CTCF      shRNA in Ribo-STAMP-293T      Batch: BGRSDLV02

Experiment Information (Status: Submitted)
BGRSDLV02-23doxBGRSDLV02-24dox
idx00
TRCN#_or_BGC#TRCN0000230191TRCN0000230191
shRNA_or_gRNA_sequenceCCGGCAAGAATGAGAAGCGCTTTAACTCGAGTTAAAGCGCTTCTCATTCTTGTTTTTGCCGGCAAGAATGAGAAGCGCTTTAACTCGAGTTAAAGCGCTTCTCATTCTTGTTTTTG
PAM
NameCTCFCTCF
Sample_IDBGRSDLV02-23doxBGRSDLV02-24dox
transduction_Date9/15/239/15/23
days4 days4 days
RBP_nameCTCFCTCF
qPCR_result83.883.1
Ave_qPCR83.4
RT-qPCR_primer-F
RT-qPCR_primer-R
protein_conc00
WB_result
Ave_WB
WB_DONE_date
MW
IP
antibody_Cat#
Antibody DCC ID
submitted_to_DCC_date
Rep1_TPM00
Rep2_TPM00
ActionReadyReady
Library_start_date
repeat_library
Note
ID92349235




Western Blot
Western Blot info was not avaliable




Experiment Status
BGRSDLV02-23doxBGRSDLV02-24dox
Sample_IDBGRSDLV02-23doxBGRSDLV02-24dox
Sample Name
Sample NameCTCF-BGRSDLV02-23doxCTCF-BGRSDLV02-24dox
RBPCTCFCTCF
Cell_LineDOX-RS293DOX-RS293
Exp UID
StatusSubmittedSubmitted
Status_date2024-12-032024-12-03
ProjectENCORE2ENCORE2
Note
ID1234212343




Library-Prep Information
BGRSDLV02-23doxBGRSDLV02-24dox
Sample #2324
Sample NameCTCF-BGRSDLV02-23doxCTCF-BGRSDLV02-24dox
Sample_Name_Alias
Index Well PositionG03H03
Index_tableIDT_UniqueDualIndex_96IDT_UniqueDualIndex_96
LibPrep_date2023-09-262023-09-26
Lib_IDLib-230926Lib-230926
Tecan_Location
Tecan
Tecan_date
Size_bp285285
Peak_Molarity68.7060.20
libSampleQC_DNA_WellDNA_Library_set65/set1/G3.pngDNA_Library_set65/set1/H3.png
RIN9.810.0
libSample_RNA_WellRNA_Library_set65/set1/G3.pngRNA_Library_set65/set1/H3.png
SampleQC_methodTapeStation_2022TapeStation_2022
SampleQC_date2023-09-272023-09-27
Sample_IDBGRSDLV02-23doxBGRSDLV02-24dox
RBPCTCFCTCF
Batch_IDBGRSDLV02BGRSDLV02
WB_result0.0000.000
Library DescriptionTruSeq mRNATruSeq mRNA
Repeat_Library_Suffix
Lib_StatusSendToSequenceSendToSequence
ProjectENCORE2ENCORE2
ID39443945




Sequencing Information
BGRSDLV02-23doxBGRSDLV02-24dox
Sample_IDBGRSDLV02-23doxBGRSDLV02-24dox
Sample NameCTCF-BGRSDLV02-23doxCTCF-BGRSDLV02-24dox
Pool IDPool-231003Pool-231003
LocalServer_folderset65set65
total_reads24,279,25121,263,665
total_aligned_reads20,996,02916,664,731
unique_aligned_reads19,416,44915,413,422
percent_uniqueAligned0.799710.72487
correlation_replicates0.9976230.997623
spikein_reads6,7846,662
percent_spikeins0.000280.00031
original_ReadLength100100
QC_StatusSubmittedSubmitted
ID26912692




Data Submission Information
DCC submission information was not avaliable




File Information
file_namefile_pathfile_formatoutput_typeassay_typelabSample IDplatformread_lengthrun_typepaired_endassemblygenome_annotationderived_fromcontrolled_byProjectNoteFILE_ID
CTCF-BGRSDLV02-23dox_S23_L001_R1_001.filtered.trimmed.paired.fastq.gzENCODE_DATA/set65/fastq_trimmedfastqreadsknockdown followed by RNA-seqGraveley Lab2691NovaSeq6000100paired-ended1NT-BGRSDLV02-3dox_S3_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDLV02-4dox_S4_L001_R1_001.filtered.trimmed.paired.fastq.gzENCORE28760
CTCF-BGRSDLV02-23dox_S23_L001_R2_001.filtered.trimmed.paired.fastq.gzENCODE_DATA/set65/fastq_trimmedfastqreadsknockdown followed by RNA-seqGraveley Lab2691NovaSeq6000100paired-ended2NT-BGRSDLV02-3dox_S3_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDLV02-4dox_S4_L001_R2_001.filtered.trimmed.paired.fastq.gzENCORE28836
CTCF-BGRSDLV02-23dox_Aligned.sortedByCoord.out.bamENCODE_DATA/set65/STAR_ENCORE2_trimmed_file_linksbamalignmentsknockdown followed by RNA-seqGraveley Lab2691GRCh38V40CTCF-BGRSDLV02-23dox_S23_L001_R1_001.filtered.trimmed.paired.fastq.gz,CTCF-BGRSDLV02-23dox_S23_L001_R2_001.filtered.trimmed.paired.fastq.gzENCORE29325
CTCF-BGRSDLV02-23dox_Signal.Unique.strand+.bwENCODE_DATA/set65/STAR_ENCORE2_trimmed_file_linksbigWig+uniqueplus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab2691GRCh38V40CTCF-BGRSDLV02-23dox/Aligned.sortedByCoord.out.bamENCORE29401
CTCF-BGRSDLV02-23dox_Signal.Unique.strand-.bwENCODE_DATA/set65/STAR_ENCORE2_trimmed_file_linksbigWig-uniqueminus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab2691GRCh38V40CTCF-BGRSDLV02-23dox/Aligned.sortedByCoord.out.bamENCORE29477
CTCF-BGRSDLV02-23dox_Signal.UniqueMultiple.strand+.bwENCODE_DATA/set65/STAR_ENCORE2_trimmed_file_linksbigWig+allplus strand signal of all readsknockdown followed by RNA-seqGraveley Lab2691GRCh38V40CTCF-BGRSDLV02-23dox/Aligned.sortedByCoord.out.bamENCORE29553
CTCF-BGRSDLV02-23dox_Signal.UniqueMultiple.strand-.bwENCODE_DATA/set65/STAR_ENCORE2_trimmed_file_linksbigWig-allminus strand signal of all readsknockdown followed by RNA-seqGraveley Lab2691GRCh38V40CTCF-BGRSDLV02-23dox/Aligned.sortedByCoord.out.bamENCORE29629
CTCF-BGRSDLV02-23dox_quant.sfENCODE_DATA/set65/salmon_ENCORE2transcript_quantificationtranscript quantificationsknockdown followed by RNA-seqGraveley Lab2691GRCh38V40CTCF-BGRSDLV02-23dox_S23_L001_R1_001.filtered.trimmed.paired.fastq.gz,CTCF-BGRSDLV02-23dox_S23_L001_R2_001.filtered.trimmed.paired.fastq.gzENCORE29705
CTCF-BGRSDLV02-24dox_S24_L001_R1_001.filtered.trimmed.paired.fastq.gzENCODE_DATA/set65/fastq_trimmedfastqreadsknockdown followed by RNA-seqGraveley Lab2692NovaSeq6000100paired-ended1NT-BGRSDLV02-3dox_S3_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDLV02-4dox_S4_L001_R1_001.filtered.trimmed.paired.fastq.gzENCORE28761
CTCF-BGRSDLV02-24dox_S24_L001_R2_001.filtered.trimmed.paired.fastq.gzENCODE_DATA/set65/fastq_trimmedfastqreadsknockdown followed by RNA-seqGraveley Lab2692NovaSeq6000100paired-ended2NT-BGRSDLV02-3dox_S3_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDLV02-4dox_S4_L001_R2_001.filtered.trimmed.paired.fastq.gzENCORE28837
CTCF-BGRSDLV02-24dox_Aligned.sortedByCoord.out.bamENCODE_DATA/set65/STAR_ENCORE2_trimmed_file_linksbamalignmentsknockdown followed by RNA-seqGraveley Lab2692GRCh38V40CTCF-BGRSDLV02-24dox_S24_L001_R1_001.filtered.trimmed.paired.fastq.gz,CTCF-BGRSDLV02-24dox_S24_L001_R2_001.filtered.trimmed.paired.fastq.gzENCORE29326
CTCF-BGRSDLV02-24dox_Signal.Unique.strand+.bwENCODE_DATA/set65/STAR_ENCORE2_trimmed_file_linksbigWig+uniqueplus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab2692GRCh38V40CTCF-BGRSDLV02-24dox/Aligned.sortedByCoord.out.bamENCORE29402
CTCF-BGRSDLV02-24dox_Signal.Unique.strand-.bwENCODE_DATA/set65/STAR_ENCORE2_trimmed_file_linksbigWig-uniqueminus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab2692GRCh38V40CTCF-BGRSDLV02-24dox/Aligned.sortedByCoord.out.bamENCORE29478
CTCF-BGRSDLV02-24dox_Signal.UniqueMultiple.strand+.bwENCODE_DATA/set65/STAR_ENCORE2_trimmed_file_linksbigWig+allplus strand signal of all readsknockdown followed by RNA-seqGraveley Lab2692GRCh38V40CTCF-BGRSDLV02-24dox/Aligned.sortedByCoord.out.bamENCORE29554
CTCF-BGRSDLV02-24dox_Signal.UniqueMultiple.strand-.bwENCODE_DATA/set65/STAR_ENCORE2_trimmed_file_linksbigWig-allminus strand signal of all readsknockdown followed by RNA-seqGraveley Lab2692GRCh38V40CTCF-BGRSDLV02-24dox/Aligned.sortedByCoord.out.bamENCORE29630
CTCF-BGRSDLV02-24dox_quant.sfENCODE_DATA/set65/salmon_ENCORE2transcript_quantificationtranscript quantificationsknockdown followed by RNA-seqGraveley Lab2692GRCh38V40CTCF-BGRSDLV02-24dox_S24_L001_R1_001.filtered.trimmed.paired.fastq.gz,CTCF-BGRSDLV02-24dox_S24_L001_R2_001.filtered.trimmed.paired.fastq.gzENCORE29706