title: gly9

extract_protocol:
For each sample, the epididymis was dissected free of fat and connective tissue, then, after cutting open the cauda, placed into 6 ml of phosphate buffer saline (PBS) for 20 minutes at room temperature. Further incubation at 4ºC will immobilize the sperm.  The tissue was then minced, the released sperm pelleted at 4ºC 3,000 x g for 10 min, then resuspended in NIM buffer and stored at -80ºC for further processing.   An appropriate amount of rat sperm suspension was used for DNA extraction. Previous studies have shown mammalian sperm heads are resistant to sonication unlike somatic cells 25,26. Somatic cells and debris were therefore removed by brief sonication (Fisher Sonic Dismembrator, model 300, power 25), then centrifugation and washing 1-2 times in 1xPBS. The resulting pellet was resuspended in 820 μL DNA extraction buffer and 80 μl 0.1M DTT added, then incubated at 65°C for 15 minutes. 80 μl proteinase K (20 mg/ml) was added and the sample was incubated at 55°C for 2-4 hours under constant rotation. Protein was removed by addition of protein precipitation solution (300 μl, Promega A795A), incubation for 15 min on ice, then centrifugation at 13,500 rpm for 30 minutes at 4°C. One ml of the supernatant was precipitated with 2 μl of glycoblue (Invitrogen, AM9516) and 1 ml of cold 100 % isopropanol. After incubation, the sample was spun at 13,500 x g for 30 min at 4°C, then washed with 70% cold ethanol. The pellet was air-dried for about 5 minutes then resuspended in 100 μl of nuclease free water.  For the MeDIP procedure, genomic DNA was sonicated and run on 1.5% agarose gel for fragment size verification. The sonicated DNA was then diluted with TE buffer to 400 μl, then heat-denatured for 10min at 95˚C, and immediately cooled on ice for 10 min to create single-stranded DNA fragments. Then 100μl of 5X IP buffer and 5μg of antibody (monoclonal mouse anti 5-methyl cytidine; Diagenode #C15200006) were added, and the mixture was incubated overnight on a rotator at 4˚C. The following day magnetic beads (Dynabeads M-280 Sheep anti-Mouse IgG; Life Technologies 11201D) were pre-washed per manufacturer’s instructions, and 50μl of beads were added to the 500μl of DNA-antibody mixture from the overnight incubation, then incubated for 2h on a rotator at 4˚C. After this incubation, the samples were washed three times with 1X IP buffer using a magnetic rack. The washed samples were then resuspended in 250μl digestion buffer (5mM Tris PH 8, 10.mM EDTA, 0.5% SDS) with 3.5μl Proteinase K (20mg/ml), and incubated for 2-3 hours on a rotator at 55˚. DNA clean-up was performed using a Phenol-Chloroform-Isoamyalcohol extraction, and the supernatant precipitated with 2μl of glycoblue (20mg/ml), 20μl of 5M NaCl and 500μl ethanol in -20˚C freezer for one to several hours. The DNA precipitate was pelleted, washed with 70% ethanol, then dried and resuspended in 20μl H2O or TE. DNA concentration was measured in Qubit (Life Technologies) with the ssDNA kit (Molecular Probes Q10212).  For histone chromatin immunoprecipitation, individual rat sperm collections were generated. To remove any somatic cell contamination sperm samples from each animal were sonicated for 10 seconds using a Sonic Dismembrator Model 300 (Thermo Scientific Fisher, USA) then centrifuged 1800xg for 5 min at 4 °C then resuspended and counted individually on a Neubauer counting chamber (Propper manufacturing Co., Inc., New York, USA) prior to pooling. The sperm samples were reconstituted up to 1 ml with PBS (phosphate buffered saline). To reduce disulfide bonds, 50 µl of 1 M DTT was added to each sample and the samples were then incubated for 2 hours at room temperature under constant rotation. To quench any residual DTT (dithiothreitol, Fisher Scientific, NY USA) in the reaction, 120 µl of fresh 1 M NEM (N-Ethylmaleimide, Thermo Scientific, Rockford, USA) was then added and the samples were incubated for 30 min at room temperature under constant rotation. The sperm cells were pelleted at 450xg for 5 min at room temperature and the supernatant was discarded. Pellets were resuspended in PBS and then spun again at 450xg for 5 min at room temperature. The supernatant was discarded and resuspended in 130 µl of complete buffer supplemented with tergitol 0.5% and DOC 1%. The samples were then sonicated using the Covaris M220. Covaris was set to a 10 min “Chromatin shearing” program and the program was run for each tube in the experiment.  After the Covaris sonication, 10 µl of each sample was run on a 1.5% agarose gel to verify fragment size. Samples were then centrifuged at 12,500xg for 10 min at room temperature. The supernatant was transferred to a fresh microfuge tube. 65 µl of protease inhibitor cocktail (1 tablet dissolved in 500 µl, 20 × concentrated) (Roche, cat. no. 11 873 580 001) were added in each sample as well as 3 µl of antibody (anti-histone H3 pan-monoclonal antibody, cat no. 05–928, Millipore Corp, Temecula CA USA). The DNA-antibody mixture was incubated overnight on a rotator at 4 °C. The following day, magnetic beads (ChIP-Grade protein G magnetic beads, Cell Signaling 9006) were pre-washed as follows: the beads were resuspended in the vial, then 30 µl per sample was transferred to a microfuge tube. The same volume of Washing Buffer (at least 1 ml) was added and the bead sample was resuspended. The tube was then placed into a magnetic rack for 1–2 min and the supernatant was discarded. The tube was removed from the magnetic rack and the beads were washed once. The washed beads were resuspended in the same volume of IP buffer as the initial volume of beads. 30 µl of beads were added to each DNA-antibody mixture from the overnight incubation, then incubated for 2 h on a rotator at 4 °C. After the incubation, the bead-antibody-DNA complex was washed three times with IP buffer as follows: the tube was placed into a magnetic rack for 1–2 min and the supernatant was discarded, then washed with IP buffer 3 times. The washed bead-antibody-DNA solution was then resuspended in 300 µl of digestion buffer (1 M Tris HCI, pH 8.0, 0.5 M EDTA, 10% SDS) and 3 µl proteinase K (20 mg/ml). The sample was incubated for 3 h on a rotator at 56 °C. After incubation the samples were extracted with Phenol-Chloroform-Isoamylalcohol and precipitated with 2 µl of Glycoblue (20 mg/ml), a one-tenth volume of 3 M sodium acetate and two volumes of ethanol overnight at −20 °C.  The precipitate was centrifuged at 18,000xg for 30 min at 4 °C and the supernatant was removed, while not disturbing the pellet. The pellet was washed with 500 µl cold 70% ethanol, then centrifuged again at 18,000xg for 10 min at 4 °C and the supernatant was discarded. The tube was spun briefly to collect residual ethanol to bottom of tube and as much liquid as possible was removed with a gel loading tip. Pellet was air-dried at RT until it looked dry (about 5 min), then resuspended in 20 µl H20. DNA concentration was measured in the Qubit (Life Technologies) with the BR dsDNA kit (Molecular Probes Q32853).
MeDIP DNA was used to create libraries for next generation sequencing (NGS) using the NEBNext Ultra RNA Library Prep Kit for Illumina (San Diego, CA) starting at step 1.4 of the manufacturer’s protocol to generate double stranded DNA from the single-stranded DNA resulting from MeDIP. After this step the MeDIP DNA, and starting with the ChIP DNA, the manufacturer’s protocol was followed indexing each sample individually with NEBNext Multiplex Oligos for Illumina.

value: Glyphosate

value: monoclonal mouse anti 5-methyl cytidine, Diagenode #C15200006

value: prostate


title: CEMBA180925_5E_7_CEMBA180925_5E_8_H10_ad002

status: Public on Sep 11 2020

type: SRA

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

country: USA

institute: HHMI-Salk-Institute

library_source: genomic

data_processing:
Library strategy: snmC-seq2
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted mm10 reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column

molecule: genomic DNA

organism: Mus musculus

source_name: C57BL/6J Male P56 Mouse Brain

growth_protocol: All mice are C57BL/6J Male, brain dissected in P56

extract_protocol:
the brain of P56 male C57BL/6J mouse will be removed and cut into 600 microns thick coronal sections using a tissue matrix. Then each region will be microdissected from the coronal tissue sections based on identified landmarks and brain atlas coordinates, as defined in Allen brain atlas CCF3 (Avaliable at: http://atlas.brain-map.org). For each dissection region, the tissue from several littermate mice will be combined together into to separate replicate groups. The number of animals in a replicate depends on the size of the tissue. Nuclei preparation will be stained with the fluorescently labeled anti-NeuN body and nucleic acid stain Hoechst 33342.
Library prepared following protocol discribed in Luo, Chongyuan, Angeline Rivkin, Jingtian Zhou, Justin P. Sandoval, Laurie Kurihara, Jacinta Lucero, Rosa Castanon, et al. 2018. “Robust Single-Cell DNA Methylome Profiling with snmC-seq2.” Nature Communications 9 (1): 3824.

tag: brain region

value: CP

tag: Sex

value: male

tag: age

tag: strain


title: CEMBA180925_5E_7_CEMBA180925_5E_8_H1_ad001


title: CEMBA180925_5E_7_CEMBA180925_5E_8_H12_ad004


title: CEMBA180925_5E_7_CEMBA180925_5E_8_H1_ad004


title: CEMBA180925_5E_7_CEMBA180925_5E_8_H1_ad002


title: CEMBA180925_5E_7_CEMBA180925_5E_8_H1_ad006


title: CEMBA180925_5E_7_CEMBA180925_5E_8_H1_ad007


title: CEMBA180925_5E_7_CEMBA180925_5E_8_G9_ad012


title: CEMBA180925_5E_7_CEMBA180925_5E_8_G9_ad001


title: CEMBA180925_5E_7_CEMBA180925_5E_8_H1_ad008


title: CEMBA180925_5E_7_CEMBA180925_5E_8_H10_ad001


title: CEMBA180925_5E_7_CEMBA180925_5E_8_G9_ad004


title: CEMBA180925_5E_7_CEMBA180925_5E_8_G9_ad010


title: CEMBA180925_5E_7_CEMBA180925_5E_8_G9_ad002


title: CEMBA180925_5E_7_CEMBA180925_5E_8_G9_ad006


title: CEMBA180925_5E_7_CEMBA180925_5E_8_G8_ad001


title: CEMBA180925_5E_7_CEMBA180925_5E_8_G8_ad004


title: CEMBA180925_5E_7_CEMBA180925_5E_8_G8_ad007


title: CEMBA180925_5E_7_CEMBA180925_5E_8_G8_ad012


title: CEMBA180925_5E_7_CEMBA180925_5E_8_G8_ad008


title: CEMBA180925_5E_7_CEMBA180925_5E_8_G7_ad012


title: CEMBA180925_5E_7_CEMBA180925_5E_8_G7_ad001


title: CEMBA180925_5E_7_CEMBA180925_5E_8_G7_ad002


title: CEMBA180925_5E_7_CEMBA180925_5E_8_G7_ad010


title: CEMBA180925_5E_7_CEMBA180925_5E_8_G7_ad007


title: CEMBA180925_5E_7_CEMBA180925_5E_8_G9_ad008


title: CEMBA180925_5E_7_CEMBA180925_5E_8_H12_ad006


title: CEMBA180925_5E_7_CEMBA180925_5E_8_G7_ad004


title: CEMBA180925_5E_7_CEMBA180925_5E_8_G7_ad006


title: CEMBA180925_5E_7_CEMBA180925_5E_8_G7_ad008


title: CEMBA180925_5E_7_CEMBA180925_5E_8_G8_ad010


title: CEMBA180925_5E_7_CEMBA180925_5E_8_G6_ad012


title: CEMBA180925_5E_7_CEMBA180925_5E_8_G6_ad007


title: CEMBA180925_5E_7_CEMBA180925_5E_8_H11_ad010


title: CEMBA180925_5E_7_CEMBA180925_5E_8_G9_ad007


title: CEMBA180925_5E_7_CEMBA180925_5E_8_G6_ad006


title: CEMBA180925_5E_7_CEMBA180925_5E_8_G6_ad008


title: CEMBA180925_5E_7_CEMBA180925_5E_8_G6_ad004


title: CEMBA180925_5E_7_CEMBA180925_5E_8_G5_ad012


title: CEMBA180925_5E_7_CEMBA180925_5E_8_G5_ad001


title: CEMBA180925_5E_7_CEMBA180925_5E_8_G6_ad002


title: CEMBA180925_5E_7_CEMBA180925_5E_8_G5_ad007


title: CEMBA180925_5E_7_CEMBA180925_5E_8_G5_ad006


title: CEMBA180925_5E_7_CEMBA180925_5E_8_G4_ad012


title: CEMBA180925_5E_7_CEMBA180925_5E_8_G5_ad008


title: CEMBA180925_5E_7_CEMBA180925_5E_8_G4_ad007


title: CEMBA180925_5E_7_CEMBA180925_5E_8_G4_ad001


title: CEMBA180925_5E_7_CEMBA180925_5E_8_G5_ad002


title: CEMBA180925_5E_7_CEMBA180925_5E_8_G3_ad001


title: CEMBA180925_5E_7_CEMBA180925_5E_8_G2_ad012


title: CEMBA180925_5E_7_CEMBA180925_5E_8_G3_ad006


title: CEMBA180925_5E_7_CEMBA180925_5E_8_G4_ad008


title: CEMBA180925_5E_7_CEMBA180925_5E_8_G3_ad008


title: CEMBA180925_5E_7_CEMBA180925_5E_8_G4_ad006


title: CEMBA180925_5E_7_CEMBA180925_5E_8_G2_ad001


title: CEMBA180925_5E_7_CEMBA180925_5E_8_G3_ad012


title: CEMBA180925_5E_7_CEMBA180925_5E_8_G4_ad002


title: CEMBA180925_5E_7_CEMBA180925_5E_8_G3_ad007


title: CEMBA180925_5E_7_CEMBA180925_5E_8_G6_ad010


title: CEMBA180925_5E_7_CEMBA180925_5E_8_G2_ad007


title: CEMBA180925_5E_7_CEMBA180925_5E_8_G3_ad004


title: CEMBA180925_5E_7_CEMBA180925_5E_8_G2_ad010


title: CEMBA180925_5E_7_CEMBA180925_5E_8_G2_ad006


title: CEMBA180925_5E_7_CEMBA180925_5E_8_G5_ad010


title: CEMBA180925_5E_7_CEMBA180925_5E_8_G2_ad002


title: CEMBA180925_5E_7_CEMBA180925_5E_8_G2_ad008


title: CEMBA180925_5E_7_CEMBA180925_5E_8_G12_ad012


title: CEMBA180925_5E_7_CEMBA180925_5E_8_G12_ad010


title: CEMBA180925_5E_7_CEMBA180925_5E_8_G12_ad008


title: CEMBA180925_5E_7_CEMBA180925_5E_8_G12_ad004


title: CEMBA180925_5E_7_CEMBA180925_5E_8_G12_ad006


title: CEMBA180925_5E_7_CEMBA180925_5E_8_G3_ad010


title: CEMBA180925_5E_7_CEMBA180925_5E_8_G12_ad001


title: CEMBA180925_5E_7_CEMBA180925_5E_8_G4_ad010


title: CEMBA180925_5E_7_CEMBA180925_5E_8_G12_ad002


title: CEMBA180925_5E_7_CEMBA180925_5E_8_G11_ad004


title: CEMBA180925_5E_7_CEMBA180925_5E_8_G11_ad007


title: CEMBA180925_5E_7_CEMBA180925_5E_8_G11_ad008


title: CEMBA180925_5E_7_CEMBA180925_5E_8_G10_ad012


title: CEMBA180925_5E_7_CEMBA180925_5E_8_G10_ad010


title: CEMBA180925_5E_7_CEMBA180925_5E_8_G11_ad006


title: CEMBA180925_5E_7_CEMBA180925_5E_8_G11_ad010


title: CEMBA180925_5E_7_CEMBA180925_5E_8_G10_ad008


title: CEMBA180925_5E_7_CEMBA180925_5E_8_G10_ad002


title: CEMBA180925_5E_7_CEMBA180925_5E_8_G11_ad012


title: CEMBA180925_5E_7_CEMBA180925_5E_8_G10_ad001


title: CEMBA180925_5E_7_CEMBA180925_5E_8_G10_ad004


title: CEMBA180925_5E_7_CEMBA180925_5E_8_G10_ad007


title: CEMBA180925_5E_7_CEMBA180925_5E_8_G2_ad004


title: CEMBA180925_5E_7_CEMBA180925_5E_8_G1_ad012


title: CEMBA180925_5E_7_CEMBA180925_5E_8_G1_ad001


title: CEMBA180925_5E_7_CEMBA180925_5E_8_G1_ad010


title: CEMBA180925_5E_7_CEMBA180925_5E_8_G1_ad006


title: CEMBA180925_5E_7_CEMBA180925_5E_8_G1_ad004


title: CEMBA180925_5E_7_CEMBA180925_5E_8_G12_ad007


title: CEMBA180925_5E_7_CEMBA180925_5E_8_G1_ad002


title: CEMBA180925_5E_7_CEMBA180925_5E_8_G1_ad008


title: CEMBA180925_5E_7_CEMBA180925_5E_8_F9_ad012


title: CEMBA180925_5E_7_CEMBA180925_5E_8_F9_ad001


title: CEMBA180925_5E_7_CEMBA180925_5E_8_G11_ad002


title: CEMBA180925_5E_7_CEMBA180925_5E_8_F9_ad006


title: CEMBA180925_5E_7_CEMBA180925_5E_8_F9_ad002


title: CEMBA180925_5E_7_CEMBA180925_5E_8_F9_ad008


title: CEMBA180925_5E_7_CEMBA180925_5E_8_F8_ad001


title: CEMBA180925_5E_7_CEMBA180925_5E_8_F8_ad006


title: CEMBA180925_5E_7_CEMBA180925_5E_8_F8_ad004


title: CEMBA180925_5E_7_CEMBA180925_5E_8_F8_ad002


title: CEMBA180925_5E_7_CEMBA180925_5E_8_F8_ad007


title: CEMBA180925_5E_7_CEMBA180925_5E_8_F8_ad010


title: CEMBA180925_5E_7_CEMBA180925_5E_8_F7_ad004


title: CEMBA180925_5E_7_CEMBA180925_5E_8_F7_ad010


title: CEMBA180925_5E_7_CEMBA180925_5E_8_F8_ad008


title: CEMBA180925_5E_7_CEMBA180925_5E_8_F7_ad006


title: CEMBA180925_5E_7_CEMBA180925_5E_8_F7_ad007


title: CEMBA180925_5E_7_CEMBA180925_5E_8_F7_ad012


title: CEMBA180925_5E_7_CEMBA180925_5E_8_F7_ad002


title: CEMBA180925_5E_7_CEMBA180925_5E_8_F7_ad008


title: CEMBA180925_5E_7_CEMBA180925_5E_8_F6_ad012


title: CEMBA180925_5E_7_CEMBA180925_5E_8_F6_ad001


title: CEMBA180925_5E_7_CEMBA180925_5E_8_F6_ad010


title: CEMBA180925_5E_7_CEMBA180925_5E_8_F9_ad004


title: CEMBA180925_5E_7_CEMBA180925_5E_8_F6_ad007


title: CEMBA180925_5E_7_CEMBA180925_5E_8_F9_ad010


title: CEMBA180925_5E_7_CEMBA180925_5E_8_F5_ad012


title: CEMBA180925_5E_7_CEMBA180925_5E_8_F6_ad008


title: CEMBA180925_5E_7_CEMBA180925_5E_8_F8_ad012


title: CEMBA180925_5E_7_CEMBA180925_5E_8_F5_ad001


title: CEMBA180925_5E_7_CEMBA180925_5E_8_F5_ad007


title: CEMBA180925_5E_7_CEMBA180925_5E_8_F5_ad010


title: CEMBA180925_5E_7_CEMBA180925_5E_8_F7_ad001


title: CEMBA180925_5E_7_CEMBA180925_5E_8_F5_ad006


title: CEMBA180925_5E_7_CEMBA180925_5E_8_F5_ad008


title: CEMBA180925_5E_7_CEMBA180925_5E_8_F4_ad012


title: CEMBA180925_5E_7_CEMBA180925_5E_8_F4_ad007


title: CEMBA180925_5E_7_CEMBA180925_5E_8_F6_ad006


title: CEMBA180925_5E_7_CEMBA180925_5E_8_F4_ad004


title: CEMBA180925_5E_7_CEMBA180925_5E_8_F4_ad002


title: CEMBA180925_5E_7_CEMBA180925_5E_8_F3_ad010


title: CEMBA180925_5E_7_CEMBA180925_5E_8_F3_ad004


title: CEMBA180925_5E_7_CEMBA180925_5E_8_F4_ad006


title: CEMBA180925_5E_7_CEMBA180925_5E_8_F4_ad010


title: CEMBA180925_5E_7_CEMBA180925_5E_8_F6_ad004


title: CEMBA180925_5E_7_CEMBA180925_5E_8_F3_ad006


title: CEMBA180925_5E_7_CEMBA180925_5E_8_F5_ad002


title: CEMBA180925_5E_7_CEMBA180925_5E_8_F3_ad007


title: CEMBA180925_5E_7_CEMBA180925_5E_8_F3_ad002


title: CEMBA180925_5E_7_CEMBA180925_5E_8_F3_ad008


title: CEMBA180925_5E_7_CEMBA180925_5E_8_F4_ad008


title: CEMBA180925_5E_7_CEMBA180925_5E_8_F2_ad012


title: CEMBA180925_5E_7_CEMBA180925_5E_8_F2_ad001


title: CEMBA180925_5E_7_CEMBA180925_5E_8_F3_ad001


title: CEMBA180925_5E_7_CEMBA180925_5E_8_F2_ad004


title: CEMBA180925_5E_7_CEMBA180925_5E_8_F2_ad010


title: CEMBA180925_5E_7_CEMBA180925_5E_8_F12_ad008


title: CEMBA180925_5E_7_CEMBA180925_5E_8_F12_ad010


title: CEMBA180925_5E_7_CEMBA180925_5E_8_F2_ad007


title: CEMBA180925_5E_7_CEMBA180925_5E_8_F2_ad002


title: CEMBA180925_5E_7_CEMBA180925_5E_8_F12_ad012


title: CEMBA180925_5E_7_CEMBA180925_5E_8_F2_ad006


title: CEMBA180925_5E_7_CEMBA180925_5E_8_F5_ad004


title: CEMBA180925_5E_7_CEMBA180925_5E_8_F12_ad007


title: CEMBA180925_5E_7_CEMBA180925_5E_8_F12_ad006


title: CEMBA180925_5E_7_CEMBA180925_5E_8_F12_ad002


title: CEMBA180925_5E_7_CEMBA180925_5E_8_F12_ad004


title: CEMBA180925_5E_7_CEMBA180925_5E_8_F12_ad001


title: CEMBA180925_5E_7_CEMBA180925_5E_8_F11_ad008


title: CEMBA180925_5E_7_CEMBA180925_5E_8_F11_ad010


title: CEMBA180925_5E_7_CEMBA180925_5E_8_F10_ad012


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title: CEMBA180925_5E_5_CEMBA180925_5E_6_B3_ad012


title: CEMBA180925_5E_5_CEMBA180925_5E_6_B4_ad012


title: CEMBA180925_5E_5_CEMBA180925_5E_6_B2_ad007


title: CEMBA180925_5E_5_CEMBA180925_5E_6_B2_ad006


title: CEMBA180925_5E_5_CEMBA180925_5E_6_B3_ad008


title: CEMBA180925_5E_5_CEMBA180925_5E_6_B3_ad002


title: CEMBA180925_5E_5_CEMBA180925_5E_6_B2_ad004


title: CEMBA180925_5E_5_CEMBA180925_5E_6_B4_ad010


title: CEMBA180925_5E_5_CEMBA180925_5E_6_B12_ad012


title: CEMBA180925_5E_5_CEMBA180925_5E_6_B12_ad007


title: CEMBA180925_5E_5_CEMBA180925_5E_6_B12_ad002


title: CEMBA180925_5E_5_CEMBA180925_5E_6_B6_ad004


title: CEMBA180925_5E_5_CEMBA180925_5E_6_B11_ad007


title: CEMBA180925_5E_5_CEMBA180925_5E_6_B6_ad006


title: CEMBA180925_5E_5_CEMBA180925_5E_6_B6_ad002


title: CEMBA180925_5E_5_CEMBA180925_5E_6_B6_ad008


title: CEMBA180925_5E_5_CEMBA180925_5E_6_B5_ad004


title: CEMBA180925_5E_5_CEMBA180925_5E_6_B5_ad010


title: CEMBA180925_5E_5_CEMBA180925_5E_6_B4_ad001


title: CEMBA180925_5E_5_CEMBA180925_5E_6_B4_ad007


title: CEMBA180925_5E_5_CEMBA180925_5E_6_B4_ad006


title: CEMBA180925_5E_5_CEMBA180925_5E_6_B4_ad002


title: CEMBA180925_5E_5_CEMBA180925_5E_6_B3_ad010


title: CEMBA180925_5E_5_CEMBA180925_5E_6_B3_ad007


title: CEMBA180925_5E_5_CEMBA180925_5E_6_B4_ad008


title: CEMBA180925_5E_5_CEMBA180925_5E_6_B3_ad006


title: CEMBA180925_5E_5_CEMBA180925_5E_6_B10_ad010


title: CEMBA180925_5E_5_CEMBA180925_5E_6_B10_ad008


title: CEMBA180925_5E_5_CEMBA180925_5E_6_B10_ad004


title: CEMBA180925_5E_5_CEMBA180925_5E_6_B2_ad001


title: CEMBA180925_5E_5_CEMBA180925_5E_6_B2_ad010


title: CEMBA180925_5E_5_CEMBA180925_5E_6_B2_ad002


title: CEMBA180925_5E_5_CEMBA180925_5E_6_B1_ad006


title: CEMBA180925_5E_5_CEMBA180925_5E_6_B1_ad008


title: CEMBA180925_5E_5_CEMBA180925_5E_6_B12_ad010


title: CEMBA180925_5E_5_CEMBA180925_5E_6_A9_ad012


title: CEMBA180925_5E_5_CEMBA180925_5E_6_B10_ad007


title: CEMBA180925_5E_5_CEMBA180925_5E_6_A9_ad007


title: CEMBA180925_5E_5_CEMBA180925_5E_6_B12_ad008


title: CEMBA180925_5E_5_CEMBA180925_5E_6_B12_ad006


title: CEMBA180925_5E_5_CEMBA180925_5E_6_B12_ad004


title: CEMBA180925_5E_5_CEMBA180925_5E_6_B11_ad012


title: CEMBA180925_5E_5_CEMBA180925_5E_6_B12_ad001


title: CEMBA180925_5E_5_CEMBA180925_5E_6_A9_ad006


title: CEMBA180925_5E_5_CEMBA180925_5E_6_B11_ad010


title: CEMBA180925_5E_5_CEMBA180925_5E_6_A8_ad012


title: CEMBA180925_5E_5_CEMBA180925_5E_6_A8_ad001


title: CEMBA180925_5E_5_CEMBA180925_5E_6_B11_ad008


title: CEMBA180925_5E_5_CEMBA180925_5E_6_A8_ad007


title: CEMBA180925_5E_5_CEMBA180925_5E_6_B11_ad006


title: CEMBA180925_5E_5_CEMBA180925_5E_6_A8_ad002


title: CEMBA180925_5E_5_CEMBA180925_5E_6_A9_ad010


title: CEMBA180925_5E_5_CEMBA180925_5E_6_B3_ad004


title: CEMBA180925_5E_5_CEMBA180925_5E_6_A7_ad010


title: CEMBA180925_5E_5_CEMBA180925_5E_6_B11_ad004


title: CEMBA180925_5E_5_CEMBA180925_5E_6_B11_ad002


title: CEMBA180925_5E_5_CEMBA180925_5E_6_A6_ad012


title: CEMBA180925_5E_5_CEMBA180925_5E_6_A7_ad012


title: CEMBA180925_5E_5_CEMBA180925_5E_6_A6_ad010


title: CEMBA180925_5E_5_CEMBA180925_5E_6_A6_ad008


title: CEMBA180925_5E_5_CEMBA180925_5E_6_A6_ad006


title: CEMBA180925_5E_5_CEMBA180925_5E_6_A5_ad010


title: CEMBA180925_5E_5_CEMBA180925_5E_6_A7_ad001


title: CEMBA180925_5E_5_CEMBA180925_5E_6_A5_ad007


title: CEMBA180925_5E_5_CEMBA180925_5E_6_A5_ad008


title: CEMBA180925_5E_5_CEMBA180925_5E_6_B11_ad001


title: CEMBA180925_5E_5_CEMBA180925_5E_6_B10_ad006


title: CEMBA180925_5E_5_CEMBA180925_5E_6_B10_ad012


title: CEMBA180925_5E_5_CEMBA180925_5E_6_A5_ad004


title: CEMBA180925_5E_5_CEMBA180925_5E_6_B10_ad002


title: CEMBA180925_5E_5_CEMBA180925_5E_6_A5_ad001


title: CEMBA180925_5E_5_CEMBA180925_5E_6_A4_ad010


title: CEMBA180925_5E_5_CEMBA180925_5E_6_B10_ad001


title: CEMBA180925_5E_5_CEMBA180925_5E_6_A4_ad008


title: CEMBA180925_5E_5_CEMBA180925_5E_6_B1_ad004


title: CEMBA180925_5E_5_CEMBA180925_5E_6_B1_ad010


title: CEMBA180925_5E_5_CEMBA180925_5E_6_A5_ad006


title: CEMBA180925_5E_5_CEMBA180925_5E_6_A9_ad004


title: CEMBA180925_5E_5_CEMBA180925_5E_6_B1_ad001


title: CEMBA180925_5E_5_CEMBA180925_5E_6_A9_ad008


title: CEMBA180925_5E_5_CEMBA180925_5E_6_A9_ad001


title: CEMBA180925_5E_5_CEMBA180925_5E_6_A7_ad002


title: CEMBA180925_5E_5_CEMBA180925_5E_6_A8_ad008


title: CEMBA180925_5E_5_CEMBA180925_5E_6_A7_ad006


title: CEMBA180925_5E_5_CEMBA180925_5E_6_A7_ad004


title: CEMBA180925_5E_5_CEMBA180925_5E_6_A3_ad007


title: CEMBA180925_5E_5_CEMBA180925_5E_6_A3_ad004


title: CEMBA180925_5E_5_CEMBA180925_5E_6_A7_ad008


title: CEMBA180925_5E_5_CEMBA180925_5E_6_A2_ad012


title: CEMBA180925_5E_5_CEMBA180925_5E_6_A6_ad001


title: CEMBA180925_5E_5_CEMBA180925_5E_6_A3_ad001


title: CEMBA180925_5E_5_CEMBA180925_5E_6_A9_ad002


title: CEMBA180925_5E_5_CEMBA180925_5E_6_A2_ad010


title: CEMBA180925_5E_5_CEMBA180925_5E_6_A5_ad012


title: CEMBA180925_5E_5_CEMBA180925_5E_6_A4_ad012


title: CEMBA180925_5E_5_CEMBA180925_5E_6_A2_ad007


title: CEMBA180925_5E_5_CEMBA180925_5E_6_A2_ad008


title: CEMBA180925_5E_5_CEMBA180925_5E_6_A4_ad007


title: CEMBA180925_5E_5_CEMBA180925_5E_6_A2_ad006


title: CEMBA180925_5E_5_CEMBA180925_5E_6_A4_ad006


title: CEMBA180925_5E_5_CEMBA180925_5E_6_A4_ad004


title: CEMBA180925_5E_5_CEMBA180925_5E_6_A4_ad002


title: CEMBA180925_5E_5_CEMBA180925_5E_6_A3_ad008


title: CEMBA180925_5E_5_CEMBA180925_5E_6_A3_ad002


title: CEMBA180925_5E_5_CEMBA180925_5E_6_A2_ad004


title: CEMBA180925_5E_5_CEMBA180925_5E_6_A11_ad012


title: CEMBA180925_5E_5_CEMBA180925_5E_6_A11_ad007


title: CEMBA180925_5E_5_CEMBA180925_5E_6_A11_ad004


title: CEMBA180925_5E_5_CEMBA180925_5E_6_A11_ad006


title: CEMBA180925_5E_5_CEMBA180925_5E_6_A12_ad001


title: CEMBA180925_5E_5_CEMBA180925_5E_6_A10_ad006


title: CEMBA180925_5E_5_CEMBA180925_5E_6_A10_ad004


title: CEMBA180925_5E_5_CEMBA180925_5E_6_A11_ad008


title: CEMBA180925_5E_5_CEMBA180925_5E_6_A10_ad002


title: CEMBA180925_5E_5_CEMBA180925_5E_6_A11_ad002


title: CEMBA180925_5E_5_CEMBA180925_5E_6_A12_ad007


title: CEMBA180925_5E_5_CEMBA180925_5E_6_A12_ad004


title: CEMBA180925_5E_5_CEMBA180925_5E_6_A2_ad001


title: CEMBA180925_5E_5_CEMBA180925_5E_6_A12_ad010


title: CEMBA180925_5E_5_CEMBA180925_5E_6_A2_ad002


title: CEMBA180925_5E_5_CEMBA180925_5E_6_A12_ad002


title: CEMBA180925_5E_5_CEMBA180925_5E_6_A12_ad012


title: CEMBA180925_5E_5_CEMBA180925_5E_6_A3_ad012


title: CEMBA180925_5E_5_CEMBA180925_5E_6_A12_ad006


title: CEMBA180925_5E_5_CEMBA180925_5E_6_A12_ad008


title: CEMBA180925_5E_5_CEMBA180925_5E_6_A3_ad006


title: CEMBA180925_5E_5_CEMBA180925_5E_6_A11_ad001


title: CEMBA180925_5E_5_CEMBA180925_5E_6_A10_ad007


title: CEMBA180925_5E_5_CEMBA180925_5E_6_A10_ad008


title: CEMBA180925_5E_5_CEMBA180925_5E_6_A1_ad010


title: CEMBA180925_5E_5_CEMBA180925_5E_6_A1_ad007


title: CEMBA180925_5E_5_CEMBA180925_5E_6_A1_ad001


title: CEMBA180925_5E_5_CEMBA180925_5E_6_A1_ad012


title: CEMBA180925_5E_5_CEMBA180925_5E_6_A1_ad002


title: CEMBA180925_5E_5_CEMBA180925_5E_6_A1_ad006


title: CEMBA180925_5E_5_CEMBA180925_5E_6_A1_ad004


title: Control_2

city: Lausanne

first: Jean-Yves

last: Roignant

address: genopode building

country: Switzerland

institute: University of Lausanne

description: Control replicate 1

library_source: transcriptomic

data_processing:
The libraries were sequenced on NextSeq500 with 42 bp paired end
After sequencing reads were mapped using STAR (v. 2.5.2b) against ensembl release 87 (BDGP6).
Counts per gene were calculated using subread (1.5.1) with ensembl release 87 as a reference.
normalized bigwig tracks were created using samtools (v.1.3.1), bedtools (2.25.0) and kentUtils (v302).
Genome_build: BDGP6
Supplementary_files_format_and_content: counts per gene as tab separated file (tsv), read depth normalized bigwig tracks (bw)

molecule: polyA RNA

organism: Drosophila melanogaster

source_name: Embryo

growth_protocol: Flies were maintained on apple juice plates supplemented with fresh yeast. Embryos were collected for two hours at 25°C and subsequently developed for 20 hours, collected in Trizol and flash frozen in liquid nitrogen.

extract_protocol:
100 lola-O mutant embryos were collected, flash frozen in liquid nitrogen, and RNA was isolated using Trizol reagent. 1 µg of Dnase I treated RNA was subjected to library preparation using the NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina®.
Librariesfor sequencing were prepared according to the NEBNext® Ultra™ Directional RNA Library Prep Kit protocol.

tag: developmental stage

value: 20-22 hours after egg laying

tag: genotype

value: Wild type / Df(2R)ED2076

tag: tissue

value: Embryo


title: Control_3

description: Control replicate 1


title: Dima_11

type: RNA

city: Roskilde

first: Vibe

last: Skov

address: Koegevej 7-13

department: Hematology

country: Denmark

institute: Roskilde Hospital

hyb_protocol: Fragmented aRNA was hybridized to Affymetrix HG-U133A 2.0 chips

scan_protocol: see standard Affymetrix protocols

data_processing: Data were analyzed in R and analyzed using rma

label: Biotin

molecule: total RNA

organism: Homo sapiens

label_protocol: total RNA was converted to amplified RNA (aRNA) and fragmented using the MessageAmpTM III RNA amplification kit

extract_protocol: Total RNA was extracted from arteries in basal state using the TRIzol protocol including an extra phenol-chloroform step

tag: diagnosis

value: uremia

value: Mammaria artery


title: Control_1

description: Control replicate 1


title: Lola-O_3

description: Lola O knockout replicate 3

value: lola-O / Df(2R)ED2076


title: Dima_9


title: Dima_2

value: normal


title: Dima_5


title: Uraemi_179F

value: Ilica artery


title: Dima_6


title: Dima_7


title: Dima_4


title: Uraemi_222F


title: Uraemi_84F


title: Uraemi_226F


title: Lola-O_2

description: Lola O knockout replicate 2


title: Uraemi_71F


title: Uraemi_232F


title: Dima_1


title: Uraemi_72F


title: Dima_10


title: Dima_8


title: Uraemi_229F


title: Uraemi_175F


title: Uraemi_150F


title: Uraemi_139F


title: Lola-O_1

description: Lola O knockout replicate 1


title: Uraemi_160F


title: CtrlF_6

description: Neuronal mCherry expression

data_processing:
The libraries were sequenced on NextSeq500 with 76 bp single read
After sequencing reads were mapped using STAR (v. 2.5.2b) against an rRNA refence and unmapped reads were mapped against ensembl release 87 (BDGP6).
normalized bigwig tracks were created using samtools (v.1.3.1), bedtools (2.25.0) and kentUtils (v302).
Genome_build: BDGP6
Supplementary_files_format_and_content: read depth normalized bigwig tracks (bw)

growth_protocol: Flies were maintained on apple juice plates supplemented with fresh yeast. Embryos were collected for three hours at 25°C and subsequently developed for 13 hours for the neuronal control and 20 hours for the octopaminergic control. Cells were isolated, FACS sorted and collected in lysis buffer.

extract_protocol:
Embryonic cells were isolated as described before (Salmand & Perrin, 2011), FACS sorted and 10 cells per replicate were collected in lysis buffer and snap-frozen at -80°C.
Libary preparation was done using the Smart-Seq 2 Kit for Illumina

value: 13-16 hours after egg laying


title: CtrlF_5

description: Neuronal mCherry expression


title: CtrlF_9

description: Neuronal mCherry expression


title: CEMBA180925_5E_5_CEMBA180925_5E_6_A6_ad004


title: CtrlO_2

description: Octopaminergic mCherry expression

value: 20-23 hours after egg laying


title: Ctrl_88

value: renal artery


title: CtrlF_3

description: Neuronal mCherry expression


title: Uraemi_163F


title: CtrlF_8

description: Neuronal mCherry expression


title: Ctrl_49F


title: Ctrl_85F


title: Tdc2-Gal4;UAS-Dam_Lola-O_2

description: Dam-Lola-O fusion protein expressed in  octopaminergic neurons

data_processing:
Library strategy: DamID-seq
The forward sequencing reads were mapped to release 6 of the Drosophila genome using Bowtie2 (see PMID: 26112292 for details of the damidseq_pipeline)
Reads were extended to adjacent GATC sites and binned for each GATC fragment
GATC fragments without any reads were excluded, followed by quantile normalization and pseudocount addition.
Ratio files (log2) were then generated from the experimental and Dam-only control data.
Genome_build: BDGP6
Supplementary_files_format_and_content: log2 normalized fold changes between the experimental and Dam-only control as bigwig tracks (converted from the gff file produced by the damidseq_pipeline)

growth_protocol: Flies were maintained on apple juice plates supplemented with fresh yeast.

extract_protocol:
Genomic DNA was isolated,RNAseA treated and DpnI digested. DamID adaptors were ligated to DpnI digested DNA followed by DpnII digestion PCR amplification, sonication and removal of DamID adaptors (Marshall et al., 2016).
Libraries were generated using the NebNext Ultra II DNA Library Kit

treatment_protocol: Embryos were collected for two hours at 25°C and subsequently developed for 20 hours, collected and frozen.

value: 22+/- 2 hours after fertilization

value: Tdc2-Gal4; UAS-Dam-Lola-O

tag: treatment

value: Dam methylase


title: Tdc2-Gal4;UAS-Dam_Lola-O_1

description: Dam-Lola-O fusion protein expressed in octopaminergic neurons


title: Uraemi_110F


title: Uraemi_101F


title: Tdc2-Gal4;UAS-Dam_PolII_2

description: Dam-PolII fusion protein expressed in octopaminergicneurons

value: Tdc2-Gal4; UAS-Dam-Lola-PolII


title: Ctrl_39F


title: Ctrl_3F


title: Ctrl_228F


title: Tdc2-Gal4;UAS-Dam_PolII_1

description: Dam-PolII fusion protein expressed in octopaminergic neurons


title: Tdc2-Gal4;UAS-Dam_Ctr_1

description: Dam alone control expressed in octopaminergic neurons (used for normalization)


title: CtrlF_2

description: Neuronal mCherry expression


title: Ctrl_196F


title: Ctrl_201F


title: Ctrl_231F


title: Ctrl_174F


title: Ctrl_221F


title: Ctrl_180F


title: Neg_M7

city: Neuherberg

first: Johannes

last: Beckers

address: Ingolstaedter Landstr. 1

department: Institute of Experimental Genetics

country: Germany

institute: Helmholtz Zentrum Muenchen

description: Gene expression data from crypt cells expressing RFP and GFP, Flattop lineage negative

scan_protocol: According to the Affymetrix expression protocol, Scanner 3000 7G

data_processing: Expression console (v.1.3.0.187, Affymetrix) was used to obtain normalized RMA gene-level data (standard settings including median polish and sketch-quantile normalisation). The 18 samples have been normalized together but RMA data provided for only 6 samples.

label: biotin

source_name: Crypt cells expressing RFP, Flattop lineage negative

label_protocol: Ovation Pico WTA System V2 in combination with the Encore Biotin Module (Nugen)

growth_protocol: No growth

extract_protocol: miRNeasy Mini Kit (Qiagen) including DNase treatment

treatment_protocol: Small intestinal crypts were isolated from FltpZV/+ mice. Single cells were pepared and FAC-sorted according to the GFP level.

value: small intestinal crypts

value: mixed C57BL/6J, CD1, 129/SvJ

value: 3-6 months

value: FltpT2AiCre crossed with Gt(ROSA)26mTmG


title: Ctrl_168F


title: Neg_M11

hyb_protocol: According to the Affymetrix expression protocol


title: Ctrl_162F


title: Tdc2-Gal4;UAS-Dam_Ctr_2

value: Embryo


title: PHH_donor2_uncultured_hepatocytes_human

city: Madison

first: Srikumar

last: Sengupta

state: WI

address: 330 N Orchard St

department: Regenerative Biology

institute: Morgridge Institute for Research

description:
uncultured_HU8295
genes.no_mt.ec.tab
genes.no_mt.tpm.rescale.tab

data_processing:
Basecalls performed using CASAVA version 1.8.2
Sequences were filtered and trimmed to remove low quality reads, adapters, and other sequencing artifacts.
Sequencing reads were mapped to chimera transcriptome using bowtie 1.2.3
Gene expected counts were calculated using RSEM 1.2.31
Genome_build: hg19
Supplementary_files_format_and_content: collated rsem output into tab files, expected counts (ec) and transcripts per million (TPMs)

growth_protocol: MEFs were cultured to passage 1 (p1) to passage 3 (p3) in growth medium (1X DMEM, 10X heat inactivated fetal bovine serum (FBS), 1X nonessential amino acids) and irradiated with a dose of 80Gy using a Mark I 137Cs irradiator (from J. L. Shepherd and Associates).

extract_protocol:
Total RNA from cells were isolated with RNeasy Plus kit (QIAGEN).
Sequencing libraries were prepared following the LM-seq protocol (Hou et al., 2015).
Sequenced on Illumina HiSeq 2500 and HiSeq 3000  at a depth of 48 samples per lane.

treatment_protocol: Irradiated MEFs were seeded onto 0.1% gelatin coated plates at a concentration of 1.8 × 10e5 cells/mL to be used for culturing SHPCs. SHPC medium was E6 based (Chen et al., 2011) and contained Dexamethasone (1 μM), epidermal growth factor (100 ng/ml), Oncostatin M (10 μg/ml), 20% FBS, insulin (2 μl/ml), Nicotinamide (100 mM), Y27632 (10 μM), A-083 (0.5 μM), CHIR99021 (3 μM), and N2 and B27 (both at 1X).

tag: passage

tag: donor


title: cholangiocyte_donor3_human

description:
human_cholangiocyte_P3_42916
genes.no_mt.ec.tab
genes.no_mt.tpm.rescale.tab


title: SHPC_donor2_hepatocytes_mag_sorted_passage_3_human

description:
HU8295_SHPC_CD44_sorted_P3
genes.no_mt.ec.tab
genes.no_mt.tpm.rescale.tab


title: Neg_F15


title: cholangiocyte_donor2_rep2_human

description:
human_cholangiocyte_P2_42116
genes.no_mt.ec.tab
genes.no_mt.tpm.rescale.tab


title: PHH_donor3_uncultured_hepatocytes_human

description:
Uncultured_hu_8290
genes.no_mt.ec.tab
genes.no_mt.tpm.rescale.tab


title: SHPC_donor3_hepatocytes_passage_3_human

description:
HU8290_SHPC_p3
genes.no_mt.ec.tab
genes.no_mt.tpm.rescale.tab


title: Ctrl_144F


title: Ctrl_159F


title: cholangiocyte_donor2_rep1_human

description:
human_cholangiocyte_P2_42316
genes.no_mt.ec.tab
genes.no_mt.tpm.rescale.tab


title: Ctrl_149F


title: hepG2_lowdensity_hepatocytes_human

description:
HepG2_low_density_DMSO
genes.no_mt.ec.tab
genes.no_mt.tpm.rescale.tab


title: SHPC_donor2_hepatocytes_passage_0_human

description:
Hu8295_P0_SHPC
genes.no_mt.ec.tab
genes.no_mt.tpm.rescale.tab


title: Ctrl_126F


title: hepG2_highdensity_hepatocytes_human

description:
HepG2_high_density_DMSO
genes.no_mt.ec.tab
genes.no_mt.tpm.rescale.tab


title: CtrlF_7

description: Neuronal mCherry expression


title: GFPlow_M13

description: Gene expression data from crypt cells expressing low levels of GFP, early Flattop lineage, RFP negative

source_name: Crypt cells expressing low levels of GFP, early Flattop lineage, RFP-negative


title: GFPlow_M9


title: CL41

city: Boston

first: Joan

middle: S.

last: Brugge

state: MA

address: 240 Longwood Avenue

department: Department of Cell Biology

institute: Harvard Medical School

data_processing:
Adapter sequence was trimmed using Trimmomatic-0.30 with the following parameters LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:30.
Trimmed reads were mapped with bowtie2-2.1.0 in paired-end mode with default parameters.
The htseq-count function of HTSeq-0.5.4 was used to summarize count data.
edgeR 3.22.3 was used for calculation of normalized count values.
Genome_build: hg19
Supplementary_files_format_and_content: Tab delimited text file include normalized counts per million (CPM) values for each sample.

source_name: OCI-C5x Clone 41

growth_protocol: The cells were cultured and passaged in OCMI-L full medium (Live Tumor Culture Core, University of Miami) in a humidified incubator at 37°C with 5% CO2.

extract_protocol:
Total RNA was extracted from each sample using the RNeasy Mini Kit according to manufacturer’s protocol (Qiagen, Inc.). The RNA concentration was measured using the Epoch microplate spectrophotometer (BioTek). Prior to library generation for RNA-sequencing, the quality of the RNA was determined on a 2200 TapeStation analyzer using RNA screen tapes (Agilent Technologies).
The mRNA libraries were generated by the Biopolymers Facility at Harvard Medical School (http://genome.med.harvard.edu, Boston, MA) and included poly-A enrichment and the Directional RNASeq Wafergen services.

tag: cell line

value: OCI-C5x single-cell clonal population

tag: tissue source

value: Ovarian clear cell carcinoma


title: CL31

source_name: OCI-C5x Clone 31


title: SHPC_donor1_hepatocytes_passage_7_human

description:
hu1962_SHPC_p7
genes.no_mt.ec.tab
genes.no_mt.tpm.rescale.tab


title: CL17

source_name: OCI-C5x Clone 17


title: CL28

source_name: OCI-C5x Clone 28


title: GFPlow_F17


title: CL44

source_name: OCI-C5x Clone 44


title: SHPC_donor1_hepatocytes_passage_5_human

description:
hu1962_SHPC_p5
genes.no_mt.ec.tab
genes.no_mt.tpm.rescale.tab


title: CL16

source_name: OCI-C5x Clone 16


title: CL12

source_name: OCI-C5x Clone 12


title: SHPC_donor1_hepatocytes_passage_3_human

description:
hu1962_SHPC_p3
genes.no_mt.ec.tab
genes.no_mt.tpm.rescale.tab


title: Ctrl_111F


title: CL09

source_name: OCI-C5x Clone 09


title: GFPhigh_M14

description: Gene expression data from crypt cells expressing high levels of GFP, late Flattop lineage, RFP negative

source_name: Crypt cells expressing high levels of GFP, late Flattop lineage, RFP-negative


title: GFPhigh_F18


title: CL49

source_name: OCI-C5x Clone 49


title: parental

source_name: OCI-C5x clear cell carcinoma line


title: Sample 10_Recovery2

city: Beijing

first: Lihui

last: Liu

address: 15 Datun Road, Chaoyang District

department: Institute of Biophysics

country: China

institute: Chinese Academy of Sciences

description: Nor-2_FCC55R9ACXX_L4_WHHUMuarNAADRAAPEI-205

data_processing:
fastqc used to check data quality
trimmomatic-0.36 to filter reads quality
STAR-2.5.1b to map reads to hg38
R language limma and edgeR package to obtein the gene of differential expression
Genome_build: hg38
Supplementary_files_format_and_content: txt file was genetrated by R language and the content in it such as gene expression ,foldchange.

source_name: IAV-infected patients' neutrophils in the recovery stage

extract_protocol:
Neutrophils and macrophages were isolated using Percoll (GE healthcare),Total RNA were extracted using TRIzol(Invitrogen) as instruction.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: patient status

value: patients infected with IAV

tag: patient id

tag: state

value: Recovery stage

tag: cell type

value: neutrophil


title: Sample 11_Recovery3

description: Nor-3_FCC56DKACXX_L7_WHHUMuarNAAFRAAPEI-207


title: Sample 9_Recovery2

description: Nor-2_FCC55R9ACXX_L3_WHHUMuarNAADRAAPEI-205


title: CL46

source_name: OCI-C5x Clone 46


title: Sample 12_Recovery3

description: Nor-3_FCC56DKACXX_L8_WHHUMuarNAAFRAAPEI-207


title: SHPC_donor1_hepatocytes_passage_1_human

description:
hu1962_SHPC_p1
genes.no_mt.ec.tab
genes.no_mt.tpm.rescale.tab


title: Nicotine-treated at 5 days, rep 1 [NI_5D_REP1_GATCAG]

city: Institute

first: Sridhar

middle: A

last: Malkaram

state: West Virginia

address: Barron Drive

department: Mathematics and Computer Sciences

institute: West Virginia State University

data_processing:
The fastq read files were quality checked using using fastqc ver. 0.11.5 and 3-prime end trimmed for the Illumina TruSeq adapters and low quality bases (phred score < 20) using trimgalore ver. 0.4.4. The reads were then aligned to the Chicken genome (ensemblgenomes Gallus gallus ver. 5.0.88) using Hisat2 ver. 2.0.5 and bowtie2 ver. 2.3.2.
The aligned reads from each sample were then assembled using stringtie ver. 1.3.3b and the ensembl gene annotation file for Gallus gallus genome version 5.0.88. A second stringtie run was used to create merged assembly combining the individual sample assemblies.
Finally stringtie was again run using the merged assembly as the reference annotation.
A table of gene expression abundances for each sample was prepared using custom perl scripts. Differential expression analysis was done using the DESeq2 package in R ver 3.3.1.
The time,  nicotine treatment, and the time:nicotine interaction variables were included in the DESeq2's model. Differential expression comparisons were made for the effect of time, effect of nicotine and the interaction effect of nicotine and time. Genes with a multiple testing adjusted p-value cutoff of < 0.05 were considered as significant.
Genome_build: ensemblgenomes Gallus gallus ver. 5.0.88
Supplementary_files_format_and_content: gene expression abundances for each sample (*.matrix); CSV format of Processed results for DESeq2 differential expression (*.all.csv).

organism: Gallus gallus

source_name: Nicotine at 5 days_spinal cord

growth_protocol: Two cohorts of 24 fertile specific pathogen-free eggs of the domestic chicken were obtained from Charles River Laboratories (Catskill, New York, USA). Eggs were randomly assigned to treatment and control cohorts.

extract_protocol:
At the time point of sacrifice (5 or 7 days), egg shells were chipped off and the animals’ viability and proper development was verified. The verification of viability was based on observation of a heartbeat. Appropriate development and lack of gross abnormalities in animals were also verified (Hamburger and Hamilton 1951).  Embryos (randomly selected 4 biological replicates for each treatment and time point) were harvested in RNAse- free conditions and dissected in cold DEPC-treated PBS. The section between the mid portion of the neck and posterior border of the anterior limb was cut out. A part of this section containing spinal cord was dissected using fine scissors, tweezers, and glass needles and then placed into a 1.5 ml tube filled with ice-cold DEPC-treated PBS. The samples were homogenized in TRI Reagent® or Trizol®(Sigma) and RNA extraction was completed using Ambion® PureLink® RNA Mini Kit (all reagents were obtained from Sigma-Aldrich (St. Louis, Missouri, USA)).  All RNA samples were stored at -80 °C before being shipped to Marshall University Genomics and Bioinformatics Core (GABC) where the expression analysis was conducted.
The RNA samples were sequenced (2 x 50 Paired End sequencing, 25 million reads per library) at  Marshall University, WV, genomics core facility
Adapter,AGATCGGAAGAGCACACGTCTGAACTCCAGTCA,,,,,,,   AdapterRead2,AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT,,,,,,,

treatment_protocol: Nicotine (nicotine hydrogen bitartrate calculated as free base) and vehicle chemicals (sodium bitartrate monohydrate) were obtained from Sigma-Aldrich (St. Louis, Missouri, USA).  Nicotine doses of 30 ng/ml and corresponding doses of vehicle control were calculated according to the weight of the egg. The injections were delivered from the blunt pole of the egg before incubation as described previously (Dalgic, Armagan et al. 2009). The drugs were dissolved in Chicken Ringer's solution and sterilized before injection using .22µm Millex® syringe filter units (Sigma-Aldrich, St. Louis, Missouri, USA).

tag: breed

value: Domestic chicken

tag: genotype/variation

value: wild type

tag: treated with

value: Nicotine (nicotine hydrogen bitartrate)

value: Spinal cord section


title: Control at 7 days, rep 4 [CT_7D_REP4_ACTTGA]

source_name: Control at 7 days_spinal cord

tag: age

value: vehicle chemicals (sodium bitartrate monohydrate)


title: RFP_GFP_F16

description: Gene expression data from crypt cells expressing RFP and GFP, Flattop positive

source_name: Crypt cells expressing RFP and GFP, Flattop-positive

tag: strain


title: human_hepatocytes_passage_1_donor_1_Matrigel_culture

description:
uncultured_Hu1962
genes.no_mt.ec.tab
genes.no_mt.tpm.rescale.tab


title: RFP_GFP_M12

tag: genotype


title: Control at 7 days, rep 3 [CT_7D_REP3_CAGATC]

tag: tissue


title: Sample 6_Hospitalized3

description: H7N9-3_FCC56A0ACXX_L2_WHHUMuarNAAARAAPEI-202

source_name: IAV-infected patients' neutrophils in the acute stage

value: being infected; acute stage


title: GFPhigh_M10


title: SHPC_donor1_hepatocytes_passage_4_human

description:
hu1962_SHPC_p4
genes.no_mt.ec.tab
genes.no_mt.tpm.rescale.tab


title: SHPC_donor1_hepatocytes_passage_2_human

description:
hu1962_SHPC_p2
genes.no_mt.ec.tab
genes.no_mt.tpm.rescale.tab


title: CL11

source_name: OCI-C5x Clone 11


title: Sample 5_Hospitalized3

description: H7N9-3_FCC56A0ACXX_L1_WHHUMuarNAAARAAPEI-202


title: Sample 8_Recovery1

description: Nor-1_FCC56DKACXX_L8_WHHUMuarNAAERAAPEI-206


title: Control at 7 days, rep 1 [CT_7D_REP1_TGACCA]


title: Sample 4_Hospitalized2

description: H7N9-2_FCC55R9ACXX_L4_WHHUMuarNAABRAAPEI-203


title: Sample 3_Hospitalized2

description: H7N9-2_FCC55R9ACXX_L3_WHHUMuarNAABRAAPEI-203


title: Nicotine-treated at 7 days, rep 3 [NI_7D_REP3_TTAGGC]

source_name: Nicotine at 7 days_spinal cord


title: Sample 7_Recovery1

description: Nor-1_FCC56DKACXX_L7_WHHUMuarNAAERAAPEI-206


title: Sample 2_Hospitalized1

description: H7N9-1_FCC55R9ACXX_L4_WHHUMuarNAACRAAPEI-204


title: Control at 7 days, rep 2 [CT_7D_REP2_GCCAAT]


title: Nicotine-treated at 7 days, rep 2 [NI_7D_REP2_CGATGT]


title: SHPC_donor1_hepatocytes_passage_0_human

description:
hu1962_SHPC_p0
genes.no_mt.ec.tab
genes.no_mt.tpm.rescale.tab


title: Sample 1_Hospitalized1

description: H7N9-1_FCC55R9ACXX_L3_WHHUMuarNAACRAAPEI-204


title: RFP_GFP_M8


title: Nicotine-treated at 7 days, rep 4 [NI_7D_REP4_ACAGTG]


title: SHPC_donor1_hepatocytes_passage_6_human

description:
hu1962_SHPC_p6
genes.no_mt.ec.tab
genes.no_mt.tpm.rescale.tab


title: Control at 5 days, rep 4 [CT_5D_REP4_CCGTCC]

source_name: Control at 5 days_spinal cord


title: CEMBA180925_5E_5_CEMBA180925_5E_6_A1_ad008

source_name: C57BL/6J Male P56 Mouse Brain

tag: brain region

value: CP

tag: Sex

value: male