title: lna_cell_jurkat_tcr_original

last: Riemondy

description:
Original single cell RNA-seq library from the 10x genomics 5' end library prep. Jurkat cells were isolated.
lna_cell_jurkattcr_bcs.txt

data_processing:
Data analysis pipeline and custom scripts are provided in a github repository (https://github.com/rnabioco/scrna-subsets). Single cell RNA-Seq libraries were preprocessed to append the read 1 sequence to the paired read 2 read id (append_read_name) followed by quality trimming and poly(A) tail removal from read 2 using cutadapt (v. 1.8.3 -a 'A{{100}}' -O 6 -m 20 -q 10) (Martin 2011). Reads were next aligned with STAR (Dobin et al. 2013) to either the human genome assembly (hg38) for the PBMC experiments or a genome with both human (hg38) and mouse (mm38) sequences for all other experiments. Sequence headers in the human/mouse combined genome were prefixed with either an “H_” or “M_” to designate human or mouse references respectively.  Following alignment, BAM files were processed to extract the cell barcode and UMI sequences into tags (CN and BX) within the BAM file (barcode_tag_bam). The cell barcode was error corrected against a list of cell barcodes, either as known well barcodes (Wafergen experiments), or generated from the original 10x genomics single cell libraries processed with the 10x genomics software cellranger (v. 2.1.1). Cell barcodes within edit distance of 1 of the known barcodes were considered valid cell barcodes and corrected to the known barcode. Alignments not designated as multi-mapping that overlapped distinct exonic features were tagged in the BAM file (subread v. 1.6.0) (Liao et al. 2014). Gencode v25 annotations was used for human data, and a union reference containing Gencode v25 and mouse v11 was used for human/mouse datasets. UMIs per gene were enumerated per cell using umi-tools (v 0.5.3) (Smith et al. 2017) using the directional method to disambiguate similar UMI sequences.
Genome_build: mm38, hg38
Supplementary_files_format_and_content: Text files containing cell barcode sequences, count matrices of UMIs per gene per cell are provided. For the TCR single cell libraries JSON files are provided with detailed annotations for each assembled contig per cell.

source_name: Jurkat cell line

extract_protocol:
Jurkat cells were isolated and resuspended in single cell suspension and captured on the 10x genomics single cell R-seq platform
10x genomics 5' end TCR enrichment single cell RNA-seq kit. Read 1 positions 1-16 contain the 16bp cell barcode, and positions 17-26 contain a 10bp UMI. The remainder of read 1 contains the 5' of the TCR alpha or beta cDNA. Read 2 also contains the cDNA.

tag: sample type

value: Jurkat cell line


title: NY15_input_ChIP_1

status: Public on Sep 04 2018

type: SRA

city: Ann Arbor

first: Mats

last: Ljungman

state: Michigan

address: NCRC, B520 Room 1346 2800 Plymouth Rd.

country: USA

institute: University of Michigan

library_source: genomic

data_processing:
Illumina Casava v1.8.2 was used for basecalling.
Reads were mapped to the reference genome (canonical chromosomes only) using bowtie v.1.1.1 and parameters -n 3 -k 1 -m 1.
Peaks were called using MACS v.1.4.2, using paired "input" samples as control and parameters --bw 300 --keep-dup 1.
BigWig files were generated using deepTools bamCoverage v.2.4.0 and parameters --binSize -normalizeTo1x hs --normalizeUsingRPKM --ignoreForNormalization chrX chrM --ignoreDuplicates --blackListFileName.  Blacklist file contained the ENCODE DAC blacklist regions (https://www.encodeproject.org/annotations/ENCSR636HFF/).
Genome_build: hg19
Supplementary_files_format_and_content: The columns of the ChIP-seq peaks files (generated by MACS) indicate: (1) chromosome; (2) start; (3) end; (4) peak name; (5) peak score
Supplementary_files_format_and_content: ChIP-seq coverage files are in the bigWig format

molecule: genomic DNA

organism: Homo sapiens

growth_protocol: NY8 and NY15 cells were grown in RPMI 1640 media with GlutaMAX-I, 10% FBS, antibiotic-antimycotic, and 100µg/ml gentamicin. Cells were cultured at 37˚C with 5% carbon dioxide.

extract_protocol:
A confluent 15cm culture plate of cells (NY8 or NY15) was used per immunoprecipitation. Cells were fixed with 1% formaldehyde for 10 minutes. Nuclei were collected and chromatin sheared to 1-10 nucleosomes using the SimpleChIP Plus Enzymatic Chromatin IP kit and protocol (Cell Signaling). HNF1A was immunoprecipitated overnight with goat polyclonal antibody C-19 (Santa Cruz) and 60µL magnetic protein G beads. Beads were washed and immunoprecipitated DNA was reverse crosslinked/purified per the SimpleChIP Plus Enzymatic Chromatin kit protocol.
10 to 500 ng of ChIPped DNA was prepared as a standard Illumina library using IntegenX Prep X (was Wafergen now Takara) reagents on the Apollo 324 instrument, where the fragments are end-repaired, A-tailed, and adapter ligated. Then the samples are PCR amplified and pooled. Final libraries were checked for quality and quantity by TapeStation (Agilent, Santa Clara, CA) and qPCR using Kapa’s library quantification kit for Illumina Sequencing platforms (catalog # KK4835) (Kapa Biosystems,Wilmington MA).  They were clustered on the cBot (Illumina) and sequenced on a 50 cycle single end run on a HiSeq 2500 in High Output mode using version 4 reagents according to manufacturer’s protocols.

treatment_protocol: NY8 and NY15 cells were grown to confluency in 15cm cell culture plates prior to ChIP.

tag: cell type

value: pancreatic cancer-derived cells

tag: cell line

tag: chip antibody


title: LK_PRMT5_KO_A

city: Miami

first: Stephen

last: Nimer

state: FL

address: 1120 NW 14th ST

department: Sylvester Comprehensive Cancer Center

institute: University of Miami

library_source: transcriptomic

data_processing:
Base calling using Illumina RTA 2.4.11
Reads mapped to GRCm38/mm10 transcriptome using STAR v2.5.3 and RSEMv1.3.0 with default parameters.
Estimated counts were obtained from RSEM.gene.results
Genome_build: GRCm38
Supplementary_files_format_and_content: Tab-delimited file contains aggragated raw RSEM expected gene level counts for all samples .

molecule: total RNA

organism: Mus musculus

source_name: sorted LK cells from Mx1-cre;PRMT5fl/fl (KO)

extract_protocol:
RNA was harvested using Qiagen Rneasy Plus Micro Kit (Cat# 74034)
RNA-Seq library prep was carried out using the Illumina TruSeq Total Stranded kit following manufacturer’s standard protocol without modification.

tag: genotype/variation

value: PRMT5fl/fl KO

value: sorted LK cells


title: PEGcaucasian: genomic DNA from whole blood of subject Sample3

type: genomic

city: Los Angeles

first: Steve

last: Horvath

state: CA

address: 695 Charles E. Young Drive South, Box 708822

department: Human Genetics

institute: University of California, Los Angeles

description: genomic DNA from Blood

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing:
BeadStudio software v3.2.
Unmethylated and methylated signal intensities and detection p values

label: Cy3 and Cy5

source_name: Whole Blood

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from EDTA tubes using the RecoverEase DNA Isolation Kit.

tag: Sex

value: male

tag: age

tag: ethnicity

value: Caucasian

tag: dnamage

tag: plasmablast

tag: nk

tag: bcell

tag: mono

tag: gran

tag: diseasestatus

value: control

tag: levodopastatus

value: no

tag: levodopaperdayincludingagonists

tag: numberofyearsinschool

tag: smokingstatus

value: never

tag: packyearstotal

tag: familyhistoryofparkinsons


title: PEGcaucasian: genomic DNA from whole blood of subject Sample2

description: genomic DNA from Blood

value: PD

value: yes

value: current


title: PEGcaucasian: genomic DNA from whole blood of subject Sample1

description: genomic DNA from Blood

value: female


title: PEGcaucasian: genomic DNA from whole blood of subject Sample5

description: genomic DNA from Blood


title: lna_gene_jurkat_cd3d_original

city: Aurora

first: Kent

middle: Augustus

state: Colorado

department: Biochemistry and Molecular Genetics

institute: University of Colorado School of Medicine

description:
Original single cell RNA-seq library from the 10x genomics 5' end library prep. Jurkat cells were isolated.
lna_gene_jurkat_bcs.txt

extract_protocol:
Jurkat cells were isolated and resuspended in single cell suspension and captured on the 10x genomics single cell R-seq platform
10x genomics 5' end single cell RNA-seq kit. Read 1 positions 1-16 contain the 16bp cell barcode, and positions 17-26 contain a 10bp UMI. The remainder of read 1 contains the 5' of the cDNA. Read 2 also contains the cDNA.

tag: sample type


title: pcr_wafergen_expt_phosphorothioate

description:
Resampled single cell RNA seq library from the Wafergen iCell 8 platform. Human Breast Cancer xenograft into mice, cells isolated from a primary fatpad tumor, a brain metastasis, a bone metastasis, or the original primary cell line. Cell barcode targeted PCR was used to reamplify selected cells for targeted resequencing. Standard PCR primers supplemented with 5' biotin and 3 phosphorotioate linkages at the 3' end of the primer were used.
pcr_wafergen_expt_bcs.txt

source_name: Human Breast Cancer Xenograft

extract_protocol: Wafergen Illumina libraries at 2 nM concentration were diluted 20 fold and PCR amplified with 1 unit of Phusion and the cell specific primer and Nextera read 2 sequencing primer to specifically amplify the sequences from the selected cells for 14 cycles.   PCR results were confirmed by gel electrophoresis and the remaining sample was purified with Ampure XP beads at a ratio of 1.8x bead/pcr volume. Samples were eluted and added in equal volume to prepared Dynabead M270 streptavidin beads. Beads were incubated for 15 minutes at room temperature with gentle rotation.  Beads were washed 5x in bind and wash buffer and eluted in 20µl of water. 10µl of streptavidin purified input DNA was added to PCR using PEPCRPrimer 1.0 (AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT)  and Nextera N703 (CAAGCAGAAGACGGCATACGAGATttctgcctGTCTCGTGGGCTCGG) for 9 cycles. PCR products were ampure purified, confirmed on the Agilent Tapestation D1000, quantified by the Qubit and submitted for sequencing. Read 1 positions 1-11 contain the 11bp cell barcode, and positions 12-22 contain a 10bp UMI. Read 2 contains the cDNA.

value: Human Breast Cancer Xenograft


title: NY15_HNF1A_ChIP_1

tag: cell type

tag: cell line

tag: chip antibody

value: HNF1A (goat polyclonal C-19 from Santa Cruz Biotechnology)


title: NY8_input_ChIP_2


title: 01-0042

city: Seattle

last: Tapscott

state: WASHINGTON

address: 1100 Fairview N. Ave

department: Human Biology

institute: Fred Hutch Cancer Research Center

data_processing:
The preprocessing of RNA-Seq data started with filtering unqualified reads, followed by trimming Illumina universal adapter using Trimmomatic-0.32.
the preprocessed reads were aligned to genome build hg38 using Tophat-21.0/Bowtie2-2.2.6.
To profile the gene expression, the gene features and annotation were first obtained from GENCODE, version 24.
Gene counts were then estimated by using Bioconductor function GenomicAlignment::summarizeOverlap() with IntersectionStrict mode, which restrict read-counts to those that fall completely within the range of exons.
Genome_build: hg38
Supplementary_files_format_and_content: (1) biopsy.dds.rda is an RDA file storing a DESeqDataSet instance containing sample info, phenotype data, gene futures, gene counts and FPKM. (2) biopsy_FPKM.csv biopsy_genecounts.csv and bopsy_normalized_genegoutns.csv contain FPKM, gene counts and normalized gene counts, respectively.

growth_protocol: Muscle biopsy samples extracted from 34 of the 36 FSHD subjects, and on 9 control quadriceps muscle biopsies from unaffected individuals.

extract_protocol:
Total RNA was extracted from whole cells using NucleoSpin RNA kit (Macherey-Nagel) following the manufacturer's instructions.
RNA-seq libraries were prepared from total RNA using the TruSeq RNA Sample Prep v2 Kit (Illumina, Inc., San Diego, CA, USA) and a Sciclone  NGSx Workstation (PerkinElmer, Waltham, MA, USA).
RNA-seq libraries were pooled (14-plex) and clustered onto two flow cell lanes.

tag: subject status

value: Control

tag: tissue

value: muscle biopsy

tag: batch

value: III


title: NY15_HNF1A_ChIP_2

value: pancreatic cancer-derived cells


title: 01-0043


title: pcr_wafergen_expt_biotinylated

description:
Resampled single cell RNA seq library from the Wafergen iCell 8 platform. Human Breast Cancer xenograft into mice, cells isolated from a primary fatpad tumor, a brain metastasis, a bone metastasis, or the original primary cell line. Cell barcode targeted PCR was used to reamplify selected cells for targeted resequencing. Standard PCR primers supplemented with 5' biotin were used.
pcr_wafergen_expt_bcs.txt


title: NY8_HNF1A_ChIP_2


title: pcr_wafergen_expt_standard

description:
Resampled single cell RNA seq library from the Wafergen iCell 8 platform. Human Breast Cancer xenograft into mice, cells isolated from a primary fatpad tumor, a brain metastasis, a bone metastasis, or the original primary cell line. Cell barcode targeted PCR was used to reamplify selected cells for targeted resequencing. Standard PCR primers were used.
pcr_wafergen_expt_bcs.txt


title: 01-0035

value: Facioscapulohumeral muscular dystrophy (FSHD)

tag: age

tag: gender

tag: inflam

tag: active

tag: stir


title: NY8_input_ChIP_1


title: 01-0030


title: 01-0033


title: Spinal cord 3

city: Bordeaux

first: Alexandre

last: FAVEREAUX

address: 146 rue leo saignat

country: France

institute: CNRS UMR 5297

data_processing:
Sequenced reads were trimmed for adaptor sequence then mapped to rat genome (Rnor6.0 ) using STAR in default parametres with quantifification mode --quantMode GeneCounts
Genome_build: Rn6.0
Supplementary_files_format_and_content: tab-delimited text files include number of reads per gene for each sample

organism: Rattus norvegicus

source_name: Spinal cord

extract_protocol:
From each rat, 5 structures of the central nervous system were dissected : the olfactory bulb, a part of the cortex, the hippocampus, the striatum and the dorsal spinal cord, and immediately placed into a 1,5 mL tube containing 700 uL of TriZol reagent (Qiagen), on ice. Samples were crushed with the Fast Prep 24 instrument (MP Biomedicals). Total RNA was extracted following the manufacturer’s instructions, allowing an isolation of all RNAs including the small RNAs (miRNeasy Micro Kit, Qiagen).
Libraries were synthesized from 1 ug of RNA for each sample, following the manufacturer’s instructions (NEXTflex Illumina Rapid directional mRNA-Seq, BiooScientific).

tag: strain

value: Wistar

value: Spinal cord


title: NY15_HNF1A_sh1_Bru_2

description: molecule: bru-labeled RNA

data_processing:
Library strategy: Bru-seq
Illumina Casava v1.8.2 was used for basecalling.
Reads were mapped to the human ribosomal DNA complete repeating unit (U13369.1) using Bowtie v.0.12.8 and parameters -n 3 -k 1 -m 1.
Reads that did not map to the ribosomal DNA were mapped to the hg19 genome using TopHat v1.4.1 and parameters –min-isoform-fraction 0, --max-multihits 1, --no-closure-search, --no-coverage-search, --bowtie-n, --initial-read-mismatches 3
A coverage determination was then made for every base in the genome using Bedtools v.2.16.2 such that a base covered by one read was recorded as having a coverage of 1/read_length
Reads Per Kilobase per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: hg19
Supplementary_files_format_and_content: The columns of the abundance measurement files indicate: (1) chromosome; (2) start; (3) end; (4) name; (5) score (placeholder); (6) strand; (7) gene span; (8) number of features (introns and exons); (9) sum of feature lengths; (10) read count (sense strand); (11) density (RPK) – count/length; (12) RPKM - count/(length/1E3)/(mapped read count/1E6)

extract_protocol:
Total RNA was isolated by using TRIzol reagent (Invitrogen), and Bru-labeled RNA was isolated from the total RNA by incubation with anti-BrdU antibodies (BD Biosciences) conjugated to magnetic beads (Dynabeads, Goat anti-Mouse IgG; Invitrogen) under gentle agitation at room temperature for 1 h. For more detail, see Paulsen et. al 2013
Bru-labeled RNA was mixed with first strand buffer and random primers and fragmented by heating at 85 ̊C for 10 minutes. The first strand cDNA was then synthesized, in the presence of Actinomycin D, to result in strand specific reads. After purifying the first strand cDNA using AMPure RNAclean beads (Beckman Coulter), the second strand cDNA was synthesized. The resulting cDNA was purified with AMPure XP beads, after which the Illumina TruSeq RNA Sample Prep Kit was used to repair the cDNA ends, adenylate and ligate adaptors to the cDNA. The samples were then run on a 3% agarose gel and size-selected by excising gel slices in the 300bp region. These gel slices were purified using the QIAEX II Gel Extraction Kit (Qiagen) and then the Illumina TruSeq Kit PCR reagents were used to enrich the DNA fragments. After a final purification using AMPure XP beads, the quality and concentration of the DNA libraries were determined using an Agilent Bioanalyzer.

treatment_protocol: Cells were transduced with lentiviruses expressing control (LacZ sh) or HNF1A targeting (sh1 and sh2). After 72 hours cells were treated with puromycin (10µg/mL) for two weeks. Puromycin treatment was withheld approximately three days before Bru-lableing. Cells were grown to approximately 60% confluency in 15cm cell culture plates prior to Bru-labeling.

tag: knockdown

tag: labeling agent

value: Bromouridine (Bru)


title: Spinal cord 2


title: Striatum 3

source_name: Striatum

value: Striatum


title: 01-0029

value: male


title: NY15_LacZ_sh_Bru_2

description: molecule: bru-labeled RNA

value: LacZ


title: 01-0041


title: Striatum 2


title: 01-0027


title: 01-0026


title: 01-0034


title: NY15_HNF1A_sh2_Bru_1

description: molecule: bru-labeled RNA


title: Striatum 1


title: NY8_HNF1A_ChIP_1


title: NY15_HNF1A_sh1_Bru_1

description: molecule: bru-labeled RNA


title: Spinal cord 1


title: 01-0025


title: Hippocampus 3

source_name: Hippocampus

value: Hippocampus


title: NY15_LacZ_sh_Bru_1

description: molecule: bru-labeled RNA


title: NY15_HNF1A_sh2_Bru_2

description: molecule: bru-labeled RNA


title: 01-0024


title: Hippocampus 2


title: NY8_HNF1A_sh1_Bru_2

description: molecule: bru-labeled RNA


title: NY8_HNF1A_sh2_Bru_2

description: molecule: bru-labeled RNA


title: NY8_LacZ_sh_Bru_2

description: molecule: bru-labeled RNA


title: Cortex 3

source_name: Cortex

value: Cortex


title: 01-0022-1


title: Cortex 2


title: 32-0009

value: II


title: NY8_HNF1A_sh2_Bru_1

description: molecule: bru-labeled RNA


title: Patient_13_Varicose

type: RNA

city: Novosibirsk

first: Mariya

middle: Alexandrovna

last: Smetanina

address: 8 Lavrentiev Avenue

country: Russia

institute: Institute of Chemical Biology and Fundamental Medicine SB RAS

description: varicose vein sample (disease condition)

hyb_protocol: Standard Illumina protocol for Direct Hybridization Gene Expression Assay

scan_protocol: Standard Illumina scanning protocol, iScan System, iScan Control Software

data_processing: The data were normalised using quantile normalisation with Illumina GenomeStudio, Gene Expression Module

label: biotin

source_name: large hollow vein

label_protocol: Biotinylated cRNA was prepared using Illumina TotalPrep RNA Amplification kit according to manufacturer’s instructions

extract_protocol: Total RNA was isolated from homogenized veins using TRIzol according to the manufacturer's protocol. Quality control was performed with electrophoresis of RNA in 1% agarose gel, and its quantity was assessed spectrophotometrically.

value: Male

tag: stage of the disease, ceap


title: Patient_27_Control

description: normal vein sample (healthy condition)


title: Cortex 1


title: 32-0008

value: female


title: NY8_HNF1A_sh1_Bru_1

description: molecule: bru-labeled RNA


title: Patient_18_Varicose

value: Female


title: Olfactory bulb 3

source_name: Olfactory bulb

value: Olfactory bulb


title: 32-0007

value: muscle biopsy


title: Patient_26_Varicose


title: Patient_1_Varicose


title: Patient_12_Varicose


title: Patient_3_Varicose


title: Hippocampus 1


title: 01-0023

value: III


title: Patient_13_Control

description: normal vein sample (healthy condition)


title: Patient_3_Control

description: normal vein sample (healthy condition)


title: NY8_LacZ_sh_Bru_1

description: molecule: bru-labeled RNA

value: pancreatic cancer-derived cells


title: 01-0037

value: Facioscapulohumeral muscular dystrophy (FSHD)


title: Patient_27_Varicose


title: Patient_12_Control

description: normal vein sample (healthy condition)


title: Patient_26_Control

description: normal vein sample (healthy condition)


title: Patient_18_Control

description: normal vein sample (healthy condition)


title: Patient_1_Control

description: normal vein sample (healthy condition)


title: Olfactory bulb 2

value: Wistar


title: lna_cell_mousehuman_resampled

description:
Resampled single cell RNA-seq library from the 10x genomics 3' end library prep. A 1:1 mixture of NIH3T3 cells and 293T cells were isolated and a LNA probe was used to hybridize selected cells for targeted resequencing.
lna_cell_mousehuman_bcs.txt

organism:
Homo sapiens
Mus musculus

source_name: 1:1 mix of NIH3T3 cell line and 293T cell line

extract_protocol: 10x Illumina libraries at 2nM concentration were diluted 20 fold and PCR amplified with Truseq Pcr F and R oligo for 14 cycles with 1 unit of Phusion.  PCR results were confirmed by gel electrophoresis and the remaining sample was Ampure XP purified at a ratio of 1.8x bead/pcr volume.  Samples were eluted in 10µl and molarity was determined using a Qubit.  10µl of 100nM library was mixed with 1 µl of 10µM LNA molecule in anneallng buffer (10mM Tris 8.0, 50mM NaCl) and heated to 98˚ for 10 minutes followed by slow cooling to 59˚-64˚ depending on the LNA and held O/N at the annealing temperature.  Annealed DNA was added in equal volume to washed  Dynabead M270 streptavidin beads at the annealing temperature.  Beads were incubated for 15 minutes with gentle shaking.  Beads were washed 5x in bind and wash buffer at the annealing temperature.  Beads were eluted in 20 µl of elution solution (50mM NaCl, .1mM EDTA) heated for 10 minutes at 100˚ and centrifuged briefly to pellet the streptavidin-bound LNA molecules which inhibit PCR, this elution was done 2 times to ensure all the DNA was removed from the LNA.   10µl of streptavidin purified input DNA was added to PCR using Truseq Pcr F and R for 8 cycles.  PCR products were ampure purified, confirmed on the Tapestation D1000, and quantified by the Qubit and submitted for sequencing.  Read 1 positions 1-16 contain the 16bp cell barcode, and positions 17-26 contain a 10bp UMI. Read 2 contains the cDNA.


title: Olfactory bulb 1


title: 01-0036


title: 32-0006

value: I


title: 32-0005


title: lna_gene_jurkat_cd3d_resampled_dna

description:
Resampled single cell RNA-seq library from the 10x genomics 5' end library prep. Jurkat cells were isolated and an DNA probe was used to hybridize CD3D mRNA for targeted resequencing.
lna_gene_jurkat_bcs.txt

extract_protocol: 10x 5' end Illumina libraries at 2nM concentration were diluted 20 fold and PCR amplified with Truseq Pcr F and R oligo for 14 cycles with 1 unit of Phusion.  PCR results were confirmed by gel electrophoresis and the remaining sample was Ampure XP purified at a ratio of 1.8x bead/pcr volume.  Samples were eluted in 10µl and molarity was determined using a Qubit.  10µl of 100nM library was mixed with 1 µl of 10µM LNA molecule in anneallng buffer (10mM Tris 8.0, 50mM NaCl) and heated to 98˚ for 10 minutes followed by slow cooling to 59˚-64˚ depending on the LNA and held O/N at the annealing temperature.  Annealed DNA was added in equal volume to washed  Dynabead M270 streptavidin beads at the annealing temperature.  Beads were incubated for 15 minutes with gentle shaking.  Beads were washed 5x in bind and wash buffer at the annealing temperature.  Beads were eluted in 20 µl of elution solution (50mM NaCl, .1mM EDTA) heated for 10 minutes at 100˚ and centrifuged briefly to pellet the streptavidin-bound LNA molecules which inhibit PCR, this elution was done 2 times to ensure all the DNA was removed from the LNA.   10µl of streptavidin purified input DNA was added to PCR using Truseq Pcr F and R for 8 cycles.  PCR products were ampure purified, confirmed on the Tapestation D1000, and quantified by the Qubit and submitted for sequencing. Read 1 positions 1-16 contain the 16bp cell barcode, and positions 17-26 contain a 10bp UMI. The remainder of read 1 contains the 5' of the cDNA. Read 2 also contains the cDNA.

value: Jurkat cell line


title: Neonatal rep3

city: Chengdu

first: Mingzhou

last: Li

state: Sichuan

address: Huimin Road 211, Gongping Street

country: China

institute: Sichuan Agricultural University

description: domestic pig

data_processing:
Illumina CASAVA ver.1.8.2 software was used for basecalling.
We removed low-quality reads including those with ≥ 10% unidentified nucleotides, > 10 nt aligned to the adapter, allowing ≤ 10% mismatches, and with > 50% of bases with phred quality < 5. Then, high-quality reads of six strand-specific libraries were mapped to the pig reference genome (Suscrofa.10.2 from Ensemble) with TopHat (v.2.1.0)
mRNA expression levels of fragments per kilobase per million mapped reads (FPKM) were obtained using Cufflinks (v.2.2.1).
Cuffquant (part of Cufflinks) was used to generate abundance files, which were applied to Cuffdiff (part of Cufflinks) to detect DE mRNAs/genes between the two groups.
Transcripts were assembled by Stringtie version 1.2.2.
AssemblyLine (http://assemblyline.googlecode.com) was used to characterize and filter background noise and to perform meta-assembly by merging the assembled transcripts.
Coffcompare (part of Cufflinks, version 2.2.1) was used to remove transcripts annotated in the reference sequence (marked by ‘c’ for partial match or ‘=’ for full match).
Each transcript sequence was translated in all six possible frames with Transeq (part of EMBOSS version 6.5.7) and the transcript with translated protein sequences that had a significant hit in the Pfam (release27) database with HMMER (v3.1b2) were excluded.
Remaining transcripts were compared with human and mouse genomes, and the UniRef database with BLASTX, then, potential coding transcripts were removed.
The Coding Potential Calculator (CPC) was used to assess the coding potential of the remaining transcripts.
To obtain genomic characterizations for all identified lncRNA transcripts, we ran FEELnc_classifier.pl (a Perl script in FEELnc).
Genome_build: Suscrofa.10.2 from Ensemble
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for each sample.

organism: Sus scrofa

source_name: Lung tissue

extract_protocol:
Total RNA was isolated from each sample with Trizol reagent (Life Technologies, Beijing, China) according to the manufacturer's instruction.
Approximately 1 µg total RNA and the Ribo-Zero™ kit (Epicentre, Madison, WI, USA) were used to generate RNA-Seq cDNA libraries from each sample, and then, RNA sequencing was performed following the manufacturer's standard procedures.

tag: development stage

value: neonatal

value: lung

value: 2 days after birth


title: Neonatal rep1

description: domestic pig


title: Neonatal rep2

description: domestic pig


title: 32-0004


title: P10 islets 3

city: Lausanne

first: Clara

last: Sanchez-Parra

state: Vaud

address: Rue de Bugnon 9

department: Department of Fundamental Neurosciences

country: Switzerland

institute: University of Lausanne

hyb_protocol: The labeled cRNAs were hybridized onto the Rat LncRNA Array v2.0 (4 x 44K, Arraystar).

scan_protocol: After having washed the slides, the arrays were scanned by the Agilent Scanner G2505C.

data_processing:
Agilent Feature Extraction software (version 11.0.1.1) was used to analyze the acquired array images. Quantile normalization and subsequent data processing were performed using the GeneSpring GX v11.5.1 software package (Agilent Technologies).
The Differentially_Expressed_LncRNAs.xls contains the list of the lncRNAs differentially expressed between adult and P10 rat islets; up or down in 'adult vs.P10' as indicated in each speadsheet.
The Differentially_Expressed_mRNAs.xls contains the list of the mRNAs differentially expressed between adult and P10 rat islets; up or down in 'adult vs.P10' as indicaterd in each spreadsheet.

source_name: islets of a pool of P10 rats 3

label_protocol: Total RNA from each sample was amplified and transcribed into fluorescent cRNA with using the manufacturer’s Agilent’s Quick Amp Labeling protocol (version 5.7, Agilent Technologies).

extract_protocol: Total RNA was extracted with the miRNeasy kit of QIAGEN following manufacturer's instructions

value: pancreatic islets

tag: developmental stage


title: lna_gene_jurkat_cd3d_resampled_lna

description:
Resampled single cell RNA-seq library from the 10x genomics 5' end library prep. Jurkat cells were isolated and an LNA probe was used to hybridize CD3D mRNA for targeted resequencing.
lna_gene_jurkat_bcs.txt

extract_protocol: 10x 5' end Illumina libraries at 2nM concentration were diluted 20 fold and PCR amplified with Truseq Pcr F and R oligo for 14 cycles with 1 unit of Phusion.  PCR results were confirmed by gel electrophoresis and the remaining sample was Ampure XP purified at a ratio of 1.8x bead/pcr volume.  Samples were eluted in 10µl and molarity was determined using a Qubit.  10µl of 100nM library was mixed with 1 µl of 10µM DNA molecule in anneallng buffer (10mM Tris 8.0, 50mM NaCl) and heated to 98˚ for 10 minutes followed by slow cooling to 59˚-64˚ depending on the LNA and held O/N at the annealing temperature.  Annealed DNA was added in equal volume to washed  Dynabead M270 streptavidin beads at the annealing temperature.  Beads were incubated for 15 minutes with gentle shaking.  Beads were washed 5x in bind and wash buffer at the annealing temperature.  Beads were eluted in 20 µl of elution solution (50mM NaCl, .1mM EDTA) heated for 10 minutes at 100˚ and centrifuged briefly to pellet the streptavidin-bound LNA molecules which inhibit PCR, this elution was done 2 times to ensure all the DNA was removed from the LNA.   10µl of streptavidin purified input DNA was added to PCR using Truseq Pcr F and R for 8 cycles.  PCR products were ampure purified, confirmed on the Tapestation D1000, and quantified by the Qubit and submitted for sequencing. Read 1 positions 1-16 contain the 16bp cell barcode, and positions 17-26 contain a 10bp UMI. The remainder of read 1 contains the 5' of the cDNA. Read 2 also contains the cDNA.

tag: sample type


title: 32-0003

value: male


title: lna_cell_pbmc_resampled

description:
Resampled single cell RNA-seq library from the 10x genomics 3' end library prep. PBMCs were isolated from a health human donor and a LNA probe was used to hybridize selected cells for targeted resequencing.
lna_cell_pbmc_bcs.txt

source_name: Human PBMCs

extract_protocol: 10x Illumina libraries at 2nM concentration were diluted 20 fold and PCR amplified with Truseq Pcr F and R oligo for 14 cycles with 1 unit of Phusion.  PCR results were confirmed by gel electrophoresis and the remaining sample was Ampure XP purified at a ratio of 1.8x bead/pcr volume.  Samples were eluted in 10µl and molarity was determined using a Qubit.  10µl of 100nM library was mixed with 1 µl of 10µM LNA molecule in anneallng buffer (10mM Tris 8.0, 50mM NaCl) and heated to 98˚ for 10 minutes followed by slow cooling to 59˚-64˚ depending on the LNA and held O/N at the annealing temperature.  Annealed DNA was added in equal volume to washed  Dynabead M270 streptavidin beads at the annealing temperature.  Beads were incubated for 15 minutes with gentle shaking.  Beads were washed 5x in bind and wash buffer at the annealing temperature.  Beads were eluted in 20 µl of elution solution (50mM NaCl, .1mM EDTA) heated for 10 minutes at 100˚ and centrifuged briefly to pellet the streptavidin-bound LNA molecules which inhibit PCR, this elution was done 2 times to ensure all the DNA was removed from the LNA.   10µl of streptavidin purified input DNA was added to PCR using Truseq Pcr F and R for 8 cycles.  PCR products were ampure purified, confirmed on the Tapestation D1000, and quantified by the Qubit and submitted for sequencing. Read 1 positions 1-16 contain the 16bp cell barcode, and positions 17-26 contain a 10bp UMI. Read 2 contains the cDNA.

value: Human PBMCs


title: Prenatal rep2

description: domestic pig

value: prenatal

value: last day before birth


title: KO_M_CC

city: Tianjin

first: Long

last: Shen

address: 22 Qixiangtai Road

institute: School of Basic Medical Sciences, Tianjin Medical University

data_processing:
Basecalls performed using BGISEQ-500.
SOAPnuke was used to get the "clean reads".
Mapping clean reads to mm10 whole genome using HISAT2.
Bowtie2 was used to get the mapping ratio.
Fragments Per Kilobase Million (FPKM) was calculated based on the RSEM.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include fpkm values for each Sample ...

source_name: peritoneal macrophage

extract_protocol:
After co-cultured with EO771 cells for 4 days, peritoneal macrophages were washed with PBS for twice, and RNA was harvested using Trizol reagent.
cDNA library construction and sequencing were performed using BGISEQ-500 platform. Transcription data were profiled and compared according to standard protocols.

value: macrophage

value: 6-8 week

tag: genotype

value: lgmn-/-


title: WT_M_CC

value: wild type


title: lna_cell_mousehuman_original

description:
Original single cell RNA-seq library from the 10x genomics 3' end library prep. A 1:1 mixture of NIH3T3 cells and 293T cells were isolated
lna_cell_mousehuman_bcs.txt

extract_protocol:
293FT and NIH3T3 cells were trpsinized and resuspended in a 1:1 mix and captured on the 10x genomics single cell R-seq platform.
10x genomics 3' end single cell RNA-seq kit. Read 1 positions 1-16 contain the 16bp cell barcode, and positions 17-26 contain a 10bp UMI. Read 2 contains the cDNA.

value: 1:1 mix of NIH3T3 cell line and 293T cell line


title: Prenatal rep1

description: domestic pig


title: 32-0002

value: Facioscapulohumeral muscular dystrophy (FSHD)

value: muscle biopsy


title: lna_cell_pbmc_original

description:
Original single cell RNA-seq library from the 10x genomics 3' end library prep. PBMCs were isolated from a health human donor.
lna_cell_pbmc_bcs.txt

extract_protocol:
PBMCs were isolated from a healthy adult using standard protocols and captured on the 10x genomics single cell R-seq platform
10x genomics 3' end single cell RNA-seq kit. Read 1 positions 1-16 contain the 16bp cell barcode, and positions 17-26 contain a 10bp UMI. Read 2 contains the cDNA.


title: Prenatal rep3

description: domestic pig


title: lna_cell_jurkat_tcr_resampled

description:
Resampled single cell RNA-seq library from the 10x genomics 5' end library prep with TCR enrichment. Jurkat cells were isolated and an LNA probe was used to hybridize selected cells for targeted resequencing.
lna_cell_jurkattcr_bcs.txt

extract_protocol: 10x Illumina libraries at 2nM concentration were diluted 20 fold and PCR amplified with Truseq Pcr F and R oligo for 14 cycles with 1 unit of Phusion.  PCR results were confirmed by gel electrophoresis and the remaining sample was Ampure XP purified at a ratio of 1.8x bead/pcr volume.  Samples were eluted in 10µl and molarity was determined using a Qubit.  10µl of 100nM library was mixed with 1 µl of 10µM LNA molecule in anneallng buffer (10mM Tris 8.0, 50mM NaCl) and heated to 98˚ for 10 minutes followed by slow cooling to 59˚-64˚ depending on the LNA and held O/N at the annealing temperature.  Annealed DNA was added in equal volume to washed  Dynabead M270 streptavidin beads at the annealing temperature.  Beads were incubated for 15 minutes with gentle shaking.  Beads were washed 5x in bind and wash buffer at the annealing temperature.  Beads were eluted in 20 µl of elution solution (50mM NaCl, .1mM EDTA) heated for 10 minutes at 100˚ and centrifuged briefly to pellet the streptavidin-bound LNA molecules which inhibit PCR, this elution was done 2 times to ensure all the DNA was removed from the LNA.   10µl of streptavidin purified input DNA was added to PCR using Truseq Pcr F and R for 8 cycles.  PCR products were ampure purified, confirmed on the Tapestation D1000, and quantified by the Qubit and submitted for sequencing. Read 1 positions 1-16 contain the 16bp cell barcode, and positions 17-26 contain a 10bp UMI. The remainder of read 1 contains the 5' of the TCR alpha or beta cDNA. Read 2 also contains the cDNA.


title: P10 islets 1

source_name: islets of a pool of P10 rats 1


title: Adult islets 2

source_name: islets of adult male rat 2

value: adult


title: P10 islets 2

source_name: islets of a pool of P10 rats 2


title: Adult islets 1

source_name: islets of adult male rat 1


title: Adult islets 3

source_name: islets of adult male rat 3


title: CL1-0_culture in conditioned media from M0 macrophage_2 weeks_rep3

status: Public on Sep 03 2018

city: Taipei

first: Sung-Liang

last: Yu

address: Jen Ai Road Section1

department: Clinical Laboratory Sciences and Medical Biotechnology

country: Taiwan

institute: National Taiwan University

description: Gene expression data from CL1-0 stable-expressing shHLJ1

hyb_protocol: Following, aminoallyl aRNA were hybridized on Phalanx Human OneArray. The hybridization was followed by single channel (Cy5) hybridization standard protocol.

scan_protocol: GeneChips were scanned using the Axon 4000B

data_processing: The expression data were analyzed by GeneSpring GX 13.0 (Silicon Genetics, Redwood City, CA). The raw signal from each array was normalized by 50 percentile shift.

source_name: lung cancer cell, CL1-0

label_protocol: Cy5-abeled aRNA was incorporated by aa-UTP prepared according to the standard protocol of AmbionMessageAmp#1705 from 12 ug total RNA

growth_protocol: The human lung cancer cell line, CL1-0, was grown in RPMI-1640 media supplemented with 10% FBS. All cell lines were incubated at 37°C in a humidified 20% O2/5% CO2 environment.

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

treatment_protocol: CL1-0 cells were individually transfected with pSilencer4.1 vector and shHLJ1. The stable-expressing cells were maintained in complete media  with 0.75 μg/ml puromycin to select for puromycin-resistant pooled clones.

tag: cell line

tag: shRNA

tag: tumor type

value: lung adenocacinoma

tag: ethnicity

value: Asian

value: 64 years


title: CL1-0_normal cuture_rep1

description: Gene expression data from CL1-0 scramble

value: scramble shRNA

tag: age


title: pituitary-4

city: Shanghai

first: Ni

state: Shanghai

address: 320 Yueyang Road, Shanghai, 200025 P.R. China

institute: Institute of Health Sciences, Shanghai Institute for Biological Sciences, Chinese Academy of Sciences

description: gene expression of normal pituitary

hyb_protocol: 0.6 μg of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/μg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 22.5μl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers' instructions. On completion of the fragmentation reaction, 22.5μl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Human Gene Expression（8*60K）for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 4x180k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities as the raw data. Raw data were normalized in quantile algorithm with Genespring 13.0(Agilent). Probe that at least 1 out of 2 samples flagged as Detected were maintained.

source_name: human normal pituitary

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 μg RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was extracted by Qiagen RNA Isolation Kit following the manufacturer's instructions.

treatment_protocol: Tissues were microdissected and removed using the surgical microscope, rinsed in sterile saline, snap-frozen in liquid nitrogen, and stored (-80 ℃) until analysis.

tag: subject gender

value: Female

tag: subject age

tag: tissue

value: pituitary


title: CL1-0_normal cuture_rep3

tag: gender

value: male


title: CL1-0_culture in conditioned media from M0 macrophage_2 weeks_rep1


title: CL1-0_culture in conditioned media from M0 macrophage_2 weeks_rep2


title: CL1-0_normal cuture_rep2


title: pituitary-L

description: gene expression of normal pituitary


title: tumor-539

description: gene expression of prolactinomas

source_name: human pituitary tumor

value: prolactinoma


title: tumor-425

description: gene expression of prolactinomas


title: tumor-534

description: gene expression of prolactinomas

value: Male


title: tumor-218

description: gene expression of prolactinomas


title: pituitary-M

description: gene expression of normal pituitary


title: tumor-469

description: gene expression of prolactinomas


title: pituitary-6

description: gene expression of normal pituitary


title: P1_D_d13_2

city: Kyoto

first: Megumu

last: Saito

address: 53, Shogoin-Kawahara

country: Japan

institute: Kyoto University

description: Gene expression in day 13 MPCs

hyb_protocol: Labelled cDNA was fragmented with Gene Expression Hybridization Kit (Agilent Technologies), followed by hybridization at 65˚C for 17 hrs.

scan_protocol: Images were acquired by DNA Microarray Scanner (Agilent Technologies)

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain signal intensity and performed the bacground correction and normalization using bioconductor package limma

source_name: Patient RD1, day13 MPCs, AK2(-), replicate 2

label_protocol: 100 ng of total RNA was first amplified with  WT-OvationTM Pico System (Nugen). The RNA was labelled with Cy3 using  Genomic DNA Enzymatic Labeling Kit (Agilent Technologies).

growth_protocol: The cells were cultured under 37°C, with 5% CO2 and 5% O2.The undifferentiated ESCs/iPSCs colonies were disseminated onto growth factor-reduced Matrigel-coated plates in mTeSR1 medium (Stem Cell Technologies) containing BMP4 (80 ng/mL). On day 4, the medium was replaced by StemPro-34 serum-free medium (Gibco) containing 2 mM glutamax (Invitrogen), VEGF (80 ng/mL), basic FGF (25 ng/ml) and SCF (100 ng/mL). On day 6, the cytokines were switched to the combination of SCF (50 ng/mL), IL-3 (50 ng/mL), TPO (5 ng/mL) and Flt-3 ligand (50 ng/mL) for myeloid differentiation.

extract_protocol: Total RNA was purified using the RNeasy mini or micro kit (Qiagen)  following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: PSCs were collected with Accumax (Innovative Cell Technologies). Flow cytometric analyses and cell sorting were performed using the FACSAriaTM II cell sorter (BD Bioscience) to collect each blood cells.

value: Blood cells

value: day 13 CD34+CD45+ myeloid progenitor cells


title: P1_D_iPS_1

description: Gene expression in PSCs

source_name: Patient RD1, iPSCs, AK2(-), replicate 1

value: iPSCs

value: Pluripotent Stem Cells


title: P1_D_d22_2

description: Gene expression in day 22 Neutrophils

source_name: Patient RD1, day22 neutrophils, AK2(-), replicate 2

value: day 22 neutrophils


title: P1_C_d22_2

description: Gene expression in day 22 Neutrophils

source_name: Patient RD1, day22 neutrophils, AK2(+), replicate 2


title: P1_D_d13_1

description: Gene expression in day 13 MPCs

source_name: Patient RD1, day13 MPCs, AK2(-), replicate 1


title: P1_C_d13_1

description: Gene expression in day 13 MPCs

source_name: Patient RD1, day13 MPCs, AK2(+), replicate 1


title: P1_C_d13_2

description: Gene expression in day 13 MPCs

source_name: Patient RD1, day13 MPCs, AK2(+), replicate 2


title: P1_C_d22_1

description: Gene expression in day 22 Neutrophils

source_name: Patient RD1, day22 neutrophils, AK2(+), replicate 1


title: P1_D_iPS_2

description: Gene expression in PSCs

source_name: Patient RD1, iPSCs, AK2(-), replicate 2


title: P1_D_d06_1

description: Gene expression in day 6 HPCs

source_name: Patient RD1, day 6 HPCs, AK2(-), replicate 1

value: day 6  CD34+KDR+ hemoangiogenic progenitors


title: P1_D_d22_1

description: Gene expression in day 22 Neutrophils

source_name: Patient RD1, day22 neutrophils, AK2(-), replicate 1


title: P1_D_d06_2

description: Gene expression in day 6 HPCs

source_name: Patient RD1, day 6 HPCs, AK2(-), replicate 2


title: OSAHS patients with hypertension-rep4

city: Wuhan

first: Xiuping

last: Yang

address: No. 1277 Jiefang Road

institute: Union Hospital, Tongji Medical College, Huazhong University of Science and Technology

description: OSAHS patients with hypertension,without other complications

hyb_protocol: 21.5ul of Biotin-labeled samples were hybridized for 16 hr at 48℃ on the GeneChip® Hybridization Oven 645(Affymetrix,USA). GeneChips were washed/stained in the GeneChip® Fluidics Station 450 (Affymetrix,USA) .

scan_protocol: Scanning procedures were conducted on the GeneChip® Scanner 3000 7G (Affymetrix,USA) following the manufacturer's instructions.

data_processing: The data were analyzed with Affymetrix ExpressionConsole-1_4_0 (EC 5.0) using Robust Multichip Average (RMA) as normalization method.

source_name: OSAHS patients with hypertension

label_protocol: Total RNA was processed with the FlashTag® Biotin HSR RNA Labeling kit (Affymetrix,USA)

growth_protocol: Blood samples of all the participants were collected at AM 8:00 after underwent full-night in-laboratory polysomnography examinations and an overnight fasting.

extract_protocol: Total RNA, including miRNA, was extracted from frozen serum between 3 groups of 15 samples, using QIAGEN RNeasy Mini Kit (217004; QIAGEN,Germany) according to the manufacturer’s instructions.

treatment_protocol: Blood was collected in inert separation gel vacuum procagulant collective tube.The serum were isolated by centrifugation at 3000 g  for 10 mins within 60 min of drawing blood, and the supernatant was transferred to without RNase Eppendorf tubes,stored at -80uC until RNA extraction.

value: serum


title: IG1

city: Rochester

first: Asha

last: Nair

address: 200 1ST ST SW

institute: Mayo Clinic

data_processing:
Base calling was performed with the Illumina CASAVA 1.9 pipeline
QC was performed on the FASTQ files using RSeQC software (http://rseqc.sourceforge.net/)
The paired end reads were aligned by TopHat 2.1.0
Gene counts were generated using subread featureCounts (http://subread.sourceforge.net/)
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include Raw counts and RPKM values for each gene per sample

source_name: gastric body

extract_protocol:
Total RNA was isolated from smooth muscle using RNA-Bee (TelTest) and then purified for sequencing using RNeasy Plus Mini Kit (Qiagen). RNA Integrity Numbers (RIN) values on all samples were > 7.0.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: smooth muscle

tag: Sex

value: female

value: idiopathic gastroparetics


title: IG4


title: OSAHS patients with hypertension-rep5

value: OSAHS patients with hypertension,without other complications


title: IG5


title: IG2


title: P1_C_d06_1

description: Gene expression in day 6 HPCs

source_name: Patient RD1, day 6 HPCs, AK2(+), replicate 1


title: OSAHS patients with hypertension-rep1


title: IG3


title: P1_C_iPS_2

description: Gene expression in PSCs

source_name: Patient RD1, iPSCs, AK2(+), replicate 2


title: OSAHS patients with hypertension-rep2


title: IC7

value: non-diabetic non-gastroparetic


title: IC6


title: IC5


title: K1_N_d22_1

description: Gene expression in day 22 Neutrophils

source_name: Kh-ES1, day22 neutrophils, control, replicate 1


title: IC4


title: P1_C_iPS_1

description: Gene expression in PSCs

source_name: Patient RD1, iPSCs, AK2(+), replicate 1


title: OSAHS patients with hypertension-rep3


title: K1_N_d13_2

description: Gene expression in day 13 MPCs

source_name: Kh-ES1, day13 MPCs, control, replicate 2


title: IC1


title: IC2


title: IC3


title: DG6

value: diabetic gastroparetics


title: DG3


title: DG2


title: DG1


title: DG5


title: simple OSAHS patients-rep4

description: OSAHS patients without any complication

source_name: simple OSAHS patients

value: OSAHS patients without any complication


title: DG4


title: simple OSAHS patients-rep3

description: OSAHS patients without any complication


title: DC7

value: diabetic non-gastroparetics controls


title: simple OSAHS patients-rep2

description: OSAHS patients without any complication


title: ribo_seq_ko_minus_r2

city: Cambridge

first: Shuping

last: Zhang

state: MA

address: 77 Massachusetts Avenue

institute: Massachusetts Institute of Technology

description: Ribosome protected RNA

data_processing:
Fastq files were trimmed by Cutadapt to remove adapters and reads with a base quality score less than 10. Reads with length less than 26 or 9 nucleotides were also discarded for Ribo-seq and mRNA-seq samples, respectively. For Ribo-seq samples, reads containing rRNA and tRNA sequences were further removed using Bowtie2.
After quality control analysis using FastQC, reads were mapped to mouse genome mm10 (UCSC) using STAR aligner with maxima of 2 mismatches and 8 multiple loci.
Quality of Ribo-seq data was examined by the triplet periodicity using RibORF.
The uniquely mapped reads were counted using Htseq. For Ribo-seq data, the first 15 and the last 5 codons were removed from reads counting to avoid the bias of pile up of reads around the start codons and stop codons.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include gene symbol on the first column and the raw read count values on the second column.

source_name: Fetal liver

extract_protocol:
For Ribo-seq, sorted erythroblasts were washed twice with cold phosphate-buffered saline and then treated with cycloheximde (100 ug/ml) at 37℃ for 5 min, followed by isolation of ribosome protected fragments (RPFs) using ARTseq-Ribosome Profiling Kit (Illumina). For mRNA-seq, total RNAs were extracted by RNeasy Plus kit (Qiagen) and polyA RNAs were isolated using an Oligotex mRNA kit (Qiagen).
Ribo-seq cDNA libraries were prepared as described (Ingolia et al. 2009, Ingolia, Lareau, and Weissman 2011). Briefly, RPFs were dephosphorylated and linkers were ligated using T4 RNA ligase. RNA samples were then reverse transcribed, circularized and PCR amplified for 12 cycles. PCR products were subjected to gel purification before sequencing. mRNA-seq cDNA libraries were prepared by the MIT BioMicro Center.

value: liver

tag: strain

tag: cell type

value: Primary basophilic erythroblasts

value: Hri-/-

tag: condition

value: Iron deficiency


title: P1_C_d06_2

description: Gene expression in day 6 HPCs

source_name: Patient RD1, day 6 HPCs, AK2(+), replicate 2

value: Blood cells


title: healthy controls-rep4

description: AHI<5;without hypertension,hyperglycemia and dyslipidemia

source_name: healthy controls

value: healthy control, without hypertension,hyperglycemia and dyslipidemia


title: simple OSAHS patients-rep1

description: OSAHS patients without any complication


title: DC3


title: healthy controls-rep5


title: healthy controls-rep2


title: ribo_seq_ko_plus_r1

description: Ribosome protected RNA

value: iron sufficiency


title: DC5


title: DC6


title: ribo_seq_ko_plus_r2

description: Ribosome protected RNA


title: DC2


title: DC1


title: K1_N_iPS_2

description: Gene expression in PSCs

source_name: Kh-ES1, ESCs, control, replicate 2

value: ESCs

value: Pluripotent Stem Cells


title: healthy controls-rep3

value: serum


title: K1_N_d13_1

description: Gene expression in day 13 MPCs

source_name: Kh-ES1, day13 MPCs, control, replicate 1

value: day 13 CD34+CD45+ myeloid progenitor cells


title: K1_N_d06_2

description: Gene expression in day 6 HPCs

source_name: Kh-ES1, day 6 HPCs, control, replicate 2

value: day 6  CD34+KDR+ hemoangiogenic progenitors


title: DC4

value: smooth muscle

value: female


title: K1_N_d06_1

description: Gene expression in day 6 HPCs

source_name: Kh-ES1, day 6 HPCs, control, replicate 1


title: K1_N_iPS_1

description: Gene expression in PSCs

source_name: Kh-ES1, ESCs, control, replicate 1


title: ribo_seq_wt_minus_r2

description: Ribosome protected RNA

value: Wild type


title: ribo_seq_wt_minus_r1

description: Ribosome protected RNA


title: ribo_seq_wt_plus_r2

description: Ribosome protected RNA


title: SplWTPHZ_3

city: Bethesda

first: Michael

last: Krause

state: MD

address: Bld. 5, Rm B104, 5 Memorial Dr.

institute: NIH/NIDDK

data_processing:
Bcl2fastq v2.18 was used to convert the bcl files to fastq files.
We aligned to GRCz10 reference genome using STAR, version 2.5.2b.
We counted number of reads mapped to genes using htseq, version 0.6.1p1.
Differential gene expression analysis was performed using DESeq2, version 1.12.3  with the cutoff of 0.05 on False Discovery Rate (FDR). R version 3.3.2 (2016-10- 31) was used, and  Bioconductor version 3.4 with BiocInstaller version 1.24.0 were used. For gene annotation, we used  Ensembl GRCz10, release 87.

organism: Danio rerio

source_name: whole animal

growth_protocol: Normal zebrafish husbandary

extract_protocol:
TRIzol + Qiagen miniRNA clean-up
NEBnext Ultra RNA prep with magnetic mRNA isolation

treatment_protocol: Adult zebrafish are treated in Phenylhydrazine-containg (2.5 µg/ml) fish water

value: spleen

value: 5-6 months old


title: SplWTPHZ_2


title: SplWTPHZ_1


title: ribo_seq_wt_plus_r1

description: Ribosome protected RNA

value: liver


title: ribo_seq_ko_minus_r1

description: Ribosome protected RNA

value: Primary basophilic erythroblasts


title: rna_seq_ko_minus_r4

molecule: polyA RNA

value: Hri-/-


title: SplWT_3


title: SplWT_1


title: SplDKOPHZ_3

value: Tu/hrg1 doulble knockout (DKO)


title: SplDKOPHZ_2


title: SplWT_2


title: DG7

value: diabetic gastroparetics


title: SplDKO_3


title: rna_seq_ko_minus_r3

value: Iron deficiency


title: healthy controls-rep1

value: healthy control, without hypertension,hyperglycemia and dyslipidemia


title: SplDKO_2


title: SplDKO_1


title: rna_seq_wt_minus_r3


title: rna_seq_ko_plus_r3

value: iron sufficiency


title: rna_seq_ko_minus_r1


title: rna_seq_ko_minus_r2


title: rna_seq_ko_plus_r2


title: rna_seq_ko_plus_r1


title: rna_seq_wt_minus_r2


title: KidWTPHZ_3

value: kidney


title: rna_seq_wt_minus_r1


title: KidWTPHZ_2


title: SplDKOPHZ_1


title: KidWTPHZ_1


title: KidWT_3


title: rna_seq_wt_plus_r3


title: rna_seq_wt_plus_r1


title: KidWT_1


title: KidDKOPHZ_3


title: S8-WT

city: haifa

first: Herman

last: Wolosker

address: 1 Efron St

department: Biochemistry

country: Israel

institute: Technion-Israel Institute of Technology

data_processing:
Quality control was assessed using Fastqc (v0.11.5) (Andrews S. (2010). FastQC: a quality control tool for high throughput sequence data), reads were trimmed for adapters, low quality 3` and minimum length of 20 using CUTADAPT (v1.1)(Marcel M. Cutadapt removes adapter sequences from high-throughput sequencing reads).
75 bp single-end reads were aligned to Mouse reference genome and annotation file (Mus_musculus.GRCm38 downloaded from ENSEMBL)(Nucleic Acids Res. 2016 44 Database issue:D710-6.) using TopHat (v2.1.1)(Bioinformatics (2009) 25 (9): 1105-1111) allowing two mismatches per read with options --verysensitive and -GTF.
. The number of reads per gene was counted using Htseq (0.6.0)(Bioinformatics. 2015 Jan 15;31(2):166-9).
A statistical analysis preformed using DESeq2 R package (version 1.12.4) (Genome Biology 2014 15:550). The number of transcripts per gene was extracted into CountWithSymbol.xls and NormalizedCountWithSymbol.xls files for raw counts and normalized counts, respectively. The similarity between samples was evaluated using correlation matrix, a heat plot and principal component analysis within DESeq2 package.
Genome_build: (Mus_musculus.GRCm38 downloaded from ENSEMBL)(Nucleic Acids Res. 2016 44 Database issue:D710-6.)
Supplementary_files_format_and_content: The files are in excell spreadsheet

source_name: Striatum- WT

extract_protocol:
Total RNA was extracted from brain tissues with the RNeasy mini kit (Qiagen, cat no. 74106) using the Qiacube automated system (Qiagen).
RNAseq libraries were produced using NEBNext® Ultra™ RNA Library Prep Kit (Illumina, cat no. E7530) starting from 800 ng total RNA/sample

value: striatum

value: 5 months

value: male

value: Wild Type


title: S7-WT


title: S6-WT


title: KidDKOPHZ_1


title: rna_seq_wt_plus_r2


title: S4-KO

source_name: Striatum- ASCT1-KO


title: S5-WT


title: KidWT_2


title: KidDKO_3


title: In Vitro sci-ATAC-seq

city: Portland

first: Andrew

last: Adey

state: OR

address: 3181 S.W. Sam Jackson Park Rd, RHH, L103

department: MMG

institute: Oregon Health & Science University

description: ATAC DNA

data_processing:
Libraries were sequenced on an Illumina NextSeq 500 using custom chemistry
Fastq files were processed using 'scitools fastq-dump', in the provided fastq files the cell barcode is the entire 36bp read 3
Reads were aligned to the mm10 reference genome using bwa (via 'scitools align')
Peaks were called and processed using macs2 with default parameters specified by 'scitools callpeak'
Count matrixes were generated using 'scitools count'
Dimensionality reduction was performed using 'scitools tfidf', 'scitools lsi', and then 'scitools tsne'
Deviation scores were generated using ChromVAR
Peak links and co-accessbility networks were generted using Cicero
Combined data files were generated using 'scitools data-combine' and can be extracted into respective components via 'scitools data-split'
Genome_build: mm10
Supplementary_files_format_and_content: data.gz files that contain all primary analyses, extract by 'scitools data-split' or gunzip and parse by section headers
Supplementary_files_format_and_content: cell barcodes can be found at the bottom of each column in the data.gz files

source_name: Cultured neurons from murine hippocampus

growth_protocol: In vitro cells were cultured in Neurobasal A containing 1xB27 and 2 mM glutamax

extract_protocol:
Nuclei were extracted using nuclei isolation buffer and then washed
sci-ATAC-seq described in the associated publicaiton and supplementary protocol
single-cell combinatorial indexing ATAC-seq

tag: assay

value: sci-ATAC-seq

tag: source

value: cultured neurons


title: In Vivo sci-ATAC-seq

description: ATAC DNA

source_name: Murine hippocampus

value: fresh tissue


title: S3-KO


title: S2-KO


title: KidDKO_2

value: 5-6 months old


title: C8-WT

source_name: Cerebral cortex- Wild type

value: cerebral cortex


title: control3

city: Wien

first: Shane

last: Cronin

address: Dr. Bohr-Gasse 3

country: Austria

institute: IMBA - Institut für Molekulare Biotechnologie GmbH

hyb_protocol: Scanned on an Agilent G2505C scanner.

scan_protocol: Images were quantified using Agilent Feature Extraction Software (version 10.7.3.1).

data_processing: Limma v3.34.3 was used for background calculation (method=normexp,offset=50), within-array (method=loess) and between-array (method=Aquantile) normalization methods.

source_name: WT.4 (experimental sample)

label_protocol: Quick Amp Labeling Kit from Agilent according to provided protocol, 500 ng total RNA were amplified and labeled according manufacturer's protocol

growth_protocol: T cells were purified from spleens and lymph nodes of mice using microbeads (naïve CD4+, Miltenyi Biotec).

extract_protocol: total RNA was extracted by sequential Qiazol extraction and purification through the RNeasy micro kit with on column genomic DNA digestion (Qiagen)

treatment_protocol: Purified naïve CD4+ were isolated and activated for 12 hours with plate-bound anti CD3(4ug/ml) and anti-CD28 (2ug/ml)

value: WT

value: TCR-activated CD4+ T cells

source_name: REFERENCE

tag: reference

value: equal mixture of experimental samples


title: C7-WT

tag: genotype


title: KidDKOPHZ_2

value: Tu/hrg1 doulble knockout (DKO)


title: Gch1;Lck sample 2

source_name: GCH.3 (experimental sample)


title: C6-WT


title: KidDKO_1


title: Gch1;Lck sample 1

source_name: GCH.2 (experimental sample)


title: Gch1;Lck sample 3

source_name: GCH.4 (experimental sample)


title: control 1

source_name: WT.2 (experimental sample)


title: control 2

source_name: WT.3 (experimental sample)


title: C5- WT


title: SC-SP_F3DTCre_rep2

city: Leuven

first: Rekin's

last: Janky

address: Herestraat 49 Box 816

department: Nucleomics Core

country: Belgium

institute: VIB

description: Gene expression in non-regenerative female mouse pituitary

hyb_protocol: 2µg of purified, amplified cDNA were used as input into the Agilent Genomic DNA Enzymatic labeling according to the manufacturers instructions, without the restriction digestion step and then labeled with cyanine 3-dUTP (Cy3). The Cy3-labeled cDNA was quantitated and dye incorporation determined by Nanodrop. 3µg labeled cDNA was hybridized on Mouse Whole Genome v2 Gene Expression 4x44K MicroArray according to the One-Color microarray-Based Gene Expression Analysis User Manual, without fragmentation step.

scan_protocol: To assess the raw probe signal intensities, arrays were scanned using the Agilent DNA MicroArray Scanner with surescan High-Resolution Technology and probe signals were quantified using Agilent’s Feature Extraction software (version 10.7.3.1).

data_processing: Data was base 2 log-transformed and a quantile normalization was applied. Control probes and probes below background were removed.

source_name: SC-SP from the pituitary

label_protocol: RNA concentration and purity were determined spectrophotometrically using the Nanodrop ND-1000 (Nanodrop Technologies) and RNA integrity was assessed using a Bioanalyser 2100 (Agilent).   Per sample, an amount of 1ng of total RNA was amplified and converted to single-stranded antisense cDNA using the NuGEN Ovation Pico WTA System v2.0. All steps were carried out according to the manufacturers protocol (NuGEN).

extract_protocol: Mice were euthanized by exposure to CO2 and the neurointermediate lobe of the pituitary was carefully removed. The AP was isolated and dissociated into single cells using trypsin. Cells were resuspended in pituitary-optimized serum-free defined medium (SFDM; Invitrogen). Dissociated AP cells were incubated with Hoechst33342 (2.5µg/ml; Sigma-Aldrich), stained with phycoerythrin (PE)-conjugated rat anti-mouse stem cell antigen-1 (Sca1; Table 1) (BD Biosciences), incubated with propidium iodide (2µg/ml; Sigma-Aldrich) and analyzed for side population (SP) by FACS (FACSVantage or FACS Aria III; BD Biosciences). To confirm the SP phenotype, verapamil was added (100µM; Sigma-Aldrich) which blocks the SP’s dye efflux. The SP fraction not expressing Sca1 at a high level (non-Sca1high SP) has been identified as the stem cell-clustering population of the pituitary, referred to as the ‘stem cell-SP’ or SC-SP. The SC-SP and the bulk Hoechstmid+high ‘main population’ (MP) were sorted by FACS after 3DT and 10DT treatment into cold lysis solution of the RNeasy Micro kit (Qiagen, Venlo, The Netherlands). Total RNA was extracted immediately after cell collection according to the manufacturer’s protocol, typically starting from 25000-50000 cells per sort. RNA samples were stored at -80°C until further processing for whole-genome microarray

treatment_protocol: -/iDTR (ctrl) and GHCre/iDTR female mice were treated with DT for 3 (3DT) or 10 (10DT) days (4 ng / g body weight, twice a day for the indicated number of days).

value: Female

value: GHCre/iDTR

tag: sorted population

tag: dt treatment


title: SC-SP_F10DTCre_rep1

description: Gene expression in control (non-injured) female mouse pituitary after 3DT


title: SC-SP_F10DTCtrl_rep1

description: Gene expression in regenerative female mouse pituitary after 3DT

value: -/iDTR


title: SC-SP_F3DTCtrl_rep1


title: SC-SP_F3DTCtrl_rep2


title: SC-SP_F3DTCre_rep1


title: C4-KO

source_name: Cerebral cortex- ASCT1-KO


title: C3-KO


title: C1-KO


title: wt60_2

city: Innsbruck

first: Ingo

last: Bauer

state: Tirol

address: Innrain 80-82

department: Institute of Molecular Biology

institute: Medical University of Innsbruck

data_processing:
Whole workflow was performed using a protocol from Trapnell et al., Nature protocols, 2012. Sequenced reads ẃere mapped to FGSC_A4 whole genome using TopHat v2.1.1 with parameters -p8 -G (including features as .gff file in version s10-m04-r06)
Fragments per kilobase of transcript per million mapped fragments (FPKM) were calculated by using Cufflinks v2.2.1 with parameters -p8 -u -N.
Cuffdiff v2.1.1 was used to produce per sample FPKM expression levels and estimate differential expression between the sample groups.
Supplementary_files_FPKM_tracking: .txt file includes FPKM values for each Sample
Genome_build: Aspergillus nidulans FGSC_A4 genome (version s10-m04-r06)
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

organism: Aspergillus nidulans

source_name: Aspergillus nidulans TIB10

growth_protocol: Fungal strains were grown as shaking cultures in liquid glucose minimal media supplemented with biotin at 37 °C

extract_protocol:
Total RNA was extracted from snap frozen fungal mycelia with TRI reagent following the manufacturer's protocol
Illumina TruSeq RNA Sample Prep Kit was used for the construction of sequencing libraries with 1 µg total RNA as input

treatment_protocol: Fungal strains were grown for 24 h and 60 h to achieve 2 time points

value: wild type

tag: growth time


title: wt60_1


title: wt60_3


title: C2-KO


title: delta_hosA24_1

source_name: Aspergillus nidulans TBF53.1

value: hosA deletion


title: delta_hosA24_3


title: delta_hosA24_2


title: delta_hosA60_1


title: delta_hosA60_3


title: S25_2

city: Ningbo

first: Zhaoshou

last: Ran

state: Zhejiang

address: Fenghua Road 818, Jiangbei Districta

department: Institute of Marine Science

institute: Ningbo University

data_processing:
Illumina Hiseq 4000 platform in Novogene Bioinformatics Technology Co., Ltd (Beijing, China) was used for base calling.
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing unknown bases of > 10% and those in which more than half of the bases gave a quality score of ≤ 20.
Transcriptome assembly was accomplished by using Trinity with min_kmer_cov set to 2 by default and all other parameters set default.
To estimate the expression level of each gene, the transcriptome obtained from Trinity was used as the reference sequence (REF), the clean reads from each sample were mapped to REF by using RSEM software (bowtie2, default parameters) (Li and Dewey, 2011). The count of mapped reads of each gene was further estimated using expected number of fragments per kilobase of transcript per millions base pairs sequenced (FPKM), which is currently the most frequently used method for estimating gene expression levels (Trapnell et al., 2010).

organism: Sinonovacula constricta

source_name: high salinity (25 psu)

extract_protocol:
Juvenile Sinonovacula constricta in whole organism was used to extract total RNA by using Trizol reagent. A total amount of 1.5 μg RNA per sample was used as input material for the RNA sample preparations.
Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) and index codes were added to attribute sequences to each sample.

value: the whole organism

value: on the 15th day after fertilization

tag: development stage

value: juvenile


title: delta_hosA60_2


title: S25_1

tag: age


title: Surf_UDW_id_52610

city: Santa Cruz

first: Jonathan

middle: David

last: Magasin

address: 1156 High Street

department: Ocean Sciences

institute: UC Santa Cruz

description: environmental sample

hyb_protocol: Cy3-labeled cDNA was hybridized at the Roy J. Carver Center for Genomics (The University of Iowa, USA) using a Gene Expression Hybridization Kit (Cat# 5188‐5242) and following a protocol based on One-Color Microarray-Based Gene Expression Analysis: Low Input Quick Amp Labeling [Version 6.7, September 2014].  From each Cy3-labeled sample, a volume equivalent to 3.0 ug of target DNA was taken and added to water to a total volume of 44.00 ul.  To each sample was added 66.0 ul of hybridization master mix (10x GE blocking agent [11.0 ul], 2x Hi-RPM Hyb Buffer [55.0 ul]) for a total volume of 110 ul.  The sample was mixed, then incubated at 95 degrees Celsius for 3 min, then placed on ice, and then briefly centrifuged. From each sample 100 ul was taken and loaded onto a MicroTOOLs microarray (4 arrays per slide).  Arrays were hybridized at 65 degrees Celsius and for ~18 hours. After hybridization, arrays were washed using the Gene Expression Wash Buffer (Cat# 5188‐5327).

scan_protocol: Microarrays were scanned at the Roy J. Carver Center for Genomics at the University of Iowa using an Agilent SureScan Microarray Scanner G2600DA (UI Tag: 607105, Serial #: SG13134301) and using the Agilent scanning protocol GE1_1105_Oct12 (Feature Extractor software version 11.5.1.1).

data_processing: All microarray analyses were done using the MicroTOOLs R package (ver. 1.0; available at https://www.jzehrlab.com). The transcription values for each gene were obtained by robust multi-array average of hybridization values for all probes and quantile normalization across all samples.  Additional data processing steps were performed for gene detection and determination of differentially expressed genes (described in our publication), but those steps do not affect the values in the sample matrices.

organism: uncultured marine microorganism

source_name: NPSG surface (25 m) water treated with deep (130 m) water.

label_protocol: cDNA was labeled at the Roy J. Carver Center for Genomics (The University of Iowa, USA) using the Agilent SureTag DNA Labeling Kit (Cat# 5190-3400) and by following a protocol based on Agilent Oligonucleotide Array‐Based CGH for Genomic DNA Analysis: Enzymatic Labeling for Blood, Cells, or Tissues [Version 7.3 March 2014].  For each sample the following steps were performed.  0.5 ug of cDNA was diluted to 19.2 ng/ul [26.0 ul total].  The diluted cDNA was then denatured and annealed with random primers: cDNA was combined with 5.0 ul of random primers and the resulting 31.0 ul sample was incubated at 95 degrees Celsius for 5 min, then immediately placed on ice for 5 min, and then centrifuged at 6kxg for 1 min.  19.0 ug of labeled master mix was prepared (5x reaction [10.0 ul], 10x dNTP [5.0 ul]; cyanine [3.0 ul]; Exo-Klenow [1.0 ul]) and then pipetted into the sample.  The sample was briefly centrifuged, then incubated at 37 degrees Celsius for 2 hrs and at 65 degrees Celsius for 10 minutes, and then transfered on ice (and possibly stored overnight at -20 Celsius).  Labeled cDNA was then cleaned using the Agilent SureTag DNA Labeling Kit, which included purification columns.  A Nanodrop spectrophotometer was used to check that the yield and specific activity of Cy3 were within expected ranges.

growth_protocol: Environmental samples were collected during the BioLINCS Cruise from 6-21 September 2011.  In situ samples were collected with an Environmental Sample Processor (ESP).  Mixing experiment samples were collected from CTD casts.

extract_protocol: RNA was extracted using the RiboPure RNA purification kit with the addition of a bead-beating step during TRI Reagent extraction as described in Shilova et al., 2014. DNA was digested using the RNase-Free DNase Kit (Qiagen) according to the manufacturer’s protocol and RNA quality and quantity was evaluated using the Agilent BioAnalyzer RNA Nano Kit and Qiagen Qubit. All samples with an RNA Integrity Number greater than 9 were processed for microarray analyses.

treatment_protocol: Environmental samples were filtered using 0.2 micron Sterivex cartridges.  Filters were immediately flash frozen with liquid nitrogen during the cruise.  After the cruise, filters were shipped to UC Santa Cruz where they were stored at -80 Celsius.

tag: category

value: mixing experiment


title: NRAS TAM 3

city: Seattle

first: Eleanor

last: Chen

state: WA

address: 1959 NE Pacific Street

department: Pathology

institute: University of Washington

data_processing:
Image analysis and base calling were performed using Illumina's Real Time Analysis v1.18 software, followed by 'demultiplexing' of indexed reads and generation of FASTQ files, using Illumina's bcl2fastq v1.8.2
Reads of low quality were filtered out prior to alignment to hg38 using TopHat v2.1.0.  Counts were generated from TopHat alignments at the gene-level,  using “intersection-strict” overlap mode in HTSeq v0.6.1.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include counts generated at the gene-level by HTSeq-count v0.6.1

source_name: 381T ERMS cell line

extract_protocol: RNA-seq libraries were prepared from total RNA using the TruSeq RNA Sample Prep v2 Kit (Illumina, Inc., San Diego, CA, USA) and a Sciclone  NGSx Workstation (PerkinElmer, Waltham, MA, USA).

tag: genotype/variation

value: NRAS knockout


title: NRAS TAM 2


title: NRAS TAM 1


title: Surf_UDW_id_52611

description: environmental sample


title: Deep_FSW_id_52606

description: environmental sample

source_name: NPSG deep (130 m) water treated with filtered surface (25 m) water.


title: S25_3

tag: tissue


title: simple OSAHS patients-rep5

description: OSAHS patients without any complication

source_name: simple OSAHS patients

value: serum

tag: sample type

value: OSAHS patients without any complication


title: ESP_Sep14_1700_id_2061

description: environmental sample

source_name: North Pacific Subtropical Gyre (NPSG) surface water (24 m)

value: in situ

value: ESP

tag: date


title: Deep_Cnt_id_52608

description: environmental sample

source_name: NPSG deep (130 m) water treated with filtered deep water (control).


title: Surf_FDW_id_52603

description: environmental sample

source_name: NPSG surface (25 m) water treated with filtered deep (130 m) water.


title: Surf_Cnt_id_52604

description: environmental sample

source_name: NPSG surface (25 m) water treated with filtered surface water (control).


title: ESP_Sep16_500_id_3052

description: environmental sample


title: Surf_Cnt_id_52605

description: environmental sample


title: S15_3

source_name: optimal salinity (15 psu)


title: NRAS No TAM 2

source_name: 381 ERMS cell line

value: Control


title: ESP_Sep15_1700_id_2041

description: environmental sample


title: Deep_FSW_id_52607

description: environmental sample


title: Deep_Cnt_id_52609

description: environmental sample


title: Surf_FDW_id_52602

description: environmental sample


title: ESP_Sep16_1700_id_3053

description: environmental sample


title: S15_2


title: ESP_Sep14_500_id_2012

description: environmental sample


title: ESP_Sep15_500_id_3045

description: environmental sample


title: NRAS No TAM 1


title: S15_1


title: S5_3

source_name: low salinity (5 psu)


title: NRAS No TAM 3


title: S5_2


title: P7 PDGFRa-GFP+ cells

city: San Diego

first: Rongbo

last: Li

address: 9500 Gilman Dr. MC0766

department: Pediatrics

institute: UC San Diego

data_processing:
Sequencing reads were first aligned to mm10 reference using STAR V2.5.1b and then aligned to annotated transcripts, which were part of the Cell Ranger version 2.1 pipeline (https://www.10xgenomics.com). A customized pre-mRNA reference package was generated to capture all the intronic reads in addition to reads that are mapped to exons. Cell Ranger filtered cells by taking > 10% of the top nth barcodes, where n is 1% of the expected number of cell counts being recovered. The filtered gene-cell matrices, output from CellRanger, was further analyzed using the Seurat package V2.3 and R 3.4. The UMI raw counts were log-normalized for each cell to its total expression and scaled to z-scored residuals of linear models that predicts gene expression using normalized UMIs. The scaled data were used to perform dimensionality reduction with Sparsesvd V0.1, graph-based clustering and visualization with t-Distributed Stochastic Neighbor Embedding (t-SNE). Differential gene expression analysis was performed using Wilcoxon rank sum test. Heatmaps, t-SNE plots and visualization of marker expression were generated using Seurat.
Genome_build: mm10

source_name: Mouse lung

extract_protocol:
Pdgfra-GFP mouse lungs at P7 and P15 were sacrificed and each lung lobes were dissected off and minced into small pieces in a conical tube containing 6ml of 2U/ml dispase (STEMCELL Technologies) followed by rotating incubation for 30 min at 37°C. The cells were placed on ice and added 15ul 10mg/ml DNase I (Sigma) for 5 min. The cells were then filtered through 40um strainers and centrifuged at 800rpm for 6 min at 4°C. The cell pellet was resuspended in 1ml of RBC lysis buffer (Abcam) and lysed for 90 s at room temperature. Addition of 6ml DMEM media (GIBCO) was followed and 500 mL of FBS (Hyclone) was slowly added in the bottom of tube. Cells were centrifuged at 800rpm for 6 min at 4°C. The cell pellet was resuspended in PBS with 3% BSA (GIBCO) for flow cytometry, 4’, 6-diamidino-2-phenylindole (DAPI) (Sigma) was used to eliminate dead cells. Cell sorting was performed with a FACS Aria II.
10X Genomics

tag: background strain

tag: developmental stage

value: lung

value: PDGFRa-GFP+ cells


title: P15 PDGFRa-GFP+ cells

tag: cell type


title: M. smemgtias MC2 155_6C sRNA inducible vector_uninduced

status: Public on Sep 02 2018

city: Toronto

first: Juntao

last: Mai

address: 661 univerisity ave

country: Canada

institute: Univerisity of Toronto

data_processing:
The raw reads were filtered by Seqtk and then mapped to the M. smegmatis mc2-155 strain reference sequence (GenBank NC_008596) using Bowtie2 (version: 2-2.0.5)
Counting of reads per gene was performed using HTSeq followed by TMM (trimmed mean of M-values) normalization
Differentially expressed genes were defined as those with a false discovery rate Q < 0.05 and fold-change ≥2 using the edgeR software
Genome_build: NC_008596
Supplementary_files_format_and_content: RPKM abundance

organism: Mycolicibacterium smegmatis

source_name: Induced

extract_protocol:
Trizol
total RNA straned

tag: strain background

value: 6C sRNA inducible vector (PMV261)

tag: treatment

value: with ATC induction


title: Input DNA_Rep2

city: San Francisco

first: Siavash

last: Fazel Darbandi

address: 1550 4th Street

department: Psychiatry

institute: University of California San Francisco

data_processing:
Clustering, base calling, and quality metrics were performed using standard Illumina software.
Sequenced libraries were analyzed for overall quality and were filtered to remove artifacts and low-quality sequences using Trim Galore version 0.4.2
reads were mapped to the mouse genome (mm9) using BWA version 0.7.16a
Significant binding peaks were called on individual replicates using MACS version 2.1.0
Genome_build: mm9
Supplementary_files_format_and_content: BED files.

source_name: P2 Wildtype Cortex_Input DNA

extract_protocol:
Lysates were clarified from sonicated nuclei and TBR1-DNA complexes were isolated with antibody.
ChIP-seq libraries were generated using Ovation Ultralow System V2 (NuGEN) following manufacturer’s protocol. Libraries were sequenced on Illumina HiSeq 4000

tag: strain

value: cortex

tag: chip antibody


title: TBR1 ChIP-seq_Rep2

source_name: P2 Wildtype Cortex_TBR1 ChIP-seq

value: TBR1 (Santa Cruz Biotech, Cat# sc-48816 X)


title: IgG ChIP-seq_Rep1

source_name: P2 Wildtype Cortex_IgG ChIP-seq

value: Rabbit IgG (Santa Cruz Biotech, Cat# sc2027)


title: IgG ChIP-seq_Rep2

value: TBR1 blocking peptide (Abcam, Cat# ab25853)


title: Input DNA_Rep1


title: M. smemgtias MC2 155_6C sRNA inducible vector_induced

source_name: Uninduced

value: with no ATC induction


title: crypt from CSN8ΔIEC mice,biological rep3

city: Louisville

first: Zhong-bin

last: Deng

address: 505 s Hancock street

department: Medicine

institute: University of Louisville

description: Gene expression data from crypt

hyb_protocol: Affymetrix Mouse ClariomTM S arrays

scan_protocol: The arrays were processed following the manufacturer’s recommended wash and stain protocol on an Affymetrix FS-450 fluidics station and scanned on an Affymetrix GeneChip® 7G scanner using the Command Console 4.0

data_processing: The data were analyzed with Partek Genomics Suite 6.6 and transcripts were normalized on a gene level using RMA as a normalization and background correction method

source_name: crypt from CSN8ΔIEC mice

label_protocol: the GeneChip® WT PLUS Reagent kit protocol from Affymetrix

extract_protocol: Total RNA from crypts was isolated using the RNeasy Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer's protocol

value: 10 week

tag: gender

value: male

tag: tissue/cell type

value: small intestinal crypts


title: crypt from CSN8ΔIEC mice,biological rep2

description: Gene expression data from crypt

value: 16 week

value: female


title: S5_1

value: the whole organism

value: on the 15th day after fertilization

value: juvenile


title: crypt from CSN8ΔIEC mice,biological rep1

description: Gene expression data from crypt


title: crypt from CSN8fl/fl mice,biological rep1

description: Gene expression data from crypt

source_name: crypt from CSN8fl/fl mice


title: crypt from CSN8fl/fl mice,biological rep2

description: Gene expression data from crypt


title: TBR1 ChIP-seq_Rep1


title: K1_N_d22_2

city: Kyoto

first: Megumu

last: Saito

address: 53, Shogoin-Kawahara

institute: Kyoto University

description: Gene expression in day 22 Neutrophils

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain signal intensity and performed the bacground correction and normalization using bioconductor package limma

source_name: Kh-ES1, day22 neutrophils, control, replicate 2

extract_protocol: Total RNA was purified using the RNeasy mini or micro kit (Qiagen)  following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

value: Blood cells

value: day 22 neutrophils


title: in vitro-activated, LKB1-deficient CD8+ T cells rep4

status: Public on Sep 01 2018

city: Grand Rapids

first: Russell

last: Jones

address: 333 Bostwick Ave. NE

institute: Van Andel Institute

description: MP.TTGAGCCT

data_processing:
Data were sequenced on HiSeq 2500 instrument (Illumina, San Diego, CA) using 41bpX18bp pair-end sequencing. Second mate was used for sample demultiplexing, at which point individual single-end fastqs were aligned to mm10 genome using STAR with following options --outFilterMultimapNmax 15 --outFilterMismatchNmax 6 --outReadsUnmapped Fastx --outSAMstrandField All.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include raw counts  for each sample

extract_protocol:
RNA was extacted using Trizol following manufacturer's protocol.
For cDNA synthesis, custom oligo-dT primers were used with a barcode and adapter-linker sequence (CCTACACGACGCTCTTCCGATCT—XXXXXXXX-T15). After first strand synthesis, samples were pooled together based on Actb qPCR values, and RNA-DNA hybrids degraded using consecutive acid-alkali treatment. A second sequencing linker (AGATCGGAAGAGCACACGTCTG) was ligated using T4 ligase (NEB) followed by SPRI clean-up. The mixture was then PCR enriched for 12 cycles and SPRI purified to yield final strand specific RNA-seq libraries as previously described (Jha et al., 2015) 3' RNA-Seq

treatment_protocol: Naïve T cells were stimulated with plate-bound anti-CD3 and anti-CD28 antibodies for 48 hours

value: CD8+ T cells

tag: genotype


title: in vitro-activated, LKB1-deficient CD8+ T cells rep2

description: MP.TTCGCTGA


title: crypt from CSN8fl/fl mice,biological rep3

description: Gene expression data from crypt


title: in vitro-activated, LKB1-deficient CD8+ T cells rep1

description: MP.GCACATCT


title: in vitro-activated, control CD8+ T cells rep4

description: MP.ACACGATC

value: LKB1 wild type


title: Col-0_monosome_rep2

city: Wageningen

first: Leónie

last: Bentsink

address: Droevendaalsesteeg 1

country: Netherlands

institute: Wageningen University

hyb_protocol: GeneChip® 3' IVT Express kit (cat. # 901229) was used for hybridization, washing and staining of the cartridges.

scan_protocol: Scanning of the arrays was performed using the Affymetrix 3000G scanner.

data_processing: The GeneChip data were analyzed using the R statistical programming environment and Bioconductor packages. The data were normalized using the RMA algorithm. The P values were adjusted for multiple testing with the Benjamini and Hochberg method to control for false positives.

organism: Arabidopsis thaliana

label_protocol: RNA was processed and cRNA synthesized according to the 3’ GeneChips OneCycle kit.

growth_protocol: For the transcriptome and  transcriptome analyses abci20 and Col-0 were grown in a randomized complete block design with three replicates. Each replicate consisted of a bulk of eight plants. The precise growth conditions used were described by (El-Lithy et al., Genetics, 2006).

extract_protocol: The total RNA and polysomal RNA were purified with TriPure Isolation Reagent (Roche, Basel, Switzerland), further purified using RNeasy Mini spin columns (Qiagen, Hilden, Germany) and dissolved in RNase-free H2O for further analyses.

treatment_protocol: RNA was extracted from freshly harvested, dry seeds of three biological replicates of each genotype.

tag: ecotype

value: wild type

value: seed

tag: rna fraction

value: Monosomal RNA


title: Col-0_total_rep2

value: Total RNA


title: Col-0_total_rep1


title: Col-0_polysome_rep3

value: Polysomal RNA


title: Col-0_monosome_rep1


title: Col-0_polysome_rep2


title: Col-0_total_rep3


title: ABCI20_polysome_rep1

value: abci20 mutant


title: ABCI20_monosome_rep3


title: in vitro-activated, control CD8+ T cells rep3

description: MP.TCGGAATG


title: in vitro-activated, control CD8+ T cells rep2

description: MP.CCAGTTAG


title: ABCI20_polysome_rep2


title: in vitro-activated, control CD8+ T cells rep1

description: MP.AGCAATTC


title: in vitro-activated, LKB1-deficient CD8+ T cells rep3

description: MP.GGTCCAGA


title: ABCI20_polysome_rep3


title: ABCI20_total_rep3


title: f_pHep_f_GF_serum_GH_3

city: St Lucia

first: Frédéric

last: Gachon

state: QLD

address: 306 Carmody Road

department: Institute for Molecular Bioscience

country: Australia

institute: University Of Queensland

data_processing:
Sequences were aligned to the full reference genome index build with Ensembl annotation to improve accuracy on splices junctions using STAR 2.4.0i
A custom Perl script was used to quantify uniquely mapped reads. For each Ensembl gene, all exons of the respective annotated protein-coding transcripts were considered.
Genome_build: mm10
Supplementary_files_format_and_content: raw counts of fragments

source_name: primay hepatocytes

extract_protocol:
RNAs was extracted using the miRNeasy Mini Kit (Qiagen) and following the manufacturer's protocol.
The RNA were quantified with Ribogreen (Life Technologies) and quality assessed on a Fragment Analyzer (Advances Analytical). Sequencing libraries were prepared from 250 ng total RNA using the TruSeq Stranded Total LT Sample Prep Kit (Illumina) with the Ribo-Zero Gold depletion set. The procedure was automated on a Sciclone NGS Workstation (Perkin Elmer). The manufacturer’s protocol was strictly followed, except for the PCR amplification step. The latter was run for 12 cycles with the KAPA HiFi HotStart ReadyMix (Kapa BioSystems). This optimal PCR cycle number has been evaluated using the Cycler Correction Factor method as described previously (Atger et al., PNAS, 2015). Purified libraries were quantified with Picogreen (Life Technologies) and the size pattern was controlled with the DNA High Sensitivity Reagent kit on a LabChip GX (Perkin Elmer). Libraries were then pooled by 24 and each pool was clustered at a concentration of 7 pmol on 8 lanes of a v3 paired-end sequencing flow cell (Illumina). Sequencing was performed for 2 x 100 cycles on a HiSeq 2500 strictly following Illumina’s recommendations.

treatment_protocol: Cryopreserved hepatocytes from a female or male (Thermo Scientific #MSCP10/20) CD-1 donor mice were seeded into Collagen I coated 24 well plates (Thermo Scientific #CM1024) (200,000 cells/well) and incubated in plating medium (Williams’ E Medium supplemented with 5% Fetal Bovine Serum, 1 μM Dexamethasone, 1% Penicillin/Streptomycin, 4 μg /mL Human Recombinant Insulin, 2 mM GlutaMAX  and 15 mM HEPES). After a 6 h incubation period to allow the cells to attach to the plate, medium was changed to a defined incubation medium (Williams E Medium supplemented with 0.1 μM Dexamethasone, 0.5% Penicillin/Streptomycin, 6.25 μg/ml human recombinant insulin, 6.25 μg/ml  human transferrin, 6.25 ng/mL  selenous acid, 1.25 mg/ml  bovine serum albumin, 5.35 μg/mL linoleic acid, 2 mM GlutaMAX  and 15 mM HEPES) and a Geltrex matrix (Thermo Scientific #A1413201) overlay was applied to the plated cells. The next day, the maintenance medium supplemented with 25% sterile-filtered serum from convR male, convR female or GF female mice was applied to the cells. After 24 h cells were then either treated with 8 ng/ml mouse growth hormone (NHPP-NIDDK #AFP-10783B) or vehicle (PBS) for 2 h before RNA extraction.

value: primay hepatocytes

tag: serum treatment

value: GF female serum

tag: growth hormone treatment

value: GH treated

tag: sex of hepatocyte donor

value: Female


title: ABCI20_monosome_rep1

tag: genotype/variation

tag: tissue


title: f_pHep_f_GF_serum_GH_1


title: f_pHep_f_GF_serum_3


title: f_pHep_f_GF_serum_1


title: f_pHep_f_GF_serum_2


title: ABCI20_monosome_rep2


title: f_pHep_f_ConvR_3

value: ConvR female serum


title: f_pHep_m_ConvR_2

value: ConvR male serum


title: f_pHep_m_ConvR_3


title: f_pHep_f_ConvR_1


title: f_pHep_f_GF_serum_GH_2


title: m_pHep_m_ConvR_3

value: Male


title: f_pHep_m_ConvR_1


title: m_pHep_m_ConvR_2


title: testis_GF3

source_name: testis

extract_protocol:
Ovaries and testis were disrupted and extracted using the tissue lyser II (Qiagen) and the miRNeasy Mini Kit (Qiagen) following the manufacturer's protocol.
The RNA were quantified with Ribogreen (Life Technologies) and quality assessed on a Fragment Analyzer (Advances Analytical). Sequencing libraries were prepared from 250 ng total RNA using the TruSeq Stranded Total LT Sample Prep Kit (Illumina) with the Ribo-Zero Gold depletion set. The procedure was automated on a Sciclone NGS Workstation (Perkin Elmer). The manufacturer’s protocol was strictly followed, except for the PCR amplification step. The latter was run for 12 cycles with the KAPA HiFi HotStart ReadyMix (Kapa BioSystems). This optimal PCR cycle number has been evaluated using the Cycler Correction Factor method as described previously (Atger et al., PNAS, 2015). Purified libraries were quantified with Picogreen (Life Technologies) and the size pattern was controlled with the DNA High Sensitivity Reagent kit on a LabChip GX (Perkin Elmer). Libraries were then pooled by 24 and each pool was clustered at a concentration of 7 pmol on 8 lanes of a v3 paired-end sequencing flow cell (Illumina). Sequencing was performed for 2 x 100 cycles on a HiSeq 2500 strictly following Illumina’s recommendations.

value: testis

tag: age

value: 15-16 weeks

tag: gut microbiome status

value: germ-free

tag: zeitgeber time

tag: Sex


title: m_pHep_m_ConvR_1

tag: cell type


title: testis_CV4

tag: strain

value: conventional raised


title: testis_GF1


title: testis_CV3


title: testis_CV2


title: ovary_GF5

source_name: ovary

value: ovary


title: ovary_GF4


title: testis_CV1


title: f_pHep_f_ConvR_2


title: ovary_GF1


title: ovary_GF3


title: ovary_GF2


title: Col-0_polysome_rep1

value: wild type

value: seed


title: ovary_CV2


title: ovary_CV3


title: ovary_CV1


title: Ghrelin_CTR_Liver_male_6

source_name: Liver

extract_protocol:
Liver RNAs were extracted as previously described (Gachon et al, 2006) with classical methods using guanidium  thiocyanate lysis buffer.
The RNA were quantified with Ribogreen (Life Technologies) and quality assessed on a Fragment Analyzer (Advances Analytical). Sequencing libraries were prepared from 250 ng total RNA using the TruSeq Stranded Total LT Sample Prep Kit (Illumina) with the Ribo-Zero Gold depletion set. The procedure was automated on a Sciclone NGS Workstation (Perkin Elmer). The manufacturer’s protocol was strictly followed, except for the PCR amplification step. The latter was run for 12 cycles with the KAPA HiFi HotStart ReadyMix (Kapa BioSystems). This optimal PCR cycle number has been evaluated using the Cycler Correction Factor method as described previously (Atger et al., PNAS, 2015). Purified libraries were quantified with Picogreen (Life Technologies) and the size pattern was controlled with the DNA High Sensitivity Reagent kit on a LabChip GX (Perkin Elmer). Libraries were then pooled by 24 and each pool was clustered at a concentration of 7 pmol on 8 lanes of a v3 paired-end sequencing flow cell (Illumina). Sequencing was performed for 2 x 125 cycles on a HiSeq 2500 strictly following Illumina’s recommendations.

treatment_protocol: Male GF animals were subcutanously injected daily with rat ghrelin (Tocris #1465, 10 µg/mouse) or PBS (at ZT 2) over a period of 5 days.

value: Liver

value: 13-16 weeks

tag: treatment

value: PBS injected


title: Ghrelin_TRT_Liver_male_5

value: ghrelin injected


title: Ghrelin_TRT_Liver_male_6


title: Ghrelin_TRT_Liver_male_4


title: Ghrelin_TRT_Liver_male_3


title: Ghrelin_TRT_Liver_male_2


title: Ghrelin_TRT_Liver_male_1


title: Ghrelin_CTR_Liver_male_4


title: testis_GF2


title: Ghrelin_CTR_Liver_male_3


title: Ghrelin_CTR_Liver_male_2


title: Ghrelin_CTR_Liver_male_1


title: Gho_TRT_Liver_male_5

treatment_protocol: Male GF animals were subcutanously injected with recombinant human growth hormone (BioVision #4769, 50µg/mouse) or PBS twice a day (ZT 2 and ZT 14) over a period of 5 days.

value: Growth hormone


title: Gho_TRT_Liver_male_6


title: ovary_CV4


title: Col-0_monosome_rep3

value: Monosomal RNA


title: Gho_TRT_Liver_male_4


title: Gho_TRT_Liver_male_3


title: ABCI20_total_rep2

value: abci20 mutant

value: Total RNA


title: Gho_TRT_Liver_male_2


title: Gho_TRT_Liver_male_1


title: Gho_CTR_Liver_male_4

value: PBS


title: Gho_CTR_Liver_male_6

value: Male


title: Gho_CTR_Liver_male_3


title: Gho_CTR_Liver_male_2


title: Ghrelin_CTR_Liver_male_5


title: Gho_CTR_Liver_male_1


title: Gho_CTR_Liver_male_5