title: liver_ATAC_733_l2_s1

description:
Sample titles are in the format liver_ATAC_[sampleID]_[libraryID]_[sequencingRun]. Note that resequenced libraries were run at a later date and were sometimes on a different sequencer than the original sequencing run, so resequenced libraries are listed as separate samples.
733_peaks.narrowPeak.gz
733_scaled.bw


title: M_DEC_PAN

status: Public on Feb 01 2025

type: SRA

city: Nagoya

first: Junfeng

last: Chen

state: 23 - 愛知県

address: Nagoya University

country: Japan

institute: Nagoya University

library_source: transcriptomic

data_processing:
Mapping and quantification were performed by bowtie (v1.2.3) and RSEM (v1.3.3).
Assembly: Mmul_10
Supplementary files format and content: Excel files include FPM values for each tissue.

molecule: total RNA

organism: Macaca mulatta

source_name: pancreas

growth_protocol: Adult rhesus macaques were kept in an open enclosure  with natural light and temperature at the Center for the Evolutionary Origins of Human Behavior, Kyoto University, Inuyama, Japan. Two meals were provided per day at the estimated ad libitum levels and water was always available ad libitum.

extract_protocol:
Total RNA was extracted using the RNeasy Plus Universal Mini Kit (Qiagen).
3'RNA-Seq library was prepared by the Lasy-Seq v1.1 protocol (https://sites.google.com/view/lasy-seq/)

treatment_protocol: Macaques were immobilized with  10 mg/kg BW ketamine hydrochloride (intramuscularly), and anaesthesized with 80 mg/kg BW pentobarbital (intravenously), and perfused with ice-cold Ames' medium.

tag: sampling point

value: December, 2019

tag: tissue

value: pancreas

tag: Sex

value: M


title: liver_ATAC_733_l1_s1

city: Chapel Hill

first: Karen

middle: L

last: Mohlke

state: NC

address: 120 Mason Farm Road

department: Genetics

country: USA

institute: University of North Carolina at Chapel Hill

library_source: genomic

data_processing:
Raw sequence reads were trimmed for adapters and low quality bases using cutadapt with parameters -q 20 --minimum-length 36. Reads were aligned to the GRCh38 version of the genome using bowtie2 with parameters --minins 36 --maxins 1000 --no-mixed --no-discordant --no-unal. Reads overlapping ENCODE exclusion regions were removed with BEDTools pairToBed. Reads on primary nuclear chromosomes (chr 1-22, X, Y) with mapq > 20 were selected with samtools. Duplicate alignments were removed using picard MarkDuplicates.
We converted BAM files to BED files using BEDTools and called peaks on each ATAC-seq library separately using MACS2 with parameters -q 0.05 –nomodel –shift -100 –extsize 200 –keep-dup all.
For each individual, we merged the BAM files of the high-quality libraries and removed duplicates using Picard MarkDuplicates because some libraries for the same donor represent re-sequencing of the same library preparation. We then called peaks on merged libraries per individual using the same procedure that we used for single libraries. We merged peaks across individuals using BEDTools and retained merged peaks found in at least 7 individuals (5% of 138). Merging peaks across individuals can result in wide peak boundaries and concatenation of multiple nearby accessible chromatin regions into one peak. Therefore, we developed a procedure to refine the boundaries of the merged peaks found in at least 7 individuals. We first calculated the number of individuals that had a peak overlapping each base of each merged peak, which we define as coverage, using BEDTools coverage. We converted the output of BEDTools coverage into a matrix of coverage values with peak IDs as rows and peak bases as columns. For each peak, we identified all local minima in coverage; peaks that contain only one peak should have only two local minima, whereas peaks containing multiple sub-peaks will have 3 or more local minima. To prevent classifying small fluctuations in coverage as sub-peaks, we only retained adjacent pairs of minima if the distance between them was at least 200 basepairs (bp) and if the maximum coverage between them was both greater than 7 and greater than twice the maximum of the two minima. To define consensus peak boundaries, we identified the position between the two local minima with maximum coverage and extended in both directions until we reached the outermost positions that had half of the maximum coverage. This is similar to the full width at half maximum procedure used to identify boundaries of DNase peaks in ENCODE.
Assembly: GRCh38
Supplementary files format and content: The bigWig (.bw) files contain ATAC-seq signal normalized by reads per million.
Supplementary files format and content: The narrowPeak files contain peaks called on individual donors and are in standard narrowPeak format from macs2. The consensus peaks bed file contains the genomic coordinates of the consensus peaks in bed4 format, with columns chr, start, stop, and peakID.

molecule: genomic DNA

organism: Homo sapiens

source_name: liver tissue

extract_protocol:
We pulverized 50-mg pieces of frozen human liver tissue in liquid nitrogen using a Cell Crusher (CellCrusher), homogenized the tissue powder in ice-cold nuclei isolation buffer (NIB: 20 mM Tris-HCl, 50 mM EDTA, 5 mM spermidine, 0.15 mM spermine, 0.1% mercaptoethanol, 40% glycerol [pH 7.5]) using a 1-mL dounce for 40 strokes, and rotated for 5 min at 4°C. We filtered the solution through a Miracloth (Calbiochem), centrifuged at 1,100 × g for 10 min at 4°C, washed the pellet with 250 μL NIB containing 0.5% Triton-X, centrifuged at 500 × g for 5 min at 4°C, and resuspended the pellet in 250 μL of resuspension buffer (10 mM Tris-HCl, 10 mM NaCl, 3 mM MgCl2 [pH 7.4]). After counting isolated nuclei, we pelleted 50,000 nuclei at 500 × g for 5 min at 4°C
We prepared ATAC-seq libraries using the omni-ATAC protocol with 5 ul Tn5 transposase per reaction, cleaned the transposase reaction and final libraries with Zymo DNA Clean and Concentrator (D4029), visualized and quantified the libraries using a TapeStation, and sequenced 150-bp paired-end reads on either an Illumina HiSeq 4000 or HiSeq X ten.

value: liver tissue


title: liver_ATAC_730_l3_s1

description:
Sample titles are in the format liver_ATAC_[sampleID]_[libraryID]_[sequencingRun]. Note that resequenced libraries were run at a later date and were sometimes on a different sequencer than the original sequencing run, so resequenced libraries are listed as separate samples.
730_peaks.narrowPeak.gz
730_scaled.bw


title: liver_ATAC_730_l2_s1


title: M_DEC_OES

source_name: oesophagus

value: oesophagus


title: liver_ATAC_765_l1_s1

description:
Sample titles are in the format liver_ATAC_[sampleID]_[libraryID]_[sequencingRun]. Note that resequenced libraries were run at a later date and were sometimes on a different sequencer than the original sequencing run, so resequenced libraries are listed as separate samples.
765_peaks.narrowPeak.gz
765_scaled.bw


title: M_DEC_NAc

source_name: nucleus accumbens

value: nucleus accumbens


title: M_DEC_SON

source_name: supraoptic nucleus

value: supraoptic nucleus


title: M_DEC_MUG

source_name: gastrocnemial muscle

value: gastrocnemial muscle


title: M_DEC_PRO

source_name: prostate gland

value: prostate gland


title: M_DEC_MUA

source_name: abdominal muscle

value: abdominal muscle


title: M_DEC_mPOA

source_name: medial preoptic area

value: medial preoptic area


title: liver_ATAC_724_l1_s1

description:
Sample titles are in the format liver_ATAC_[sampleID]_[libraryID]_[sequencingRun]. Note that resequenced libraries were run at a later date and were sometimes on a different sequencer than the original sequencing run, so resequenced libraries are listed as separate samples.
724_peaks.narrowPeak.gz
724_scaled.bw


title: liver_ATAC_724_l2_s1


title: M_DEC_mPFC

source_name: medial prefrontal cortex

value: medial prefrontal cortex


title: M_DEC_MMB

source_name: mammilary nuclei

value: mammilary nuclei


title: M_DEC_PVN

source_name: paraventricular nucleus

value: paraventricular nucleus


title: liver_ATAC_720_l2_s1

description:
Sample titles are in the format liver_ATAC_[sampleID]_[libraryID]_[sequencingRun]. Note that resequenced libraries were run at a later date and were sometimes on a different sequencer than the original sequencing run, so resequenced libraries are listed as separate samples.
720_peaks.narrowPeak.gz
720_scaled.bw


title: liver_ATAC_720_l3_s1


title: M_DEC_MEL

source_name: mesenteric lymph node

value: mesenteric lymph node


title: liver_ATAC_733_l3_s1


title: liver_ATAC_720_l1_s1


title: M_DEC_OLB

source_name: olfactory bulb

value: olfactory bulb


title: M_DEC_LUN

source_name: lung

value: lung


title: M_DEC_LIV

source_name: liver

value: December, 2019

value: liver


title: liver_ATAC_711_l3_s1

description:
Sample titles are in the format liver_ATAC_[sampleID]_[libraryID]_[sequencingRun]. Note that resequenced libraries were run at a later date and were sometimes on a different sequencer than the original sequencing run, so resequenced libraries are listed as separate samples.
711_peaks.narrowPeak.gz
711_scaled.bw


title: liver_ATAC_730_l1_s1


title: liver_ATAC_711_l2_s1


title: liver_ATAC_744_l2_s1

description:
Sample titles are in the format liver_ATAC_[sampleID]_[libraryID]_[sequencingRun]. Note that resequenced libraries were run at a later date and were sometimes on a different sequencer than the original sequencing run, so resequenced libraries are listed as separate samples.
744_peaks.narrowPeak.gz
744_scaled.bw


title: M_DEC_NM

source_name: nasal mucosa

value: nasal mucosa

value: M


title: M_DEC_LHA

source_name: lateral hypothalamic nucleus

value: lateral hypothalamic nucleus


title: liver_ATAC_724_l3_s1

source_name: liver tissue

value: liver tissue


title: liver_ATAC_711_l1_s1


title: M_DEC_KIM

source_name: kidney medulla

value: kidney medulla


title: liver_ATAC_687_l3_s1

description:
Sample titles are in the format liver_ATAC_[sampleID]_[libraryID]_[sequencingRun]. Note that resequenced libraries were run at a later date and were sometimes on a different sequencer than the original sequencing run, so resequenced libraries are listed as separate samples.
687_peaks.narrowPeak.gz
687_scaled.bw


title: liver_ATAC_687_l2_s1


title: liver_ATAC_687_l1_s1


title: M_DEC_KIC

source_name: kidney cortex

value: kidney cortex


title: M_DEC_LC

source_name: locus coeruleus

value: locus coeruleus


title: liver_ATAC_669_l2_s1

description:
Sample titles are in the format liver_ATAC_[sampleID]_[libraryID]_[sequencingRun]. Note that resequenced libraries were run at a later date and were sometimes on a different sequencer than the original sequencing run, so resequenced libraries are listed as separate samples.
669_peaks.narrowPeak.gz
669_scaled.bw


title: M_DEC_IRI

source_name: iris

value: iris


title: liver_ATAC_669_l3_s1


title: M_DEC_ILE

source_name: ileum

value: ileum


title: liver_ATAC_669_l1_s1


title: M_DEC_HEA

source_name: heart

value: heart


title: liver_ATAC_659_l3_s1

description:
Sample titles are in the format liver_ATAC_[sampleID]_[libraryID]_[sequencingRun]. Note that resequenced libraries were run at a later date and were sometimes on a different sequencer than the original sequencing run, so resequenced libraries are listed as separate samples.
659_peaks.narrowPeak.gz
659_scaled.bw


title: liver_ATAC_659_l1_s1


title: M_DEC_JEJ

source_name: jejunum

value: jejunum


title: M_DEC_GUM

source_name: gum

value: gum


title: liver_ATAC_659_l2_s1


title: M_DEC_GPi

source_name: globus pallidus internal segment

value: globus pallidus internal segment


title: M_DEC_GPe

source_name: globus pallidus external segment

value: globus pallidus external segment


title: liver_ATAC_657_l2_s1

description:
Sample titles are in the format liver_ATAC_[sampleID]_[libraryID]_[sequencingRun]. Note that resequenced libraries were run at a later date and were sometimes on a different sequencer than the original sequencing run, so resequenced libraries are listed as separate samples.
657_peaks.narrowPeak.gz
657_scaled.bw


title: liver_ATAC_651_l2_s1

description:
Sample titles are in the format liver_ATAC_[sampleID]_[libraryID]_[sequencingRun]. Note that resequenced libraries were run at a later date and were sometimes on a different sequencer than the original sequencing run, so resequenced libraries are listed as separate samples.
651_peaks.narrowPeak.gz
651_scaled.bw


title: M_DEC_FOV

source_name: fovea centralis

value: fovea centralis


title: M_DEC_GAL

source_name: gallbladder

value: December, 2019

value: gallbladder


title: liver_ATAC_657_l1_s1


title: M_DEC_EPI

source_name: epididymis

value: epididymis


title: liver_ATAC_649_l3_s1

description:
Sample titles are in the format liver_ATAC_[sampleID]_[libraryID]_[sequencingRun]. Note that resequenced libraries were run at a later date and were sometimes on a different sequencer than the original sequencing run, so resequenced libraries are listed as separate samples.
649_peaks.narrowPeak.gz
649_scaled.bw


title: M_DEC_DMH

source_name: dorsomedial hypothalamic nucleus

value: dorsomedial hypothalamic nucleus

value: M


title: liver_ATAC_651_l1_s1

value: liver tissue


title: liver_ATAC_649_l2_s1


title: M_DEC_CRB

source_name: cerebellum

value: cerebellum


title: liver_ATAC_644_l3_s1

description:
Sample titles are in the format liver_ATAC_[sampleID]_[libraryID]_[sequencingRun]. Note that resequenced libraries were run at a later date and were sometimes on a different sequencer than the original sequencing run, so resequenced libraries are listed as separate samples.
644_peaks.narrowPeak.gz
644_scaled.bw


title: M_DEC_COR

source_name: cornea

value: cornea


title: liver_ATAC_644_l2_s1

source_name: liver tissue


title: M_DEC_DRN

source_name: dorsal raphe

value: dorsal raphe


title: M_DEC_CEC

source_name: cecum

value: cecum


title: liver_ATAC_649_l1_s1


title: liver_ATAC_657_l3_s1


title: liver_ATAC_644_l1_s1


title: M_DEC_CAU

source_name: caudate nucleus

value: caudate nucleus


title: M_DEC_COL

source_name: colon

value: colon


title: M_DEC_CAT

source_name: cartilage

value: cartilage


title: liver_ATAC_639_l3_s1

description:
Sample titles are in the format liver_ATAC_[sampleID]_[libraryID]_[sequencingRun]. Note that resequenced libraries were run at a later date and were sometimes on a different sequencer than the original sequencing run, so resequenced libraries are listed as separate samples.
639_peaks.narrowPeak.gz
639_scaled.bw


title: liver_ATAC_639_l1_s1


title: liver_ATAC_636_l2_s1

description:
Sample titles are in the format liver_ATAC_[sampleID]_[libraryID]_[sequencingRun]. Note that resequenced libraries were run at a later date and were sometimes on a different sequencer than the original sequencing run, so resequenced libraries are listed as separate samples.
636_peaks.narrowPeak.gz
636_scaled.bw


title: M_DEC_CA1

source_name: hippocampus CA1

value: hippocampus CA1


title: M_DEC_DUO

source_name: duodenum

value: duodenum


title: M_DEC_CA3

source_name: hippocampus CA3

value: hippocampus CA3


title: liver_ATAC_634_l2_s1

description:
Sample titles are in the format liver_ATAC_[sampleID]_[libraryID]_[sequencingRun]. Note that resequenced libraries were run at a later date and were sometimes on a different sequencer than the original sequencing run, so resequenced libraries are listed as separate samples.
634_peaks.narrowPeak.gz
634_scaled.bw


title: liver_ATAC_636_l1_s1


title: M_DEC_BON

source_name: bone

value: bone


title: liver_ATAC_634_l3_s1


title: liver_ATAC_634_l1_s1


title: M_DEC_HAB

source_name: habenula

value: December, 2019

value: habenula


title: M_DEC_BNST

source_name: bed nucleus of the stria terminalis

value: bed nucleus of the stria terminalis


title: M_DEC_PT

source_name: pars tuberalis of the pituitary

value: pars tuberalis of the pituitary


title: M_DEC_BLA

source_name: urinary bladder

value: urinary bladder

value: M


title: M_DEC_BAT

source_name: brown adipose tissue

value: brown adipose tissue


title: liver_ATAC_633_l2_s1

description:
Sample titles are in the format liver_ATAC_[sampleID]_[libraryID]_[sequencingRun]. Note that resequenced libraries were run at a later date and were sometimes on a different sequencer than the original sequencing run, so resequenced libraries are listed as separate samples.
633_peaks.narrowPeak.gz
633_scaled.bw

value: liver tissue


title: liver_ATAC_633_l3_s1


title: liver_ATAC_639_l2_s1


title: liver_ATAC_632_l1_s1

description:
Sample titles are in the format liver_ATAC_[sampleID]_[libraryID]_[sequencingRun]. Note that resequenced libraries were run at a later date and were sometimes on a different sequencer than the original sequencing run, so resequenced libraries are listed as separate samples.
632_peaks.narrowPeak.gz
632_scaled.bw


title: M_DEC_AXL

source_name: axillary lymph node

value: axillary lymph node


title: M_DEC_AMYL

source_name: amygdala lateral nucleus

value: amygdala lateral nucleus


title: liver_ATAC_631_l4_s1

description:
Sample titles are in the format liver_ATAC_[sampleID]_[libraryID]_[sequencingRun]. Note that resequenced libraries were run at a later date and were sometimes on a different sequencer than the original sequencing run, so resequenced libraries are listed as separate samples.
631_peaks.narrowPeak.gz
631_scaled.bw

source_name: liver tissue


title: M_DEC_ANU

source_name: anus

value: anus


title: liver_ATAC_632_l2_s1


title: liver_ATAC_632_l3_s1


title: liver_ATAC_631_l3_s1


title: M_DEC_BOM

source_name: bone marrow

value: bone marrow


title: M_DEC_AMYC

source_name: amygdala central nucleus

value: amygdala central nucleus


title: liver_ATAC_631_l2_s1


title: liver_ATAC_631_l1_s1


title: M_AUG_WAT

source_name: white adipose tissue

value: August, 2020

value: white adipose tissue


title: M_DEC_ADG

source_name: adrenal gland

value: adrenal gland


title: liver_ATAC_630_l3_s1

description:
Sample titles are in the format liver_ATAC_[sampleID]_[libraryID]_[sequencingRun]. Note that resequenced libraries were run at a later date and were sometimes on a different sequencer than the original sequencing run, so resequenced libraries are listed as separate samples.
630_peaks.narrowPeak.gz
630_scaled.bw


title: M_AUG_VMH

source_name: ventromedial  hypothalamic nucleus

value: ventromedial  hypothalamic nucleus


title: liver_ATAC_633_l1_s1


title: M_DEC_BRO

source_name: bronchus

value: December, 2019

value: bronchus


title: liver_ATAC_630_l1_s1


title: M_AUG_VIC

source_name: visual cortex

value: visual cortex


title: liver_ATAC_629_l2_s1

description:
Sample titles are in the format liver_ATAC_[sampleID]_[libraryID]_[sequencingRun]. Note that resequenced libraries were run at a later date and were sometimes on a different sequencer than the original sequencing run, so resequenced libraries are listed as separate samples.
629_peaks.narrowPeak.gz
629_scaled.bw


title: M_AUG_THR

source_name: thyroid

value: thyroid


title: M_DEC_AOR

source_name: aorta

value: aorta


title: M_DEC_ARC

source_name: arcuate nucleus

value: arcuate nucleus

value: M


title: liver_ATAC_629_l3_s1

value: liver tissue


title: liver_ATAC_629_l1_s1


title: M_AUG_VTA

source_name: ventral tegmental area

value: ventral tegmental area


title: M_AUG_STM

source_name: stomach

value: stomach


title: liver_ATAC_627_l3_s1

description:
Sample titles are in the format liver_ATAC_[sampleID]_[libraryID]_[sequencingRun]. Note that resequenced libraries were run at a later date and were sometimes on a different sequencer than the original sequencing run, so resequenced libraries are listed as separate samples.
627_peaks.narrowPeak.gz
627_scaled.bw


title: M_AUG_TES

source_name: testis

value: testis


title: liver_ATAC_627_l1_s1


title: liver_ATAC_627_l2_s1


title: M_AUG_THA

source_name: thalamus

value: thalamus


title: liver_ATAC_623_l3_s1

description:
Sample titles are in the format liver_ATAC_[sampleID]_[libraryID]_[sequencingRun]. Note that resequenced libraries were run at a later date and were sometimes on a different sequencer than the original sequencing run, so resequenced libraries are listed as separate samples.
623_peaks.narrowPeak.gz
623_scaled.bw


title: M_AUG_SPL

source_name: spleen

value: spleen


title: M_AUG_SON

source_name: supraoptic nucleus

value: August, 2020

value: supraoptic nucleus


title: liver_ATAC_623_l2_s1

source_name: liver tissue


title: M_AUG_SN

source_name: substantia nigra

value: substantia nigra


title: liver_ATAC_623_l1_s1


title: M_AUG_SKNH

source_name: skin in the hindquarter

value: skin in the hindquarter


title: liver_ATAC_630_l2_s1


title: M_AUG_SKNB

source_name: skin on the back

value: skin on the back


title: liver_ATAC_620_l2_s1

description:
Sample titles are in the format liver_ATAC_[sampleID]_[libraryID]_[sequencingRun]. Note that resequenced libraries were run at a later date and were sometimes on a different sequencer than the original sequencing run, so resequenced libraries are listed as separate samples.
620_peaks.narrowPeak.gz
620_scaled.bw


title: liver_ATAC_620_l1_s1


title: liver_ATAC_619_l3_s1

description:
Sample titles are in the format liver_ATAC_[sampleID]_[libraryID]_[sequencingRun]. Note that resequenced libraries were run at a later date and were sometimes on a different sequencer than the original sequencing run, so resequenced libraries are listed as separate samples.
619_peaks.narrowPeak.gz
619_scaled.bw


title: M_AUG_RPE

source_name: pigmental epithelial cells

value: pigmental epithelial cells


title: M_AUG_SCN

source_name: suprachiasmatic nucleus

value: suprachiasmatic nucleus


title: M_AUG_RET

source_name: retina

value: retina


title: liver_ATAC_619_l1_s1


title: liver_ATAC_619_l2_s1


title: M_AUG_REC

source_name: rectum

value: rectum


title: liver_ATAC_618_l3_s1

description:
Sample titles are in the format liver_ATAC_[sampleID]_[libraryID]_[sequencingRun]. Note that resequenced libraries were run at a later date and were sometimes on a different sequencer than the original sequencing run, so resequenced libraries are listed as separate samples.
618_peaks.narrowPeak.gz
618_scaled.bw


title: M_AUG_PVN

source_name: paraventricular nucleus

value: paraventricular nucleus


title: M_AUG_PUT

source_name: putamen

value: putamen

value: M


title: liver_ATAC_618_l1_s1

value: liver tissue


title: liver_ATAC_618_l2_s1


title: liver_ATAC_617_l3_s1

description:
Sample titles are in the format liver_ATAC_[sampleID]_[libraryID]_[sequencingRun]. Note that resequenced libraries were run at a later date and were sometimes on a different sequencer than the original sequencing run, so resequenced libraries are listed as separate samples.
617_peaks.narrowPeak.gz
617_scaled.bw


title: M_AUG_TON

source_name: tongue

value: tongue


title: M_AUG_PIN

source_name: pineal gland

value: pineal gland


title: liver_ATAC_617_l1_s1


title: M_AUG_PD

source_name: pars distalis of the pituitary

value: pars distalis of the pituitary


title: liver_ATAC_617_l2_s1


title: M_AUG_PRO

source_name: prostate gland

value: prostate gland


title: liver_ATAC_493_l2_s1

description:
Sample titles are in the format liver_ATAC_[sampleID]_[libraryID]_[sequencingRun]. Note that resequenced libraries were run at a later date and were sometimes on a different sequencer than the original sequencing run, so resequenced libraries are listed as separate samples.
493_peaks.narrowPeak.gz
493_scaled.bw


title: liver_ATAC_620_l3_s1


title: liver_ATAC_493_l3_s1


title: M_AUG_SG

source_name: salivary gland

value: August, 2020

value: salivary gland


title: liver_ATAC_493_l1_s1


title: M_AUG_OES

source_name: oesophagus

value: oesophagus


title: liver_ATAC_492_l3_s1

description:
Sample titles are in the format liver_ATAC_[sampleID]_[libraryID]_[sequencingRun]. Note that resequenced libraries were run at a later date and were sometimes on a different sequencer than the original sequencing run, so resequenced libraries are listed as separate samples.
492_peaks.narrowPeak.gz
492_scaled.bw


title: M_AUG_NAc

source_name: nucleus accumbens

value: nucleus accumbens


title: M_AUG_NM

source_name: nasal mucosa

value: nasal mucosa


title: M_AUG_OLB

source_name: olfactory bulb

value: olfactory bulb


title: liver_ATAC_492_l1_s1

source_name: liver tissue


title: liver_ATAC_492_l2_s1


title: M_AUG_MUG

source_name: gastrocnemial muscle

value: gastrocnemial muscle


title: liver_ATAC_489_l3_s1

description:
Sample titles are in the format liver_ATAC_[sampleID]_[libraryID]_[sequencingRun]. Note that resequenced libraries were run at a later date and were sometimes on a different sequencer than the original sequencing run, so resequenced libraries are listed as separate samples.
489_peaks.narrowPeak.gz
489_scaled.bw


title: M_AUG_MUA

source_name: abdominal muscle

value: abdominal muscle


title: liver_ATAC_489_l2_s1


title: M_AUG_PT

source_name: pars tuberalis of the pituitary

value: pars tuberalis of the pituitary


title: liver_ATAC_489_l1_s1


title: M_AUG_mPOA

source_name: medial preoptic area

value: medial preoptic area


title: liver_ATAC_484_l2_s1

description:
Sample titles are in the format liver_ATAC_[sampleID]_[libraryID]_[sequencingRun]. Note that resequenced libraries were run at a later date and were sometimes on a different sequencer than the original sequencing run, so resequenced libraries are listed as separate samples.
484_peaks.narrowPeak.gz
484_scaled.bw


title: M_AUG_MMB

source_name: mammilary nuclei

value: mammilary nuclei


title: M_AUG_PAN

source_name: pancreas

value: pancreas

value: M


title: M_AUG_MEL

source_name: mesenteric lymph node

value: mesenteric lymph node


title: M_AUG_mPFC

source_name: medial prefrontal cortex

value: medial prefrontal cortex


title: M_AUG_LUN

source_name: lung

value: lung


title: liver_ATAC_484_l3_s1

value: liver tissue


title: M_AUG_LIV

source_name: liver

value: August, 2020

value: liver


title: liver_ATAC_479_l3_s1

description:
Sample titles are in the format liver_ATAC_[sampleID]_[libraryID]_[sequencingRun]. Note that resequenced libraries were run at a later date and were sometimes on a different sequencer than the original sequencing run, so resequenced libraries are listed as separate samples.
479_peaks.narrowPeak.gz
479_scaled.bw


title: M_AUG_LC

source_name: locus coeruleus

value: locus coeruleus


title: liver_ATAC_478_l4_s1

description:
Sample titles are in the format liver_ATAC_[sampleID]_[libraryID]_[sequencingRun]. Note that resequenced libraries were run at a later date and were sometimes on a different sequencer than the original sequencing run, so resequenced libraries are listed as separate samples.
478_peaks.narrowPeak.gz
478_scaled.bw


title: liver_ATAC_479_l1_s1


title: liver_ATAC_479_l2_s1


title: M_AUG_KIM

source_name: kidney medulla

value: kidney medulla


title: M_AUG_JEJ

source_name: jejunum

value: jejunum


title: liver_ATAC_478_l2_s1


title: M_AUG_KIC

source_name: kidney cortex

value: kidney cortex


title: liver_ATAC_478_l1_s1


title: M_AUG_IRI

source_name: iris

value: iris


title: liver_ATAC_478_l3_s1


title: liver_ATAC_477_l4_s1

description:
Sample titles are in the format liver_ATAC_[sampleID]_[libraryID]_[sequencingRun]. Note that resequenced libraries were run at a later date and were sometimes on a different sequencer than the original sequencing run, so resequenced libraries are listed as separate samples.
477_peaks.narrowPeak.gz
477_scaled.bw


title: M_AUG_ILE

source_name: ileum

value: ileum


title: liver_ATAC_477_l2_s1

source_name: liver tissue


title: liver_ATAC_477_l3_s1


title: M_AUG_HEA

source_name: heart

value: heart


title: M_AUG_HAB

source_name: habenula

value: habenula


title: liver_ATAC_476_l3_s1

description:
Sample titles are in the format liver_ATAC_[sampleID]_[libraryID]_[sequencingRun]. Note that resequenced libraries were run at a later date and were sometimes on a different sequencer than the original sequencing run, so resequenced libraries are listed as separate samples.
476_peaks.narrowPeak.gz
476_scaled.bw


title: M_AUG_GUM

source_name: gum

value: gum


title: M_AUG_GPe

source_name: globus pallidus external segment

value: globus pallidus external segment


title: M_AUG_LHA

source_name: lateral hypothalamic nucleus

value: lateral hypothalamic nucleus

value: M


title: M_AUG_GAL

source_name: gallbladder

value: gallbladder


title: liver_ATAC_477_l1_s1


title: liver_ATAC_476_l2_s1


title: liver_ATAC_484_l1_s1


title: liver_ATAC_475_l2_s1

description:
Sample titles are in the format liver_ATAC_[sampleID]_[libraryID]_[sequencingRun]. Note that resequenced libraries were run at a later date and were sometimes on a different sequencer than the original sequencing run, so resequenced libraries are listed as separate samples.
475_peaks.narrowPeak.gz
475_scaled.bw


title: M_AUG_DUO

source_name: duodenum

value: duodenum


title: liver_ATAC_475_l4_s1

value: liver tissue


title: M_AUG_EPI

source_name: epididymis

value: August, 2020

value: epididymis


title: M_AUG_FOV

source_name: fovea centralis

value: fovea centralis


title: liver_ATAC_475_l1_s1


title: M_AUG_DRN

source_name: dorsal raphe

value: dorsal raphe


title: liver_ATAC_475_l3_s1


title: liver_ATAC_470_l3_s1

description:
Sample titles are in the format liver_ATAC_[sampleID]_[libraryID]_[sequencingRun]. Note that resequenced libraries were run at a later date and were sometimes on a different sequencer than the original sequencing run, so resequenced libraries are listed as separate samples.
470_peaks.narrowPeak.gz
470_scaled.bw


title: M_AUG_DMH

source_name: dorsomedial hypothalamic nucleus

value: dorsomedial hypothalamic nucleus


title: M_AUG_COR

source_name: cornea

value: cornea


title: liver_ATAC_470_l2_s1


title: M_AUG_CRB

source_name: cerebellum

value: cerebellum


title: liver_ATAC_470_l1_s1


title: liver_ATAC_465_l3_s1

description:
Sample titles are in the format liver_ATAC_[sampleID]_[libraryID]_[sequencingRun]. Note that resequenced libraries were run at a later date and were sometimes on a different sequencer than the original sequencing run, so resequenced libraries are listed as separate samples.
465_peaks.narrowPeak.gz
465_scaled.bw


title: liver_ATAC_465_l2_s1


title: M_AUG_GPi

source_name: globus pallidus internal segment

value: globus pallidus internal segment


title: M_AUG_COL

source_name: colon

value: colon


title: liver_ATAC_476_l1_s1


title: M_AUG_CEC

source_name: cecum

value: cecum


title: liver_ATAC_458_l3_s1

description:
Sample titles are in the format liver_ATAC_[sampleID]_[libraryID]_[sequencingRun]. Note that resequenced libraries were run at a later date and were sometimes on a different sequencer than the original sequencing run, so resequenced libraries are listed as separate samples.
458_peaks.narrowPeak.gz
458_scaled.bw

source_name: liver tissue


title: M_AUG_CAT

source_name: cartilage

value: cartilage


title: liver_ATAC_458_l1_s1


title: M_AUG_CA1

source_name: hippocampus CA1

value: hippocampus CA1


title: liver_ATAC_458_l2_s1


title: M_AUG_BRO

source_name: bronchus

value: bronchus


title: M_AUG_BON

source_name: bone

value: bone

value: M


title: liver_ATAC_450_l2_s1

description:
Sample titles are in the format liver_ATAC_[sampleID]_[libraryID]_[sequencingRun]. Note that resequenced libraries were run at a later date and were sometimes on a different sequencer than the original sequencing run, so resequenced libraries are listed as separate samples.
450_peaks.narrowPeak.gz
450_scaled.bw


title: liver_ATAC_450_l3_s1


title: M_AUG_CA3

source_name: hippocampus CA3

value: hippocampus CA3


title: M_AUG_BOM

source_name: bone marrow

value: bone marrow


title: M_AUG_BLA

source_name: urinary bladder

value: August, 2020

value: urinary bladder


title: liver_ATAC_444_l2_s1

description:
Sample titles are in the format liver_ATAC_[sampleID]_[libraryID]_[sequencingRun]. Note that resequenced libraries were run at a later date and were sometimes on a different sequencer than the original sequencing run, so resequenced libraries are listed as separate samples.
444_peaks.narrowPeak.gz
444_scaled.bw

value: liver tissue


title: liver_ATAC_444_l1_s1


title: liver_ATAC_440_l2_s1

description:
Sample titles are in the format liver_ATAC_[sampleID]_[libraryID]_[sequencingRun]. Note that resequenced libraries were run at a later date and were sometimes on a different sequencer than the original sequencing run, so resequenced libraries are listed as separate samples.
440_peaks.narrowPeak.gz
440_scaled.bw


title: liver_ATAC_440_l3_s1


title: M_AUG_BAT

source_name: brown adipose tissue

value: brown adipose tissue


title: M_AUG_BNST

source_name: bed nucleus of the stria terminalis

value: bed nucleus of the stria terminalis


title: M_AUG_CAU

source_name: caudate nucleus

value: caudate nucleus


title: M_AUG_ARC

source_name: arcuate nucleus

value: arcuate nucleus


title: liver_ATAC_439_l3_s1

description:
Sample titles are in the format liver_ATAC_[sampleID]_[libraryID]_[sequencingRun]. Note that resequenced libraries were run at a later date and were sometimes on a different sequencer than the original sequencing run, so resequenced libraries are listed as separate samples.
439_peaks.narrowPeak.gz
439_scaled.bw


title: liver_ATAC_439_l2_s1


title: liver_ATAC_465_l1_s1


title: liver_ATAC_440_l1_s1


title: M_AUG_ANU

source_name: anus

value: anus


title: liver_ATAC_439_l1_s1


title: liver_ATAC_437_l2_s1

description:
Sample titles are in the format liver_ATAC_[sampleID]_[libraryID]_[sequencingRun]. Note that resequenced libraries were run at a later date and were sometimes on a different sequencer than the original sequencing run, so resequenced libraries are listed as separate samples.
437_peaks.narrowPeak.gz
437_scaled.bw


title: liver_ATAC_450_l1_s1


title: M_AUG_AOR

source_name: aorta

value: aorta


title: M_AUG_AMYL

source_name: amygdala lateral nucleus

value: amygdala lateral nucleus


title: M_AUG_AMYC

source_name: amygdala central nucleus

value: amygdala central nucleus


title: M_AUG_ADG

source_name: adrenal gland

value: adrenal gland


title: liver_ATAC_437_l1_s1

source_name: liver tissue


title: M_APR_WAT

source_name: white adipose tissue

value: April, 2020

value: white adipose tissue


title: M_APR_VTA

source_name: ventral tegmental area

value: ventral tegmental area

value: M


title: M_APR_VMH

source_name: ventromedial  hypothalamic nucleus

value: ventromedial  hypothalamic nucleus


title: liver_ATAC_436_l2_s1

description:
Sample titles are in the format liver_ATAC_[sampleID]_[libraryID]_[sequencingRun]. Note that resequenced libraries were run at a later date and were sometimes on a different sequencer than the original sequencing run, so resequenced libraries are listed as separate samples.
436_peaks.narrowPeak.gz
436_scaled.bw


title: liver_ATAC_436_l3_s1


title: liver_ATAC_435_l3_s1

description:
Sample titles are in the format liver_ATAC_[sampleID]_[libraryID]_[sequencingRun]. Note that resequenced libraries were run at a later date and were sometimes on a different sequencer than the original sequencing run, so resequenced libraries are listed as separate samples.
435_peaks.narrowPeak.gz
435_scaled.bw


title: liver_ATAC_436_l1_s1


title: M_APR_VIC

source_name: visual cortex

value: visual cortex


title: M_AUG_AXL

source_name: axillary lymph node

value: August, 2020

value: axillary lymph node


title: liver_ATAC_435_l1_s1

value: liver tissue


title: M_APR_THR

source_name: thyroid

value: thyroid


title: liver_ATAC_435_l2_s1


title: liver_ATAC_434_l3_s1

description:
Sample titles are in the format liver_ATAC_[sampleID]_[libraryID]_[sequencingRun]. Note that resequenced libraries were run at a later date and were sometimes on a different sequencer than the original sequencing run, so resequenced libraries are listed as separate samples.
434_peaks.narrowPeak.gz
434_scaled.bw


title: M_APR_TES

source_name: testis

value: testis


title: M_APR_STM

source_name: stomach

value: stomach


title: liver_ATAC_434_l1_s1


title: M_APR_SPL

source_name: spleen

value: spleen


title: liver_ATAC_437_l3_s1


title: liver_ATAC_434_l2_s1


title: liver_ATAC_433_l1_s1

description:
Sample titles are in the format liver_ATAC_[sampleID]_[libraryID]_[sequencingRun]. Note that resequenced libraries were run at a later date and were sometimes on a different sequencer than the original sequencing run, so resequenced libraries are listed as separate samples.
433_peaks.narrowPeak.gz
433_scaled.bw


title: liver_ATAC_431_l3_s1

description:
Sample titles are in the format liver_ATAC_[sampleID]_[libraryID]_[sequencingRun]. Note that resequenced libraries were run at a later date and were sometimes on a different sequencer than the original sequencing run, so resequenced libraries are listed as separate samples.
431_peaks.narrowPeak.gz
431_scaled.bw


title: liver_ATAC_433_l2_s1


title: M_APR_SKNB

source_name: skin on the back

value: skin on the back


title: M_APR_SON

source_name: supraoptic nucleus

value: supraoptic nucleus


title: M_APR_SKNH

source_name: skin in the hindquarter

value: skin in the hindquarter


title: M_APR_SG

source_name: salivary gland

value: salivary gland


title: M_APR_SCN

source_name: suprachiasmatic nucleus

value: April, 2020

value: suprachiasmatic nucleus


title: liver_ATAC_403_l3_s1

description:
Sample titles are in the format liver_ATAC_[sampleID]_[libraryID]_[sequencingRun]. Note that resequenced libraries were run at a later date and were sometimes on a different sequencer than the original sequencing run, so resequenced libraries are listed as separate samples.
403_peaks.narrowPeak.gz
403_scaled.bw


title: M_APR_SN

source_name: substantia nigra

value: substantia nigra


title: M_APR_RPE

source_name: pigmental epithelial cells

value: pigmental epithelial cells

value: M


title: M_APR_TON

source_name: tongue

value: tongue


title: liver_ATAC_431_l1_s1

source_name: liver tissue


title: liver_ATAC_403_l2_s1


title: M_APR_RET

source_name: retina

value: retina


title: M_APR_THA

source_name: thalamus

value: thalamus


title: liver_ATAC_401_l4_s1

description:
Sample titles are in the format liver_ATAC_[sampleID]_[libraryID]_[sequencingRun]. Note that resequenced libraries were run at a later date and were sometimes on a different sequencer than the original sequencing run, so resequenced libraries are listed as separate samples.
401_peaks.narrowPeak.gz
401_scaled.bw

value: liver tissue


title: liver_ATAC_401_l3_s1


title: M_APR_PVN

source_name: paraventricular nucleus

value: paraventricular nucleus


title: M_APR_REC

source_name: rectum

value: rectum


title: liver_ATAC_401_l2_s1


title: M_APR_PT

source_name: pars tuberalis of the pituitary

value: pars tuberalis of the pituitary


title: M_APR_PUT

source_name: putamen

value: putamen


title: liver_ATAC_399_l3_s1

description:
Sample titles are in the format liver_ATAC_[sampleID]_[libraryID]_[sequencingRun]. Note that resequenced libraries were run at a later date and were sometimes on a different sequencer than the original sequencing run, so resequenced libraries are listed as separate samples.
399_peaks.narrowPeak.gz
399_scaled.bw


title: liver_ATAC_401_l1_s1


title: M_APR_PRO

source_name: prostate gland

value: prostate gland


title: liver_ATAC_431_l2_s1


title: liver_ATAC_433_l3_s1


title: liver_ATAC_399_l2_s1


title: M_APR_PD

source_name: pars distalis of the pituitary

value: pars distalis of the pituitary


title: liver_ATAC_399_l1_s1


title: liver_ATAC_39_l1_s1

description:
Sample titles are in the format liver_ATAC_[sampleID]_[libraryID]_[sequencingRun]. Note that resequenced libraries were run at a later date and were sometimes on a different sequencer than the original sequencing run, so resequenced libraries are listed as separate samples.
39_peaks.narrowPeak.gz
39_scaled.bw


title: M_APR_OLB

source_name: olfactory bulb

value: olfactory bulb


title: M_APR_NAc

source_name: nucleus accumbens

value: nucleus accumbens


title: liver_ATAC_156_l2_s1

description:
Sample titles are in the format liver_ATAC_[sampleID]_[libraryID]_[sequencingRun]. Note that resequenced libraries were run at a later date and were sometimes on a different sequencer than the original sequencing run, so resequenced libraries are listed as separate samples.
156_peaks.narrowPeak.gz
156_scaled.bw


title: liver_ATAC_39_l2_s1


title: M_APR_NM

source_name: nasal mucosa

value: April, 2020

value: nasal mucosa


title: liver_ATAC_156_l3_s1


title: M_APR_MUG

source_name: gastrocnemial muscle

value: gastrocnemial muscle


title: M_APR_MUA

source_name: abdominal muscle

value: abdominal muscle


title: M_APR_OES

source_name: oesophagus

value: oesophagus

value: M


title: liver_ATAC_403_l1_s1


title: liver_ATAC_152_l3_s1

description:
Sample titles are in the format liver_ATAC_[sampleID]_[libraryID]_[sequencingRun]. Note that resequenced libraries were run at a later date and were sometimes on a different sequencer than the original sequencing run, so resequenced libraries are listed as separate samples.
152_peaks.narrowPeak.gz
152_scaled.bw


title: M_APR_PIN

source_name: pineal gland

value: pineal gland


title: liver_ATAC_152_l1_s1


title: M_APR_mPFC

source_name: medial prefrontal cortex

value: medial prefrontal cortex


title: M_APR_mPOA

source_name: medial preoptic area

value: medial preoptic area


title: M_APR_MMB

source_name: mammilary nuclei

value: mammilary nuclei


title: liver_ATAC_151_l2_s1

description:
Sample titles are in the format liver_ATAC_[sampleID]_[libraryID]_[sequencingRun]. Note that resequenced libraries were run at a later date and were sometimes on a different sequencer than the original sequencing run, so resequenced libraries are listed as separate samples.
151_peaks.narrowPeak.gz
151_scaled.bw

source_name: liver tissue

value: liver tissue


title: M_APR_MEL

source_name: mesenteric lymph node

value: mesenteric lymph node


title: liver_ATAC_151_l1_s1


title: M_APR_PAN

source_name: pancreas

value: pancreas


title: liver_ATAC_151_l3_s1


title: liver_ATAC_122_l3_s1

description:
Sample titles are in the format liver_ATAC_[sampleID]_[libraryID]_[sequencingRun]. Note that resequenced libraries were run at a later date and were sometimes on a different sequencer than the original sequencing run, so resequenced libraries are listed as separate samples.
122_peaks.narrowPeak.gz
122_scaled.bw


title: liver_ATAC_122_l2_s1


title: liver_ATAC_122_l1_s1


title: M_APR_LIV

source_name: liver

value: liver


title: liver_ATAC_156_l1_s1


title: M_APR_LHA

source_name: lateral hypothalamic nucleus

value: lateral hypothalamic nucleus


title: M_APR_LC

source_name: locus coeruleus

value: locus coeruleus


title: liver_ATAC_1_l3_s1

description:
Sample titles are in the format liver_ATAC_[sampleID]_[libraryID]_[sequencingRun]. Note that resequenced libraries were run at a later date and were sometimes on a different sequencer than the original sequencing run, so resequenced libraries are listed as separate samples.
1_peaks.narrowPeak.gz
1_scaled.bw


title: liver_ATAC_1_l1_s1


title: liver_ATAC_1_l2_s1


title: M_APR_KIM

source_name: kidney medulla

value: kidney medulla


title: M_APR_KIC

source_name: kidney cortex

value: April, 2020

value: kidney cortex


title: M_APR_JEJ

source_name: jejunum

value: jejunum


title: liver_ATAC_152_l2_s1


title: M_APR_ILE

source_name: ileum

value: ileum


title: M_APR_IRI

source_name: iris

value: iris


title: Biol rept 2_FT_6h

city: Houston

first: Ann-Bin

last: Shyu

state: Texas

address: 6431 Fannin Street, Rm 6.200

institute: The University of Texas Health Science Center at Houston

data_processing:
Adapters were trimmed with trim_galore with default parameter.
Bowtie2 was used for the mapping of the trimmed reads to the hg19 transcripts set and RSEM v1.3.0 was used for the gene counting.
TPM method was used for the gene expression normalization.
Assembly: hg19
Supplementary files format and content: Tab-delimited text files contain transcripts per million for each sample.

source_name: human bone osteosarcoma

growth_protocol: Human U2OS cell line was purchased from ATCC and cultured following the manufacturer's protocol.

extract_protocol:
RNA samples were extracted using RNeasy Mini Kit (QIAGEN) following manufacture's protocol.
cDNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were labeled with BrU for two hours and were collected at different times after BrU removal for total cytoplasmic RNA extraction. BrU-RNA IP was performed to isolated BrU-RNA. BrU-RNA samples were subject to m6A-RNA IP to separate m6A-mRNAs from unmethylated mRNAs.

value: human bone osteosarcoma

tag: cell line

tag: cell type

value: epithelial cells

tag: genotype

value: WT

tag: treatment

value: BrU labeling for 2 hours

tag: treatment (time-course_in_hours)


title: Biol rept 2_FT_4h


title: Biol rept 2_FT_2h


title: M_APR_HEA

source_name: heart

value: heart

value: M


title: Biol rept 2_FT_1h


title: M_APR_GUM

source_name: gum

value: gum


title: M_APR_LUN

source_name: lung

value: lung


title: Biol rept 2_FT_0h


title: M_APR_HAB

source_name: habenula

value: habenula


title: Biol rept 2_FT_0.5h


title: M_APR_GPe

source_name: globus pallidus external segment

value: globus pallidus external segment


title: Biol rept 2_IP_6h


title: Biol rept 2_IP_4h


title: M_APR_GPi

source_name: globus pallidus internal segment

value: globus pallidus internal segment


title: M_APR_GAL

source_name: gallbladder

value: gallbladder


title: Biol rept 2_IP_0.5h


title: M_APR_DUO

source_name: duodenum

value: April, 2020

value: duodenum


title: M_APR_DRN

source_name: dorsal raphe

value: dorsal raphe


title: Biol rept 2_IP_1h


title: Biol rept 2_IP_0h


title: M_APR_EPI

source_name: epididymis

value: epididymis


title: Biol rept 2_IP_2h


title: M_APR_CRB

source_name: cerebellum

value: cerebellum


title: Biol rept 2_INPUT_4h

value: human bone osteosarcoma


title: M_APR_COR

source_name: cornea

value: cornea


title: Biol rept 2_INPUT_6h

value: epithelial cells

value: WT


title: Biol rept 2_INPUT_0.5h

value: BrU labeling for 2 hours


title: Biol rept 2_INPUT_1h


title: Biol rept 2_INPUT_2h


title: M_APR_CEC

source_name: cecum

value: cecum

value: M


title: M_APR_CAU

source_name: caudate nucleus

value: caudate nucleus


title: Biol rept 1_FT_6h


title: Biol rept 1_FT_1h


title: Biol rept 1_FT_4h


title: M_APR_CA3

source_name: hippocampus CA3

value: hippocampus CA3


title: M_APR_COL

source_name: colon

value: colon


title: Biol rept 2_INPUT_0h

source_name: human bone osteosarcoma


title: M_APR_CAT

source_name: cartilage

value: cartilage


title: M_APR_CA1

source_name: hippocampus CA1

value: hippocampus CA1


title: Biol rept 1_FT_0.5h


title: M_APR_FOV

source_name: fovea centralis

value: April, 2020

value: fovea centralis


title: M_APR_BRO

source_name: bronchus

value: bronchus


title: M_APR_BON

source_name: bone

value: bone


title: M_APR_BOM

source_name: bone marrow

value: bone marrow


title: M_APR_BNST

source_name: bed nucleus of the stria terminalis

value: bed nucleus of the stria terminalis


title: M_APR_DMH

source_name: dorsomedial hypothalamic nucleus

value: dorsomedial hypothalamic nucleus


title: Biol rept 1_IP_6h

value: human bone osteosarcoma

value: epithelial cells


title: Biol rept 1_IP_4h

value: WT

value: BrU labeling for 2 hours


title: M_APR_BLA

source_name: urinary bladder

value: urinary bladder

value: M


title: Biol rept 1_IP_2h


title: M_APR_BAT

source_name: brown adipose tissue

value: brown adipose tissue


title: Biol rept 1_IP_1h


title: M_APR_AXL

source_name: axillary lymph node

value: axillary lymph node


title: Biol rept 1_FT_2h


title: Biol rept 1_IP_0.5h


title: Biol rept 1_IP_0h


title: Biol rept 1_INPUT_4h


title: M_APR_AMYC

source_name: amygdala central nucleus

value: amygdala central nucleus


title: M_APR_AOR

source_name: aorta

value: aorta


title: Biol rept 1_INPUT_0.5h


title: M_APR_ARC

source_name: arcuate nucleus

value: April, 2020

value: arcuate nucleus


title: Biol rept 1_INPUT_2h


title: Biol rept 1_INPUT_0h


title: F_OCT_WAT

source_name: white adipose tissue

value: October, 2019

value: white adipose tissue

value: F


title: M_APR_ADG

source_name: adrenal gland

value: adrenal gland


title: M_APR_AMYL

source_name: amygdala lateral nucleus

value: amygdala lateral nucleus


title: F_OCT_VTA

source_name: ventral tegmental area

value: ventral tegmental area


title: F_OCT_UTE

source_name: uterus

value: uterus


title: F_OCT_VIC

source_name: visual cortex

value: visual cortex


title: Biol rept 1_FT_0h

source_name: human bone osteosarcoma

value: human bone osteosarcoma

value: epithelial cells

value: WT

value: BrU labeling for 2 hours


title: Input_repeat 2

data_processing:
Reads are aligned to hg38 genome by HISAT2 and only uniquely mapped reads are kept.
reads are sorted and marked for duplication using PicardTools.
MoAIMS was used to perform the m6A peak calling.
(Fastq files from two replicates were merged first before m6A peak calling.)
Assembly: hg38
Supplementary files format and content: Tab-delimited text file contains m6A peaks sites for newly synthesized mRNA population.

treatment_protocol: Cells were labeled with BrU for two hours and were collected for total cytoplasmic RNA extraction. BrU-RNA IP was performed to isolated BrU-RNA. Following RNA fragmentation step, fragmented BrU-RNA samples were subject to m6A-RNA IP.

value: epithelial cell

value: no


title: m6A-IP_repeat 1

value: anti-m6A antibody (SYSY #202003)


title: Biol rept 1_INPUT_6h


title: F_OCT_VMH

source_name: ventromedial  hypothalamic nucleus

value: ventromedial  hypothalamic nucleus


title: M_APR_ANU

source_name: anus

value: April, 2020

value: anus

value: M


title: DF2 siRNA #2_INPUT_4h

data_processing:
Adapters were trimmed with trim_galore with default parameter.
Bowtie2 was used for the mapping of the trimmed reads to the hg19 transcripts set and RSEM v1.3.0 was used for the gene counting.
TPM method was used for the gene expression normalization.
Assembly: hg19
Supplementary files format and content: Tab-delimited text file contains transcripts per million for each sample.

treatment_protocol: Cells with or without DF2 knock-down were collected for total cytoplasmic RNA extraction. Total RNA samples were subject to m6A-RNA IP to separate m6A-mRNAs from unmethylated mRNAs.

value: epithelia cells

value: DF2 siRNA #2


title: F_OCT_THA

source_name: thalamus

value: October, 2019

value: thalamus

value: F


title: F_OCT_THR

source_name: thyroid

value: thyroid


title: DF2 siRNA #2_INPUT_1h

value: human bone osteosarcoma


title: F_OCT_SN

source_name: substantia nigra

value: substantia nigra


title: F_OCT_STM

source_name: stomach

value: stomach


title: Biol rept 1_INPUT_1h

value: epithelial cells

value: WT

value: BrU labeling for 2 hours


title: DF2 siRNA #2_INPUT_2h


title: m6A-IP_repeat 2

value: epithelial cell

value: anti-m6A antibody (SYSY #202003)


title: DF2 siRNA #2_INPUT_0h


title: DF2 siRNA #2_FT_6h


title: F_OCT_SPL

source_name: spleen

value: spleen


title: F_OCT_SKNH

source_name: skin in the hindquarter

value: skin in the hindquarter


title: F_OCT_SON

source_name: supraoptic nucleus

value: supraoptic nucleus


title: F_OCT_TON

source_name: tongue

value: tongue


title: DF2 siRNA #2_INPUT_0.5h

value: epithelia cells

value: DF2 siRNA #2


title: DF2 siRNA #2_FT_4h


title: F_OCT_SKNB

source_name: skin on the back

value: October, 2019

value: skin on the back


title: F_OCT_SG

source_name: salivary gland

value: salivary gland

value: F


title: Input_repeat 1

value: human bone osteosarcoma

value: no


title: F_OCT_RPE

source_name: pigmental epithelial cells

value: pigmental epithelial cells


title: DF2 siRNA #2_FT_2h

value: WT


title: DF2 siRNA #2_FT_1h


title: F_OCT_SCN

source_name: suprachiasmatic nucleus

value: suprachiasmatic nucleus


title: DF2 siRNA #2_INPUT_6h


title: DF2 siRNA #2_FT_0h


title: F_OCT_RET

source_name: retina

value: retina


title: DF2 siRNA #2_IP_6h


title: DF2 siRNA #2_FT_0.5h


title: F_OCT_REC

source_name: rectum

value: rectum


title: F_OCT_PUT

source_name: putamen

value: putamen


title: F_OCT_PIN

source_name: pineal gland

value: pineal gland


title: DF2 siRNA #2_IP_0.5h

source_name: human bone osteosarcoma


title: DF2 siRNA #2_IP_4h


title: F_OCT_PVN

source_name: paraventricular nucleus

value: paraventricular nucleus


title: DF2 siRNA #2_IP_2h


title: DF2 siRNA #1_INPUT_6h


title: DF2 siRNA #2_IP_1h


title: F_OCT_PD

source_name: pars distalis of the pituitary

value: pars distalis of the pituitary


title: DF2 siRNA #2_IP_0h

value: epithelia cells


title: F_OCT_OVA

source_name: ovary

value: ovary


title: F_OCT_PAN

source_name: pancreas

value: October, 2019

value: pancreas


title: DF2 siRNA #1_FT_6h

value: DF2 siRNA #1


title: F_OCT_NM

source_name: nasal mucosa

value: nasal mucosa

value: F


title: DF2 siRNA #1_INPUT_4h

value: human bone osteosarcoma


title: F_OCT_OVI

source_name: oviduct

value: oviduct


title: DF2 siRNA #1_INPUT_2h

value: WT


title: F_OCT_NAc

source_name: nucleus accumbens

value: nucleus accumbens


title: DF2 siRNA #1_INPUT_1h


title: F_OCT_OLB

source_name: olfactory bulb

value: olfactory bulb


title: F_OCT_MUG

source_name: gastrocnemial muscle

value: gastrocnemial muscle


title: DF2 siRNA #1_INPUT_0h


title: DF2 siRNA #1_INPUT_0.5h


title: F_OCT_MUA

source_name: abdominal muscle

value: abdominal muscle


title: F_OCT_OES

source_name: oesophagus

value: oesophagus


title: DF2 siRNA #1_FT_4h


title: DF2 siRNA #1_FT_2h


title: DF2 siRNA #1_FT_1h


title: F_OCT_mPFC

source_name: medial prefrontal cortex

value: medial prefrontal cortex


title: DF2 siRNA #1_FT_0.5h


title: F_OCT_PT

source_name: pars tuberalis of the pituitary

value: pars tuberalis of the pituitary


title: F_OCT_LUN

source_name: lung

value: lung


title: DF2 siRNA #1_FT_0h

value: epithelia cells


title: F_OCT_MMB

source_name: mammilary nuclei

value: October, 2019

value: mammilary nuclei


title: F_OCT_mPOA

source_name: medial preoptic area

value: medial preoptic area


title: DF2 siRNA #1_IP_2h

source_name: human bone osteosarcoma

value: DF2 siRNA #1


title: DF2 siRNA #1_IP_4h


title: DF2 siRNA #1_IP_1h


title: F_OCT_LIV

source_name: liver

value: liver

value: F


title: Ctrl siRNA_INPUT_1h

value: human bone osteosarcoma

value: control siRNA


title: F_OCT_LHA

source_name: lateral hypothalamic nucleus

value: lateral hypothalamic nucleus


title: DF2 siRNA #1_IP_0.5h

value: WT


title: F_OCT_LC

source_name: locus coeruleus

value: locus coeruleus


title: DF2 siRNA #1_IP_0h


title: Ctrl siRNA_FT_6h


title: Ctrl siRNA_FT_4h


title: Ctrl siRNA_INPUT_6h


title: F_OCT_KIM

source_name: kidney medulla

value: kidney medulla


title: DF2 siRNA #1_IP_6h


title: F_OCT_JEJ

source_name: jejunum

value: jejunum


title: F_OCT_KIC

source_name: kidney cortex

value: kidney cortex


title: Ctrl siRNA_INPUT_0.5h


title: Ctrl siRNA_INPUT_4h


title: Ctrl siRNA_FT_2h


title: F_OCT_IRI

source_name: iris

value: iris


title: F_OCT_MEL

source_name: mesenteric lymph node

value: mesenteric lymph node


title: Ctrl siRNA_INPUT_0h

value: epithelia cells


title: F_OCT_ILE

source_name: ileum

value: October, 2019

value: ileum


title: F_OCT_HEA

source_name: heart

value: heart


title: F_OCT_GUM

source_name: gum

value: gum


title: F_OCT_HAB

source_name: habenula

value: habenula


title: F_OCT_GPe

source_name: globus pallidus external segment

value: globus pallidus external segment

value: F


title: F_OCT_DRN

source_name: dorsal raphe

value: dorsal raphe


title: Ctrl siRNA_FT_0.5h

value: human bone osteosarcoma

value: control siRNA


title: Ctrl siRNA_INPUT_2h

value: WT


title: Ctrl siRNA_FT_1h


title: F_OCT_GAL

source_name: gallbladder

value: gallbladder


title: F_OCT_DMH

source_name: dorsomedial hypothalamic nucleus

value: dorsomedial hypothalamic nucleus


title: F_OCT_FOV

source_name: fovea centralis

value: fovea centralis


title: F_OCT_CRB

source_name: cerebellum

value: cerebellum


title: Ctrl siRNA_FT_0h

source_name: human bone osteosarcoma


title: F_OCT_DUO

source_name: duodenum

value: duodenum


title: Ctrl siRNA_IP_0.5h

value: epithelia cells


title: Ctrl siRNA_IP_4h


title: Ctrl siRNA_IP_2h


title: F_OCT_GPi

source_name: globus pallidus internal segment

value: October, 2019

value: globus pallidus internal segment


title: F_OCT_COL

source_name: colon

value: colon


title: Ctrl siRNA_IP_0h


title: Ctrl siRNA_IP_1h


title: DF2 siRNA #2_FT_6h

data_processing:
Adapters were trimmed with trim_galore with default parameter
Bowtie2 was used for the mapping of the trimmed reads to the hg19 transcripts set and RSEM v1.3.0 was used for the gene counting
TPM method was used for the gene expression normalization
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text file contains transcripts per million for each sample.

source_name: human bone osteosarcoma epithelial cells

value: DF2 siRNA #2

tag: time (hours)

tag: molecule subtype

value: unmethylated mRNA


title: F_OCT_CAU

source_name: caudate nucleus

value: caudate nucleus


title: F_OCT_CEC

source_name: cecum

value: cecum

value: F


title: F_OCT_COR

source_name: cornea

value: cornea


title: F_OCT_CAT

source_name: cartilage

value: cartilage


title: Ctrl siRNA_IP_6h

value: human bone osteosarcoma

value: WT

value: control siRNA


title: DF2 siRNA #2_FT_4h

value: human bone osteosarcoma epithelial cells


title: F_OCT_CA3

source_name: hippocampus CA3

value: hippocampus CA3


title: DF2 siRNA #2_IP_6h

value: m6A mRNA


title: DF2 siRNA #2_FT_2h


title: F_OCT_BOM

source_name: bone marrow

value: bone marrow


title: F_OCT_CA1

source_name: hippocampus CA1

value: October, 2019

value: hippocampus CA1


title: DF2 siRNA #2_FT_1h


title: DF2 siRNA #2_IP_4h


title: F_OCT_BLA

source_name: urinary bladder

value: urinary bladder


title: DF2 siRNA #2_IP_1h

value: DF2 siRNA #2


title: DF2 siRNA #2_IP_2h


title: DF2 siRNA #2_FT_0.5h

value: unmethylated mRNA


title: F_OCT_BAT

source_name: brown adipose tissue

value: brown adipose tissue


title: F_OCT_BNST

source_name: bed nucleus of the stria terminalis

value: bed nucleus of the stria terminalis


title: DF2 siRNA #2_IP_0.5h


title: DF2 siRNA #2_IP_0h


title: DF2 siRNA #2_INPUT_6h

value: Total cytoplasmic RNA


title: F_OCT_AOR

source_name: aorta

value: aorta

value: F


title: F_OCT_ANU

source_name: anus

value: anus


title: DF2 siRNA #2_INPUT_4h


title: F_OCT_BRO

source_name: bronchus

value: bronchus


title: F_OCT_AMYL

source_name: amygdala lateral nucleus

value: amygdala lateral nucleus


title: DF2 siRNA #2_INPUT_2h

value: human bone osteosarcoma epithelial cells


title: DF2 siRNA #2_FT_0h


title: F_OCT_BON

source_name: bone

value: bone


title: F_OCT_AMYC

source_name: amygdala central nucleus

value: amygdala central nucleus


title: DF2 siRNA #2_INPUT_1h

source_name: human bone osteosarcoma epithelial cells


title: DF2 siRNA #2_INPUT_0h


title: F_OCT_ADG

source_name: adrenal gland

value: adrenal gland


title: F_JUN_WAT

source_name: white adipose tissue

value: white adipose tissue


title: DF2 siRNA #1_FT_2h

value: DF2 siRNA #1


title: DF2 siRNA #2_INPUT_0.5h


title: DF2 siRNA #1_FT_6h


title: F_JUN_VIC

source_name: visual cortex

value: visual cortex


title: F_JUN_VTA

source_name: ventral tegmental area

value: ventral tegmental area


title: F_JUN_VMH

source_name: ventromedial  hypothalamic nucleus

value: ventromedial  hypothalamic nucleus


title: F_OCT_AXL

source_name: axillary lymph node

value: October, 2019

value: axillary lymph node


title: F_JUN_THR

source_name: thyroid

value: thyroid


title: DF2 siRNA #1_FT_0.5h

value: unmethylated mRNA


title: DF2 siRNA #1_FT_1h


title: F_JUN_STM

source_name: stomach

value: stomach

value: F


title: DF2 siRNA #1_IP_2h

value: m6A mRNA


title: F_JUN_TON

source_name: tongue

value: tongue


title: DF2 siRNA #1_IP_6h

value: human bone osteosarcoma epithelial cells


title: F_JUN_SON

source_name: supraoptic nucleus

value: supraoptic nucleus


title: DF2 siRNA #1_IP_4h


title: F_JUN_SKNH

source_name: skin in the hindquarter

value: skin in the hindquarter


title: F_JUN_SN

source_name: substantia nigra

value: substantia nigra


title: DF2 siRNA #1_IP_0.5h


title: F_JUN_THA

source_name: thalamus

value: thalamus


title: F_OCT_ARC

source_name: arcuate nucleus

value: arcuate nucleus


title: DF2 siRNA #1_IP_1h

value: DF2 siRNA #1


title: DF2 siRNA #1_IP_0h


title: F_JUN_SPL

source_name: spleen

value: spleen


title: F_JUN_SG

source_name: salivary gland

value: salivary gland


title: F_JUN_SKNB

source_name: skin on the back

value: skin on the back


title: DF2 siRNA #1_INPUT_2h

source_name: human bone osteosarcoma epithelial cells

value: Total cytoplasmic RNA


title: F_JUN_SCN

source_name: suprachiasmatic nucleus

value: suprachiasmatic nucleus


title: F_JUN_RET

source_name: retina

value: retina


title: F_JUN_RPE

source_name: pigmental epithelial cells

value: pigmental epithelial cells


title: F_JUN_UTE

source_name: uterus

value: uterus

value: F


title: DF2 siRNA #1_INPUT_6h


title: DF2 siRNA #1_FT_0h

value: unmethylated mRNA


title: Ctrl siRNA_FT_4h

value: control siRNA

value: human bone osteosarcoma epithelial cells


title: F_JUN_PIN

source_name: pineal gland

value: pineal gland


title: Ctrl siRNA_FT_0h


title: F_JUN_PAN

source_name: pancreas

value: pancreas


title: Ctrl siRNA_FT_2h


title: Ctrl siRNA_FT_0.5h


title: Ctrl siRNA_IP_6h

value: m6A mRNA


title: Ctrl siRNA_IP_4h


title: DF2 siRNA #1_INPUT_0.5h


title: DF2 siRNA #1_INPUT_1h


title: F_JUN_OVA

source_name: ovary

value: ovary


title: F_JUN_NM

source_name: nasal mucosa

value: nasal mucosa


title: DF2 siRNA #1_INPUT_0h

value: DF2 siRNA #1


title: F_JUN_REC

source_name: rectum

value: rectum


title: Ctrl siRNA_FT_6h


title: F_JUN_PVN

source_name: paraventricular nucleus

value: paraventricular nucleus


title: F_JUN_MUA

source_name: abdominal muscle

value: abdominal muscle


title: DF2 siRNA #1_FT_4h


title: Ctrl siRNA_INPUT_1h

value: Total cytoplasmic RNA


title: F_JUN_PT

source_name: pars tuberalis of the pituitary

value: pars tuberalis of the pituitary


title: F_JUN_MEL

source_name: mesenteric lymph node

value: mesenteric lymph node


title: Ctrl siRNA_INPUT_0.5h


title: F_JUN_MMB

source_name: mammilary nuclei

value: mammilary nuclei


title: F_JUN_PD

source_name: pars distalis of the pituitary

value: pars distalis of the pituitary

value: F


title: F_JUN_OES

source_name: oesophagus

value: oesophagus


title: F_JUN_PUT

source_name: putamen

value: putamen


title: F_JUN_OLB

source_name: olfactory bulb

value: olfactory bulb


title: Ctrl siRNA_IP_1h

source_name: human bone osteosarcoma epithelial cells

value: control siRNA


title: F_JUN_LUN

source_name: lung

value: lung


title: Ctrl siRNA_IP_2h

value: human bone osteosarcoma epithelial cells

value: m6A mRNA


title: Ctrl siRNA_IP_0.5h


title: F_JUN_NAc

source_name: nucleus accumbens

value: nucleus accumbens


title: Ctrl siRNA_FT_1h

value: unmethylated mRNA


title: F_JUN_LIV

source_name: liver

value: liver


title: Ctrl siRNA_INPUT_6h


title: F_JUN_MUG

source_name: gastrocnemial muscle

value: gastrocnemial muscle


title: Ctrl siRNA_INPUT_4h

value: Total cytoplasmic RNA


title: F_JUN_mPOA

source_name: medial preoptic area

value: medial preoptic area


title: F_JUN_mPFC

source_name: medial prefrontal cortex

value: medial prefrontal cortex


title: Ctrl siRNA_INPUT_0h


title: Ctrl siRNA_IP_0h


title: F_JUN_KIM

source_name: kidney medulla

value: kidney medulla


title: m6A-IP_control 2

description:
RNA fragments from m6A-RIP
Control_m6A_peaks.txt

data_processing:
Reads are aligned to hg38 genome by HISAT2 and only uniquely mapped reads are kept.
reads are sorted and marked for duplication using PicardTools.
MoAIMS was used to perform the m6A peak calling.
(Note that control files and DF2 knockdown files were merged before m6A peak calling.)
Genome_build: hg38
Supplementary_files_format_and_content: Tab-delimited text files contains m6A peaks sites for control and DF2 knockdown.

treatment_protocol: Cells with or without DF2 knock-down were collected for total cytoplasmic RNA extraction. Following RNA fragmentation step, fragmented RNA samples were subject to m6A-RNA IP.

value: control 2

tag: m6a-rip antibody


title: m6A-IP_DF2 siRNA #1

description:
RNA fragments from m6A-RIP
DF2_knockdown_m6A_peaks.txt

value: DF2 siRNA #1


title: F_JUN_ILE

source_name: ileum

value: ileum

value: F


title: m6A-IP_DF2 siRNA #2

value: DF2 siRNA #2


title: INS-1E cell_UA_rep2 [A_2]

city: guangzhou

first: li

last: xueyan

address: NO.74 2nd Zhongshan Road

country: China

institute: Sun Yat-Sen University

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9)
We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.0.4) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-1.3.4d) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.

organism: Rattus norvegicus

source_name: INS-1E cell

extract_protocol:
Total RNA was extracted using Trizol reagent following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit, high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
After total RNA was extracted, mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase, which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I, RNase H and dUTP Solution. An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 (LC-Bio Technology CO., Ltd., Hangzhou, China) following the vendor's recommended protocol.

value: pancreas

value: treated with UA for 24 hours

value: Insulin secreting beta cell derived line


title: Input_DF2 siRNA #1

description: Fragmented total cytoplasmic RNA

value: no


title: F_JUN_KIC

source_name: kidney cortex

value: kidney cortex


title: m6A-IP_control 1

value: control 1


title: Input_DF2 siRNA #2

description: Fragmented total cytoplasmic RNA


title: Ctrl siRNA_INPUT_2h

value: control siRNA

value: human bone osteosarcoma epithelial cells


title: INS-1E cell_basal-con_rep2 [Ba_2]

value: untreated


title: Input_control 2

description: Fragmented total cytoplasmic RNA


title: F_JUN_LC

source_name: locus coeruleus

value: locus coeruleus


title: DF2 siRNA #1_INPUT_4h

value: Total cytoplasmic RNA


title: INS-1E cell_basal-con_rep1 [Ba_1]


title: F_JUN_IRI

source_name: iris

value: iris


title: F_JUN_GAL

source_name: gallbladder

value: gallbladder


title: F_JUN_JEJ

source_name: jejunum

value: jejunum


title: F_JUN_FOV

source_name: fovea centralis

value: fovea centralis


title: F_JUN_DUO

source_name: duodenum

value: duodenum

value: F


title: F_JUN_HAB

source_name: habenula

value: habenula


title: INS-1E cell_UA_rep3 [A_3]

value: pancreas

value: treated with UA for 24 hours


title: F_JUN_DMH

source_name: dorsomedial hypothalamic nucleus

value: dorsomedial hypothalamic nucleus


title: F_JUN_HEA

source_name: heart

value: heart


title: F_JUN_GPi

source_name: globus pallidus internal segment

value: globus pallidus internal segment


title: F_JUN_GUM

source_name: gum

value: gum


title: INS-1E cell_UA_rep1 [A_1]

value: Insulin secreting beta cell derived line


title: F_JUN_LHA

source_name: lateral hypothalamic nucleus

value: lateral hypothalamic nucleus


title: F_JUN_GPe

source_name: globus pallidus external segment

value: globus pallidus external segment


title: AECII transfected with shMettl3_SUP_rep1

type: RNA

city: Shanghai

first: Qiuyun

last: Wang

state: Shanghai

address: 197 Ruijin Er Road, Shanghai

institute: Ruijin Hospital

description:
T-1(Sup,Normalized)
IP and Sup RNAs were amplified as cRNAs and labeled with Cy5 and Cy3 respectively using Arraystar Super RNA labeling Kit.

hyb_protocol: Cy3 and Cy5 labeled cRNAs were  combined together and hybridized to Arraystar Human mRNA&lncRNA Epitranscriptomic Arrays (8x60K, Arraystar) at 65°C for 17 hours in an Agilent Hybridization Oven.

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

data_processing:
Hierarchical clustering heatmap analysis was performed for differentially m6A-methylated RNAs. Differentially m6A-methylated mRNAs were analyzed for GO and pathway enrichment.
Raw intensities of IP (immunoprecipitated, Cy5-labelled) and/or Sup (supernatant, Cy3-labelled) were normalized with average of log2-scaled Spike-in RNA intensities.

organism: Mus musculus

source_name: AECII transfected with shMettl3

label_protocol: Total RNAs were  immunoprecipitated with anti-N6-methyadenosine(m6A) antibody. The immunoprecipitated IP fraction contained enriched m6A methylated RNAs, and the supernatant  Sup fraction contained unmodified RNAs.IP and Sup RNAs were amplified as cRNAs and labeled with Cy5 and Cy3 respectively using Arraystar Super RNA Labeling Kit.

growth_protocol: Collected samples are maintained in liquid nitrogen

extract_protocol: Total RNA extracted using Trizol reagent.The purity and amount of total RNA samples were determined with NanoDrop ND-1000. Results were provided in Sample QC report.

value: AECII

value: transfected with shMettl3

value: unmodified RNAs

tag: molecule type

value: SUP RNA


title: AECII transfected with shMettl3_SUP_rep3

description:
T-3(Sup,Normalized)
IP and Sup RNAs were amplified as cRNAs and labeled with Cy5 and Cy3 respectively using Arraystar Super RNA labeling Kit.


title: F_JUN_CAT

source_name: cartilage

value: cartilage


title: AECII_SUP_rep3

description:
NC-3(Sup,Normalized)
IP and Sup RNAs were amplified as cRNAs and labeled with Cy5 and Cy3 respectively using Arraystar Super RNA labeling Kit.

source_name: Normal AECII


title: AECII_SUP_rep1

description:
NC-1(Sup,Normalized)
IP and Sup RNAs were amplified as cRNAs and labeled with Cy5 and Cy3 respectively using Arraystar Super RNA labeling Kit.


title: AECII_SUP_rep2

description:
NC-2(Sup,Normalized)
IP and Sup RNAs were amplified as cRNAs and labeled with Cy5 and Cy3 respectively using Arraystar Super RNA labeling Kit.


title: Input_control 1

description: Fragmented total cytoplasmic RNA

source_name: human bone osteosarcoma epithelial cells

value: control 1

value: no


title: F_JUN_DRN

source_name: dorsal raphe

value: dorsal raphe

value: F


title: F_JUN_CRB

source_name: cerebellum

value: cerebellum


title: F_JUN_COR

source_name: cornea

value: cornea


title: INS-1E cell_basal-con_rep3 [Ba_3]

source_name: INS-1E cell

value: pancreas

value: untreated


title: F_JUN_COL

source_name: colon

value: colon


title: AECII_IP_rep3

description:
NC-3(IP,Normalized)
IP and Sup RNAs were amplified as cRNAs and labeled with Cy5 and Cy3 respectively using Arraystar Super RNA labeling Kit.

value: immunoprecipitated with anti-N6-methyadenosine(m6A) antibody

value: IP RNA


title: AECII transfected with shMettl3_SUP_rep2

description:
T-2(Sup,Normalized)
IP and Sup RNAs were amplified as cRNAs and labeled with Cy5 and Cy3 respectively using Arraystar Super RNA labeling Kit.


title: F_JUN_CEC

source_name: cecum

value: cecum


title: AECII_IP_rep1

description:
NC-1(IP,Normalized)
IP and Sup RNAs were amplified as cRNAs and labeled with Cy5 and Cy3 respectively using Arraystar Super RNA labeling Kit.

value: AECII


title: AECII transfected with shMettl3_IP_rep3

description:
T-3(IP,Normalized)
IP and Sup RNAs were amplified as cRNAs and labeled with Cy5 and Cy3 respectively using Arraystar Super RNA labeling Kit.

value: transfected with shMettl3


title: NP cell, control 3

city: Guangzhou

first: Huichuan

last: Yu

state: Guangdong

address: 26 Yuancun Erheng Road

institute: Sun Yat-sen University

data_processing:
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 ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using STAR and paired-end clean reads were aligned to the reference genome using STAR (v2.5.1b). STAR used the method of Maximal Mappable Prefix(MMP) which can generate a precise mapping result for junction reads.
HTSeq v0.6.0 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.10.1). DESeq2 provide statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate . Genes with an adjusted P-value <0.05 found by DESeq2 were assigned as differentially expressed.
Alternative Splicing is an important mechanism for regulate the expression of genes and the variable of protein. rMATS(3.2.1) software was used to analysis the ASevent.
Genome_build: GRCh38 for HCT116 and Rnor_6.0 for NP
Supplementary_files_format_and_content: xls files include FPKM values for each Sample

source_name: Rat nucleus pulposus cells

growth_protocol: All cell lines were either purchased from ATCC or provided by Shanghai Institutes for Biological Sciences, which had their identity confirmed by DNA genotyping and cultured according to manufacturer’s protocol.

extract_protocol:
RNA was isolated from cells of each group using RNeasy mini kit (Qiagen) according to manufacturer’s protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The cells were treated by 50 mM PDS for 24 hours.

tag: passages

value: Rat NP

value: control


title: AECII transfected with shMettl3_IP_rep1

description:
T-1(IP,Normalized)
IP and Sup RNAs were amplified as cRNAs and labeled with Cy5 and Cy3 respectively using Arraystar Super RNA labeling Kit.


title: F_JUN_CA3

source_name: hippocampus CA3

value: hippocampus CA3


title: NP cell, control 2


title: NP cell, control 1


title: F_JUN_CAU

source_name: caudate nucleus

value: caudate nucleus


title: Zebrafish, RIP-seq, Rbm24a Knock-in2 IP2

city: Tsingtao

middle: pan

last: feng

state: shandong

address: Ao Shan Wei Street

department: College of Life Sciences

institute: shandong university

description:
Library name: Sample4
antibody GFP

data_processing:
Each library was amplified by a 15-cycle PCR, and 150 bp paired-end sequencing was subjected to Illumina Nova seq 6000 to obtain the raw data.
Assembly: GRCz11
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: Bigwig file for each Sample

organism: Danio rerio

source_name: whole embryo

growth_protocol: Zebrafish embryos were maintained in 1/3x Ringer's at 28.5C

extract_protocol:
Total RNAs were extracted from Mrbm24a embryos at 4-cell sphere 24-hpf stage, using TRIzol reagent (Invitrogen), and were precipitated by cold isopropanol (50%, v/v) in the presence of carrier glycogen (20 µg/each sample).
1 μg of immunoprecipitated RNA was utilized for library construction. Ribosomal RNA depletion was performed using RNase H-based probes followed by magnetic bead purification. RNA fragmentation was achieved through magnesium-catalyzed hydrolysis under elevated temperature (94°C for 6 min). First-strand cDNA synthesis was initiated with random hexamer primers and reverse transcriptase, followed by second-strand synthesis using DNA polymerase I with dUTP incorporation for strand marking. Double-stranded cDNA fragments underwent end repair and 3'-adenylation using a single-tube enzymatic reaction system. Illumina-compatible adaptors with unique dual indexes were ligated to both ends of the DNA fragments. Size selection of adaptor-ligated products (180-250 bp) was performed using double-sided SPRI bead purification. PCR amplification was conducted with P5/P7 primers for 12 cycles, followed by AMPure XP bead purification to remove primer dimers. Library quality was verified by Agilent 2100 Bioanalyzer DNA High Sensitivity chip analysis. Indexed libraries were pooled in equimolar ratios and subjected to paired-end sequencing (2×150 bp) on an Illumina NovaSeq 6000 platform following the manufacturer's standardized workflow.

value: whole embryo

value: 4-cell stage

value: embryonic cell

value: knock-in


title: F_JUN_CA1

source_name: hippocampus CA1

value: hippocampus CA1

value: F


title: F_JUN_AXL

source_name: axillary lymph node

value: axillary lymph node


title: NP cell, PDS-treat 3

value: PDS


title: AECII transfected with shMettl3_IP_rep2

description:
T-2(IP,Normalized)
IP and Sup RNAs were amplified as cRNAs and labeled with Cy5 and Cy3 respectively using Arraystar Super RNA labeling Kit.

value: immunoprecipitated with anti-N6-methyadenosine(m6A) antibody


title: F_JUN_BRO

source_name: bronchus

value: bronchus


title: F_JUN_AOR

source_name: aorta

value: aorta


title: NP cell, PDS-treat 2


title: Zebrafish, RIP-seq, Rbm24a Knock-in1 IgG1

description:
Library name: Sample1
antibody GFP


title: F_JUN_ANU

source_name: anus

value: anus


title: F_JUN_BON

source_name: bone

value: bone


title: NP cell, PDS-treat 1

value: Rat NP


title: F_JUN_BNST

source_name: bed nucleus of the stria terminalis

value: bed nucleus of the stria terminalis


title: F_JUN_AMYL

source_name: amygdala lateral nucleus

value: amygdala lateral nucleus


title: F_JUN_BOM

source_name: bone marrow

value: bone marrow


title: F_JUN_BLA

source_name: urinary bladder

value: urinary bladder


title: AECII_IP_rep2

description:
NC-2(IP,Normalized)
IP and Sup RNAs were amplified as cRNAs and labeled with Cy5 and Cy3 respectively using Arraystar Super RNA labeling Kit.

source_name: Normal AECII

value: AECII

value: IP RNA


title: F_JUN_BAT

source_name: brown adipose tissue

value: brown adipose tissue


title: mutant embryos (pool of 5)_3

city: Jerusalem

first: Inbar

last: Plaschkes

address: The Hebrew University of Jerusalem - Ein Kerem

department: The Faculty of Medicine - Ein Kerem

country: Israel

institute: HUJI

data_processing:
Raw reads were processed for quality trimming and adaptors removal using fastx_toolkit v0.0.14 and cutadapt v2.10 (ref 1).
The processed reads were aligned to the zebrafish transcriptome and genome version GRCz11 with annotations from Ensembl release 106 using TopHat v2.1.1 (ref 2).
Counts per gene quantification was done with htseq-count v2.01 (ref. 3). Normalization and differential expression analysis were done with the DESeq2 package v 1.36.0 (ref 4.). The normalized counts were further batch corrected for the effect of the 3 repeats of the biological procedure.
The normalized counts were further batch corrected for the effect of the 3 repeats of the biological procedure.
Assembly: GRCz11, with annotations from Ensembl release 99
Supplementary files format and content: txt table with DESeq2 normalized counts per gene (rows) per sample (column)

molecule: polyA RNA

growth_protocol: zebrafish mbryos were produced by pair mating (heterozygotes for atad3-KO) and raised at 28.5°C in egg water

extract_protocol:
RNA was extracted using the NucleoSpin® RNA kit (MACHEREY-NAGEL; 740955) according to the manufacturer instructions.
PolyA-selection, mRNA libraries were prepared using KAPA mRNA HyperPrep Kit

treatment_protocol: atad3 knockout by CRISPR/Cas9

value: whole embryo


title: F_JUN_ARC

source_name: arcuate nucleus

value: arcuate nucleus

value: F


title: Zebrafish, RIP-seq, Rbm24a Knock-in1 IP1

description:
Library name: Sample3
antibody GFP

value: 4-cell stage

value: embryonic cell

value: knock-in


title: wild-type embryos (pool of 5)_3

value: wild-type


title: mutant embryos (pool of 5)_1


title: Zebrafish, RIP-seq, Rbm24a Knock-in2 IgG2

description:
Library name: Sample2
antibody GFP


title: wild-type embryos (pool of 5)_2


title: F_JUN_AMYC

source_name: amygdala central nucleus

value: amygdala central nucleus


title: F_FEB_WAT

source_name: white adipose tissue

value: February, 2020

value: white adipose tissue


title: F_FEB_TON

source_name: tongue

value: tongue


title: wild-type embryos (pool of 5)_1

source_name: whole embryo


title: F_JUN_ADG

source_name: adrenal gland

value: adrenal gland


title: F_FEB_THA

source_name: thalamus

value: thalamus


title: F_FEB_VMH

source_name: ventromedial  hypothalamic nucleus

value: ventromedial  hypothalamic nucleus


title: F_FEB_SPL

source_name: spleen

value: spleen


title: mutant embryos (pool of 5)_2


title: F_FEB_VTA

source_name: ventral tegmental area

value: ventral tegmental area


title: uc4_seedling_rep2

city: SAINT PAUL

first: Gary

last: Muehlbauer

state: MN

address: 1991 Upper Buford Circle 411 Borlaug Hall

department: Agronomy and Plant Genetics

institute: University of Minnesota

description: Gene expression data from seedling tissue

hyb_protocol: Labeled RNA (15 μg) was chemically fragmented using the Affymetrix GeneChip sample cleanup module (Affymetrix) and used for hybridization. The Affymetrix Barley1 GeneChip hybridizations, washes were conducted following standard  Affymetrix procedures.

scan_protocol: Chip reading was conducted using standard Affymetrix procedures using an Affymetrix gene chip scanner.

data_processing: GeneChip data were inspected for quality using the Expressionist Pro Refiner, v. 1.0 (Genedata, San Francisco, CA, USA). Normalization and summarization was performed with Microarray Suite version 5.0 (MAS 5.0)

label: biotin

organism: Hordeum vulgare

source_name: Seedling tissue was collected from 2-3 day old plants.

label_protocol: Biotinylated cRNA was produced by transcribing the cDNA was transcribed in vitro using the Enzo BioArray HighYield RNA transcript labeling kit (Enzo Life Sciences, Farmingdale, NY, U.S.A.) in the presence of biotinylated UTP and CTP. The biotin-labeled cRNA was purified with the Affymetrix Gene-Chip Sample Cleanup Module (Affymetrix).

growth_protocol: Seeds for each genotype were surface sterilized with bleach. For seedling samples seeds were germinated in sterile plastic petri dishes containing three layers of filter paper saturated with distilled H2O. The petri dishes were covered  with foil and transferred to a growth chamber set at 17 °C for 16 h and 12 °C for 8 h. For crown tissue plants were grown on vermiculite and for inflorescence and embryo tissue in potting mix in a growth chamber set at 17 °C for 16 h in light (200±20 μEm−1s−1) followed by 12 °C for 8 h in the dark.

extract_protocol: Tissue was pooled and ground to a fine powder in liquid nitrogen. Total RNA was extracted using the Trizol (Invitrogen, Carlsbad, CA, U.S.A.) protocol. Genomic DNA was digested using RNasefree DNase and the RNA was purified on RNeasy columns (Promega Corp., Madison, WI, U.S.A.). RNA quality was examined using an Agilent 2100 bioanalyzer. For cDNA synthesis an T7-Oligo(dT) primer (Proligo, Boulder, CO, U.S.A.) and the SuperScript Double-Stranded cDNA Synthesis Kit (Invitrogen) was used and cDNA was purified with the Affymetrix Gene-Chip sample cleanup module (Affymetrix, Santa Clara, CA,U.S.A.).

tag: tissue type

value: seedling

value: uniculm 4 (cul4)


title: F_FEB_THR

source_name: thyroid

value: thyroid


title: F_FEB_STM

source_name: stomach

value: stomach

value: F


title: F_FEB_SN

source_name: substantia nigra

value: substantia nigra


title: F_FEB_SKNB

source_name: skin on the back

value: skin on the back


title: F_FEB_UTE

source_name: uterus

value: uterus


title: F_FEB_VIC

source_name: visual cortex

value: visual cortex


title: F_FEB_SKNH

source_name: skin in the hindquarter

value: February, 2020

value: skin in the hindquarter


title: F_FEB_SON

source_name: supraoptic nucleus

value: supraoptic nucleus


title: uc4_seedling_rep3


title: F_FEB_SG

source_name: salivary gland

value: salivary gland


title: F_FEB_SCN

source_name: suprachiasmatic nucleus

value: suprachiasmatic nucleus


title: F_FEB_RPE

source_name: pigmental epithelial cells

value: pigmental epithelial cells


title: uc4_inflorescence_rep3

description: Gene expression data from inflorescence tissue

source_name: Immature inflorescences were sampled 16-20 days after pollination.

value: inflorescence


title: uc4_seedling_rep1


title: F_FEB_RET

source_name: retina

value: retina


title: uc4_inflorescence_rep1


title: uc2_seedling_rep3

value: seedling

value: uniculm 2 (cul2)


title: uc4_inflorescence_rep2

value: uniculm 4 (cul4)


title: F_FEB_PUT

source_name: putamen

value: putamen


title: uc4_embryo_rep3

description: Gene expression data from embryo tissue

source_name: Embryo tissue was sampled 16-20 days after pollination.

value: embryo


title: uc4_crown_rep3

description: Gene expression data from crown tissue

source_name: Crown tissue was sampled from 10 - 14 day old plants.

value: crown


title: uc2_seedling_rep2

source_name: Seedling tissue was collected from 2-3 day old plants.


title: uc4_crown_rep1

description: Gene expression data from crown tissue


title: F_FEB_REC

source_name: rectum

value: rectum

value: F


title: F_FEB_PT

source_name: pars tuberalis of the pituitary

value: pars tuberalis of the pituitary


title: F_FEB_PVN

source_name: paraventricular nucleus

value: February, 2020

value: paraventricular nucleus


title: uc4_crown_rep2

description: Gene expression data from crown tissue


title: F_FEB_PD

source_name: pars distalis of the pituitary

value: pars distalis of the pituitary


title: uc4_embryo_rep1

description: Gene expression data from embryo tissue


title: uc2_inflorescence_rep3


title: uc4_embryo_rep2

description: Gene expression data from embryo tissue


title: F_FEB_PAN

source_name: pancreas

value: pancreas


title: F_FEB_PIN

source_name: pineal gland

value: pineal gland


title: uc2_inflorescence_rep2


title: uc2_embryo_rep3

description: Gene expression data from embryo tissue


title: F_FEB_OVI

source_name: oviduct

value: oviduct


title: F_FEB_OVA

source_name: ovary

value: ovary


title: F_FEB_OLB

source_name: olfactory bulb

value: olfactory bulb


title: F_FEB_NAc

source_name: nucleus accumbens

value: nucleus accumbens


title: F_FEB_MUG

source_name: gastrocnemial muscle

value: gastrocnemial muscle


title: F_FEB_MUA

source_name: abdominal muscle

value: abdominal muscle


title: F_FEB_NM

source_name: nasal mucosa

value: nasal mucosa


title: uc2_embryo_rep1

description: Gene expression data from embryo tissue

value: embryo

value: uniculm 2 (cul2)


title: F_FEB_mPOA

source_name: medial preoptic area

value: medial preoptic area


title: uc2_inflorescence_rep1

source_name: Immature inflorescences were sampled 16-20 days after pollination.

value: inflorescence


title: lnt_seedling_rep3

value: seedling

value: low number of tillers (lnt1)


title: lnt_seedling_rep2


title: lnt_seedling_rep1


title: F_FEB_mPFC

source_name: medial prefrontal cortex

value: February, 2020

value: medial prefrontal cortex

value: F


title: uc2_crown_rep1

description: Gene expression data from crown tissue

source_name: Crown tissue was sampled from 10 - 14 day old plants.

value: crown


title: lnt_inflorescence_rep3


title: lnt_embryo_rep3

description: Gene expression data from embryo tissue

source_name: Embryo tissue was sampled 16-20 days after pollination.


title: F_FEB_MMB

source_name: mammilary nuclei

value: mammilary nuclei


title: F_FEB_OES

source_name: oesophagus

value: oesophagus


title: lnt_inflorescence_rep2


title: uc2_crown_rep2

description: Gene expression data from crown tissue


title: uc2_crown_rep3

description: Gene expression data from crown tissue


title: lnt_inflorescence_rep1


title: uc2_seedling_rep1

source_name: Seedling tissue was collected from 2-3 day old plants.


title: F_FEB_MEL

source_name: mesenteric lymph node

value: mesenteric lymph node


title: lnt_embryo_rep2

description: Gene expression data from embryo tissue


title: F_FEB_LUN

source_name: lung

value: lung


title: F_FEB_LIV

source_name: liver

value: liver


title: lnt_crown_rep3

description: Gene expression data from crown tissue


title: lnt_embryo_rep1

description: Gene expression data from embryo tissue


title: F_FEB_LHA

source_name: lateral hypothalamic nucleus

value: lateral hypothalamic nucleus


title: F_FEB_LC

source_name: locus coeruleus

value: locus coeruleus


title: lnt_crown_rep2

description: Gene expression data from crown tissue


title: F_FEB_KIM

source_name: kidney medulla

value: kidney medulla


title: F_FEB_KIC

source_name: kidney cortex

value: kidney cortex


title: lnt_crown_rep1

description: Gene expression data from crown tissue


title: Bowman_seedling_rep3

value: Bowman


title: Bowman_seedling_rep2


title: F_FEB_JEJ

source_name: jejunum

value: jejunum


title: F_FEB_IRI

source_name: iris

value: iris


title: F_FEB_ILE

source_name: ileum

value: ileum


title: F_FEB_GPi

source_name: globus pallidus internal segment

value: February, 2020

value: globus pallidus internal segment


title: uc2_embryo_rep2

description: Gene expression data from embryo tissue

value: embryo

value: uniculm 2 (cul2)


title: F_FEB_HEA

source_name: heart

value: heart

value: F


title: F_FEB_HAB

source_name: habenula

value: habenula


title: Bowman_seedling_rep1

value: seedling


title: F_FEB_GPe

source_name: globus pallidus external segment

value: globus pallidus external segment


title: F_FEB_FOV

source_name: fovea centralis

value: fovea centralis


title: F_FEB_GAL

source_name: gallbladder

value: gallbladder


title: F_FEB_DUO

source_name: duodenum

value: duodenum


title: F_FEB_DRN

source_name: dorsal raphe

value: dorsal raphe


title: Bowman_inflorescence_rep2

source_name: Immature inflorescences were sampled 16-20 days after pollination.

value: inflorescence

value: Bowman


title: Bowman_inflorescence_rep1


title: F_FEB_CRB

source_name: cerebellum

value: cerebellum


title: Bowman_embryo_rep1

description: Gene expression data from embryo tissue

source_name: Embryo tissue was sampled 16-20 days after pollination.


title: als_seedling_rep2

source_name: Seedling tissue was collected from 2-3 day old plants.

value: absent lower laterals (als)


title: F_FEB_COR

source_name: cornea

value: February, 2020

value: cornea


title: F_FEB_CEC

source_name: cecum

value: cecum


title: F_FEB_DMH

source_name: dorsomedial hypothalamic nucleus

value: dorsomedial hypothalamic nucleus


title: F_FEB_COL

source_name: colon

value: colon


title: Bowman_embryo_rep2

description: Gene expression data from embryo tissue

value: embryo


title: Bowman_crown_rep2

description: Gene expression data from crown tissue

source_name: Crown tissue was sampled from 10 - 14 day old plants.

value: crown


title: Bowman_inflorescence_rep3


title: als_seedling_rep1

value: seedling


title: Bowman_crown_rep3

description: Gene expression data from crown tissue


title: als_seedling_rep3


title: Bowman_embryo_rep3

description: Gene expression data from embryo tissue


title: Bowman_crown_rep1

description: Gene expression data from crown tissue


title: als_inflorescence_rep3


title: als_inflorescence_rep1


title: als_embryo_rep1

description: Gene expression data from embryo tissue


title: als_inflorescence_rep2


title: als_embryo_rep2

description: Gene expression data from embryo tissue


title: F_FEB_GUM

source_name: gum

value: gum

value: F


title: als_crown_rep2

description: Gene expression data from crown tissue


title: F_FEB_CA1

source_name: hippocampus CA1

value: hippocampus CA1


title: F_FEB_BRO

source_name: bronchus

value: bronchus


title: als_crown_rep3

description: Gene expression data from crown tissue


title: F_FEB_CAT

source_name: cartilage

value: cartilage


title: F_FEB_BON

source_name: bone

value: bone


title: F_FEB_CAU

source_name: caudate nucleus

value: caudate nucleus


title: F_FEB_BNST

source_name: bed nucleus of the stria terminalis

value: bed nucleus of the stria terminalis


title: F_FEB_BLA

source_name: urinary bladder

value: urinary bladder


title: F_FEB_BAT

source_name: brown adipose tissue

value: February, 2020

value: brown adipose tissue


title: F_FEB_ARC

source_name: arcuate nucleus

value: arcuate nucleus


title: F_FEB_AOR

source_name: aorta

value: aorta


title: COLON_468_SALMON_baseline

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

country: Netherlands

institute: Wageningen University

description: no history of polyps

hyb_protocol: Hybridisation of 10ug cRNA on  NuGO_Hs1a52018 arrays was done overnight for 16 hours at 45ºC in a Hybridisation Oven 640 (Affymetrix). The protocol is conducted as described in the Genechip Expression Analysis Technical Manual, section 2 (Eukaryotic Sample and Array Processing), chapter 2 (Eukaryotic Target Hybridization) (P/N 701027, revision 5).

scan_protocol: Arrays were scanned on an Affymetrix 3000 7G scanner, as described n the Genechip Expression Analysis Technical Manual, section 2 (Eukaryotic Sample and Array Processing), chapter 2 (Eukaryotic Arrays: Washing, Staining and Scanning (P/N 701028, revision 5).

data_processing: Expression estimates were calculated using GCRMA, applying the Emperical Bayes estimate for background correction.

source_name: colon biopsy

label_protocol: The Ambion MessageAmp aRNA Amplification Kit was used to prepare labelled cRNA from 350ng of total RNA. The protocol was conducted using the reagents provided by Ambion (P/N 1751), as per the manufacturer's instructions.

growth_protocol: Volounteers were recruited for the study through gastroenterology clinics across The Netherlands and the UK. Biopsies of 28 participants (15 female and 13 male) were used for array analyses. These subjects had a mean age of 56±11 years and a BMI of 26.5 kg m-2. All were disease free although 19 had previously had polyps removed. This study was approved by the Medical Ethical Committee of Nijmegen University Medical Centre St. Radboud, Netherlands (reference 2004/111), and the King’s Lynn Local Research Ethics Committee (reference 04/Q0105/8). All subjects gave written informed consent after the study was explained to them both in writing and verbally. The trial was registered at www.clinicaltrials.gov under identifier NCT00145015.

extract_protocol: Biopsies were put immediately into RNAlater (Qiagen), and total RNA was isolated from the samples using the RNeasy Plus Mini kit (Qiagen).

treatment_protocol: Subjects were randomised into one of three dietary interventions: salmon (300g/week), cod (300g/week) or no additional fish in a diet for six months. Dietary advice was offered to all three groups. Biopsies were taken from the sigmoid colon, and were collected at baseline and after 6 months dietary intervention.

tag: protocol

value: extra salmon

tag: time

value: baseline

tag: individual

value: subject 468

tag: gender

value: Male

tag: age


title: COLON_9232_SALMON_6months_after_intervention

description: history of polyps

value: after six months of intervention

value: subject 9232

value: Female


title: COLON_7413_COD_baseline

description: no history of polyps

value: extra cod

value: subject 7413


title: COLON_2267_SALMON_6months_after_intervention

description: history of polyps

value: subject 2267


title: COLON_7815_COD_baseline

description: history of polyps

value: subject 7815


title: COLON_9232_SALMON_baseline

description: history of polyps


title: F_FEB_AXL

source_name: axillary lymph node

tag: sampling point

tag: tissue

value: axillary lymph node

tag: Sex

value: F