title: O-GlcNAcseq_wt Drosophila larvae (biological rep 2)_150uM GalNAz media for 36h followed by 36h growth on DMSO media

description:
wt.r2_36
processed data file: TC-O-GlcNAc-seq-peaks.bed
O-GlcNAc-seq in wt Drosophila larvae (biological replicate 2) grown on 150uM GalNAz media for 36h followed by 36h growth on DMSO media

source_name: O-GlcNAc-seq_wt larvae_150uM GalNAz media for 36h followed by 36h growth on DMSO media

treatment_protocol: Wild-type Oregon R (WT) Drosophila were expanded in 50 mL bottles of cornmeal molasses media at 25°C. Drosophila parents from approximately 25 of these bottles were required for each time course replicate. Time course Ac4GalNAz feeding was performed on 10 mL petri dishes. Just under 10 mL of cornmeal molasses media supplemented with Ac4GalNAz dissolved in DMSO to a final concentration of 150 uM or DMSO only in the same volume added to the Ac4GalNAz plates (control) were made. Adult Drosophila parents from the bottles were then transferred to the control plates for 2 hours (on cages) for a pre-egg laying period. This facilitated the laying of eggs that were not synchronized. These adult Drosophila were then transferred to either 150 uM Ac4GalNAz or control plates for 2 hours (enabling the laying of synchronized eggs). After a 36 h incubation period, the resulting larvae were transferred to control plates or collected and snap frozen (0 h time point). Larvae that were initially grown on control plates were collected at this time as well (no feed control). The larvae transferred from Ac4GalNAz plates to control plates were then collected after 4, 8, 12, 16, 20, 24, and 36 hours of feeding on these control plates.


title: ACL.ESCs.r1

status: Public on Jan 07 2020

type: SRA

city: Guangzhou

first: Lin

last: Li

address: Shatai South Road

department: Pathophysiology

country: China

institute: Southern Medical University

description: polyA RNA

library_source: transcriptomic

data_processing:
Illumina CASAVA version 1.8 were used to the basecalling.
Reads were trimmed to remove adaptor sequences and low quality bases;
For whole genome bisulfite sequencing (WGBS), the clean reads were first mapped to mouse reference genome mm10 with Bismark (v0.7.6) in paired-end and non-directional module, and then the unmapped reads were realigned to the same reference genome in single-end and non-directional module; while for RNA-seq, the cleaned reads were aligned to the mouse mm10 reference genome using Tophat (v2.0.12) with default settings (Trapnell et al., 2009).
For WGBS, methylation level of covered cytosines, including CpG, CHH and CHG were estimated using comstomized perl scripts; while for RNA-seq, HTSeq (0.6.1) was used to do the reads counting and then gene expression level was calculated using the RPKM method (Reads Per Kilobase transcriptome per million reads).
Genome_build: mm10
Supplementary_files_format_and_content: Methylation calling txt files include the methylation level of covered cytosines, including CpG, CHH and CHG context; while gene RPKM txt files include the RPKM values of RefSeq genes.

molecule: total RNA

organism: Mus musculus

source_name: Embryonic stem cell

extract_protocol:
The isolated genomic DNA were used to construct the WGBS library, as previously described (Zhang et al., 2017). RNA-seq were performed under the instruction of mRNA library construction kit (NEB).
Total RNA were extracted from approximately one million to two million cells using RNeasy Mini Kit (QIAGEN) according to the recommendation of manufacturer and then NEBNext® Poly(A) mRNA Magnetic Isolation Module was used to isolate mRNA from total RNA. Using mRNA as input, the first and second strand cDNAs were synthesized by NEBNext® RNA First Strand Synthesis Module and NEBNext® Ultra II Non-Directional RNA Second Strand Synthesis Module, respectively. Final libraries were prepared using KAPA Hyper Prep Kits (8 PCR cycles) and sequenced on HiSeq4000 platform. Following the manufacturer’s instructions, genomic DNA was extracted from stem cells using the DNeasy Blood & Tissue Kit (Qiagen). Remaining RNA was removed by treating with RNase A. Three replicated samples from each of these stem cells were used for library preparation to ensure repeatability of experiment. In short, 2 μg of genomic DNA spiked with 10 ng of lambda DNA were fragmented to about 300 bp with Covaris S220. Next, end repair and A-ligation were performed to the DNA fragments. Methylated Adaptor (NEB) was then ligated to the DNA fragments. In order to reach >99% bisulfite conversion, the adaptor-ligated DNA was treated twice using EZ-96 DNA Methylation-Direct™ MagPrep (Zymo Research). The resulting single-strand DNA fragments were amplified by 4 PCR cycles using the KAPA HiFi HotStart Uracil+ ReadyMix (2×). At last, the libraries were sequenced on HiSeq4000 platform to generate 150-bp paired-end reads.

tag: strain

tag: cell type

value: Embryonic stem cell

tag: passages


title: SUZ12_chiapet_rep5

city: Farmington

first: Chia-Lin

last: Wei

state: CT

address: 10 Discovery Drive

department: Genome Technologies

country: USA

institute: The Jackson Laboratory

description:
allPRC2_chiapet.narrowPeak.gz
allPRC2.cis.chiasig.sigf.interactions.gz

library_source: genomic

data_processing:
ChIA-PET data was processed by ChIA-PET Utilities (CPU) v0.0.1a (https://github.com/cheehongsg/CPU). CPU (options: tag -W) removed the adaptors, and extracted the intra-molecular and inter-molecular paired tags based on the linker sequence identified in the read and the remaining read-pairs without linker sequence. Tags (>=18bp) and reads without linker sequence were mapped to mouse genome (mm10) independently  using CPU (options: memaln -T 15), which utilized BWA (options: aln and mem) according to the tag/read length. CPU (options: pair) further separated the mapping results into uniquely-mapped, multiply-mapped, and unmapped classes with the pairing consideration. Next, deduplication of uniquely-mapped pair-end tags/reads arising from clonal PCR amplification was performed with CPU (options: dedup).
The non-redundant uniquely-mapped pair-end tags are merged with samtools and deduplicated with CPU (options: dedup) for all replicates of each factor separately, producing 3 factor-level (i.e. Suz12, Ezh2, Eed) alignment files. PRC2 binding peaks were called with MACS v2.1.1.20160309 (options: --keep-dup all --nomodel --extsize 250 -B –SPMR -g mm) where the 3 factor-level alignment files are specified as the treatment file and the combined 28 input files (23 E14_input, 2 CTCF ChIP input, 2 H3K27me3 ChIP input and RNAPolII_ChIP_r1_input) as the input control.
The non-redundant uniquely-mapped pair-end tags are merged with samtools and deduplicated with CPU (options: dedup) for all replicates of each factor separately, producing 3 factor-level (i.e. Suz12, Ezh2, Eed) alignment files. These 3 factor-level alignment files were merged using samtools and clustering of the pair-end tags were performed with CPU (options: cluster -M -B 1000 -v 3 -5 5,-20 -3 5,980 -g) to produce cis-interactions and trans-interactions. Statistical assessment of the cis-interaction significance was performed using ChiaSigScaled (https://github.com/cheehongsg/ChiaSigScaled ; options: -p -m 3000). Cis-interaction clusters with member size 3 and above (iPET 3+) and FDR<0.05 were reported, excluding any interaction should any of its anchors overlap the blacklist (see publication supplementary table).
Illumina RTA-1.12 to 1.18 software used for basecalling depending on when library is sequenced.
Genome_build: mm10

molecule: genomic DNA

source_name: Mouse embryonic stem cells

growth_protocol: ES E14 were cultured routinely under feeder-free conditions on 0.1% gelatin coated dishes in Knockout DMEM supplemented with 15% FBS, 2 mM L-glutamine , 0.1 mM non-essential amino acids, 100 U/ml Penicillin/Streptomycin, 0.05 mM 2-mercaptoethanol, 1,000 U/ml ESGRO mouse LIF Medium Supplement (Leukemia Inhibitory Factor) and maintained at 37ºC with 5% CO2.

extract_protocol:
Cells were lysed using SDS-based lysis buffer and sonicated, protein-DNA complexes were then isolated with antibody.
Immunoprecipitated protein-DNA complex were ligated with linkers. The proximity ligated chromatin complex was eluted with 1% SDS and de-crosslinked using proteinase K and purified. The purified fragments were tagmented using the Nextera DNA Sample Preparation Kit (Illumina). The linker ligated ChIA-PET constructs were selected using streptavidin magnetic beads. The magnetic beads were blocked with yeast tRNA prior to the selection. The streptavidin selected constructs were amplified with PCR and purified.

tag: cell line

value: E14 cell line

value: embryonic stem cells

tag: ip antibody

value: Suz12 (Abcam ab12073)


title: SUZ12_chiapet_rep6


title: O-GlcNAcseq_wt Drosophila larvae (biological rep 2)_150uM GalNAz media for 36h followed by 24h growth on DMSO media

city: Burnaby

first: David

last: Vocadlo

state: British Columbia

address: 8888 University Drive

department: Chemistry

country: Canada

institute: Simon Fraser University

description:
wt.r2_24
processed data file: TC-O-GlcNAc-seq-peaks.bed
O-GlcNAc-seq in wt Drosophila larvae (biological replicate 2) grown on 150uM GalNAz media for 36h followed by 24h growth on DMSO media

data_processing:
O-GlcNAc-seq: FASTQ sequencing files were aligned to a concatenated reference genome of D. melanogaster (dm3), S. cerevisiae (sacCer3), and the three synthetic gBlock fragments using the snap-aligner single command from SNAP version 1.0beta.18. The yeast chromosomes were re-name with the prefix "yeast" to avoid conflicts with the same chromosome names as Drosophila.
O-GlcNAc-seq: The resulting BAM-format alignment files were sorted, cleared of duplicates and indexed using the SAMtools commands sort, rmdup -s, and index, respectively, using SAMtools version 0.1.19-96b5f2294a
O-GlcNAc-seq: BDG files were generated from the BAM files using the command bedtools genomecov -ibam -bg command using bedtools v2.17.0. Yeast spike-in normalized BDG files were generated by multiplying by the fourth column, which specifies the sequencing coverage, of the BDG file by the normalization constants. These normalization constants were calculated by dividing the number of base pairs that aligned to the sacCer3 genome from the time point that had the least sacCer3 aligned base pairs by the number of base pairs that aligned to the sacCer3 reference genome from each time point. This was done within each replicate separately. The command awk -F'\t' '{$4=$4*a;print}' a=NF OFS='\t' <$.bdg> was used to do this, where NF is the normalization factor, which are specified in Table 1, and <$.bdg> is the appropriate time course input BDG file.
O-GlcNAc-seq: Peaks were called by calculating the coordinates that contained 5 times the average base pair sequencing coverage within each time course experiment. This was done for the no feed controls as well. The coordinates of base pairs that satisfied this requirement were then merged if they were within 30 base pairs of each other. This was done with the command awk '{ if( $4 > 5X) print}' <$.bdg> | cut -f 1,2,3 | bedtools merge -d 30, where 5X indicates 5 times the average base pair sequencing coverage within each time course experiment and <$.bdg> indicates the appropriate time course BDG file. For each time point, the peaks that occurred from the no feed controls were eliminated from the time course experiment peaks using the bedtools intersect -v command. This effectively removed false positives from the analysis. Peaks resulting from the intersection of replicate time points were kept using the regular bedtools intersect command. Peaks at time point 0 for WT and OGA-null were then intersected using the bedtools intersect command. Peaks that were less than 20 base pairs were then expanded from their midpoint by 10 base pairs on each side to a peak length of 20 base pairs. This strategy resulted in 1883 peaks and enabled focus on coordinates that consistently contained O-GlcNAz peaks within both WT and OGA-null and each replicate.
O-GlcNAc-seq pilot study: FASTQ sequencing files were aligned to the D. melanogaster (dm3) genome using the snap-aligner single command from SNAP version 1.0beta.18.
O-GlcNAc-seq pilot study: The resulting BAM-format alignment files were sorted, cleared of duplicates and indexed using the SAMtools commands sort, rmdup -s, and index, respectively, using SAMtools version 0.1.19-96b5f2294a
O-GlcNAc-seq pilot study: BDG files were generated from the BAM files using the command bedtools genomecov -ibam -bg command using bedtools v2.17.0.
OGA ChIP-seq: Fastq files were aligned to the dm3 genome the Burrows–Wheeler Aligner version 0.7.5a-r405 algorithm. The resulting BAM-format alignment files were sorted, cleared of duplicates and indexed using the SAMtools commands sort, rmdup -s, and index, respectively, using SAMtools version 0.1.19-96b5f2294a.
OGA ChIP-seq: BDG files were generated from the BAM files using the command bedtools genomecov -ibam -bg command using bedtools v2.17.0.
OGA ChIP-seq: Peaks were called by calculating the coordinates that contained 5 times the average base pair sequencing coverage within both OGA ChIP-seq experiments (WT and OGA-null). Peaks within the OGA-null experiment were considered false positives and were subtracted from the peaks called in the WT experiment using the bedtools intersect -v command to yield the final OGA ChIP-seq peaks.
Genome_build: dm3, sacCer3 and synthetic DNA probes.
Supplementary_files_format_and_content: Bdg files and bed files containing ChIP-seq and O-GlcNAc-seq loci. Bed files of O-GlcNAc-seq data contain normalized sequencing depth at each O-GlcNAc bearing locus accross time points for WT and OGA-null replicates.

organism: Drosophila melanogaster

source_name: O-GlcNAc-seq_wt larvae_150uM GalNAz media for 36h followed by 24h growth on DMSO media

extract_protocol:
The larvae were collected and rinsed with PBST (PBS + 0.1% Triton X-100) three times to remove adhering corn food. One volume of hexanes (a mixture of isomers) was equilibrated for 30 min against 0.175 vol of 37% formaldehyde and 0.130 vol of 10X PBS (1.37 M NaCl, 27 mM KCl, 43 mM Na2HPO4 and 14 mM KH2PO4), pH 7.5, to make the mixture 5% formaldehyde and 1X PBS. Only the upper organic phase was used for crosslinking. Larvae were fixed in 10 ml of buffered 5% formaldehyde/hexanes per gram of larvae by vigorous shaking for 5 min at room temperature. The larvae were allowed to settle, and the formaldehyde/hexanes solution was removed by centrifugation (3,000 x g for 5 min at RT). The larvae were washed twice in a solution containing 1X PBS and 0.5% Triton X- 100 (0.5% PBST), using the five volumes as used for fixing. They were then stored at -80°C. Chromatin was purified by quickly thawing frozen larvae and resuspending them in buffer A [0.3 M sucrose, 15 mM NaCl, 5 mM MgCl2, 15 mM Tris pH 7.5, 60 mM KCl, 0.1 mM EDTA, 0.1 mM EGTA, 0.5 mM dithiothreitol (DTT) and 1 mM phenylmethylsulfonyl fluoride (PMSF)]. They were homogenized with 20-25 strokes of a hand-held type B Dounce homogenizer. Triton X-100 was added to 0.3%, and the homogenate was centrifuged (2,000 x g for 15 min at 4°C). The pellet was resuspended in buffer B (100 mM NaCl, 10 mM Tris pH 7.9, 1 mM EDTA, 0.1% v/v NP-40 and 1 mM PMSF) and homogenized with ~5 strokes of a hand-held type B Dounce homogenizer. The homogenate was then sheared by 20 cycles (20 × 20 s on and 50 s off cycles, 40% power settings) through a sonicator (Sonic Dismembrator Model 500, Fisher Scientific) to an average size of ~200 to 700 bp chromatin fragments. After sonication, debris was removed by centrifugation at 4°C for 10 min at 13,000 r.p.m., and an equal amount of 6 M urea was added to the solution and then incubated for 10 min at 4°C on a rotating wheel. The soluble chromatin was dialyzed using a membrane with a molecular weight cut-off of 3.5 kDa, at 4°C against 2 L dialysis buffer (10 mM Tris-HCl pH 8.0, 1 mM EDTA, 0.5 mM EGTA, 4% glycerol) overnight. Insoluble debris was removed by quick centrifugation (7,500 r.p.m., 2 min). The chromatin solution was pre-cleared with 100 μl Streptavidin-agarose slurry (Sigma) beads for O-GlcNAz modified or vehicle-only chromatin separately and incubated for 1 hour at 4°C on a rotating wheel. The pre-cleared chromatin was aliquoted after centrifugation at 4°C for 2 min at 7,500 r.p.m., snap-frozen in liquid nitrogen and stored at −80°C for future use. For click chemistry, 20-50 μg chromatin DNA was incubated with iodoacetamide (IAA) to a final concentration of 15 mM, agitate mildly for 30 min at RT then added DMSO solution of dibenzylcyclooctyne-S-S-PEG3-Biotin (DBCO-S-S-PEG3-Biotin, Jena Bioscience GmbH) to a final concentration of 40 μM. The samples were protected from light and agitated mildly for 1 hour at RT. The unreacted probe was filtered off by the Amicon Ultra-0.5 mL centrifugal filter (15K cut-off) (EMD Millipore). Biotinylated-probe-chromatin complexes were captured by incubation with 50 μl Streptavidin magnetic beads (NEB) at 4°C for 2 hours. Beads were washed with 0.5 ml of the following buffers: three washes with low-salt wash buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl pH 8.0, 150 mM NaCl), followed by three washes with high-salt wash buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl pH 8.0, 500 mM NaCl), then three washes with lithium wash buffer (0.25 M LiCl, 1% NP-40, 1% sodium deoxycholate, 1 mM EDTA, 10 mM Tris-HCl pH 8.0); then two washes with TE (10 mM Tris-HCl pH 8.0, 1 mM EDTA). Beads were resuspended in 100 μl TE containing 0.5% SDS, 15 mM DTT and incubated with 0.15 mg/ml proteinase K at 55°C for 3-4 hours. DNA-protein complex was de-crosslinked by incubating overnight at 65°C (not more than 15 hours). ChIP-DNA was purified with QIAquick PCR Purification Kit and stored at -20°C.
The libraries were prepared according to the manufacturer’s instructions using the NEBNext kit (E6200). Briefly, DNA was fragmented by sonication to a maximum of 300 bp. Next, the ends of the fragments were repaired with a combination of fill-in reactions and exonuclease activity to produce blunt ends that were then tailed with an A-base. Illumina-specific adaptors were ligated followed by removal of unligated adaptors using AMpure XP beads (Beckman Coulter). Finally, a PCR with 12-15 cycles for both kits was performed to enrich final adaptor-ligated fragments. Quality and quantity were assessed on High Sensitivity dsDNA Agilent Bioanalyzer Chips and Quibit. WT and OGA-null O-GlcNAc-seq libraries and OGA ChIP-seq libraries were sequenced on the Illumina NextSeq 500 High Output (75 cycles, 400M reads) platform. The additional replicates for both WT and OGA-null DMSO control from an earlier pilot study were sequenced on the MiSeq platform, using v3, 150-cycle reagent kits (Illumina).

tag: strain background

value: Oregon R

tag: genotype/variation

value: wild type

tag: stage/tissue

value: larvae

tag: chip strategy

value: GalNAz feeding, strain-promoted click reaction and streptavidin purification


title: Glia cells at P8 replicate 2 [Glia_P8_r2]

city: Ashburn

first: Ken

last: Sugino

state: VA

address: 19700 Helix Dr

institute: Janelia Research Campus

data_processing:
Basecalls performed using CASAVA
Reads were mapped to mm10 genome using STAR v2.4.0i with parameters  --chimSegmentMin 15 --outFilterMismatchNmax 3.
Mapped reads were processed with featureCounts with gencode.vM15 annotation to obtain read counts for genes
Genome_build: mm10
Supplementary_files_format_and_content: tab deliminated file including read counts

source_name: Glia cells at P8

extract_protocol:
Mouse cochlea or inner ear was dissected, digested with pronase for 30-45 mins at RT, triturated and tdtomato labeled cells were sorted manually. RNA was extracted using PicoPure kit (life technologies, KIT0204).
Extracted RNA was amplified using Ovation RNA-Seq System V2 (NuGEN, #7102-32). 1.8~2.25 ug of the amplified material was used for library construction using Ovation Rapid DR multiplex system (NuGEN, #0319-32).

tag: age

tag: tissue

value: Cochlear

value: Glia

tag: number of cells


title: O-GlcNAcseq_wt Drosophila larvae (biological rep 2)_150uM GalNAz media for 36h followed by 20h growth on DMSO media

description:
wt.r2_20
processed data file: TC-O-GlcNAc-seq-peaks.bed
O-GlcNAc-seq in wt Drosophila larvae (biological replicate 2) grown on 150uM GalNAz media for 36h followed by 20h growth on DMSO media

source_name: O-GlcNAc-seq_wt larvae_150uM GalNAz media for 36h followed by 20h growth on DMSO media


title: SUZ12_chiapet_rep10


title: O-GlcNAcseq_wt Drosophila larvae (biological rep 2)_150uM GalNAz media for 36h followed by 16h growth on DMSO media

description:
wt.r2_16
processed data file: TC-O-GlcNAc-seq-peaks.bed
O-GlcNAc-seq in wt Drosophila larvae (biological replicate 2) grown on 150uM GalNAz media for 36h followed by 16h growth on DMSO media

source_name: O-GlcNAc-seq_wt larvae_150uM GalNAz media for 36h followed by 16h growth on DMSO media


title: O-GlcNAcseq_wt Drosophila larvae (biological rep 2)_150uM GalNAz media for 36h followed by 12h growth on DMSO media

description:
wt.r2_12
processed data file: TC-O-GlcNAc-seq-peaks.bed
O-GlcNAc-seq in wt Drosophila larvae (biological replicate 2) grown on 150uM GalNAz media for 36h followed by 12h growth on DMSO media

source_name: O-GlcNAc-seq_wt larvae_150uM GalNAz media for 36h followed by 12h growth on DMSO media


title: O-GlcNAcseq_wt Drosophila larvae (biological rep 2)_150uM GalNAz media for 36h followed by 8h growth on DMSO media

description:
wt.r2_8
processed data file: TC-O-GlcNAc-seq-peaks.bed
O-GlcNAc-seq in wt Drosophila larvae (biological replicate 2) grown on 150uM GalNAz media for 36h followed by 8h growth on DMSO media

source_name: O-GlcNAc-seq_wt larvae_150uM GalNAz media for 36h followed by 8h growth on DMSO media


title: Glia cells at P8 replicate 1 [Glia_P8_r1]


title: HC cells at P12 replicate 3 [HC_P12_r3]

source_name: HC cells at P12

value: inner ear (both cochlear and vestibular organs)

value: HC


title: O-GlcNAcseq_wt Drosophila larvae (biological rep 2)_150uM GalNAz media for 36h followed by 4h growth on DMSO media

description:
wt.r2_4
processed data file: TC-O-GlcNAc-seq-peaks.bed
O-GlcNAc-seq in wt Drosophila larvae (biological replicate 2) grown on 150uM GalNAz media for 36h followed by 4h growth on DMSO media

source_name: O-GlcNAc-seq_wt larvae_150uM GalNAz media for 36h followed by 4h growth on DMSO media


title: O-GlcNAcseq_wt Drosophila larvae (biological rep 1)_DMSO media for 36h

description:
wt.r1_no-feed
processed data file: TC-O-GlcNAc-seq-peaks.bed
O-GlcNAc-seq in wt Drosophila larvae (biological replicate 1) grown on DMSO media for 36h

source_name: O-GlcNAc-seq_wt larvae_DMSO media for 36h


title: HC cells at P12 replicate 2 [HC_P12_r2]


title: O-GlcNAcseq_wt Drosophila larvae (biological rep 2)_150uM GalNAz media for 36h followed by 0h growth on DMSO media

description:
wt.r2_0
processed data file: TC-O-GlcNAc-seq-peaks.bed
O-GlcNAc-seq in wt Drosophila larvae (biological replicate 2) grown on 150uM GalNAz media for 36h followed by 0h growth on DMSO media

source_name: O-GlcNAc-seq_wt larvae_150uM GalNAz media for 36h followed by 0h growth on DMSO media


title: Raly_ChIPSeq3

city: Los Angeles

first: Zhengyi

last: Zhang

address: Westwood

institute: UCLA

data_processing:
RNA-seq reads were aligned with TopHatv2.0.2 to the mouse genome, version mm9. Transcripts were assessed and quantities were determined by Cufflinks v2.0.2, using a GTF file based on Ensembl mouse NCBI37. Comparison expression levels were made using FPKM values using Cuffdiff from the Cufflinks package 26.
For ChIP-seq, Bowtie2 was used for alignment and we identified Raly enriched peaks in using by Homer findPeaks with FDR < 0.01. The called peaks were subsequently used for identifying the motifs enrichment by PscanChIP.
For ATAC-seq, reads were mapped to the mouse genome (NCBI37/mm9) using Bowtie2 and were removed from the subsequent analysis if they were duplicated, mapped to mitochondrial genome, or aligned to unmapped contiguous sequences. Peak calling was performed using MACS2. The reads were converted to reads per thousand base pairs peak per million mapped reads (RPKM) by dividing by the total number of reads per sample. The average RPKM from four replicates was used to quantify the accessibility across all called peaks.
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited text files include RPKM values for each Sample. Bedgraph filescontained ChIP-seq peaks or ATAC-seq peaks.

source_name: Hepa1-6 cells

growth_protocol: Hepa1-6 cells were originally obtained from ATCC and cultured in DMEM medium with 10% FBS.

extract_protocol:
RNA from cells or tissues was harvested using Trizol reagent following purinfication by Qiagen Rneasy microKit.  For ChIP-seq, lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody. ATAC-seq was optimized in liver after several modifications from original Buenstero protocol (Curr Protoc Mol Biol. 2015)
Libraries for RNA-Seq were prepared with KAPA Stranded RNA-Seq Kit on RNA isolated from livers of chow diet feeding mice with AAV-GFP or AAV-Cre transduction. ChIP-Seq libraries were prepared using the Kapa LTP Library Preparation Kit (Kapa Biosystems). ATAC-Seq libraries were prepared using the Nextera Tn5 Transposase and DNA library preparation kit (Illumina)

value: Hepa1-6 cells

tag: chip antibody

value: Raly (Abcam, Ab170105)


title: Glia cells at P8 replicate 3 [Glia_P8_r3]


title: SUZ12_chiapet_rep4


title: O-GlcNAcseq_wt Drosophila larvae (biological rep 1)_150uM GalNAz media for 36h followed by 36h growth on DMSO media

description:
wt.r1_36
processed data file: TC-O-GlcNAc-seq-peaks.bed
O-GlcNAc-seq in wt Drosophila larvae (biological replicate 1) grown on 150uM GalNAz media for 36h followed by 36h growth on DMSO media


title: HC cells at P12 replicate 1 [HC_P12_r1]


title: O-GlcNAcseq_wt Drosophila larvae (biological rep 1)_150uM GalNAz media for 36h followed by 24h growth on DMSO media

description:
wt.r1_24
processed data file: TC-O-GlcNAc-seq-peaks.bed
O-GlcNAc-seq in wt Drosophila larvae (biological replicate 1) grown on 150uM GalNAz media for 36h followed by 24h growth on DMSO media


title: SGN cells at P30 replicate 3 [SGN_P30_r3]

source_name: SGN cells at P30

value: spiral ganglion neurons (SGNs)


title: Raly_ChIPSeq2

treatment_protocol: RNA isolated from livers of chow diet feeding mice with AAV-GFP or AAV-Cre transduction.


title: O-GlcNAcseq_wt Drosophila larvae (biological rep 1)_150uM GalNAz media for 36h followed by 20h growth on DMSO media

description:
wt.r1_20
processed data file: TC-O-GlcNAc-seq-peaks.bed
O-GlcNAc-seq in wt Drosophila larvae (biological replicate 1) grown on 150uM GalNAz media for 36h followed by 20h growth on DMSO media


title: SUZ12_chiapet_rep2


title: Raly_ChIPSeq4


title: SGN cells at P30 replicate 2 [SGN_P30_r2]


title: Raly_ChIPSeq1


title: O-GlcNAcseq_wt Drosophila larvae (biological rep 1)_150uM GalNAz media for 36h followed by 16h growth on DMSO media

description:
wt.r1_16
processed data file: TC-O-GlcNAc-seq-peaks.bed
O-GlcNAc-seq in wt Drosophila larvae (biological replicate 1) grown on 150uM GalNAz media for 36h followed by 16h growth on DMSO media


title: SGN cells at P30 replicate 1 [SGN_P30_r1]


title: O-GlcNAcseq_wt Drosophila larvae (biological rep 1)_150uM GalNAz media for 36h followed by 12h growth on DMSO media

description:
wt.r1_12
processed data file: TC-O-GlcNAc-seq-peaks.bed
O-GlcNAc-seq in wt Drosophila larvae (biological replicate 1) grown on 150uM GalNAz media for 36h followed by 12h growth on DMSO media


title: RNA-seq_KO_Rep3

source_name: Liver

tag: genotype

value: RALY-KO


title: SGN cells at P14 replicate 3 [SGN_P14_r3]

source_name: SGN cells at P14


title: MG132_24HR_rep2

type: RNA

city: RTP

first: Trevor

last: Archer

address: 111 TW Alexander

institute: NIH

description: Gene expression after 24 H MG132 treatment

hyb_protocol: For each sample, 1.65ug of Cy3 labeled cRNAs were fragmented and hybridized for 17 hours in a rotating hybridization oven.

scan_protocol: Slides were washed and then scanned with an Agilent Scanner.

data_processing: Data was obtained using the Agilent Feature Extraction software (v9.5), using the 1-color defaults for all parameters.

organism: Homo sapiens

source_name: MCF7 cell with 24 hr MG132 treatment

label_protocol: Starting with 500ng of total RNA, Cy3 labeled cRNA was produced according to manufacturer’s protocol.

growth_protocol: MCF-7 cells were grown in a humidified incubator at 37°C with 5% CO2 in MEM, supplemented with 10% fetal bovine serum 100 μg/mL penicillin/streptomycin, 2 mM glutamine and 10 mM HEPES. For MG132 treatment, cells were seeded overnight in phenol red-free MEM supplemented with 5% charcoal-stripped calf serum and 2 mM glutamate. Next day, cells were treated with, vehicle (DMSO) or 1uM MG132 for 4 or 24 hours.

extract_protocol: Total RNA was collected using Applied Biosystem mirVana RNA Isolation Kit (AM1560, suggested by Agilent miRNA array protocol)

treatment_protocol: Total RNA was collected from MCF7 cells cultured in phenol red free MEM, supplemented with charcoal stripped serum and containing  0.1% DMSO or 1 uM MG132 for 4 or 24H.  Cells were incubated for 4 or 24 hours at 37 ºC in a humidified incubator with 5% CO2.

value: breast cancer cells

tag: treatment

value: with 24 hr MG132 treatment


title: MG132_24HR_rep1


title: MG132_4HR_rep2

description: Gene expression after 4 H MG132 treatment

source_name: MCF7 cell with 4 hr MG132 treatment

value: with 4 hr MG132 treatment


title: O-GlcNAcseq_wt Drosophila larvae (biological rep 1)_150uM GalNAz media for 36h followed by 8h growth on DMSO media

description:
wt.r1_8
processed data file: TC-O-GlcNAc-seq-peaks.bed
O-GlcNAc-seq in wt Drosophila larvae (biological replicate 1) grown on 150uM GalNAz media for 36h followed by 8h growth on DMSO media


title: MG132_4HR_rep3


title: MG132_24HR_rep3


title: SGN cells at P14 replicate 2 [SGN_P14_r2]


title: RNA-seq_KO_Rep1


title: O-GlcNAcseq_wt Drosophila larvae (biological rep 1)_150uM GalNAz media for 36h followed by 4h growth on DMSO media

description:
wt.r1_4
processed data file: TC-O-GlcNAc-seq-peaks.bed
O-GlcNAc-seq in wt Drosophila larvae (biological replicate 1) grown on 150uM GalNAz media for 36h followed by 4h growth on DMSO media


title: O-GlcNAcseq_wt Drosophila larvae (biological rep 1)_150uM GalNAz media for 36h followed by 0h growth on DMSO media

description:
wt.r1_0
processed data file: TC-O-GlcNAc-seq-peaks.bed
O-GlcNAc-seq in wt Drosophila larvae (biological replicate 1) grown on 150uM GalNAz media for 36h followed by 0h growth on DMSO media


title: RNA-seq_KO_Rep2


title: SGN cells at P14 replicate 1 [SGN_P14_r1]


title: MG132_4HR_rep1


title: RNA-seq_WT_Rep2


title: SGN cells at P8 replicate 2 [SGN_P8_r2]

source_name: SGN cells at P8


title: RNA-seq_WT_Rep3


title: SGN cells at P8 replicate 3 [SGN_P8_r3]


title: RNA-seq_WT_Rep1


title: SGN cells at P8 replicate 1 [SGN_P8_r1]


title: DMSO_CTL_rep3

description: Gene expression control

source_name: MCF7 cell controls

value: control


title: DMSO_CTL_rep2

description: Gene expression control


title: highfat_lgRNA3

city: West Lafayette

first: Theresa

middle: M

last: Casey

state: Indiana

address: 175 S. University Street

department: Animal Sciences

institute: Purdue University

description:
highfat_3
highfat diet
70_accepted_hits.bam

data_processing:
The the quality of the raw sequence reads were checked by fastqc; adapter sequences were removed and quality trimmed using trimmomatic; ribosomal RNA contamination was checked with by bowtie2; other possible contaminants were checke by blasting sequences using blast in the NCBI website.
Map reads to reference genome by Tophat
Run cufflinks to assemble FPKM transcription level
Run HTSeq to get counts based on reference genome
Differential gene expression analysis using DESeq2
Supplementary_files_format_and_content: FPKM

source_name: milk fat

extract_protocol:
Milk fat layer was isolated by centrifugation (1000-g for 5 min) at 4 °C from lactation day 10 samples, and transferred to a new microfuge.  An equal volume of PBS was added and mixed with milk fat by vortexing. Milk-fat PBS mixture was centrifuged for 5 min in 4 °C at 3000 rpm to remove cells and other debris that may have been trapped in fat. The miRNeasy Mini Kit (cat. No. 217004, company: QIAGEN) was used to isolate total RNA following manufacturer’s directions using these specifications; Lysis Reagent was added to sample at a 1:3.5 ratio (200ul milk sample to 700ul QIAzol) followed by disruption and homogenization using vortex. Total RNA was eluted from final column with 20 µl of RNase-Free water and stored at -80° C, until sequencing.
TruSeq Stranded Total RNA Library Prep Kit

treatment_protocol: Nine 4-week old female ICR (CD1; Envigo) mice were matched by weight and divided into two treatment groups: control (n=5) and high fat (HF; n=4) diet. Mice were exposed to a 12h light: 12h dark cycle throughout entire study.  For the 4 weeks prior to mating, female mice were housed in pairs within treatment and fed a high fat diet (HF; Research Diets #D12492, 60% of total kcal energy is fat and 7% of total kcal is sucrose; 5.24kcal/gm; Brunswick, NJ) or control diet that was matched for sucrose (C; Research Diets #D12450J, 10% of total kcal energy is fat and  7% of total kcal is sucrose; 3.85 kcal/gm). Dams remained on respective diets throughout pregnancy and lactation. Milk was collected from each dam on post-natal day 10.

value: ICR

value: primiparous

value: lactation day 10

tag: Sex

value: female

tag: biosample

tag: bioproject


title: highfat_lgRNA4

description:
highfat_4
highfat diet
71_accepted_hits.bam

tag: strain


title: SGN cells at P1 replicate 3 [SGN_P1_r3]

source_name: SGN cells at P1

tag: cell type


title: highfat_lgRNA2

description:
highfat_2
highfat diet
68_accepted_hits.bam


title: SGN cells at P1 replicate 2 [SGN_P1_r2]


title: water column RNA_ETSP_Sample10_30m

type: mixed

city: Princeton

first: Bess

middle: B

last: Ward

state: NJ

address: Washington Road

department: Geosciences

institute: Princeton University

description: PCR fragment amplified from total cDNA prepared from RNA extract

hyb_protocol: Samples were hybridized to duplicate arrays by overnight incubation at 64°C and washed.

scan_protocol: The arrays were scanned with a laser scanner (Molecular Devices 4300) Images were analyzed with Gene Pix Pro 6.0 software (Molecular Devices)

data_processing: Quality control was employed to remove noise by eliminating features in which the Cy3 signal was not at least twice the value of the control probes.

molecule: other

organism: synthetic construct

source_name: Universal Internal Standard + 70-mer

label_protocol: PCR products derived from both DNA and cDNA were labeled with amino-allyl-dUTP (Ambion) during linear amplification using random octamers and a Klenow polymerase (Applied Biosystems). The reaction contained 3.96 mM d(AGC)TP, 0.44 mM dTTP, and 4.84 mM dUaa and was amplified for 3 h at 37°C. The Klenow product was purified and conjugated with Cy3. The Cy3-labelled target (200 ng) was combined with 2x hybridization buffer (1x final concentration; Agilent) and 0.25 pmol of a Cy5-labelled complementary 20-mer standard oligonucleotide and incubated at 95°C for 5 min before being cooled to room temperature.

extract_protocol: DNA and RNA were extracted simultaneously from the same filters using the AllPrep DNA/RNA Mini Kit (Qiagen Sciences, Maryland, USA) with slight modifications (as in Rees et al. 2016).

tag: sample type

value: 20-mer DNA oligo

organism: seawater metagenome

source_name: seawater

tag: location

value: Oxygen Minimum Zone nitrogen cycling experiments in the Eastern Tropical South Pacific Ocean

value: PCR fragment


title: water column RNA_ETSP_Sample11_120m


title: water column RNA_ETSP_Sample19_145m


title: WT2

city: Shanghai

first: Luo

last: Guo

address: 83# fenyang road, 9# building, room 613

institute: Fudan University

data_processing:
Sequencing results were analyzed using Tophat2 and are expressed in fragments per kilobase of transcript per million mapped reads (FPKM).
differetailly expressed genes were called by cuffdiff
Genome_build: mm10
Supplementary_files_format_and_content: excel file with FPKM values, p value, adjusted p value and fold changes for wild-type and knockout groups

source_name: Laryngeal tissue

extract_protocol:
Total RNA was extracted from mouse laryngeal tissues using TRIzol reagent (Life Technologies; Carlsbad, CA, USA). The RNA quantity and integrity were analyzed with an Agilent 2100 Bioanalyzer (Santa Clara, CA, USA).
PolyA mRNA purification, fragmentation, cDNA synthesis, reverse transcription, and amplification were performed using the Illumina TruSeq RNA Sample Preparation Kit. cDNA libraries were sequenced using the Illumina HiSeq 2000 platform.

value: larynx

value: wild type


title: WT3


title: highfat_lgRNA1

description:
highfat_1
highfat diet
62_accepted_hits.bam


title: water column RNA_ETSP_Sample9_190m


title: SGN cells at P1 replicate 1 [SGN_P1_r1]

value: Cochlear


title: KO4


title: WT1


title: control_lgRNA4

description:
control_4
control diet
73_accepted_hits.bam


title: water column RNA_ETSP_Sample18_5m


title: KO3


title: control_lgRNA5

description:
control_5
control diet
74_accepted_hits.bam


title: SGN cells at E15.5 replicate 2 [SGN_E15.5_r2]

source_name: SGN cells at E15.5


title: water column RNA_ETSP_Sample17_100m


title: control_lgRNA2

description:
control_2
control diet
64_accepted_hits.bam


title: water column RNA_ETSP_Sample16_10m


title: SGN cells at E15.5 replicate 1 [SGN_E15.5_r1]


title: DMSO_CTL_rep1

description: Gene expression control

tag: cell line


title: KO2


title: water column RNA_ETSP_Sample15_130m


title: KO1


title: water column RNA_ETSP_Sample1_250m


title: control_lgRNA1

description:
control_1
control diet
63_accepted_hits.bam


title: B6NJ_si_chr7_F4_RNA-seq_rep2

data_processing:
Raw reads were trimmed with Trim Galore v0.4.0 (options: -q 30 -e .20 --length 15). Trimmed reads were mapped to mm10 genome with hisat2 v2.1.0 (options: --dta-cufflinks -x).
Genes expression were computed by HTSeq v0.6.1 (options: -s=reverse –nonunique=all) for all gene models in gencode.vm14.grcm38 excluding those known as not transcribed by RNA polymerase II like pseudogenes, snoRNA, snRNA, miscRNA and riboRNA.
Illumina RTA-1.12 to 1.18 software used for basecalling depending on when library is sequenced.
Genome_build: mm10

molecule: polyA RNA

source_name: Mouse embryonic stem cells

growth_protocol: ES B6NJ and its derivative KO lines were cultured rountined on irradiated MEF-feeder layer with high glucose DMEM supplemented with 15% ES Cell FBS, 1X non-essential amino acids, 1X Glutamax, 100 U/ml Penicillin/Streptomycin, 1mM sodium pyruvate, 0.1mM 2-mercaptoethanol and further supplemented with PD0325901 and CHIR99021.

extract_protocol:
Total RNA was extracted from cell pellets using Trizol reagent followed by a purification with Qiagen RNeasy column.
RNA-seq libraries were prepared using illumina Truseq mRNA stranded protocol following manufacturer's instructions.

value: B6NJ derived KO cells

value: knock-out targeted region chr7:143440438-143450716 on B6NJ

tag: clone

value: F4 (clone of the generated knockout)


title: CrePos_RM650

city: Durham

first: Yen-Rei

middle: Andrea

last: Yu

state: NC

address: 40 Duke Medicine Circle

department: Medicine

institute: Duke University School of Medicine

data_processing:
The sequencing reads were trimmed to remove the Illumina adapters and any low-quality base at the ends (the Phred quality score less than 30) by using Cutadapt (v1.12)
The pair end reads for each sample were successfully aligned to the mouse reference transcriptomes, GRCm38, using Tophat (v2.1.1)
The read-count-per-gene measurements for each sample were performed by htseq-count (HTSeq v0.6.0)
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files

source_name: Hif1α Δ/Δ

growth_protocol: Primary cells

extract_protocol:
Libraries were prepared using SMARTer@ Stranded Total RNA-seq Kit - Pico Input Mammalian library Prep kit per the manufacturer’s protocol. Library qualities and quantities were verified using Agilent Bioanalyzer system (Agilent, Santa Clara, CA) and Qubit fluorometric quantification (Thermo Fisher Scientific, Carlsbad, CA).
SMARTer@ Stranded Total RNA-seq Kit - Pico Input Mammalian library Prep kit

treatment_protocol: Animals were exposed to hypoxia plus weekly dose of SU5416 for 3 weeks. Non-classical monocytes and pulmonry intersitial macropahges (~250 per sample were sorted directly in lysis solution).

tag: cells

value: Primary Cells

value: Hypoxia + Su5416

value: Non-classical Monocytes


title: B6NJ_si_chr7_F4_RNA-seq_rep3


title: CrePos_RM661


title: ATAC-seq_KO_Rep4

value: RALY-KO


title: SGN cells at E15.5 replicate 3 [SGN_E15.5_r3]

value: spiral ganglion neurons (SGNs)


title: water column RNA_ETSP_Sample6_305m


title: ATAC-seq_KO_Rep3


title: water column RNA_ETSP_Sample7_270m


title: B6NJ_si_chr7_D4_RNA-seq_rep3

value: D4 (clone of the generated knockout)


title: CreNeg_RM659

source_name: Hif1α flox/lox


title: B6NJ_si_chr7_F4_RNA-seq_rep1


title: ATAC-seq_KO_Rep2


title: water column RNA_ETSP_Sample5_75m


title: ATAC-seq_KO_Rep1


title: B6NJ_si_chr7_D4_RNA-seq_rep2


title: CreNeg_RM657


title: ATAC-seq_WT_Rep4


title: B6NJ_si_chr7_D4_RNA-seq_rep1


title: water column RNA_ETSP_Sample3_260m


title: water column RNA_ETSP_Sample4_220m


title: B6NJ_si_chr9_G9_RNA-seq_rep3

value: knock-out targeted region chr9:37451506-37461721 on B6NJ

value: G9 (clone of the generated knockout)


title: CreNeg_RM648


title: water column RNA_ETSP_Sample1_350m

value: 20-mer DNA oligo


title: ATAC-seq_WT_Rep3


title: ATAC-seq_WT_Rep2


title: CrePos_RM649


title: CrePos_IM650

value: Intersitial Macrophages


title: ATAC-seq_WT_Rep1


title: water column RNA_ETSP_Sample2_300m

value: Oxygen Minimum Zone nitrogen cycling experiments in the Eastern Tropical South Pacific Ocean

value: PCR fragment


title: B6NJ_si_chr9_G9_RNA-seq_rep2


title: SUZ12_chiapet_rep1

description:
allPRC2_chiapet.narrowPeak.gz
allPRC2.cis.chiasig.sigf.interactions.gz

value: E14 cell line

value: embryonic stem cells

tag: ip antibody

value: Suz12 (Abcam ab12073)


title: CrePos_IM649


title: water column DNA_ETSP_Sample19_145m

description: PCR fragment amplified from total DNA extract


title: E14_Input_9

data_processing:
Raw reads were quality trimmed along with the adapter using cutadapt v1.14  (options: -e 0.2 -a AGATCGGAAGAGC --minimum-length 20 --trim-n -n 3). The trimmed-reads were mapped on the mm10 genome using BWA v0.7.12  (options: aln –l 25 followed by samse). Only the de-duplicated uniquely mapped reads were used for downstream analysis.
Illumina RTA-1.12 to 1.18 software used for basecalling depending on when library is sequenced.
Genome_build: mm10

extract_protocol:
Cells were lysed using SDS-based lysis buffer and sonicated, protein-DNA complexes were then isolated with antibody.
Immunoprecipitated protein-DNA complex were ligated with illumina-compatible adaptors, amplified by PCR and sequenced.


title: B6NJ_si_chr9_G9_RNA-seq_rep1

value: B6NJ derived KO cells


title: water column DNA_ETSP_Sample11_120m


title: CreNeg_IM660


title: B6NJ_si_chr9_F1_RNA-seq_rep2

value: F1 (clone of the generated knockout)


title: B6NJ_si_chr9_F1_RNA-seq_rep1


title: water column DNA_ETSP_Sample10_30m


title: E14_Input_4


title: B6NJ_RNA-seq_rep3

value: B6NJ primary cells


title: water column DNA_ETSP_Sample9_190m


title: CTCF_ChIP_rep2_input

data_processing:
Raw reads were quality trimmed along with the adapter using cutadapt v1.14  (options: -e 0.2 -a AGATCGGAAGAGC --minimum-length 20 --trim-n -n 3). The trimmed-reads were mapped on the mm10 genome using BWA v0.7.12  (options: aln –l 25 followed by samse). Only the de-duplicated uniquely mapped reads were used for downstream analysis.
Peak calling was performed on the pair of ChIP and input dataset with MACS v2.1.1.20160309 (options: --nomodel --extsize 250 -B –SPMR -g mm ; broad peak additional options: --broad --broad-cutoff 0.1). bedGraphToBigWig from kentUtils was used to convert MACS2 generated bedgraph to bigWig format. Fold enrichment was computed with MACS2 bdgcmp and the output bedgraph file was converted to bigWig with bedGraphToBigWig.
Illumina RTA-1.12 to 1.18 software used for basecalling depending on when library is sequenced.
Genome_build: mm10


title: CreNeg_IM648

value: Primary Cells

value: Hypoxia + Su5416


title: CTCF_ChIP_rep2

description:
CTCF_ChIP_treat.bigWig
CTCF_ChIP_foldEnrich.bigWig
CTCF_ChIP.narrowPeak.gz

value: CTCF (Abcam ab70303)


title: CrePos_IM661


title: water column DNA_ETSP_Sample17_100m


title: B6NJ_RNA-seq_rep1


title: H3K27me3_ChIP_rep1_input


title: water column DNA_ETSP_Sample18_5m


title: SL.ESCs.r3

description: polyA RNA

source_name: Embryonic stem cell

value: Embryonic stem cell

tag: passages


title: IL-17A+ GDT

city: Saint Louis

first: Yee-shiuan

last: Chen

state: MO

address: 660 S Euclid Ave

department: Department of Medicine

institute: Washington University School of Medicine

description: Sorted IL-17A producing gamma-delta T cells

data_processing:
Basecalling was performed using HiSeq Control Software
Sequence alignment to mouse reference genome (Ensembl_R67) was performed using the splice junction aligner, Tophat
Gene-level expression (Reads Per Kilobase of exon per Megabase of library size (RPKM)) were calculated using Cufflinks
Transcript-level expression (Reads Per Kilobase of exon per Megabase of library size (RPKM)) were calculated using Cufflinks
Genome_build: Mus_musculus reference build Ensembl_R67
Supplementary_files_format_and_content: tab-delimited text files contain gene-level and transcript-level coordinates and expression values generated by Cufflinks

source_name: C.difficile infected mice

growth_protocol: Adult C57BL/6 mice were purchased from Jackson Laboratory

extract_protocol:
Mice were sacrificed on day 4 post-infection and mesenteric lymphe nodes were dissected. Cells were then stimulated with PMA/ionomycin in vitro for 3 hours at 37°C. IL-17A-producing cells were labeled using Mouse IL-17 Secretion Assay (Miltenyi Biotec) and additionally stained with APC-TCRgamma-delta, PerCP/Cy5.5-TCRβ, PerCP/Cy5.5-CD19 and PO-PRO-1 (Invitrogen) to exclude dead cells. Labeled cells were sorted on BD Aria-II (BD Biosciences). Total RNA was isolated using RNeasy Mini Kit (Qiagen).
Library construction were performed by the Genome Technology Access Center at Washington University in St. Louis School of Medicine

treatment_protocol: Mice were provided with water containing kanamycin (0.4 mg/ml), gentamicin (0.035 mg/ml), vancomycin (0.045 mg/ml), colistin (0.057 mg/ml) and metronidazole (0.215 mg/ml) for 5 days. A single dose of clindamycin-2-phosphate (30 mg/kg) was given 48 hours later by intraperitoneal (i.p.) injection. Mice were then orally gavaged 48 hours later with C. difficile spores (4x10^5 CFU) diluted in 400 ul of DMEM.

tag: tissue

value: mesenteric lymph node

tag: developmental stage

value: Adult


title: IL-17A- GDT

description: Sorted IL-17A non-producing gamma-delta T cells


title: Fmr1_KO_GC_TRAP_3

city: Cambridge

first: Kirsty

last: Sawicka

address: Robinson Way

department: University of Cambridge

country: United Kingdom

institute: CRUK Cambridge Insititute

description:
TRAP RNA from cerebellar granule cells Fmr1 KO
processed data file:
featureCounts_Cb_GC_input_and_trap.txt

data_processing:
Library strategy: TRAP
alignment with STAR to mm10 genome
read counts per gene with featureCounts and GENCODE annotation
Genome_build: mm10

growth_protocol: Hippocampal tissue from postnatal day 28-32 male littermates or Cerebellar tissue from 6-8 week old male littermates

extract_protocol:
For input samples, RNA was extracted directly from tissue lysate with Trizol LS. For TRAP samples, ribosome bound transcripts were immunoprecipitated with anti-HA and eluted from the bead with Trizol. RNA was further purified using the High Pure RNA isolation kit with on-column DNase treatment (Roche)
Illumina Ribo-Zero rRNA removal kit and Illumina TruSeq RNA library prep kit

value: Neurod1-Cre +/- RiboTag +/- Fmr1 -/Y

value: cerebellum

value: male

tag: age

value: 6-8 weeks


title: water column DNA_ETSP_Sample16_10m

value: 20-mer DNA oligo

value: Oxygen Minimum Zone nitrogen cycling experiments in the Eastern Tropical South Pacific Ocean

value: PCR fragment


title: RNApolII_chiapet_rep4

data_processing:
ChIA-PET data was processed by ChIA-PET Utilities (CPU) v0.0.1a (https://github.com/cheehongsg/CPU). CPU (options: tag -W) removed the adaptors, and extracted the intra-molecular and inter-molecular paired tags based on the linker sequence identified in the read and the remaining read-pairs without linker sequence. Tags (>=18bp) and reads without linker sequence were mapped to mouse genome (mm10) independently  using CPU (options: memaln -T 15), which utilized BWA (options: aln and mem) according to the tag/read length. CPU (options: pair) further separated the mapping results into uniquely-mapped, multiply-mapped, and unmapped classes with the pairing consideration. Next, deduplication of uniquely-mapped pair-end tags/reads arising from clonal PCR amplification was performed with CPU (options: dedup).
The non-redundant uniquely-mapped pair-end tags are merged with samtools and deduplicated with CPU (options: dedup), producing a single RNA PolII alignment file. RNA PolII binding peaks were called with MACS v2.1.1.20160309 (options: --keep-dup all --nomodel --extsize 250 -B –SPMR -g mm) where the single RNA PolII alignment file is specified as the treatment file and the combined 28 input files (23 E14_input, 2 CTCF ChIP input, 2 H3K27me3 ChIP input and RNAPolII_ChIP_r1_input) as the input control.
Illumina RTA-1.12 to 1.18 software used for basecalling depending on when library is sequenced.
Genome_build: mm10

value: E14 cell line

value: embryonic stem cells

value: RNA polymerase II clone (Covance MMS126R-500)


title: SL.ESCs.r2

description: polyA RNA


title: CreNeg_IM659

value: Intersitial Macrophages


title: water column DNA_ETSP_Sample15_130m


title: water column DNA_ETSP_Sample1_250m


title: SL.ESCs.r1

description: polyA RNA


title: WT_GC_TRAP_3

description:
TRAP RNA from cerebellar granule cells wildtype
processed data file:
featureCounts_Cb_GC_input_and_trap.txt

tag: genotype

value: Neurod1-Cre +/- RiboTag +/-


title: EED_chiapet_rep6

value: EED (Abcam ab4469)


title: RNApolII_chiapet_rep1


title: Fmr1_KO_GC_TRAP_2

source_name: TRAP RNA from cerebellar granule cells Fmr1 KO


title: B6NJ_RNA-seq_rep2

value: B6NJ primary cells


title: water column DNA_ETSP_Sample7_270m


title: blASCs.r3

description: polyA RNA

value: Embryonic stem cell


title: EED_chiapet_rep5


title: WT_GC_TRAP_2

source_name: TRAP RNA from cerebellar granule cells wildtype


title: water column DNA_ETSP_Sample6_305m


title: Fmr1_KO_GC_TRAP_1


title: water column DNA_ETSP_Sample5_75m


title: EED_chiapet_rep4


title: H3K27me3_ChIP_rep1

description:
H3K27me3_ChIP_treat.bigWig
H3K27me3_ChIP_foldEnrich.bigWig
H3K27me3_ChIP.broadPeak.gz


title: WT_GC_TRAP_1


title: Cb_Fmr1_KO_input_3

description:
cerebellar RNA Fmr1 KO
processed data file:
featureCounts_Cb_GC_input_and_trap.txt

source_name: cerebellar RNA Fmr1 KO


title: blASCs.r1

description: polyA RNA


title: water column DNA_ETSP_Sample4_220m


title: EpiSCs.r2

description: polyA RNA

source_name: Epiblast stem cell

value: Epiblast stem cell


title: EED_chiapet_rep1


title: Cb_WT_input_3

description:
cerebellar RNA wildtype
processed data file:
featureCounts_Cb_GC_input_and_trap.txt

source_name: cerebellar RNA wildtype


title: EpiSCs.r1

description: polyA RNA


title: Cb_Fmr1_KO_input_2


title: B6NJ_si_chr7_F4_Ezh2_chiapet_rep2

data_processing:
ChIA-PET data was processed by ChIA-PET Utilities (CPU) v0.0.1a (https://github.com/cheehongsg/CPU). CPU (options: tag -W) removed the adaptors, and extracted the intra-molecular and inter-molecular paired tags based on the linker sequence identified in the read and the remaining read-pairs without linker sequence. Tags (>=18bp) and reads without linker sequence were mapped to mouse genome (mm10) independently  using CPU (options: memaln -T 15), which utilized BWA (options: aln and mem) according to the tag/read length. CPU (options: pair) further separated the mapping results into uniquely-mapped, multiply-mapped, and unmapped classes with the pairing consideration. Next, deduplication of uniquely-mapped pair-end tags/reads arising from clonal PCR amplification was performed with CPU (options: dedup).
Illumina RTA-1.12 to 1.18 software used for basecalling depending on when library is sequenced.
Genome_build: mm10

extract_protocol:
Cells were lysed and digested with AluI.
Digested DNA fragment on the protein-DNA complex were ligated with linkers by proximity. The complex is then sheared by sonication and subjected to immunoprecipitation with antibody. The immunoprecipitated DNA were tagmented using the Nextera enzyme (Illumina), the linker-containing ChIA-PET constructs were  selected using streptavidin magnetic beads, amplified with PCR and purified.

value: B6NJ derived KO cells

value: Ezh2 (Active Motif 39875)


title: Input DNA

source_name: Hepa1-6 cells

value: Hepa1-6 cells

tag: chip antibody


title: Cb_WT_input_2

value: cerebellum

tag: Sex

value: male


title: water column DNA_ETSP_Sample1_350m

value: 20-mer DNA oligo


title: water column DNA_ETSP_Sample2_300m

value: Oxygen Minimum Zone nitrogen cycling experiments in the Eastern Tropical South Pacific Ocean


title: EpiSCs.r3

description: polyA RNA

data_processing:
Illumina CASAVA version 1.8 were used to the basecalling.
Reads were trimmed to remove adaptor sequences and low quality bases;
For whole genome bisulfite sequencing (WGBS), the clean reads were first mapped to mouse reference genome mm10 with Bismark (v0.7.6) in paired-end and non-directional module, and then the unmapped reads were realigned to the same reference genome in single-end and non-directional module; while for RNA-seq, the cleaned reads were aligned to the mouse mm10 reference genome using Tophat (v2.0.12) with default settings (Trapnell et al., 2009).
For WGBS, methylation level of covered cytosines, including CpG, CHH and CHG were estimated using comstomized perl scripts; while for RNA-seq, HTSeq (0.6.1) was used to do the reads counting and then gene expression level was calculated using the RPKM method (Reads Per Kilobase transcriptome per million reads).
Genome_build: mm10
Supplementary_files_format_and_content: Methylation calling txt files include the methylation level of covered cytosines, including CpG, CHH and CHG context; while gene RPKM txt files include the RPKM values of RefSeq genes.


title: EZH2_chiapet_rep5

data_processing:
ChIA-PET data was processed by ChIA-PET Utilities (CPU) v0.0.1a (https://github.com/cheehongsg/CPU). CPU (options: tag -W) removed the adaptors, and extracted the intra-molecular and inter-molecular paired tags based on the linker sequence identified in the read and the remaining read-pairs without linker sequence. Tags (>=18bp) and reads without linker sequence were mapped to mouse genome (mm10) independently  using CPU (options: memaln -T 15), which utilized BWA (options: aln and mem) according to the tag/read length. CPU (options: pair) further separated the mapping results into uniquely-mapped, multiply-mapped, and unmapped classes with the pairing consideration. Next, deduplication of uniquely-mapped pair-end tags/reads arising from clonal PCR amplification was performed with CPU (options: dedup).
The non-redundant uniquely-mapped pair-end tags are merged with samtools and deduplicated with CPU (options: dedup) for all replicates of each factor separately, producing 3 factor-level (i.e. Suz12, Ezh2, Eed) alignment files. PRC2 binding peaks were called with MACS v2.1.1.20160309 (options: --keep-dup all --nomodel --extsize 250 -B –SPMR -g mm) where the 3 factor-level alignment files are specified as the treatment file and the combined 28 input files (23 E14_input, 2 CTCF ChIP input, 2 H3K27me3 ChIP input and RNAPolII_ChIP_r1_input) as the input control.
The non-redundant uniquely-mapped pair-end tags are merged with samtools and deduplicated with CPU (options: dedup) for all replicates of each factor separately, producing 3 factor-level (i.e. Suz12, Ezh2, Eed) alignment files. These 3 factor-level alignment files were merged using samtools and clustering of the pair-end tags were performed with CPU (options: cluster -M -B 1000 -v 3 -5 5,-20 -3 5,980 -g) to produce cis-interactions and trans-interactions. Statistical assessment of the cis-interaction significance was performed using ChiaSigScaled (https://github.com/cheehongsg/ChiaSigScaled ; options: -p -m 3000). Cis-interaction clusters with member size 3 and above (iPET 3+) and FDR<0.05 were reported, excluding any interaction should any of its anchors overlap the blacklist (see publication supplementary table).
Illumina RTA-1.12 to 1.18 software used for basecalling depending on when library is sequenced.
Genome_build: mm10


title: water column DNA_ETSP_Sample3_260m

value: PCR fragment


title: epiASCs.r2

description: polyA RNA


title: EZH2_chiapet_rep7

value: E14 cell line


title: Cb_Fmr1_KO_input_1

value: Neurod1-Cre +/- RiboTag +/- Fmr1 -/Y

value: 6-8 weeks


title: EZH2_chiapet_rep4

value: embryonic stem cells


title: epiASCs.r1

description: polyA RNA


title: epiASCs.r3

description: polyA RNA


title: B6NJ_si_chr7_D4_Ezh2_chiapet_rep2


title: Cb_WT_input_1

value: Neurod1-Cre +/- RiboTag +/-


title: EZH2_chiapet_rep1

value: Ezh2 (Millipore 07-689)


title: control_lgRNA3

description:
control_3
control diet
67_accepted_hits.bam

source_name: milk fat

value: ICR

value: primiparous

value: lactation day 10

value: female

tag: biosample


title: EZH2_chiapet_rep6

value: Ezh2 (Active Motif 39875)


title: Fmr1_KO_CA1_TRAP_3

description:
TRAP RNA from CA1 pyramidal neurons Fmr1 KO
processed data file:
featureCounts_CA1_input_and_trap.txt

value: Camk2a-Cre +/- RiboTag +/- Fmr1 -/Y

value: hippocampus

value: postnatal day 28-32


title: esASCs.r3

description: polyA RNA

value: Embryonic stem cell


title: SUZ12_chiapet_rep11

value: Suz12 (Abcam ab12073)


title: WT_CA1_TRAP_3

description:
TRAP RNA from CA1 pyramidal neurons wildtype
processed data file:
featureCounts_CA1_input_and_trap.txt

value: Camk2a-Cre +/- RiboTag +/-

value: male


title: B6NJ_si_chr9_G9_Ezh2_chiapet_rep2

value: B6NJ derived KO cells


title: esASCs.r2

description: polyA RNA


title: B6NJ_si_chr7_D4_Ezh2_chiapet_rep1


title: SUZ12_chiapet_rep3

value: E14 cell line


title: Fmr1_KO_CA1_TRAP_2

source_name: TRAP RNA from CA1 pyramidal neurons Fmr1 KO


title: 2iL.ESCs.r3

description: polyA RNA


title: B6NJ_si_chr9_F1_Ezh2_chiapet_rep2


title: B6NJ_si_chr7_F4_Ezh2_chiapet_rep1


title: WT_CA1_TRAP_2

source_name: TRAP RNA from CA1 pyramidal neurons wildtype


title: B6NJ_si_chr9_G9_Ezh2_chiapet_rep1


title: 2iL.ESCs.r2

description: polyA RNA


title: Fmr1_KO_CA1_TRAP_1


title: B6NJ_si_chr9_F1_Ezh2_chiapet_rep1

value: B6NJ primary cells


title: 2iL.ESCs.r1

description: polyA RNA


title: B6NJ_Ezh2_chiapet_rep2


title: WT_CA1_TRAP_1


title: EED_chiapet_rep3

value: embryonic stem cells

value: EED (Abcam ab4469)


title: B6NJ_Ezh2_chiapet_rep1


title: EpiSCs.WGBS.r2

description: genomic DNA

value: Epiblast stem cell


title: rep3_poly_6

city: Stockholm

first: Christian

last: Oertlin

address: Tomtebodavägen 23A

country: Sweden

institute: Karolinska Institutet

description:
P13171_136
P13171_136_S36_bothLanes

data_processing:
Nextflow RNAseq pipeline (version 1.3) default settings.
Genome_build: GRCm38
Supplementary_files_format_and_content: raw_counts.txt: Genes were filtered to only contain genes mapping to chromosomes 1 to 22, X, Y and MT as well as only to contain protein-coding genes. Genes with 0 counts in at least one sample were removed.

source_name: RAW cells

growth_protocol: RAW264.7 cells were seeded in a 15-cm Petri dish.

extract_protocol:
Cells were harvested at 80% confluency, washed twice with ice-cold PBS containing 100 µg/mL cycloheximide and then lysed in hypotonic lysis buffer (5 mM Tris HCl, pH 7.5, 2.5 mM MgCl2, 1.5 mM KCl, 100 µg/ml cycloheximide, 2 mM dithiothreitol (DTT), 0.5% Triton, and 0.5% sodium deoxycholate).
Illumina TruSeq Ribozero

treatment_protocol: 2 h or 6 h with a vehicle (DMSO), 500 ng/mL LPS from Salmonella enterica serotype minnesota Re 595, 100 nM torin1 for 2 h only, or the combination of LPS (500 ng/mL) and torin1 (100 nM) whereby cells were pre-treated for 15 minutes with torin1 before stimulation with LPS.

tag: treatment

tag: rna source

value: Polysome-associated mRNA

tag: replicate


title: Hipp_WT_input_3

description:
hippocampal RNA wildtype
processed data file:
featureCounts_CA1_input_and_trap.txt

source_name: hippocampal RNA wildtype

tag: strain


title: EpiSCs.WGBS.r1

description: genomic DNA

tag: cell type


title: rep3_poly_5

description:
P13171_135
P13171_135_S35_bothLanes

tag: cell line


title: epiASCs.WGBS.r3

description: genomic DNA


title: rep3_poly_1

description:
P13171_131
P13171_131_S31_bothLanes

value: Veh


title: Hipp_WT_input_2


title: Hipp_Fmr1_KO_input_3

description:
hippocampal RNA Fmr1 KO
processed data file:
featureCounts_CA1_input_and_trap.txt

source_name: hippocampal RNA Fmr1 KO


title: rep3_total_6

description:
P13171_130
P13171_130_S30_bothLanes

value: Total mRNA


title: Est2_ChIP_replicate 8

type: genomic

city: Bonn

first: Katrin

last: Paeschke

address: Sigmund Freud Str. 25

department: Department of Oncology, Hematology and Rheumatology

country: Germany

institute: University Hospital Bonn

description: Immunoprecipitated DNA was amplified and amplified as per instructions described in Agilent Yeast ChIP on chip analysis protocol v9.2

hyb_protocol: Hybridization was carried out at 65°C for 18 hr at 20 rpm

scan_protocol: Arrays were scanned using an Agilent Microarray Scanner.

data_processing:
Data extraction, dye normalization, and spatial derendering were done using default settings of the Agilent Feature Extractor.
The resulting log2 ratio of Cy3 and Cy5 signal at each array spot was median-standardized across the biological replicates.

organism: Saccharomyces cerevisiae

source_name: Yeast

label_protocol: Labelling was performed with minor modifications according to the instructions described in the Agilent Yeast ChIP on chip analysis protocol v9.2

growth_protocol: S. cerevisiae cells were grown in YPD (1% Yeast extract, 2% Peptone, 2% Glucose) to exponential phase at 30 °C, 250 rpm

extract_protocol: Immunoprecipitated DNA was extracted using Qiagen PCR purification kits.

treatment_protocol: untreated

tag: Stage

value: exponential


title: Est2_ChIP_replicate 4


title: Est2_ChIP_replicate 7


title: epiASCs.WGBS.r1

description: genomic DNA

extract_protocol:
The isolated genomic DNA were used to construct the WGBS library, as previously described (Zhang et al., 2017). RNA-seq were performed under the instruction of mRNA library construction kit (NEB).
Total RNA were extracted from approximately one million to two million cells using RNeasy Mini Kit (QIAGEN) according to the recommendation of manufacturer and then NEBNext® Poly(A) mRNA Magnetic Isolation Module was used to isolate mRNA from total RNA. Using mRNA as input, the first and second strand cDNAs were synthesized by NEBNext® RNA First Strand Synthesis Module and NEBNext® Ultra II Non-Directional RNA Second Strand Synthesis Module, respectively. Final libraries were prepared using KAPA Hyper Prep Kits (8 PCR cycles) and sequenced on HiSeq4000 platform. Following the manufacturer’s instructions, genomic DNA was extracted from stem cells using the DNeasy Blood & Tissue Kit (Qiagen). Remaining RNA was removed by treating with RNase A. Three replicated samples from each of these stem cells were used for library preparation to ensure repeatability of experiment. In short, 2 μg of genomic DNA spiked with 10 ng of lambda DNA were fragmented to about 300 bp with Covaris S220. Next, end repair and A-ligation were performed to the DNA fragments. Methylated Adaptor (NEB) was then ligated to the DNA fragments. In order to reach >99% bisulfite conversion, the adaptor-ligated DNA was treated twice using EZ-96 DNA Methylation-Direct™ MagPrep (Zymo Research). The resulting single-strand DNA fragments were amplified by 4 PCR cycles using the KAPA HiFi HotStart Uracil+ ReadyMix (2×). At last, the libraries were sequenced on HiSeq4000 platform to generate 150-bp paired-end reads.


title: rep3_total_5

description:
P13171_129
P13171_129_S29_bothLanes


title: Hipp_WT_input_1


title: EpiSCs.WGBS.r3

description: genomic DNA


title: Est2_ChIP_replicate 6


title: Est2_ChIP_replicate 3


title: Est2_ChIP_replicate 5


title: Hipp_Fmr1_KO_input_2

value: Camk2a-Cre +/- RiboTag +/- Fmr1 -/Y


title: Est2_ChIP_replicate 1


title: esASCs.WGBS.r3

description: genomic DNA


title: esASCs.WGBS.r2

description: genomic DNA


description:
ogako.pilot-study_no-feed
processed data file: TC-O-GlcNAc-seq-peaks.bed
O-GlcNAc-seq pilot study in OGA knockout Drosophila larvae grown on DMSO media for 36h

data_processing:
O-GlcNAc-seq: FASTQ sequencing files were aligned to a concatenated reference genome of D. melanogaster (dm3), S. cerevisiae (sacCer3), and the three synthetic gBlock fragments using the snap-aligner single command from SNAP version 1.0beta.18. The yeast chromosomes were re-name with the prefix "yeast" to avoid conflicts with the same chromosome names as Drosophila.
O-GlcNAc-seq: The resulting BAM-format alignment files were sorted, cleared of duplicates and indexed using the SAMtools commands sort, rmdup -s, and index, respectively, using SAMtools version 0.1.19-96b5f2294a
O-GlcNAc-seq: BDG files were generated from the BAM files using the command bedtools genomecov -ibam -bg command using bedtools v2.17.0. Yeast spike-in normalized BDG files were generated by multiplying by the fourth column, which specifies the sequencing coverage, of the BDG file by the normalization constants. These normalization constants were calculated by dividing the number of base pairs that aligned to the sacCer3 genome from the time point that had the least sacCer3 aligned base pairs by the number of base pairs that aligned to the sacCer3 reference genome from each time point. This was done within each replicate separately. The command awk -F'\t' '{$4=$4*a;print}' a=NF OFS='\t' <$.bdg> was used to do this, where NF is the normalization factor, which are specified in Table 1, and <$.bdg> is the appropriate time course input BDG file.
O-GlcNAc-seq: Peaks were called by calculating the coordinates that contained 5 times the average base pair sequencing coverage within each time course experiment. This was done for the no feed controls as well. The coordinates of base pairs that satisfied this requirement were then merged if they were within 30 base pairs of each other. This was done with the command awk '{ if( $4 > 5X) print}' <$.bdg> | cut -f 1,2,3 | bedtools merge -d 30, where 5X indicates 5 times the average base pair sequencing coverage within each time course experiment and <$.bdg> indicates the appropriate time course BDG file. For each time point, the peaks that occurred from the no feed controls were eliminated from the time course experiment peaks using the bedtools intersect -v command. This effectively removed false positives from the analysis. Peaks resulting from the intersection of replicate time points were kept using the regular bedtools intersect command. Peaks at time point 0 for WT and OGA-null were then intersected using the bedtools intersect command. Peaks that were less than 20 base pairs were then expanded from their midpoint by 10 base pairs on each side to a peak length of 20 base pairs. This strategy resulted in 1883 peaks and enabled focus on coordinates that consistently contained O-GlcNAz peaks within both WT and OGA-null and each replicate.
O-GlcNAc-seq pilot study: FASTQ sequencing files were aligned to the D. melanogaster (dm3) genome using the snap-aligner single command from SNAP version 1.0beta.18.
O-GlcNAc-seq pilot study: The resulting BAM-format alignment files were sorted, cleared of duplicates and indexed using the SAMtools commands sort, rmdup -s, and index, respectively, using SAMtools version 0.1.19-96b5f2294a
O-GlcNAc-seq pilot study: BDG files were generated from the BAM files using the command bedtools genomecov -ibam -bg command using bedtools v2.17.0.
OGA ChIP-seq: Fastq files were aligned to the dm3 genome the Burrows–Wheeler Aligner version 0.7.5a-r405 algorithm. The resulting BAM-format alignment files were sorted, cleared of duplicates and indexed using the SAMtools commands sort, rmdup -s, and index, respectively, using SAMtools version 0.1.19-96b5f2294a.
OGA ChIP-seq: BDG files were generated from the BAM files using the command bedtools genomecov -ibam -bg command using bedtools v2.17.0.
OGA ChIP-seq: Peaks were called by calculating the coordinates that contained 5 times the average base pair sequencing coverage within both OGA ChIP-seq experiments (WT and OGA-null). Peaks within the OGA-null experiment were considered false positives and were subtracted from the peaks called in the WT experiment using the bedtools intersect -v command to yield the final OGA ChIP-seq peaks.
Genome_build: dm3, sacCer3 and synthetic DNA probes.
Supplementary_files_format_and_content: Bdg files and bed files containing ChIP-seq and O-GlcNAc-seq loci. Bed files of O-GlcNAc-seq data contain normalized sequencing depth at each O-GlcNAc bearing locus accross time points for WT and OGA-null replicates.

source_name: O-GlcNAc-seq pilot study in OGA knockout larvae_DMSO media for 36h

treatment_protocol: Wild-type OGA knockout (OGA-null) Drosophila (P. T. Radermacher, F. Myachina, F. Bosshardt, R. Pandey, D. Mariappa, H.-A. J. Müller, C. F. Lehner, Proc. Natl. Acad. Sci. U.S.A. 2014, 111, 5592–5597) were expanded in 50 mL bottles of cornmeal molasses media at 25°C. Drosophila parents from approximately 25 of these bottles were required for each time course replicate. Time course Ac4GalNAz feeding was performed on 10 mL petri dishes. Just under 10 mL of cornmeal molasses media supplemented with Ac4GalNAz dissolved in DMSO to a final concentration of 150 uM or DMSO only in the same volume added to the Ac4GalNAz plates (control) were made. Adult Drosophila parents from the bottles were then transferred to the control plates for 2 hours (on cages) for a pre-egg laying period. This facilitated the laying of eggs that were not synchronized. These adult Drosophila were then transferred to either 150 uM Ac4GalNAz or control plates for 2 hours (enabling the laying of synchronized eggs). After a 36 h incubation period, the resulting larvae were transferred to control plates or collected and snap frozen (0 h time point). Larvae that were initially grown on control plates were collected at this time as well (no feed control). The larvae transferred from Ac4GalNAz plates to control plates were then collected after 4, 8, 12, 16, 20, 24, and 36 hours of feeding on these control plates.

tag: strain background

value: Oregon R

tag: genotype/variation

value: OGA knockout

tag: stage/tissue

value: larvae

tag: chip strategy

value: GalNAz feeding, strain-promoted click reaction and streptavidin purification


title: Est2_ChIP_replicate 2


title: epiASCs.WGBS.r2

description: genomic DNA

value: Embryonic stem cell

tag: passages


title: Hipp_Fmr1_KO_input_1

tag: tissue

value: hippocampus

value: male

tag: age

value: postnatal day 28-32


title: esASCs.WGBS.r1

description: genomic DNA


title: 2iL.ESCs.WGBS.r3

description: genomic DNA


title: rep2_poly_1

description:
P13171_119
P13171_119_S19_bothLanes


title: rep2_poly_5

description:
P13171_123
P13171_123_S23_bothLanes


title: CA1_FMRP_cTag_CLIP_2

data_processing:
filtering and demultiplexing using fastq_filter.pl (CTK package, Zhang lab, min:0-15:20,mean:16-41:20)
trim 3' linker sequence using cutadapt (GTGTCAGTCACTTCCAGCGG)
collapse exact  duplicates using fastq2collapse.pl (CTK package, Zhang lab)
trim 5' barcode and linker using stripBarcode.pl (CTK package, Zhang lab)
alignment with STAR to refseq mm10 transcriptome
collapse PCR duplicates using tag2collapse.pl (CTK package, Zhang lab)
selected most abundant transcript per gene, removed multimapped reads and reads not mapping in the appropriate direction in the transcriptome
Genome_build: mm10
Supplementary_files_format_and_content: number of unique clip tags that were mapped to each transcript or to the coding region of these transcripts.

source_name: FMRP cTag CLIP from CA1 pyramidal neurons

growth_protocol: Hippocampal tissue from postnatal day 28-32 male mice

extract_protocol:
Tissue was UV crosslinked and processed for FMRP cTag CLIP (see associated paper for method)
RNA tags cloned using BrdU-CLIP cloning method (see associated paper for method)

tag: genotype

value: Camk2a-Cre +/- Fmr1-cTag +/Y


title: HDLEC control siRNA mix 72h

city: Takamatsu

first: Tatsuo

last: Furuyama

state: Kagawa

address: 281-1 Murecho-hara

country: Japan

institute: Kagawa Prefectural University of Health Sciences

hyb_protocol: 0.6ug of Cy3-labelled cRNA was fragmented at 60°C for 30min in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Human GE 8x60K v2 Microarray for 17h at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1min at room temperature with GE Wash Buffer 1 (Agilent) and 1min with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2600D).

data_processing: The scanned images were analyzed with Feature Extraction 11.5.1.1(Agilent) using default parameters (protocol GE1_1105 and Grid: 039494_D_F_20140813) to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: HDLEC

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100ng RNA using the Low Input Quick Amp Labeling Kit, one color (Agilent) according to the manufacturer's instructions

growth_protocol: HDLEC was purchased from PromoCell (C-12216, lot number 3061302.3). It was cultured in MV2 medium (PromoCell, Germany).

extract_protocol: Total RNAs were extracted from cells at 72h after siRNA treatment using PureLink RNA mini kit (Ambion, USA) following manufacture's manual.

treatment_protocol: 70% confluent HDLEC were transfected with siRNA mix for Foxo1 (siGENOME human FOXO1 smart pool, Dahmacon, USA) or random mix (non-targetting siRNA #3, Dahmacon) using Lipofectamine RNAiMax (Invitrogen, USA) and then were further cultured for 72h.

value: primary human dermal lymphatic endothelial cells

tag: gender

value: 72h after control siRNA treatment


title: rep2_total_6

description:
P13171_118
P13171_118_S18_bothLanes


title: 2iL.ESCs.WGBS.r1

description: genomic DNA

source_name: Embryonic stem cell


title: HDLEC Foxo1 siRNA mix 72h

value: 72h after Foxo1 siRNA treatment


title: 2iL.ESCs.WGBS.r2

description: genomic DNA


title: esASCs.r1

description: polyA RNA


title: CreNeg_FMRP_cTag_CLIP_3

source_name: Negative control

value: Fmr1-cTag +/Y

tag: Sex


title: rep2_poly_6

description:
P13171_124
P13171_124_S24_bothLanes

tag: treatment

value: Polysome-associated mRNA


title: blASCs.r2

description: polyA RNA


title: CreNeg_FMRP_cTag_CLIP_1


title: CA1_FMRP_cTag_CLIP_1


title: water column RNA_ETSP_Sample21_140m

data_processing: Quality control was employed to remove noise by eliminating features 1) in which the Cy3 signal was not at least twice the value of the control probes, and 2) in which the Cy3/Cy5 could not pass a Z test to find out the outlier values. The Z test was performed by calculating Zi = ri/(s/square root of 3), i = 1, 2, or 3, where ri represents Cy3/Cy5, s the standard deviation of the triplicate Cy3/Cy5 values. A feature is considered as an outlier if the Z is greater than 1.9 (CI = 80%).

source_name: Universal Internal Standard + 70-mer

tag: sample type

value: 20-mer DNA oligo

source_name: seawater

tag: location

value: Oxygen Minimum Zone nitrogen cycling experiments in the Eastern Tropical South Pacific Ocean

tag: depth

value: PCR fragment amplified from total cDNA prepared from RNA extract


title: CA1_FMRP_cTag_CLIP_3

tag: strain


title: T2DN [DN322]

city: Taichung

first: Fuu-Jen

last: Tsai

address: No.2, Yude Rd., North Dist.

department: Department of Medical Research

country: Taiwan

institute: China Medical University Hospital

description:
DN322
DNA methylation data from whole blood samples of Taiwanese patients with nephropathy of Type-2 Diabetes (T2DN).

hyb_protocol: The hybridization was performed against the Affymetrix GeneChip® Human Promoter 1.0R array by following the Affymetrix protocol for 17 hours at 45oC and 60 rpm.

scan_protocol: The arrays were subsequently washed (Affymetrix Fluidics Station 450) and stained with streptavidin-phycoerythrin (GeneChip® Hybridization, Wash, and Stain Kit, 900720), and were scanned on an Affymetrix GeneChip® Scanner 3000 7G.

data_processing:
The output data was annotated and the differential methylation of the compared arrays was performed with the tilling analysis software (TAS) of Affymetrix update to 1.0.3 version. It resulted in CHP files and text files.
The differential methylation levels were determined by the MAT (Model-based Analysis of Tiling-array) score which based on T value of ANOVA method, which was performed by the Partek Genomics suite (version 7.18.0723).

label: Biotin

source_name: Blood, T2DN

label_protocol: The 50 ng of methylated DNA from MeDIP immunoprecipitations and MBD-Capture reactions was amplified with GenomePlex Single Cell Whole Genome Amplification Kit (Sigma, Catalog No. WGA4) in each amplification performance was instructed by the company protocol. Then, cDNA was purified using cDNA cleanup columns (Affymetrix, Catalog No. 900371), and 7.5 ug of amplified DNA was fragmented and labeled following Affymetrix Chromatin Immunoprecipitation Assay Protocol (P/N: 702238 Rev. 3).

growth_protocol: The patients have been diagnosed with resulting to classified groups as Control, Type-2 diabetes with non-complication (T2D), Type-2 diabetes with nephropathy (T2DN), Type-2 diabetes with non-proliferative retinopathy (T2NPDR) and Type-2 diabetes with proliferative retinopathy (T2PDR). The blood samples were collected individually for the only research purposes with their voluntary participation. Whole blood of these samples was contained individually in the EDTA tubes for further steps of array analysis.

extract_protocol: The MethylMiner Methylated DNA Enrichment Kit (Invitrogen) was used to isolate the methylated DNA. One microgram of genomic DNA was sonicated to 100–500 bp. Then 3.5 mg (7 mL) of MBD-Biotin Protein was coupled to 10 mL of Dynabeads M-280 Streptavidin according to the manufacturer’s instructions.

treatment_protocol: Not applicable.

value: Whole blood

tag: disease group

value: Type-2 Diabetes with nephropathy

tag: phenotype

tag: blood glucose

value: Glucose (AC):185 mg/dL; HbA1C:7.8%.

tag: bmi (kg/m2)

tag: duration (yr)

tag: age (yr)

tag: population

value: Taiwanese


title: rep2_total_1

description:
P13171_113
P13171_113_S13_bothLanes

tag: cell line

value: Veh

tag: rna source

value: Total mRNA

tag: replicate


title: rep2_total_5

description:
P13171_117
P13171_117_S17_bothLanes


title: CreNeg_FMRP_cTag_CLIP_2

tag: genotype

tag: tissue

value: hippocampus

value: male

tag: age


title: water column RNA_ETSP_Sample20_150m

tag: sample type


title: rep3_total_1

description:
P13171_125
P13171_125_S25_bothLanes

tag: treatment


title: rep1_poly_6

description:
P13171_112
P13171_112_S12_bothLanes


title: rep1_poly_5

description:
P13171_111
P13171_111_S11_bothLanes


title: water column RNA_ETSP_Sample19_145m

tag: location

tag: depth


title: T2DN [DN297]

description:
DN297
DNA methylation data from whole blood samples of Taiwanese patients with nephropathy of Type-2 Diabetes (T2DN).

tag: disease group

value: Glucose (AC):79 mg/dL; HbA1C:7.9%.

tag: gender


title: T2DN [DN228]

description:
DN228
DNA methylation data from whole blood samples of Taiwanese patients with nephropathy of Type-2 Diabetes (T2DN).

tag: phenotype

tag: blood glucose

value: Glucose (AC):165 mg/dL; HbA1C:7.6%.


title: E14_Input_8

source_name: Mouse embryonic stem cells

value: E14 cell line

tag: cell type

value: embryonic stem cells

tag: ip antibody


title: rep1_total_6

description:
P13171_106
P13171_106_S6_bothLanes


title: E14_Input_3


title: T2DN [DN313]

description:
DN313
DNA methylation data from whole blood samples of Taiwanese patients with nephropathy of Type-2 Diabetes (T2DN).

value: Glucose (AC):176 mg/dL; HbA1C:8.3%.

tag: bmi (kg/m2)

tag: duration (yr)

tag: age (yr)

tag: population


title: rep1_total_5

description:
P13171_105
P13171_105_S5_bothLanes

tag: cell line

tag: rna source

tag: replicate


title: E14_Input_17


title: water column RNA_ETSP_Sample12_180m

tag: sample type


title: water column RNA_ETSP_Sample10_30m


description:
wt.pilot-study_no-feed
processed data file: TC-O-GlcNAc-seq-peaks.bed
O-GlcNAc-seq pilot study in wt Drosophila larvae grown on DMSO media for 36h

source_name: O-GlcNAc-seq pilot study in wt larvae_DMSO media for 36h

extract_protocol:
The larvae were collected and rinsed with PBST (PBS + 0.1% Triton X-100) three times to remove adhering corn food. One volume of hexanes (a mixture of isomers) was equilibrated for 30 min against 0.175 vol of 37% formaldehyde and 0.130 vol of 10X PBS (1.37 M NaCl, 27 mM KCl, 43 mM Na2HPO4 and 14 mM KH2PO4), pH 7.5, to make the mixture 5% formaldehyde and 1X PBS. Only the upper organic phase was used for crosslinking. Larvae were fixed in 10 ml of buffered 5% formaldehyde/hexanes per gram of larvae by vigorous shaking for 5 min at room temperature. The larvae were allowed to settle, and the formaldehyde/hexanes solution was removed by centrifugation (3,000 x g for 5 min at RT). The larvae were washed twice in a solution containing 1X PBS and 0.5% Triton X- 100 (0.5% PBST), using the five volumes as used for fixing. They were then stored at -80°C. Chromatin was purified by quickly thawing frozen larvae and resuspending them in buffer A [0.3 M sucrose, 15 mM NaCl, 5 mM MgCl2, 15 mM Tris pH 7.5, 60 mM KCl, 0.1 mM EDTA, 0.1 mM EGTA, 0.5 mM dithiothreitol (DTT) and 1 mM phenylmethylsulfonyl fluoride (PMSF)]. They were homogenized with 20-25 strokes of a hand-held type B Dounce homogenizer. Triton X-100 was added to 0.3%, and the homogenate was centrifuged (2,000 x g for 15 min at 4°C). The pellet was resuspended in buffer B (100 mM NaCl, 10 mM Tris pH 7.9, 1 mM EDTA, 0.1% v/v NP-40 and 1 mM PMSF) and homogenized with ~5 strokes of a hand-held type B Dounce homogenizer. The homogenate was then sheared by 20 cycles (20 × 20 s on and 50 s off cycles, 40% power settings) through a sonicator (Sonic Dismembrator Model 500, Fisher Scientific) to an average size of ~200 to 700 bp chromatin fragments. After sonication, debris was removed by centrifugation at 4°C for 10 min at 13,000 r.p.m., and an equal amount of 6 M urea was added to the solution and then incubated for 10 min at 4°C on a rotating wheel. The soluble chromatin was dialyzed using a membrane with a molecular weight cut-off of 3.5 kDa, at 4°C against 2 L dialysis buffer (10 mM Tris-HCl pH 8.0, 1 mM EDTA, 0.5 mM EGTA, 4% glycerol) overnight. Insoluble debris was removed by quick centrifugation (7,500 r.p.m., 2 min). The chromatin solution was pre-cleared with 100 μl Streptavidin-agarose slurry (Sigma) beads for O-GlcNAz modified or vehicle-only chromatin separately and incubated for 1 hour at 4°C on a rotating wheel. The pre-cleared chromatin was aliquoted after centrifugation at 4°C for 2 min at 7,500 r.p.m., snap-frozen in liquid nitrogen and stored at −80°C for future use. For click chemistry, 20-50 μg chromatin DNA was incubated with iodoacetamide (IAA) to a final concentration of 15 mM, agitate mildly for 30 min at RT then added DMSO solution of dibenzylcyclooctyne-S-S-PEG3-Biotin (DBCO-S-S-PEG3-Biotin, Jena Bioscience GmbH) to a final concentration of 40 μM. The samples were protected from light and agitated mildly for 1 hour at RT. The unreacted probe was filtered off by the Amicon Ultra-0.5 mL centrifugal filter (15K cut-off) (EMD Millipore). Biotinylated-probe-chromatin complexes were captured by incubation with 50 μl Streptavidin magnetic beads (NEB) at 4°C for 2 hours. Beads were washed with 0.5 ml of the following buffers: three washes with low-salt wash buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl pH 8.0, 150 mM NaCl), followed by three washes with high-salt wash buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl pH 8.0, 500 mM NaCl), then three washes with lithium wash buffer (0.25 M LiCl, 1% NP-40, 1% sodium deoxycholate, 1 mM EDTA, 10 mM Tris-HCl pH 8.0); then two washes with TE (10 mM Tris-HCl pH 8.0, 1 mM EDTA). Beads were resuspended in 100 μl TE containing 0.5% SDS, 15 mM DTT and incubated with 0.15 mg/ml proteinase K at 55°C for 3-4 hours. DNA-protein complex was de-crosslinked by incubating overnight at 65°C (not more than 15 hours). ChIP-DNA was purified with QIAquick PCR Purification Kit and stored at -20°C.
The libraries were prepared according to the manufacturer’s instructions using the NEBNext kit (E6200). Briefly, DNA was fragmented by sonication to a maximum of 300 bp. Next, the ends of the fragments were repaired with a combination of fill-in reactions and exonuclease activity to produce blunt ends that were then tailed with an A-base. Illumina-specific adaptors were ligated followed by removal of unligated adaptors using AMpure XP beads (Beckman Coulter). Finally, a PCR with 12-15 cycles for both kits was performed to enrich final adaptor-ligated fragments. Quality and quantity were assessed on High Sensitivity dsDNA Agilent Bioanalyzer Chips and Quibit. WT and OGA-null O-GlcNAc-seq libraries and OGA ChIP-seq libraries were sequenced on the Illumina NextSeq 500 High Output (75 cycles, 400M reads) platform. The additional replicates for both WT and OGA-null DMSO control from an earlier pilot study were sequenced on the MiSeq platform, using v3, 150-cycle reagent kits (Illumina).

tag: strain background

value: Oregon R

tag: genotype/variation

value: wild type

tag: stage/tissue

value: larvae

tag: chip strategy

value: GalNAz feeding, strain-promoted click reaction and streptavidin purification


title: water column RNA_ETSP_Sample14_90m

value: 20-mer DNA oligo

tag: location

value: Oxygen Minimum Zone nitrogen cycling experiments in the Eastern Tropical South Pacific Ocean

tag: depth

value: PCR fragment amplified from total cDNA prepared from RNA extract


title: E14_Input_2


title: water column RNA_ETSP_Sample11_120m


title: rep1_total_1

description:
P13171_101
P13171_101_S1_bothLanes

tag: treatment


title: E14_Input_15

tag: cell type


title: E14_Input_7

tag: ip antibody


title: E14_Input_1


title: water column RNA_ETSP_Sample13_125m


title: ATAC-seq_rep2

description: ATAC-seq.bigWig

data_processing:
Raw reads were trimmed with Trim Galore v0.4.0 (options: --length 20 --stringency 5 --fastqc -e 0.2). The trimmed-reads were mapped on the mm10 genome using BWA v0.7.12  (options: aln –l 25 followed by samse). Only the de-duplicated uniquely mapped reads were used for downstream analysis.
Peak calling was performed with MACS v2.1.1.20160309 (options: --nomodel --shift 125 --extsize 250 -B -SPMR -g mm). bedGraphToBigWig from kentUtils was used to convert MACS2 generated bedgraph to bigWig format.
Illumina RTA-1.12 to 1.18 software used for basecalling depending on when library is sequenced.
Genome_build: mm10

extract_protocol:
Freshly harvested cell were processed according published method by Buenrostro et al (doi:10.1038/nmeth.2688) .
PCR amplification was performed to generate a library.


title: OVCAR8 NR Tx-3 [272 DS-24]

city: Nashville

first: Dhivya

last: Sudhan

state: TN

address: 777 Preston Research Building

department: Hematology/Oncology Division

institute: Vanderbilt University

data_processing:
Quality control on raw reads was performed using FastQC.
STAR v2.5.3a used for reads mapping.
FeatureCounts v1.15.2 was used to count the number of mapped reads to each gene.
BiomaRt package was used to map mouse genes to human genes, and only uniquely mapped genes between human and mouse were kept.
Significantly differentially expressed genes with FDR-adjusted p-value≤0.01 and absolute fold-change≥2.0 were detected by DESeq2 (v1.18.1).
Genome Ontology and Kyoto Encyclopedia of Genes and Genome (KEGG) pathway over-representation analysis was performed on differentially expressed genes using the WebGestaltR package.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include count values for each Sample.

source_name: OVCAR8 NR Tx

growth_protocol: 5637NR and OVCAR8NR cells were maintained under drug-free conditions for 1 week prior to seeding.

extract_protocol:
RNA was extracted using ReliaPrep RNA Cell Miniprep system (Promega). Total RNA was quantified using the Quant-iT Ribo-Green RNA Assay Kit (Invitrogen).
Automated Illumina  Tru Seq Sample Preparation protocol was used to separate mRNA from total RNA, followed by cDNA  18  synthesis. Libraries were prepared using TruSeq® Stranded mRNA Library Prep kit (Illumina). Following  quality check, the libraries were quantified using the KAPA Library Quantification Kits for Next-Generation  Sequencing (Kapa biosystems), pooled and sequenced on the HiSEq3000 platform targeting 50 million  paired end reads/sample.

treatment_protocol: Parental and neratinib-resistant cells were seeded in triplicate in 10-cm dishes and then treated with or without neratinib (5637 – 600 nM; OVCAR8 – 1 μM); 24h later, cells were harvested and RNA was extracted.

tag: phenotype

value: neratinib-resistant cells

value: neratinib


title: H139

city: YangLing

first: bai

middle: sheng

last: sheng

state: ShaanXi

address: Xi Nong Road

department: College of Agronomy

institute: 西北农林科技大学

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.

data_processing: The array image was acquired using Affymetrix GeneChip® Operating Software (GCOS version 1.4). Copy number values for individual SNPs were extracted and converted from CEL files into signal intensities using GTYPE 4.1 and Affymetrix Copy Number Analysis Tool (CNAT 4.0.1) softwares. Genomic Smoothing analysis was performed by using the smoothing window of 0 Mb, and inferred copy number states were derived from a Hidden Markov Model (HMM) based algorithm implemented in CNAT 4.0.1. Circular Binary Segmentation (Ohlsen et al., 2004) was applied using DNAcopy package for R Bioconductor on raw data.

label: biotin

organism: Triticum aestivum

source_name: leaf

label_protocol: Biotinylated DNA were prepared according to the standard Affymetrix protocol

growth_protocol: H139 seeds germinate at room temperature. When the seedlings reach the two leaf stage, the leaves of several plants are cut off to extract plant genomic DNA.

extract_protocol: Extraction of total DNA was performed according to CTAB

treatment_protocol: The leaves of H139 are frozen by liquid nitrogen and ground into powder.

value: Wheat-Psathyrostachys huashania 2Ns/2D Substitution Line


title: water column RNA_ETSP_Sample18_5m

extract_protocol: DNA and RNA were extracted simultaneously from the same filters using the AllPrep DNA/RNA Mini Kit (Qiagen Sciences, Maryland, USA) with slight modifications (as in Rees et al. 2016).


title: T2DN [DN301]

description:
DN301
DNA methylation data from whole blood samples of Taiwanese patients with nephropathy of Type-2 Diabetes (T2DN).

tag: tissue

value: Whole blood

tag: disease group

value: Type-2 Diabetes with nephropathy

tag: blood glucose

value: Glucose (AC):119 mg/dL; HbA1C:6.6%.

tag: bmi (kg/m2)

tag: duration (yr)

tag: gender

value: Taiwanese


title: OVCAR8 NR Tx-2 [272 DS-23]

tag: cell line


title: rep1_poly_1

description:
P13171_107
P13171_107_S7_bothLanes

value: Veh

tag: rna source

value: Polysome-associated mRNA

tag: replicate


title: T2DN [DN184]

description:
DN184
DNA methylation data from whole blood samples of Taiwanese patients with nephropathy of Type-2 Diabetes (T2DN).

value: Glucose (AC):147 mg/dL; HbA1C:5.9%.

tag: age (yr)

value: female

tag: population


title: water column RNA_ETSP_Sample17_100m

tag: sample type

tag: location


title: ATAC-seq_rep1

city: Farmington

first: Chia-Lin

last: Wei

address: 10 Discovery Drive

institute: The Jackson Laboratory

description: ATAC-seq.bigWig

value: E14 cell line

value: embryonic stem cells


title: T2DN [DN314]

description:
DN314
DNA methylation data from whole blood samples of Taiwanese patients with nephropathy of Type-2 Diabetes (T2DN).

value: Glucose (AC):101 mg/dL; HbA1C:6.7%.


title: T2DN [DN304]

description:
DN304
DNA methylation data from whole blood samples of Taiwanese patients with nephropathy of Type-2 Diabetes (T2DN).

value: Glucose (AC):163 mg/dL; HbA1C:8.1%.


title: OVCAR8 NR control-3 [272 DS-21]

source_name: OVCAR8 NR control

tag: treatment

value: control


title: OVCAR8 NR Tx-1 [272 DS-22]


title: T2DR [DR265]

description:
DR265
DNA methylation data from whole blood samples of Taiwanese patients with proliferative retinopathy of Type-2 Diabetes (T2PDR).

source_name: Blood, T2DR

value: Type-2 Diabetes with proliferative retinopathy

value: Pan retinal photocoagulation with non-neovascularization and Non-diabetic macular edema in both eyes


title: T2DN [DN270]

description:
DN270
DNA methylation data from whole blood samples of Taiwanese patients with nephropathy of Type-2 Diabetes (T2DN).

value: Glucose (AC):114 mg/dL; HbA1C:10.1%.


title: H3K27me3_ChIP_rep2_input

data_processing:
Raw reads were quality trimmed along with the adapter using cutadapt v1.14  (options: -e 0.2 -a AGATCGGAAGAGC --minimum-length 20 --trim-n -n 3). The trimmed-reads were mapped on the mm10 genome using BWA v0.7.12  (options: aln –l 25 followed by samse). Only the de-duplicated uniquely mapped reads were used for downstream analysis.
Peak calling was performed on the pair of ChIP and input dataset with MACS v2.1.1.20160309 (options: --nomodel --extsize 250 -B –SPMR -g mm ; broad peak additional options: --broad --broad-cutoff 0.1). bedGraphToBigWig from kentUtils was used to convert MACS2 generated bedgraph to bigWig format. Fold enrichment was computed with MACS2 bdgcmp and the output bedgraph file was converted to bigWig with bedGraphToBigWig.
Illumina RTA-1.12 to 1.18 software used for basecalling depending on when library is sequenced.
Genome_build: mm10

tag: cell type


title: RNAPolII_ChIP_rep4_input

tag: ip antibody


title: OVCAR8 NR control-2 [272 DS-20]

tag: phenotype

value: neratinib-resistant cells


title: water column RNA_ETSP_Sample16_10m

value: 20-mer DNA oligo

value: Oxygen Minimum Zone nitrogen cycling experiments in the Eastern Tropical South Pacific Ocean

tag: depth

value: PCR fragment amplified from total cDNA prepared from RNA extract


title: T2DR [DR261]

description:
DR261
DNA methylation data from whole blood samples of Taiwanese patients with proliferative retinopathy of Type-2 Diabetes (T2PDR).

tag: tissue

value: Whole blood

tag: disease group

value: Not available

value: Taiwanese


title: water column RNA_ETSP_Sample1_250m


title: T2DN [DN060]

description:
DN060
DNA methylation data from whole blood samples of Taiwanese patients with nephropathy of Type-2 Diabetes (T2DN).

value: Type-2 Diabetes with nephropathy

tag: blood glucose

value: Glucose (AC):220 mg/dL; HbA1C:6.1%.

tag: bmi (kg/m2)


title: T2DR [DR259]

description:
DR259
DNA methylation data from whole blood samples of Taiwanese patients with proliferative retinopathy of Type-2 Diabetes (T2PDR).

tag: duration (yr)

tag: gender

value: male


title: water column RNA_ETSP_Sample15_130m


title: H3K27me3_ChIP_rep2

description:
H3K27me3_ChIP_treat.bigWig
H3K27me3_ChIP_foldEnrich.bigWig
H3K27me3_ChIP.broadPeak.gz

tag: cell line

value: E14 cell line

value: embryonic stem cells


title: OVCAR8 NR control-1 [272 DS-19]


title: water column RNA_ETSP_Sample9_190m


title: water column RNA_ETSP_Sample7_270m


title: T2DR [DR229]

description:
DR229
DNA methylation data from whole blood samples of Taiwanese patients with proliferative retinopathy of Type-2 Diabetes (T2PDR).

value: Glucose (AC):196 mg/dL; HbA1C:8.5%.


title: RNAPolII_ChIP_rep3_input


title: RNAPolII_ChIP_rep2_input


title: T2DR [DR227]

description:
DR227
DNA methylation data from whole blood samples of Taiwanese patients with proliferative retinopathy of Type-2 Diabetes (T2PDR).

value: Pan retinal photocoagulation with non-neovascularization and Mild diabetic macular edema in both eyes

value: Glucose (AC):194 mg/dL; HbA1C:7%.

value: female


title: OVCAR8 parental Tx-3 [272 DS-18]

source_name: OVCAR8 parental Tx

value: parental

value: neratinib


title: RNAPolII_ChIP_rep1_input


title: OVCAR8 parental Tx-2 [272 DS-17]


title: water column RNA_ETSP_Sample6_305m

value: 20-mer DNA oligo


title: water column RNA_ETSP_Sample5_75m

value: Oxygen Minimum Zone nitrogen cycling experiments in the Eastern Tropical South Pacific Ocean


title: T2DR [DR226]

description:
DR226
DNA methylation data from whole blood samples of Taiwanese patients with proliferative retinopathy of Type-2 Diabetes (T2PDR).

value: Type-2 Diabetes with proliferative retinopathy

value: Pan retinal photocoagulation with non-neovascularization and Non-diabetic macular edema in both eyes

value: Glucose (AC):144 mg/dL; HbA1C:7.2%.


title: OVCAR8 parental Tx-1 [272 DS-16]


title: RNAPolII_ChIP_rep3

description:
RNAPolII_ChIP_treat.bigWig
RNAPolII_ChIP_foldEnrich.bigWig
RNAPolII_ChIP.narrowPeak.gz

value: RNA polymerase II clone (Covance MMS126R-500)


title: water column RNA_ETSP_Sample4_220m

value: PCR fragment amplified from total cDNA prepared from RNA extract