title: EPS-blastoid7 [A7]

first: gene

last: E

address: Julong Street

institute: egene

description: Smart-seq2 approach for mRNA sequencing library contructions

data_processing:
Basecalls performed using CASAVA
RNA reads are removed adaptor sequences and low quality sequences using software cutadapt-1.9 with parameters -a AGATCGGAAGAGC -A AGATCGGAAGAGC -a CTGTCTCTTATA -A CTGTCTCTTATA -g AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT -G AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT -g AAGCAGTGGTATCAACGCAGAGTACATGGG -G AAGCAGTGGTATCAACGCAGAGTACATGGG -u 10 -U 10-n 4 aligned to the genome Mus musculus GRCm38 using hisat2-2.1.0  with default parameters
Fragments per kilobase of exon per million fragments mapped (FPKM) are caculated using the stringtie-1.3.4d following the default options and added the -G/--GTF guide
Genome_build: Mus musculus GRCm38
Supplementary_files_format_and_content: tab-delimited FPKM files for all the samples generated using ballgown

source_name: EPS-blasotids

growth_protocol: EPS colonies were dissociated into single cells by incubation with TrypLE (Gibco). To remove irradiated MEF cells, cell resuspension was transferred into a 0.1% gelatin-coated plate and incubated at 37°C for 30 min. EPS cells were collected, filtered through a 40 μm cell strainer, and counted. AggreWell 400 (STEMCELL Technology) were prepared following the manufacturer’s instructions. The basal medium for the EPS-blastoid induction medium is composed of 25% TSC basal medium, 25% N2B27 basal medium, and 50% KSOM (homemade or Millipore, MR020P5D). Approximately 6,000 cells (five cells per microwell for 1200 microwells) were resuspended in basal medium supplemented with 2μM ROCK inhibitor Y-27632 (Reagents Direct, 53-B80-50), 12.5ng/ml rhFGF4 (R&D, 235F4025), 12.5ng/ml Heparin (Sigma, H3149), 3μM GSK3 inhibitor CHIR99021 (Axon Medchem, 27-H76), 5ng/ml BMP4 (Proteintech, HZ-1040), and 0.5μM A83-01 (Axon Medchem, 1421) and seeded into the AggreWell 400. The plate was centrifuged at 300g for one minute and transferred into a incubator. The next day, the medium was removed and replaced with fresh induction medium without Y- 27632. Blastoids were manually picked up under a stereomicroscope for downstream experiments or analysis

extract_protocol:
EPS-blastoids were manually picked up using mouthpipette and washed three times. Total RNA was isolated from eight individual EPS-blastoids at day five of induction using the TRIzol method.
RNA-Seq libraries were constructed using the Illumina Smart- Seq2, and 2x150 bp pair-end sequencing was performed in an Illumina HiSeq Xten.

tag: Sex

value: male

value: embryo

value: Blastoids generated from EPS cells


title: EPS-blastoid6 [A6]

status: Public on Aug 03 2019

type: SRA

city: Shenzhen

country: China

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: tissue

tag: cell type


title: EPS-blastoid8 [A8]


title: EMM3

city: New York

first: Juhee

last: Jeong

state: New York

address: 345 E 24th St

department: Basic sciences and Craniofacial development

country: USA

institute: New York University College of Dentistry

data_processing:
Sequencing results were demultiplexed and converted to FASTQ format by using Illumina bcl2fastq software
Sequencing reads were aligned to the mouse genome mm10 using STAR aligner
Read counts were normalized and used to test for differential expression with DESeq2
Genome_build: mm10
Supplementary_files_format_and_content: comma-separated values' file with normalized counts for all genes in each sample, along with Fold Change and p value for the comparison of expression levels between EMM and SOM.

source_name: early migrating cranial mesenchyme

extract_protocol:
Apical and basolateral areas of the head were dissected in ice cold PBS, and subject to dispase treatment 3 U/ml, 37 C, 10 min. Subsequently, the surface ectoderm and the brain were removed to isolate the mesenchyme, which was flash frozen on dry ice and stored at -80 C. After enough tissue was collected, it was homogenized with a pestle and QIAshredder (QIAgen), and total RNA was extracted using RNeasy Mini kit (QIAgen).
Illumina TruSeq kit following standard Illumina protocol

tag: strain

tag: age

tag: genotype

value: wild type


title: EPS-blastoid5 [A5]


title: EPS-blastoid4 [A4]


title: EMM2


title: EPS-blastoid3 [A3]


title: EPS-blastoid2 [A2]


title: EMM1


title: EPS-blastoid1 [A1]


title: Tumor- P152Lp53 - 2

status: Public on Aug 02 2019

city: Bangalore

first: madavan

last: vasudevan

state: Karnataka

address: Kasturi Nagar

country: India

institute: Theomics International Private Limited

data_processing:
Quality check on Fastq files for tumor samples were performed using fastQC -0.11.6
Human reference genome version GRCH38p10 was indexed using STAR Aligner- 2.5
Fastq files were aligned on reference genome using STAR Aligner-2.5
Read alignment Counts were generated using QoRTs v1.3.0
Deseq2 used get differetially expressed genes Tumor Control vs Mutated
Genome_build: Release 27 (GRCh38.p10)
Supplementary_files_format_and_content: .txt Count files generated using STAR Alingment and QoRTs.

organism: Homo sapiens

source_name: Tumor generated from H1299 cell line

growth_protocol:
Human lung carcinoma H1299 (p53 null) cell line was cultured in RPMI supplemented with 10% (v/v) FCS (Gibco). Proliferating cell cultures were main¬tained in a 5% CO2 humidified incubator at 37 °C.
H1299 cell line stably expressing P152L p53 and vector control were injected subcutaneously  into  the  right  flank  region  of nude mice. After 38 days, when tumors were visible, mice were sacrificed

extract_protocol:
Total RNA was isolated and harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
The sequencing library is prepared by random fragmentation of the cDNA sample, followed by 5' and 3' adapter ligation, after end-repair and the addition of an ‘A’ base and SPRI cleanup. The prepared cDNA library was amplified using PCR for the enrichment of the adapter-ligated fragments. Alternatively, "tagmentation" combines the fragmentation and ligation reactions into a single step that greatly increases the efficiency of the library preparation process. . The individual libraries were quantified using a NanoDrop spectrophotometer (Thermo Scientific) and validated for quality with a Bioanalyzer (Agilent Technologies). Adapter-ligated fragments are then PCR amplified and gel purified

value: H1299 cells stably transfected with p FLAG-CMV10 P152Lp53

value: P152Lmutant p53


title: Tumor- P152Lp53 - 1


title: Tumor- pCMV10Ctrl -2

value: H1299 cells stably transfected with p FLAG-CMV10 vector control


title: Tumor- pCMV10Ctrl -1


title: CD4+ T cells, EAE+Vehicle

type: RNA

city: Columbia

first: Prakash

last: Nagarkatti

state: SC

address: 6439 Garners Ferry Road

institute: University of South Carolina School of Medicine

hyb_protocol: Labeled samples were hybridized to miRNA 4.0 chips overnight (16h, 48°C, 60 RPM) then washed and stained on an Affymetrix GCS 3000 system Fluidics station using the FS450_0002 protocol.

scan_protocol: Chips were scanned on a Affymetrix GCS 3000 system scanner.

data_processing: Affymetrix Expression Console Version 1.4.1.46 was used for quality control, data summarization, and normalization. The processing algorithm used was RMA-DABG. Affymetrix Transcriptome Analysis Console Version 3.1.0.5 was used to perform differential expression analyses. MicroRNAs were considered differentially expressed between the two groups if linear fold change was greater than ±2 and the ANOVA p-value was less than 0.05

label: Biotin

source_name: Brain CD4+

label_protocol: 500ng total RNA was used as starting material for labeling according to the Affymetrix FlashTag Biotin HSR RNA Labeling Kit manufacturer protocol.

growth_protocol: EAE disease was induced in 6-8 week old mice by immunization with MOG peptide. Mice were treated daily with vehicle or 10mg/kg each (i.p.) of (THC+CBD) starting on day 10 post immunization.

extract_protocol: Total RNA was isolated with Qiagen miRNeasy micro kit.

treatment_protocol: Brain mononuclear cells were isolated by enzymatic digestion followed by overnight culture and CD4+ immunomagnetic selection.

tag: disease state

value: EAE

tag: gender

value: Female

value: 6-8 weeks

value: brain

value: CD4+ T cells

tag: treatment

value: Vehicle


title: KO-M-FA-3

city: hershey

first: Nithyananda

last: Thorenoor

state: PA

address: 500 University Drive

department: Pediatrics

institute: Penn State University College of Medicine

description:
Small RNA-seq libraries were generated by NEXTflex Small RNA Library Prep Kit v3 for Illumina (BioO Scientific, Austin, TX), followed by deep sequencing on an Illumina HiSeq 2500 as per the manufacturer’s instructions.  Briefly, 1-2 ng of total RNA was ligated with chemically modified 3’- and 5’- adapters that can specifically bind to mature micro RNAs, followed by reverse transcription and PCR amplification.  Unique index sequence tags were introduced during PCR to enable multiplexed sequencing.  Each library was assessed for the presence of desired micro RNA population and approximate library quantity by Bioanalyzer High Sensitivity DNA Kit (Agilent Technologies).  Pooled libraries were denatured and loaded onto a TruSeq Rapid flow cell on an Illumina HiSeq 2500 and run for 50 cycles using a single-read recipe according to the manufacturer's instructions.  De-multiplexed sequencing reads passed the default purify filtering of Illumina CASAVA pipeline (released version 1.8) and were quality trimmed/filtered using The FASTX-Toolkit (http://hannonlab.cshl.edu/fastx_toolkit).  The filtered reads were further trimmed with both 5’ and 3’ adapter sequences and subjected to Chimira suite to align and count miRNA expression (Vitsios and Enright, 2015).
KO male_deseq2.txt
JFRm140

data_processing:
De-multiplexed sequencing reads passed the default purify filtering of Illumina CASAVA pipeline (released version 1.8) and were quality trimmed/filtered using The FASTX-Toolkit (http://hannonlab.cshl.edu/fastx_toolkit).  The filtered reads were further trimmed with both 5’ and 3’ adapter sequences and subjected to Chimira suite to align and count miRNA expression (Vitsios and Enright, 2015).  The differentially expressed miRNAs (DEG) between FA to O3, males and females were identified by using the edgeR (Robinson et al., 2010) and the TCC v1.14.0 R package (Sun et al., 2013) with false discovery rate (FDR) adjusted p value of 0.1 as a significance cutoff.
miRNAs with good correlation between mice (3 out of 4).  We used two different parameters (methods) to analyze the identified miRNA expression (fold change).  a) The expression levels (fold change) of miRNAs from co-ex (FA to O3 for males and females) and KO (FA to O3 for males and females) were analyzed and differentially expressed miRNAs in co-ex and KO males and females were identified in response to FA or O3.  b) The changes in miRNA expression in co-ex were calculated by normalizing to KO, i.e., the level of expression of each individual experimental miRNA in co-ex males and females exposed to FA or O3 was divided by the corresponding miRNA in the KO.  Next, the differentially expressed miRNAs between co-ex males and females were determined by dividing a specific individual male miRNA by the corresponding female miRNA.
Supplementary_files_format_and_content: normalized counts

source_name: Male mouse exposed to Filtered air-Alveolar Macrophage (AM) cells

extract_protocol:
AM cells were isoalated from Broncho alveolar lavage, Total RNA extracted
Small RNA-seq libraries were generated by NEXTflex Small RNA Library Prep Kit v3 for Illumina (BioO Scientific, Austin, TX), followed by deep sequencing on an Illumina HiSeq 2500 as per the manufacturer’s instructions.  Briefly, 1-2 ng of total RNA was ligated with chemically modified 3’- and 5’- adapters that can specifically bind to mature micro RNAs, followed by reverse transcription and PCR amplification.  Unique index sequence tags were introduced during PCR to enable multiplexed sequencing.  Each library was assessed for the presence of desired micro RNA population and approximate library quantity by Bioanalyzer High Sensitivity DNA Kit (Agilent Technologies).  Pooled libraries were denatured and loaded onto a TruSeq Rapid flow cell on an Illumina HiSeq 2500 and run for 50 cycles using a single-read recipe according to the manufacturer's instructions.

treatment_protocol: The animals were exposed to FA or O3 in parallel as described previously (Haque et al., 2007).  A group of 4 animals (males, females) were exposed to FA or O3 for 3 h, and alveolar macrophages (AM) were isolated after 4 h of recovery

tag: exposure time

value: 3 hours

value: Male


title: KO-F-FA-3

description:
Small RNA-seq libraries were generated by NEXTflex Small RNA Library Prep Kit v3 for Illumina (BioO Scientific, Austin, TX), followed by deep sequencing on an Illumina HiSeq 2500 as per the manufacturer’s instructions.  Briefly, 1-2 ng of total RNA was ligated with chemically modified 3’- and 5’- adapters that can specifically bind to mature micro RNAs, followed by reverse transcription and PCR amplification.  Unique index sequence tags were introduced during PCR to enable multiplexed sequencing.  Each library was assessed for the presence of desired micro RNA population and approximate library quantity by Bioanalyzer High Sensitivity DNA Kit (Agilent Technologies).  Pooled libraries were denatured and loaded onto a TruSeq Rapid flow cell on an Illumina HiSeq 2500 and run for 50 cycles using a single-read recipe according to the manufacturer's instructions.  De-multiplexed sequencing reads passed the default purify filtering of Illumina CASAVA pipeline (released version 1.8) and were quality trimmed/filtered using The FASTX-Toolkit (http://hannonlab.cshl.edu/fastx_toolkit).  The filtered reads were further trimmed with both 5’ and 3’ adapter sequences and subjected to Chimira suite to align and count miRNA expression (Vitsios and Enright, 2015).
KO female_deseq2.txt
JFRm138

source_name: Female mouse exposed to Filtered air-Alveolar Macrophage (AM) cells


title: KO-M-O3-2

description:
Small RNA-seq libraries were generated by NEXTflex Small RNA Library Prep Kit v3 for Illumina (BioO Scientific, Austin, TX), followed by deep sequencing on an Illumina HiSeq 2500 as per the manufacturer’s instructions.  Briefly, 1-2 ng of total RNA was ligated with chemically modified 3’- and 5’- adapters that can specifically bind to mature micro RNAs, followed by reverse transcription and PCR amplification.  Unique index sequence tags were introduced during PCR to enable multiplexed sequencing.  Each library was assessed for the presence of desired micro RNA population and approximate library quantity by Bioanalyzer High Sensitivity DNA Kit (Agilent Technologies).  Pooled libraries were denatured and loaded onto a TruSeq Rapid flow cell on an Illumina HiSeq 2500 and run for 50 cycles using a single-read recipe according to the manufacturer's instructions.  De-multiplexed sequencing reads passed the default purify filtering of Illumina CASAVA pipeline (released version 1.8) and were quality trimmed/filtered using The FASTX-Toolkit (http://hannonlab.cshl.edu/fastx_toolkit).  The filtered reads were further trimmed with both 5’ and 3’ adapter sequences and subjected to Chimira suite to align and count miRNA expression (Vitsios and Enright, 2015).
KO male_deseq2.txt
JFRm124

source_name: Male mouse exposed to Ozone (O3)-Alveolar Macrophage (AM) cells


title: KO-F-O3-1

description:
Small RNA-seq libraries were generated by NEXTflex Small RNA Library Prep Kit v3 for Illumina (BioO Scientific, Austin, TX), followed by deep sequencing on an Illumina HiSeq 2500 as per the manufacturer’s instructions.  Briefly, 1-2 ng of total RNA was ligated with chemically modified 3’- and 5’- adapters that can specifically bind to mature micro RNAs, followed by reverse transcription and PCR amplification.  Unique index sequence tags were introduced during PCR to enable multiplexed sequencing.  Each library was assessed for the presence of desired micro RNA population and approximate library quantity by Bioanalyzer High Sensitivity DNA Kit (Agilent Technologies).  Pooled libraries were denatured and loaded onto a TruSeq Rapid flow cell on an Illumina HiSeq 2500 and run for 50 cycles using a single-read recipe according to the manufacturer's instructions.  De-multiplexed sequencing reads passed the default purify filtering of Illumina CASAVA pipeline (released version 1.8) and were quality trimmed/filtered using The FASTX-Toolkit (http://hannonlab.cshl.edu/fastx_toolkit).  The filtered reads were further trimmed with both 5’ and 3’ adapter sequences and subjected to Chimira suite to align and count miRNA expression (Vitsios and Enright, 2015).
KO female_deseq2.txt
JFRm119

source_name: Female mouse exposed to Ozone (O3)-Alveolar Macrophage (AM) cells


title: KO-F-O3-2

description:
Small RNA-seq libraries were generated by NEXTflex Small RNA Library Prep Kit v3 for Illumina (BioO Scientific, Austin, TX), followed by deep sequencing on an Illumina HiSeq 2500 as per the manufacturer’s instructions.  Briefly, 1-2 ng of total RNA was ligated with chemically modified 3’- and 5’- adapters that can specifically bind to mature micro RNAs, followed by reverse transcription and PCR amplification.  Unique index sequence tags were introduced during PCR to enable multiplexed sequencing.  Each library was assessed for the presence of desired micro RNA population and approximate library quantity by Bioanalyzer High Sensitivity DNA Kit (Agilent Technologies).  Pooled libraries were denatured and loaded onto a TruSeq Rapid flow cell on an Illumina HiSeq 2500 and run for 50 cycles using a single-read recipe according to the manufacturer's instructions.  De-multiplexed sequencing reads passed the default purify filtering of Illumina CASAVA pipeline (released version 1.8) and were quality trimmed/filtered using The FASTX-Toolkit (http://hannonlab.cshl.edu/fastx_toolkit).  The filtered reads were further trimmed with both 5’ and 3’ adapter sequences and subjected to Chimira suite to align and count miRNA expression (Vitsios and Enright, 2015).
KO female_deseq2.txt
JFRm120


title: KO-M-O3-1

description:
Small RNA-seq libraries were generated by NEXTflex Small RNA Library Prep Kit v3 for Illumina (BioO Scientific, Austin, TX), followed by deep sequencing on an Illumina HiSeq 2500 as per the manufacturer’s instructions.  Briefly, 1-2 ng of total RNA was ligated with chemically modified 3’- and 5’- adapters that can specifically bind to mature micro RNAs, followed by reverse transcription and PCR amplification.  Unique index sequence tags were introduced during PCR to enable multiplexed sequencing.  Each library was assessed for the presence of desired micro RNA population and approximate library quantity by Bioanalyzer High Sensitivity DNA Kit (Agilent Technologies).  Pooled libraries were denatured and loaded onto a TruSeq Rapid flow cell on an Illumina HiSeq 2500 and run for 50 cycles using a single-read recipe according to the manufacturer's instructions.  De-multiplexed sequencing reads passed the default purify filtering of Illumina CASAVA pipeline (released version 1.8) and were quality trimmed/filtered using The FASTX-Toolkit (http://hannonlab.cshl.edu/fastx_toolkit).  The filtered reads were further trimmed with both 5’ and 3’ adapter sequences and subjected to Chimira suite to align and count miRNA expression (Vitsios and Enright, 2015).
KO male_deseq2.txt
JFRm123


title: KO-M-O3-3

description:
Small RNA-seq libraries were generated by NEXTflex Small RNA Library Prep Kit v3 for Illumina (BioO Scientific, Austin, TX), followed by deep sequencing on an Illumina HiSeq 2500 as per the manufacturer’s instructions.  Briefly, 1-2 ng of total RNA was ligated with chemically modified 3’- and 5’- adapters that can specifically bind to mature micro RNAs, followed by reverse transcription and PCR amplification.  Unique index sequence tags were introduced during PCR to enable multiplexed sequencing.  Each library was assessed for the presence of desired micro RNA population and approximate library quantity by Bioanalyzer High Sensitivity DNA Kit (Agilent Technologies).  Pooled libraries were denatured and loaded onto a TruSeq Rapid flow cell on an Illumina HiSeq 2500 and run for 50 cycles using a single-read recipe according to the manufacturer's instructions.  De-multiplexed sequencing reads passed the default purify filtering of Illumina CASAVA pipeline (released version 1.8) and were quality trimmed/filtered using The FASTX-Toolkit (http://hannonlab.cshl.edu/fastx_toolkit).  The filtered reads were further trimmed with both 5’ and 3’ adapter sequences and subjected to Chimira suite to align and count miRNA expression (Vitsios and Enright, 2015).
KO male_deseq2.txt
JFRm125


title: ZH487_mock_rep2

city: Heidelberg

first: Bernhard

last: Radlwimmer

address: Im Neuenheimer Feld 280

department: Department of Molecular Genetics

country: Germany

institute: Deutsches Krebsforschungszentrum / German National Cancer Research Centre

hyb_protocol: Affymetrix standard protocol

scan_protocol: Affymetrix standard protocol

data_processing: Raw microarray .CEL files were read into R (3.4.3) and normalized using the ‘gcrma’ R package (2.50.0). Probes without an annotated gene were removed from the analysis, leaving 41941 annotated probes. R annotation package versions: hgu133plus2probe_2.18.0,  hgu133plus2cdf_2.18.0, hgu133plus2.db_3.2.3

label: biotin

source_name: gliomasphere patient-derived cell line

label_protocol: Affymetrix standard protocol

growth_protocol: The human glioblastoma cell line LN229 was obtained from ATCC (cat. CRL-2611). Cells were cultured in DMEM containing 1 g/L glucose (D5921, Sigma) supplemented with 10% tetracycline-free fetal bovine serum (Clontech), 1% penicillin and streptomycin (P/S) mix, and glutamine (0.5 mM).     The ZH487 glioblastoma spheroid primary cells were originally established at the University of Zurich Hospital.  ZH487 cells were cultured in Neurobasal medium (Cat. 12348017, NBM) supplemented with 2% B27 (cat. 12587010, retinoic acid-free, Invitrogen), EGF (20 ng/ml, AF-100-15, Peprotech), FGF (20 ng/ml, cat. 100-18B, Peprotech) and glutamine (0.5 mM).     DNA methylation array (Illumina EPIC) analysis classified the ZH487 primary tumour and derived cell line as part of the RTK I subtype.    All cell lines were cultured under 10% CO2 at 37℃ with humidity.    Cell identities were verified by the Multiplex human Cell line Authentication Test (MCA). Cells were also tested for mycoplasma contamination with the Multiplex cell test (Multiplexion GmbH, Friedrichshafen, Germany).

extract_protocol: Total RNA was isolated using the RNeasy Microkit (Qiagen) according to the manufacturer's standard protocol.

treatment_protocol: Inducible SOX10 knockdown cells were established by infecting cells with pLKO-Tet-On non-targeting (nt) shRNA and pLKO-Tet-On SOX10 shRNA (TRCN0000018988) lentiviral particles and puromycin selection (1 µg/ml) for 7 days. shRNA expression was induced by adding 0.1 µg/ml doxycycline to the medium for at least 7 days.

tag: subtype

value: RTK_I-like glioblastoma cell line


title: ZH487_shSOX10_2_rep2


title: ZH487_shSOX10_3_rep2


title: ZH487_shSOX10_1_rep2


title: KO-F-FA-2

description:
Small RNA-seq libraries were generated by NEXTflex Small RNA Library Prep Kit v3 for Illumina (BioO Scientific, Austin, TX), followed by deep sequencing on an Illumina HiSeq 2500 as per the manufacturer’s instructions.  Briefly, 1-2 ng of total RNA was ligated with chemically modified 3’- and 5’- adapters that can specifically bind to mature micro RNAs, followed by reverse transcription and PCR amplification.  Unique index sequence tags were introduced during PCR to enable multiplexed sequencing.  Each library was assessed for the presence of desired micro RNA population and approximate library quantity by Bioanalyzer High Sensitivity DNA Kit (Agilent Technologies).  Pooled libraries were denatured and loaded onto a TruSeq Rapid flow cell on an Illumina HiSeq 2500 and run for 50 cycles using a single-read recipe according to the manufacturer's instructions.  De-multiplexed sequencing reads passed the default purify filtering of Illumina CASAVA pipeline (released version 1.8) and were quality trimmed/filtered using The FASTX-Toolkit (http://hannonlab.cshl.edu/fastx_toolkit).  The filtered reads were further trimmed with both 5’ and 3’ adapter sequences and subjected to Chimira suite to align and count miRNA expression (Vitsios and Enright, 2015).
KO female_deseq2.txt
JFRm137


title: KO-M-FA-2

description:
Small RNA-seq libraries were generated by NEXTflex Small RNA Library Prep Kit v3 for Illumina (BioO Scientific, Austin, TX), followed by deep sequencing on an Illumina HiSeq 2500 as per the manufacturer’s instructions.  Briefly, 1-2 ng of total RNA was ligated with chemically modified 3’- and 5’- adapters that can specifically bind to mature micro RNAs, followed by reverse transcription and PCR amplification.  Unique index sequence tags were introduced during PCR to enable multiplexed sequencing.  Each library was assessed for the presence of desired micro RNA population and approximate library quantity by Bioanalyzer High Sensitivity DNA Kit (Agilent Technologies).  Pooled libraries were denatured and loaded onto a TruSeq Rapid flow cell on an Illumina HiSeq 2500 and run for 50 cycles using a single-read recipe according to the manufacturer's instructions.  De-multiplexed sequencing reads passed the default purify filtering of Illumina CASAVA pipeline (released version 1.8) and were quality trimmed/filtered using The FASTX-Toolkit (http://hannonlab.cshl.edu/fastx_toolkit).  The filtered reads were further trimmed with both 5’ and 3’ adapter sequences and subjected to Chimira suite to align and count miRNA expression (Vitsios and Enright, 2015).
KO male_deseq2.txt
JFRm122


title: ZH487_NT_rep2


title: hASCs_RCP

city: Tsukuba

first: Hitomi

last: Takada

state: Ibaraki

address: Higashi 1-1-1

country: Japan

institute: National Institute for Advanced Industrial Science and Technology

description: Gene expression in hASCs cultured on RCP

hyb_protocol: 0.6 ug Cy3-labelled cRNA (specific activity >9.0 pmol Cy3/ug cRNA)  was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Fragmentation buffer and 2x Blocking agent. 25 uL of 2x Hi-RPM Hybridization buffer was added to the fragmentation mixture and hybridized to SurePrint G3 Human GE microarray 8360K (G4851A; Agilent Technologies) for 17 hours at 65 °C. After hybridization, the array slides were washed 1 minute with Agilent Gene Expression Wash Buffer1 at room temperature,1 minute with Agilent Gene Expression Wash Buffer 2 at 37°C, 15 seconds with acetonitrile (Wako), and dried immediately.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 8x60k array slides.

data_processing: The scanned images were analyzed with Feature Extraction Software 11.5.1.1 (Agilent) using default parameters (protocol GE1_1105_Oct12 and Grid:028004_D_F_20140326 ) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: ASCs_normal adhesive dish_2 days

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using the Quick Amp Labeling kit (Agilent) according to manufacturer's instructions, followed by Rneasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000c Sepctrophotometer.

extract_protocol: hASCs with RCP scaffold were mechanically homogenized and dissolved with Isogen, and fine fragments of the RCP were discarded by following centrifugation. hASCs cultured in normal culture dish were harvested with 0.25% trypsin and 2mM EDTA for 5 minutes at 37 ℃, and the cell suspension were collected and dissolved with Isogen. Total RNAs of the both group were purified using the RNeasy mini kit (Qiagen, Hilden, Germany) according to the manufacturer’s recommendations.

treatment_protocol: hASCs were culutred on RCP scaffold or on normal adhesive dish for 2days.

value: Adipose tissue-derived stem cells (ASCs)

tag: cultured on

value: recombinant collagen peptide (RCP) scaffold


title: co-ex- O3-M-4

description:
Small RNA-seq libraries were generated by NEXTflex Small RNA Library Prep Kit v3 for Illumina (BioO Scientific, Austin, TX), followed by deep sequencing on an Illumina HiSeq 2500 as per the manufacturer’s instructions.  Briefly, 1-2 ng of total RNA was ligated with chemically modified 3’- and 5’- adapters that can specifically bind to mature micro RNAs, followed by reverse transcription and PCR amplification.  Unique index sequence tags were introduced during PCR to enable multiplexed sequencing.  Each library was assessed for the presence of desired micro RNA population and approximate library quantity by Bioanalyzer High Sensitivity DNA Kit (Agilent Technologies).  Pooled libraries were denatured and loaded onto a TruSeq Rapid flow cell on an Illumina HiSeq 2500 and run for 50 cycles using a single-read recipe according to the manufacturer's instructions.  De-multiplexed sequencing reads passed the default purify filtering of Illumina CASAVA pipeline (released version 1.8) and were quality trimmed/filtered using The FASTX-Toolkit (http://hannonlab.cshl.edu/fastx_toolkit).  The filtered reads were further trimmed with both 5’ and 3’ adapter sequences and subjected to Chimira suite to align and count miRNA expression (Vitsios and Enright, 2015).
Coex_male_deseq2.txt
JFRm88


title: KO-F-FA-1

description:
Small RNA-seq libraries were generated by NEXTflex Small RNA Library Prep Kit v3 for Illumina (BioO Scientific, Austin, TX), followed by deep sequencing on an Illumina HiSeq 2500 as per the manufacturer’s instructions.  Briefly, 1-2 ng of total RNA was ligated with chemically modified 3’- and 5’- adapters that can specifically bind to mature micro RNAs, followed by reverse transcription and PCR amplification.  Unique index sequence tags were introduced during PCR to enable multiplexed sequencing.  Each library was assessed for the presence of desired micro RNA population and approximate library quantity by Bioanalyzer High Sensitivity DNA Kit (Agilent Technologies).  Pooled libraries were denatured and loaded onto a TruSeq Rapid flow cell on an Illumina HiSeq 2500 and run for 50 cycles using a single-read recipe according to the manufacturer's instructions.  De-multiplexed sequencing reads passed the default purify filtering of Illumina CASAVA pipeline (released version 1.8) and were quality trimmed/filtered using The FASTX-Toolkit (http://hannonlab.cshl.edu/fastx_toolkit).  The filtered reads were further trimmed with both 5’ and 3’ adapter sequences and subjected to Chimira suite to align and count miRNA expression (Vitsios and Enright, 2015).
KO female_deseq2.txt
JFRm118


title: hASCs_control

description: Gene expression in hASCs cultured on normal adhesive dish

source_name: ASCs_RCP_2 days

value: adhesive dish


title: Thoracic Aorta SMCs, Tsc1+/+  (aka Cntrl)

city: New Haven

first: George

last: Tellides

state: CT- CONNECTICUT

address: 10 Amistad St, 337B

department: Surgery

institute: Yale University

description: Control

data_processing:
I1 read: contains the sample index.
R1 read: contains the cell barcode (first 16 nt) and UMI (next 10 nt).
R2 read: contains the RNA sequence.
The data from sequencer was processed using bcl2fastq progam provided by the vendor (10X genomics).  This program demultiplexes the data.
The resulting output was procssed using cellranger program provided by the vendor (10X genomics).  This program aligns, the reads, and uses the barcode information to generate diigital gene expression matrix data.
This data was read into the Seurat package (version 2.0).  The data was filtered and normalized in Seurat.
After principal component analysis, first 30 principal components were used for clustering.  The data was further visualized using Seurat and R.
Genome_build: mm10 with added sequences for GFP, and tdTomato
Supplementary_files_format_and_content: average gene expression values for each cluster for each original condition.

source_name: Thoracic Aorta GFP+ SMCs

extract_protocol:
Thoracic aortas were rapidly excised, rinsed in cold PBS, opened longitudinally, sliced into small fragments around 3 mm in size, incubated in 0.5 ml DMEM with 10% FBS, 1.5 mg/ml collagenase A, and 0.5 mg/ml elastase for 60 min at 37°C while the tissue fragments were gently triturated using a pipette every 15 min, passed through a 40 μm filter, incubated with cell-impermeant viability dye for 20 min at 4°C
The selected cells were processed for single-cell RNA-seq library preparation using the Chromium™ Single Cell Platform (10x Genomics) as per the manufacturer’s protocol: single cells were partitioned into Gel Beads in Emulsion using the Chromium™ system (10x Genomics), followed by cell lysis and barcoded reverse transcription of RNA, cDNA amplification and shearing, and 5’ adaptor and sample index attachment. The single-cell RNA-seq libraries were sequenced on a HiSeq 4000 System (Illumina) at the Yale Center for Genome Analysis.

value: male

tag: time

value: 24 weeks postnatal

value: Tsc+/+

value: Thoracic Aorta

value: SMCs


title: Thoracic Aorta SMCs, Tsc1−/−  (aka KO)

description: KO

value: Tsc-/-


title: co-ex- O3-M-3

description:
Small RNA-seq libraries were generated by NEXTflex Small RNA Library Prep Kit v3 for Illumina (BioO Scientific, Austin, TX), followed by deep sequencing on an Illumina HiSeq 2500 as per the manufacturer’s instructions.  Briefly, 1-2 ng of total RNA was ligated with chemically modified 3’- and 5’- adapters that can specifically bind to mature micro RNAs, followed by reverse transcription and PCR amplification.  Unique index sequence tags were introduced during PCR to enable multiplexed sequencing.  Each library was assessed for the presence of desired micro RNA population and approximate library quantity by Bioanalyzer High Sensitivity DNA Kit (Agilent Technologies).  Pooled libraries were denatured and loaded onto a TruSeq Rapid flow cell on an Illumina HiSeq 2500 and run for 50 cycles using a single-read recipe according to the manufacturer's instructions.  De-multiplexed sequencing reads passed the default purify filtering of Illumina CASAVA pipeline (released version 1.8) and were quality trimmed/filtered using The FASTX-Toolkit (http://hannonlab.cshl.edu/fastx_toolkit).  The filtered reads were further trimmed with both 5’ and 3’ adapter sequences and subjected to Chimira suite to align and count miRNA expression (Vitsios and Enright, 2015).
Coex_male_deseq2.txt
JFRm87


title: ZT23_KO3

city: Lisboa

first: Miguel

middle: Alves

last: Rendas

state: Lisbon

address: Av. Brasília, 1400-038 Lisboa

country: Portugal

institute: Champalimaud Foundation

data_processing:
Global quality of RNA-Seq data was assessed Global quality of FASTQ files with raw RNA-seq reads was analysed using fastqc (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
vast-tools (Tapial, J. et al., 2017) (version 2.0.0) aligning and read processing software was used for quantification of gene expression in read counts from FASTQ files using VASTD-DB56 transcript annotation for mouse genome assembly mm9.
Only the 8443 genes with read count information in all 12 samples and an average greater than 1.25 reads/sample were considered informative enough for subsequent analyses.
Preprocessing of read count data, namely transforming them to log2-counts per million (logCPM), was performed with voom (Law et al., 2014), included in the Bioconductor (Huber et al., 2015) package limma (Ritchie et al., 2015) for the statistical software environment R.
Linear models and empirical Bayes statistics were employed in differential gene expression analysis, using limma.
Genome_build: mm9
Supplementary_files_format_and_content: CSV file containing the Log2 (counts per million) for each sample

source_name: Small intestina lamina propria

extract_protocol:
Cells were sorted to complete RPMI medium with a purity always greater than 95%. RNA extraction was then performed using the RNeasy Micro Kit (Qiagen) following the manufacturer instructions. Samples were processed following the Smart-Seq 2 guidelines. Briefly, polyA mRNA was initially purified using oligo-dT magnetic beads and then converted to cDNA. Library preparation was achieved using the Nextera XT DNA sample preparation kit (illumina). Libraries were sequenced on a Illumina HiSeq4000 (paired-end, 100bp).
Mice were sacrificed with CO2. Small intestines were harvested and thoroughly rinsed with cold PBS1X and had the Peyer patches removed. Intestines were then cut in 1cm pieces, and shaken for 30min in PBS containing 2% FBS, 1% HEPES and 5mM EDTA to remove intraepithelial and epithelial cells. Intestines were then digested with collagenase D (0.5mg/mL; Roche) and DNase I (20U/mL; Roche) in complete RPMI for 30 min at 37 °C, under gentle agitation. Sequentially cells were passed through a 100μM cell strainer and purified by centrifugation 30min at 2400rpm in 40/80 Percoll (GE Healthcare) gradient. Erythrocytes from small intestine were lysed using RBC lysis buffer (eBioscience). Cells were stained and ILC3 were sorted as CD45.2+ Lin- Thy1.2hi KLRG1- cells
Libraries were prepared according to Smart-Seq 2 guidelines, using the Nextera XT DNA sample preparation kit (illumina).

value: KO (Rorc-Cre.Arntlfl/fl)

value: Small intestine lamina propria

tag: timepoint


title: KO-M-FA-1

description:
Small RNA-seq libraries were generated by NEXTflex Small RNA Library Prep Kit v3 for Illumina (BioO Scientific, Austin, TX), followed by deep sequencing on an Illumina HiSeq 2500 as per the manufacturer’s instructions.  Briefly, 1-2 ng of total RNA was ligated with chemically modified 3’- and 5’- adapters that can specifically bind to mature micro RNAs, followed by reverse transcription and PCR amplification.  Unique index sequence tags were introduced during PCR to enable multiplexed sequencing.  Each library was assessed for the presence of desired micro RNA population and approximate library quantity by Bioanalyzer High Sensitivity DNA Kit (Agilent Technologies).  Pooled libraries were denatured and loaded onto a TruSeq Rapid flow cell on an Illumina HiSeq 2500 and run for 50 cycles using a single-read recipe according to the manufacturer's instructions.  De-multiplexed sequencing reads passed the default purify filtering of Illumina CASAVA pipeline (released version 1.8) and were quality trimmed/filtered using The FASTX-Toolkit (http://hannonlab.cshl.edu/fastx_toolkit).  The filtered reads were further trimmed with both 5’ and 3’ adapter sequences and subjected to Chimira suite to align and count miRNA expression (Vitsios and Enright, 2015).
KO male_deseq2.txt
JFRm121


title: ZT23_KO1


title: KO-F-O3-3

description:
Small RNA-seq libraries were generated by NEXTflex Small RNA Library Prep Kit v3 for Illumina (BioO Scientific, Austin, TX), followed by deep sequencing on an Illumina HiSeq 2500 as per the manufacturer’s instructions.  Briefly, 1-2 ng of total RNA was ligated with chemically modified 3’- and 5’- adapters that can specifically bind to mature micro RNAs, followed by reverse transcription and PCR amplification.  Unique index sequence tags were introduced during PCR to enable multiplexed sequencing.  Each library was assessed for the presence of desired micro RNA population and approximate library quantity by Bioanalyzer High Sensitivity DNA Kit (Agilent Technologies).  Pooled libraries were denatured and loaded onto a TruSeq Rapid flow cell on an Illumina HiSeq 2500 and run for 50 cycles using a single-read recipe according to the manufacturer's instructions.  De-multiplexed sequencing reads passed the default purify filtering of Illumina CASAVA pipeline (released version 1.8) and were quality trimmed/filtered using The FASTX-Toolkit (http://hannonlab.cshl.edu/fastx_toolkit).  The filtered reads were further trimmed with both 5’ and 3’ adapter sequences and subjected to Chimira suite to align and count miRNA expression (Vitsios and Enright, 2015).
KO female_deseq2.txt
JFRm126

value: Female


title: co-ex- O3-M-1

description:
Small RNA-seq libraries were generated by NEXTflex Small RNA Library Prep Kit v3 for Illumina (BioO Scientific, Austin, TX), followed by deep sequencing on an Illumina HiSeq 2500 as per the manufacturer’s instructions.  Briefly, 1-2 ng of total RNA was ligated with chemically modified 3’- and 5’- adapters that can specifically bind to mature micro RNAs, followed by reverse transcription and PCR amplification.  Unique index sequence tags were introduced during PCR to enable multiplexed sequencing.  Each library was assessed for the presence of desired micro RNA population and approximate library quantity by Bioanalyzer High Sensitivity DNA Kit (Agilent Technologies).  Pooled libraries were denatured and loaded onto a TruSeq Rapid flow cell on an Illumina HiSeq 2500 and run for 50 cycles using a single-read recipe according to the manufacturer's instructions.  De-multiplexed sequencing reads passed the default purify filtering of Illumina CASAVA pipeline (released version 1.8) and were quality trimmed/filtered using The FASTX-Toolkit (http://hannonlab.cshl.edu/fastx_toolkit).  The filtered reads were further trimmed with both 5’ and 3’ adapter sequences and subjected to Chimira suite to align and count miRNA expression (Vitsios and Enright, 2015).
Coex_male_deseq2.txt
JFRm85


title: co-ex- O3- M-2

description:
Small RNA-seq libraries were generated by NEXTflex Small RNA Library Prep Kit v3 for Illumina (BioO Scientific, Austin, TX), followed by deep sequencing on an Illumina HiSeq 2500 as per the manufacturer’s instructions.  Briefly, 1-2 ng of total RNA was ligated with chemically modified 3’- and 5’- adapters that can specifically bind to mature micro RNAs, followed by reverse transcription and PCR amplification.  Unique index sequence tags were introduced during PCR to enable multiplexed sequencing.  Each library was assessed for the presence of desired micro RNA population and approximate library quantity by Bioanalyzer High Sensitivity DNA Kit (Agilent Technologies).  Pooled libraries were denatured and loaded onto a TruSeq Rapid flow cell on an Illumina HiSeq 2500 and run for 50 cycles using a single-read recipe according to the manufacturer's instructions.  De-multiplexed sequencing reads passed the default purify filtering of Illumina CASAVA pipeline (released version 1.8) and were quality trimmed/filtered using The FASTX-Toolkit (http://hannonlab.cshl.edu/fastx_toolkit).  The filtered reads were further trimmed with both 5’ and 3’ adapter sequences and subjected to Chimira suite to align and count miRNA expression (Vitsios and Enright, 2015).
Coex_male_deseq2.txt
JFRm86


title: coex-FA-M-3

description:
Small RNA-seq libraries were generated by NEXTflex Small RNA Library Prep Kit v3 for Illumina (BioO Scientific, Austin, TX), followed by deep sequencing on an Illumina HiSeq 2500 as per the manufacturer’s instructions.  Briefly, 1-2 ng of total RNA was ligated with chemically modified 3’- and 5’- adapters that can specifically bind to mature micro RNAs, followed by reverse transcription and PCR amplification.  Unique index sequence tags were introduced during PCR to enable multiplexed sequencing.  Each library was assessed for the presence of desired micro RNA population and approximate library quantity by Bioanalyzer High Sensitivity DNA Kit (Agilent Technologies).  Pooled libraries were denatured and loaded onto a TruSeq Rapid flow cell on an Illumina HiSeq 2500 and run for 50 cycles using a single-read recipe according to the manufacturer's instructions.  De-multiplexed sequencing reads passed the default purify filtering of Illumina CASAVA pipeline (released version 1.8) and were quality trimmed/filtered using The FASTX-Toolkit (http://hannonlab.cshl.edu/fastx_toolkit).  The filtered reads were further trimmed with both 5’ and 3’ adapter sequences and subjected to Chimira suite to align and count miRNA expression (Vitsios and Enright, 2015).
Coex_male_deseq2.txt
JFRm83


title: coex-FA-M-4

description:
Small RNA-seq libraries were generated by NEXTflex Small RNA Library Prep Kit v3 for Illumina (BioO Scientific, Austin, TX), followed by deep sequencing on an Illumina HiSeq 2500 as per the manufacturer’s instructions.  Briefly, 1-2 ng of total RNA was ligated with chemically modified 3’- and 5’- adapters that can specifically bind to mature micro RNAs, followed by reverse transcription and PCR amplification.  Unique index sequence tags were introduced during PCR to enable multiplexed sequencing.  Each library was assessed for the presence of desired micro RNA population and approximate library quantity by Bioanalyzer High Sensitivity DNA Kit (Agilent Technologies).  Pooled libraries were denatured and loaded onto a TruSeq Rapid flow cell on an Illumina HiSeq 2500 and run for 50 cycles using a single-read recipe according to the manufacturer's instructions.  De-multiplexed sequencing reads passed the default purify filtering of Illumina CASAVA pipeline (released version 1.8) and were quality trimmed/filtered using The FASTX-Toolkit (http://hannonlab.cshl.edu/fastx_toolkit).  The filtered reads were further trimmed with both 5’ and 3’ adapter sequences and subjected to Chimira suite to align and count miRNA expression (Vitsios and Enright, 2015).
Coex_male_deseq2.txt
JFRm84


title: coex-FA-M-1

description:
Small RNA-seq libraries were generated by NEXTflex Small RNA Library Prep Kit v3 for Illumina (BioO Scientific, Austin, TX), followed by deep sequencing on an Illumina HiSeq 2500 as per the manufacturer’s instructions.  Briefly, 1-2 ng of total RNA was ligated with chemically modified 3’- and 5’- adapters that can specifically bind to mature micro RNAs, followed by reverse transcription and PCR amplification.  Unique index sequence tags were introduced during PCR to enable multiplexed sequencing.  Each library was assessed for the presence of desired micro RNA population and approximate library quantity by Bioanalyzer High Sensitivity DNA Kit (Agilent Technologies).  Pooled libraries were denatured and loaded onto a TruSeq Rapid flow cell on an Illumina HiSeq 2500 and run for 50 cycles using a single-read recipe according to the manufacturer's instructions.  De-multiplexed sequencing reads passed the default purify filtering of Illumina CASAVA pipeline (released version 1.8) and were quality trimmed/filtered using The FASTX-Toolkit (http://hannonlab.cshl.edu/fastx_toolkit).  The filtered reads were further trimmed with both 5’ and 3’ adapter sequences and subjected to Chimira suite to align and count miRNA expression (Vitsios and Enright, 2015).
Coex_male_deseq2.txt
JFRm81


title: co-ex- O3-F-3

description:
Small RNA-seq libraries were generated by NEXTflex Small RNA Library Prep Kit v3 for Illumina (BioO Scientific, Austin, TX), followed by deep sequencing on an Illumina HiSeq 2500 as per the manufacturer’s instructions.  Briefly, 1-2 ng of total RNA was ligated with chemically modified 3’- and 5’- adapters that can specifically bind to mature micro RNAs, followed by reverse transcription and PCR amplification.  Unique index sequence tags were introduced during PCR to enable multiplexed sequencing.  Each library was assessed for the presence of desired micro RNA population and approximate library quantity by Bioanalyzer High Sensitivity DNA Kit (Agilent Technologies).  Pooled libraries were denatured and loaded onto a TruSeq Rapid flow cell on an Illumina HiSeq 2500 and run for 50 cycles using a single-read recipe according to the manufacturer's instructions.  De-multiplexed sequencing reads passed the default purify filtering of Illumina CASAVA pipeline (released version 1.8) and were quality trimmed/filtered using The FASTX-Toolkit (http://hannonlab.cshl.edu/fastx_toolkit).  The filtered reads were further trimmed with both 5’ and 3’ adapter sequences and subjected to Chimira suite to align and count miRNA expression (Vitsios and Enright, 2015).
Coex_female_deseq2.txt
JFRm95


title: co-ex- O3-F-2

description:
Small RNA-seq libraries were generated by NEXTflex Small RNA Library Prep Kit v3 for Illumina (BioO Scientific, Austin, TX), followed by deep sequencing on an Illumina HiSeq 2500 as per the manufacturer’s instructions.  Briefly, 1-2 ng of total RNA was ligated with chemically modified 3’- and 5’- adapters that can specifically bind to mature micro RNAs, followed by reverse transcription and PCR amplification.  Unique index sequence tags were introduced during PCR to enable multiplexed sequencing.  Each library was assessed for the presence of desired micro RNA population and approximate library quantity by Bioanalyzer High Sensitivity DNA Kit (Agilent Technologies).  Pooled libraries were denatured and loaded onto a TruSeq Rapid flow cell on an Illumina HiSeq 2500 and run for 50 cycles using a single-read recipe according to the manufacturer's instructions.  De-multiplexed sequencing reads passed the default purify filtering of Illumina CASAVA pipeline (released version 1.8) and were quality trimmed/filtered using The FASTX-Toolkit (http://hannonlab.cshl.edu/fastx_toolkit).  The filtered reads were further trimmed with both 5’ and 3’ adapter sequences and subjected to Chimira suite to align and count miRNA expression (Vitsios and Enright, 2015).
Coex_female_deseq2.txt
JFRm94


title: ZT23_WT1

value: WT


title: ZT05_WT1


title: ZT05_WT3


title: ZT05_KO1


title: ZT23_WT2


title: co-ex- O3-F-4

description:
Small RNA-seq libraries were generated by NEXTflex Small RNA Library Prep Kit v3 for Illumina (BioO Scientific, Austin, TX), followed by deep sequencing on an Illumina HiSeq 2500 as per the manufacturer’s instructions.  Briefly, 1-2 ng of total RNA was ligated with chemically modified 3’- and 5’- adapters that can specifically bind to mature micro RNAs, followed by reverse transcription and PCR amplification.  Unique index sequence tags were introduced during PCR to enable multiplexed sequencing.  Each library was assessed for the presence of desired micro RNA population and approximate library quantity by Bioanalyzer High Sensitivity DNA Kit (Agilent Technologies).  Pooled libraries were denatured and loaded onto a TruSeq Rapid flow cell on an Illumina HiSeq 2500 and run for 50 cycles using a single-read recipe according to the manufacturer's instructions.  De-multiplexed sequencing reads passed the default purify filtering of Illumina CASAVA pipeline (released version 1.8) and were quality trimmed/filtered using The FASTX-Toolkit (http://hannonlab.cshl.edu/fastx_toolkit).  The filtered reads were further trimmed with both 5’ and 3’ adapter sequences and subjected to Chimira suite to align and count miRNA expression (Vitsios and Enright, 2015).
Coex_female_deseq2.txt
JFRm96


title: co-ex-FA-F-4

description:
Small RNA-seq libraries were generated by NEXTflex Small RNA Library Prep Kit v3 for Illumina (BioO Scientific, Austin, TX), followed by deep sequencing on an Illumina HiSeq 2500 as per the manufacturer’s instructions.  Briefly, 1-2 ng of total RNA was ligated with chemically modified 3’- and 5’- adapters that can specifically bind to mature micro RNAs, followed by reverse transcription and PCR amplification.  Unique index sequence tags were introduced during PCR to enable multiplexed sequencing.  Each library was assessed for the presence of desired micro RNA population and approximate library quantity by Bioanalyzer High Sensitivity DNA Kit (Agilent Technologies).  Pooled libraries were denatured and loaded onto a TruSeq Rapid flow cell on an Illumina HiSeq 2500 and run for 50 cycles using a single-read recipe according to the manufacturer's instructions.  De-multiplexed sequencing reads passed the default purify filtering of Illumina CASAVA pipeline (released version 1.8) and were quality trimmed/filtered using The FASTX-Toolkit (http://hannonlab.cshl.edu/fastx_toolkit).  The filtered reads were further trimmed with both 5’ and 3’ adapter sequences and subjected to Chimira suite to align and count miRNA expression (Vitsios and Enright, 2015).
Coex_female_deseq2.txt
JFRm92


title: ZT05_WT2


title: C50-Non-Ep

city: Baltimore

first: yang

last: song

state: MD

address: HSF-3, 3rd Floor; 670 W Baltimore St.

department: Department: Institute for Genome Sciences

institute: University of Maryland in Baltimore

library_source: genomic

data_processing:
FASTQ files were aligned to mm10 using bwa mem, and converted to BAM format
Only mapped reads were filtered out.
BAM files were converted to BED format
Nuclease accessible regions were called using F-seq peak calling
Blacklist regions were removed
Genome_build: mm10

molecule: genomic DNA

source_name: Cochlea Non-Epithelial

extract_protocol:
Cochleae were removed and dissociated to obtained a single cell suspension, incubated with an CD326-APC antibody to label epithelial cells. Cells were then sorted into cochlear CD326 (+) cells (epithelial) and cochlear CD326 (-) cells (non-epithelial) by FACS using a BD FACS Aria II Cell Sorter (BD Biosciences)
Library were prepared following the protocol described in Buenrostro et al. (2015) with the Nextera kit (Illumina)

value: Post-natal day 2

value: non-epithelial cochlear cells

tag: antibody for facs

value: CD326-APC (BioLegend cat# 118213)

tag: cell number


title: C100-Non-Ep


title: ZT05_KO3


title: ZT05_KO2


title: ZT23_WT3


title: C100-Ep

source_name: Cochlea Epithelial

value: epithelial cochlear cells


title: C50-Ep


title: co-ex-FA-F-2

description:
Small RNA-seq libraries were generated by NEXTflex Small RNA Library Prep Kit v3 for Illumina (BioO Scientific, Austin, TX), followed by deep sequencing on an Illumina HiSeq 2500 as per the manufacturer’s instructions.  Briefly, 1-2 ng of total RNA was ligated with chemically modified 3’- and 5’- adapters that can specifically bind to mature micro RNAs, followed by reverse transcription and PCR amplification.  Unique index sequence tags were introduced during PCR to enable multiplexed sequencing.  Each library was assessed for the presence of desired micro RNA population and approximate library quantity by Bioanalyzer High Sensitivity DNA Kit (Agilent Technologies).  Pooled libraries were denatured and loaded onto a TruSeq Rapid flow cell on an Illumina HiSeq 2500 and run for 50 cycles using a single-read recipe according to the manufacturer's instructions.  De-multiplexed sequencing reads passed the default purify filtering of Illumina CASAVA pipeline (released version 1.8) and were quality trimmed/filtered using The FASTX-Toolkit (http://hannonlab.cshl.edu/fastx_toolkit).  The filtered reads were further trimmed with both 5’ and 3’ adapter sequences and subjected to Chimira suite to align and count miRNA expression (Vitsios and Enright, 2015).
Coex_female_deseq2.txt
JFRm90

value: 3 hours


title: co-ex-FA-F-3

description:
Small RNA-seq libraries were generated by NEXTflex Small RNA Library Prep Kit v3 for Illumina (BioO Scientific, Austin, TX), followed by deep sequencing on an Illumina HiSeq 2500 as per the manufacturer’s instructions.  Briefly, 1-2 ng of total RNA was ligated with chemically modified 3’- and 5’- adapters that can specifically bind to mature micro RNAs, followed by reverse transcription and PCR amplification.  Unique index sequence tags were introduced during PCR to enable multiplexed sequencing.  Each library was assessed for the presence of desired micro RNA population and approximate library quantity by Bioanalyzer High Sensitivity DNA Kit (Agilent Technologies).  Pooled libraries were denatured and loaded onto a TruSeq Rapid flow cell on an Illumina HiSeq 2500 and run for 50 cycles using a single-read recipe according to the manufacturer's instructions.  De-multiplexed sequencing reads passed the default purify filtering of Illumina CASAVA pipeline (released version 1.8) and were quality trimmed/filtered using The FASTX-Toolkit (http://hannonlab.cshl.edu/fastx_toolkit).  The filtered reads were further trimmed with both 5’ and 3’ adapter sequences and subjected to Chimira suite to align and count miRNA expression (Vitsios and Enright, 2015).
Coex_female_deseq2.txt
JFRm91


title: coex-FA-M-2

description:
Small RNA-seq libraries were generated by NEXTflex Small RNA Library Prep Kit v3 for Illumina (BioO Scientific, Austin, TX), followed by deep sequencing on an Illumina HiSeq 2500 as per the manufacturer’s instructions.  Briefly, 1-2 ng of total RNA was ligated with chemically modified 3’- and 5’- adapters that can specifically bind to mature micro RNAs, followed by reverse transcription and PCR amplification.  Unique index sequence tags were introduced during PCR to enable multiplexed sequencing.  Each library was assessed for the presence of desired micro RNA population and approximate library quantity by Bioanalyzer High Sensitivity DNA Kit (Agilent Technologies).  Pooled libraries were denatured and loaded onto a TruSeq Rapid flow cell on an Illumina HiSeq 2500 and run for 50 cycles using a single-read recipe according to the manufacturer's instructions.  De-multiplexed sequencing reads passed the default purify filtering of Illumina CASAVA pipeline (released version 1.8) and were quality trimmed/filtered using The FASTX-Toolkit (http://hannonlab.cshl.edu/fastx_toolkit).  The filtered reads were further trimmed with both 5’ and 3’ adapter sequences and subjected to Chimira suite to align and count miRNA expression (Vitsios and Enright, 2015).
Coex_male_deseq2.txt
JFRm82

value: Male


title: Lmx1bCKO_caudal_2

city: Cleveland

first: Evan

last: Deneris

state: OH

address: 2109 Adelbert Rd.

department: Neurosciences

institute: Case Western Reserve University

data_processing:
Illumina Casava1.8.2 software used for basecalling.
Sequenced reads were filtered for low-quality sequence, then mapped to mm10 whole genome using tophat2.
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using cufflinks.
Reads were mapped to the Mus musculus genome (UCSC mm10) using the Burroughs-Wheeler Aligner (BWA) and were filtered to select reads that map to a single location (Li and Durbin, 2009). Peak calling was performed with MACS2 v2.1.1 (Zhang et al., 2008).
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for each sample in the control vs. Lmx1bCKO and Pet1CKO generated by cufflinks. For ChIP-seq, a BED file of mycPet-1 ChIP peaks is provided.

source_name: 5-HT neuron

growth_protocol: Animals were reared in standard housing conditions.

extract_protocol:
EYFP+ 5-HT neurons were sorted using a BD FACSAria or Sony iCyt into Trizol reagent and extracted RNA was Dnase I treated and purified using the RNA Clean & Concentrator-5 kit (Zymo). Purified total RNA was amplified with the TRIO RNA-seq kit (Nugen) or SMARTer v2 (Clontech). Dissected YFP+ tissue between the mid-hindbrain boundary and pontine flexure (rostral) and pontine flexure to the spinal cord boundary (caudal) of E17.5 hindbrains from Lmx1bfl/fl;ePet-EYFP, Pet1fl/fl;ePet-EYFP, ePet-Cre;Lmx1bfl/fl;ePet-EYFP, or ePet-Cre;Pet1fl/fl;ePet-EYFP embryos.
RNA libraries were prepared for sequencing using either Clontech SMARTer v2 RNA-seq (P2) or NuGen TRIO RNA-Seq (E17.5).

value: 5-HT neuron


title: CUTLL1 DMSO Arima rep1 (Hi-C)

status: Public on Aug 04 2019

city: Braunschweig

first: Andreas

last: Kloetgen

state: NI

address: Inhoffenstr 7

department: Department for Computational Biology of Infection Research

institute: Helmholtz Centre for Infection Research

description:
CUTLL1 cell line model for T-ALL. Enzymatic restriction was peformed using commercial Arima kit.
CUTLL1_DMSO_Arima_TADs_hicratio-500kb-activity.bed
HiC_cscore_compartment-scores.tsv
HiC_hicratio-scores.tsv

data_processing:
Read alignment: bowtie2 2.2.3. Paired-end reads were mapped against the hg19 reference sequence using bowtie2 (special paramters: --very-sensitive-local --local)
Filtering: GenomicTools "gtools-hic filter". Discards read-pairs marked as multihits, only one mappable read, positional duplicates, low mapping quality (MAPQ < 20), self-ligated fragments, short-range interactions (<25 kb)
Matrix generation: HicBench. For each sample and each chromosome, a matrix with binned interactions (bin-size 40kb) was generated.
Normalization: ICE normalization as described in Imakaev et al. (2012) was employed first. We then applied normalization by distance as recently described (Gong et al., 2018)
Topologically Associated Domains (TAD) calls: TADs were called using the algorithm developed within hic-bench, setting the insulating window to 500kb.
Genome_build: hg19
Supplementary_files_format_and_content: TAD bed files, scores.tsv files

source_name: T-ALL Cell line

growth_protocol: CUTLL1 and Jurkat cells were grown in RPMI medium with 10% FBS ; Primary T-ALL cells isolated from the peripheral blood of T-ALL patients were xenogroafted in immunocompromised NOD SCID gamma mice (NSG) . Following xenograft, T-ALL cells were isolated from spleen by flow cytometer using hCD45 as marker;  Healthy T cells were purchased from Lonza (catalog no: 2W-200)

extract_protocol:
Nuclear extraction and DNA purification using Amicon Ultra 30K
End-repair was performed using T4 DNA polymerase (NEB), T4 DNA polynucleotide kinase (NEB), Klenow (NEB) and dNTPs in 1× T4 DNA ligase reaction buffer (NEB), followed by dATP-addition with Klenow. Paired-end (PE) adapters (Illumina) were ligated to DNA fragments using 15 U of the T4 DNA ligase (Invitrogen) for 2 hours at room temperature. Bead-bound DNA was amplified with 6 PCR amplification cycles using PE PCR 1.0 and PE PCR 2.0 primers (Illumina). Library prepartion of samples prcoessed using Arima HiC kit were prepared using Kap Hper library prep kit (KK8504)as per manufacturer's guidelines.

treatment_protocol: CUTLL1 cells were treated with DMSO or gamma-secretase inhibitor (1 uM) for 72 hours or THZ1 (100 nM) for 24 hours.

tag: cell line

value: T-ALL

value: DMSO

tag: enzymatic restriction

value: commercial Arima kit


title: co-ex-FA-F-1

description:
Small RNA-seq libraries were generated by NEXTflex Small RNA Library Prep Kit v3 for Illumina (BioO Scientific, Austin, TX), followed by deep sequencing on an Illumina HiSeq 2500 as per the manufacturer’s instructions.  Briefly, 1-2 ng of total RNA was ligated with chemically modified 3’- and 5’- adapters that can specifically bind to mature micro RNAs, followed by reverse transcription and PCR amplification.  Unique index sequence tags were introduced during PCR to enable multiplexed sequencing.  Each library was assessed for the presence of desired micro RNA population and approximate library quantity by Bioanalyzer High Sensitivity DNA Kit (Agilent Technologies).  Pooled libraries were denatured and loaded onto a TruSeq Rapid flow cell on an Illumina HiSeq 2500 and run for 50 cycles using a single-read recipe according to the manufacturer's instructions.  De-multiplexed sequencing reads passed the default purify filtering of Illumina CASAVA pipeline (released version 1.8) and were quality trimmed/filtered using The FASTX-Toolkit (http://hannonlab.cshl.edu/fastx_toolkit).  The filtered reads were further trimmed with both 5’ and 3’ adapter sequences and subjected to Chimira suite to align and count miRNA expression (Vitsios and Enright, 2015).
Coex_female_deseq2.txt
JFRm89

tag: Sex


title: co-ex- O3-F-1

description:
Small RNA-seq libraries were generated by NEXTflex Small RNA Library Prep Kit v3 for Illumina (BioO Scientific, Austin, TX), followed by deep sequencing on an Illumina HiSeq 2500 as per the manufacturer’s instructions.  Briefly, 1-2 ng of total RNA was ligated with chemically modified 3’- and 5’- adapters that can specifically bind to mature micro RNAs, followed by reverse transcription and PCR amplification.  Unique index sequence tags were introduced during PCR to enable multiplexed sequencing.  Each library was assessed for the presence of desired micro RNA population and approximate library quantity by Bioanalyzer High Sensitivity DNA Kit (Agilent Technologies).  Pooled libraries were denatured and loaded onto a TruSeq Rapid flow cell on an Illumina HiSeq 2500 and run for 50 cycles using a single-read recipe according to the manufacturer's instructions.  De-multiplexed sequencing reads passed the default purify filtering of Illumina CASAVA pipeline (released version 1.8) and were quality trimmed/filtered using The FASTX-Toolkit (http://hannonlab.cshl.edu/fastx_toolkit).  The filtered reads were further trimmed with both 5’ and 3’ adapter sequences and subjected to Chimira suite to align and count miRNA expression (Vitsios and Enright, 2015).
Coex_female_deseq2.txt
JFRm93


title: Lmx1bCKO_caudal_1

tag: tissue


title: WT_caudal_2

tag: strain


title: WT_caudal_3

tag: age


title: Pet1CKO_ros_1

tag: genotype


title: Pet1CKO_ros_2


title: WT_caudal_1


title: ZT23_KO2

tag: cell type


title: CD4+ T cells, EAE+(THC+CBD)

tag: disease state

value: EAE

tag: gender

value: 6-8 weeks

value: brain

value: CD4+ T cells

value: THC+CBD


title: WT_ros_2


title: Bin1-WT-F-0224

city: Cambridge

first: Jacob

last: Gagnon

state: Massachusetts

address: 225 Binney St

institute: Biogen

data_processing:
Single-end sequencing data were generated on an Illumina Illumina HiSeq 2500, at a depth of 30 million reads per sample, with read length 50bp.The reads were aligned with the OmicSoft OSA4 to the mouse genome (mm10) and the Ensembl.R84 gene model.
Gene counts were estimated using RSEM.  Two samples were removed (one sample from WT_Female cohort and one samples from Heterozygote_Male cohort) due to low fraction of uniquely mapped single reads and higher than expected duplication.  Of note, these samples with poor technical QC metrics were also clear outliers in PCA.
Normalization and differential expression analysis were carried out with the Bioconductor package DESeq2. Differentially expressed genes (DEGs) were defined as having adjpval < 0.05, and |FC| > 1.5.
Genome_build: mm10
Supplementary_files_format_and_content: Gene counts were estimated using RSEM

source_name: Microglia

growth_protocol: Mice were housed with a 12h light/dark cycle, and food and water were provided ad libitum for 3 month after birth.

extract_protocol:
Microglia Isolation: Briefly, animals were anesthetized with Ketamine/Xylazine i.p. injection (1:1, concentration) and ice-cold PBS was used for perfusion and brains collection. After removing Cerebellum and Olfactory bulbs, remaining brain tissue was minced in Petri dish and transferred to 15ml tube with 3ml of Accutase (Cat: SCR005, Millipore); and incubated at 4°C for 30min in a rotary shaker. Then, large tissue chunks were allowed to settle at the bottom by gravity, and the cell suspension from the top of the tube were passed through pierce tissue strainer (Cat: 87791, Thermo Fisher) and collected in fresh tubes. Two ml of HBSS (Cat: 14185-052, Life Technologies)/HEPES (Cat: 15630-080, Life Technologies) buffer was added to the chunk tissues and triturated with 5ml pipette until almost homogenous. Following gravity separation, supernatants were passed through a pierce tissue strainer and pooled to the same tube containing cell suspension from previous step. Trituration was repeated with the remaining tissue chunks with a 1ml pipette until completely homogenous and passed through a pierce strainer and pooled to the rest of the cell suspension. Then, the strainer was rinsed with HBSS/HEPES buffer to bring the cell suspension to 15ml, prior to a spin at 600xg for 5min at 4°C (brake 5).  The supernatant was aspirated, and the pellet was resuspended with 1ml of 100% FBS. Nine milliliters of 33% Percoll (Cat: 17089102, GE Life Science) was added to the cell suspension and mixed well. One milliliter of 10%FBS was overlayed on the Percoll/cell suspension and spun at 800g at 4°C for 15min (break 1 or lowest possible). The supernatant was aspirated without disturbing the pellet, and the pellet was resuspended with 1ml of FACS buffer (HBSS, 1%BSA, 2mM EDTA, 25mM HEPES, 0.09% NaN3). Additional FACS buffer was added to bring the cell suspension to 15mL before spinning at 600g for 10min at 4°C. Following centrifugation, the pellet was resuspended with 300μl of FACS buffer and filtered through 30μm filter (Partec Celltrics, 04-004-2326) for further analysis. Microglia sorting: Filtered cells were pelleted down with gentle centrifugation and incubated with 50μl of Fc blocker anti-mouse CD16/32 (Cat: 101321, Biolegend) on ice for 10min. Then 50μl of CD11b-PE Rat anti-mouse antibody (Cat: 553311, BD Bioscience) and CD45 BV421 anti-mouse antibody (Cat: 563890, BD Bioscience) were mixed with the cells and incubated for 30min on ice. Following incubation, cells were washed and resuspended in 200μl of FACS buffer. Cells were filtered through a 30μm filter before FACS sorting (BD FACS Aria Fusion) and collecting approximately 20,000-100,000 CD11b+; CD45med cells in FACS buffer. Unstained and single-stained cells were used as controls for gating the cells in FACS. Sorted cells were centrifuged at 6800g for 15min and the cell pellets were snap frozen and stored at -80°C until RNA extraction. RNA extraction: Qiagen All Prep kit (Cat: 80224, Qiagen) was used for RNA extraction from previously frozen microglia cells. Briefly, cells were lysed with RLT Buffer (with β-mercaptoethanol added), and passed through QIA shredder (Cat: 79654, Qiagen). Flow-through from the QIA shredder was then passed through a DNA Mini column to remove the DNA from the lysate. DNA mini columns were stored at 4°C for DNA purification later; and the passed-through lysates were treated with proteinase K. Following treatment, 100% ethanol was added to the lysates and passed through an RNeasy Mini spin column. In-column DNase treatment was also performed. Subsequently, RNA was eluted with RNase-free water, quantified in Nano-drop and stored at -70°C until samples were submitted for sequencing.
mRNA profile of  microglia cells FACS-sorted from brains of mice homozygous and heterozygous conditional knock-out for Bin1 in excitatory neurons  (B6.129S6-Bin1tm2Gcp/J (Bin1flox/flox), <FVB/N-Tg(Thy1-cre)1Vln/J> (Thy1-Cre) ) and Bin1-expressing littermates at 3 month of age had been generated from 10ng of total RNA using SMARTer Ultra Low Input RNA kit v4 (Clontech).  The cDNA was amplified by 8 PCR cycles, followed by QC analysis on BioAnalyzer 2100 (Agilent).  Sequence libraries were produced from 150pg of cDNA using Nextera XT DNA library kit (Illumina), cleaned up with AMPure XP beads, and QC checked with Caliper LabChip GX.

value: 3 month-old mice

value: Female

value: Bin1flox/wt Thy1-Cre- (WT)

value: CD11b+; CD45med FACS sorted Microglia


title: Bin1-WT-F-0232


title: Bin1-Homo-M-0437

value: Bin1flox/flox X Thy1-Cre+ (Homo-cKO)


title: Lmx1bCKO_ros_2


title: Lmx1bCKO_ros_1


title: Bin1-Homo-M-0329


title: Bin1-WT-M-0214


title: Bin1-Homo-M-0436


title: Bin1-WT-F-0210


title: Bin1-WT-M-0215


title: WT_ros_3


title: Bin1-WT-M-0222


title: Bin1-WT-M-0211


title: WT_ros_1


title: Bin1-Homo-M-0328


title: Bin1-Homo-F-0440


title: NSCLC 1017

city: Daejeon

first: Jeongyeon

last: Kim

address: 291 Daehakro

country: South Korea

institute: Korea Advanced Institute of Science and Technology

data_processing:
Alignment was performed using STAR (2.5.3)
gene expression values were quantified using RSEM (1.3.1)
Genome_build: hg19
Supplementary_files_format_and_content: gene expression matrix (tab-delimited text file; TPM unit)

source_name: NSCLC

extract_protocol:
RNA was extracted from same tumour tissue using Allprep DNA/RNA Mini Kit (Qiagen
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: subject status

value: advanced non-small cell lung carcinoma (NSCLC) patient treated with anti-PD-1/PD-L1

value: male

tag: progression-free survival (pfs)

value: tumor tissue


title: NSCLC 1066

value: female


title: NSCLC 1079


title: Bin1-Homo-F-0432


title: NSCLC 1104


title: Bin1-Homo-M-0344

value: Male


title: NSCLC 1145


title: NSCLC 1155


title: NSCLC 1164


title: NSCLC 1203


title: Bin1-Homo-F-0357


title: NSCLC 1352


title: NSCLC 1425


title: Bin1-Het-M-0212

value: Bin1flox/wt Thy1-Cre+ (Het-cKO)


title: Bin1-Het-M-0217


title: NSCLC 1401


title: NSCLC 1412


title: Bin1-Het-F-0219


title: Bin1-Het-F-0207


title: Bin1-Het-M-0227


title: Bin1-Het-M-0216


title: Bin1-Het-F-0201


title: Bin1-Het-F-0206


title: NSCLC 1508


title: NSCLC 1528


title: NSCLC 1510


title: Bin1-Homo-F-0333


title: Bin1-Homo-F-0342


title: NSCLC 1554


title: Thoracic Aorta SMCs, Tsc1−/− (iii)

data_processing:
The reads were trimmed for quality using custom scripts.  The trimmed reads were aligned to the reference mouse genome (mm10 UCSC) using TopHat2.
cufflinks and cuffdiff was used to estimate transcript abundances, and to determine differentially expressed genes.  The cuffdiff output was processed further with R and cummeRbund for visualizations and downstream analyses.
Genome_build: mm10
Supplementary_files_format_and_content: The processed file is a table with FPKM values for all the samples used in the analysis.

source_name: Thoracic Aorta

extract_protocol:
Thoracic aortas were rapidly excised, flash frozen in liquid nitrogen, crushed tissue was immersed in RLT lysis buffer (Qiagen) and vigorously vortexed, total RNA was isolated using a RNeasy Mini Kit and DNase Digestion Set (Qiagen) according to the manufacturer’s protocol, and 500 ng of intact total RNA (RIN>7) was used for polyA selection and construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: 24 weeks postnatal

value: Tsc-/-

value: Thoracic Aorta

value: SMCs


title: Thoracic Aorta SMCs, Tsc1−/− (i)


title: NSCLC 1327


title: NSCLC 1358


title: Thoracic Aorta SMCs, Tsc1+/+ (iv)

value: Tsc+/+


title: NSCLC 1708


title: Pull Bioitin OPC mirctr 2 [Dutta_miRNA_Pulldown_Set_2_RandID_4_S4]

city: Portland

first: Selva

last: Baltan

state: OR

address: 3181 S.W. Sam Jackson Park Rd.

department: Anesthesia and Perioperative Medicine (APOM)

institute: Oregon Health and Science University

data_processing:
Post-sequencing, raw demultiplexed fastq paired end read files were trimmed of adapters and filtered using the program skewer to throw out any with an average phred quality score of less than 30 or a length of less than 36.
Trimmed reads were then aligned using the HISAT2 aligner to the Mus musculus NCBI reference genome assembly (v GRCm38) and sorted using SAMtools.
Aligned reads were counted and assigned to gene meta-features using the program featureCounts part of the Subread package.
These count files were imported into the R programming language and were assessed for quality control, normalized, and analyzed using an in-house pipeline utilizing the edgeR Bioconductor library for differential gene expression testing.
Genome_build: mm8
Supplementary_files_format_and_content: Comma Separated Values (CSV) files include CPM values for each Sample ...

source_name: Pull Bioitin OPC mirctr

growth_protocol: OPCs proliferation in SATO+PDGFRA media

extract_protocol:
RNA isolated from biotin-tagged miRNA mimic (control and miR-27a)-transfected OPCs, as well as pulldown assays using TRIZOL method.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: miRNA mimic transfection (Control and miR-27a)

value: Post natal day 6-7

value: brain

value: Oligodendrocyte progenitor cells (OPCs)

tag: genotype/variation

value: biotin-tagged miRNA mimic control


title: NSCLC 1809


title: NSCLC 1873


title: Thoracic Aorta SMCs, Tsc1+/+ (i)

tag: time


title: Thoracic Aorta SMCs, Tsc1−/− (iv)


title: Thoracic Aorta SMCs, Tsc1+/+ (ii)


title: Thoracic Aorta SMCs, Tsc1−/− (ii)


title: NSCLC 378


title: t2160_rep3

city: Logrono

first: María

last: de Toro

state: La Rioja

address: C/Piqueras 98

department: Genomics & Bioinformatics Core Facility

country: Spain

institute: Centro de Investigación Biomédica de La Rioja

data_processing:
Quality analysis of raw reads with FastQC
Sequenced reads were trimmed for adaptor sequence and masked for low-quality sequence with Trim-Galore software
Quality analysis of clean reads with FastQC
Clean reads were mapped against the reference genome with Tophat2 software
Resulting mapping files (bam files) were sorted and indexed with the Samtools software
Quality analysis of Bam files with Qualimap tool
FeatureCounts tools was used to obtain raw counts over gene features.
Differential expression analysis with DESeq2 and edgeR Bioconductor packages
Resulting tables annotated with Biomart, WormBase and org.Ce.eg.db databases in R platform
Common up- and down- regulated genes from both statistical protocols were used for the wnrichment analysis for GO, Kegg and Reactome terms/pathways.
Genome_build: Ensemble version of C. elegans WBcel235.85
Supplementary_files_format_and_content: raw counts obtained from FeatureCounts

molecule: polyA RNA

organism: Caenorhabditis elegans

growth_protocol: Synchronized wild type and nxf-1(t2160) worms were grown at 15˚C until adult stage in standart conditions

extract_protocol:
RNA, Rneasy Mini kit Qiagen, following manufacturer's recommendations
TruSeq mRNA (Illumina)

treatment_protocol: 16 hours at 25 C after one day adult stage

value: adults worms grown at 15C

tag: treatment

value: shifted to 25 C for 16 hours before collected

value: ts allele


title: NSCLC 1619

value: advanced non-small cell lung carcinoma (NSCLC) patient treated with anti-PD-1/PD-L1

value: male


title: t2160_rep2


title: NSCLC 573

value: tumor tissue


title: Thoracic Aorta SMCs, Tsc1+/+ (iii)


title: NSCLC 825

value: female


title: N2_Ang_rep3

source_name: wild type_rep3


title: NSCLC 947


title: N2_Ang_rep2

source_name: wild type_rep2


title: NSCLC 990


title: t2160_rep1


title: Unstable_Patient4

city: Edinburgh

first: Julie

last: Rodor

address: 47 Little France Crescent

department: Centre for Cardiovascular Science

country: United Kingdom

institute: UNIVERSITY OF EDINBURGH

data_processing:
Fastq files obtained from GENEWIZ
Gene quantification (read count and normalised expression value as FPKM) was obtained using RSEM 1.3.0 (options: -bowtie2 -forward-prob 0.5 -paired-end), based on GENCODE annotation version 25 (primary assembly).
Genome_build: GRCh38
Supplementary_files_format_and_content: txt file with FPKM

source_name: unstable section of human atherosclerotic plaque

growth_protocol: Carotid plaques were obtained from patients undergoing endarterectomy. Plaques harvested at the time of surgery were transported in 0.9% sodium chloride solution, and examined and dissected within 1 hour.

extract_protocol:
The plaque samples are homogenised with a tissue homogeniser, in Qiazol (Qiagen). Total RNA was extracted using miRNeasy mini kit (Qiagen) following manufacturer’s instructions including on-column DNase digestion.
Ribosomal-depleted unstranded libraries were prepared and sequenced on Illumina HiSeq by GENEWIZ, Inc.

treatment_protocol: Plaques were dissected into stable and unstable regions based on macroscopic appearance. Unstable regions were characterised as the visible zone of plaque rupture, and the surrounding abnormal tissue, including obvious calcification and intra-plaque haemorrhage. Stable regions were macroscopically normal adjacent areas. The appropriate dissection of stable and unstable regions was confirmed in other plaque samples with an Ex vivo 18F- sodium fluoride imaging.

tag: stability of region

value: unstable

tag: patient

value: Patient 4


title: N2_Ang_rep1

source_name: wild type_rep1


title: Stable_Patient4

source_name: stable section of human atherosclerotic plaque

value: stable


title: 25: Obese (HFD) rep 5

city: Oklahoma City

first: Jonathan

middle: D

last: Wren

state: OK

address: 825 N.E. 13th Street

department: Genes and Human Disease

institute: Oklahoma Medical Research Foundation

data_processing:
Illumina RTA v2 used for base calling
Alignment performed using Strand NGS
Genome_build: mm10
Supplementary_files_format_and_content: csv delimited file contains raw count expression matrix for each sample on all detected genes

source_name: Perigondal adipose tissue

extract_protocol:
RNA was extractedfrom a guanidinium isothiocyanate extract and purified over a CsCl gradient.  Poly A+ RNA was selected by affinity purification using an oligo dT column
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Beginning at 8 weeks of age, mice were fed either chow diet (lean) or 60% high fat diet (obese) for 5 weeks.  After 5 weeks, 1/2 of the obese mice were swtiched back to chow diet to induce weight loss (SWAP) for 1 week.  At the end of the SWAP period all mice were killed.  Perigonadal fat pads were removed and snap frozen in liquid nitrogen.  RNA was extracted and purified over a CsCl gradient.  Poly A+ RNA was isolated using oligodT affinity purification

tag: group

value: Obese (HFD)

value: Perigondal adipose tissue

value: 14 weeks


title: Unstable_Patient3

value: Patient 3


title: 24: Weight loss (SWAP) rep5

value: Weight loss (SWAP)


title: Stable_Patient3


title: 23: Lean (RD) rep 5

value: Lean (RD)


title: Unstable_Patient2

value: Patient 2


title: HCC1599

type: genomic

city: Rotterdam

first: Marcel

last: Smid

address: Dr. Molewaterplein 50

department: Medical Oncology

country: Netherlands

institute: Erasmus MC

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix protocol

data_processing:
Data was processed using default settings in Genotyping Console Software (Affymetrix). Copy number values for individual SNPs were extracted, smoothed and segmented into copy number states according to the default settings in Genotyping Console
log2ratio copy number

source_name: Breast cancer cell line

label_protocol: Standard Affymetrix protocol

growth_protocol: Cell lines were grown according to standard conditions.

extract_protocol: Genomic DNA was extracted using the DNeasy kit of Qiagen

tag: cell line


title: 22: Lean (RD) rep 4


title: HCC1806


title: HCC1395


title: HCC1500


title: HCC1143


title: HCC1569


title: ZR-75.30


title: HCC38


title: HCC202


title: HCC1954


title: HCC70


title: HCC1419


title: Stable_Patient2


title: 21: Obese (HFD) rep 4


title: UACC812


title: SUM149-PT


title: SUM185PE


title: HCC2218


title: Stable_Patient1

value: Patient 1


title: 20: Weight loss (SWAP) rep4


title: HCC1008


title: SUM229PE


title: Unstable_Patient1


title: SUM102-PT


title: SUM190PT


title: UACC893


title: siCONT_3

data_processing:
Fastq files obtained from GENEWIZ
Gene quantification (read count and normalized expression value as FPKM) was obtained using RSEM 1.3.0 (options: -bowtie2 -forward-prob 0 -paired-end), based on GENCODE annotation version 25 (primary assembly).
Genome_build: GRCh38
Supplementary_files_format_and_content: txt file with FPKMs

source_name: depletion control in HSVSMCs treated with IL1a and PDGFbb

growth_protocol: Primary human saphenous vein derived smooth muscle cells (HSVSMC) were isolated from medial explants (Southgate et al., 1992) and maintained in Smooth Muscle Cell Growth Medium 2 (PromoCell) with supplements at 37°C in a humidified atmosphere containing 5% CO2. All cells were used between passages 3-5.

extract_protocol:
miRNeasy mini kit (Qiagen) with on-column DNAse digestion
Ribosomal-depleted unstranded libraries were prepared and sequenced on Illumina HiSeq by GENEWIZ, Inc.

treatment_protocol: For SMILR depletion experiments, double stranded dicer substrate siRNA targeting SMILR (CCAUAAUUUACAUGGAUG) and siControl (CUUCCUCUCUUUCUCUCC) were obtained from Integrated DNA Technologies (See Supplementary Table 2 for sequences). Transient transfection was performed with Lipofectamine RNAiMAX (Life Technologies) following the manufacturer’s guidelines. Cells were transfected with siRNA and five hours post transfection, cells were quiesced for 48 h in DMEM supplemented with 100 mg/mL of penicillin, 100 IU/mL streptomycin, 2 mM L-glutamine, and 0.2% [v/v] FCS and then stimulated for a further 48 or 96h with fresh 0.2% media containing 10 ng/mL IL1α and 20 ng/mL PDGF-ββ (R&D Systems). For SMILR overexpression, SMILR sequence, based RACE data from Ballantyne et al, 2016, was cloned into pLNT/SFFV-MCS plasmid. Lentiviral vectors were produced by triple transient transfection of HEK293T cells with a packaging plasmid (pCMV∆8.74), a plasmid encoding the envelope of vesicular stomatitis virus (VSVg) (pMDG) (Plasmid Factory) and pLNT/SFFV-MCS plasmid employing polyethylenimine (PEI; Sigma-Aldrich) as previously described. A confluent monolayer of smooth muscle cells were plated and infected with either SMILR_LNT or CTRL_LNT. Following 24 h infection, media was changed to 0.2% media for a further 24h before being stimulated with 10 ng/mL IL1α and 20 ng/mL PDGF-ββ for further 96h.

value: depletion control

value: HSVSMCs

value: IL1a and PDGFbb

tag: replicate


title: SUM225CWN


title: HCC1187


title: 19: Obese (HFD) rep 3

tag: tissue


title: siCONT_2


title: 18: Lean (RD) rep 3

tag: strain


title: ZR-75.1


title: 17: Weight loss (SWAP) rep3

tag: age


title: SUM1315MO2


title: SUM52PE


title: T47D


title: globular-seed-YAB1-like ChIP replicate 1

city: Los Angeles

first: Bob

last: Goldberg

state: CA

address: 610 Charles E Young Drive East

department: Molecular, Cell and Developmental Biology

institute: University of California, Los Angeles

description: Whole seeds 1.0 - 1.5 mm in length were collected

data_processing:
Basecalls performed using RTA version 1.12.4.2
Sequenced reads passing Illumina quality filter were aligned to the Glycine max genome (Wm82.a2.v1) using Bowtie v0.12.7 with parameters -v 2 -5 0 -3 0 -m 1 --best --strata
Reads were filtered to remove PCR duplicates using samtools (v.0.1.18).
Peaks were identified using MACS2 with default parameters and a q-value threshold of 0.01.
Genome_build: Wm82.a2.v1
Supplementary_files_format_and_content: NarrowPeak files generated by MACS2

organism: Glycine max

source_name: Soybean seeds containing globular stage embryos

growth_protocol: Soybean plants (Williams 82) were grown under standard greenhouse conditions (Le et al., PNAS 2010).

extract_protocol:
Chromatin isolation and immunoprecipitation were performed as described in Gendrel AV, Lippman Z, Martienssen R, Colot V. Nat Methods. 2005;2:213–218, except that the isolated nuclei were resuspended in lysis buffer described in by Johnson et al. (2002) and sonicated to achieve chromatin fragments ranging from 100 to 500 bp. Nuclear extracts were either set aside for whole genome extracts (input control) or incubated overnight with 10ug of polyclonal antibody raised against GmYAB1-like peptide STSFSPDQQHLSPSD in rabbit. Crosslinks were reversed and protein digested as described in Dahl and Collas, Nat Protoc. 2008;3(6):1032-45, extracted with phenol:chloroform and precipitated using standard procedures.
ChIP and Input libraries were generated using Nugen Ovation Ultralow DR Multiplex System, following the manufaturer's instructions and enriched by PCR using 15 cycles.

treatment_protocol: Whole seeds were collected and crosslinked under vaccuum for 10 minutes in Buffer A (0.4M sucrose, 10mM Tris pH 8.0, 1mM EDTA pH 8.0) containing 1% formaldehyde, at room temperature, then quenched in 100 mM Glycine for 5 minutes. Tissues were rinsed twice with deionized water and stored at -80C until use.

tag: cultivar

value: Williams 82

tag: developmental stage

value: globular stage

value: whole seeds

tag: chip antibody

value: anti-peptide GmYAB1-like


title: globular-seed-input replicate 1 (YAB1 study)


title: 15: Lean (RD) rep 2


title: SUM159-PT


title: siSMILR_2

source_name: depletion of SMILR in HSVSMCs treated with IL1a and PDGFbb

tag: genotype

value: SMILR depletion

tag: cell type


title: heart-seed-input replicate 2 (WOX9 study)

description: Whole seeds 1.7 - 2.1 mm in length were collected

source_name: Soybean seeds containing heart stage embryos

extract_protocol:
Chromatin isolation and immunoprecipitation were performed as described in Gendrel AV, Lippman Z, Martienssen R, Colot V. Nat Methods. 2005;2:213–218, except that the isolated nuclei were resuspended in lysis buffer described in by Johnson et al. (2002) and sonicated to achieve chromatin fragments ranging from 100 to 500 bp. Nuclear extracts were either set aside for whole genome extracts (input control) or incubated overnight with 10ug of polyclonal antibody raised against GmWOX9-like peptide NHHTPTSLPQTATTA in rabbit. Crosslinks were reversed and protein digested as described in Dahl and Collas, Nat Protoc. 2008;3(6):1032-45, extracted with phenol:chloroform and precipitated using standard procedures.
ChIP and Input libraries were generated using Nugen Ovation Ultralow DR Multiplex System, following the manufaturer's instructions and enriched by PCR using 15 cycles.

treatment_protocol: Whole seeds were collected and crosslinked under vaccuum for 10 minutes in Buffer A (0.4M sucrose, 10 mM Tris pH 8.0, 1mM EDTA pH 8.0) containing 1% formaldehyde, at room temperature, then quenched in 100 mM Glycine for 5 minutes. Tissues were rinsed twice with deionized water and stored at -80C until use.

value: heart stage


title: 14: Weight loss (SWAP) rep2


title: heart-seed-input replicate 1 (WOX9 study)


title: siSMILR_1


title: 13: Lean (RD) rep 1


title: heart-seed-WOX9-like ChIP replicate 2

value: anti-peptide GmWOX9-like


title: SK-BR-7


title: globular-seed-input replicate 1 (WOX9 study)


title: 12: Weight loss (SWAP) rep1

value: Perigondal adipose tissue


title: SUM44PE


title: LNT_CONT_3

source_name: overexpression control in HSVSMCs treated with IL1a and PDGFbb

value: overexpression control


title: LNT_CONT_2


title: 11: Obese (HFD) rep 1

value: Obese (HFD)

value: 14 weeks


title: LNT_SMILR_3

source_name: overexpression of SMILR in HSVSMCs treated with IL1a and PDGFbb

value: SMILR overexpression


title: Lmx1bCKO_ros_P2_3

source_name: 5-HT neuron

value: 5-HT neuron


title: Lmx1bCKO_ros_P2_4


title: LNT_SMILR_2


title: Lmx1bCKO_ros_P2_2


title: siSMILR_3


title: LNT_CONT_1


title: Lmx1bCKO_ros_P2_1


title: LNT_SMILR_1


title: single-cells_#16_Enc2

city: Planegg-Martinsried

first: Eduardo

last: Beltrán

state: Bayern

address: Großhaderner Str. 9

department: Institute of Clinical Neuroimmunology

institute: University Hospital, LMU Munich

data_processing:
Short sequencing reads were aligned to the UCSC hg38 transcriptome using HISAT2
featureCounts to count mapped reads
Data were log-transformed [log(TPM + 1)] for all downstream analyses
unbiased graph-based clustering of single cell data, and identification of markers for each cluster, were performed with Seurat
Genome_build: UCSC hg38
Supplementary_files_format_and_content: first tab-delimited text file include TPM values of all single-cells in all samples; first tab-delimited text file include single-cell information (metadata)

source_name: CSF sample

value: CSF

tag: cell types

value: ALL cells types in the CSF sample

tag: diagnosis

value: autoimmune encephalitis

tag: Sex

value: male


title: SK-BR-5


title: globular-seed-AGL62-like ChIPreplicate 1

extract_protocol:
Chromatin isolation and immunoprecipitation were performed as described in Gendrel AV, Lippman Z, Martienssen R, Colot V. Nat Methods. 2005;2:213–218, except that the isolated nuclei were resuspended in lysis buffer described in by Johnson et al. (2002) and sonicated to achieve chromatin fragments ranging from 100 to 500 bp. Nuclear extracts were either set aside for whole genome extracts (input control) or incubated overnight with 10ug of polyclonal antibody raised against GmAGL62-like peptide ERKHAEKLNRKQKEA in rabbit. Crosslinks were reversed and protein digested as described in Dahl and Collas, Nat Protoc. 2008;3(6):1032-45, extracted with phenol:chloroform and precipitated using standard procedures.
ChIP and Input libraries were generated using Nugen Ovation Ultralow DR Multiplex System, following the manufaturer's instructions and enriched by PCR using 15 cycles.

value: Williams 82

value: anti-peptide AGL62-like


title: globular-seed-input replicate 1 (AGL62 study)

value: globular stage

value: whole seeds


title: plX_HALO_empty_ampDAPseq

city: London

first: Alex

last: de Mendoza

address: Mile End Road. Fogg Building 5.14

department: School of Biological and Behavioural Sciences

institute: Queen Mary University of London

data_processing:
Library strategy: ampDAP-seq
CASAVA v1.8.2
For Bisulfite-seq and TAB-seq, adapters were trimmed using fastp as default, then aligned to the reference genome using Bowtie2 and BSseeker2 with the option --bt2--end-to-end. PCR duplicates were removed using Sambamba v.0.6.6 before methylation quantification with BSseeker2. For DAP-seq and ampDAP-seq, reads where trimmed with fastp and mapped to the genome using bowtie with the parameters "-m 1 -v 1", then peaks where called using macs2 using pIX Halo empty bam as background and parameters "-q 0.05 --down-sample -g 166679601".
Genome_build: Amphimedon queenslandica genome assembly was downloaded from ftp://ftp.ensemblgenomes.org/pub/metazoa/release-40/fasta/amphimedon_queenslandica/dna/Amphimedon_queenslandica.Aqu1.dna.toplevel.fa.gz, Sycon ciliatum genome assembly was downloaded from http://www.compagen.org/datasets/SCIL_WGA_130802.zip, Nematostella vectensis genome assembly was downloaded from ftp://ftp.ensemblgenomes.org/pub/metazoa/release-40/fasta/nematostella_vectensis/dna/Nematostella_vectensis.ASM20922v1.dna.toplevel.fa.gz, Mnemiopsis leidyi genome assembly was downloaded from ftp://ftp.ensemblgenomes.org/pub/metazoa/release-40/fasta/mnemiopsis_leidyi/dna/Mnemiopsis_leidyi.MneLei_Aug2011.dna.toplevel.fa.gz
Supplementary_files_format_and_content: Bisulfite-seq files (CGmap files) are the direct output from BSseeker2 (https://github.com/BSSeeker/BSseeker2), they contain chromosome position, (1) chromosome  (2) nucleotide on Watson (+) strand  (3) position  (4) context (CG/CHG/CHH)  (5) dinucleotide-context (CA/CC/CG/CT)  (6) methylation-level = #_of_C / (#_of_C + #_of_T). (7) #_of_C (methylated C, the count of reads showing C here) (8) = #_of_C + #_of_T (all Cytosines, the sum of reads showing C or T in that position). Macs2 xls files are described in https://github.com/taoliu/MACS/blob/master/README.rst.

organism: Amphimedon queenslandica

extract_protocol:
Phenol-chloroform extraction
Genomic DNA was fragmented with a Covaris S2 sonicator to a mean length of 200 bp, then end-repaired, A-tailed, ligated to Illumina TruSeq adapters and amplified 11 cycles, next it was incubated with in-vitro translated HaloTag and affinity purified. The resulting DNA was amplified 20 cycles.

tag: individuals

value: individuals from Heron Island

tag: experimental variable


title: single-cells_#15_Enc1

value: female


title: WT_ros_P2_2


title: SK-BR-3


title: single-cells_#14_Twin4.2

value: non-inflammatory control


title: WT_ros_P2_1


title: heart-seed-WOX9-like ChIP replicate 1

value: heart stage

value: anti-peptide GmWOX9-like


title: single-cells_#13_Twin4.1

value: clinically definite MS


title: Null_HFD_3

city: Philadelphia

first: Ellen

last: Pure

address: 380 S University Ave

institute: University of Pennsylvania

data_processing:
fastq files were aligned to version 79 of mouse reference genome GRCm38 using Kallisto (Bray, Pimentel, Melsted, & Pachter, 2016) .
.tsv files resulting from imported to R using Tximport
Expression data was normalized using the VOOM function in the Limma package in R
Differentially expressed genes (³1.5-fold and £5% false discovery rate) were identified by linear modeling and Bayesian statistics using the Limma package
GSEA analysis was carried out  in R using the GSVA package
Genome_build: version 79 of mouse reference genome GRCm38
Supplementary_files_format_and_content: tab-delimited text file includes log2 transcripts per million (TPM) values for each sample

source_name: Null_HFD, total subcutaneous mammary adipose

extract_protocol:
Inguinal fat pads were flash frozen and then homogenized in QIAzol reagent using an OMNI tissue homogenizer. RNA was isolated using the RNeasy Mini Kit (Qiagen) and processed as per manufacturer’s instructions.
Libraries were prepared using the TruSeq Stranded Total RNA LT Kit with Ribo-Zero Gold, according to the manufacturer’s instructions.

treatment_protocol: Female FVB mice were fed on ingredient matched low- or high-fat diet from 12 weeks of age to 30 weeks of age

value: FVB

value: FAP-/-

tag: diet

value: High fat diet (60% kcal from fat)

value: total subcutaneous mammary adipose


title: 16: Obese (HFD) rep 2

tag: group

value: Obese (HFD)

value: Perigondal adipose tissue

value: 14 weeks


title: siCONT_1

value: depletion control

value: HSVSMCs

tag: treatment

value: IL1a and PDGFbb


title: single-cells_#12_Twin3.2

value: CSF

value: ALL cells types in the CSF sample


title: OCUB-F

tag: cell line

value: OCUB-F


title: plX_HALO_EGR_DBD_ampDAPseq

extract_protocol:
Phenol-chloroform extraction
Genomic DNA was fragmented with a Covaris S2 sonicator to a mean length of 200 bp, then end-repaired, A-tailed, ligated to Illumina TruSeq adapters and amplified 11 cycles, next it was incubated with in-vitro translated AquEGR DNA binding domain fused to HaloTag and affinity purified. The resulting DNA was amplified 20 cycles.

value: individuals from Heron Island


title: MDA-MB-468


title: Null_HFD_1

tag: tissue


title: plX_HALO_SP41_DBD_ampDAPseq

extract_protocol:
Phenol-chloroform extraction
Genomic DNA was fragmented with a Covaris S2 sonicator to a mean length of 200 bp, then end-repaired, A-tailed, ligated to Illumina TruSeq adapters and amplified 11 cycles, next it was incubated with in-vitro translated AquSP41 DNA binding domain fused to HaloTag and affinity purified. The resulting DNA was amplified 20 cycles.


title: Null_HFD_2

tag: strain


title: plX_HALO_GLI_DBD_ampDAPseq

extract_protocol:
Phenol-chloroform extraction
Genomic DNA was fragmented with a Covaris S2 sonicator to a mean length of 200 bp, then end-repaired, A-tailed, ligated to Illumina TruSeq adapters and amplified 11 cycles, next it was incubated with in-vitro translated AquGLI DNA binding domain fused to HaloTag and affinity purified. The resulting DNA was amplified 20 cycles.