CNBP RNA-Seq in Ribo-STAMP-293T

Experiment Information (Status: Submitted)

	BGRSLV03-15	BGRSLV03-16
idx	0	0
TRCN#_or_BGC#	TRCN0000218324	TRCN0000218324
shRNA_or_gRNA_sequence	GTACCGGATTGAGGCTACAGCCTAATTACTCGAGTAATTAGGCTGTAGCCTCAATTTTTTTG	GTACCGGATTGAGGCTACAGCCTAATTACTCGAGTAATTAGGCTGTAGCCTCAATTTTTTTG
PAM
Name	CNBP	CNBP
Sample_ID	BGRSLV03-15	BGRSLV03-16
transduction_Date	1/30/23	1/30/23
days	D4	D4
RBP_name	CNBP	CNBP
qPCR_result	90.6	90.1
Ave_qPCR	90.4
RT-qPCR_primer-F	tatcgctgtggtgagtctgg
RT-qPCR_primer-R	gcattgctctcgctctctct
protein_conc	0	0
WB_result
Ave_WB
WB_DONE_date
MW
IP
antibody_Cat#
Antibody DCC ID
submitted_to_DCC_date
Rep1_TPM	0	0
Rep2_TPM	0	0
Action	Ready	Ready
Library_start_date
repeat_library
Note
ID	8325	8326

Western Blot Western Blot info was not avaliable

Experiment Status

	BGRSLV03-15	BGRSLV03-16
Sample_ID	BGRSLV03-15	BGRSLV03-16
Sample Name
Sample Name	CNBP-BGRSLV03-15	CNBP-BGRSLV03-16
RBP	CNBP	CNBP
Cell_Line	Ribo-STAMP-293T	Ribo-STAMP-293T
Exp UID
Status	Submitted	Submitted
Status_date	2024-12-03	2024-12-03
Project	ENCORE2	ENCORE2
Note
ID	11380	11381

Library-Prep
Sequencing

Library-Prep Information

	BGRSLV03-15	BGRSLV03-16
Sample #	11	12
Sample Name	CNBP-BGRSLV03-15	CNBP-BGRSLV03-16
Sample_Name_Alias
Index Well Position	C08	D08
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2023-02-15	2023-02-15
Lib_ID	Lib-230215	Lib-230215
Tecan_Location
Tecan
Tecan_date
Size_bp	287	282
Peak_Molarity	52.70	72.00
libSampleQC_DNA_Well	DNA_Library_set58/set1/C8.png	DNA_Library_set58/set1/D8.png
RIN	9.8	10.0
libSample_RNA_Well	RNA_Library_set58/set1/C2.png	RNA_Library_set58/set1/D2.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-02-17	2023-02-17
Sample_ID	BGRSLV03-15	BGRSLV03-16
RBP	CNBP	CNBP
Batch_ID	BGRSLV03	BGRSLV03
WB_result	0.000	0.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	3518	3519

Sequencing Information

	BGRSLV03-15	BGRSLV03-16
Sample_ID	BGRSLV03-15	BGRSLV03-16
Sample Name	CNBP-BGRSLV03-15	CNBP-BGRSLV03-16
Pool ID	Pool-230217	Pool-230217
LocalServer_folder	set58	set58
total_reads	51,180,668	57,723,005
total_aligned_reads	44,517,420	50,396,749
unique_aligned_reads	41,579,181	47,068,384
percent_uniqueAligned	0.81240	0.81542
correlation_replicates	0.997289	0.997289
spikein_reads	352,250	349,644
percent_spikeins	0.00688	0.00606
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	2389	2390

Data Submission Information DCC submission information was not avaliable

File Information

file_name	file_path	file_format	output_type	assay_type	lab	Sample ID	platform	read_length	run_type	paired_end	assembly	genome_annotation	derived_from	controlled_by	Project	FILE_ID
CNBP-BGRSLV03-15_S145_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set58/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2389	NovaSeq6000	100	paired-ended	1				NT-BGRSLV03-1_S135_L004_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV03-2_S136_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8134
CNBP-BGRSLV03-15_S145_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set58/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2389	NovaSeq6000	100	paired-ended	2				NT-BGRSLV03-1_S135_L004_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV03-2_S136_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8176
CNBP-BGRSLV03-15_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set58/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2389					GRCh38	V40	CNBP-BGRSLV03-15_S145_L004_R1_001.filtered.trimmed.paired.fastq.gz,CNBP-BGRSLV03-15_S145_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	11255
CNBP-BGRSLV03-15_Signal.Unique.strand+.bw	ENCODE_DATA/set58/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2389					GRCh38	V40	CNBP-BGRSLV03-15/Aligned.sortedByCoord.out.bam		ENCORE2	11297
CNBP-BGRSLV03-15_Signal.Unique.strand-.bw	ENCODE_DATA/set58/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2389					GRCh38	V40	CNBP-BGRSLV03-15/Aligned.sortedByCoord.out.bam		ENCORE2	11339
CNBP-BGRSLV03-15_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set58/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2389					GRCh38	V40	CNBP-BGRSLV03-15/Aligned.sortedByCoord.out.bam		ENCORE2	11381
CNBP-BGRSLV03-15_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set58/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2389					GRCh38	V40	CNBP-BGRSLV03-15/Aligned.sortedByCoord.out.bam		ENCORE2	11423
CNBP-BGRSLV03-15_quant.sf	ENCODE_DATA/set58/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2389					GRCh38	V40	CNBP-BGRSLV03-15_S145_L004_R1_001.filtered.trimmed.paired.fastq.gz,CNBP-BGRSLV03-15_S145_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	11465
CNBP-BGRSLV03-16_S146_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set58/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2390	NovaSeq6000	100	paired-ended	1				NT-BGRSLV03-1_S135_L004_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV03-2_S136_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8135
CNBP-BGRSLV03-16_S146_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set58/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2390	NovaSeq6000	100	paired-ended	2				NT-BGRSLV03-1_S135_L004_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV03-2_S136_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8177
CNBP-BGRSLV03-16_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set58/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2390					GRCh38	V40	CNBP-BGRSLV03-16_S146_L004_R1_001.filtered.trimmed.paired.fastq.gz,CNBP-BGRSLV03-16_S146_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	11256
CNBP-BGRSLV03-16_Signal.Unique.strand+.bw	ENCODE_DATA/set58/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2390					GRCh38	V40	CNBP-BGRSLV03-16/Aligned.sortedByCoord.out.bam		ENCORE2	11298
CNBP-BGRSLV03-16_Signal.Unique.strand-.bw	ENCODE_DATA/set58/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2390					GRCh38	V40	CNBP-BGRSLV03-16/Aligned.sortedByCoord.out.bam		ENCORE2	11340
CNBP-BGRSLV03-16_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set58/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2390					GRCh38	V40	CNBP-BGRSLV03-16/Aligned.sortedByCoord.out.bam		ENCORE2	11382
CNBP-BGRSLV03-16_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set58/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2390					GRCh38	V40	CNBP-BGRSLV03-16/Aligned.sortedByCoord.out.bam		ENCORE2	11424
CNBP-BGRSLV03-16_quant.sf	ENCODE_DATA/set58/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2390					GRCh38	V40	CNBP-BGRSLV03-16_S146_L004_R1_001.filtered.trimmed.paired.fastq.gz,CNBP-BGRSLV03-16_S146_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	11466