title: Genomic DNA from adult human whole blood [C480349644]


title: Genomic DNA from adult human whole blood [C480322687]

status: Public on Dec 18 2018

type: genomic

city: Kansas City

first: Devin

middle: Charles

last: Koestler

state: KS

address: 3901 Rainbow Boulevard

department: Biostatistics

country: USA

institute: The University of Kansas Cancer Center

description: DNA methylation profiling of adult human whole blood (WB)

hyb_protocol: Standard Illumina Protocol

scan_protocol: Standard Illumina Protocol

data_processing: The methylation signal intensities were generated with minfi Bioconductor package. Functional normalization (e.g., Funnorm) was applied to normalized the between array technical variation. Poor quality samples and probes were excluded based on their detection p-values. The SNP-associated (reported SNPs at the queried CpG site and at the single-base extension (SBE) site) and cross-reactive CpGs were also removed. As we observed statistically significant association between beadchip and the first principal component, we conducted batch-effect correction using ComBat (implemented using the ComBat() function in the sva Bioconductor package).

label: Cy5 and Cy3

molecule: genomic DNA

organism: Homo sapiens

source_name: Adult human whole blood

label_protocol: Standard Illumina Protocol

growth_protocol: Not applicable

extract_protocol: DNA extraction was conducted from buffy coats using QIAamp Blood Mini Kit

treatment_protocol: Not applicable

tag: individual id

tag: year of collection

tag: age

tag: nk

tag: bcell

tag: mono

tag: gran


title: Genomic DNA from adult human whole blood [C480323241]


title: 25_IL-23_Vehicle_0mpk_IP

type: SRA

city: Cambridge

first: Radhika

last: Goenka

state: MA

address: 200 Sidney St.

institute: Abbvie

library_source: transcriptomic

data_processing:
FastQC was applied on raw fastq files to examine the sequence quality
STAR v2.52 reads aligner
Apply featureCounts  of the subread v1.5.0 package to generate read counts
Genome_build: GRCm38
Supplementary_files_format_and_content: Raw reads counts data matrix by featureCounts

molecule: total RNA

organism: Mus musculus

source_name: IL-23 Vehicle with Intraperitoneal dosing route

extract_protocol: Illumina stranded RNA-seq workflow (TruSeq Stranded Total RNA Library Prep Kit) was used followed by sequencing using Illumina HiSeq 2500

tag: agent

value: IL-23 Vehicle IP


title: RCH-ACV SOX11 KO repl. 3

city: Tampere

first: Saara

last: Laukkanen

address: Arvo Ylpön Katu 34

country: Finland

institute: University of Tampere

description:
RA_raw_read_counts
RCH-ACV_SOX11_3

data_processing:
The samples were sequenced with Illumina HiSeq 2500 instrument using Truseq v2 Rapid sequencing chemistry. The samples were normalized and pooled for the automated onboard cluster preparation in HiSeq 2500. The 18 libraries were pooled into one pool and run in 2 lanes. Single-read sequencing with 1 x 50 bp read length was used, followed by 8 + 8 bp dual index run. The base calling was performed using Illumina's standard bcl2fastq2 software, automatic adapter trimming was used.
The quality of the raw sequencing reads was ensured with FastQC (v0.10.1) and reads were quality filtered using FASTX Toolkit (0.0.14) (-q 15 -p 93,3).
Reads were mapped to human reference genome version hg19 using STAR aligner software (2.5.3a modified) and reads aligning to more than two locations were discarded
The alignment file was turned into tag directories and raw read counts were calculated using HOMER tool kit (v4.8).
Genome_build: hg19
Supplementary_files_format_and_content: raw counts of sequencing reads for the features of interest

source_name: RCH-ACV cell line

growth_protocol: Cells were cultured in RPMI (Gibco, Thermo Fisher Scientific, Waltham, MA, USA) supplemented with 2 mM L-glut, 100 U penicillin, 100 ug/ml streptomycin and 10% FBS (Gibco).

extract_protocol:
Total RNA extraction was performed with PureLink™ RNA Mini Kit and On-Column PureLink® DNase Treatment Protocol was used to avoid contamination by genomic DNA (Ambion® by Life Technologies and Invitrogen). The quality of the total RNA samples was ensured with Advanced Analytical Fragment Analyzer.
Library preparation was done according to Illumina TruSeq® Stranded mRNA Sample Preparation Guide (part # 15031047) (Illumina, San Diego, CA, USA). The high quality of the libraries was confirmed with Advanced Analytical Fragment Analyzer and the concentrations of the libraries were quantified with Qubit® Fluorometric Quantitation (Life Technologies). Good quality libraries were exclusively selected and sequenced.

treatment_protocol: Cells were transfected with 300nM of either SOX11 specific or non-specific control siRNA (SR30005, OriGene, Rockville, MD, USA) using 4D-Nucleofector™ (Lonza, Basel, Switzerland). Total RNA samples were harvested 48h hours after transfection.

tag: sirna

tag: replicate

tag: cell line

value: RCH-ACV cell line

tag: cell type

value: B-ALL cells


title: 14_IL-23_Vehicle_0mpk_PO

source_name: IL-23 Vehicle with per os dosing route

value: IL-23 Vehicle PO


title: Genomic DNA from adult human whole blood [C480321479]


title: Genomic DNA from adult human whole blood [C480322033]


title: Genomic DNA from adult human whole blood [C480353268]


title: Genomic DNA from adult human whole blood [C480345021]


title: RCH-ACV SOX11 KO repl. 1

description:
RA_raw_read_counts
RCH-ACV_SOX11_1


title: US-1622997: 29-1

city: Seattle

first: Hannele

last: Ruohola-Baker

state: WA

address: 850 Republican Street

institute: Institute for Stem Cell and Regenerative Medicine

data_processing:
RNA-seq reads in fastq files were aligned to hg19 using Tophat (version 2.0.13).
Gene-level read counts were quantified using htseq-count 62 using Ensembl GRCh37 gene annotations.
FeatureCounts was used to do gene-level quantification.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited file of gene-level read counts for each sample.

source_name: human dental pulp stem cell

growth_protocol: Dental pulp stem cells were isolated from human third molars or exfoliated deciduous teeth   from 300 patients ranging from 9 to 58 years old. Teeth were obtained from the University of Washington dental clinic after consent from the patient or legal guardian. This study was approved by the Human Subjects Division of the University of Washington (HSD#51634-EJ).  The teeth were stored in DMEM Glutamax® media (Gibco) with 10% Fetal Bovine serum (FBS) (VWR) solution immediately after tooth extraction. Each individual tooth was cut using a dremel at the cemento-enamel junction which exposed the pulp chamber. The pulp was then removed and minced into small pieces. The isolated pulp tissue underwent an enzymatic digestion with a solution of collagenase type I (92μM) (Sigma-Aldrich, 9001-12-1) and dispase (444μM) (Gibco, 17105-041) for an hour at 37°C with occasional vortexing. Digested pulp pieces were centrifuged to remove the enzyme solution and seeded into proliferation media containing DMEM Glutamax® media (Gibco), 10% FBS (Invitrogen), ascorbic acid (0.1mM) and 1X antibiotic antimycotic solution (Sigma-Aldrich) in a 35-mm cell culture plate. Pulp tissues from the deciduous teeth were isolated with the same protocol and seeded in proliferation media supplemented with insulin growth factor (IGF-1) to increase proliferation success. Once seeded, the pulp pieces were incubated at 37°C with 5% CO2 with media changed every 3 days until cells migrated out and optimal confluence was achieved. When the cells were ~70% confluent, they were trypsinized and passaged to allow expansion in a 10cm plate for cryopreservation or further experimentation. The passaged DPSCs were cultured and maintained in media containing 10% FBS and 1% Penicillin-Streptomycin (Invitrogen) in DMEM.

extract_protocol:
RNA was extracted using Trizol (Life Technologies) according to manufacturer’s instructions. RNA samples were treated with Turbo DNase (Thermo Fisher Scientific) and quantified using Nanodrop ND-1000. Reverse transcription was performed using iScript cDNA Synthesis Kit (Bio-Rad). 10 ng of cDNA was used to perform qRT-PCR using SYBR Green (Applied Biosystems) or TaqMan (Applied Biosystems) on a 7300 real time PCR system (Applied Biosystems). The PCR conditions were set up as the following: stage 1 50°C for 2mins, stage 2 as 95°C for 10mis, 95°C for 15sec, 60°C for 1min (40 Cycles). ß-actin was used as an endogenous control. The primer sequences used in this work are shown in Supplementary Table S5.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: DPSCs were cultred to specific passages (early v.s late) under the growth protocol described above

tag: tissue

value: human dental pulp stem cell


title: Genomic DNA from adult human whole blood [C480320825]


title: mm_krit1_control_rep3

city: Chicago

first: Yan

last: Li

state: IL

address: 900 East 57th St.

department: Center for Research Informatics

institute: The University of Chicago

data_processing:
Raw sequencing QC assessement: FastQC v0.115
Alignment: STAR v2.5.3a
Post alignement QC assessment: RSeQC and Picard tools v2.9.0
Gene transcripts assembly: featureCounts
Differentially expressed genes analysis: DESeq2
Genome_build: UCSC human genome model: hg19; GENCODE mouse genome model: GRCm38 V13 (release_M13); ENSEMBLE worm genome model: c. elegans WBcel235 V87 (release-87)
Supplementary_files_format_and_content: tab-delimited text files include gene features raw counts values summarized by featureCouts for each Sample.

source_name: brain microvascular endothelial cells

extract_protocol:
For human samples, RNAs was extracted using an RNA isolation kit (RNeasy® Micro Kit, Qiagen, Hilden, Germany). For mouse and C. elegans samples, RNA was extracted using the TRIzol protocol (ThermoFisher, Waltman, MA).
RNA libraries were prepared for sequencing using commercially low-input strand specific RNA-Seq kits (Clontech, California, USA) for human specimens and TruSeq Stranded mRNA Sample Prep Kit (Illumina, San Diego, CA) for mouse and C. elegans samples

tag: genotype

value: Krit1 control (Cre negative; Krit1fl/fl)

value: 2 to 4 months

tag: background

value: brain microvascular endothelial cells (BMECs)


title: Genomic DNA from adult human whole blood [C480323895]


title: 697 ctrl repl. 3

description:
697_raw_read_counts
697_CTRL_3

source_name: 697 cell line

value: CTRL

value: 697 cell line


title: Genomic DNA from adult human whole blood [C480336438]


title: Genomic DNA from adult human whole blood [C480352614]


title: 24_IL-23_Vehicle_0mpk_PO


title: 697 ctrl repl. 2

description:
697_raw_read_counts
697_CTRL_2


title: mm_krit1_control_rep1


title: Genomic DNA from adult human whole blood [C480318409]


title: Genomic DNA from adult human whole blood [C480317846]


title: Genomic DNA from adult human whole blood [C480320271]


title: Genomic DNA from adult human whole blood [C480352060]


title: Genomic DNA from adult human whole blood [C480351406]


title: Genomic DNA from adult human whole blood [C480353822]


title: Genomic DNA from adult human whole blood [C480335230]


title: 697 SOX11 KO repl. 3

description:
697_raw_read_counts
697_SOX11_3


title: Genomic DNA from adult human whole blood [C480350852]


title: mm_krit1_rep2

value: Krit1 null (Pdgfb-iCreERT2; Krit1fl/fl)


title: Genomic DNA from adult human whole blood [C480343695]


title: 697 SOX11 KO repl. 2

description:
697_raw_read_counts
697_SOX11_2


title: mm_krit1_rep1


title: 697 SOX11 KO repl. 1

description:
697_raw_read_counts
697_SOX11_1


title: mm_krit1_control_rep2


title: Genomic DNA from adult human whole blood [C480317292]


title: Undifferentiated_H3K27me3 IP 3

city: New York

first: Aarthi

last: Ramakrishnan

state: New York

address: 1425 Madison Avenue

department: Neuroscience

institute: Icahn School of Medicine at Mount Sinai

library_source: genomic

data_processing:
Illumina Casava1.7 software used for basecalling.
ChIPseq: For H3K4me3, H3K4me3Q5ser and Taf3 ChIP-seq in RN46A-B14 cells, raw sequencing reads were aligned to the rat genome (rn6) using default settings of Bowtiev2.2.0. Only uniquely mapped reads were retained. Alignments were filtered using SAMtoolsv0.1.19 to remove duplicated reads. Peak-calling–normalized to respective inputs–was performed using MACSv2.1.150 with default settings and filtered for FDR < 0.05 and fold change > 1.2; the window size was set as 300 bp.  Raw sequencing reads from mouse brains (H3K4me3 vs. H3K4me3Q5ser) were aligned to the mouse genome (mm10) using default settings of HISATv0.1.6b. Only uniquely mapped reads were retained. Alignments were filtered using SAMtoolsv0.1.19 to remove duplicate reads, and peak-calling–normalized to respective inputs–was performed using MACSv2.1.1 with default settings and filtered for FDR < 0.05 and fold change > 1.2. Raw sequencing reads from human PSCs vs. ¬5-HT neurons (H3K4me3Q5ser) were aligned to the human genome (hg38) using default settings of HISAT2v2.1.0. Again, only uniquely mapped reads were retained. Alignments were filtered using SAMtoolsv1.8 to remove duplicated reads, and peak-calling–normalized to respective inputs–was performed using MACSv2.1.1 with default settings and filtered for FDR < 0.05 and fold change > 1.2.
RNAseq: Raw sequencing reads from RN46A-B14 cells were mapped to rn6 using TopHat2v2.1.051. Counts of reads mapping to genes were obtained using HTSeq-count against Ensembl v81 annotation. Differential expression analysis was done using the DESeq2 package52 (v1.6.3) at an FDR cutoff of 0.05. Raw RNA-seq reads obtained from mouse brains were mapped to mm10 using HISAT v0.1.6b. StringTie v1.2.1 was used to obtain gene-level FPKM values against Ensembl v84. Raw RNA-seq reads obtained from human cells were mapped to the human genome (hg38) using HISAT2v2.1.0. Counts of reads mapping to genes were obtained using HTSeq-count against Ensembl v90 annotation. Differential expression analysis was done using the DESeq2 package (v1.6.3), again with a FDR<0.05 cutoff.
Genome_build: rn6, mm10, hg38
Supplementary_files_format_and_content: Peaks called using MACS and annotated using region_analysis in tab delimited text file. Counts in tab delimited text files generated using HTSeq-count against Ensembl v81 annotation; Tab delimited text files include gene level FPKM values for each sample obtained using StringTiev1.2.1 against Ensembl v84 annotation

organism: Rattus norvegicus

source_name: Serotonergic tissue culture cells

growth_protocol: For RN46A-B14 cell differentiation, a modified version of published protocols was used. Briefly, RN46A-B14 cells were cultured and maintained in DMEM with 10% FBS, 1% Pen/Strep and 250 ug/ml Geneticin at 33°C with 5% CO2 on 10 cm cell culture dishes. The day before differentiation, cell culture dishes were coated with 6 ml of a matrigel/DMEM mixture for 1 hr at RT. After matrigel polymerization, 0.7-0.8 x 10^6 cells were seeded onto each plate with 10 ml regular growth media. Plates were then incubated at 33°C overnight allowing the cells to adhere to the plate. On the day of differentiation, regular growth media was removed from plates and 10 ml of differentiation media (1% Pen/Strep, 1% B-27 supplement, 0.1% Insulin, 0.1% apotransferrin, 0.1% putrescine, in B16 Base media) was added to each plate. Cells were then incubated at 39°C with 5% CO2, 95% humidity for three days. On the fourth day, differentiation media was changed conditionally at a 1:1 ratio. Differentiated RN46A-B14 cells were collected on the sixth day with 0.05% trypsin by centrifugation, washed several times and then reconstituted in DPBS on ice. Induced pluripotent stem cells were derived from human fibroblasts and cultured on Matrigel-coated plastic plates using a modified recipe of mTeSR1 medium (Stemcell Technologies). Briefly, hPSCs were maintained as colonies and passaged by mechanical and enzymatic dissociation (Dispase). Cells were cultured for 1 week with daily media changes prior to harvesting. Serotonergic neurons were generated using a modified version of a previously described method24. Briefly, floating embyroid bodies (EBs) were generated by mechanical and enzymatic (collagenase) dissociation of hPSC colonies. EBs were cultured for one week with DMEM/F12-Glutamax:Neurobasal (1:1) including: N2, B27 supplements, 1x non essential amino acids, SB431542 (2 μM), DMH-1 (2 μM) and CHIR99021 (1.4µM) (Serotonergic medium). EBs were plated onto to poly-ornithine/laminin (Sigma)-coated plastic plates in Serotonergic medium with the addition of Sonic hedgehog protein (Shh, 500 ng/ml) for another week. Rosette-forming EBs and derived neural precursor cells were selected and cultured as monolayers in Serotonergic medium containing Shh (500 ng/ml) and FGF-4 (10 ng/ml), and were then maintained at high densities. Serotonergic neurons were derived by culturing for an additional 3 weeks at lower densities in serotonergic differentiation medium comprised of a base of Neurobasal medium containing GDNF (10 ng/ml), BDNF (10 ng/ml) (Peprotech), dibutyrl-cyclicAMP (1 mM, Sigma), ascorbic acid (200 nM, Sigma), laminin (1 μg/ml), DAPT (2.5 µM) and TGF-beta3 (1 ng/ml). Medium was changed every other day for 3 weeks before cells were harvested for further processing. All protocols were performed in accordance with the Salk Institute’s IRB.

extract_protocol:
Cell pellets (>10 x 10^6/n) and brain tissues were crosslinked and quenched. Samples were washed thoroughly before being subjected to lysis and sonication. Samples were then incubated with specific antibodies (7.5 μg/sample) bound to M-280 Dynabeads on a rotator at 4°C overnight. The following day, immunoprecipitates were washed, eluted and reverse crosslinked. Following RNA and protein digestion, DNA fragments were purified using a Qiagen PCR purification kit.
RNA and ChIP libraries were prepared for sequencing using standard Illumina protocols

tag: cell/region

value: RN46A-B14 Cells

tag: chip antibody

value: H3K27me3 (Cell Signaling 9733; Lot#8)

tag: differentiation status

value: Undifferentiated


title: Differentiated_H3K27me3 IP 1

value: Differentiated


title: REH ctrl repl. 3

description:
REH_raw_read_counts
REH_CTRL_3

source_name: REH cell line

value: REH cell line


title: 697 ctrl repl. 1

description:
697_raw_read_counts
697_CTRL_1


title: E17.5_RNA 2

source_name: Embryonic 17.5

value: Whole brain

value: Embryonic 17.5


title: Genomic DNA from adult human whole blood [C480319063]

tag: individual id

tag: year of collection


title: RCH-ACV SOX11 KO repl. 2

description:
RA_raw_read_counts
RCH-ACV_SOX11_2

value: RCH-ACV cell line


title: Undifferentiated_H3K27me3 IP 1


title: E9.5_RNA 2

source_name: Embryonic 9.5

value: Embryonic 9.5


title: REH ctrl repl. 2

description:
REH_raw_read_counts
REH_CTRL_2

value: B-ALL cells


title: Undifferentiated_H3K27me3 IP 2


title: E9.5_RNA 1


title: Differentiated_H3K27me3 IP 2


title: Genomic DNA from adult human whole blood [C480316084]

tag: age

tag: nk


title: H3.3Q5A_RNA 4

tag: virus

value: Lenti-H3.3 Q5A


title: Differentiated_H3K27me3 IP 3


title: H3.3Q5A_RNA 3


title: Genomic DNA from adult human whole blood [C480319617]

tag: bcell

tag: mono

tag: gran


title: Genomic DNA from adult human whole blood [C480316638]


title: REH SOX11 KO repl. 3

description:
REH_raw_read_counts
REH_SOX11_3

tag: sirna

tag: replicate


title: mm_krit1_rep3

tag: cell type


title: E17.5_RNA 1


title: H3.3Q5A_RNA 2


title: Genomic DNA from adult human whole blood [C480339417]


title: H3.3Q5A_RNA 1


title: Genomic DNA from adult human whole blood [C480347219]


title: H3.3Q5A_RNA 6


title: E9.5_RNA 3


title: Genomic DNA from adult human whole blood [C480314876]


title: REH SOX11 KO repl. 2

description:
REH_raw_read_counts
REH_SOX11_2

tag: cell line


title: REH SOX11 KO repl. 1

description:
REH_raw_read_counts
REH_SOX11_1


title: H3.3WT_RNA 3

value: Lenti-H3.3 WT


title: H3.3Q5A_RNA 5


title: E17.5_Input 2

value: Input


title: H3.3WT_RNA 2


title: H3.3WT_RNA 5


title: E17.5_RNA 3


title: E9.5_Input IP 2


title: Genomic DNA from adult human whole blood [C480346665]


title: MEL501_TDG_KD_3

city: Camden

first: Jaroslav

last: Jelinek

state: NJ

address: 403 Haddon Avenue

department: Research Labs

institute: Coriell Institute for Medical Research

description: TDG knockdown replicate 3

data_processing:
Library strategy: DREAM
Sequencing reads were mapped to SmaI sites in the human genome (hg19) and signatures corresponding to methylated (starting with CCGGG) and unmethylated (starting with GGG) CpG were enumerated for each SmaI/XmaI site.
At each SmaI/XmaI site, let sm be the number of tags corresponding to methylated CpG (i.e., tags starting with CCGGG) and u be the number of tags corresponding to unmethylated CpG (i.e., tags starting with GGG), the methylation value was calculated as 100%*(c*sm/(c*sm+u)), where c is the correction factor based on observed vs expected methylation of spiked-in standards.
Genome_build: hg19
Supplementary_files_format_and_content: The processed data are in tab-delimited text file. The columns of the file are: ID_SmaI_hg19 (CCCGGG site ID), chromosome (chromosome of the CCCGGG site), position (position of the CCCGGG site), meth_reads (observed number of reads corresponding to methylated CpG, Xma),  unmeth_reads (observed number of reads corresponding to unmethylated CpG, Sma), total_reads, raw_methylation (unadjusted methylation value), adjusted_methylation (methylation value adjusted based on the spiked in standards).

growth_protocol: SK28 and MEL501 cells were cultured in RPMI-1640 supplemented with 10% fetal bovine serum

extract_protocol:
DNA isolation: The pellet was lysed in the solution containing 2% sodium dodecyl sulphate and 25 mM EDTA. Proteins were precipitated by adding 1/3 volume of 10 M ammonium acetate and removed as a pellet by centrifugation. DNA was precipitated from the supernatant with isopropanol, washed with 70% ethanol and dissolved in TE (10 mM TRIS pH 8.0, 1 mM EDTA).
Two micrograms of genomic DNA spiked with 5 methylation standards with defined methylation levels were digested with 20 units of SmaI endonuclease (NEB) for 8 hours at 25°C. Subsequently, 20 units of XmaI endonuclease (NEB) were added and the digestion was continued for an additional 16 hours at 37°C. Digested DNA with methylation-specific signatures at the ends of restriction fragments was end repaired using dCTP, dGTP and dATP (0.4 mM final concentration of each) and 15 units of Klenow Fragment (3'>5' exonuclease deficient) DNA polymerase (NEB).
Illumina paired end (Quail et al. 2008) or barcoded Truseq (Illumina, San Diego, CA) sequencing adapters were then ligated at 10:1 adapter:fragment ratio using Rapid T4 DNA ligase (Enzymatics, Beverly, MA). The ligation mix was size selected by electrophoresis in 2% agarose. Two slices corresponding to 250-350 bp and 350-500 bp sizes based on a 100 bp DNA ladder (NEB) were cut out and DNA was extracted from agarose. DNA eluted from the slices was separately amplified with Illumina paired end PCR primers (Quail et al. 2008) using iProof high-fidelity DNA polymerase (Bio-Rad Laboratories, Hercules, CA) and 18 cycles of amplification. Resulting sequencing libraries were purified with AMPure magnetic beads (Agencourt, Beverly, MA).

treatment_protocol: Knockdown was performed by infection with TDG shRNA lentivirus C8 or emty vector control pLKO.1. Control pLKO.1 and TDG shRNA lentivirus-infected melanoma cell lines were selected in puromycin (0.5 μg/mL) for 3 days.

value: adult

value: Melanoma cell

tag: shRNA

value: TDG knockdown


title: MEL501_TDG_KD_2

description: TDG knockdown replicate 2


title: Genomic DNA from adult human whole blood [C480315430]


title: MEL501_TDG_KD_1

description: TDG knockdown replicate 1


title: E17.5_Input 1


title: MEL501_Empty  pLKO.1 Vector_3

description: Empty vector replicate 3

value: control


title: E17.5_Input 3


title: Genomic DNA from adult human whole blood [C480334676]


title: MEL501_Empty  pLKO.1 Vector_2

description: Empty vector replicate 2


title: E9.5_Input 3


title: Genomic DNA from adult human whole blood [C480338863]


title: Genomic DNA from adult human whole blood [C480314222]


title: H3.3WT_RNA 4

value: RN46A-B14 Cells


title: Genomic DNA from adult human whole blood [C480312460]


title: MEL501_Empty pLKO.1 Vector_1

description: Empty vector replicate 1


title: SK28_TDG_KD_2

description: TDG knockdown replicate 2


title: E9.5_H3K4me3 IP 2


title: SK28_TDG_KD_3

description: TDG knockdown replicate 3


title: Genomic DNA from adult human whole blood [C480349090]


title: SK28_TDG_KD_1

description: TDG knockdown replicate 1


title: SK28_Empty  pLKO.1 Vector_3

description: Empty vector replicate 3


title: Genomic DNA from adult human whole blood [C480313668]


title: H3.3WT_RNA 1


title: G4_3_leaf_RNA-seq

city: Wuhan

first: Yuhua

last: Fu

state: Hubei

address: No.1, Shizishan Street, 430070, Wuhan, China

department: College of Animal Science and Technology

country: China

institute: Huazhong Agricultural University

data_processing:
To avoid reads with low-quality, we removed the following types of reads: (a) reads with ≥ 10% unidentified nucleotides (N); (b) reads with > 10 nt aligned to the adapter, allowing ≤ 10% mismatches; and (c) reads with > 50% bases having phred quality < 5.
High-quality RNA-seq data were aligned to the swine Sscrofa10.2 reference genome using Tophat (v2.1.0) with 2 nt fault tolerance
Reads count for each protein-coding gene were extracted by using the HTseq (v 0.6.1) and only uniquely aligned reads were remained.
The reads count were normalized by using TMM method from R package edgeR (v 3.16.3)
Genome_build: Oryza_indica.ASM465v1
Supplementary_files_format_and_content: Reads count for each gene in twelve  library

organism: Oryza sativa

source_name: Leaf

growth_protocol: The aerial tissues of one-month-old plants from four different areas

extract_protocol:
Total RNA was extracted from the twelve Oryza sativa L. spp. indica cultivars TU100 (hybrid rice) leaf samples using TRIzol (Invitrogen). RNase-free DNase I (TaKaRa) was used to remove genomic DNA from the RNA samples. Those RNA samples, with no smear seen on agarose gels, a 260/280 ratio above 2.0, and a RNA integrity number greater than 8.0 were used.
Twelve cDNA libraries were sequenced by Illumina Hiseq 2500 (Illumina, San Diego, CA, USA) with 125 bp paired-end reads according to the manufacturer’s instructions.

tag: treatment

value: VdAL+ azoxystrobin


title: E17.5_H3K4me3Q5ser IP 2

tag: cell/region

value: H3K4me3Q5ser (Millipore 4491a; Lot#RA1608107)


title: E9.5_H3K4me3 IP 1

tag: chip antibody


title: E17.5_H3K4me3 IP 3

tag: differentiation status


title: E9.5_H3K4me3Q5ser IP 2


title: Genomic DNA from adult human whole blood [C480347873]

tag: individual id


title: E9.5_H3K4me3Q5ser IP 1


title: E17.5_H3K4me3 IP 1


title: RPL13A_WT-ES-4

city: jerusalem

first: Manar

last: Abu Diab

address: Shmu'el Bait St 12, Jerusalem, 9103102

department: Genetics

country: Israel

institute: Shaare Zedek Medical Center

description: bisulfite footprinting in a non-repetitive control locus

data_processing:
bisulfite DNA-seq reads were aligned to the FMR1/C9orf72/RPL13A reference loci from genome (hg19) using ApE
To align each read to a reference sequence, we wrote a simple perl script, which first filtered out PCR errors with reads containing inaccurate repeat number. The reference sequences were manually prepared according to the known repeat tract length for each sample. Next we divided template from non-template reads (based upon the conversion pattern at the repeats) to generate two separate matrices containing coded information on each nucleotide according to the reference sequence. In addition, a third matrix was generated, containing the remaining reads. The coded information is as follows: non-C nucleotide marked with 0; Unconverted C (dsDNA structure) with 1; Converted C (single stranded) with 2 if the conversion is to T (correct conversion) and 3 if the conversion is to A or G, most probably due to sequencing errors, which were found to be uncommon. Reads with over 10 sequencing errors (numbers 3) were excluded. For clustering and heatmaps, we randomly selected 10,000 reads using the R statistical gplots library and generated heatmaps using the heatmap.2 function. At FMR1, the total number of compatible reads was less than 10,000, and therefore the heatmaps were generated from the entire population of molecules.
Analysis was performed using either a reverse primer (FMR1 and C9orf72) or a forward primer (RPL13A). Bisulfite foorprinting: "Find_Repeats_FRM1_FASTQ.pl": will extract reads that contain 3bp repeats of the CGG and all possible conversion combinations. The repeats number is dictated by the first foreach loop. The script will define "sense" vs "antisense" slipouts and all undefined/unmodified reads as "oops". "Find_Repeats_C9_FASTQ.pl" is similar to "Find_Repeats_FRM1_FASTQ.pl" but for GGGGCC 6bp repeats conversion combinations. "Find_RPL13A_FASTQ.pl" designed to work on control locus (non-repetative R-loop forming locus) to define "sense" vs "antisense" slipouts and undefined/unmodified reads as "oops". Nucleotide_to_Number_based_coding.pl will produce a number based matrix according to conversion patterns relativle to the uncoverted reference sequence: C -> C = "1" C -> T = "2" C -> A/G = "9" G -> G = "4" G -> A = "5" G-> T/C = "7" In positions of which the refernce sequence is not G or C it will produce "0". For the RPL13A we used a pl script ("Find_RPL13A_FASTQ.pl") that uploads "RPL13A_WT-ES-4_TXT" that can be found in  "https://github.com/RachelEiges/Bisulfite_Footprinting". The txt file includes a list of converted and unconverted cytosines for each read in the relevent fastq file. The columns in the text file are for:   1. Number of bp identical to the reference squence.  2. Number of G to G  3. Number of G to A  4. Number of C to C  5. Number of C to T  6. G to A positions  7. C to T positions
Genome_build: hg19
Supplementary_files_format_and_content: Raw data for the bisulfite footprinting analysis is provided for FMR1, C9orf72 and RPL13A as fastq files, while the processed data for FMR1,C9orf72 and RPL13A as TEXT doc..

source_name: B-200: wild type XY hESC line

growth_protocol: hESCs were grown in feeder-free culture conditions using defined Essential 8 medium combined with Vitronectin (Gibco) coated surfaces (Cohen-Hada et al. et al., 2016).

extract_protocol:
DNA extracted under native conditions
First PCR products were purified using SPRI beads (X1), and then a second PCR was performed to add Illumina adapters with the indices. PCR products were cleaned again using SPRI beads (X1) and eluted in 25 ul elution buffer. To confirm the length and purity of the library; 1 µl was loaded onto an Agilent TapeStation 2200 using the D1000 ScreenTape assay (Agilent Technologies, Santa Clara, USA). Library concentration was measured using the Qubit® dsDNA HS (High Sensitivity) Assay Kit. The libraries were normalized to 4 nM and loaded on a Miseq (Illumina, USA) using the MiSeq Reagent Kit v2 (500 cycles) with the following conditions: 250x2 in final concentration of 8pM and 20% phiX spike-in.

treatment_protocol: bisulfite conversion of genomic DNA under non-denatured conditions

value: hESCs


title: E9.5_Input 1


title: G3_3_leaf_RNA-seq

value: VdAL


title: E9.5_H3K4me3 IP 3

value: Whole brain


title: SK28_Empty pLKO.1 Vector_1

description: Empty vector replicate 1


title: Genomic DNA from adult human whole blood [C480313014]

tag: year of collection


title: C9orf72_C9-ES-2

description: bisulfite footprinting in C9orf72 of wild type alleles (2 repeat copies each)

source_name: SZ-ALS3: C9 mutant hESC line


title: C9orf72_C9-ES-1

description: bisulfite footprinting in C9orf72 of wild type alleles (5 repeat copies each)

source_name: SZ-ALS1: C9 mutant hESC line


title: C9orf72_WT-ES-1

source_name: SZ-13: wild type XY hESC line


title: C9orf72_WT-ES-5

description: bisulfite footprinting in C9orf72 of wild type alleles (carrying either 2 or 5 repeat copies)

source_name: SZ-FX C15B: wild type XY hESC line for the C9 locus

value: SZ-FX C15B


title: E17.5_H3K4me3Q5ser IP 1

value: Embryonic 17.5


title: E17.5_H3K4me3Q5ser IP 3


title: REH ctrl repl. 1

description:
REH_raw_read_counts
REH_CTRL_1

value: CTRL

value: REH cell line


title: G3_1_leaf_RNA-seq


title: G4_1_leaf_RNA-seq


title: FMR1_ WT-ES-4

description: bisulfite footprinting in FMR1 of a wild type allele


title: G2_3_leaf_RNA-seq

value: azoxystrobin


title: G4_2_leaf_RNA-seq


title: E9.5_H3K4me3Q5ser IP 3

value: Embryonic 9.5


title: Lamtor1_KO_2_long_N2B27

city: Basel

first: Joerg

last: Betschinger

address: Maulbeerstrasse 66

country: Switzerland

institute: Friedrich Miescher Institute

data_processing:
Reads were aligned using qAlign from the Bioconductor package QuasR (Gaidatzis et al., 2015) (package version 1.16.0) to mouse GRCm38/mm10 genome with default parameters except for splicedAlignment=TRUE, which performs spliced alignments by internally running SpliceMap (Au et al., 2010).
Alignments were quantified with qCount from the Bioconductor package QuasR (Gaidatzis et al., 2015) (package version 1.16.0) for known UCSC genes obtained from the TxDb.Mmusculus.UCSC.mm10.knownGene package (package version 3.4.0) using default parameters.
Statistically significantly deregulated genes were identified using edgeR (Robinson et al., 2010) (package version 3.18.0) and these genes were fitted to five separate generalized linear models for different sets of samples. Raw P values were corrected for multiple testing by calculating false discovery rates (FDR) (Benjamini et al., 1995).
RNA log2 fold changes were used from edgeR. For centred expression, read counts were normalized (dividing by the total number of aligned reads and multiplying with minimal library size, and adding a pseudocount of 8), log2 transformed and differences in log-space of each gene in each sample to its average over all samples was calculated.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text file containing RPKM values for each Sample (column) and gene (row).

molecule: polyA RNA

source_name: mouse embryonic stem cells RGd2

growth_protocol: ESCs (RGd2 containing a Rex1:GFPd2-IRES-Blasticidin reporter (Wray et al., 2011) (gift from Martin Leeb, Vienna) were cultured on plastic coated with gelatin or laminin (Sigma) in N2B27 medium (DMEM/F12 (Life Technologies), Neurobasal (Gibco) supplemented with N2 (homemade) and B-27 Serum-Free Supplement (Gibco), 1mM sodium pyruvate (Gibco), 2mM L-glutamine (Gibco), 0.1 mM 2-mercaptoethanol (Sigma)), and where indicated with 2i for ESC maintenance (3µM CHIR99021 and 1µM PD0325901 (Steward lab, Dresden)) and 4-hydroxytamoxifen (0.1mM, Sigma).

extract_protocol:
Cellular RNA from ESCs, cells 34h after 2i withdrawal, and long-term differentiated cells sorted for Rex1 expression was purified using RNAeasy (Qiagen).
Strand-specific RNA-seq libraries were generated using TruSeq mRNA Library preparation kit (Illumina).

treatment_protocol: For differentiation, ESCs were plated on gelatin-coated plates at 1.5 x 104 cells/cm2 and, the following day, 2i was withdrawn for 34h or cells were passaged further on laminin-coated plates for long-term differentiation.

tag: tissue

value: mouse embryonic stem cells RGd2

tag: genotype

value: Lamtor1 KO.2

tag: timepoint

value: long N2B27


title: FMR1_uFM-ES-2

description: bisulfite footprinting in FMR1 of a methylated wild type allele

source_name: SZ-FX7: FXS XX hESC line with skewed X-inactivation


title: G2_2_leaf_RNA-seq


title: G3_2_leaf_RNA-seq


title: G2_1_leaf_RNA-seq


title: Lamtor1_KO_1_long_N2B27

value: Lamtor1 KO.1


title: Tfe3-ERT2_Tam_long_N2B27

value: long Tam


title: G1_3_leaf_RNA-seq

value: Water


title: Flcn_KO_1_long_N2B27

treatment_protocol: For differentiation, ESCs were plated on gelatin-coated plates at 1.5 x 104 cells/cm2 and, the following day, 2i was withdrawn for 32h or cells were passaged further on laminin-coated plates for long-term differentiation.

value: Flcn KO.1


title: Flcn_KO_1_34h_N2B27_II


title: G1_1_leaf_RNA-seq


title: Flcn_KO_1_34h_N2B27_I


title: Flcn_KO_2_long_N2B27

value: Flcn KO.2


title: G1_2_leaf_RNA-seq


title: Flcn_WT_34h_N2B27_II

value: wildtype


title: Tfe3-ERT2_34h_Tam_N2B27_II

value: 34h Tam


title: Flcn_WT_34h_N2B27_I


title: 58_6W_Heart_minus6_S93

first: Yang

last: Lin

state: NY

address: 455 Main Street 06W

institute: Weill Cornell Medicine

description: processed data file: ILMN_176_190_mRNAseq_STAR_featureCoutns_edgeR_20171220.xlsx

data_processing:
HiSeq4000 using HiSeq 3000/4000 PE SBS Kit.
Mapped to the mm10 mouse genome using STAR RNA-seq aligner.
Sequencing reads were assigned to mm10 refGene genes using featureCounts.
Differential expression analysis was performed using exactTest and glmLRT (edgeR).
Genome_build: mm10
Supplementary_files_format_and_content: ILMN_176_190_mRNAseq_STAR_featureCoutns_edgeR_20171220.xlsx: Excel file content sample information, QC results, Raw counts and RPKM for each sample.

source_name: 6W Heart EC TdTomato- 6

growth_protocol: Abcg2CreERT mice were crossed with ROSATdTomato mice to make Abcg2CreERT;ROSATdTomato mice.

extract_protocol:
Tissues were digested by collagenase and cell suspensions were stained with antibodies that label CD31, CD45, Ter119. The TdTomato+ and ToTomato- EC were isolated by Aria II flow cytometer. RNA was isolated by Qiagen RNeasy Micro kit. PolyA selection for mRNASeq.
Illumina TruSeq RNA Access Library Prep Kit.

treatment_protocol: 50mg/kg tamoxifen was intraperitoneally injected into mice 24 hours before tissue collection.

tag: strain

value: Abcg2CreERT; ROSATdTomato

value: Muscle

tag: age

value: 6 weeks

value: Endothelial Cells

tag: tdtomato +/-

value: Negative


title: 56_6W_Heart_plus6_S91

source_name: 6W Heart EC TdTomato+ 6

value: Positive


title: 55_6W_Heart_plus5_S90

source_name: 6W Heart EC TdTomato+ 5


title: 57_6W_Heart_minus5_S92

source_name: 6W Heart EC TdTomato- 5


title: 54_6W_Muscle_minus5_S89

source_name: 6W Muscle EC TdTomato- 5


title: Tfe3-ERT2_34h_Tam_N2B27_I


title: 53_6W_Muscle_minus4_S88

source_name: 6W Muscle EC TdTomato- 4


title: DRG_SNI_RFP_1

city: Montreal

first: Arkady

last: Khoutrosky

state: Quebec

address: 3655 Prom. Sir-William-Osler

department: Department of Anesthesia

country: Canada

institute: McGill University

description: Ribosome footprint

data_processing:
fastx_clipper from FASTX Toolkit v0.0.14 was employed to remove the adapter sequence from raw sequencing read, reads shorter than 18 bp were removed
Bowtie v1.1.2 was used to remove reads of undesired sequences (i.e. rRNAs and tRNAs)
Reference alignment was performed with STAR v2.5.2b using a reference index built from GRCm38 primary genome assembly and corresponding gene structure information retrieved from GENCODE
Only uniquely mapped reads were considered for the output, and raw count tables were generated by STAR in the fashion of HTSeq-count
An R script was used to calculate RPKM for each gene
Translation Efiiciency was calculated for each gene
Genome_build: GRCm38.p5
Supplementary_files_format_and_content: The file (.csv) contains counts and RPKM values for all 16 samples (F in the column name dentes ribosome footprint sample and T denotes total mRNA samples), and translation efficiency (TE) for the 8 respective ribosome footprinting samples w.r.t. Ensembl_gene_id, Entrez_gene_id, gene_symbol, gene_type, gene_description, chromosome, non_coding, pseudogene, gene_length, exonic_length

source_name: Lumbar(L3 to L5) dorsal root ganglion

growth_protocol: C57BL/6J female mice, at 8 weeks of age

extract_protocol:
The animals were sacrificed 30 days post-surgery, and lumbar DRG (L3 to L5) and dorsal horn of corresponding spinal cord section were extracted and frozen at -80 °C. Tissues from ten animals were pooled per sample and two independent replicates were made for each of the four conditions. Pooled tissue were lysed in lysis buffer containing cyclohexamide and the lysate was divided into two fractions. One fraction was used to purify poly(A) mRNA for RNA-seq and the remaining fraction was used to isolate ribosome footprints. For the former, poly(A) mRNA were purified using magnetic oligo-dT DynaBeads. The purified RNA was then subjected to alkaline fragmentation. Fragmented mRNAs were size-selected on a denaturing 10% polyacrylamide-urea gel and the bands corresponding to 30–50 nucleotides were excised, eluted, and precipitated with Isopropanol. For the later, lysate was treated with RNAse 1 followed by ultracentrifugation through a sucrose cushion. The resulting RNA pellet was resuspended in Tris HCl buffer and purified by double acid Phenol and one Chloroform extraction. Purified RNA was resolved on a 15% polyacrylamide urea gel and bands corresponding to 28–32 nucleotides, containing the desired ribosome footprints (RFPs), was excised and extracted for RNA using Costar Spin-X columns (Sigma).
Fragmented mRNA and RFPs were subjected to PNK dephosphorylation and 10 pmol of the dephosphorylated RNA fragments were used for ligation to a pre-adenylated and 3′-blocked linker, followed by separation on a 10% polyacrylamide urea gel. Linker ligated bands were excised and extracted for RNA, which was reverse transcribed using oNTI223 adapter (Illumina) and SuperScript III reverse transcriptase (Invitrogen) according to the manufacturer’s instruction manual. The resulting cDNA was purified by size selection on a 10% polyacrylamide Tris/Borate/EDTA-urea (TBE-urea) gel. The cDNA was then circularized using CircLigase (Epicentre, CL4111K). Products arising from ribosomal sequences were depleted using biotinylated rDNA complementary oligos (Ingolia et al., 2012) and MyOne Streptavidin C1 dynabeads. The remaining products were amplified by PCR (11 cycles) using indexed primers, size-selected on a 8% polyacrylamide gel and purified. At these intermediate steps, bands in the gels that were very close to the fragment size + adapter were excised and purified. The resulting cDNA library samples were analyzed on an Agilent Bioanalyzer High Sensitivity DNA chip to confirm the size and concentration.

treatment_protocol: Mice underwent the bilateral Spared Nerve Injury surgical procedure. The mouse was returned to its home-cage for recovery. Sham animals were used as controls, where the surgical procedure was carried out identically but all three branches of the sciatic nerve were left untouched and unharmed.

value: Lumbar(L3 to L5) dorsal root ganglion

tag: procedure

value: Spared Nerve Injury (SNI) surgery

value: 8 weeks

tag: Sex

value: female


title: DRG_SNI_mRNA_2

data_processing:
Library strategy: Ribo-seq
fastx_clipper from FASTX Toolkit v0.0.14 was employed to remove the adapter sequence from raw sequencing read, reads shorter than 18 bp were removed
Bowtie v1.1.2 was used to remove reads of undesired sequences (i.e. rRNAs and tRNAs)
Reference alignment was performed with STAR v2.5.2b using a reference index built from GRCm38 primary genome assembly and corresponding gene structure information retrieved from GENCODE
Only uniquely mapped reads were considered for the output, and raw count tables were generated by STAR in the fashion of HTSeq-count
An R script was used to calculate RPKM for each gene
Translation Efiiciency was calculated for each gene
Genome_build: GRCm38.p5
Supplementary_files_format_and_content: The file (.csv) contains counts and RPKM values for all 16 samples (F in the column name dentes ribosome footprint sample and T denotes total mRNA samples), and translation efficiency (TE) for the 8 respective ribosome footprinting samples w.r.t. Ensembl_gene_id, Entrez_gene_id, gene_symbol, gene_type, gene_description, chromosome, non_coding, pseudogene, gene_length, exonic_length

tag: replicate


title: Tfe3-ERT2_34h_EtOH_N2B27_II

value: mouse embryonic stem cells RGd2

value: 34h EtOH


title: DRG_SNI_RFP_2

description: Ribosome footprint


title: 52_6W_Muscle_minus3_S87

source_name: 6W Muscle EC TdTomato- 3

tag: cell type


title: Slide9_Array2

city: Wilayah Persekutuan Kuala Lumpur

first: Prevathe

last: Poniah

address: Lembah Pantai

department: Pharmacology

country: Malaysia

institute: University of Malaya

hyb_protocol: 1,350 μL of DNase/RNase-free distilled water was added to the vial containing lyophilized 10× aCGH Blocking Agent (included in the Oligo aCGH/ChIP-on-chip Hybridization Kit) to prepare 10x blocking agent. 245 μL of sample after yield-testing and addition of hybridization master mix were then hybridized following manufacturer's protocol.

scan_protocol: Scanning was done using the Agilent Technologies Scanner G2505C US81403231 by selecting Protocol CGH_107_Sep09.

data_processing: Scanned images derived from the SurePrint Scanner were extracted using Agilent Feature Extraction for Cytogenomics Software, version 2.7.8.0 (Agilent Technologies, USA) using the CGH_107_Sep09 protocol and CGH_QCMT_Sep09 metric set for background subtraction and normalization. Extracted data were analysed using the Agilent Cytogenomics Software, version 2.7 (Agilent Technologies).

source_name: Peripheral Blood

label_protocol: 5 μL of Random Primer was added to each reaction tube containing 26 μL of gDNA to make a total volume of 31 μL. Samples are centrifuged in a centrifuge for 1 minute at 6,000 × g. 19 μL of Labeling Master Mix was added to each reaction tube to make a total volume 50 μL. Samples were then subjected to clean-up process by adding 430 μL of 1× TE (pH 8.0), Molecular grade to each reaction tube. After discarding the flow-through, this step is repeated by adding 480 μL of 1× TE (pH 8.0), Molecular grade to each column. Upon adding 1× TE (pH 8.0), Molecular grade, 1.5 μL of each sample is tested for yield and specific activity/ degree of labeling.

growth_protocol: Genomic DNA was extracted from peripheral blood of human PCa and BPH subjects and were stored in EDTA tubes in -80°C freezer until use.

extract_protocol: gDNA was extracted from whole blood samples using QiAmp DNA Blood Mini Kit (Qiagen, Hilden, Germany). The direct method was used for sample preparation prior to labelling according to manufacturer's protocol.

treatment_protocol: Samples were thawed to room temperature and vortexed prior to extraction.

tag: gender

value: Male

tag: tumour stage

value: Advanced PCa

tag: prostate condition

value: BPH


title: Slide9_Array1


title: DRG_Sham_RFP_2

description: Ribosome footprint

value: Sham surgery


title: DRG_Sham_mRNA_2


title: E17.5_H3K4me3 IP 2

source_name: Embryonic 17.5

tag: cell/region

value: Whole brain

tag: chip antibody

value: Embryonic 17.5


title: DRG_Sham_RFP_1

description: Ribosome footprint


title: Slide5_Array2


title: Slide3_Array1


title: Slide6_Array1


title: Slide8_Array1


title: Slide3_Array2


title: Slide5_Array1


title: Slide6_Array2


title: 51_6W_Muscle_minus2_S86

source_name: 6W Muscle EC TdTomato- 2

value: Abcg2CreERT; ROSATdTomato

value: Muscle


title: DRG_SNI_mRNA_1


title: Lamtor1_KO_2_ESC_II

value: Lamtor1 KO.2

tag: treatment

value: ESC


title: SC_SNI_mRNA_2

source_name: Dorsal section of lumbar spinal cord

value: Dorsal section of lumbar spinal cord


title: Slide8_Array2


title: Tfe3-ERT2_34h_EtOH_N2B27_I


title: DRG_Sham_mRNA_1

value: Lumbar(L3 to L5) dorsal root ganglion


title: Lamtor1_KO_2_ESC_I


title: Slide7_Array1


title: 49_6W_Muscle_plus5_S85

source_name: 6W Muscle EC TdTomato+ 5

value: 6 weeks

value: Endothelial Cells

value: Positive


title: 48_6W_Muscle_plus4_S84

source_name: 6W Muscle EC TdTomato+ 4


title: Slide4_Array1


title: Lamtor1_KO_1_ESC_II

value: mouse embryonic stem cells RGd2

value: Lamtor1 KO.1


title: Slide2_Array2

value: Male


title: SC_Sham_mRNA_2

value: 8 weeks

value: female


title: SC_Sham_RFP_2

description: Ribosome footprint

value: Sham surgery


title: Slide1_Array1

value: Advanced PCa

value: BPH


title: SC_Sham_RFP_1

description: Ribosome footprint


title: SC_SNI_mRNA_1

value: Spared Nerve Injury (SNI) surgery


title: Slide7_Array2


title: Slide2_Array1


title: Lamtor1_KO_1_ESC_I


title: Slide4_Array2


title: 44_P6_Mus_5_S36

source_name: P6 Muscle EC TdTomato-5

value: Abcg2CreERT; ROSATdTomato

value: Muscle

value: Postnatal day 6

value: Negative


title: Slide1_Array2


title: SC_Sham_mRNA_1

value: Dorsal section of lumbar spinal cord


title: 43_P6_Mus_4_S35

source_name: P6 Muscle EC TdTomato-4


title: 46_6W_Muscle_plus2_S82

source_name: 6W Muscle EC TdTomato+ 2

value: 6 weeks


title: Lamtor1_WT_ESC_II

source_name: mouse embryonic stem cells RGd2

value: wildtype

value: ESC


title: LC_KO_4 [RMN039]

city: Singapore

first: Kaibo

last: Duan

address: 8A Biomedical Grove, Immunos Building, Level 4

country: Singapore

institute: Singapore Immunology Network

data_processing:
Paired-end reads were mapped to GRCm38 reference genome using STAR version 2.5.2b
Mapped paired-end reads were summarized to gene level using featureCounts v.1.5.0 and with GENCODE GRCm38 vM7 gene annotation
Genes with zero read counts in all samples were filtered out
Genome_build: GRCm38 / mm10
Supplementary_files_format_and_content: Tab-delimited text file includes gene-level read counts for all samples

source_name: EZH2 -/-_Langerhans cells

extract_protocol:
Mouse skin cells were isolated as described previously (Ginhoux et al., 2007). Briefly, mouse ears were split into dorsal and ventral halves and floated in RPMI-1640 medium (Sigma) containing 1 mg/ml dispase (Invitrogen) for 60 min at 37°C to allow separation of epidermal and dermal sheets. The separated epidermis were then cut into small pieces and incubated in RPMI containing 10% serum, Collagenase IV (0.2mg / ml, Roche) and DNAse I (20000U / ml, Roche) for 1 hr at 37°C. Cells were then passed through 19 G needle and filtered through a 100 µM cell strainer (BD Falcon) to obtain a homogenous cell suspension. Langerhans cells has been sorted based on this phenotype: DAPI- CD45+ Ly6G- CD103- MHCII+ CD24+ EpCAM+. post sort purity has been  chacked and only 99.5 % purity sor or above has been selected for bulk RNA sequencing
RNA libraries were prepared for sequencing using standard  protocols

tag: strain background

tag: genotype/variation

value: skin

value: Langerhans cells


title: 47_6W_Muscle_plus3_S83

source_name: 6W Muscle EC TdTomato+ 3

tag: tissue

value: Endothelial Cells

value: Positive


title: LC_KO_1 [RMN032]


title: LC_KO_3 [RMN038]


title: LC_KO_2 [RMN033]


title: LC_WT_3 [RMN036]

source_name: WT_Langerhans cells

value: wild type


title: 42_P6_Mus_3_S34

source_name: P6 Muscle EC TdTomato-3


title: Flcn_KO_2_ESC_II

value: mouse embryonic stem cells RGd2

tag: genotype

value: Flcn KO.2

tag: timepoint


title: LC_WT_4 [RMN037]


title: LC_WT_2 [RMN031]


title: LC_WT_1 [RMN030]


title: Lamtor1_WT_ESC_I


title: Flcn_KO_2_ESC_I


title: 41_P6_Mus_2_S33

source_name: P6 Muscle EC TdTomato-2

tag: strain

tag: age


title: Flcn_KO_1_ESC_I

value: Flcn KO.1


title: Flcn_KO_1_ESC_II


title: 40_P6_Mus_1_S32

source_name: P6 Muscle EC TdTomato-1

tag: tdtomato +/-


title: Flcn_WT_ESC_II


title: 39_P6_Mus_5_S31

source_name: P6 Muscle EC TdTomato+5


title: Tfe3-ERT2_34h_Tam_ESC_II

value: 34h Tam


title: Flcn_WT_ESC_I


title: 37_P6_Mus_3_S29

source_name: P6 Muscle EC TdTomato+3

value: Abcg2CreERT; ROSATdTomato


title: 36_P6_Mus_2_S28

source_name: P6 Muscle EC TdTomato+2

value: Muscle


title: Tfe3-ERT2_34h_EtOH_ESC_II

value: 34h EtOH


title: 35_P6_Mus_1_S27

source_name: P6 Muscle EC TdTomato+1

value: Postnatal day 6


title: 32_P1_Lung_8_S26

source_name: P1 Lung EC TdTomato- 8

value: Lung

value: Postnatal day 1

value: Negative


title: Tfe3-ERT2_34h_EtOH_ESC_I

value: ESC


title: 31_P1_Lung_7_S25

source_name: P1 Lung EC TdTomato- 7


title: sample B, uncontrolled hypertensive 13b

type: RNA

city: São Paulo

first: Michelle Sabrina

last: Moreira Silva

state: SP

address: Av. Dr. Enéas de Carvalho Aguiar

country: Brazil

institute: Heart Institute - InCor

hyb_protocol: IVT followed Affymetrix's instructions for hybridization to Gene Chip® Human Gene 1.0 ST Arrays.

scan_protocol: standard Affymetrix protocol

data_processing: Raw data were preprocessed in R with Bioconductor packages for normalization and probe annotation (RMA). The replicate log2 transformed expression values of 28,231 transcripts were used for subsequent statistical analyses in R, after control probesets were removed. Replicate samples of the same individuals were used to increase accuracy in detecting true positives in subsequent association analyses. Affy annotation package: na35_hg9

label: biotin

source_name: fasting blood

label_protocol: Washing, staining and scanning followed Affymetrix guidelines.

extract_protocol: Total RNA was extracted from PBMCs isolated with Ficoll-Paque. All samples were processed within 2 hours of collection. Purified RNA was hybridized in Affymetrix Human Gene 1.0 ST Arrays.

treatment_protocol: Fasting blood samples for gene expression measurements and biochemical markers were withdrawn on two evaluations five months apart.

value: peripheral blood mononuclear cells

value: female

tag: race

value: black

tag: height

tag: weight

tag: sistolic blood pressure in a sample

tag: sistolic blood pressure in b sample

tag: diastolic blood pressure in a sample

tag: diastolic blood pressure in b sample


title: Tfe3-ERT2_3h_Tam_ESC_II

value: 3h Tam


title: sample B, uncontrolled hypertensive 15b

tag: gender

value: male

value: white


title: 30_P1_Lung_6_S24

source_name: P1 Lung EC TdTomato- 6

tag: cell type

value: Endothelial Cells


title: Tfe3-ERT2_3h_Tam_ESC_I

value: mouse embryonic stem cells RGd2

tag: treatment


title: sample B, uncontrolled hypertensive 19b

value: brown


title: sample B, uncontrolled hypertensive 16b


title: sample B, controlled hypertensive 11b


title: 38_P6_Mus_4_S30

source_name: P6 Muscle EC TdTomato+4

value: Abcg2CreERT; ROSATdTomato

value: Positive


title: sample B, controlled hypertensive 12b


title: sample B, controlled hypertensive 14b


title: sample B, uncontrolled hypertensive 10b


title: sample B, uncontrolled hypertensive 6b


title: sample B, uncontrolled hypertensive 9b


title: 29_P1_Lung_5_S23

source_name: P1 Lung EC TdTomato- 5


title: Tfe3-ERT2_34h_Tam_ESC_I

source_name: mouse embryonic stem cells RGd2

value: 34h Tam


title: sample B, controlled hypertensive 18b


title: Tfe3-ERT2_3h_EtOH_ESC_II

value: 3h EtOH


title: 28_P1_Lung_8_S22

source_name: P1 Lung EC TdTomato+ 8

value: Lung


title: sample B, controlled hypertensive 4b


title: sample B, controlled hypertensive 5b


title: Tfe3-ERT2_3h_EtOH_ESC_I


title: 25_P1_Lung_5_S19

source_name: P1 Lung EC TdTomato+ 5

value: Postnatal day 1


title: 21_P1_Lung_1_S18

source_name: P1 Lung EC TdTomato- 1

value: Negative


title: 26_P1_Lung_6_S20

source_name: P1 Lung EC TdTomato+ 6


title: SC_SNI_RFP_2

description: Ribosome footprint

source_name: Dorsal section of lumbar spinal cord

value: Dorsal section of lumbar spinal cord

tag: procedure

value: Spared Nerve Injury (SNI) surgery

value: 8 weeks

tag: Sex

tag: replicate


title: 27_P1_Lung_7_S21

source_name: P1 Lung EC TdTomato+ 7

tag: tissue


title: sample B, controlled hypertensive 3b

value: peripheral blood mononuclear cells

value: female


title: sample B, controlled hypertensive 8b


title: sample B, controlled hypertensive 17b


title: 17_P1_Lung_1_S17

source_name: P1 Lung EC TdTomato+ 1

tag: strain


title: SC_SNI_RFP_1

description: Ribosome footprint

tag: age


title: sample B, controlled hypertensive 7b


title: 34_P1_Heart_5_S16

source_name: P1 Heart EC TdTomato- 5

value: Heart

tag: tdtomato +/-


title: sample B, controlled hypertensive 2b

value: male

tag: race

value: white


title: sample A, uncontrolled hypertensive 9a

tag: height


title: sample A, controlled hypertensive 3a

tag: weight


title: sample A, controlled hypertensive 5a

tag: sistolic blood pressure in a sample


title: 16_6W_Heart_4_S14

source_name: 6W Heart EC TdTomato- 4

value: 6 weeks

value: Endothelial Cells


title: sample A, controlled hypertensive 17a

tag: sistolic blood pressure in b sample


title: sample A, controlled hypertensive 8a

tag: diastolic blood pressure in a sample


title: 14_6W_Heart_2_S13

source_name: 6W Heart EC TdTomato- 2

value: Abcg2CreERT; ROSATdTomato


title: sample A, controlled hypertensive 20a

tag: diastolic blood pressure in b sample


title: sample B, uncontrolled hypertensive 1b

tag: gender

value: brown


title: sample A, controlled hypertensive 18a


title: 12_6W_Heart_4_S11

source_name: 6W Heart EC TdTomato+ 4

tag: cell type

value: Positive


title: sample A, uncontrolled hypertensive 10a

value: black


title: 9_6W_Heart_1_S9

source_name: 6W Heart EC TdTomato+ 1


title: 33_P1_Heart_5_S15

source_name: P1 Heart EC TdTomato+ 5


title: 8_P1_Heart_4_S8

source_name: P1 Heart EC TdTomato- 4


title: sample A, uncontrolled hypertensive 1a

source_name: fasting blood


title: sample A, uncontrolled hypertensive 19a


title: sample A, controlled hypertensive 14a


title: 6_P1_Heart_2_S6

source_name: P1 Heart EC TdTomato- 2


title: sample A, controlled hypertensive 2a


title: sample A, uncontrolled hypertensive 13a


title: sample A, uncontrolled hypertensive 15a


title: sample A, controlled hypertensive 11a


title: sample A, uncontrolled hypertensive 6a


title: 13_6W_Heart_1_S12

source_name: 6W Heart EC TdTomato- 1


title: sample A, uncontrolled hypertensive 4a


title: mm_ccm3_control_rep1

source_name: brain microvascular endothelial cells

tag: genotype

value: Pdcd10 control (Cre negative; Pdcd10fl/fl)

value: 2 to 4 months

tag: background

value: brain microvascular endothelial cells (BMECs)


title: sample B, controlled hypertensive 20b


title: 2_P1_Heart_2_S2

source_name: P1 Heart EC TdTomato+ 2

value: Postnatal day 1


title: 10_6W_Heart_2_S10

source_name: 6W Heart EC TdTomato+ 2


title: mm_ccm3_control_rep2


title: 1_P1_Heart_1_S1

description:
Did not pass QC (MeanDiffPlots). Removed from downstream analysis.
processed data file: ILMN_176_190_mRNAseq_STAR_featureCoutns_edgeR_20171220.xlsx

source_name: P1 Heart EC TdTomato+ 1


title: 4_P1_Heart_4_S4

source_name: P1 Heart EC TdTomato+ 4


title: 5_P1_Heart_1_S5

description:
Matched sample (1_P1_Heart_1_S1) did not pass QC (MeanDiffPlots). Removed from downstream analysis.
processed data file: ILMN_176_190_mRNAseq_STAR_featureCoutns_edgeR_20171220.xlsx

source_name: P1 Heart EC TdTomato- 1

value: Negative


title: 3_P1_Heart_3_S3

source_name: P1 Heart EC TdTomato+ 3


title: sample A, uncontrolled hypertensive 16a


title: mm_ccm3_rep2

value: Pdcd10 null (Pdgfb-iCreERT2; Pdcd10fl/fl)


title: mm_ccm3_rep3


title: mm_ccm3_rep1


title: hs_ccm_control_rep2

source_name: neurovascular unit (NVU)

tag: source of nvu

value: autopsy contol

value: neurovascular unit (NVU)


title: 7_P1_Heart_3_S7

source_name: P1 Heart EC TdTomato- 3

value: Heart


title: hs_ccm_control_rep1


title: hs_ccm_control_rep3


title: sample A, controlled hypertensive 7a

value: peripheral blood mononuclear cells

value: female


title: mm_ccm3_control_rep3


title: hs_ccm_rep2

value: cerebral cavernous malformation

value: sporadic


title: chicken forelimb bud_PBS_3hr_rep2

city: Loma Linda

first: Kerby

middle: Clyde

last: Oberg

state: CA

address: 24785 Stewart Street

department: Pathology and Human Anatomy

institute: Loma Linda University

data_processing:
Reads were aligned with Hisat2 alignment algorithm to release-87 of gallus gallus genome build 5
Fold changes and statistical comparisons were obtained using EdgeR
Genome_build: Galgal5 release-87
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample …

organism: Gallus gallus

source_name: chicken forelimb bud PBS 3hrs

growth_protocol: Fertile chicken eggs were incubated in a humidified chamber for 4 days or until embryos reached desired developmental stage (HH23).

extract_protocol:
RNA was extracted using QIAGEN RNeasy Plus Micro kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Using tungsten needle and forceps, FGF-2 soaked beads were implanted in the posteror mesoderm of HH23 Chicken limb buds about 500microns from the distal tip. Embryos were incubated for an additional 3hrs then treated tissue was harvested and flash frozen using liquid nitrogen.

tag: treatment

value: PBS


title: chicken forelimb bud_FGF2_3hr_rep3

source_name: chicken forelimb bud FGF2 3hrs


title: hs_ccm_rep5


title: hs_ccm_rep4


title: chicken forelimb bud_FGF2_3hr_rep2


title: hs_ccm_rep1


title: chicken forelimb bud_PBS_3hr_rep3


title: hs_ccm_rep3


title: Amphetamine Hyperthermic #7 [H78778/FG204_L8.LB14]

city: Jefferson

first: John

middle: Francis

last: Bowyer

state: AR

address: 3900 NCTR Drive

department: Neurotoxicology

institute: National Center for Toxicological Research FDA

data_processing:
basic fastq.gs read files were initially trimmed/ processed for alignment using fastq-mcf.Any read that has a base at ≥ 95% frequency of the entire sequence is removed. Any read with more than 4 Ns within its sequence is removed (filtered). N’s at either end of reads are clipped.  Reads with an average Q score below 25 is removed. Nucleotide stretches with a quality score below 7 at the end of reads are clipped.  Sequence corresponding to Illumina sequencing adapters or other library preparation oligos are clipped. If the read resulting from steps 4 or 5 is shorter than 13 nt in length, it is removed.
After trimming reads are aligned with quality control sequences from ribosomal RNA or spiked RNA to enable clipping
Phase 1 - mature miRNA alignment was the performed on the clipped sequence reads less than 26 nt using Bowtie 0.12.97 which produces a SAM format file and miRBase definition
Phase 2 - in this second alignment, immature/ haripin miRNAs to other clipped reads that are > 26nt in length were aligned again with  Bowtie and miRBase
Phase 3 - in the last alignmen, reads not alignedi in phase 1 or 2 were aligned using the Ensamble ncRNA database these alignment reads are designated as noncoding RNA alignments.
Supplementary_files_format_and_content: There are three processed data files - matrix with miRNA annotated counts in text file format is "miRNA_counts_norm.annotated_matrix.txt"; matrix with haripin RNA annotated counts in text file format is "hairpin_counts_norm.annotated_matrix.txt"; and matrix with ncRNA annotated counts in text file format is "ncRNA_counts_norm.annotated_matrix.txt"

source_name: AMPH hot ID 204

growth_protocol: Animals used in these experiments were Charles River male Sprague-Dawley. They were given access to water and food ad lib and kept on a 12 hour light cycle 6:00am to 6:00pm until testing

extract_protocol:
Total RNA was extracted using Tri Reagent (Molecular Research Center Inc., Cincinnati, OH) (Chomczynski and Mackey, 1995) with modifications similar to those previously described (Bowyer et al., 2007).
miRNA sequencing was performed by EA Quintiles - Briefly, sequencing libraries were created using an adaptation of the Illumina TruSeq Small RNA method.  Briefly, a single stranded adenylated DNA adapters were added to the 3’ hydroxyl group of the sample RNAs using T4 RNA Ligase 2, deletion mutant enzyme.  This enzyme prevents ligation of the adapter to the 5’ end due to the absence of ATP.   5’ adapters were then added to the 5’ phosphate using T4 RNA Ligase in the presence of ATP.  Following adapter ligation, single stranded cDNA was created by a reverse transcription reaction.
The cDNA is then PCR amplified for 14 cycles using a common sequencing primer and an indexed primer that is unique to each sample.  The cDNA libraries were then size selected using the Pippin HT to ensure sequencing of small RNAs from 15-35 base pairs. The resulting libraries were quantified, normalized and pooled in preparation for sequencing. Ten million reads per sample were generated from the libraries .

treatment_protocol: Whole blood was obtained via cardiac puncture at 4:30 to 5:30 pm, and immediately frozen, from adult 85 to 90 day old male Sprague-Dawley rats at 3 hr after four sequential injections of saline, saline in a cool  environmental, saline in a hot envrionment (39°C), amphetamine or amphetamine in a cool environment

value: Sprague-Dawley

value: adult

tag: Sex

value: male

tag: tissue

value: whole blood


title: THP1_INPUT [NM-L8_S8_L001_R1_001]

city: Boston

first: Trevor

last: Siggers

address: 24 Cummington Mall

department: Department of Biology

institute: Boston University

description: Input DNA (3 biological replicates)

data_processing:
fastq files for HiSeq 4000 reads were generated using the Illumina pipeline (1.8). NextSeq 500 data (IRF8 and associated Input) fastq files were generated and pre-processed by Illumina BaseSpace
reads not demonstrating a minimal quality level (at least 60% of the read must have PHRED score of at least 20) were filtered prior to mapping using the fastx-toolkit (fastq_quality_filter -q 20 -p 60)
filtered reads were mapped to the reference genome (hg19) using bowtie2 (default parameters, --local)
mapped reads were filtered for high-quality, uniquely mappable reads using samtools (samtools view -b -F 1548 -q 30)
peaks were called on both biological replicates separately using MACS2 with relaxed parameters (-p 1e-3)
transcription factor peaks (PU.1, C/EBPa, IRF8) were then filtered for stringent reproducibility across biological replicates (IDR < 0.01) using IDR and used to design the nextPBM microarray. Peaks shared across the punctate histone mark (H3K4me1 and H3K27ac) replicates were also used
Genome_build: hg19
Supplementary_files_format_and_content: bigWig, narrowPeak (relaxed parameters from MACS2), bed (cross-replicate IDR format)

source_name: THP-1 cell line

growth_protocol: THP-1 cells were purchased from ATCC (cat # TIB-202) and cultured in RPMI 1640 media with 10% FBS supplemented by 50 unit/ml Penicillin and 50ug/ml Streptomycin

extract_protocol:
Soluble-chromatin was prepared from 40,000,000 THP-1 cells according to previously described protocols with some modifications (outlined below). Briefly, cells were crosslinked with 1% formaldehyde (final concentration) (Fisher Scientific, cat # F79-500) for 10 minutes at room temperature with gentle shaking. Crosslinking was stopped by adding 125 mM final concentration of glycine solution in PBS . Fixed cells were pelleted at 800xg for 5 minutes at 4˚Ϲ and washed twice with 10 ml of cold PBS in a 15 ml conical tube and pelleted at 800xg for 5 minutes at 4˚Ϲ.  Washed cell pellet was re-suspended in 10 ml of Lysis Buffer 133, nutated for 10 minutes at 4˚Ϲ,  and pelleted at 2000xg for 5 minutes at 4˚Ϲ. The same procedure was repeated with Lysis Buffer 233 at room temperature followed by pelleting at 2000xg for 5 minutes at 4˚Ϲ. To release nuclei from hard-to-disrupt THP-1 membranes, cells were re-suspended in 10 ml of Lysis Buffer 333 and were shaken vigorously (225 rpm) at room temperature for 30 minutes. Cells then were passed through an 18-gauge needle (VWR, cat # BD305195) for 25 times using a 10ml syringe. Nuclei were pelleted at 3000xg for 20 minutes at 4˚Ϲ and re-suspended in 500 μl of Lysis Buffer 3 and then transferred into a 1.5 ml microfuge tube placed in Benchtop 1.5 ml Tube Cooler (Active Motif, cat # 53076).  The nuclei were sonicated using Active Motif Q120AM sonicator with a 3.2 mm Probe (Active motif cat # 53053) at 25% amplitude for 15 minutes with 20 seconds ON and 30 seconds OFF cycles (45 cycles total). Cell-debris was pelleted at 21,000xg for 30 minutes at 4˚Ϲ. 50 μl of the combined soluble-chromatin was saved to be used as the input DNA upon reverse-crosslinking. For immunoprecipitation, 500 μl of the soluble chromatin was mixed with 30 μg of either PU.1, C/EBPα, H3K4me or H3K27ac antibodies (60 μg of IRF8 antibody was mixed with 1 ml of the soluble chromatin), and a tubes were rotated at 25 rpm for one hour at 4˚Ϲ using HulaMixer (ThermoFisher Scientific cat # 15920). 125 μl of the protein A Dynabead slurry (ThermoFisher Scientific cat # 10001D) per each rabbit antibody (PU.1. C/EBPα, H3K4me or H3K27ac), and 250 μl of the protein G Dynabead slurry (ThermoFisher Scientific cat # 10003D) for the goat-IRF8 antibody, were transferred into 1.5 ml microfuges and placed on DynaMag magnet (ThermoFisher Scientific, cat # 12321D) until all beads collected on the side of tubes. The solution was gently aspirated off from each tube and then the rack was removed from the magnet and beads were re-suspended in 1 ml of the Lysis Buffer 3 with several gentle inversions and then the rack was put back on the magnet and the buffer was aspirated off after all beads were collected on the side of the tube. Each bead then re-suspended in 50 μl of Lysis Buffer 3 and were added to the corresponding tube and returned to HulaMixer to rotate at 35 rpm for over-night at 4˚Ϲ. Dynabeads were collected with placing the tubes in the magnet. Beads were washed for 6 times with 1 ml of the Lysis Buffer 3 and two times with 1 ml of the Wash Buffer (RIPA). All ChIP samples along with the 50 μl of the soluble-chromatin were reverse-crosslinked by adding 200 μl of the Elution buffer and 3 μl of 20 mg/ml Proteinase K (ThermoFisher Scientific, cat # AM2546) and incubated at 65˚Ϲ for over-night. Beads were collected by magnets and the solutions were transferred into a new 1.5 microfuges containing 1 μl of 10 mg/ml RNase A (ThermoFisher Scientific, cat # EN0531) and left at room temperature for an hour. The ChIP and input DNA were purified using QIAquick PCR Purification Kit (QIAGEN, cat # 28104) and eluted in 50 μl of 50˚Ϲ Nuclease-Free Water (Thermo Fisher Scientific, AM9932). The concentration and size distribution of the ChIP-DNA samples were defined using Agilent 2100 Bioanalyser
DNA libraries were prepared using NEBNext Ultr II DNA Library Prep kit (NEB, E7645S) following the provider’s instruction manual. Amplified libraries were Bioanalyzed again to check the size selection efficiency and to define the concentrations of libraries before preparing the library pool involving the same molarity of each library

treatment_protocol: untreated

value: untreated monocytes

tag: chip antibody

tag: cell line


title: Amphetamine Hyperthermic #6 [H78778/FG199_L8.LB11]

source_name: AMPH hot ID 199

tag: strain

tag: age


title: THP1_INPUT [NM-L16_S16_L002_R1_001]

description: Input DNA (3 biological replicates)


title: THP1_H3K27AC [NM-L14_S14_L002_R1_001]

description:
H3K27ac (2 biological replicates)
MACS2_IDR_H3K27AC.txt

value: H3K27ac (Abcam ab177178)


title: chicken forelimb bud_PBS_3hr_rep1


title: glaucoma aqeous humor (AH) lncRNAs 7

city: Changsha

first: li

middle: li

last: xie

address: No.139 Remin Middle Road

department: Ophthalmology

institute: the Second Xiangya Hospital, Central South University

description: lncRNA expression data from glaucoma aqueous humor

hyb_protocol: The labeled cRNAs were hybridized onto the Arraystar Human lncRNA Arrays, and incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: After washing, slides were scanned with the Agilent Scanner G2505C.

data_processing: Data was extracted using Agilent Feature Extraction software.A series of data processing including quantile normalization were performed using the R software package. The lncRNAs that at least 5 out of 10 samples have flags in P or M (“All Targets Value”) were retained for further differential analyses. Differentially expressed lncRNAs with statistical significance between the two groups were identified through Volcano Plot filtering.

source_name: glaucoma aqeous humor (AH)

label_protocol: Total RNA from each sample was amplified and transcribed into fluorescent cRNA utilizing ramdom primer according to Arraystar Super RNA Labeling protocol (Arraystar, Inc.)

growth_protocol: glaucoma and matched age-related cataract aqeous humor

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

treatment_protocol: aqeous humor from surgury were collected and preserved at -80 ℃.

value: glaucoma aqeous humor (AH)

value: 60 years


title: glaucoma aqeous humor (AH) lncRNAs 6

value: 65 years


title: glaucoma aqeous humor (AH) lncRNAs 3

value: 66 years


title: glaucoma aqeous humor (AH) lncRNAs 2

value: 61 years


title: glaucoma aqeous humor (AH) lncRNAs 4


title: THP1_H3K4ME1 [NM-L13_S13_L002_R1_001]

description:
H3K4me1 (2 biological replicates)
MACS2_IDR_H3K4ME1.txt

value: H3K4me1 (Abcam ab8895)


title: glaucoma aqeous humor (AH) lncRNAs 1

description: lncRNA expression data from age-related cataract aqueous humor

value: 59 years


title: glaucoma aqeous humor (AH) lncRNAs 9

value: 67 years


title: glaucoma aqeous humor (AH) lncRNAs 8

value: 68 years


title: glaucoma aqeous humor (AH) lncRNAs 5

value: female


title: Amphetamine Hyperthermic #5 [H78778/FG198_L8.LB10]

source_name: AMPH hot ID 198


title: glaucoma aqeous humor (AH) lncRNAs 10


title: chicken forelimb bud_FGF2_3hr_rep1


title: THP1_H3K4ME1 [NM-L5_S5_L001_R1_001]


title: Amphetamine Hyperthermic #4 [H78778/FG197_L8.LB9]

source_name: AMPH hot ID 197


title: THP1_H3K27AC [NM-L6_S6_L001_R1_001]


title: THP1_IRF8 [NM-L11_S11_L002_R1_001]

description:
IRF8 (2 biological replicates)
MACS2_IDR_IRF8.txt

value: IRF8 (Santa Cruz sc-6058x)


title: Amphetamine Hyperthermic #3 [H78778/FG189_L8.LB6]

source_name: AMPH hot ID 189

value: Sprague-Dawley


title: Amphetamine Hyperthermic #2 [H78778/FG188_L8.LB5]

source_name: AMPH hot ID 188

value: adult


title: Amphetamine Hyperthermic #1 [H78778/FG184_L8.LB3]

source_name: AMPH hot ID 184

value: male


title: THP1_CEBPA [NM-L2_S2_L001_R1_001]

description:
C/EBPa (2 biological replicates)
MACS2_IDR_CEBPA.txt

value: C/EBPa (Santa Cruz sc-61x)


title: age-related cataract aqeous humor (AH) lncRNAs 10

source_name: age-related cataract aqeous humor (AH)

value: age-related cataract aqeous humor (AH)


title: age-related cataract aqeous humor (AH) lncRNAs 8


title: age-related cataract aqeous humor (AH) lncRNAs 9


title: age-related cataract aqeous humor (AH) lncRNAs 6


title: THP1_PU1 [NM-L9_S9_L002_R1_001]

description:
PU.1 (2 biological replicates)
MACS2_IDR_PU1.txt

value: untreated monocytes

value: PU.1 (Santa Cruz sc-352x)


title: Saline Control #6 [H78778/FG200_L8.LB12]

source_name: Control ID FG200

value: whole blood


title: age-related cataract aqeous humor (AH) lncRNAs 7


title: THP1_CEBPA [NM-L10_S10_L002_R1_001]


title: Saline Control #7 [H78778/FG202_L8.LB13]

source_name: Control ID FG202


title: hPSCs_H3K4me3Q5ser IP 4

source_name: Human IPSCs

tag: cell/region

value: hPSCs

value: H3K4me3Q5ser (Millipore 4491a; Lot#RA1608107)

tag: differentiation status

value: Undifferentiated PSCs


title: 5-HT Neurons_H3K4me3Q5ser IP 1

source_name: 5-HT Neurons

value: hPSC derived 5-HT neurons

value: Differentiated 5-HT neurons


title: hPSCs_H3K4me3Q5ser IP 2


title: Saline Control #4 [H78778/FG195_L8.LB7]

source_name: Control ID FG195


title: Saline Control #2 [H78778/FG181_L8.LB2]

source_name: Control ID FG181


title: hPSCs_H3K4me3Q5ser IP 3


title: Saline Control #1 [H78778/FG180_L8.LB1]

source_name: Control ID FG180


title: PBM_NE_PHOS_PU1

type: protein

hyb_protocol: Microarray DNA double stranding and basic PBM protocols are as previously described (Berger & Bulyk, 2009)

scan_protocol: Microarrays were scanned with a GenePix 4400A scanner and fluorescence was quantified using GenePix Pro 7.2

data_processing:
Exported data were normalized using MicroArray LINEar Regression. The platforms used comprise essentially the same DNA sequences so the results across experiments from the 085624 and 085106 platforms were integrated together (using a common sequence ID) to facilitate interpretation by the community.
Processed data corresponds to replicate probe-averaged z-scores normalized against a distribution of background probes

label: alexa fluor conjugated antibody

molecule: protein

source_name: THP-1 cell line nuclear extract (pan-phosphatase-treated)

label_protocol: Arrays were incubated with the protein sample (IVT protein or THP-1 nuclear lysate) for one hour in a binding reaction buffer containing: 2% milk (final concentration); 20 mM Hepes buffer, pH 7.9; 100 mM NaCl; 1 mM DTT; 0.2 mg/mL BSA; 0.02% Triton X-100; and 0.4 mg/mL salmon testes DNA (Sigma D7656). After protein incubation, microarrays were washed with PBS containing 0.5% Tween-20 (3 min), then in PBS containing 0.01% Triton X-100 (2 min), followed by a brief PBS rinse. Microarrays were then incubated with 10 μg/mL of primary antibody in 2% milk in PBS (20 min). After primary antibody incubtion, microarrays were washed with PBS containing 0.5% Tween-20 (3 min), then in PBS containing 0.01% Triton X-100 (2 min), followed by a brief PBS rinse. Microarrays were then incubated with 7.5 μg/mL of alexa488-conjugated secondary antibody in 2% milk in PBS (20 min). Excess antibody was removed by washing with PBS containing 0.05% Tween-20 (3 min), then PBS (2 min).

growth_protocol: THP-1 cells were purchased from ATCC (cat # TIB-202) and cultured in RPMI 1640 media with 10% FBS supplemented by 50 unit/ml Penicillin and 50 μg /ml Streptomycin. HEK-293T cells for Lentivirus packaging (gift from Thomas Gilmore, Boston University) were cultured in DMEM media with 10% FBS supplemented by 50 unit/ml Penicillin and 50 μg /ml Streptomycin. In vitro transcription/translation (IVT) samples of PU.1 (full-length, untagged) were generated using 1-Step Human Coupled IVT Kit – DNA (Thermo Fisher Scientific Cat# 88881) following the provider’s instructions. Protein expression was confirmed by western analysis.

extract_protocol: 5 × 10^6 THP-1 cells pelleted at 500xg for 5 minutes at 4˚Ϲ in a 15 ml conical tube. The pellet resuspended and washed twice with PBS. Cell pellet was resuspended in 1 ml of ‘low-salt buffer’ (10 mM HEPES (pH 7.9), 1.5 mM MgCl2, 10 mM KCl plus 1 μl protease inhibitor cocktail (Sigma-Aldrich, cat # P8340) and incubated for 10 minutes on ice. 50 μl of 5% IGEPAL (Sigma-Aldrich, cat # I8896) was added to the cell suspension followed by a harsh vortex for 10 seconds. Released nuclei were immediately pelleted at 750xg for 5 minutes at 4˚Ϲ. The supernatant was transferred to another tube and saved as the ‘cytosolic fraction’. To wash the remaining cytosolic proteins from the surface of the nuclear pellet, 100 μl of the low-salt buffer was gently pipetted onto the side of the tube and allowed to wash the pellet, but making sure to not disrupt the pellet.   This wash was then gently transferred to the cytosolic fraction without dislodging the nuclear pellet. 200 μl of ‘high-salt buffer’ (20 mM HEPES (pH 7.9), 25% Glycerol, 1.5 mM MgCl2, 0.2 mM EDTA, 420 mM NaCl plus 1 μl protease inhibitor cocktail) was pipetted on the pellet and the tube went through a vigorous vortex for 30 seconds followed by nutation at 4˚Ϲ for 1 hour. The nuclei were pelleted at 4˚Ϲ for 20 minutes at 21,000xg. The supernatant was transferred into another tube as the nuclear soluble protein fraction. Final nuclear extract samples used in nextPBM assays were 9.6 mg/ml.

treatment_protocol: See individual sample descriptions

value: pan-phosphatase

tag: target protein

tag: primary antibody

tag: primary antibody concentration

tag: secondary antibody

value: Alexa 647-conjugated anti-rabbit (A32733)

tag: secondary antibody concentration


title: 5-HT Neurons_H3K4me3Q5ser IP 4


title: PBM_NE_IRF8ID_PU1

source_name: THP-1 cell line nuclear extract (IRF8 depleted)

value: IRF8 immune-depletion


title: PBM_NE_DIL_QUARTER_PU1

source_name: THP-1 cell line nuclear extract (diluted 1/4)

value: untreated (diluted 1/4)


title: Saline Control #3 [H78778/FG185_L8.LB4]

source_name: Control ID FG185

value: Sprague-Dawley


title: hPSCs_H3K4me3Q5ser IP 1


title: age-related cataract aqeous humor (AH) lncRNAs 4

tag: gender

value: female

value: 66 years


title: age-related cataract aqeous humor (AH) lncRNAs 3

value: 65 years


title: age-related cataract aqeous humor (AH) lncRNAs 5

value: age-related cataract aqeous humor (AH)


title: Saline Control #5 [H78778/FG196_L8.LB8]

source_name: Control ID FG196

value: adult

value: male


title: PBM_NE_DIL_EIGHTH_PU1

source_name: THP-1 cell line nuclear extract (diluted 1/8)

value: untreated (diluted 1/8)


title: age-related cataract aqeous humor (AH) lncRNAs 1

value: 61 years


title: PBM_NE_DIL_HALF_PU1

source_name: THP-1 cell line nuclear extract (diluted 1/2)

value: untreated (diluted 1/2)


title: 5-HT Neurons_H3K4me3Q5ser IP 3

value: H3K4me3Q5ser (Millipore 4491a; Lot#RA1608107)


title: wtBT14IP

city: Martinsried

first: Christoph

last: Ziegenhain

state: Bavaria

address: Großhaderner Str. 2

department: Department Biology II

country: Germany

institute: Ludwig-Maximilians University Munich

data_processing:
Samples were demultiplexed using deML (Renaud et al., 2015)
Reads were mapped with ngm (Sedlazeck et al., 2013)
HTseq was used to count reads overlapping genes unambigiously (Anders et al., 2015)
Genome_build: mm10
Supplementary_files_format_and_content: Gene/Sample-wise counts

source_name: wild type_cortex_IP

extract_protocol:
Cell type–specific RNA purification by translating ribosome affinity purification (BacTRAP):
Mice (3 months old) were decapitated and fresh brains immediately processed according to Heiman et al. Cortical hemispheres from one animal were dissected from diencephalon and basal ganglia structures, hippocampus and a tip of a rostral cortex, and processed in 2mL of tissue-lysis buffer. 30µl of the supernatant (S20) was collected as an input sample immediately before immunopurification (IP). Affinity matrix was prepared with Dynabeads Protein G (Life Technologies, Novex) (50µl per sample) and anti-GFP rabbit serum (Life Technologies, Molecular Probes) (10µl per sample), and beads were washed in a low-salt buffer.
Library preparation for RNA sequencing was performed using the Smart-seq2 protocol (Picelli et al., 2014)

tag: strain background

tag: genotype/variation

value: wild type

value: 3 months

value: cortex

tag: bactrap sample

value: IP


title: PBM_NE_IRF8ID_IRF8

tag: treatment

value: IRF8 immune-depletion

value: Alexa 488-conjugated anti-goat (A11055)


title: 5-HT Neurons_Input 1

data_processing:
Illumina Casava1.7 software used for basecalling.
ChIPseq: For H3K4me3, H3K4me3Q5ser and Taf3 ChIP-seq in RN46A-B14 cells, raw sequencing reads were aligned to the rat genome (rn6) using default settings of Bowtiev2.2.0. Only uniquely mapped reads were retained. Alignments were filtered using SAMtoolsv0.1.19 to remove duplicated reads. Peak-calling–normalized to respective inputs–was performed using MACSv2.1.150 with default settings and filtered for FDR < 0.05 and fold change > 1.2; the window size was set as 300 bp.  Raw sequencing reads from mouse brains (H3K4me3 vs. H3K4me3Q5ser) were aligned to the mouse genome (mm10) using default settings of HISATv0.1.6b. Only uniquely mapped reads were retained. Alignments were filtered using SAMtoolsv0.1.19 to remove duplicate reads, and peak-calling–normalized to respective inputs–was performed using MACSv2.1.1 with default settings and filtered for FDR < 0.05 and fold change > 1.2. Raw sequencing reads from human PSCs vs. ¬5-HT neurons (H3K4me3Q5ser) were aligned to the human genome (hg38) using default settings of HISAT2v2.1.0. Again, only uniquely mapped reads were retained. Alignments were filtered using SAMtoolsv1.8 to remove duplicated reads, and peak-calling–normalized to respective inputs–was performed using MACSv2.1.1 with default settings and filtered for FDR < 0.05 and fold change > 1.2.
RNAseq: Raw sequencing reads from RN46A-B14 cells were mapped to rn6 using TopHat2v2.1.051. Counts of reads mapping to genes were obtained using HTSeq-count against Ensembl v81 annotation. Differential expression analysis was done using the DESeq2 package52 (v1.6.3) at an FDR cutoff of 0.05. Raw RNA-seq reads obtained from mouse brains were mapped to mm10 using HISAT v0.1.6b. StringTie v1.2.1 was used to obtain gene-level FPKM values against Ensembl v84. Raw RNA-seq reads obtained from human cells were mapped to the human genome (hg38) using HISAT2v2.1.0. Counts of reads mapping to genes were obtained using HTSeq-count against Ensembl v90 annotation. Differential expression analysis was done using the DESeq2 package (v1.6.3), again with a FDR<0.05 cutoff.
Genome_build: rn6, mm10, hg38
Supplementary_files_format_and_content: Peaks called using MACS and annotated using region_analysis in tab delimited text file. Counts in tab delimited text files generated using HTSeq-count against Ensembl v81 annotation; Tab delimited text files include gene level FPKM values for each sample obtained using StringTiev1.2.1 against Ensembl v84 annotation

value: hPSC derived 5-HT neurons

value: Input

value: Differentiated 5-HT neurons


title: hPSCs_Input 4

source_name: hPSCs

value: hPSCs

value: Undifferentiated PSCs


title: age-related cataract aqeous humor (AH) lncRNAs 2

source_name: age-related cataract aqeous humor (AH)

tag: tissue

value: age-related cataract aqeous humor (AH)

value: female

value: 59 years


title: hetBT14IXX

value: heterozygous Foxp2 deletion


title: wtBT13IN

source_name: wild type_cortex_Input


title: wtBT14IN


title: PBM_NE_PHOS_IRF8

value: pan-phosphatase


title: 5-HT Neurons_H3K4me3Q5ser IP 2

tag: chip antibody

value: H3K4me3Q5ser (Millipore 4491a; Lot#RA1608107)


title: hPSCs_Input 1


title: hPSCs_Input 3


title: hPSCs_Input 2


title: hetBT13IN


title: PBM_NE_IRF8KO_PU1

source_name: THP-1 IRF8 (-/-) line nuclear extract

value: untreated

value: Alexa 647-conjugated anti-rabbit (A32733)


title: hetBT13IP

source_name: heterozygous Foxp2 deletion_cortex_IP

value: 3 months

value: cortex


title: PBM_NE_IRF8KO_IRF8


title: 5-HT Neurons_Input 3

source_name: 5-HT Neurons


title: 5-HT Neurons_Input 4


title: het786IN


title: PBM_NE_DIL_HALF_IRF8

value: untreated (diluted 1/2)


title: PBM_NE_DIL_QUARTER_IRF8

value: untreated (diluted 1/4)

value: Alexa 488-conjugated anti-goat (A11055)


title: 5-HT Neurons_Input 2

value: hPSC derived 5-HT neurons

value: Input


title: PBM_NE_UT_PU1_REP2

source_name: THP-1 cell line nuclear extract (second replicate)


title: PBM_NE_DIL_EIGHTH_IRF8

value: untreated (diluted 1/8)


title: Xorna

city: Austin

first: Rebecca

middle: L

last: Young

state: TX

address: 2415 Speedway

department: Integrative Biology

institute: University of Texas at Austin

data_processing:
An aliquot of total RNA was then run on a Bioanalyzer Nano RNA chip (Agilent) to confirm RNA integrity score was above 7 for each sample
Trimmomatic was used to filter and trim reads using the following parameters: -phred33 ILLUMINACLIPadapters.fa:3:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36
A transcriptome was assembled de novo using Trinity from the reads of each sample/species
de novo assembled contigs were annotated to reference genomes using blastx
Reads were mapped the the annotated de novo assembly using bwa mem
Raw reads were calculated as the sum of transcript counts using SAMtools and Reads Per Million of library size (RPM) were calculated as the reads mapping to de novo assembled contigs  of annotated as the same gene and normalized by the size the size of the library.
Supplementary_files_format_and_content: fasta files including the de novo assembled contigs annotated using closely related reference genomes for each Sample
Supplementary_files_format_and_content: csv files including raw reads and RPMs for each sample

organism: Xenotilapia ornatipinnis

source_name: fore- and mid-brain

extract_protocol:
fore- and mid-brains were rapidly dissected and flash frozen on dry ice or preserved in RNAlater and stored at -80C until RNA was extracted using Trizol
RNA libraries were prepared for sequencing using the NEB small RNA kit (cat #E6160L or #E6160S) Illumina protocols by the University of Texas at Austin Genome Sequencing and Analysis Facility (GSAF)

value: fore- and mid-brain

tag: Sex

value: male

tag: state

value: reproductive

tag: number of individuals pooled

tag: annotation genome


title: Xspil

organism: Xenotilapia spiloptera


title: het786IP

tag: age

value: IP


title: wt736IN

value: wild type


title: ce_ccm3_control_rep2

first: Yan

last: Li

address: 900 East 57th St.

institute: The University of Chicago

data_processing:
Raw sequencing QC assessement: FastQC v0.115
Alignment: STAR v2.5.3a
Post alignement QC assessment: RSeQC and Picard tools v2.9.0
Gene transcripts assembly: featureCounts
Differentially expressed genes analysis: DESeq2
Genome_build: UCSC human genome model: hg19; GENCODE mouse genome model: GRCm38 V13 (release_M13); ENSEMBLE worm genome model: c. elegans WBcel235 V87 (release-87)
Supplementary_files_format_and_content: tab-delimited text files include gene features raw counts values summarized by featureCouts for each Sample.

organism: Caenorhabditis elegans

source_name: entire organism

extract_protocol:
For human samples, RNAs was extracted using an RNA isolation kit (RNeasy® Micro Kit, Qiagen, Hilden, Germany). For mouse and C. elegans samples, RNA was extracted using the TRIzol protocol (ThermoFisher, Waltman, MA).
RNA libraries were prepared for sequencing using commercially low-input strand specific RNA-Seq kits (Clontech, California, USA) for human specimens and TruSeq Stranded mRNA Sample Prep Kit (Illumina, San Diego, CA) for mouse and C. elegans samples

tag: genotype

value: Pdcd10 wild type control (N2)

value: 24 hours past the L4 state

tag: cell type

value: entire organism


title: Mpen

organism: Microtus pennsylvanicus


title: Op

organism: Oophaga pumilio


title: Ri

organism: Ranitomeya imitator


title: wt785IP


title: ce_ccm3_control_rep3


title: ce_ccm3_control_rep1


title: sample A, controlled hypertensive 12a

source_name: fasting blood

value: peripheral blood mononuclear cells

value: female

tag: race

value: white

tag: height

tag: weight

tag: sistolic blood pressure in a sample

tag: sistolic blood pressure in b sample

tag: diastolic blood pressure in a sample

tag: diastolic blood pressure in b sample


title: wt736IP

tag: strain background

tag: genotype/variation

value: 3 months

value: cortex

tag: bactrap sample


title: wt734IN

tag: tissue


title: ce_ccm3_rep3

value: Pdcd10 null (ccm3/pdcd10(tm2806) knock-out )


title: PBM_NE_UT_PU1

source_name: THP-1 cell line nuclear extract

tag: treatment

value: untreated

tag: target protein

tag: primary antibody

tag: primary antibody concentration

tag: secondary antibody

value: Alexa 647-conjugated anti-rabbit (A32733)

tag: secondary antibody concentration


title: PBM_NE_UT_FLI1


title: wt734IP

tag: age


title: PBM_IVT_PU1

source_name: in vitro transcribed/translated PU.1


title: het730IXX

value: heterozygous Foxp2 deletion

value: Input


title: PBM_NE_UT_IRF8

value: Alexa 488-conjugated anti-goat (A11055)


title: ce_ccm3_rep1

tag: genotype

tag: cell type


title: wt785IN


title: ce_krit1_control_rep3

value: Kri-1 wild type control (N2)


title: het729IN


title: Differentiated_Taf3 IP 2

first: Aarthi

last: Ramakrishnan

address: 1425 Madison Avenue

institute: Icahn School of Medicine at Mount Sinai

source_name: Serotonergic tissue culture cells

extract_protocol:
Cell pellets (>10 x 10^6/n) and brain tissues were crosslinked and quenched. Samples were washed thoroughly before being subjected to lysis and sonication. Samples were then incubated with specific antibodies (7.5 μg/sample) bound to M-280 Dynabeads on a rotator at 4°C overnight. The following day, immunoprecipitates were washed, eluted and reverse crosslinked. Following RNA and protein digestion, DNA fragments were purified using a Qiagen PCR purification kit.
RNA and ChIP libraries were prepared for sequencing using standard Illumina protocols

tag: cell/region

value: RN46A-B14 cells

tag: chip antibody

tag: differentiation status

value: Differentiated


title: Differentiated_Taf3 IP 1


title: ce_krit1_control_rep2


title: Undifferentiated_Taf3 IP 3

value: Undifferentiated


title: Dp

organism: Prunella modularis

value: fore- and mid-brain

tag: Sex

value: male

tag: state

value: reproductive

tag: number of individuals pooled

tag: annotation genome


title: ce_krit1_rep3

value: Kri-1 null (ccm1/kri-1(ok1251) knock out)

value: 24 hours past the L4 state

value: entire organism


title: CONTROL

city: Giessen

first: Daniel

last: Amsel

address: Aulweg 128

institute: Justus Liebig University

data_processing:
mining of novel miRNAs using miRDeep2 resulting in miRDeep2_output.csv
target prediction using microPIECE resulting in microPIECE_target_prediction.csv
calculating ReadsPerMillion from alignment file Sample1_aln.sam, Sample2_aln.sam, Sample3_aln.sam
Genome_build: GCA_002589825.1
Supplementary_files_format_and_content: mining file in CSV format contains miRDeep2 output of novel miRNAs; microPIECE output file is a CSV file containing the miRNA target prediction

organism: Galleria mellonella

source_name: mock-infected larvae

extract_protocol:
miRNeasy Mini Kit (Qiagen)
according to manufacturer

tag: infection

value: Mock-injected host

tag: tissue

value: larva


title: Differentiated_Taf3 IP 3


title: het729IP

tag: strain background

tag: genotype/variation

value: 3 months

value: cortex

tag: bactrap sample

value: IP


title: ce_krit1_control_rep1

city: Chicago


title: Undifferentiated_Taf3 IP 2

city: New York


title: As

organism: Anthus spinoletta


title: ABU

source_name: infected larvae

value: host infected with ABU (ABU83972) strain


title: ce_ccm3_rep2

value: Pdcd10 null (ccm3/pdcd10(tm2806) knock-out )


title: Undifferentiated_Taf3 IP 1


title: ce_krit1_rep1


title: UPEC

value: host infected with UPEC (CFT073) strain


title: Pcal

organism: Peromyscus californicus


title: het730IX

value: heterozygous Foxp2 deletion

value: Input


title: Pman

organism: Peromyscus maniculatus


title: gRNA

status: Public on Dec 17 2018

city: La Jolla

first: Dario

last: Meluzzi

address: 9500 Gilman Drive #0648

department: School of Medicine

institute: UC San Diego

description:
Sample name:
31
gRNA = Cas13b gRNA described in: Cox, D. B. T. et al. RNA editing with CRISPR-Cas13. Science 358, 1019 1027 (2017). This gRNA was expressed from a U6 promoter.

data_processing:
Basecalls were performed using Illumina RTA 2.7.7.0, and fastq files were then generated using Illumina bcl2fastq v2.18.0.12. Both tasks were carried out by the UCSD IGM Genomics Center.
RNA-seq read pairs with 100 bases per read mate were aligned to the GRCh38 reference genome using STAR aligner version 2.6.0c (Dobin A et al 2013). The genome index was built using primary assembly annotations from GENCODE release 28 (GRCh38.p12). Default parameters were used to run STAR, except for the following relevant settings: readMapNumber=-1, alignSJoverhangMin=5, alignSJDBoverhangMin=1, alignEndsType=EndToEnd, outFilterMismatchNmax=10, outFilterMultimapNmax=1, outSAMunmapped=None, outSAMmultNmax=1
The reads of the resulting uniquely aligned pairs were sorted by genomic coordinate using samtools sort (Li H. et al 2009). Duplicated read pairs were marked using samtools markdup and were removed from subsequent RNA-editing analysis.
The uniquely aligned reads for each sample were down-sampled using samtools view with option -s. Down-sampling fractions were calculated by dividing the smallest number of uniquely aligned reads among all samples by the number of uniquely aligned reads available for the sample being down-sampled. Down-sampling was not performed on the reads of the control sample. The down-sampled reads where then fed to samtools mpileup, whose output was parsed to extract the counts of each base found at each A-site and T-site in the GRCh38 reference genome. Insertions and deletions were ignored. Reference sites with read coverage less than 10 were discarded. From the remaining reference A- and T-sites a final list was selected by choosing sites common to all samples and with at least one G or C at a reference A- or T-site, respectively, in at least one sample.
For each pair of compared control and treatment samples, and for each reference A- or T- site selected as described above, a Fisher exact test was carried out to calculate the p-value for the change in proportion of G or C bases, respectively, at that site. The p-values for all selected reference sites were adjusted for multiple testing using the Benjamini-Hochberg method.
Genome_build: GRCh38
Supplementary_files_format_and_content: pm_adar_rned_003-mcpspc_bfscr_res-bpr-000.tsv.gz: Proportions of G or C bases counted from aligned reads at each selected reference A- or T-site (row), respectively, for each biological sample (column).
Supplementary_files_format_and_content: pm_adar_rned_003-mcpspc_bfscr_res-pad-000.tsv.gz: Adjusted p-values for comparisons of proportions of G or C bases between each treatment sample and control sample, at each selected reference A- or T-site, respectively.

source_name: HEK 293T

growth_protocol: All HEK 293T cells were grown in Dulbecco’s Modified Eagle Medium supplemented with 10% FBS and 1% Antibiotic-Antimycotic (Thermo Fisher) in an incubator at 37 °C and 5% CO2 atmosphere.

extract_protocol:
Cells were harvested 60 hours post transfection. RNA was extracted using the Qiagen RNeasy mini kit.
RNA-seq libraries were prepared from 300ng of RNA, using the NEBNext Poly(A) mRNA magnetic isolation module and NEBNext Ultra RNA Library Prep Kit for Illumina. Samples were pooled and loaded on an Illumina Hiseq (100bp paired-end run).

treatment_protocol: Cells were transfected with lipofectamine 2000 at 25-30% confluence.

tag: cell line

value: HEK 293T

tag: transfected with

value: gRNA


title: GluR2 adRNA

description:
Sample name:
30

value: GluR2 adRNA


title: 293T TR4

description:
Sample name:
26
technical replicate (i.e., separate lanes of the flow cell, or different sequencing runs) of the same RNA-seq library that was used for sample 0.

value: untransfected control


title: MS2 adRNA

description:
Sample name:
29

value: MS2 adRNA


title: Cas13b-ADAR2 DD (E488Q) - gRNA

description:
Sample name:
24
gRNA = Cas13b gRNA described in: Cox, D. B. T. et al. RNA editing with CRISPR-Cas13. Science 358, 1019 1027 (2017). This gRNA was expressed from a U6 promoter.

value: Cas13b-ADAR2 DD (E488Q) - gRNA


title: ADAR2 (E488Q) - Glu R2adRNA

description:
Sample name:
22

value: ADAR2 (E488Q) - Glu R2adRNA


title: Cas13b-ADAR2 DD (E488Q) + gRNA

description:
Sample name:
25
gRNA = Cas13b gRNA described in: Cox, D. B. T. et al. RNA editing with CRISPR-Cas13. Science 358, 1019 1027 (2017). This gRNA was expressed from a U6 promoter.

value: Cas13b-ADAR2 DD (E488Q) + gRNA