title: 3532_Testis


title: 3568_Testis

status: Public on Dec 15 2019

type: SRA

city: Indianapolis

first: Kamin

last: Johnson

state: IN

address: 9330 Zionsville Rd

country: USA

institute: Corteva Agriscience

description: Day after mating designated gestation day 0. Loading dose delivered on gestation day 6 via oral gavage. Daily maintenance doses delivered from gestation day 7 to 20 via oral gavage. Samples analyzed 30 minutes following the last dosing.

library_source: transcriptomic

data_processing:
Basecalls performed using Illumina CASAVA software version 1.8.
Raw sequencing reads were trimmed and filtered for low quality bases using the fastq-mcf tool from the ea-utils software package (v1.1.0) with the minimum remaining sequence length option set to 50 and quality threshold set to 30.
Trimmed reads were subsequently mapped to the rat reference genome (version 6.0.80) using the hisat2 mapping software (v2.0.3) run using default parameter settings and in stranded mode.
Using HTSeq (v0.7.2), the reads mapped to the antisense strand of each gene were counted.
Genome_build: Rattus norvegicus (version 6.0.80)
Supplementary_files_format_and_content: *.raw_gene_counts.txt: Tab-delimited text files include raw gene count values for each Sample.

molecule: total RNA

organism: Rattus norvegicus

source_name: Fetal testis

extract_protocol:
Total RNA was extracted from organs stored in RNAlater using a Qiagen RNeasy kit. Samples were digested with DNase during the RNA isolation process to avoid DNA contamination. RNA quantity was measured using a NanoDrop ND-1000 spectrophotometer. Total RNA quality was examined using the HT RNA Std Sens assay on a LabChip GX instrument (PerkinElmer; Waltham, MA) according to the manufacturer’s instructions.
The Illumina TruSeq Stranded mRNA library preparation kit was used to prepare mRNA library templates following the manufacturer’s recommended protocol. In brief, poly-A containing mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Purified mRNA was fragmented to approximately 200 bp average length using divalent cations under high temperature. Following fragmentation, SuperScript II reverse transcriptase and random primers were used to copy the mRNA into first strand cDNA. The cDNA was further converted into double stranded cDNA using DNA polymerase I and RNase H. These double stranded cDNA fragments then underwent end repair, A-tailing, and ligation to indexed Illumina adapters. Finally, adapter-ligated library products were enriched with 15 cycles of PCR and purified.

tag: strain/background

value: Cr1:CD (SD); Sprague-Dawley

tag: tissue

value: Fetal testis

tag: developmental stage

value: Gestation day 20

tag: Sex

value: Male

tag: molecule exposure

value: TCDF

tag: exposure

value: Gestation day 8 - 20

tag: loading dose level (ug/kg)

tag: maintenance dose level (ug/kg)

tag: experimental block

tag: sample deemed an outlier

value: No


title: 3530_Testis

description: Day after mating designated gestation day 0. A single dose was administered on gestation day 15.

value: Corn oil (vehicle)

value: Gestation day 15 - 20

value: Not applicable


title: 3574_Testis


title: 3566_Testis


title: 3564_Testis


title: 3563_Testis


title: 3561_Testis


title: 3565_Testis


title: 3567_Testis


title: 3560_Testis


title: 3559_Testis


title: 3558_Testis


title: 3554_Testis

value: TCDD


title: 3556_Testis


title: 3555_Testis


title: 3549_Testis


title: 3548_Testis


title: 3547_Testis


title: 3545_Testis


title: 3546_Testis


title: 3544_Testis


title: 3542_Testis


title: 3543_Testis


title: 3541_Testis


title: 3540_Testis


title: 3539_Testis


title: 3538_Testis


title: 3537_Testis


title: 3535_Testis


title: 3536_Testis


title: 3529_Testis


title: 3528_Testis


title: 3527_Testis


title: 3525_Testis


title: 3842_Testis


title: 3838_Testis


title: 3839_Testis


title: 3840_Testis


title: 3835_Testis


title: 3841_Testis


title: 3837_Testis


title: 3833_Testis


title: 3832_Testis


title: 3830_Testis


title: 3827_Testis


title: 3829_Testis


title: 3828_Testis


title: 3823_Testis


title: 3826_Testis


title: 3824_Testis


title: 3825_Testis


title: 3822_Testis


title: 3817_Testis


title: 3821_Testis


title: 3819_Testis


title: 3818_Testis


title: 3820_Testis


title: 3526_Testis


title: 3815_Testis


title: 3816_Testis


title: 3813_Testis


title: 3834_Testis


title: 3836_Testis


title: 3814_Testis


title: 3831_Testis


title: 3812_Testis


title: 3808_Testis


title: 3574_Pituitary

source_name: Fetal pituitary

value: Fetal pituitary


title: 3571_Pituitary


title: 3572_Pituitary


title: 3811_Testis


title: 3554_Pituitary


title: 3809_Testis


title: 3573_Pituitary


title: 3553_Pituitary


title: 3570_Pituitary


title: 3552_Pituitary


title: 3534_Pituitary


title: 3532_Pituitary


title: 3550_Pituitary

value: Yes


title: 3533_Pituitary


title: 3531_Pituitary


title: 3551_Pituitary


title: 3566_Pituitary


title: 3567_Pituitary


title: 3530_Pituitary


title: 3565_Pituitary


title: 3564_Pituitary


title: 3569_Pituitary


title: 3563_Pituitary


title: 3560_Pituitary


title: 3562_Pituitary


title: 3561_Pituitary


title: 3559_Pituitary


title: 3558_Pituitary


title: 3555_Pituitary


title: 3548_Pituitary


title: 3557_Pituitary


title: 3546_Pituitary


title: 3547_Pituitary


title: 3568_Pituitary


title: 3544_Pituitary


title: 3542_Pituitary


title: 3540_Pituitary


title: 3545_Pituitary


title: 3541_Pituitary


title: 3539_Pituitary


title: 3556_Pituitary


title: 3549_Pituitary


title: 3538_Pituitary


title: 3543_Pituitary


title: 3529_Pituitary


title: 3528_Pituitary


title: 3535_Pituitary


title: 3536_Pituitary


title: 3537_Pituitary


title: 3842_Pituitary


title: 3525_Pituitary


title: 3527_Pituitary


title: 3526_Pituitary


title: 3841_Pituitary


title: 3840_Pituitary


title: 3837_Pituitary


title: CD8_siFOXP3_rep5

city: Bethesda

first: Clifton

middle: Lee

last: Dalgard

state: Maryland

address: 4301 Jones Bridge Road B2038

department: Anatomy Physiology & Genetics

institute: Uniformed Services University

data_processing:
Raw paired-end sequencing reads were aligned to the human reference genome (hg19) using STAR (version 2.4.2a).
Gene quantification was performed with RSEM (version 1.2.22)
Genome_build: hg19
Supplementary_files_format_and_content: FOXP3_sample_gene_expected_counts.txt – Expected gene counts for samples produced by RSEM
Supplementary_files_format_and_content: FOXP3_sample_gene_FPKMs.txt - Gene FPKM values for samples produced by RSEM

organism: Homo sapiens

source_name: CD8 T cells

growth_protocol: T cells were purified from PBMC by immunomagnetic negative selection using the specific EasySep Human T cell isolation kit

extract_protocol:
Total RNA was isolated from primary T cells using the Qiagen RNeasy Plus Mini Kit with on-column DNase digestion.  Total RNA integrity was assessed using automated capillary electrophoresis on a AATI Fragment Analyzer.   The integrity of all samples are RQI > 8.0
A minimum starting amount of 75 ng was used as input for library preparation using the Illumina TruSeq Stranded mRNA Library Preparation Kit

treatment_protocol: T cells were electroporated with siRNAs against FOXP3 (FOXP3HSS121456) using the Amaxa Nucleofection 4D system and the P3 Primary Cell kit (Lonza). Stealth RNAi negative control medium GC duplex siRNA (ThermoFisher) was used as a non-specific (NS) control, and all assays were conducted 4 days post electroporation for peak knockdown efficiency.

tag: sirna

tag: t cell subtype

tag: antibody blockade


title: 3839_Pituitary


title: 3838_Pituitary


title: CD8_siFOXP3_rep4


title: CD8_siFOXP3_rep2


title: 3835_Pituitary


title: RS59 Genomic DNA from R05C01

type: genomic

city: Cheongju

first: Yong-June

last: Kim

state: Chungbuk

address: Chungdae-ro 1, Seowon-Gu

department: College of Medicine

country: South Korea

institute: Chungbuk National University

description: surrounding tissue

hyb_protocol: Standard Illumina

scan_protocol: Standard Illumina procedures using Illumina iScan scanner

data_processing: Each methylation data point is represented by fluorescent signals from the M (methylated) and U (unmethylated) alleles. Background intensity computed from a set of negative controls was subtracted from each analytical data point. The ratio of fluorescent signals was then computed from the two alleles = (max(M, 0))/(|U| + |M| + 100). The   -value reflects the methylation level of each CpG site.A   -value of 0~1 was reported signifying percent methylation, from 0% to 100%, respectively, for each CpG site. Software Array data export processing and analysis was performed using Illumina GenomeStudio v2011.1 (Methylatioin Module v1.9.0) and R 3.0.2 (http://www.r-project.org).

label: biotin

molecule: genomic DNA

label_protocol: The A and T nucleotides are biotin labeled. The C and G nucleotides are labeled with dinintrophenol.

extract_protocol: Genomic DNA was extracted by standard methods by using the Wizard Genomic DNA Purification System (Promega, Madison, WI). Bisulfite modified gDNA was prepared using EZ DNA Methylation-Lightning kit (Zymo Research, Orange, CA) according to the manufacturer's instructions. The methylation status were assayed using the Infinium HumanMethylation450 (Infinium Methylation 450K; Illumina, Inc. CA, USA).

tag: tumor stage


title: Tu162 Genomic DNA from R06C02

description: surrounding tissue


title: 3833_Pituitary


title: CD8_siFOXP3_rep1


title: RS84 Genomic DNA from R04C02

description: surrounding tissue


title: RS79 Genomic DNA from R02C01

description: surrounding tissue


title: RS72 Genomic DNA from R03C02

description: surrounding tissue


title: R87 Genomic DNA from R06C02

description: cancer

tag: gender

value: male

tag: age

tag: recur


title: RS140 Genomic DNA from R05C02

description: surrounding tissue


title: Rs139 Genomic DNA from R06C01

description: surrounding tissue


title: RS171 Genomic DNA from R02C02

description: surrounding tissue


title: RS80 Genomic DNA from R03C01

description: surrounding tissue


title: 3832_Pituitary

tag: strain/background


title: RCC74 Genomic DNA from R03C02

description: cancer

value: female


title: RS60 Genomic DNA from R01C01

description: surrounding tissue


title: CD8_siNS_rep5

value: siNS


title: 3831_Pituitary

tag: tissue


title: R59 Genomic DNA from R05C01

description: cancer


title: CD8_siNS_rep4


title: R171 Genomic DNA from R02C02

description: cancer


title: 3830_Pituitary

tag: developmental stage


title: 3836_Pituitary

tag: Sex


title: RS169 Genomic DNA from R04C01

description: surrounding tissue


title: R149 Genomic DNA from R01C02

description: cancer


title: CD8_siNS_rep3


title: RS149 Genomic DNA from R01C02

description: surrounding tissue


title: R140 Genomic DNA from R05C02

description: cancer


title: RCC86 Genomic DNA from R04C02

description: cancer


title: 3829_Pituitary

tag: molecule exposure


title: mESCs, RING1B_EPZ_2

city: Edinburgh

first: Rob

middle: S

last: Illingworth

state: Midlothian

address: Centre for Regenerative Medicine

department: Centre for regenerative Medicine

country: United Kingdom

institute: The University of Edinburgh

description:
ChIP-seq for RING1B from mESCs treated with EPZ for 24 h. Replicate 2 of 2.
ChIP-seq

library_source: genomic

data_processing:
Base Calling. Basecalling, quality scoring and de-multiplexing was performed directly using the NextSeq 550 software (RTAv2). Alignment. ChIP-seq data was mapped to the mouse genome (mm9 build) using bowtie2 with the --local --threads 3 -S options to generate SAM files. Processing. Using the HOMER package, SAM files were converted into tag directories and multi-mapping reads were removed using makeTagDirectory -unique -fragLength 150. Mapped regions which, due to fragment processing, extended beyond the end of the chromosomes were removed using removeOutOfBoundsReads.pl  with chromosome lengths for mm9. Genome browser files (.bw) were generated using makeUCSCfile (HOMER package) with the -bigWig -fsize 1e20 -norm 10e7 options. H3K27me3 genome browser files were generated using the same parameters but normalised to a calibrator value that preserved the relative contribution of Drosophila spike-in reads between the input and immunoprecipitated samples.
Genome_build: mm9
Supplementary_files_format_and_content: .bigWig files contain information on both the genomic distribution and signal strength of the mapped reads (representative of the sample composition).  .bigWig files are in an indexed binary format.

organism: Mus musculus

source_name: Embryonic Stem Cells

growth_protocol: Feeder-free mouse embryonic stem cells (mESCs; E14tg2A - 129/Ola) were cultured on 0.1% gelatin (Sigma - catalogue no. G1890) coated Corning flasks in GMEM BHK-21 (Gibco - catalogue no. 21710-025) supplemented with 10 % foetal calf serum (FCS; Sigma - catalogue no. F-7524), 1,000 units/ml LIF, non-essential amino acids (Gibco - catalogue no. 11140-035), sodium pyruvate (Gibco - catalogue no. 11360-039), 50 μM 2-β-mercaptoethanol (Gibco - catalogue no. 31350-010) and L-glutamine. For passaging, 60–90% confluent ESC culture flasks were washed with PBS, incubated for 2–3 min at RT in trypsin (0.05% v/v;  Gibco 25300-054), and tapped to release. Trypsin was inactivated by adding 9 volumes of ESC medium and this mixture was repeatedly pipetted to obtain a single cell suspension. ESCs were centrifuged, resuspended in ESC medium and re-plated onto gelatin coated flasks at a density of ~4 × 104 cells/cm2 (determined using a hemocytometer - Neubauer).All centrifugation steps with live cells were performed at 330 x g for 3 min at room temperature (RT). All ESC lines used in this study were routinely tested for mycoplasma.

extract_protocol:
Trypsinized mESCs (20 x 10e6) were washed twice in PBS. Cells were resuspended in 250 µl of PBS and fixed by the addition of an equal volume of PBS containing 2% methanol free formaldehyde (Thermo Scientific Pierce PN28906; final concentration of 1%) and incubated at RT for 10 min. Fixation was stopped by 5 min incubation with 125 mM glycine at room temperature. Fixed cells were washed in PBS and combined at this stage with 1.3x10e6 formaldehyde fixed S2 cells (Drosophila melanogaster cells; for downstream calibration of ChIP-seq data). All buffers were supplemented with 1 mM DTT and 1x Protease inhibitors (Roche, 11836170001) just prior to use. Cell pellets were resuspended in lysis buffer (50 mM Tris-HCl pH 8.1, 10 mM EDTA and 20% SDS) and incubated for 10 min at 4 °C. Lysates were diluted 1:10 in ChIP Dilution Buffer (1% Triton X-100, 2 mM EDTA, 150 mM NaCl, 2 0mM and Tris-HCl pH8.1) and sonicated, first with a single 30s pulse with a probe sonicator (labtech Soniprep 150) on ice followed by a further 45 cycles using a cooled Bioruptor (Diagenode; 1 min cycles of 30sec on / 30 sec off on ‘high’ setting at 4 °C). The sonicated extract was pre-cleared by centrifugation at 16000 g for 10 min at 4 °C. The supernatant was transferred to a fresh tube and supplemented with BSA to a final concentration of 25 mg/ml. Anti-RING1B (Cell Signalling D22F2) antibodies were pre-coupled to a protein A Dynabeads (Life Technologies; catalogue no. 10001D) at a ratio of 1 mg antibody per 30 ml of dynabead suspension by rotation at 4 °C for 1 h. 12 x 10e6 cell equivalents of lysate were added to 7.5 µg of antibody bound beads and incubated for 6 h on a rotating wheel at 4 ºC. Following incubation, bead-associated immune complexes were washed sequentially with ChIP dilution buffer, wash buffer A and wash buffer B, each for 10 min at 4 ºC on a rotating wheel followed by two washes in TE buffer at RT (wash buffer A - 1% Triton X-100, 0.1% Sodium-Deoxycolate, 0.1% SDS, 1mM EDTA, 500 mM NaCl, 50 mM HEPES pH7.9; wash buffer B – 0.5% NP40, 0.5% Sodium-Deoxycolate, 1 mM EDTA, 250 mM LiCl, and 20 mM Tris-HCl pH8.1). Chromatin was released by incubating the beads in 100 µl of elution buffer (0.1 M NaHCO3 and 1 % SDS) for 15 min at 37 ºC, followed by the addition of 50 µg of RNaseA and 6µl of 2 M Tris pH6.8 and incubation at 65 ºC for 2 h and finally by the addition of 50 µg of proteinase K and incubation at 65 ºC for 8 h to degrade proteins and reverse the cross-links. Dynabeads were removed using a magnetic rack and the chromatin purified using PCR Purification columns (Qiagen) according to manufacturer’s instructions.
Libraries were constructed using the NEBNext® Ultra™ II DNA Library Prep Kit for Illumina according to manufacturer’s instructions (NEB - catalogue no. E7645S). Library PCRs were supplemented with 2x SYBR dye (Sigma – catalogue no. S9430) so that amplification could be monitored by quantitative PCR on a Roche lightcycler 480. To allow for sample multiplexing, PCRs were performed using index primers (NEBNext Multiplex Oligos for Illumina - Set 1. Catalogue no. E7335) and amplified to linear phase. Size selection purifications following the ligation and amplification PCR steps were performed with 1x and 0.9x reaction volumes of Agencourt AMPure XP beads (Beckman Coulter - A63880). Purified libraries were combined as a 12 sample equimolar pool containing the indexes 1-12 and sequenced on an Illumina NextSeq on a single high-output flow cell (single-end 75 bp reads).

treatment_protocol: Mouse ESCs were plated in standard medium at 4 × 104 cells/cm2 and cultured for 24 h. The medium was then replaced with medium supplemented with either EPZ-6438 (BioVision - catalogue no. 2383-5; reconstituted in DMSO) at a final concentration of 2.5µM or DMSO and cultured for a further 24 h prior to harvesting.

tag: cell type

value: mESC

tag: treatment

tag: cell line

tag: strain

tag: chip antibody

value: anti-RING1B (Cell Signalling D22F2)


title: R169 Genomic DNA from R04C01

description: cancer


title: 3828_Pituitary

value: Cr1:CD (SD); Sprague-Dawley

tag: exposure

tag: loading dose level (ug/kg)

tag: maintenance dose level (ug/kg)

tag: experimental block

tag: sample deemed an outlier


title: 3827_Pituitary

value: Gestation day 20


title: CLIP-seq_HSV-1-2

city: Irvine

first: Yongsheng

last: Shi

state: California

address: 811 Health Sciences Rd

institute: University of California, Irvine

description: ICP27-bound RNA

data_processing:
Library strategy: CLIP-Seq
Reads from CLIP-seq data were trimmed to remove the primers and polyA tails.
Both 4SU-Seq and CLIP-seq were aligned to human(hg19)(+HSV for infected cells) genome using STAR. Multi-mapping was not allowed.
Mapped reads were converted to bigwig files using deepTools.
Genome_build: Hg19
Supplementary_files_format_and_content: Bigwig

source_name: Hela + KOS

extract_protocol:
(1) For 4SU-seq: 4sU was added to 5 ml medium at 500 μM for each 10 cm dish and incubated for 1 hr before cells were harvested. For HSV1-infected cells, 4sU was added at 7 hr post infection. Discard medium and add 3 ml Trizol (Invitrogen) in dark. Total RNA were isolated from the cells as per instruction. 700 μl thiol-specific biotinylation reaction contained 70 μg total RNA, 70 μl 10x Biotinylation Buffer (100 mM Tris-Cl pH 7.5 and 10 mM EDTA), 140 μl biotin-HPDP (in 1 mg/ml DMF), 70 ul DMF. Incubate the reaction at room temperature for 1.5 hr with rotation. Add an equal volume of chloroform. Mix vigorously. Centrifuge at 14,000 rpm for 10 min at 4 °C and transfer aqueous phase into a new tube. Repeat chloroform extract once. Add 1/10 the volume of 5 M NaCl and an equal volume of isopropanol to precipitate RNA. Centrifuge at 14,000 × g for 20 min at 4 °C. Discard supernatant and wash once with 75% ethanol. Re-suspend biotinylated RNA in 100 μl H2O. Wash 50 μl streptavidin-magnetic beads (Invitrogen) with solution A (0.1 M NaOH and 0.05 M NaCl) for 2 x 2 min followed by solution B (0.1 M NaCl) for 2 x 2 min. Keep beads in 100 μl 2 x B&W buffer (10 mM Tris-Cl pH 7.5, 1 mM EDTA and 2 M NaCl). Heat 100 μl biotinylated RNA samples to 65 °C for 10 min to denature and immediately place on ice. Add 100 μl pre-washed streptavidin-magnetic beads  to roate for 1hr. Wash beads with 800 μl 1 x B&W buffer (5 mM Tris-Cl pH 7.5, 0.5 mM EDTA and 1 M NaCl) for 3 x 5 min and incubate beads-4SU-RNA with 100 μl 0.1 M DTT for 2 x 5 min at room temperature. Add 1/10 the volume of 5 M NaCl and an equal volume of isopropanol and 1ul glycoblue to precipitate RNA. Centrifuge at 14,000 × g for 20 min at 4 °C. Discard supernatant and wash once with 75% ethanol. Re-suspend newly transcribed RNA in 20 μl H2O for libraries preparation. (2) For CLIP-seq: The approach is modified from eCLIP. Briefly, Infected and transfected Hela cells were exposed to 254 nM UV with 400 mJ/cm2. Cells were scrapped and re-suspended in lysis buffer (50 mM Tris-HCl pH 7.4, 100 mM NaCl, 1% NP-40, 0.1% SDS, 0.5% sodium deoxycholate and Protease Inhibitor). After RNase I digestion, 80 μl of protein G Dynabeads beads and 5 μg ICP27 antibody per IP were used for immunoprecipitation overnight. After washing with High salt buffer (50 mM Tris-HCl pH 7.4, 1 M NaCl, 1 mM EDTA, 1% NP-40, 0.1% SDS and 0.5% sodium deoxycholate) and wash buffer (20 mM Tris-HCl pH 7.4, 10 mM MgCl2 and 0.2% Tween-20), phosphates at 5’ and 3’ end of RNA were removed by CIP for 15 min at 37oC . 3’ RNA linker was added by T4 RNA ligase overnight and [γ-32P]ATP was used to label 5’ end of RNA by T4 PNK. ICP27/RNA complex was resolved in SDS-PAGE and transfered to NC membrane. Proper regions of membrane were cut out to extract RNA in PK/Urea buffer. Extracted RNA was added with 5’ RNA linker by T4 RNA ligase and reverse-transcribed with Superscript III. Libraries for CLIP-seq were got after PCR using illumina universal primer and index primers.
(1) For 4SU-seq: Libraries were directly fragmented and prepared according to Illumina's instructions; (2) For CLIP-seq: RNA linkers for CLIP-seq are designed according to illumina universal primers and index primers, and the final libraries were got by PCR.

treatment_protocol: (1) For infection: HeLa cells with 100% confluence in 10 cm dish were washed once with PBS plus MgCl2. Add 5 ml PBS plus MgCl2 containing HSV-1 (MOI=10) and incubate cells at 37 oC for 45 min. Remove viral suspension and add 8 ml fresh growth media to culture until cells were harvested. (2) For transfection, 10 μg plasmid (for 10-cm dish) was incubated with 30 μl of 1 mg/ml PEI in 1 ml DMEM for 20 min at RT, and then PEI/DNA complex was added in Hela cells. Transfected cells were harvested 2 days post transfection.

value: cervical carcinoma

value: HeLa

value: HSV-1 infection


title: R80 Genomic DNA from R03C01

description: cancer

tag: tumor stage

tag: gender

tag: age


title: CLIP-seq_ICP27-2

description: ICP27-bound RNA

source_name: Hela

value: ICP27 overexpression


title: 3826_Pituitary

tag: strain/background

tag: tissue

value: Male

value: TCDF

value: Gestation day 8 - 20

value: No


title: RCC81 Genomic DNA from R02C01

description: cancer

tag: recur


title: CD4_siFOXP3_rep5

source_name: CD4 T cells

tag: sirna

tag: t cell subtype

tag: antibody blockade


title: R60 Genomic DNA from R01C01

description: cancer


title: CLIP-seq_HSV-1-1

description: ICP27-bound RNA

tag: cell type

tag: cell line

tag: treatment


title: mESCs, K27me3_EPZ_2

description:
Calibrated ChIP-seq for H3K27me3 from mESCs treated with EPZ for 24 h. Replicate 2 of 2.
ChIP-seq (Calibrated)

extract_protocol:
Trypsinized mESCs (20 x 10e6) were washed twice in PBS. Cells were resuspended in 250 µl of PBS and fixed by the addition of an equal volume of PBS containing 2% methanol free formaldehyde (Thermo Scientific Pierce PN28906; final concentration of 1%) and incubated at RT for 10 min. Fixation was stopped by 5 min incubation with 125 mM glycine at room temperature. Fixed cells were washed in PBS and combined at this stage with 1.3x10e6 formaldehyde fixed S2 cells (Drosophila melanogaster cells; for downstream calibration of ChIP-seq data). All buffers were supplemented with 1 mM DTT and 1x Protease inhibitors (Roche, 11836170001) just prior to use. Cell pellets were resuspended in lysis buffer (50 mM Tris-HCl pH 8.1, 10 mM EDTA and 20% SDS) and incubated for 10 min at 4 °C. Lysates were diluted 1:10 in ChIP Dilution Buffer (1% Triton X-100, 2 mM EDTA, 150 mM NaCl, 2 0mM and Tris-HCl pH8.1) and sonicated, first with a single 30s pulse with a probe sonicator (labtech Soniprep 150) on ice followed by a further 45 cycles using a cooled Bioruptor (Diagenode; 1 min cycles of 30sec on / 30 sec off on ‘high’ setting at 4 °C). The sonicated extract was pre-cleared by centrifugation at 16000 g for 10 min at 4 °C. The supernatant was transferred to a fresh tube and supplemented with BSA to a final concentration of 25 mg/ml. Anti-H3K27me3 (Cell Signalling C36B11) antibodies were pre-coupled to a protein A Dynabeads (Life Technologies; catalogue no. 10001D) at a ratio of 1 mg antibody per 30 ml of dynabead suspension by rotation at 4 °C for 1 h. 6 x 10e6 cell equivalents of lysate were added to 5 µg of antibody bound beads and incubated for 6 h on a rotating wheel at 4 ºC. Following incubation, bead-associated immune complexes were washed sequentially with ChIP dilution buffer, wash buffer A and wash buffer B, each for 10 min at 4 ºC on a rotating wheel followed by two washes in TE buffer at RT (wash buffer A - 1% Triton X-100, 0.1% Sodium-Deoxycolate, 0.1% SDS, 1mM EDTA, 500 mM NaCl, 50 mM HEPES pH7.9; wash buffer B – 0.5% NP40, 0.5% Sodium-Deoxycolate, 1 mM EDTA, 250 mM LiCl, and 20 mM Tris-HCl pH8.1). Chromatin was released by incubating the beads in 100 µl of elution buffer (0.1 M NaHCO3 and 1 % SDS) for 15 min at 37 ºC, followed by the addition of 50 µg of RNaseA and 6µl of 2 M Tris pH6.8 and incubation at 65 ºC for 2 h and finally by the addition of 50 µg of proteinase K and incubation at 65 ºC for 8 h to degrade proteins and reverse the cross-links. Dynabeads were removed using a magnetic rack and the chromatin purified using PCR Purification columns (Qiagen) according to manufacturer’s instructions.
Libraries were constructed using the NEBNext® Ultra™ II DNA Library Prep Kit for Illumina according to manufacturer’s instructions (NEB - catalogue no. E7645S). Library PCRs were supplemented with 2x SYBR dye (Sigma – catalogue no. S9430) so that amplification could be monitored by quantitative PCR on a Roche lightcycler 480. To allow for sample multiplexing, PCRs were performed using index primers (NEBNext Multiplex Oligos for Illumina - Set 1. Catalogue no. E7335) and amplified to linear phase. Size selection purifications following the ligation and amplification PCR steps were performed with 1x and 0.9x reaction volumes of Agencourt AMPure XP beads (Beckman Coulter - A63880). Purified libraries were combined as a 12 sample equimolar pool containing the indexes 1-12 and sequenced on an Illumina NextSeq on a single high-output flow cell (single-end 75 bp reads).

tag: strain

tag: chip antibody

value: anti-H3K27me3 (Cell Signalling C36B11)


title: CD8_siNS_rep1


title: mESCs, RING1B_DMSO_1

description:
ChIP-seq for RING1B from mESCs treated with DMSO for 24 h. Replicate 1 of 2.
ChIP-seq

value: 24 h DMSO


title: mESCs, RING1B_DMSO_2

description:
ChIP-seq for RING1B from mESCs treated with DMSO for 24 h. Replicate 2 of 2.
ChIP-seq


title: 3825_Pituitary

value: Fetal pituitary

tag: developmental stage

tag: Sex

tag: molecule exposure

tag: exposure

tag: loading dose level (ug/kg)

tag: maintenance dose level (ug/kg)


title: CLIP-seq_ICP27-1

description: ICP27-bound RNA


title: CD4_siFOXP3_rep4


title: mESCs, K27me3_EPZ_1

description:
Calibrated ChIP-seq for H3K27me3 from mESCs treated with EPZ for 24 h. Replicate 1 of 2.
ChIP-seq (Calibrated)


title: mESCs, RING1B_EPZ_1

description:
ChIP-seq for RING1B from mESCs treated with EPZ for 24 h. Replicate 1 of 2.
ChIP-seq


title: R139 Genomic DNA from R06C01

description: cancer

tag: tumor stage

tag: gender

value: male

tag: age


title: 3824_Pituitary

tag: strain/background

tag: tissue

tag: experimental block

tag: sample deemed an outlier


title: 4SU-seq_HSV-1-1

description: 4SU labeled total RNA

data_processing:
Library strategy: 4SU-Seq
Reads from CLIP-seq data were trimmed to remove the primers and polyA tails.
Both 4SU-Seq and CLIP-seq were aligned to human(hg19)(+HSV for infected cells) genome using STAR. Multi-mapping was not allowed.
Mapped reads were converted to bigwig files using deepTools.
Genome_build: Hg19
Supplementary_files_format_and_content: Bigwig

tag: cell type

tag: cell line


title: CD4_siFOXP3_rep2

tag: sirna

tag: t cell subtype

tag: antibody blockade


title: 4SU-seq_ICP27-2

description: 4SU labeled total RNA

tag: treatment


title: 3823_Pituitary

tag: developmental stage

tag: Sex

tag: molecule exposure


title: mESCs, K27me3_DMSO_1

description:
Calibrated ChIP-seq for H3K27me3 from mESCs treated with DMSO for 24 h. Replicate 1 of 2.
ChIP-seq (Calibrated)

tag: strain

tag: chip antibody


title: CD4_siFOXP3_rep1


title: 4SU-seq_ICP27-1

description: 4SU labeled total RNA


title: mESCs, K27me3_DMSO_2

description:
Calibrated ChIP-seq for H3K27me3 from mESCs treated with DMSO for 24 h. Replicate 2 of 2.
ChIP-seq (Calibrated)


title: 4SU-seq_HSV-1-2

description: 4SU labeled total RNA


title: CD4_siNS_rep5

value: siNS


title: mESCs, Input_EPZ_2

description:
Deep sequenced input chromatin from mESCs treated with EPZ for 24 h. Replicate 2 of 2.
ChIP-seq (Input)

extract_protocol:
Trypsinized mESCs (20 x 10e6) were washed twice in PBS. Cells were resuspended in 250 µl of PBS and fixed by the addition of an equal volume of PBS containing 2% methanol free formaldehyde (Thermo Scientific Pierce PN28906; final concentration of 1%) and incubated at RT for 10 min. Fixation was stopped by 5 min incubation with 125 mM glycine at room temperature. Fixed cells were washed in PBS and combined at this stage with 1.3x10e6 formaldehyde fixed S2 cells (Drosophila melanogaster cells; for downstream calibration of ChIP-seq data). All buffers were supplemented with 1 mM DTT and 1x Protease inhibitors (Roche, 11836170001) just prior to use. Cell pellets were resuspended in lysis buffer (50 mM Tris-HCl pH 8.1, 10 mM EDTA and 20% SDS) and incubated for 10 min at 4 °C. Lysates were diluted 1:10 in ChIP Dilution Buffer (1% Triton X-100, 2 mM EDTA, 150 mM NaCl, 2 0mM and Tris-HCl pH8.1) and sonicated, first with a single 30s pulse with a probe sonicator (labtech Soniprep 150) on ice followed by a further 45 cycles using a cooled Bioruptor (Diagenode; 1 min cycles of 30sec on / 30 sec off on ‘high’ setting at 4 °C). The sonicated extract was pre-cleared by centrifugation at 16000 g for 10 min at 4 °C. The supernatant was transferred to a fresh tube and supplemented with BSA to a final concentration of 25 mg/ml. A sample of the chromatin was retained as an input reference.
Libraries were constructed using the NEBNext® Ultra™ II DNA Library Prep Kit for Illumina according to manufacturer’s instructions (NEB - catalogue no. E7645S). Library PCRs were supplemented with 2x SYBR dye (Sigma – catalogue no. S9430) so that amplification could be monitored by quantitative PCR on a Roche lightcycler 480. To allow for sample multiplexing, PCRs were performed using index primers (NEBNext Multiplex Oligos for Illumina - Set 1. Catalogue no. E7335) and amplified to linear phase. Size selection purifications following the ligation and amplification PCR steps were performed with 1x and 0.9x reaction volumes of Agencourt AMPure XP beads (Beckman Coulter - A63880). Purified libraries were combined as a 12 sample equimolar pool containing the indexes 1-12 and sequenced on an Illumina NextSeq on a single high-output flow cell (single-end 75 bp reads).

value: mESC


title: CD8_siNS_rep2


title: CD8_siFOXP3_rep3


title: CD4_siNS_rep4


title: 3821_Pituitary

tag: exposure

tag: loading dose level (ug/kg)

tag: maintenance dose level (ug/kg)


title: 4SU-seq_WT-1

description: 4SU labeled total RNA

value: WT


title: 4SU-seq_WT-2

description: 4SU labeled total RNA


title: CD4_siNS_rep3


title: mESCs, Input_EPZ_1

description:
Deep sequenced input chromatin from mESCs treated with EPZ for 24 h. Replicate 1 of 2.
ChIP-seq (Input)


title: 3822_Pituitary

tag: strain/background

value: Cr1:CD (SD); Sprague-Dawley

tag: tissue


title: CD4_siFOXP3_rep3


title: mESCs, Input_DMSO_2

description:
Deep sequenced input chromatin from mESCs treated with DMSO for 24 h. Replicate 2 of 2.
ChIP-seq (Input)


title: CD4_siNS_rep2


title: 3819_Pituitary

value: Gestation day 20

tag: experimental block

tag: sample deemed an outlier


title: mESCs, Input_DMSO_1

description:
Deep sequenced input chromatin from mESCs treated with DMSO for 24 h. Replicate 1 of 2.
ChIP-seq (Input)

tag: cell type

tag: cell line


title: Vaseline treated (vehicle control)

city: Boston

first: Natasha

last: Frank

state: MA

address: 77 Avenue Louis Pasteur

department: Medicine

institute: Brigham and Women's Hospital

description: 3670BWH_hMeDIP_mergedregs_WT_topdiffsites_tags50fc2x.xlsx

data_processing:
Read sequences were aligned to the mouse genome (mm10) using ELAND v2 in the CASAVA package.
MACS2 was used to identify differentially hydroxymethylated genes.
Genome_build: mm10

source_name: Epidermal tissue

extract_protocol:
Punch biopsies of mouse skin were obtained. Isolation of the epidermis from shaved biopsies was performed by soaking the samples in 0.2% dispase at 4°C for 6 hours and manually separating epidermis from dermis.
Genomic DNA from the epithelium of mouse models was purified, sonicated, and ligated to Illumina barcode adapters before hMeDIP-seq. Adaptor-ligated DNA was denatured and incubated with 3 μL of 5-hmC antibody at 4°C overnight. Antibody-DNA complexes were captured by protein A/G beads. The immunoprecipitated DNA was purified and sequenced using the Illumina platform followed by standard Illumina protocols.

treatment_protocol: Mice at 6 weeks of age received a topical dose of 62.5 μg of Imiquimod (Aldara) 5% cream daily onto the shaved back and right ear for 6 consecutive days. This translates to a daily dose of 3.125 mg of the active compound. Control mouse skin was similarly treated with Vaseline as a control vehicle cream.

value: Epidermis

tag: age

value: postnatal 6 weeks

value: Vaseline


title: Imiquimod (IMQ) treated

value: Imiquimod


title: 3818_Pituitary

value: Male


title: CD4_siNS_rep1

tag: sirna

tag: t cell subtype

tag: antibody blockade


title: mESCs, totRNA_EPZ_2

description:
RNA-seq of total RNA peformed on mESCs treated with EPZ for 24 h. Replicate 2 of 2.
RNA-seq (Total RNA)

data_processing:
Base Calling. Basecalling, quality scoring and de-multiplexing was performed directly using the NextSeq 550 software (RTAv2). Alignment. For each de-multiplexed sample, multiple fastq files were merged using the ‘cat’ function for both read 1 and 2. Merged files were aligned to the mouse genome (mm9) using bowtie2 v2.2.6 for paired end sequence data (options: --local --threads 3) to generate .SAM files. Further processing. Aligned read data was processed using HOMER v4.8. SAM files were converted into tag directories using ‘makeTagDirectory’ with the following parameters: -format sam -flip –sspe. Genomic intervals which extended beyond the end of the chromosomes were removed using ‘removeOutOfBoundsReads.pl’. Strand specific browser track files (bigwig format; ‘.bigWig’) for each replicate were generated using ‘makeUCSCfile’ with the following parameters: -fsize 1e20 -strand + (or -) -norm 1e8. Supplementary files format and content. Processed files are in bigwig format with files representing read data mapped to the positive or negative strand indicated by ‘*PosStr*‘ or ‘*NegStr*‘ respectively.
Genome_build: mm9
Supplementary_files_format_and_content: .bigWig files contain information on both the genomic distribution and signal strength of the mapped reads (representative of the sample composition).  .bigWig files are in an indexed binary format.

extract_protocol:
4SU-seq was performed essentially as described previously (Rabani et al, 2011 PMID: 21516085). Briefly, 4-thiouridine (4SU; Sigma - catalogue no. T4509) was added to ESCs in culture to a final concentration of 500 µM and incubated at 37°C for 20 min. Cells were harvested by trypsinisation and washed twice with PBS at RT. Total RNA was isolated from 7x10e6 cells using trizol according to the manufacturer’s instructions (Invitrogen - catalogue no. 15596026). Following precipitation, purified RNA was resuspended in 100 μl RNase-free water and DNase treated using the TURBO DNA-free kit according to the manufacturer’s instructions (Invitrogen - catalogue no. AM1907M). Residual inactivation beads were removed by spinning the RNA sample through a QIAshredder column at 1000 g for 1 min (Qiagen- catalogue no. 79654). 2μg of RNA input was retained for direct sequencing of the total RNA pool and 30 μg was incubated for 1.5 h at RT with 100 μg of Biotin-HPDP (Pierce - catalogue no. 21341; reconstituted in Dimethylformamide at 1 mg/ml) in 1x Biotinylation Buffer (10 mM Tris pH 7.4 and 1 mM EDTA) to a total volume of 500 μl. Uncoupled biotin was removed through two consecutive rounds of 1:1 v/v chloroform extraction followed by isopropanol/NaCl precipitation. RNA was resuspended in 100 μl of RNase free water and mixed 1:1 w/w with µMacs Streptavidin beads (miltenyi - catalogue no. 130-074-101) and incubated for 15 min at RT with rotation. The RNA / bead mixture was applied to a µMacs column following pre-equilibration with wash buffer (100 mM Tris pH 7.5, 10 mM EDTA, 1 M NaCl and 0.1% Tween20). The captured beads were then washed with 3 x 900 µl of 65 oC wash buffer and 3 x 900 µl RT wash buffer. RNA was then eluted from the column by adding two consecutive rounds of 100 mM DTT. The eluate was added to 700 µl Buffer RLT (RNeasy MinElute Cleanup Kit; Qiagen catalogue no. 74204) and then purified according to the manufacturer’s instructions. Prior to library preparation, ribosomal RNA was depleted from both the total and purified nascent RNA using the low Input RiboMinus Eukaryote System v2 kit according to the manufacturer’s instructions (Ambion - catalogue no. A15027).
Libraries were constructed using the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina according to the protocol for ribosome depleted RNA and with a 11 min RNA fragmentation step (NEB - catalogue no. E7760). Library PCRs were supplemented with 2x SYBR dye (Sigma – catalogue no. S9430) so that amplification could be monitored by quantitative PCR on a Roche lightcycler 480. To allow for sample multiplexing, PCRs were performed using index primers (NEBNext Multiplex Oligos for Illumina - Set 1. Catalogue no. E7335) and amplified to linear phase. Size selection purifications following the ligation and amplification PCR steps were performed with 1x and 0.9x reaction volumes of Agencourt AMPure XP beads (Beckman Coulter - A63880). Purified libraries were combined as an 8 sample equimolar pool containing the indexes 5-12 and sequenced on an Illumina NextSeq on a single high-output flow cell (paired-end 75 bp reads).

tag: treatment


title: CD4_siCD48_CD48_Ab_rep5

description:
processed data file:
CD48_sample_gene_counts.txt
CD48_sample_gene_FPKMs.txt

data_processing:
Raw paired-end sequencing reads were aligned to the human reference genome (hg38) using MapSplice version 2.2.1.
Gene read counts against GENCODE v28 basic gene models were calculated by HTSeq version 0.9.1 with parameters: -m intersection-nonempty -i gene_name -s reverse
Gene read count normalization and differential expression analysis was performed with DESeq2 version 1.16.1.
Genome_build: hg38
Supplementary_files_format_and_content: CD48_sample_gene_counts.txt - raw gene counts for siCD48 samples group
Supplementary_files_format_and_content: CD48_sample_gene_FPKMs.txt - gene FPKM values for siCD48 samples group

treatment_protocol: T cells were electroporated with siRNAs against CD48 (assay ID s2689)  (ThermoFisher) using the Amaxa Nucleofection 4D system and the P3 Primary Cell kit (Lonza). Stealth RNAi negative control medium GC duplex siRNA (ThermoFisher) was used as a non-specific (NS) control, and all assays were conducted 4 days post electroporation for peak knockdown efficiency.

tag: knockdown

value: CD48 Ab


title: Sample 1_Ath_mRNA_PacBio

city: Yangzhou

first: Biao

last: Jin

state: Jiangsu

address: Wenhui east road no. 48

department: College of Horticulture and Plant Protection

country: China

institute: Yangzhou University

data_processing:
For ONT sequencing, sequenced reads were trimmed for adaptor sequence, low-quality sequence and the percentage of unknown bases (N) is greater than 10%. At last, the obtained “clean bases” for further analysis.
Then filtered reads were mapped to A. thaliana genome (TAIR 10) using minimap2.
Expression levels of the assembled transcripts were calculated and normalized using RPT10K/RPG10K（Reads Per Transcript/Gene per 10,000 reads）
For Pacbio sequencing, subreads were filtered using the standard protocols in the SMRT Analysis software suite (http://www.pacificbiosciences.com), and reads of insert (ROIs) were obtained. After examining for poly(A) signal and 5’ and 3’ adaptors, full-length and non-full-length cDNA reads were recognized. Consensus isoforms were identified using the algorithm of iterative clustering for error correction and further polished to obtain high-quality consensus isoforms. Then the high quality consensus isoforms were mapped to the A.thaliana genome to identifying transcripts.
Then, the functional annotations of identified transcripts were conducted by using BLASTX (cutoff E-value ≤ 1e-5) against different protein and nucleotide databases of COG (Clusters of Orthologous Groups), GO (Gene Ontology), KEGG (Kyoto Encyclopedia of Genes and Genomes), Pfam (a database of conserved Protein families or domains), Swiss-prot (a manually annotated, non-redundant protein database), TrEMBL (an automatically annotated protein database), NR (NCBI non-redundant proteins), and NT (the NCBI nucleotide database). For each transcript in each database searching, the functional information of the best matched sequence was assigned to the query transcript.
Genome_build: TAIR10
Supplementary_files_format_and_content: Text file "PB_transcript annotation.txt" includes Gene family and  transcript ID. Text file “gene.expression.txt” includes Gene_ID, the gene expression level of CK1,CK2,CK3

organism: Arabidopsis thaliana

source_name: overall ground parts of plants_PacBio

growth_protocol: Wild-type (WT) A. thaliana Columbia ecotype (Col-0) was cultivated at 23/18℃ under 16/8 light/dark cycle.

extract_protocol:
Total RNA was extracted using RNAprep Pure Plant Kit (Tiangen, Beijing, China).
For Pacbio sequencing, the cDNA from the Arabidopsis RNA samples  was synthesized using the SMARTer PCR cDNA Synthesis Kit. After PCR amplification, products were sequenced on Pacbio Sequel platform.   For ONT sequencing, cDNA-PCR libraries were built using the Ligation Sequencing Kit (SQK-LSK109) and sequenced on Nanopore PromethION platform.

tag: ecotype

tag: genotype/variation

value: wild type

tag: developmental stages

value: at growth stage of rosette growth complete

tag: tag

value: Pacbio sequel


title: 3820_Pituitary

description: Day after mating designated gestation day 0. Loading dose delivered on gestation day 6 via oral gavage. Daily maintenance doses delivered from gestation day 7 to 20 via oral gavage. Samples analyzed 30 minutes following the last dosing.

tag: developmental stage

tag: Sex

tag: molecule exposure

value: TCDF

tag: exposure

value: Gestation day 8 - 20

tag: loading dose level (ug/kg)

tag: maintenance dose level (ug/kg)

value: No


title: 3817_Pituitary

tag: strain/background

tag: tissue

value: Fetal pituitary

tag: experimental block

tag: sample deemed an outlier


title: CD4_siCD48_CD48_Ab_rep3

tag: t cell subtype

tag: antibody blockade


title: SART3_siRNA_TNFalpha+_rep2

city: Pamplona

first: Maite

last: Huarte

state: Navarra

address: c/ Avd Pio XII, 55

country: Spain

institute: Centro de Investigación Médica Aplicada

data_processing:
The generated BCL files were demultiplexed using bcl2fastq conversion software (version 2.17)
Quality control of the obtained reads was performed using fastqc and Trimmomatic
Filtered reads were mapped to the hg19 version using STAR (Dobin et al., 2013)
Read summarization was done with the featureCounts program and using the gencode.v19.hg19.gtf annotation
Differential gene expression was performed using the R package DESeq2.
Genome_build: hg19
Supplementary_files_format_and_content: matrix table of normalised counts sequencing reads

source_name: HCC95 cells

growth_protocol: HCC95 cells were cultured at 37ºC in the presence of 5% CO2 using  RPMI 1640 medium supplemented with 10% fetal bovine serum and 1% of pen strep

extract_protocol:
Total RNA from HCC95 cells was extracted using Maxwell® 16 Total RNA Purification Kit (Promega). RNA quality was assessed using Agilent 2200 TapeStation.
Quality-verified RNA was used for library preparation. First strand cDNA synthesis was carried out using dT oligos

treatment_protocol: For RNAi, 200,000 HCC95 cells per well were plated in a 6-well plate. The next day siRNAs at a final concentration of 30 nM were transfected using Lipofectamine 2000 (Invitrogen) following manufacturers protocol. TNFalpha treatment was performed using a concentration of 10 ng/ml (R&D systems) for 4 hours.

tag: treatment

tag: RNAi


title: 3814_Pituitary


title: CD4_siCD48_CD48_Ab_rep4

tag: knockdown


title: CD4_siCD48_CD48_Ab_rep2


title: 3815_Pituitary


title: SART3_siRNA_TNFalpha+_rep1


title: mESCs, totRNA_DMSO_1

description:
RNA-seq of total RNA peformed on mESCs treated with DMSO for 24 h. Replicate 1 of 2.
RNA-seq (Total RNA)

tag: cell type

value: mESC

value: 24 h DMSO

tag: cell line

tag: strain


title: SART3_siRNA_rep3


title: CD4_siCD48_CD48_Ab_rep1


title: 3813_Pituitary

value: Cr1:CD (SD); Sprague-Dawley

tag: developmental stage

tag: Sex


title: mESCs, totRNA_DMSO_2

description:
RNA-seq of total RNA peformed on mESCs treated with DMSO for 24 h. Replicate 2 of 2.
RNA-seq (Total RNA)


title: 3812_Pituitary

value: Gestation day 20

tag: molecule exposure

value: Corn oil (vehicle)

tag: exposure


title: mESCs, 4SU_EPZ_2

description:
4sU-seq peformed on mESCs treated with EPZ for 24 h. Replicate 2 of 2.
RNA-seq (4sU-seq)

data_processing:
Library strategy: 4sU-seq
Base Calling. Basecalling, quality scoring and de-multiplexing was performed directly using the NextSeq 550 software (RTAv2). Alignment. For each de-multiplexed sample, multiple fastq files were merged using the ‘cat’ function for both read 1 and 2. Merged files were aligned to the mouse genome (mm9) using bowtie2 v2.2.6 for paired end sequence data (options: --local --threads 3) to generate .SAM files. Further processing. Aligned read data was processed using HOMER v4.8. SAM files were converted into tag directories using ‘makeTagDirectory’ with the following parameters: -format sam -flip –sspe. Genomic intervals which extended beyond the end of the chromosomes were removed using ‘removeOutOfBoundsReads.pl’. Strand specific browser track files (bigwig format; ‘.bigWig’) for each replicate were generated using ‘makeUCSCfile’ with the following parameters: -fsize 1e20 -strand + (or -) -norm 1e8. Supplementary files format and content. Processed files are in bigwig format with files representing read data mapped to the positive or negative strand indicated by ‘*PosStr*‘ or ‘*NegStr*‘ respectively.
Genome_build: mm9
Supplementary_files_format_and_content: .bigWig files contain information on both the genomic distribution and signal strength of the mapped reads (representative of the sample composition).  .bigWig files are in an indexed binary format.


title: SART3_siRNA_rep2


title: mESCs, 4SU_EPZ_1

description:
4sU-seq peformed on mESCs treated with EPZ for 24 h. Replicate 1 of 2.
RNA-seq (4sU-seq)


title: mESCs, 4SU_DMSO_2

description:
4sU-seq peformed on mESCs treated with DMSO for 24 h. Replicate 2 of 2.
RNA-seq (4sU-seq)


title: 3811_Pituitary

tag: loading dose level (ug/kg)

tag: maintenance dose level (ug/kg)


title: SART3_siRNA_rep1


title: mESCs, totRNA_EPZ_1

description:
RNA-seq of total RNA peformed on mESCs treated with EPZ for 24 h. Replicate 1 of 2.
RNA-seq (Total RNA)


title: SART3_siRNA_TNFalpha+_rep3


title: 3816_Pituitary

tag: strain/background

tag: tissue


title: mESCs, 4SU_DMSO_1

description:
4sU-seq peformed on mESCs treated with DMSO for 24 h. Replicate 1 of 2.
RNA-seq (4sU-seq)


title: CD4_siNS_isotype_rep4

value: siNS

value: isotype control


title: 3834_Pituitary

value: TCDD

tag: experimental block

tag: sample deemed an outlier


title: CD4_siNS_isotype_rep5

tag: t cell subtype

tag: antibody blockade


title: ALAL1_siRNA_TNFalpha+_rep3

tag: treatment

tag: RNAi


title: CD4_siNS_isotype_rep3

tag: knockdown


title: 3809_Pituitary

value: Male


title: E14 RING1B KO 2

city: Basel

first: Ilya

middle: M.

last: Flyamer

address: Maulbeerstrasse 66

country: Switzerland

institute: Friedrich Miescher Institute for Biomedical Research

description: Test sequencing (smaller run) was carried out using NextSeq 550.

data_processing:
Fastq files were generated by the sequencing facilities (Wellcome Trust Clinical Research Facility for test sequencing on NextSeq 550, BGI for deep sequencing on HiSeq 4000).
Reads were processed using distiller (https://github.com/mirnylab/distiller-nf) on the high-performance computing cluster of the University of Edinburgh (Eddie3). Mapping was performed to the mm9 genome build. Hi-C pairs with exactly matching coordinates were removed as PCR or optical duplicates (pcr_dups_max_mismatch_bp: 0). The output statistics information and Cooler files were used in downstream analyses. 1000 bp resolution Cooler files were used to create multi-resolution files for visualization in HiGlass.
Genome_build: mm9
Supplementary_files_format_and_content: We provide 2 processed files for each biological sample, and three for combined data for each condition. They are (i) a gzip-compressed .pairs file (https://pairtools.readthedocs.io/en/latest/index.html, (ii) multiresolution cooler (https://github.com/mirnylab/cooler) .mcool files storing data, which can be used for data analysis or in HiGlass (https://github.com/hms-dbmi/higlass) for interactive visualization.  We also provide a file with all statistics information provided in distiller output for the samples and merged data.

source_name: Mouse ES cells

growth_protocol: Feeder-free mouse embryonic stem cells (mESCs) including E14tg2A (129/Ola; Ring1B+/+) and the derivative lines (Ring1B I53A/I53A and Ring1B -/-, PMID:26385961) were cultured on 0.1% gelatin (Sigma - catalogue no. G1890) coated Corning flasks in GMEM BHK-21 (Gibco - catalogue no. 21710-025) supplemented with 10 % foetal calf serum (FCS; Sigma - catalogue no. F-7524), 1,000 units/ml LIF, non-essential amino acids (Gibco - catalogue no. 11140-035), sodium pyruvate (Gibco - catalogue no. 11360-039), 50 μM 2-β-mercaptoethanol (Gibco - catalogue no. 31350-010) and L-glutamine. For passaging, 60–90% confluent ESC culture flasks were washed with PBS, incubated for 2–3 min at 37°C in trypsin (0.05% v/v;  Gibco 25300-054), and tapped to release. Trypsin was inactivated by adding 9 volumes of ESC medium and this mixture was repeatedly pipetted to obtain a single cell suspension. ESCs were centrifuged, resuspended in ESC medium and re-plated onto gelatin coated flasks at a density of ~4 × 104 cells/cm2 (determined using a hemocytometer - Neubauer). All centrifugation steps with live cells were performed at 330 x g for 3 min at room temperature (RT).

extract_protocol:
Hi-C was performed largely as described (Rao et. el., 2014) with minor modifications. Briefly, ES cells were crosslinked in 1% formaldehyde for 10 minutes, snap-frozen in 2-5 mln aliquots and stored at -80°C. After permeabilization in lysis buffer (0.2% Igepal, 10 mM Tris-HCl pH 8.0, 10 mM NaCl, 1x Halt Protease inhibitor cocktail) nuclei were isolated in 0.3% SDS in NEBuffer 3 at 62° for 10 minutes. SDS was quenched with 1% Triton X-100 at 37° for 1 h, then the nuclei were pelleted and resuspended in 250 ul DpnII buffer with 600 U DpnII. After overnight digestion, 200 more units were added for 2 hours. Then the ends were filled-in using Klenow, d(G/C/T)TPs and biotin-14-dATP for 1.5 hrs at 37°. After ligation at room temperature for 4 hrs the nuclei were spun down, resuspended in 200 ul mQ and digested with proteinase K for 30 min at 55° in presence of 1% SDS. Then the cross-links were reversed at 65° overnight after addition of NaCl to a final concentration of 1.85 M. In the morning, after ethanol precipitation and a wash with 70-80% Ethanol, DNA was resuspended in 500 ul of sonication buffer (50 mM Tris pH 8.0, 0.1%SDS, 10 mM EDTA), incubated on ice for 15 min and then sheared using a probe sonicator to fragment size of 200-700 bp. Then the DNA was concentrated on Amicon filter units, bound to MyOne T1 Streptavidin beads and used for Illumina library preparation. Small aliquots were taken before and after DpnII treatment, and before sonication to confirm efficient DNA digestion and ligation by running them on 1% agarose gel. Samples were first test-sequenced on NextSeq 550 (WTCRF, Edinburgh) to check library quality, and then selected libraries were sequenced deeply on HiSeq 4000 (BGI).
In house Illumina library protocol from Rao et. al., 2014.

value: Mouse ES cells

tag: genotype

value: RING1B KO

tag: biologial replicate

tag: molecule subtype

value: Proximity-ligated gDNA


title: ALAL1_siRNA_TNFalpha+_rep2


title: 3808_Pituitary

tag: developmental stage

tag: Sex


title: E14 RING1B KO 1


title: CD4_siNS_isotype_rep2


title: ALAL1_siRNA_TNFalpha+_rep1


title: ALAL1_siRNA_rep3


title: E14 RING1B I53A 2

value: RING1B I53A


title: OLN93 Sox10-deficient (Sox10ko) cells, clone A

city: Erlangen

first: Michael

last: Wegner

state: Bavaria

address: Fahrstr. 17

department: Institut of Biochemistry

country: Germany

description:
OLN93_Sox10ko_1
RNAseq data from OLN93 cells (Sox10ko).
processed data file: OLN93_Sox10_ko_CrisprCas_vs_ctrl.xlsx

data_processing:
Sequencing data were pooled using the Illumina HiSeq 2500 platform and converted into fastq files.
Reads from rRNA, tRNA, mt-rRNA and mt-tRNA were purged from demultiplexed reads.
Reads were aligned to rn5 reference genome using STAR (version 2.5.1.b).
Unique maps were generated using HTSeq count relating to Ensembl gene identifier version 75.
Statistical analysis of raw data was done with DESeq2 by R version 1.8.1.
Genome_build: rn5 (Rnor_5.0)
Supplementary_files_format_and_content: *_rn5_htseq-count.tabular.txt: Tab-delimited text files
Supplementary_files_format_and_content: OLN93_Sox10_ko_CrisprCas_vs_ctrl.txt: Tab-delimited text file

source_name: OLN93 cell line, Crispr/Cas9-mediated Sox10 inactivation

growth_protocol: OLN93 cells were kept in DMEM medium with 10% FCS and PenStrep and split every 96 hours.

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit according to QIAGEN protocol.
RNA libraries were prepared for sequencing using Illumina Stranded mRNA Kit.

treatment_protocol: The genome of OLN93 cells was edited using Crispr/Cas9 to inactivate the Sox10 gene.

tag: cell line

tag: cell type

value: Oligodendrocytes cell line

tag: genotype/variation


title: OLN93 Sox10-deficient (Sox10ko) cells, clone B

description:
OLN93_Sox10ko_2
RNAseq data from OLN93 cells (Sox10ko).
processed data file: OLN93_Sox10_ko_CrisprCas_vs_ctrl.xlsx


title: E14 RING1B I53A 1


title: OLN93 control (ctrl) cells, biological replicate 1

description:
OLN93_ctrl_1
RNAseq data from OLN93 cells (ctrl).
processed data file: OLN93_Sox10_ko_CrisprCas_vs_ctrl.xlsx

source_name: OLN93 cell line


title: ALAL1_siRNA_rep1


title: ALAL1_siRNA_rep2


title: E14 WT 3

value: WT


title: Control_siRNA_TNFalpha+_treated rep3

value: control


title: Ribo WT  rep2

city: Beijing

first: Zonggui

last: Chen

state: Beijing

address: No.5 Yiheyuan Road Haidian District

department: Academy for Advanced Interdisciplinary Studies

institute: Peking University

description:
different_translation_efficiency_rep2.tsv
Paired-end reads - average insert size: 28.5, standard deviation: 10.3.

data_processing:
Library strategy: Ribo-seq
Adapter sequences were trimmed using Cutadapt(2.5) program.
Potential ribosomal RNA contamination were eliminated by using Bowtie(1.2.2) program to align reads to reference ribosomal RNA sequences.
Reads were mapped to GRCm38 by using STAR(STAR_2.5.0a) program. Only proper-pair and primary alingments were retained.
Fragment counts on CDS region of transcripts were counted by using custom scripts.
FPKM of each transcript was calculated on CDS region.
Translation efficiency was calculated as FPKM(RPF)/FPKM(Input).
Genome_build: GRCm38
Supplementary_files_format_and_content: Tab-delimited text files include the fragment count and FPKM values for all samples and foldchanges of FPKM between different conditions.

source_name: testes

extract_protocol:
The DNase-treated lysates were clarified by centrifugation and subjected to RNA extraction & sequencing or ribosome profiling analyses.
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: strain

value: testes

tag: age

value: post natal day 24

tag: fraction

value: ribosome protected fragments


title: Ribo Miwi-null  rep2

description:
different_translation_efficiency_rep2.tsv
Paired-end reads - average insert size: 28.5, standard deviation: 17.3

value: Miwi-null

tag: tissue


title: Ribo Miwi-null  rep1

description:
different_translation_efficiency_rep1.tsv
Paired-end reads - average insert size: 28.5, standard deviation: 7.7.


title: 3fep_2_WGBS.fastq.gz

city: Los Angeles

first: Eric

middle: Alva

last: Webb

state: CA

address: 3616 Trousdale Parkway

institute: University of Southern California

description: Cells were grown semi-continuously in Aquil medium in Fe/P co-limitation in 380 µatm CO2 for 1 year. Samples for WGBS were taken in the middle of the photoperiod (i.e. midday)

data_processing:
Raw read files were downloaded from the USC Genomics and Cytometry Core server upon completion
Raw reads were quality processed and trimmed using Trimmomatic (v0.32) with the following settings: LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:35. Next, reads were mapped using the BSMAP package with default settings followed by methylation identification and site-specific estimation of methylation levels by the MethPiPe pipeline. A cytosine was deemed methylated if the residue had a combined coverage of >5 reads and if methylation was detected in all biological replicates with at least 20% of total reads being methylated in at least one experimental treatment (n = 6 treatments).
Bisulfite conversion rates were estimated using MethPipe
We performed differential methylation analysis with a modified version of RADMeth. The modified program skips the step where significance of each site is adjusted based on the significance of its neighbors. This step was originally designed to enable detection of regional changes in mammalian methylomes at sites with relatively low coverage. The coverages in our samples are high enough to enable detection of methylation changes without this adjustment. A differentially methylated cytosine was considered significant if the change in the cytosine-specific (Smet) methylation level was >1/3 relative to the corresponding cytosine in the stated reference treatment and if it retained a Benjamini-Hochberg false discovery rate (FDR) < 0.001.
Genome_build: NC_008312.1: https://www.ncbi.nlm.nih.gov/nuccore/113473942?report=fasta
Supplementary_files_format_and_content: The Methyl_all_final.bed has 7 columns as follows: 1) chromosome number (1 chromosome) 2) Methylation coordinate 3) Methylation coordinate repeated 4) Sequence context 5) Methylation level 6) strand 7) Full or hemimethylated indicator
Supplementary_files_format_and_content: The all_diff_3f_001_33_mat.txt is a matrix of all differentially methylated sites. The first column has the methylated genome coordinate followed by methylation levels of that coordinate per biological replicate. Finally the last two columns contain the strand and if the coordinate is fully or hemimethylated
Supplementary_files_format_and_content: T_erythraeum_IMS101.fasta is a fasta file of the closed genome of Trichodesmum erythraeum IMS101 that was used in this study.

organism: Trichodesmium erythraeum IMS101

source_name: cell population

growth_protocol: Briefly, IMS101 cell lines that were bubbled with 380 µatm CO2 air in nutrient replete media for ~7 years were then subjected to simultaneous Fe/P co-limitation for ~1 year (0.25 µM PO43- and 10 nM Fe). Following ~1 year of Fe/P co-limitation, 10 µm PO4 was supplied to Fe/P co-limited cultures generating steady-state Fe-limited cultures, which were grown for ~2 months prior to sampling.

extract_protocol:
sampling protocol: Biological replicates from each treatment were gently filtered onto 5 µm polycarbonate filters (Whatman) during the middle of the photoperiod, immediately flash frozen, and stored in liquid nitrogen until extraction DNA extraction.
DNA was extracted from frozen filters with the FastDNA Spin Kit for Soil (MP Biomedicals, Santa Ana, CA, USA) following the manufacturer’s protocol.
Extracted DNA was then sent to the USC Genomics and Cytometry Core for library construction and sequencing (http://upcgenomecore.usc.edu/site/Home.html). The USC Genomics Core employs the NEXTflex Bisulfite-Seq library preparation kit (BIOO Scientific) followed by sequencing on the Illumina HiSeq 2500.

tag: environment

value: cell culture

tag: co2 concentration

value: 380 µatm

tag: medium

value: Aquil medium w/o fixed nitrogen, with 0.25 uM PO4 and 10nM Fe

tag: location

value: University of Southern California


title: Ribo WT  rep1

description:
different_translation_efficiency_rep1.tsv
Paired-end reads - average insert size: 28.5, standard deviation: 9.7.


title: Control_siRNA_TNFalpha+_treated rep2

tag: treatment

tag: RNAi


title: 3fep_1_WGBS.fastq.gz


title: E14 WT 2

tag: genotype

tag: biologial replicate


title: E14 WT 1

tag: molecule subtype


title: 3f_2_WGBS.fastq.gz

description: Cells were grown semi-continuously in Aquil medium in Fe-limitation in 380 µatm CO2 for 2 months. Samples for WGBS were taken in the middle of the photoperiod (i.e. midday)

value: Aquil medium w/o fixed nitrogen, with 10nM Fe and 10 uM PO4


title: Control_siRNA_TNFalpha+_treated rep1


title: Miwi-null input rep1

description:
different_translation_efficiency_rep1.tsv
Paired-end reads - average insert size: 287.6, standard deviation: 88.6.

data_processing:
Adapter sequences were trimmed using Cutadapt(2.5) program.
Potential ribosomal RNA contamination were eliminated by using Bowtie(1.2.2) program to align reads to reference ribosomal RNA sequences.
Reads were mapped to GRCm38 by using STAR(STAR_2.5.0a) program. Only proper-pair and primary alingments were retained.
Fragment counts on CDS region of transcripts were counted by using custom scripts.
FPKM of each transcript was calculated on CDS region.
Translation efficiency was calculated as FPKM(RPF)/FPKM(Input).
Genome_build: GRCm38
Supplementary_files_format_and_content: Tab-delimited text files include the fragment count and FPKM values for all samples and foldchanges of FPKM between different conditions.

value: total RNAs


title: CD4_siNS_isotype_rep1

description:
processed data file:
CD48_sample_gene_counts.txt
CD48_sample_gene_FPKMs.txt

tag: knockdown

value: siNS

tag: t cell subtype

tag: antibody blockade

value: isotype control


title: Miwi-null input rep2

description:
different_translation_efficiency_rep2.tsv
Paired-end reads - average insert size: 284, standard deviation: 89.1.


title: 3f_1_WGBS.fastq.gz


title: Control_siRNA_not_treated rep3


title: OLN93 control (ctrl) cells, biological replicate 2

description:
OLN93_ctrl_2
RNAseq data from OLN93 cells (ctrl).
processed data file: OLN93_Sox10_ko_CrisprCas_vs_ctrl.xlsx

tag: cell line

tag: cell type

tag: genotype/variation


title: WT input rep2

description:
different_translation_efficiency_rep2.tsv
Paired-end reads - average insert size: 244.5, standard deviation: 62.2.

tag: strain

tag: age

tag: fraction


title: Sample 3_Ath_mRNA_Nanopore

description: repeat 2 (CK2)

source_name: overall ground parts of plants_Nanopore

tag: ecotype

value: wild type

tag: developmental stages

value: at growth stage of rosette growth complete

tag: tag

value: Nanopore PromethION platform


title: Sample 4_Ath_mRNA_Nanopore

description: repeat 3 (CK3)


title: Control_siRNA_not_treated rep2

tag: treatment


title: E14 WT 4

tag: tissue

value: Mouse ES cells

value: WT

value: Proximity-ligated gDNA


title: r3_1_WGBS.fastq.gz

description: Cells were grown semi-continuously in Aquil medium with replete nutrients in 380 µatm CO2. Samples for WGBS were taken in the middle of the photoperiod (i.e. midday)

tag: environment

tag: co2 concentration

tag: medium

value: Aquil medium w/o fixed nitrogen, with 10 uM PO4 and 250 nM Fe

tag: location


title: Sample 2_Ath_mRNA_Nanopore

description: repeat 1 (CK1)


title: WT input rep1

description:
different_translation_efficiency_rep1.tsv
Paired-end reads - average insert size: 266, standard deviation: 78.4.

tag: genotype

value: testes

value: post natal day 24


title: r3_2_WGBS.fastq

value: cell culture


title: Control_siRNA_not_treated rep1

tag: RNAi

value: control


title: 4T1

status: Public on Dec 14 2019

city: CABA

first: Soledad

last: Mac Keon

state: Buenos Aires

address: Av patricias argentinas 435

country: Argentina

institute: Fundacion Instituto Leloir

data_processing:
During the QC steps, Agilent 2100 Bioanaylzer and ABI StepOnePlus Real-Time PCR System were used by BGI in quantification and qualification of the sample library
BGI internal software was used to filter reads, fllowed as: 1) Remove reads with adaptors; 2) Remove reads in which unknown bases(N) are more than 5%;3) Remove low quality reads (defining low quality read as the percentage of base which quality is lesser than 15 is greater than 20% in a read). After filtering, the remaining reads are called "Clean Reads" and stored in FASTQ format.
BGI used HISAT to perform genome mapping (version: v0.1.6-beta; parameters: --phred64 --sensitive --no-discordant --no-mixed -I 1 -X 1000)
BGI used StringTie to reconstruct transcripts (version: v1.0.4; parameters: -f 0.3 -j 3 -c 5 -g 100 -s 10000 -p 8), and use cuffcompare to compare reconstructed transcripts to reference annotation (version: v2.2.1; parameters: -p 12).
BGI used CPC to predict coding potential of novel transcripts (version: v0.9-r2; parameters: default), then merged coding novel transcripts with reference transcripts to get a complete reference, and downstream analysis was based on this reference.
Genome_build: We take the mouse genome (mm10) as the reference genome for this project which is available at http://hgdownload.cse.ucsc.edu/goldenPath/mm10/bigZips/.

source_name: murine mammary carcinoma cell line

growth_protocol: RPMI 10%FBS

extract_protocol:
Cell pellet was snap-frozen in liquid nitrogen and shipped to BGI for RNA extraction After extract total RNA and treated with DNase I, Oligo(dT) were used to isolate mRNA.Mixed with the fragmentation buffer, the mRNA were fragmented. Then cDNA was synthesized using the mRNA fragments as templates. Short fragments were purified and resolved with EB buffer for end reparation and single nucleotide A (adenine) addition. After that, the short fragments are connected with adapters. The suitable fragments were selected for the PCR amplification.
Agilent 2100 Bioanaylzer and ABI StepOnePlus Real-Time PCR System are used in quantification and qualification of the sample library.

tag: disease state

value: mammary carcinoma


title: PGC-1β Liver LivPGC-1β 1

type: RNA

city: Bari

first: Elena

last: Piccinin

state: Bari

address: Piazza Giulio Cesare, 11

department: Department of Translational Biomedicine and Neuroscience

country: Italy

institute: University of Bari

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in R

source_name: TG Mouse Liver

label_protocol: standard Illumina protocol

extract_protocol: Tissues were snap frozen in liquid nitrogen and stored at ������80  C. Total RNA was isolated by  QIAzol reagent (Qiagen, Hilden, Germany) following the manufacture’s instruction, after tissue  homogenization through Qiagen TissueLyser (Qiagen, Hilden, Germany). To avoid possible DNA  contamination, RNA was treated with DNase (Thermo Fisher Scientific,Waltham, MA, USA). RNA  purity and concentration were checked by spectrophotometer, while the RNA integrity was assessed  by Bio-RadExperion(Bio-Rad, Hercules, CA, USA). Only samples with Relative Quality Index (RQI)  > N8 were used for microarray analysis

value: FVBN

value: 4 months

value: Liver


title: Cloudman S91

source_name: murine skin melanoma cell lines

growth_protocol: DMEM 10%FBS

value: DBA

value: skin melanoma


title: B16-F1

source_name: murine skin melanoma cell line


title: PGC-1β Liver LivPGC-1β 2


title: PGC-1α Liver WT 4

source_name: WT Mouse Liver

extract_protocol: Tissues were snap frozen in liquid nitrogen and stored at -80  C. Total RNA was isolated by QIAzol reagent (Qiagen, Hilden, Germany) following the manufacture’s instruction, after tissue homogenization through Qiagen TissueLyser (Qiagen, Hilden, Germany). To avoid possible DNA contamination, RNA was treated with DNase (Thermo Fisher Scientific,Waltham, MA, USA). RNA purity and concentration were checked by spectrophotometer, while the RNA integrity was assessed by Bio-RadExperion(Bio-Rad, Hercules, CA, USA). Only samples with Relative Quality Index (RQI) > N8 were used for microarray analysis


title: PGC-1α Liver LivPGC-1α 5


title: PGC-1β Liver WT 2


title: PGC-1β Liver WT 4


title: PGC-1β Liver WT 5


title: PGC-1β Liver WT 3


title: PGC-1β Liver WT 1


title: PGC-1α Liver WT 5


title: PGC-1α Liver LivPGC-1α 1


title: PGC-1α Liver LivPGC-1α 4


title: PGC-1α Liver WT 3


title: PGC-1β Liver LivPGC-1β 4


title: PGC-1β Liver LivPGC-1β 6


title: PGC-1β Liver LivPGC-1β 3


title: PGC-1β Liver LivPGC-1β 5


title: PGC-1α Liver LivPGC-1α 3


title: PGC-1α Liver LivPGC-1α 2


title: rat-drug concetration 3.2g/kg-repH4

city: Tongliao

first: Xiulan

last: Wang

state: Inner Mongolia

address: HuoLinhe

department: Affiliated Hospital

institute: Inner Mongolia University For The Nationlities

description: miRNA expression data from drug group

hyb_protocol: Following fragmentation, mirRNA targets were hybridized for 16 hr at 48C on mirRNA-40 Affymetrix. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Command Console (AGCC)

data_processing: The data were preprocessed with R/Bioconductor package Affy ,and the processing algorithm used Range Migration Algorithm (RMA)

source_name: rat-drug concetration 3.2g/kg-kidney

label_protocol: After validation of the RNA quality with Bioanalyzer 2100, 1 µg of total RNA was biotin labelled following the FlashTag Ligation Mix Biotin   (Affymetrix)

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

value: Sprague Dawley

tag: sample group

value: Mongolian medicine Narenmandula group

value: Narenmandula 3.2g/kg

value: renal tissues


title: N13B

city: New York

first: Weijia

last: Zhang

state: NY

address: 1 Gustave L. Levy Pl

department: Renal

institute: Icahn School of Medicine at Mount Sinai

data_processing:
The reads with good quality were firstly aligned to several human reference databases including hg19 human genome, exon, splicing junction segment and contamination database including ribosome and mitochondria sequences using STAR alignment algorithm. After filtering reads mapped to contamination database, the reads that are uniquely aligned to the exon and splicing-junction segments with a maximal 2 mis-matches for each transcript were then counted as expression level for corresponding transcript.  After filtering out of the transcripts with low read (<100) across all samples, the read counts were log2 transformed and quantile-normalized at an equal global median value in order to compare transcription level across samples.
Genome_build: hg19
Supplementary_files_format_and_content: txt files with normalized log2 transfromed read counts

source_name: kidney biopsy

extract_protocol:
Total RNA was extracted using TRIzol (Thermo Fisher Scientific). The RNA quality was evaluated by an Agilent 2100 Bioanalyzer.
The total RNA sample was treated using a Ribo-Zero Magnetic Gold Kit to deplete rRNA, and cDNA libraries were prepared and sequenced at BGI using a HiSeq 4000 system.

tag: group

value: Control


title: rat-drug concetration 3.2g/kg-repH12

description: miRNA expression data from drug group

tag: strain


title: rat-drug concetration 3.2g/kg-repH9

description: miRNA expression data from drug group


title: PGC-1α Liver WT 2

tag: age


title: PGC-1α Liver WT 1


title: N10B


title: N12B


title: N8B


title: rat-drug concetration 3.2g/kg-repH8

description: miRNA expression data from drug group


title: rat-drug concetration 3.2g/kg-repH2

description: miRNA expression data from drug group


title: N7B


title: N6B


title: N3A


title: rat-model group-repF8

description: miRNA expression data from model group

source_name: rat-model group-kidney

value: doxorubicin nephropathy model


title: rat-normal group-repE6

description: miRNA expression data from normal group

source_name: rat-normal group-kidney

value: normal


title: B9B


title: N2A


title: rat-normal group-repE10

description: miRNA expression data from normal group


title: rat-model group-repF2

description: miRNA expression data from model group


title: rat-model group-repF9

description: miRNA expression data from model group


title: NKT.19-8-TCRb+CD1daGalCerTet+.Lv#1_RNA-seq

first: Liang

last: Yang

department: Pathology

institute: Harvard Medical School

description:
iNKT Cell
SK-3N77_G2

data_processing:
Reads were mapped to the mouse reference genome (mm10) with STAR 2.5.4a
Non-uniquely mapped reads were discarded.
The uniquely mapped reads were assigned to genes using featureCounts with GENCODE annotation (vM16)
Genome_build: mm10
Supplementary_files_format_and_content: raw read counts

source_name: Liver

growth_protocol: 6 week old C57BL/6J mice from the Jackson Laboratory (Bar Harbor, ME) housed in facility at least one week before harvesting cells

extract_protocol:
Extractions follow ImmGen standard operating protocol (available on https://www.immgen.org/). Briefly, organs are harvested at 9am on day of sort, perterbed as little as possible during preparation, and 1000 cells are double sorted into TCL buffer (Qiagen, Hilden, Germany) containing 1% BME.
Libraries are constructed according to the standard protocol for Smart-seq2 (Picelli et al, 2013) at the Broad Techology Labs in Cambridge, MA

value: 6 weeks old

tag: sorting markers

tag: cell type

value: ab T Cell


title: T.4.19-8-TCRb+CD4+.Sp#2_RNA-seq

description:
CD4 T Cell
SK-3N77_G6

source_name: Spleen

value: Spleen


title: rat-model group-repF3

description: miRNA expression data from model group


title: NKT.19-8-TCRb+CD1daGalCerTet+.Lv#3_RNA-seq

description:
iNKT Cell
SK-3N77_G4


title: NKT.19-8-TCRb+CD1daGalCerTet+.Lv#2_RNA-seq

description:
iNKT Cell
SK-3N77_G3


title: T.4.19-8-TCRb+CD4+.Sp#1_RNA-seq

description:
CD4 T Cell
SK-3N77_G5


title: rat-model group-repF6

description: miRNA expression data from model group


title: B8B


title: rat-normal group-repE4

description: miRNA expression data from normal group


title: NKT.19-8-TCRb+CD1daGalCerTet+.Th#3_RNA-seq

description:
iNKT Cell
SK-3N77_F8

source_name: Thymus

value: Thymus


title: N5B


title: B6B


title: NKT.19-8-TCRb+CD1daGalCerTet+.Th#1_RNA-seq

description:
iNKT Cell
SK-3N77_F6


title: B5B


title: rat-normal group-repE1

description: miRNA expression data from normal group


title: rat-normal group-repE2

description: miRNA expression data from normal group


title: 550971A05_CichlCGH09.wa01

city: Portland

first: Suzy

middle: CP

last: Renn

state: Oregon

address: 3203 SE Woodstock Blvd., Biology Room B124

department: Biology

institute: Reed College

description: multi-species aCGH

hyb_protocol: Arrays were hybridized for 64hrs at 42ºC in a NimbleGen Hybridization Station 4, then arrays were washed and dried according to manufactured protocol

scan_protocol: Arrays were scanned on the GenPix 4000 Scanner at a resolution of 5um/pixel

data_processing:
High-resolution pictures were processed with DEVA v.2.1 (NimbleGen). Dual-color signal-intensity matrices were exported and analyzed in R using the Ringo and limma packages
GC-Loess normalized data (ch1 bias = negative, ch2 bias = positive).

label: AlexaFluor 555

organism: Maylandia zebra

label_protocol: Genomic DNA was labeled using dual-color labeling kits from NimbleGen, following standard protocol.

extract_protocol: For each sample used in this study DNA was extracted from muscle or fin tissue from a single individual using a standard phenol-chloroform protocol.

tag: genome

value: Maylandia zebra

label: AlexaFluor 647

organism: Oreochromis niloticus

source_name: Oreochromis.niloticus XX clone

value: Oreochromis niloticus


title: 545409A05_CichlCGH05.wa04

description: multi-species aCGH


title: 545385A05_CichlCGH03.wa05

description: multi-species aCGH


title: B3B


title: NKT.19-8-TCRb+CD1daGalCerTet+.Sp#3_RNA-seq

description:
iNKT Cell
SK-3N77_G1


title: NKT.19-8-TCRb+CD1daGalCerTet+.Sp#2_RNA-seq

description:
iNKT Cell
SK-3N77_F12


title: NKT.19-8-TCRb+CD1daGalCerTet+.Sp#1_RNA-seq

description:
iNKT Cell
SK-3N77_F11


title: Patient 3 GC　NT

city: Kyoto

first: Kenji

last: Nanishi

state: Kyoto

address: Kawaramachi-Hirokoji, Kamigyo-ku

country: Japan

institute: Kyoto Prefectural University of Medicine

hyb_protocol: The labeled cRNAs were hybridized onto the Arraystar Human circRNA Arrays V2 (8x15K, Arraystar), and incubated for 17 hours at 65°C in an Agilent Hybridization Oven.  The labeled cRNAs were hybridized onto the Arraystar Human circRNA Arrays V2 (8x15K, Arraystar), and incubated for 17 hours at 65°C in an Agilent Hybridization Oven.  The labeled cRNAs were hybridized onto the Arraystar Human circRNA Arrays V2 (8x15K, Arraystar), and incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: The hybridized arrays were washed, fixed and scanned using the Agilent DNA Microarray Scanner (part number G2505C).

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. For each sample the gProcessedSignal was extracted from the Agilent Feature Extraction Files and the log2 values were quantile normalized.

source_name: gastric normal tissue

label_protocol: Total RNAs were digested with Rnase R (Epicentre, Inc.) to remove linear RNAs and to enrich circular RNAs. The enriched circular RNAs were amplified and transcribed into fluorescent cRNA utilizing a random priming method (Arraystar Super RNA Labeling Kit; Arraystar).

extract_protocol: Total RNA were extracted from frozen samples using the AllPrep® DNA/RNA/miRNA universal kit (Qiagen, Hilden, Germany) according to the manufacturer’s instructions.

tag: gender

value: M

tag: Stage

value: adjacent normal gastric mucosa


title: 545383A05_CichlCGH02.WS1

description: multi-species aCGH


title: NKT.19-8-TCRb+CD1daGalCerTet+.Lu#2_RNA-seq

description:
iNKT Cell
SK-3N77_F10

source_name: Lung

tag: tissue

value: Lung


title: A33A


title: Opn3 KO Liver tissue n=3

city: Cincinnati

first: Gowri

last: Nayak Sarangdhar

state: Ohio

address: 3333 Burnet Avenue

description:
Samples collected at 1 hour after lights on (ZT1)
Affymetrix Clariom™ D Assay mouse (formerly known at GeneChip® Mouse Transcriptome Assay 1.0)

hyb_protocol: Standard Affymetrix Protocol

scan_protocol: Standard Affymetrix Protocol

data_processing:
The data were analyzed using Altanalyze developed by Dr. Nathan Salomonis at Cincinnati Children's Hospital Medical Center.
Altanalyze output, where normalized gene-level expression values are Log2 transformed.

label: Biotin

source_name: Liver, ZT1

label_protocol: Standard Affymetrix Protocol

extract_protocol: Trizol extraction and column purification according to manufacturer's (Genejet) instructions

tag: postnatal age


title: Opn3 KO Liver tissue n=1

institute: Cincinnati Children's Hospital Medical Center


title: Opn3 KO Liver tissue n=2


title: A31A


title: A32A


title: A30A


title: Patient 3 GC　T

source_name: primary gastric cancer tissue

value: IIIA


title: B4B


title: Patient 2 GC　NT

value: F


title: Flower buds, RNA-seq_Date3_3

city: Villenave d'Ornon

first: Benedicte

last: Wenden

address: 71 avenue Edouard Bourlaux

country: France

institute: INRA

description: Prunus avium L.

data_processing:
For RNA-seq, Trimmed reads were mapped to the peach (Prunus persica (L) Batsch) reference genome v1.0 (Verde et al., 2013) using Tophat (Trapnell et al., 2009).
Possible optical duplicates were removed using Picard tools (https://github.com/broadinstitute/picard).
For RNA-seq data, for each gene, TPM (Transcripts Per Million) numbers were calculated (Wagner, 2003).
Genome_build: Prunus persica (L) Batsch reference genome v1.0 (Verde et al., 2013)
Supplementary_files_format_and_content: RNA-seq processed data files are txt files that contains a gene_id column that defines the gene name corresponding to the peach locus, locus information (chromosome, position), and the TPM (transcripts per million reads) per locus.
Gene list and homology information for Prunus persica genome v1.0 are available at https://www.rosaceae.org/analysis/11

organism: Prunus avium

source_name: Sweet cherry flower buds

growth_protocol: Branches and flower buds were collected from the sweet cherry cultivars (Prunus avium L.) 'Burlat'. The trees were grown in an orchard located at the Fruit Experimental Unit of INRA in the South West of France (44° 19′ 56′′ N, 0° 24′ 47′′ E). Sweet cherry flower buds used for the ChIP-seq experiment were collected on October 21st 2014 (Date 1) and December 5th 2014 (Date 2) for dormant buds and January 27th 2015 (Date 3) for non-dormant buds. For each date, buds were harvested from the same branches, flash frozen in liquid nitrogen and stored at -80°C prior to performing RNA-seq and ChIP-seq.

extract_protocol:
Total RNA was extracted from 50-70 mg of frozen and pulverised flower buds using RNeasy Plant Mini kit (Qiagen) with minor modification: 1.5% PVP-40 was added in the RLT buffer. RNA quality was evaluated using Tapestation 4200 (Agilent Genomics).
For RNA-seq libraries, library preparation was performed on 1 μg of high quality RNA (RNA integrity number equivalent superior or equivalent to 8.5) using the TruSeq Stranded mRNA Library Prep Kit High Throughput (Illumina cat. no. RS-122-2103). DNA quality from libraries was evaluated using Tapestation 4200. The libraries were sequenced on a NextSeq500, at the Sainsbury Laboratory Cambridge University (SLCU), using paired-end sequencing of 75 bp in length.

tag: cultivar

value: Burlat

value: Flower buds

tag: time-point

tag: lane


title: Stomach

city: Toronto

first: Tae-Hee

last: Kim

state: Ontario

address: 686 Bay Street. Room 16.9709

department: Developmental & Stem Cell Biology

country: Canada

institute: The Hospital for Sick Children

data_processing:
Base-calls were performed with Illumina bcl2fastq
Sequenced reads were trimmed for adaptor sequence.Then reads in bam files were tagged with the cell and molecular (UMI) barcode sequences using Drop-seq_tools-1.12.The cell barcodes are tagged as XC in the bam file and the UMI is tagged as XM in the bam file. The reads quality under 10 were removed.
ScRNA-seq reads were aligned to the Mus_musculus.GRCm38.88 genome assembly using STAR with default configurations.
Each aligned exonic read was tagged with a gene name. A digital expression matrix was built by counting the number of unique UMIs per gene within each cell; columns are cells, and rows are genes. The first inflection point was estimated on a cumulative sum plot of the digital expression matrix to determine the number of cells in the sample.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files of digital expression matrix (dge) based on raw UMI counts, columns are cells, and rows are genes.

source_name: Stomach

extract_protocol:
Tissue (Stomach and intestine) was collected from male mouse. Epithelial cells were removed by EDTA shaking, and mesenchyme was digested with digestion buffer (Protease, dispase, DANase). Single cells wer sorted for Tdtomato+ve cells.
RNA libraries were prepared for sequencing using standard Illumina protocols
Drop-seq. single cell RNA-seq

value: Stomach stromal cells

value: Stomach

tag: allele

tag: developmental stage

value: Postnatal day 40

tag: sorting

value: Tdtomato+ cells were sorted


title: Opn3 Wildtype Liver tissue n=3


title: Patient 1 GC　NT


title: Patient 1 GC　T

value: IIIC


title: Patient 2 GC　T


title: A29A


title: Flower buds, RNA-seq_Date3_2

description: Prunus avium L.


title: NKT.19-8-TCRb+CD1daGalCerTet+.Lu#1_RNA-seq

description:
iNKT Cell
SK-3N77_F9

value: 6 weeks old

value: ab T Cell


title: Opn3 Wildtype Liver tissue n=2


title: A28A


title: Opn3 Wildtype Liver tissue n=1


title: Flower buds, RNA-seq_Date3_1

description: Prunus avium L.


title: Rbp4-Cre (KL100) x Rosa26-LSL-TRAP dentate gyrus IP Rep2 [1923]

first: Laura

last: Kus

address: 1230 York Avenue # 260

department: Heintz Laboratory

institute: The Rockefeller University

description:
Ribosomal-bound RNA
1923_Rbp4_Cre_KL100::Rosa26_LSL_TRAP_dentate_gyrus_Rep2_GTGAAA_L001

data_processing:
FASTX Toolkit 0.0.13 was used to assess the quality of reads and trim trailing adaptors.
Trimmed reads were aligned to annotated exons using the mm10 genome using STAR v2.0.0e_r291 using default settings.
Raw counts of mapped reads were generated with HTSeq framework v0.6.0 using the htseq-count module with the "union" mode and default settings.
Genome_build: mm10
Supplementary_files_format_and_content: Text files of counts

source_name: Dentate gyrus

growth_protocol: Not applicable

extract_protocol:
The cerebral cortex and dentate gyrus were dissected and homogenized seperately and tagged polysomes were immunopurified with monoclonal anti-EGFP antibodies bound to biotinylated-Protein L (Thermo Fisher) coated streptavidin-conjugated magnetic beads (Life Technologies). Total RNA from IPs was purified with the Agilent Nanoprep kit following manufacturer's protocol.
Ribosomal-bound RNA was extracted and treated as described in PMID 24810037, Heiman M, Kulicke R, Fenster RJ, Greengard P, Heintz N. (2014) Cell type-specific mRNA purification by translating ribosome affinity purification (TRAP). Nat Protoc. 9:1282-1291

treatment_protocol: No treatment

value: Dentate gyrus

tag: animal line

value: Rbp4-Cre KL100

tag: antibody

value: anti-EGFP Immunopurified (IP)


title: Flower buds, RNA-seq_Date2_3

description: Prunus avium L.


title: Rbp4-Cre (KL100) x Rosa26-LSL-TRAP cerebral cortex IP Rep2 [1922]

description:
Ribosomal-bound RNA
1922_Rbp4_Cre_KL100::Rosa26_LSL_TRAP_cerebral_cortex_Rep2_ACAGTG_L001

source_name: Cerebral cortex

value: Cerebral cortex


title: A26A

tag: group


title: intestine

source_name: Intestine

value: Intestinal stromal cells

value: Intestine


title: Opn3 KO Inguinal white adipose tissue n=3

source_name: Inguinal White Adipose Tissue, ZT1


title: Opn3 KO Inguinal white adipose tissue n=2


title: Flower buds, RNA-seq_Date2_1

description: Prunus avium L.


title: A24A

source_name: kidney biopsy


title: Opn3 KO Inguinal white adipose tissue n=1


title: Opn3 Wildtype Inguinal white adipose tissue n=3


title: A25A


title: Flower buds, RNA-seq_Date2_2

description: Prunus avium L.


title: Rbp4-Cre (KL100) x Rosa26-LSL-TRAP cerebral cortex IP Rep1 [1920]

description:
Ribosomal-bound RNA
1920_Rbp4_Cre_KL100::Rosa26_LSL_TRAP_cerebral_cortex_Rep1_GCCAAT_L001


title: Rbp4-Cre (KL100) x Rosa26-LSL-TRAP dentate gyrus IP Rep3 [1924]

description:
Ribosomal-bound RNA
1924_Rbp4_Cre_KL100::Rosa26_LSL_TRAP_dentate_gyrus_Rep3_CGATGT_L001


title: A22A


title: Flower buds, RNA-seq_Date1_2

description: Prunus avium L.


title: MT_stomach_RNASeq_Rep2

data_processing:
fastq reads were aligned to the mm9 transcriptome using kallisto 0.42.2 with default parameters
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited files containing transcript ID, transcript length, effective length, estimated counts, and abundance in TPM were generated using kallisto 0.42.2

source_name: E17.5 stomach

extract_protocol:
Control and Sufu and Spop double knockout E17.5 stomachs were removed, and their epithelial and mesenchymal tissues were separated using EDTA. The mesenchymal part was kept at -20°C prior to RNA extraction with RNeasy kit (Qiagen). The integrity of the samples was checked on Agilent Bioanalyzer, and the samples with a RIN>8.5 were used. 1 to 2µg of RNA were used to prepare the PolyA RNA library.
Libraries were prepared according to manfacturer's instructions for the NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® kit.

value: stomach

tag: genotype/variation

value: Sufu;Spop double knockout


title: A23A


title: Flower buds, RNA-seq_Date1_1

description: Prunus avium L.

value: Burlat


title: A21A


title: MT_stomach_RNASeq_Rep1


title: Opn3 Wildtype Inguinal white adipose tissue n=1


title: Opn3 Wildtype Inguinal white adipose tissue n=2


title: A20A


title: CT_stomach_RNASeq_Rep1

value: WT


title: CT_stomach_RNASeq_Rep2


title: Flower buds, ChIP-seq_date3_3_K4

description:
Prunus avium L.
date3_3_K4_40193923_count.txt

data_processing:
The quality of reads was assessed using FastQC (www.bioinformatics.babraham.ac.uk/projects/fastqc/) and possible adaptor contaminations and low quality trailing sequences were removed using Trimmomatic (Bolger et al., 2014).
For ChIP-seq data, adaptor-trimmed reads were mapped to the peach (Prunus persica (L) Batsch) reference genome v1.0 (Verde et al., 2013) using Bowtie2 (Langmead et al., 2009).
Possible optical duplicates were removed using Picard tools (https://github.com/broadinstitute/picard).
We used a gene-centric approach to identify genes with significant changes in the strength of H3K4me3 signal between time-points. The DiffBind R package was used for the read counting and differential binding analysis steps (Stark and Brown, 2011; Ross-Innes et al., 2012). Firstly, to quantify H3K4me3 signal at genes, we measured the number of H3K4me3 ChIP reads in a 2000bp window around the TSS of each gene, normalised by H3. Two biological replicates were present for each time point, and DiffBind combines the available information to provide a statistical estimate of the normalised H3K4me4 signal for any particular gene.
Genome_build: Prunus persica (L) Batsch reference genome v1.0 (Verde et al., 2013)
Supplementary_files_format_and_content: ChIP-seq processed data files are txt files that contains the gene_id column that defines the gene name corresponding to the peach locus, locus information (chromosome, position), and the TMM (i.e. counts of H3K4me3 signal normalized by H3 signals at the TSS of each gene) per locus.
Gene list and homology information for Prunus persica genome v1.0 are available at https://www.rosaceae.org/analysis/11

extract_protocol:
For ChIP-seq, ChIP was conducted on 300-500 mg of frozen and pulverized flower buds using the procedure described in Leida et al. (2012) with minor modifications (1% PVP-40was added to the different buffers and DNA extraction and purification was carried out using SPRI beads). For immunoprecipitation , we used anti-trimethyl-histone 3 Lys 4 antibody (Millipore cat#17-614).
For ChIP-seq libraries, library preparation was performed using all the volume for IPs (50µL) and 20 ng in 50µL using the TruSeq ChIP Library Preparation kit (48 samples, 12 indexes, Illumina, cat. no. IP-202-1012). DNA quality from libraries was evaluated using Tapestation 4200. The libraries were sequenced on a NextSeq500, at the Sainsbury Laboratory Cambridge University (SLCU), using paired-end sequencing of 75 bp in length.

value: Flower buds

tag: chip antibody


title: Opn3 KO Interscapular adipose tissue n=3

source_name: Interscapular Adipose Tissue, ZT1


title: input DNA_Rep2

data_processing:
Adaptor sequences were trimmed using Trimmomatic 0.36 with adaptor sequence file TruSeq3-PE-2.fa
Reads were aligned to the mm9 reference genome using default parameters of BWA MEM
Aligned reads were filtered using bamtools to exclude unmappped reads, mapping quality < 5, and not proper pairs.
ENCODE blacklist regions in mm9 were filtered out using bedtools
Peaks were called using MACS2 with q = 0.05. --broad option was used for histone marks
Genome_build: mm9
Supplementary_files_format_and_content: peaks called from MACS2

extract_protocol:
E17.5 stomachs were dissected, cut into small pieces, and crosslinked in solution A (1% formaldehyde, 50mM Hepes-KOH, 100 mM NaCl, 1mM EDTA, 0.5 mM EGTA) for 20 minutes at room temperature. 1/20 volume of 2.5 M glycine was added to quench formaldehyde. Tissues were rinsed in ice-cold PBS and dounced in Wheaton tissue grinder. Cell suspensions were passed through a 100μm cell strainer to remove connective tissues, then centrifuged at 4 °C at 2500 × rcf for 3 min, followed by a wash in PBS. Gli2, H27K27ac, or H3K36me3 antibodies were incubated with pre-blocked magnetic beads in 250μL total volume for 8 hours at 4 °C, then washed and resuspended in 100μL 0.5% BSA (w/v) solution. Cell pellets were lysed by sequentially resuspending and centrifuging in LB1 (50 mM Hepes-KOH, pH 7.5; 140 mM NaCl; 1mM EDTA; 10% Glycerol; 0.5% NP-40 or Igepal CA-630; 0.25% Triton X-100), and LB2 (10 mM Tris-HCL, pH8.0; 200 mM NaCl; 1 mM EDTA; 0.5 mM EGTA). Pellet was resuspended in LB3 (10 mM Tris-HCl, pH 8; 100 mM NaCl; 1 mM EDTA; 0.5 mM EGTA; 0.1% Na-Deoxycholate; 0.5% N-lauroylsarcosine) and sonicated into 200-400bp fragments. Sonicated lysates were diluted with LB3. After saving 50μL for input control, they were split into tubes containing 10% v/v Triton X-100 with Gli2 (homemade), H3K27ac (Millipore 05-1334 lot 2489078), or H3K36me3 (Abcam ab9050 lot GR204353-1) antibody, and incubated overnight. Beads were washed 6 times in RIPA buffer (50 mM Hepes-KOH, pH 7.5; 500 mM LiCl; 1mM EDTA; 1% NP-40 or Igepal CA-630; 0.7% Na-Deoxycholate), and once in TBS (20 mM Tris-HCl, pH 7.6; 150 mM NaCl). Protein-DNA complexes were eluted and crosslink reversed with 200 μL of elution buffer (50 mM Tris-HCl, pH 8; 10 mM EDTA; 1% SDS). The 50μL input lysate was also included in this step. Eluted DNA was diluted with 200 μL of TE, and treated with RNaseA for 30 min at 37°C, and subsequently with proteinase K for 2 hours at 55°C. Phenol:chloroform:isoamyl alcohol was used to extract DNA.
Libraries were prepared according to manfacturer's instructions for the NEBNext® Ultra™ DNA Library Prep Kit for Illumina® kit.


title: Flower buds, ChIP-seq_date3_3_INPUT


title: A19A


title: Opn3 KO Interscapular adipose tissue n=2


title: Rbp4-Cre (KL100) x Rosa26-LSL-TRAP dentate gyrus IP Rep1 [1921]

description:
Ribosomal-bound RNA
1921_Rbp4_Cre_KL100::Rosa26_LSL_TRAP_dentate_gyrus_Rep1_CTTGTA_L001


title: A18A


title: Flower buds, ChIP-seq_date3_3_H3

value: Anti-Histone H3 antibody (Abcam, ab1791)


title: Opn3 KO Interscapular adipose tissue n=1


title: input DNA_Rep1


title: Flower buds, RNA-seq_Date1_3

description: Prunus avium L.


title: A17A


title: Opn3 Wildtype Interscapular adipose tissue n=3


title: A15A


title: Flower buds, ChIP-seq_date3_2_K4

description:
Prunus avium L.
date3_2_K4_40220194_count.txt

value: anti-trimethyl-histone 3 Lys 4 antibody (Millipore cat#17-614)


title: H3K36me3_ChIPSeq_Rep2


title: Flower buds, ChIP-seq_date3_2_INPUT


title: Opn3 Wildtype Interscapular adipose tissue n=2


title: H3K36me3_ChIPSeq_Rep1


title: Opn3 Wildtype Interscapular adipose tissue n=1


title: Flower buds, ChIP-seq_date3_2_H3


title: H3K27ac_ChIPSeq_Rep2


title: A13A


title: Flower buds, ChIP-seq_date2_3_K4

description:
Prunus avium L.
date2_3_K4_40217306_count.txt


title: A12A


title: H3K27ac_ChIPSeq_Rep1


title: Flower buds, ChIP-seq_date2_3_INPUT


title: Flower buds, ChIP-seq_date2_3_H3


title: A11A