Dr George Pratt Pdf Download

Enhanced crosslinking and immunoprecipitation (eCLIP) identifies transcriptome wide RBP occupancy sites23. By modifying steps in CLIP-seq and iCLIP protocols, eCLIP requires fewer amplification cycles and results in fewer redundant reads. Additionally, with the eCLIP protocol, size-matched inputs are generated to serve as controls for peak calling and other downstream analyses. The experimental protocol is available at -5396-424a-a1a3-3f18707c3222/@@download/attachment/eCLIP_SOP_v1.P_110915.pdf.

Dr George Pratt Pdf Download

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We require all eCLIP antibodies to undergo primary and secondary characterizations. Detailed RBP antibody standards are available at -8a2d-425b-b2a0-9c39fa296816/@@download/attachment/ENCODE_Approved_Nov_2016_RBP_Antibody_Characterization_Guidelines.pdf.

RNA Bind-n-Seq characterizes RBPs and their motifs in vitro61. Recombinant RBPs are purified and incubated with randomized RNAs. The RBPs are then captured, and bound RNAs are sequenced. The experimental protocol is available at -aaee-4358-a834-c6ee002938b8/@@download/attachment/RBNSExperimentalProtocol_Feb2016_96well.pdf.

We required all commercial histone antibodies to be validated by at least two independent methods, and antibody lots to be analysed independently. Detailed histone mark antibody standards are available at -387a-47c4-ab24-cebe64ead5ae/@@download/attachment/ENCODE_Approved_Oct_2016_Histone_and_Chromatin_associated_Proteins_Antibody_Characterization_Guidelines.pdf.

We required antibodies to undergo primary and secondary characterizations for each lot. For epitope-tagged proteins, we developed a protocol that includes genomic DNA characterization followed by immuno-characterization. Additional details are available at -7e5f-455e-9119-46a54f160711/@@download/attachment/ENCODE_Approved_May_2016_TF_Antibody%20Characterization_Guidelines.pdf (TF antibodies) and -dd6a-44e3-8795-50ead83f34f7/@@download/attachment/Guidelines_for_Use_of_Epitope_Tags_in_ChIP-seq_Jan_2017.pdf (epitope-tagged proteins).

DNase-seq surveys open chromatin regions through genomic cleavage by endonuclease DNase I followed by sequencing. For ENCODE phase III, the DNase-seq protocol was updated, allowing for smaller quantities of input material. Experimental protocols are available at -d14c-4e77-bc52-5517b56daac0/@@download/attachment/Culturedcells_SOP_nuclei_DNase_crosslink_RNA_V1.pdf (cultured cells) and -9a7a-4277-b7be-4a3c1ce1cfc6/@@download/attachment/08112010_nuclei_isolation_human__tissue_V6_3.pdf (tissues). Additional details are available at -standards/dnase-seq/.

To map DNA methylation, WGBS uses bisulfite treatment to convert unmethylated cytosines into uracils, leaving methylated cytosines unchanged. Through sequencing and alignment to a transformed genome, CpG, CHG, and CHH methylation levels can be extracted. The experimental protocol is available at -5ebe-482b-9fa3-d93a968a7045/@@download/attachment/WGBS_V4_protocol.pdf (human) and -cf8f-4f26-b76b-d14a3b9721bd/@@download/attachment/Ecker_Methyl_Protocol_022315.pdf (mouse). Additional details are available at -standards/wgbs/.

DNA replication timing provides insights into both gene regulation and spatiotemporal genome compartmentalization65. Production documents were generated for each experiment, and a representative experimental protocol for Repli-seq is available at: -9f55-41c1-b5ce-78dc7bd59a1e/@@download/attachment/Repliseq_Protocol.pdf.

We downloaded the SNPs tested by MPRA50 in human lymphoblastoid cells from Supplementary Table 1 of that study and reconstructed tested regions by generating a 75-bp window around each SNP. We then intersected cCREs with these regions using bedtools intersect, requiring at least 25% of each cCRE to overlap. Of the cCREs that overlapped a tested region, we calculated the percentage that overlapped an MPRA+ region. We analysed all cCREs and GM12878-specific cCREs stratified by the cCRE group.

We downloaded SuRE peaks in human K562 cells from the Supplementary Data Set of an earlier study51. Using bedtools intersect, we compared the SuRE peaks with the hg38 cCREs lifted down to the hg19 genome version, counting the number of base pairs overlapping each cCRE or region of interest. We then calculated the total percentage of base pairs for each cCRE group that overlapped a SuRE peak.

All of the older issues of the Bulletin have been scanned and PDF copies can be freely downloaded using the link beside each issue below. Many of the PDF files are large, as the original publications often exceeded 100 printed pages, so downloads could take a long time if your internet connection speed is relatively slow.