.1016/j.stem.2015.02.013). Of note, in this protocol NKX6.1-positive cultures at day 10 are labeled pancreatic endoderm. For consistent labeling we refer to pancreatic progenitors instead.

extract_protocol:
Cells were harvested at day 5 (corresponding to gut tube endoderm (GTE)) or day 10 (coressponding to NKX6.1-positive pancreatic progenitors  (PP). ChIP-IT High-Sensitivity kit (Active Motif) was used for chromatin isolation followed by immunoprecipitation with Monoclonal Rat Nkx6.1 raised in Mouse - Antibody RES310 (http://www.betacell.org/pdf/betacell-resource-310.pdf )
KAPA DNA Library Preparation Kits for Illumina® (Kapa Biosystems)

value: hESC

tag: Stage

value: PP stage


title: LAP B-ALL 4 (BLNK1)

description: Gene expression data from mouse ALL


title: LAP/Blnk preB-ALL 2 (BLNK1)

description: Gene expression data from mouse ALL


title: 293 CU1 rep 2


title: NKX6.1_D13


title: Co-X-79B

city: Berlin

first: Mathias

last: Dahlmann

address: Robert-Rössle-Str. 10

department: Experimental and Clinical Research Center

institute: Charité University Medicine

description:
cryo pulverization after growth matrix removal
PD3D_culture_tpm.tsv

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using fastp (v0.19.5), using base correcton for paired end data.
Transcript abundances (TPM, FPKM, raw counts) were calculated with RSEM (v1.3.0), using STAR (v2.70) to align reads to the reference sequence (GRC38.p12).
Raw counts were normalized with DESeq2 for differential expression analysis.
Genome_build: hg38
Supplementary_files_format_and_content: Tab-delimited matrix containing TPM values for each sample type (patient metastasis, PDX tumor, PD3D culture)
Supplementary_files_format_and_content: GCT file (v1.3) DESeq2 normalized count matrix

source_name: PD3D cell culture

extract_protocol:
Total RNA was extracted from cryo pulverized samples using the Qiagen AllPrep DNA/RNA Mini Kit.
Libraries were generated from 750ng total RNA using the Illumina TruSeq Stranded mRNA Kit.

value: PD3D culture cells


title: Co-X-79A


title: 293 CU1 rep 1


title: run6: Lung L3

city: Pessac Cedex

first: Justine

last: Rudewicz

address: Allée Geoffroy Saint Hilaire Bâtiment B2, Rez-de-Chaussée

department: SVS

institute: University of Bordeaux

data_processing:
Filters FASTQ file generated by CASAVA 2.17
fastq files were trimmed for adapters and low quality bases with Trim Galore (v0.4.4, calling cutadapt 1.3)
Fastq files were aligned with Bismark (v0.17.1_dev) against the GRCm38.p5 mus musculus genome (download from http://www.ensembl.org/, release 89)  with following parameters -N 0  and --maxins 800.
Bismark use Bowtie 2 (v2.3.4.3) and samtools (v1.9).
Incomplete bisulfite conversion filtering were done on Bismark BAM files in order to remoove reads that exceed a certain threshold of methylated calls in non-CG context.
Then deduplication was apply (deduplicate_bismark) followed by extraction of methylated positions (bismark_methylation_extractor).
For memory purpose, only non 0 CG position are reported.
Genome_build: mm10
Supplementary_files_format_and_content: CX report

source_name: Lung L3

extract_protocol:
WGBS libraries have been prepared according to Biooscientific’s protocol using the Biooscientific NEXTflex™ Bisulfite Library Prep Kit for Illumina Sequencing. Briefly, DNA was fragmented by sonication, size selection was performed using Agencourt AMPure beads XP and adaptators were ligated to be sequenced. Then, bisulfite treatment was performed for 2.5 hours using the EZ DNA Methylation-Gold™ Kit from Zymo Research, and 12 cycles of PCR were performed. Library quality was assessed using an Advanced Analytical Fragment Analyser and libraries were quantified by QPCR using the Kapa Library Quantification Kit.
Illumina HiSeq3000 using a paired-end read length of 2x150 pb

tag: protocol

value: Mouse renal carcinoma cell line RENCA (expressing GFP for visualisation) are implanted in syngeneic (and thus immunocompetent) mouse model under the kidney capsule leading to formation of a primary tumour and subsequent metastasis to the lungs. Lungs metastasis are explanted and cell lines purified for re-implantation into the kidney.


title: run7: Lung L3


title: 293 T1 rep 2


title: run5: Lung L3


title: 293 T2 rep 2


title: Blnk preB-ALL 4 (BLNK1)

description: Gene expression data from mouse ALL


title: Blnk preB-ALL 3 (BLNK1)

description: Gene expression data from mouse ALL


title: Co-X-77B


title: Co-X-78


title: Blnk preB-ALL 1 (BLNK1)

description: Gene expression data from mouse ALL


title: 293 empty vector rep 2


title: BKO408 LAP 2 (BLNK1)

description: Gene expression data from mouse ALL

source_name: preB-ALL cell line developed in Blnk KO mice and transduced with Cebpb LAP retrovirus

value: preB-ALL cell line BKO408

tag: transduced with

value: Cebpb LAP retrovirus


title: BKO408 LAP 1 (BLNK1)

description: Gene expression data from mouse ALL


title: BKO408 LAP 3 (BLNK1)

description: Gene expression data from mouse ALL


title: BKO408 4 (BLNK1)

description: Gene expression data from mouse ALL

source_name: preB-ALL cell line developed in Blnk KO mice


title: 293 T1 rep 1

tag: tissue


title: run4: Lung L3


title: Co-X-83B


title: run3: Lung L3


title: BKO408 2 (BLNK1)

description: Gene expression data from mouse ALL


title: BKO408 1 (BLNK1)

description: Gene expression data from mouse ALL


title: Co-X-64A


title: Blnk preB-ALL 2 (BLNK1)

description: Gene expression data from mouse ALL


title: run1: Lung L3


title: BKO408 3 (BLNK1)

description: Gene expression data from mouse ALL


title: Co-X-80


title: 293 empty vector rep 1


title: Co-X-77A


title: Co14452A

description:
cryo pulverization of fresh frozen tissue
PDX_tumor_tpm.tsv

source_name: PDX

value: PDX tumor


title: Co13947B


title: 293 parental rep 1


title: 293 T2 rep 1


title: Co13573


title: run5: Lung L2

source_name: Lung L2


title: run6: Lung L2


title: Cardiac cells, STDP, rep2

city: Hangzhou

first: penghui

last: Yang

state: Zhejiang

address: 866 Yuhangtang Road

institute: Pharmaceutical Informatics Institute

data_processing:
The quality of the raw sequencing data was controlled and the acquired raw image files were converted to sequential reads by CASAVA (Illumina, Inc) and stored in FASTQ format. Next, genomic alignment and quantification of gene expression levels were performed using Hisat2 v2.0.5 and featureCounts v1.5.0.
DESeq2 (v1.16.1) package was used to analyze the gene expression difference between two groups. The P value and the fold change were obtained to select the differentially expressed genes (DEGs) between Sham and Model or Model and STDP groups.
Genome_build: mm10
Supplementary_files_format_and_content: gene_count.txt

source_name: Cardiac cells

extract_protocol: Total RNA from heart tissue was extracted with the TRIzolTM Reagent (Thermo Fisher Scientific, MA, USA), and the purity and integrity of RNA were detected by agarose gel electrophoresis. Second, sequencing libraries were generated using the Illumina NEBNext® UltraTM RNA Library Prep Kit (NEB, USA) according to the protocols recommended by the manufacturer. Briefly, the mRNA was randomly interrupted and reverse transcription was performed to synthesize double-stranded cDNA, which was purified (~200bp) by the AMPure XP beads after ligation of adaptors to obtain the sequencing library. Third, the content of DNA was detected by a Qubit 2.0 Fluorometer (Invitrogen, Carlsbad, CA, USA), and the quality of the library DNA integrity was assessed using an Agilent 2100 Bioanalyzer (CA, USA). Last, the qualified samples were sequenced on an illumine HiSeq X Ten platform by Novogene (Beijing, China).

treatment_protocol: First, the mouse model of CHF was established by the transverse aortic constriction (TAC) surgery, and the efficacy of STDP against CHF was evaluated by assessing the alterations in cardiac function, myocardial fibrosis, and cardiomyocyte hypertrophy with echocardiography, Masson's trichrome staining, and wheat germ agglutinin staining. Next, a CHF disease network was constructed by integrating cardiovascular disease-related genes and the transcriptome sequencing data of mouse heart tissue, which was used to explore the underlying mechanism of action of STDP in CHF. Then, the key targets involved in the effects of STDP on CFH were determined by network analysis algorithms, and pathway enrichment analysis was performed to these key genes. Finally, important targets in the critical pathway were verified in vivo.

value: Cardiac cells

tag: treatment

value: transverse aortic constriction; intragastrically administered STDP at 86 mg/kg bw once a day for 6 weeks

tag: disease state

value: model of CHF


title: Cardiac cells, Model, rep4

tag: strain

value: transverse aortic constriction; intragastrically administered 1% sodium carboxymethyl cellulose at 0.1 mL/10 g bw once a day for 6 weeks


title: Cardiac cells, STDP, rep3


title: Co13422B


title: Cardiac cells, STDP, rep4


title: Cardiac cells, STDP, rep1


title: Co13947A


title: 293 parental rep 2

tag: cell line


title: run4: Lung L2


title: run3: Lung L2


title: Cardiac cells, Model, rep2

tag: cell type


title: run2: Lung L2


title: Cardiac cells, Sham, rep4

value: sham-operation; intragastrically administered 1% sodium carboxymethyl cellulose at 0.1 mL/10 g body weight once a day for 6 weeks

value: vehicle


title: run7: Lung L2


title: Cardiac cells, Model, rep1


title: Cardiac cells, Model, rep3


title: Co13422A


title: Co13196D


title: Co13261B


title: Cardiac cells, Sham, rep3


title: run7: Lung L1

source_name: Lung L1


title: run6: Lung L1


title: Co13196A


title: run5: Lung L1


title: Co13022


title: HSD_4

city: Solna

first: Hong

state: Stockholm

address: Tomtebodavägen 23A

department: Systems Biology

country: Sweden

institute: KTH Royal Institute of Technology/Science For Life Laboratory

data_processing:
Kallisto
Genome_build: GRCm38
Supplementary_files_format_and_content: Tab-delimited Raw counts for every gene and samples
Supplementary_files_format_and_content: Tab-delimited TPM counts for every gene and samples

source_name: liver

extract_protocol: C57BL/6J mice were fed a standard mouse chow diet and housed in a 12‐h light–dark cycle. From the age of 8 weeks, the mice were then divided into two groups of 5 mice fed with chow diet, 4 mice fed with high-sucrose diet for 3 weeks, respectively. At the age of 11 weeks, we performed a genome-wide transcriptomic analysis on tissue samples obtained from these mice.

value: liver

value: HSD

tag: age

value: 11 weeks


title: Co13120


title: CRC-69A

description:
cryo pulverization of fresh frozen tissue
Patient_sample_tpm.tsv

source_name: pmCRC

value: patient metastasis


title: Cardiac cells, Sham, rep2


title: HSD_3


title: Co12969


title: run1: Lung L2


title: Co12908B


title: run2: Lung L1


title: HSD_2


title: HSD_1


title: run4: Lung L1


title: run3: Lung L1


title: Cardiac cells, Sham, rep1


title: CRC-55A


title: run5: Tail T4

source_name: Tail T4

value: Mouse renal carcinoma cell line RENCA (expressing GFP for visualisation) are injected directly into the blood stream (tail vein) leading to formation of tumours in the lungs in the absence of a tumour in the kidney. Lungs metastasis are explanted and cell lines purified for re-injection into the tail vein.


title: CRC-39


title: run6: Tail T4


title: run7: Tail T4


title: Chow_5

value: Chow


title: Chow_2


title: run4: Tail T4


title: Co12908A


title: CRC-28B


title: run3: Tail T4


title: CRC-55B


title: run1: Lung L1


title: CRC-28A


title: Chow_3


title: ela6h-3

city: Shanghai

first: Ruoxuan

last: Bao

address: Dongan road

institute: Fudan University

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Mus musculus whole genome using hisat v2.1.0 with default parameter
The expression level of each transcript was calculated according to the (TPM) method. RSEM v1.3.1 was used to quantify gene abundances
Differential gene expression analysis was done using R package DESeq2 v1.24.0
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each sample.

source_name: primary hepatocytes

growth_protocol: Hepatocytes were isolated from wild-type C57BL/6 mice using the two-step collagenase perfusion method. Cells were cultured in DMEM medium (Invitrogen) supplemented with 10% fetal bovine serum (Gibco) and 50 μg/ml of penicillin/streptomycin.

extract_protocol:
Cells were harvested with TRIzol reagent (Invitrogen) and kept at -80 °C . RNA extraction was performed by Shanghai Majorbio.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: One replicate was treated with DMSO or elaiophylin for 6 hours.

value: primary hepatocytes

value: treated with elaiophylin for 6 hours


title: run2: Tail T4


title: run7: Tail T3

source_name: Tail T3


title: Chow_4


title: run1: Tail T4


title: LAP/Blnk preB-ALL 3 (BLNK1)

description: Gene expression data from mouse ALL

value: preB-ALL tumor

value: Blnk KO/LAP tg mice


title: CRC-21


title: Chow_1


title: DMSO-3

value: treated with DMSO for 6 hours


title: CRC-19D


title: CRC-19A


title: ela6h-2


title: DMSO-1


title: DMSO-2


title: CRC-09


title: ela6h-1


title: CRC-13


title: run3: Tail T3


title: CRC-06


title: run5: Tail T3


title: CRC-05A


title: KO2_RNA-seq

city: Wuhan

first: Andi

last: Wang

address: Luojiashan Road

institute: Wuhan University

data_processing:
Cutadapt (version 1.16, http:// cutadapt.readthedocs.io/en/stable/guide.html) was used for adaptor sequence remove with the parameters -u 0 -u -30 -U 0 -U -30 -m 30
Cleaned reads were mapped to the mouse reference genome (mm10) using TopHat (version 2.1.1, http://ccb.jhu.edu/software/tophat/index.shtml) with default settings.
The gene expression level was calculated by Cufflinks (version 2.2.1, http://cole-trapnell-lab.github.io/ cufflinks) and normalized by fragments per kilobase of bin per million mapped reads (FPKM).
Principal component analysis (PCA) of the quality control matrices was employed to determine the presence of RNA-Seq sample outliers.
Differentially expressed genes are defined as ones with the p value less than 0.05.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include raw count and RPKM values for each Sample.

source_name: neurospheres

extract_protocol:
RNA isolation was performed using the TRIZOL reagent (Invitrogen) according to manufacturer’s instructions. Tissue or cells were homogenized using a glass-Teflon in 1 ml or 500 µl TRIZOL reagent on ice and phase separation was achieved with 200 µl or 100 µl chloroform. After centrifugation at 12,000× g for 15 min at 4°C, RNA was precipitated by mixing aqueous phase with equal volumes of isopropyl alcohol and 0.5 µl 20 mg/ml glycogen. Precipitation were dissolved in DNase/RNase-free water (not diethylpyrocarbonate treated, Ambion).
Total RNA was extracted as described above. The concentration and quality of RNA was measured with Nanodrop 2000c (Thermo Fisher Scientific) and an Agilent 2100 Bioanalyzer (Agilent Technologies), respectively. RNA-seq libraries were constructed by NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB E7490) and NEBNext Ultra II Non-Directional RNA Second Strand Synthesis Module (NEB E6111). Briefly, mRNA was extracted by poly-A selected with magnetic beads with poly-T and transformed into cDNA by first and second strand synthesis. Newly synthesized cDNA was purified by AMPure XP beads (1:1) and eluted in 50 μl nucleotide-free water. RNA-seq libraries were sequenced by Illumina NovaSeq 6000 platform with pair-end reads of 150 bp. The sequencing depth was 60 million reads per library.

value: cortex

tag: developmental stage

value: Embryo 12.5

value: neurospheres

tag: genotype

value: LncBAR-KO


title: THESC + AG-205 rep 3

city: Brussels

first: Patrick

last: Henriet

address: Avenue Hippocrate, 75

department: De Duve Institute

country: Belgium

institute: Université Catholique de Louvain

description: Sample 12

data_processing:
Low quality reads were trimmed and adapters were removed using Trimmomatic software v0.38. Reads were aligned using HISAT2 software v2.1.0 on GRCh38 genome . Gene counts were generated using featureCounts software from subread-2.0.0  and Homo_sapiens.GRCh38.94.gtf annotation file Homo_sapiens.GRCh38.94.gtf annotation file.
Genome_build: GRCh38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: THESC

extract_protocol:
After incubation, cells were lysed and RNA harvested using TRIzol Reagent (Ambion, Life Technologies). An additional step was performed to remove excess DNA with the TURBO DNA-free kit (Invitrogen) according to manufacturer’s recommendations except that a longer centrifugation step (3 min) was carried out.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Triplicate of epithelial or stromal endometrial cells treated with 15µM or DMSO control for 32h

value: endometrial

tag: origin

value: fibroblastic origin

value: THESC

value: treated with 15µM AG-205 for 32 hours


title: run2: Tail T3

tag: passage


title: KO1_RNA-seq


title: run1: Tail T3


title: THESC + DMSO rep3

description: Sample 11

value: treated with DMSO for 32 hours


title: BKO408 LAP 4 (BLNK1)

description: Gene expression data from mouse ALL

value: preB-ALL cell line BKO408

value: Blnk KO mice

value: Cebpb LAP retrovirus


title: run7: Tail T1

source_name: Tail T1

value: Mouse renal carcinoma cell line RENCA (expressing GFP for visualisation) are injected directly into the blood stream (tail vein) leading to formation of tumours in the lungs in the absence of a tumour in the kidney. Lungs metastasis are explanted and cell lines purified for re-injection into the tail vein.


title: WT1_RNA-seq

value: WT


title: WT2_RNA-seq


title: run4: Tail T3


title: THESC + AG-205 rep 2

description: Sample 10


title: run5: Tail T1


title: THESC + DMSO rep2

description: Sample 9


title: regression_Ntn1

city: New York

first: Emily

last: Brown

state: NY

address: 435 E 30th St

department: Medicine

institute: NYU Langone

data_processing:
quality control, Cell Ranger Single Cell Software Suite
sample de-multiplexing, Cell Ranger Single Cell Software Suite
barcode processing, Cell Ranger Single Cell Software Suite
single cell 3' gene counting, Cell Ranger Single Cell Software Suite
alignment, Cell Ranger Single Cell Software Suite
Genome_build: mm10
Supplementary_files_format_and_content: Filtered matrix of gene expression by cell, file with barcodes and file with expressed genes.  Files are ready to be import into Seurat package or similar.

source_name: regression of pooled CD45+ aortic leukocytes after deletion of netrin-1

extract_protocol: The whole aorta was carefully isolated, and the perivascular fat was removed. Then the aortic tissue was cut into as small pieces as possible and incubated at 37°C for 15 minutes with enzyme mixture containing DNase I (40 U/ml), liberase (4 U/ml), hyaluronidase (60 U/ml). Live CD45+ cells were sorted out using BD FACSAriaIII. The cells are resuspended in final concentration of ~500 cells/µL in 1X HBSS containing 0.04% BSA to minimize cell loss and aggregation. ~12,000 cells are partitioned into nanoliter-scale Gel Bead-In-EMulsions (GEMs) to achieve single cell resolution for a maximum recovery of 10,000 individual cells per sample. Utilizing the v2 Chromium™ Single Cell 3' Library Kit and Chromium instrument (10x Genomics), poly-adenylated mRNA from an individual cell is tagged with a unique 16bp 10x barcode and 10bp Unique Molecular Identifier. Full length cDNA is then amplified to generate sufficient mass for library construction. Enzymatic fragmentation and size selection are used to optimize the cDNA amplicon size (~400bp) for library construction. The final library is sequence ready and contains four unique sample indexes. The concentration of the 10x single cell library will be accurately determined through qPCR (Kapa Biosystems) to produce cluster counts appropriate for the HiSeq4000 platform (Illumina). 26x98nt read lengths are generated targeting 50,000 reads per cell.

value: Atherosclerotic aoric arch

value: PCSK9 treated Ntn1 fl/fl-Cx3cr1+/-  (TMX induced Ntn1 deletion)

value: atherosclerosis regression (20wks HFD, followed by 5d TMX and 4 weeks chow diet)

value: CD45+ aortic leukcytes


title: THESC + AG-205 rep 1

description: Sample 8


title: THESC + DMSO rep1

description: Sample 7


title: HEC1A + DMSO rep3

description: Sample 6

value: epithelial origin


title: run3: Tail T1


title: baseline_Ntn1

source_name: baseline of pooled Ntn1 CD45+ aortic leukocytes, prior to deletion of netrin-1

value: PCSK9 treated Ntn1 fl/fl-Cx3cr1+/-  (no TMX)

value: atherosclerosis progression (20wks HFD)


title: HEC1A + AG-205 rep3

description: Sample 5

value: endometrial


title: run2: Tail T1


title: run7: Kidney K5

source_name: Kidney K5

value: Mouse renal carcinoma cell line RENCA (expressing GFP for visualisation) are implanted in syngeneic (and thus immunocompetent) mouse model under the kidney capsule leading to formation of a primary tumour and subsequent metastasis to the lungs. The primary tumour is explanted and cell lines purified for re-implantation into the kidney.


title: NA-SD-29

city: Jena

first: Marco

last: Groth

address: Beutenbergstraße 11

department: Core Facility - Next Generation Sequencing

institute: Leibniz Institute on Aging - FLI

data_processing:
Reads were extracted in FastQ format using Illumina’s bcl2FastQ v2.20.0.422
The R1 reads were mapped to the mouse reference genome (GRCm38) with the Ensembl gene annotation (release 92) with TopHat2 v2.1.0 (parameters: --no-convert-bam –no-coverage-search -x 1 -g 1).
All reads mapped to an Ensembl gene were counted using FeatureCounts v1.6.2 (parameters: -s 2).
Genome_build: GRCm38
Supplementary_files_format_and_content: excel file containing reads counts, RPMs and RPKMs per gene over all samples

source_name: Bone Marrow Mononuclear Cells (BMMCs)

growth_protocol: Bone marrow was cultured in IMDM (PAA) (with 10% FCS, 100U/ml penicillin, 100mg/ml streptomycin, 50mM β-mercaptoethanol, 20ng/ml X63Ag-653 BPV-rmIL-3 supernatant). When cultures consisted of 95% BMMCs (after 4 weeks) culture cells were used for experiments. BMMC purity was estimated by the surface expression of c-Kit and the FcεRI via flow cytometry.

extract_protocol:
Total RNA was isolated with Qiazol reagent (Qiagen).
Preparation of libraries was done using NEBNext Ultra II directional library preparation kit including enrichment of polyA RNAs using NEBNext Poly(A) mRNA Magnetic Isolation Module by introducing unique dual indices  (all ourchased from NEB)  according the manufacturer‘s description.

treatment_protocol: In presence of IL-3 BMMCs treated with Dex (5µM) or stimulated TGFb (50ng/ml) or IL-33 (50ng/ml) for 24h.

value: 4 weeks of differentiation


title: NA-SD-30


title: NA-SD-28


title: run6: Tail T1


title: HEC1A + DMSO rep2

description: Sample 4


title: run6: Kidney K5


title: HEC1A + AG-205 rep 2

description: Sample 3

value: treated with 15µM AG-205 for 32 hours


title: regression_ctl

source_name: regression of pooled CD45+ aortic leukocytes with netrin-1

value: PCSK9 treated Ntn1 fl/fl-Cx3cr1-/-


title: NA-SD-27


title: NA-SD-26


title: HEC1A + DMSO rep1

description: Sample 2

value: treated with DMSO for 32 hours


title: run5: Kidney K5


title: RNA-seq Con PDX1-NKX6.1-pos Rep6

data_processing:
HiSeq 3000/4000 System (Illumina®) with single-end reads of 50bp
Reads were aligned with STAR aligner (Dobin, 2013; Version 2.5.2b) on  human genome hg38 and using Ensembl Transcriptome Annotation e87 as  transcriptome reference.
DESeq2 (version 1.22.1) was used for  normalization and differential expression analysis (Love, 2014). Only  genes with at least 10 reads, an adjusted p-value < 0.05 and abs(FC) >  1.5 were considered
Deeptools and R were used for further processing
Genome_build: hg38
Supplementary_files_format_and_content: We provide bigwig, VST(Variance Stabilizing Transformation) model count and FPKM(Fragments Per Kilobase Million)

growth_protocol: HUES8  were subjected to in vitro pancreatic differentiation.

extract_protocol:
Cells were harvested at definitve endoderm (DE), pancreatic endoderm (PE) and pancreatic progenitor (PP) stage. Total RNA from ESC-derived pancreatic cells was isolated using GeneJET RNA Purification Kit (Thermo Fisher Scientific) according to manufacturer’s instructions.
After quality check with samples reaching RNA integrity values RIN>8, up to 1µg of total RNA was used for poly-A enrichment and subsequent library preparation with the TrueSeq stranded mRNA Kit from Illumina (HUES8 n=6)

value: embryonic stem cells, HUES8

value: wild type

value: pancreatic progenitors, sorted PDX1+/NKX6.1+


title: baseline_ctl

source_name: baseline of pooled WT CD45+ aortic leukocytes


title: NA-SD-24


title: run4: Kidney K5


title: NA-SD-25


title: HEC1A + AG-205 rep1

description: Sample 1


title: run4: Tail T1

value: Mouse renal carcinoma cell line RENCA (expressing GFP for visualisation) are injected directly into the blood stream (tail vein) leading to formation of tumours in the lungs in the absence of a tumour in the kidney. Lungs metastasis are explanted and cell lines purified for re-injection into the tail vein.


title: run3: Kidney K5


title: NA-SD-23


title: run2: Kidney K5


title: RNA-seq Con PDX1-NKX6.1-pos Rep5


title: run1: Tail T1


title: run6: Tail T3


title: NA-SD-22


title: run1: Kidney K5


title: run7: Kidney K4

source_name: Kidney K4


title: RNA-seq Con PDX1-NKX6.1-pos Rep3


title: run2: Lung L3

source_name: Lung L3

value: Mouse renal carcinoma cell line RENCA (expressing GFP for visualisation) are implanted in syngeneic (and thus immunocompetent) mouse model under the kidney capsule leading to formation of a primary tumour and subsequent metastasis to the lungs. Lungs metastasis are explanted and cell lines purified for re-implantation into the kidney.


title: NA-SD-20


title: RNA-seq Con PDX1-NKX6.1-pos Rep2


title: NA-SD-21


title: run6: Kidney K4


title: run5: Kidney K4


title: NA-SD-19


title: RNA-seq Con PP Rep6

value: pancreatic progenitors


title: run4: Kidney K4


title: RNA-seq Con PP Rep5


title: run2: Kidney K4


title: run3: Kidney K4


title: run1: Kidney K4


title: RNA-seq Con PDX1-NKX6.1-pos Rep4


title: Female_CAST_PolyA_RNA_Repl4_G164_M19

city: Boston

first: David

middle: J.

last: Waxman

state: MA

address: 5 Cummington Mall

department: Department of Biology and Bioinformatics Program

institute: Boston University

description: RNA-seq Library

data_processing:
READ MAPPING: Sequence reads were mapped to the mouse genome (mm9) using TopHat2 (Trapnell et al, Nat. Biotech, 2010)
QUANTIFICATION: FeatureCounts (Liao, 2014, Bioinformatics) was used to obtain read counts for RefSeq and long noncoding genes (Lodato et al 2017). Transcripts were quantified by counting sequence reads that map to a the gene body of a gene.
DIFFERENTIAL EXPRESSION: Quantification of differential expression was performed using edgeR (Robinson, 2010, Bioinformatics)
Genome_build: mm9
Supplementary_files_format_and_content: EdgeR output for CAST and B6 strains, and FPKM normalized read counts for protein coding and noncoding genes (FPKM_perGene.txt), where BM indicates livers of five individual C57BL/6J males, BF indicates C57BL/6J females, CM indicates livers of five individual CAST/EiJ males, CF indicates CAST/EiJ females.

source_name: Liver

growth_protocol: Male and female C57BL/6J and CAST/EiJ mice, 8-9 weeks of age, were purchased from Jackson Labs.

extract_protocol:
Snap frozen liver was used as input for RNA purification using TRIzol reagent (Invitrogen, cat#:15596026) following the manufacturer’s directions. Total RNA was quantified using the Qubit RNA BR kit (Invitrogen, cat#:Q10210). 1 microgram of total RNA per sample was used as input for library preparation.
Samples were prepared for sequencing with NEBNext Ultra Directional RNA Library Prep kit for Illumina (NEB, cat#:E7420) with the PolyA selection with the NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB, cat#:E7490).

value: CAST/EiJ (Jackson Labs, cat#:000928)

tag: rna isolation

value: 1 microgram total liver RNA

tag: Sex

value: Female

value: 8 weeks


title: Female_CAST_PolyA_RNA_Repl2_G164_M17

description: RNA-seq Library


title: RNA-seq Con PP Rep2


title: run6: Kidney K2

source_name: Kidney K2


title: RNA-seq Con PP Rep3


title: RNA-seq Con PP Rep4


title: Female_CAST_PolyA_RNA_Repl1_G164_M16

description: RNA-seq Library


title: RPE1 180m G1 Lb1 cTSA-seq StrePD Rep1

city: Baltimore

first: Joseph

last: Tran

state: MD

address: 3520 San Martin Drive

department: Embryology

institute: Carnegie Institution for Science

data_processing:
RNAseq data was aligned using Tophat v2.1.1 / Bowtie v2.3.2
RNAseq reads were counted using featurecounts from the Subread v1.5.2 package
RNAseq differential expression was calculated using the glmFit method in EdgeR v3.24.3 under R v3.5.2. SLAMseq was analyzed using the GrandSLAM package v2.0.5
DNA was aligned using bowtie v2.3.2
DNA reads were counted into 10kb or 100kb windows using bedtools v2.26.0 coverage, and calculated as a log2(StrepD/input). The data was covnerted to a z-score and these z-score values were averaged for the indicated samples. Bigwigs were made with kentutils v3.62
Hidden Markov Model (HMM) was called using depmixS4 v1.4-0 in RStudio v0.98.953 (R v3.5.1). Note we used a three state model
HMM calls were intersected between replicates to generate a consensus bed file for downstream analysis.
Genome_build: hg19
Supplementary_files_format_and_content: Original featureCounts output, bigwig files for cell cycle LADs, bedgraph files for the K562 APEXID LADs, bedgraph files for the cell cycle H3K9me3 ChIPseq, HMM calls in bed format for cell cycle LADs

source_name: Immortalized cell line

growth_protocol: For bulk experiments. HCT116 or hTERT-RPE1 cells were cultured on 10cm plates to 80-90% confluency, harvested and fixed with 1% PFA. The fixed cells were counted with a hemacytometer. The K562 cells were grown in suspension in T25 flasks. The cells were collected, fixed and counted.

extract_protocol:
Cells were permeabilized with PBS +0.25% Triton X-100 and stained for Lamin B1, and then a secondary HRP antibody. THe TSA reaction was performed according the kit [Biotin-XX-Tyramide Superboost kit (Invitrogen, #2005939)]. The cells were then further solubilized in RIPA buffer and sonicated with a Bioruptor Pico prior to Streptavidin pulldown.
Libraries were produced with the Illumina TruSeq RNA library kit v2 (for RNA) or the Rubicon Genomics (Takara) ThruPlex 48 kit.

treatment_protocol:
For release experiments. Cells were first blocked with nocodazole for 16h. Next the cells were gently washed 2x with warm media and then shaken off. The shake-off cells were seeded on poly-lysine coated 10cm plates and processed as described above prior to FACS sorting.
For SLAM-seq, cells were treated with 4sU for 1hr prior to harvest. RNA was isolated using the Qiagen RNeasy Plus kit. RNA was treated with iodoacetimide and then reextracted with the Qiagen RNeasy Plus kit.

value: Immortalized cell line

tag: type

value: Streptavidin pull-down (StrePD)

tag: cell cycle stage

value: Later G1

tag: treatments

value: Nocodazole (16h), release and FACS for G1


title: RNA-seq Con PP Rep1

tag: Stage


title: RPE1 G1 Lb1 cTSA-seq StrePD Rep1


title: Male_CAST_PolyA_RNA_Repl5_G164_M15

description: RNA-seq Library

value: C57BL/6J (Jackson Labs, cat#:000664)

value: Male


title: run5: Kidney K2

tag: protocol

value: Mouse renal carcinoma cell line RENCA (expressing GFP for visualisation) are implanted in syngeneic (and thus immunocompetent) mouse model under the kidney capsule leading to formation of a primary tumour and subsequent metastasis to the lungs. The primary tumour is explanted and cell lines purified for re-implantation into the kidney.


title: RNA-seq Con PDX1-NKX6.1-pos Rep1

tag: tissue

value: embryonic stem cells, HUES8


title: RNA-seq Con PE Rep6

value: wild type

value: pancreatic endoderm


title: Female_CAST_PolyA_RNA_Repl5_G164_M20

description: RNA-seq Library


title: Male_CAST_PolyA_RNA_Repl4_G164_M14

description: RNA-seq Library


title: run4: Kidney K2


title: RPE1 G1 Lb1 cTSA-seq input Rep1

value: None / input


title: Male_CAST_PolyA_RNA_Repl3_G164_M13

description: RNA-seq Library


title: Female_CAST_PolyA_RNA_Repl3_G164_M18

description: RNA-seq Library


title: RNA-seq Con PE Rep4


title: run3: Kidney K2


title: run7: Kidney K2


title: RPE1 180m G1 Lb1 cTSA-seq input Rep1


title: Male_CAST_PolyA_RNA_Repl2_G164_M12

description: RNA-seq Library


title: Male_CAST_PolyA_RNA_Repl1_G164_M11

description: RNA-seq Library


title: RPE1 90m G1 Lb1 cTSA-seq input Rep1

value: Early G1


title: RNA-seq Con PE Rep3


title: run2: Kidney K2


title: RPE1 90m G1 Lb1 cTSA-seq StrePD Rep1


title: RNA-seq Con PE Rep2


title: HCT116 1e6 cells Lb1 cTSA-seq StrePD Rep1

value: Asynchronous low-cell (counted)


title: run1: Kidney K2


title: RNA-seq Con PE Rep5


title: Female_B6_PolyA_RNA_Repl5_G164_M10

description: RNA-seq Library

value: CAST/EiJ (Jackson Labs, cat#:000928)


title: RNA-seq Con PE Rep1


title: run7: RENCA – parental cell line

source_name: RENCA – parental cell line

value: no implantation


title: Female_B6_PolyA_RNA_Repl4_G164_M9

description: RNA-seq Library

value: 1 microgram total liver RNA

value: Female


title: RNA-seq Con DE Rep6

value: definitive endoderm


title: Female_B6_PolyA_RNA_Repl3_G164_M8

description: RNA-seq Library

value: 8 weeks


title: HCT116 200k cells Lb1 cTSA-seq StrePD Rep2

value: Immortalized cell line

value: Streptavidin pull-down (StrePD)

value: Asynchronous low-cell


title: HCT116 200k cells Lb1 cTSA-seq StrePD Rep1


title: run4: RENCA – parental cell line


title: run5: RENCA – parental cell line


title: Female_B6_PolyA_RNA_Repl2_G164_M7

description: RNA-seq Library


title: RNA-seq Con DE Rep5


title: RNA-seq Con DE Rep4


title: Female_B6_PolyA_RNA_Repl1_G164_M6

description: RNA-seq Library


title: HCT116 200k cells Lb1 cTSA-seq input Rep1


title: run3: RENCA – parental cell line


title: RNA-seq Con DE Rep3


title: HCT116 50k cells Lb1 cTSA-seq StrePD Rep2


title: HCT116 1e6 cells Lb1 cTSA-seq input Rep1


title: HCT116 50k cells Lb1 cTSA-seq StrePD Rep1


title: Male_B6_PolyA_RNA_Repl5_G164_M5

description: RNA-seq Library

value: C57BL/6J (Jackson Labs, cat#:000664)

value: Male


title: RNA-seq Con DE Rep2

value: embryonic stem cells, HUES8


title: run2: RENCA – parental cell line


title: run6: RENCA – parental cell line


title: HCT116 50k cells Lb1 cTSA-seq input Rep1


title: RNA-seq Con ESC Rep6

value: wild type

value: undifferentiated


title: RNA-seq Con DE Rep1


title: Male_B6_PolyA_RNA_Repl4_G164_M4

description: RNA-seq Library


title: run1: RENCA – parental cell line


title: T-allo-957

city: Stanford

first: Pauline

last: Chen

address: 265 Campus Drive

department: Pediatrics

institute: Stanford University

data_processing:
Library strategy: TcR-Seq
Basecalls output were from Miseq Real-time analysis (RTA) software.
Alignment of raw sequences,  extraction of clonotypes were performed by MiXCR Immune Repertoire Analyzer software (Illumina)
Abundance measurements and statistical analysis of the resultant clonotype sets were performed by using an R package-tcR.
Amino acid motifs of the TCRa and b repertoires were identified by GLIPH algorithm (Glanville et al., Nature, 2017)

source_name: CD4+  T cells

extract_protocol:
Cells were lysed in RLT solution and  RNA extracted using RNeasy Mini Plus kit (Qiagen) . RNA quality was verified using Agilent RNA Pico Kit (Agilent Technologies).
Bulk TCRab libraries were prepared using SMARTer® Human TCR a/b Profiling Kit (Takara ) with inputting 10 ng total RNA from each sample.

value: Control Teff cells

tag: sequencing run

value: pair-ended 2x300

tag: treatment

value: untreated


title: Male_B6_PolyA_RNA_Repl2_G164_M2

description: RNA-seq Library

tag: strain


title: RNA-seq Con ESC Rep5


title: HCT116 G1 SLAM-seq Rep1

tag: cell line

tag: cell type

value: SLAM-seq (RNA-seq)


title: non-Tr1-957

source_name: T-allo10 cells

value: sorted from T-allo10 cells


title: RNA-seq Con ESC Rep4


title: HCT116 180m G1 SLAM-seq Rep2

value: Later G1

value: Nocodazole (16h), release and FACS for G1


title: RNA-seq Con ESC Rep3


title: Tr1-957


title: T-allo10-957

source_name: CD4+ T cells

value: DC-derived T regulatory type I cells


title: Female_CAST_DNaseI_Repl4_G163_M19

description: DNase-seq Library

data_processing:
READ MAPPING: DNase-seq reads were aligned using Bowtie2 (Langmead et al 2009, Genome Biology) with default settings. Reads were filtered so that only uniquely-aligned reads were used for downstream analysis.
PEAK CALLING: Peaks were called using Macs2 (Zhang et al 2008, Genome Biology) with default parameters without filtering for PCR duplicates. Peaks were filtered to remove blacklisted regions (www.sites.google.com/site/anshulkundaje/projects/blacklists) and also regions called as peaks that contain only PCR duplicated reads.
Genome_build: mm9
Supplementary_files_format_and_content: Replicate merged peak lists for DNase-seq, merged by strain and sex. Samples were combined at the fastq level and processed through a standard ChIP-seq pipeline as described. Columns are in BED6+4 format from MACS2 narrowPeak defaults. Specifically, columns 1-3 represent genomic coordinates of the indicated peak; column 4 is the peak name (unique identifier); column 5 is an integer score for display calculated as -10*log10(qvalue); column 6 indicates the strand; column 7 indicates the fold-change over background; column 8 indicates -(log10pvalue); column 9 indicates -log10(qvalue); and column 10 indicates the summit position relative to the 5' end of the peak.

extract_protocol:
Liver was homogenized, nuclei were suspended in a high sucrose buffer, and then ultra centrifuged to obtain purified intact nuclei. 50 million liver nuclei per sample were incubated with 32 U of RQ1 RNase-free DNase I (Promega, cat#:M6101) for 2 min at 37C. From the purified DNA, fragments between 125-400 bp long were isolated using a sucrose gradient and with Agencourt AMPure XP beads (Beckman Coulter, Cat# A63881) size selection.
Samples were prepared for sequencing with NEBNext Ultra II DNA Library Prep Kit for Illumina according to the manufacturer's directions for low input samples (New England Biolabs, #E7645). All samples were subjected to double-sided SPRI size selection prior to PCR amplification (Agencourt AMPure XP; Beckman Coulter: A63882). Samples were barcoded using New England Biolabs NEBNext Multiplex Oligos for Illumina (#E7335) with 8 rounds of PCR per the manufacturer's instructions.

value: CAST/EiJ (Jackson Labs, cat#:000928)

tag: units dnasei

value: 32U (RQ1; Promega cat#:M6101)

value: Female

tag: age

value: 8 weeks


title: Female_CAST_DNaseI_Repl3_G163_M18

description: DNase-seq Library


title: RNA-seq Con ESC Rep2

tag: genotype


title: Female_CAST_DNaseI_Repl2_G163_M17

description: DNase-seq Library


title: Male_B6_PolyA_RNA_Repl3_G164_M3

description: RNA-seq Library

value: C57BL/6J (Jackson Labs, cat#:000664)

value: 1 microgram total liver RNA


title: HCT116 G1 SLAM-seq Rep2

value: Immortalized cell line


title: CD4-957

source_name: PBMC

value: positive isolated from PBMC


title: T-allo-789


title: HCT116 90m G1 SLAM-seq Rep2

value: Early G1


title: HCT116 90m G1 SLAM-seq Rep1


title: RNA-seq Con ESC Rep1

value: embryonic stem cells, HUES8

value: wild type

value: undifferentiated


title: Female_CAST_DNaseI_Repl1_G163_M16

description: DNase-seq Library


title: ATAC-seq Con PP Rep2

data_processing:
Reads were trimmed with skewer and aligned with Bowtie2 to the human hg19 genome. Only properly mapped pairs were further considered and duplicates were removed.
We used MACS2 with FDR of 5% to find condition specific peaks using corresponding input DNA and replicates.
Genome_build: hg19
Supplementary_files_format_and_content: Clusters on wild-type(Con_Clusters), and Wild-type versus Knock-out differential peaks on each stages (Diff-peaks)

source_name: embryonic stem cells, HUES8

growth_protocol: HUES8 control and HNF6 KO hESC were subjected to in vitro pancreatic differentiation.

extract_protocol:
Single cells were harvested at definitve endoderm (DE), gut tube  (GT), pancreatic endoderm (PE) and pancreatic progenitor (PP) stage. Cells were directly lysed in tagmentation buffer (Nextera DNA Library Preparation Kit, Illumina) followed by DNA extraction.
Nextera DNA Library Preparation Kit, Illumina

value: embryonic stem cells

value: pancreatic progenitors


title: HCT116 G1 no 4sU label SLAM-seq Rep2

value: No 4sU control RNAseq


title: ATAC-seq Con PP Rep3


title: Male_B6_PolyA_RNA_Repl1_G164_M1

description: RNA-seq Library

value: Male


title: Male_CAST_DNaseI_Repl4_G163_M15

description: DNase-seq Library


title: non-Tr1-789

value: sorted from T-allo10 cells

value: pair-ended 2x300

value: untreated


title: HCT116 G2 Lb1 cTSA-seq StrePD Rep2

value: Streptavidin pull-down (StrePD)


title: HCT116 G1 no 4sU label SLAM-seq Rep1


title: Male_CAST_DNaseI_Repl3_G163_M14

description: DNase-seq Library

value: CAST/EiJ (Jackson Labs, cat#:000928)

value: 32U (RQ1; Promega cat#:M6101)

value: 8 weeks


title: CD4-789


title: HCT116 180m G1 SLAM-seq Rep1

value: Immortalized cell line

value: SLAM-seq (RNA-seq)

value: Later G1

value: Nocodazole (16h), release and FACS for G1


title: ATAC-seq Con PP Rep1

value: wild type


title: T-allo10-789

value: DC-derived T regulatory type I cells


title: T-allo-869

value: Control Teff cells

value: pair-ended 2x250


title: Female_B6_DNaseI_Repl4_G163_M10

description: DNase-seq Library

value: C57BL/6J (Jackson Labs, cat#:000664)

value: Female


title: ATAC-seq Con PE Rep3

value: embryonic stem cells

value: pancreatic endoderm


title: Tr1-789

value: sorted from T-allo10 cells

value: pair-ended 2x300

value: untreated


title: Male_CAST_DNaseI_Repl1_G163_M11

description: DNase-seq Library

value: CAST/EiJ (Jackson Labs, cat#:000928)

value: 32U (RQ1; Promega cat#:M6101)

value: Male


title: Male_CAST_DNaseI_Repl2_G163_M13

description: DNase-seq Library

value: 8 weeks


title: HCT116 G2 Lb1 cTSA-seq input Rep1

value: Immortalized cell line

value: None / input


title: Female_B6_DNaseI_Repl3_G163_M9

description: DNase-seq Library


title: Tr1-869


title: HCT116 G2 Lb1 cTSA-seq StrePD Rep1

value: Streptavidin pull-down (StrePD)


title: ATAC-seq Con PE Rep2

value: wild type


title: ATAC-seq Con GT Rep3

value: primitive gut tube


title: Female_B6_DNaseI_Repl1_G163_M6

description: DNase-seq Library


title: T-allo10-869

value: DC-derived T regulatory type I cells

value: pair-ended 2x250


title: CD4-869

value: positive isolated from PBMC


title: ATAC-seq Con PE Rep1

value: embryonic stem cells


title: HCT116 G2 Lb1 cTSA-seq input Rep2


title: ATAC-seq Con DE Rep3

value: definitive endoderm


title: non-Tr1-869

value: sorted from T-allo10 cells


title: HCT116 S Lb1 cTSA-seq StrePD Rep1

value: S


title: ATAC-seq Con GT Rep2


title: HCT116 S Lb1 cTSA-seq StrePD Rep2


title: Male_B6_DNaseI_Repl4_G163_M4

description: DNase-seq Library

value: C57BL/6J (Jackson Labs, cat#:000664)


title: Female_B6_DNaseI_Repl2_G163_M7

description: DNase-seq Library

value: Female


title: ATAC-seq Con GT Rep1


title: HCT116 S Lb1 cTSA-seq input Rep1


title: HCT116 G1 Lb1 cTSA-seq StrePD Rep2


title: ATAC-seq Con DE Rep2


title: HCT116 G1 Lb1 cTSA-seq StrePD Rep1


title: HCT116 S Lb1 cTSA-seq input Rep2


title: Male_B6_DNaseI_Repl3_G163_M3

description: DNase-seq Library

value: 32U (RQ1; Promega cat#:M6101)


title: ATAC-seq Con DE Rep1


title: Male_B6_DNaseI_Repl2_G163_M2

description: DNase-seq Library

value: Male


title: Female_CAST_INPUT_G162_M24

description: Input Control Library

data_processing:
READ MAPPING: ChIP-seq reads were aligned using Bowtie2 (Langmead et al 2009, Genome Biology) with default settings. Reads were filtered so that only uniquely-aligned reads were used for downstream analysis.
PEAK CALLING: Peaks were called using Macs2 (Zhang et al 2008, Genome Biology) with default parameters without filtering for PCR duplicates. Peaks were filtered to remove blacklisted regions (www.sites.google.com/site/anshulkundaje/projects/blacklists) and also regions called as peaks that contain only PCR duplicated reads.
Genome_build: mm9
Supplementary_files_format_and_content: Replicate merged peak lists for H3K27ac ChIP-seq, merged by strain and sex. Samples were combined at the fastq level and processed through a standard ChIP-seq pipeline as described. Columns are in BED6+4 format from MACS2 narrowPeak defaults. Specifically, columns 1-3 represent genomic coordinates of the indicated peak; column 4 is the peak name (unique identifier); column 5 is an integer score for display calculated as -10*log10(qvalue); column 6 indicates the strand; column 7 indicates the fold-change over background; column 8 indicates -(log10pvalue); column 9 indicates -log10(qvalue); and column 10 indicates the summit position relative to the 5' end of the peak.

extract_protocol:
Liver was dounce homogenized, passed through a 70 micron filter, and then crosslinked with 1% formaldehyde for 10 minutes. Samples were sonicated with a Bioruptor Pico (Diagenode, cat#:B01060010) until the majority of DNA fragments were between 100-400bp (25 cycles total, 30 sec ON 30 sec OFF). Chromatin was quantified and 15 ug of chromatinized DNA was incubated with anti-H3K27ac antibody (Abcam, cat#:ab4729).
Samples were prepared for sequencing with NEBNext Ultra II DNA Library Prep Kit for Illumina according to the manufacturer's directions for low input samples (New England Biolabs, #E7645). All samples were subjected to double-sided SPRI size selection prior to PCR amplification (Agencourt AMPure XP; Beckman Coulter: A63882). Samples were barcoded using New England Biolabs NEBNext Multiplex Oligos for Illumina (#E7335) with 8 rounds of PCR per the manufacturer's instructions.

value: CAST/EiJ (Jackson Labs, cat#:000928)

tag: chip antibody

value: 8 weeks


title: Male_B6_DNaseI_Repl1_G163_M1

description: DNase-seq Library


title: HCT116 G1 Lb1 cTSA-seq input Rep2

value: Immortalized cell line

value: None / input


title: HCT116 G1 Lb1 cTSA-seq input Rep1


title: ATAC-seq Con ESC Rep3

value: undifferentiated

value: wild type


title: ATAC-seq Con ESC Rep2


title: Male_CAST_INPUT_G162_M23

description: Input Control Library


title: HCT116 180m G1 Lb1 cTSA-seq StrePD Rep2

value: Streptavidin pull-down (StrePD)

value: Later G1

value: Nocodazole (16h), release and FACS for G1


title: Tr1-2443

first: Alma-Martina

last: Cepika

address: 265 Campus Drive West

institute: Stanford University School of Medicine

data_processing:
Sequencing reads were mapped and aligned to the reference human genome (GENCODE v32) using Salmon v1.0.0
Reads were quantified using Salmon v1.0.0, then aggregated to gene level and imported into R using tximport
Counts were generated from abundances and scaled using the average transcript length, averaged over samples and to library size
Counts were filtered by expression and retained if a min count per group (Cell_Type) was 15
Count data was transformed to log2-counts per million (logCPM), cmbining observational-level weights from voom with sample-specific weights
Genome_build: GENCODE v32
Supplementary_files_format_and_content: comma-separated values (csv) file containing log2-counts per million (logCPM) for every gene and sample

growth_protocol: ex vivo, or T-allo10 or T-allo culture

extract_protocol:
T cells were lysed using RNAqueous lysis buffer (Invitrogen), lysates purified from genomic DNA using gDNA Eliminator Columns (Qiagen),  and RNA extracted using RNAqueous Micro Total RNA Isolation Kit (Invitrogen)
cDNA was generated from total RNA using SMARTer Ultra Low Input RNA Kit for Sequencing (Takara Bio).  RNA-seq libraries were generated from by Nextera XT Library Prep Kit (Illumina)

treatment_protocol: ex vivo isolated total CD4+ T cells, or FACS-sorted CD49b+LAG3+ or CD49b-LAG3- memory CD4 T cells from the T-allo10 culture, or FACS-sorted CD49b-LAG3- memory CD4 T cells from the T-allo culture


title: Male_B6_INPUT_G162_M21

description: Input Control Library


title: Female_B6_INPUT_G162_M22

description: Input Control Library


title: ATAC-seq Con ESC Rep1

value: embryonic stem cells


title: HCT116 180m G1 Lb1 cTSA-seq input Rep2


title: ExVivoTissue_CRLM_rep2

city: Chongqing

first: Bosheng

last: Li

address: Gaotanyan Street

institute: Army Medical University

description: Arraystar Human lncRNA microarray V3

hyb_protocol: Agilent Gene Expression Hybridization Kit (Agilent p/n 5188-5242) was used according to the manufacturer' protocol

scan_protocol: Agilent Microarray Scanner (Agilent p/n G2565BA) was used to scan

data_processing: Agilent Feature Extraction was used to extract data

source_name: CRLM tissue, replicate 2

label_protocol: Quick Amp Labeling Kit, One-Color (Agilent p/n 5190-0442) was used according to the manufacturer' instructions and RNA was purified using RNeasy Mini Kit (Qiagen p/n 74104)

extract_protocol: Cryopulverization of tissue using the Biopulverizer；Place the BioPulverizer™ in a shallow container and cool thoroughly with either liquid nitrogen；Place prefrozen tissue in the well of the mortar；Remove the mortar from the shallow container, place it on the lab bench and pulverize the tissue with one or two blows to the pestle with a hammer (models 59012MS)；Empty the powdered contents for subsequent homogenization or extraction procedures.

tag: gender

value: male


title: ExVivoTissue_CRLM_rep1

description: Arraystar Human lncRNA microarray V3

source_name: CRLM tissue, replicate 1


title: ExVivoTissue_CRLM_rep3

description: Arraystar Human lncRNA microarray V3

source_name: CRLM tissue, replicate 3


title: Tr1-0789a


title: ExVivoTissue_Normal_rep2

description: Arraystar Human lncRNA microarray V3

source_name: Normal tissue, replicate 2


title: ExVivoTissue_Normal_rep3

description: Arraystar Human lncRNA microarray V3

source_name: Normal tissue, replicate 3


title: ExVivoTissue_Normal_rep1

description: Arraystar Human lncRNA microarray V3

source_name: Normal tissue, replicate 1


title: Tr1-0789b


title: HCT116 180m G1 Lb1 cTSA-seq StrePD Rep1


title: HCT116 90m G1 Lb1 cTSA-seq StrePD Rep2

value: Early G1


title: Teff-0789b

source_name: T-allo

value: Teff


title: Female_CAST_H3K27ac_Repl5_G162_M20

description: ChIP-seq Library

value: Abcam anti H3K27ac (cat# Ab4729)

tag: Sex


title: Female_CAST_H3K27ac_Repl4_G162_M19

description: ChIP-seq Library

value: Female


title: Teff-2443


title: Female_CAST_H3K27ac_Repl2_G162_M17

description: ChIP-seq Library


title: Teff-0789a


title: ExVivoTissue_CRC_rep3

description: Arraystar Human lncRNA microarray V3

source_name: CRC tissue, replicate 3


title: ExVivoTissue_CRC_rep2

description: Arraystar Human lncRNA microarray V3

source_name: CRC tissue, replicate 2


title: ExVivoTissue_CRC_rep1

description: Arraystar Human lncRNA microarray V3

source_name: CRC tissue, replicate 1


title: FB:  DP T cell

city: Seoul

first: Jaeil

last: Lee

address: 103 Daehak-ro, Jongno-gu

country: South Korea

institute: Seoul National University

description: Cell Surface Protein Library

library_source: other

data_processing:
We used Cell Ranger v3.1.0 (10X Genomics) pipeline for FASTQ file generation from raw sequencing data,
Illumina basecall files from Illumina sequencing instrument were converted to FASTQ format for each sample using the ‘mkfastq’ command.0
Sequencing reads were aligned to the Macaca_fascicularis_6.0 genome reference for Macaca fascicularis using STAR (v2.5.1b) aligner. Those of feature barcoded libraries were matched to the target feature barcode reference.
gene and cell surface protein expression profiling in each cell was performed with the information of unique molecular identifier (UMI) and 10X cell barcode. Then, cells were grouped into clusters by their gene expression.
Raw count matrices of 10x genomics were imported to Seurat 3.1.3.
Genome_build: Macaca_fascicularis_6.0
Supplementary_files_format_and_content: The lists of cell barcode and features in tsv format, filtered gene matrix table with raw gene counts in mtx and HDF5 format.

molecule: other

organism: Macaca fascicularis

source_name: CD4, CD8 cell surface protein

extract_protocol:
CD4+ T cells were first separated from fresh PBMC using the REAlease CD4 MicroBead kit  according to the manufacturer's instructions. And then, CD4+CD8+ DP T cells were separated from isolated CD4+ T cells using CD8 Microbeads kit.
Libraries were prepared using the Chromium controller according to the 10x Chromium Single Cell V(D)J User Guide (10x Genomics).

value: Peripheral blood

value: circulating CD4+CD8+ double positive T cells

value: 10 years old

value: untreated


title: Male_CAST_H3K27ac_Repl5_G162_M15

description: ChIP-seq Library

source_name: Liver

value: C57BL/6J (Jackson Labs, cat#:000664)

value: Male

value: 8 weeks


title: DN-2443

value: DN


title: HCT116 90m G1 Lb1 cTSA-seq StrePD Rep1

source_name: Immortalized cell line

value: Immortalized cell line

tag: type

value: Streptavidin pull-down (StrePD)


title: Female_CAST_H3K27ac_Repl3_G162_M18

description: ChIP-seq Library

value: CAST/EiJ (Jackson Labs, cat#:000928)


title: RNA: DP T cell

description: 5’ Gene Expression Library

source_name: circulating CD4+CD8+ double positive T cells Gene expression


title: HCT116 90m G1 Lb1 cTSA-seq input Rep2

value: None / input

tag: cell cycle stage

value: Nocodazole (16h), release and FACS for G1


title: HCT116 180m G1 Lb1 cTSA-seq input Rep1

value: Later G1

tag: treatments


title: Female_CAST_H3K27ac_Repl1_G162_M16

description: ChIP-seq Library


title: HCT116 90m G1 Lb1 cTSA-seq input Rep1

value: Early G1


title: HCT116 Bulk Lb1 cTSA-seq StrePD Rep1

value: Asynchronous bulk


title: CD4-2443


title: DN-0789b


title: CD4-0789


title: HCT116 Bulk Lb1 cTSA-seq StrePD Rep2


title: DN-0789a


title: Male_CAST_H3K27ac_Repl2_G162_M12

description: ChIP-seq Library

value: Abcam anti H3K27ac (cat# Ab4729)


title: Male_CAST_H3K27ac_Repl4_G162_M14

description: ChIP-seq Library


title: FB2271-t

first: Jens

last: Hansen

address: 1425 Madison Ave

department: Department of Pharmacological Sciences

institute: Icahn School of Medicine at Mount Sinai

data_processing:
Random removal of reads from each fastq-file to ensure that all samples that are subjected to the same comparison have the same final read counts (e.g. all mouse samples have the same read counts before alignment)
Alignment to the reference genome using Tophat 2.0.8
Identification of differentially expressed genes using Cufflinks 1.3.0
Genome_build: h19 and mm9

source_name: Thoracic aortic wall

extract_protocol: none provided by the submitter

value: thoracic aortic tissue of Marfan patient


title: HCT116 Bulk Lb1 cTSA-seq input Rep2


title: Male_CAST_H3K27ac_Repl3_G162_M13

description: ChIP-seq Library


title: K562 Bulk Lb1 cTSA-seq StrePD Rep2


title: Male_CAST_H3K27ac_Repl1_G162_M11

description: ChIP-seq Library


title: FB490-t


title: HCT116 Bulk Lb1 cTSA-seq input Rep1


title: K562 Bulk Lb1 cTSA-seq StrePD Rep1


title: Female_B6_H3K27ac_Repl5_G162_M10

description: ChIP-seq Library

value: Female


title: FB1334-t


title: K562 Bulk Lb1 cTSA-seq input Rep1


title: sternohyoid muscle biopsies from hyperthyroid donor 2

city: Debrecen

first: Szilard

last: Poliska

address: Egyetem ter 1.

department: Biochemistry and Molecular Biology

country: Hungary

institute: University of Debrecen

hyb_protocol: Samples were hybridized at 45 degrees Celsius for 16 hours and then standard washing protocol was performed using GeneChip Fluidics Station 450 (Affymetrix).

scan_protocol: Arrays were scanned on GeneChip Scanner 7G (Affymetrix), Affymetrix GeneChip Command Console (AGCC) was used to obtain image files.

data_processing:
CHP files were generated using Affymetrix Expression Control.
log2 RMA signals

label_protocol: Ambion WT Expression Kit (Applied Biosystems) and GeneChip WT Terminal Labeling and Control Kit (Affymetrix) were used for amplifying and labeling 150 ng of RNA

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Human biopsies were taken from eu- and hyperthyroid patients without any preliminary treatments from female donors  in accordance with guidelines of the European Union Council and Hungarian regulations under license number DEOEC RKEB/IKEB 3517-2011.

tag: individual

value: hyperthyroid donor 2

value: Human sternohyoid muscle biopsy


title: Female_B6_H3K27ac_Repl4_G162_M9

description: ChIP-seq Library


title: AS1207-t

value: control thoracic aortic tissue


title: K562 Bulk Lb1 cTSA-seq input Rep2


title: Female_B6_H3K27ac_Repl3_G162_M8

description: ChIP-seq Library


title: AS1088-t


title: sternohyoid muscle biopsies from hyperthyroid donor 3

value: hyperthyroid donor 3


title: sternohyoid muscle biopsies from hyperthyroid donor 1

value: hyperthyroid donor 1


title: sternohyoid muscle biopsies from euthyroid donor 2

value: euthyroid donor 2


title: sternohyoid muscle biopsies from euthyroid donor 1

value: euthyroid donor 1


title: sternohyoid muscle biopsies from euthyroid donor 3

value: euthyroid donor 3


title: Female_B6_H3K27ac_Repl1_G162_M6

description: ChIP-seq Library

value: CAST/EiJ (Jackson Labs, cat#:000928)

value: 8 weeks


title: RVSMC transfected with AlivecGap and treated with AngII 3hr, biological rep3

city: Duarte

first: Rama

last: Natarajan

state: California

address: 1500 E Duarte Rd

department: Department of Diabetes Complications and Metabolism

institute: Beckman Research Institute, City of Hope

description: Gene expression data from RVSMC transfected with Alivec GapmeR (100nM) for 48 hours and treated with Angiotensin II (100 nM) for 3 hours

hyb_protocol: The chips were hybridized in Affymetrix Hybridization Oven 640 and washed using Affymetrix Fluidics Station 450 according to manufacturer's protocols.

scan_protocol: The chips were scanned by Affymetrix scanner 3000 7G using manufacturer's default settings

data_processing: Raw Affymetrix intensity measurements of all probe sets were background-corrected, normalized, and summarized into gene level expression measurements using RMA method implemented in Partek Genomic Suite V6.6.

organism: Rattus norvegicus

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 200 ng total RNA.

growth_protocol: Rat vascular smooth muscle cells (RVSMCs) were isolated from thoracic aortas of male Sprague-Dawley rats by enzymatic digestion and cultured in M199 medium supplemented with 10% FBS and antibiotics.

extract_protocol: Total RNA was isolated using RNeasy reagent (Qiagen) following manufacturer's instructions.

treatment_protocol: Cells were transfected with either negative control GapmeR (NCGap) or rat Alivec Gapmer (AlivecGap) for 48 hours, and then treated with either 100 nM of Angiotensin II or equivalent volume of 1x PBS for 3 hours.

value: rat vascular smooth muscle cells


title: RVSMC transfected with AlivecGap and treated with AngII 3hr, biological rep2

value: transfected with Alivec GapmeR (100nM) for 48 hours and treated with Angiotensin II (100 nM) for 3 hours


title: RVSMC transfected with AlivecGap and treated with AngII 3hr, biological rep1


title: Male_B6_H3K27ac_Repl5_G162_M5

description: ChIP-seq Library

value: C57BL/6J (Jackson Labs, cat#:000664)

value: Male


title: LC476

city: Parkville

first: Peter

last: Hickey

address: 1G Royal Parade

country: Australia

institute: WEHI

description: A backup plate containing the same samples as LCE475

data_processing:
gene and ERCC count matrix generated using scPipe 1.10.0
reads were aligned using Rsubread 2.2.6
All code used to perform data processing and analysis of the RNA-seq data are available from https://github.com/WEHISCORE/C084_Hayman_Pasricha
Genome_build: GRCh38.p12
Supplementary_files_format_and_content: CSV, gene count matrix, rows represent genes and each column is a well, values corresponding to UMI counts
Supplementary_files_format_and_content: CSV, ERCC count matrix, rows represent ERCC spike-in sequences and each column is a well, values corresponding to UMI counts
Supplementary_files_format_and_content: CSV, sample sheet, rows represent a well and columns contain metadata on the sample in the well

source_name: Peripheral blood

extract_protocol:
Whole blood was stored and frozen in RNA-later. Frozen samples were thawed at room temperature and RNA was isolated immediately using the RiboPure Blood Kit (Ambion) as per manufacturers protocol.
Transcriptome libraries were generated by adapting the CelSeq2 protocol[12] as follows: Samples were pooled after first strand cDNA synthesis, treated with Exonuclease 1 for 30 minutes, followed by a 1.2X bead clean-up. Second strand synthesis was performed using NEBNext Second Strand Synthesis module (NEB #E6111S) i and NucleoMag NGS Clean-up and Size select magnetic beads (Macherey-Nagel - 7449970.5) were used for all DNA purification and size selection steps.

treatment_protocol: Children received one of the following interventions daily for six months: 1) MNPs containing 10 mg of zinc (Treatment A); 2) dispersible tablet containing 10 mg zinc (Treatment B); or 3) placebo powder (Treatment C)

value: Peripheral blood


title: LC475

description: A 1:10 dilution of plate number LCE475


title: Failed plate LC475

description: Plate number LCE475 failed library preparation. Following the failure of LCE475, the library preparation was repeated to generate ‘C084_LC475_mini_bulk_back_up_1:10’ and ‘LCE_476_BU_8_cycle’


title: Female_B6_H3K27ac_Repl2_G162_M7

description: ChIP-seq Library

value: Abcam anti H3K27ac (cat# Ab4729)