CNOT4 RNA-Seq in Ribo-STAMP-293T

Experiment Information (Status: Submitted)

	BGRSDLV03-5	BGRSDLV03-6
idx	0	0
TRCN#_or_BGC#	TRCN0000015215	TRCN0000015215
shRNA_or_gRNA_sequence	GCCTCTTCACATCAGAAACAACTCGAGTTGTTTCTGATGTGAAGAGGC	GCCTCTTCACATCAGAAACAACTCGAGTTGTTTCTGATGTGAAGAGGC
PAM
Name	CNOT4	CNOT4
Sample_ID	BGRSDLV03-5	BGRSDLV03-6
transduction_Date	9/29/23	9/29/23
days	4 days	4 days
RBP_name	CNOT4	CNOT4
qPCR_result	52.4	57.4
Ave_qPCR	54.9
RT-qPCR_primer-F	CCATTGACAAACCTTCAGATTC
RT-qPCR_primer-R	ACAAACCAGGTGGTGGTGA
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	9319	9320

Western Blot Western Blot info was not avaliable

Experiment Status

	BGRSDLV03-5	BGRSDLV03-6
Sample_ID	BGRSDLV03-5	BGRSDLV03-6
Sample Name
Sample Name	CNOT4-BGRSDLV03-5	CNOT4-BGRSDLV03-6
RBP	CNOT4	CNOT4
Cell_Line	DOX-RS293	DOX-RS293
Exp UID
Status	Submitted	Submitted
Status_date	2024-12-03	2024-12-03
Project	ENCORE2	ENCORE2
Note
ID	12602	12603

Library-Prep
Sequencing

Library-Prep Information

	BGRSDLV03-5	BGRSDLV03-6
Sample #	5	6
Sample Name	CNOT4-BGRSDLV03-5	CNOT4-BGRSDLV03-6
Sample_Name_Alias
Index Well Position	E05	F05
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2023-10-17	2023-10-17
Lib_ID	Lib-231017	Lib-231017
Tecan_Location
Tecan
Tecan_date
Size_bp	282	287
Peak_Molarity	39.40	49.40
libSampleQC_DNA_Well	DNA_Library_set66/set1/E6.png	DNA_Library_set66/set1/F6.png
RIN	9.6	9.5
libSample_RNA_Well	RNA_Library_set66/set1/E1.png	RNA_Library_set66/set1/F1.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-10-18	2023-10-18
Sample_ID	BGRSDLV03-5	BGRSDLV03-6
RBP	CNOT4	CNOT4
Batch_ID	BGRSDLV03	BGRSDLV03
WB_result	0.000	0.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4038	4039

Sequencing Information

	BGRSDLV03-5	BGRSDLV03-6
Sample_ID	BGRSDLV03-5	BGRSDLV03-6
Sample Name	CNOT4-BGRSDLV03-5	CNOT4-BGRSDLV03-6
Pool ID	Pool-231018	Pool-231018
LocalServer_folder	set66	set66
total_reads	16,257,015	14,496,588
total_aligned_reads	14,167,502	12,695,636
unique_aligned_reads	13,222,692	11,873,178
percent_uniqueAligned	0.81335	0.81903
correlation_replicates	0.997669	0.997669
spikein_reads	3,006	4,792
percent_spikeins	0.00018	0.00033
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	2757	2758

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
CNOT4-BGRSDLV03-5_S5_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set66/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2757	NovaSeq6000	100	paired-ended	1				NT-BGRSDLV03-1_merged_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDLV03-2_merged_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8906
CNOT4-BGRSDLV03-5_S5_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set66/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2757	NovaSeq6000	100	paired-ended	2				NT-BGRSDLV03-1_merged_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDLV03-2_merged_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8946
CNOT4-BGRSDLV03-5_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set66/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2757					GRCh38	V40	CNOT4-BGRSDLV03-5_S5_L001_R1_001.filtered.trimmed.paired.fastq.gz,CNOT4-BGRSDLV03-5_S5_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	8986
CNOT4-BGRSDLV03-5_Signal.Unique.strand+.bw	ENCODE_DATA/set66/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2757					GRCh38	V40	CNOT4-BGRSDLV03-5/Aligned.sortedByCoord.out.bam		ENCORE2	9026
CNOT4-BGRSDLV03-5_Signal.Unique.strand-.bw	ENCODE_DATA/set66/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2757					GRCh38	V40	CNOT4-BGRSDLV03-5/Aligned.sortedByCoord.out.bam		ENCORE2	9066
CNOT4-BGRSDLV03-5_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set66/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2757					GRCh38	V40	CNOT4-BGRSDLV03-5/Aligned.sortedByCoord.out.bam		ENCORE2	9106
CNOT4-BGRSDLV03-5_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set66/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2757					GRCh38	V40	CNOT4-BGRSDLV03-5/Aligned.sortedByCoord.out.bam		ENCORE2	9146
CNOT4-BGRSDLV03-5_quant.sf	ENCODE_DATA/set66/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2757					GRCh38	V40	CNOT4-BGRSDLV03-5_S5_L001_R1_001.filtered.trimmed.paired.fastq.gz,CNOT4-BGRSDLV03-5_S5_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9186
CNOT4-BGRSDLV03-6_S6_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set66/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2758	NovaSeq6000	100	paired-ended	1				NT-BGRSDLV03-1_merged_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDLV03-2_merged_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8907
CNOT4-BGRSDLV03-6_S6_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set66/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2758	NovaSeq6000	100	paired-ended	2				NT-BGRSDLV03-1_merged_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDLV03-2_merged_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8947
CNOT4-BGRSDLV03-6_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set66/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2758					GRCh38	V40	CNOT4-BGRSDLV03-6_S6_L001_R1_001.filtered.trimmed.paired.fastq.gz,CNOT4-BGRSDLV03-6_S6_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	8987
CNOT4-BGRSDLV03-6_Signal.Unique.strand+.bw	ENCODE_DATA/set66/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2758					GRCh38	V40	CNOT4-BGRSDLV03-6/Aligned.sortedByCoord.out.bam		ENCORE2	9027
CNOT4-BGRSDLV03-6_Signal.Unique.strand-.bw	ENCODE_DATA/set66/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2758					GRCh38	V40	CNOT4-BGRSDLV03-6/Aligned.sortedByCoord.out.bam		ENCORE2	9067
CNOT4-BGRSDLV03-6_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set66/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2758					GRCh38	V40	CNOT4-BGRSDLV03-6/Aligned.sortedByCoord.out.bam		ENCORE2	9107
CNOT4-BGRSDLV03-6_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set66/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2758					GRCh38	V40	CNOT4-BGRSDLV03-6/Aligned.sortedByCoord.out.bam		ENCORE2	9147
CNOT4-BGRSDLV03-6_quant.sf	ENCODE_DATA/set66/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2758					GRCh38	V40	CNOT4-BGRSDLV03-6_S6_L001_R1_001.filtered.trimmed.paired.fastq.gz,CNOT4-BGRSDLV03-6_S6_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9187