CNOT4 RNA-Seq in Ribo-STAMP-293T

Experiment Information (Status: Submitted)

	BGRSDLV03-7dox	BGRSDLV03-8dox
idx	0	0
TRCN#_or_BGC#	TRCN0000015215	TRCN0000015215
shRNA_or_gRNA_sequence	GCCTCTTCACATCAGAAACAACTCGAGTTGTTTCTGATGTGAAGAGGC	GCCTCTTCACATCAGAAACAACTCGAGTTGTTTCTGATGTGAAGAGGC
PAM
Name	CNOT4	CNOT4
Sample_ID	BGRSDLV03-7dox	BGRSDLV03-8dox
transduction_Date	9/29/23	9/29/23
days	4 days	4 days
RBP_name	CNOT4	CNOT4
qPCR_result	54.7	51.4
Ave_qPCR	53.0
RT-qPCR_primer-F
RT-qPCR_primer-R
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	9321	9322

Western Blot Western Blot info was not avaliable

Experiment Status

	BGRSDLV03-7dox	BGRSDLV03-8dox
Sample_ID	BGRSDLV03-7dox	BGRSDLV03-8dox
Sample Name
Sample Name	CNOT4-BGRSDLV03-7dox	CNOT4-BGRSDLV03-8dox
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	12604	12605

Library-Prep
Sequencing

Library-Prep Information

	BGRSDLV03-7dox	BGRSDLV03-8dox
Sample #	7	8
Sample Name	CNOT4-BGRSDLV03-7dox	CNOT4-BGRSDLV03-8dox
Sample_Name_Alias
Index Well Position	G05	H05
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	278	312
Peak_Molarity	45.10	48.50
libSampleQC_DNA_Well	DNA_Library_set66/set1/G6.png	DNA_Library_set66/set1/H6.png
RIN	9.6	9.7
libSample_RNA_Well	RNA_Library_set66/set1/G1.png	RNA_Library_set66/set1/H1.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-10-18	2023-10-18
Sample_ID	BGRSDLV03-7dox	BGRSDLV03-8dox
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	4040	4041

Sequencing Information

	BGRSDLV03-7dox	BGRSDLV03-8dox
Sample_ID	BGRSDLV03-7dox	BGRSDLV03-8dox
Sample Name	CNOT4-BGRSDLV03-7dox	CNOT4-BGRSDLV03-8dox
Pool ID	Pool-231018	Pool-231018
LocalServer_folder	set66	set66
total_reads	14,617,845	15,918,331
total_aligned_reads	12,909,532	14,858,707
unique_aligned_reads	12,065,249	13,880,340
percent_uniqueAligned	0.82538	0.87197
correlation_replicates	0.996084	0.996084
spikein_reads	3,410	6,730
percent_spikeins	0.00023	0.00042
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	2759	2760

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-BGRSDLV03-7dox_S7_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set66/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2759	NovaSeq6000	100	paired-ended	1				NT-BGRSDLV03-3dox_S3_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDLV03-4dox_merged_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8908
CNOT4-BGRSDLV03-7dox_S7_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set66/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2759	NovaSeq6000	100	paired-ended	2				NT-BGRSDLV03-3dox_S3_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDLV03-4dox_merged_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8948
CNOT4-BGRSDLV03-7dox_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set66/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2759					GRCh38	V40	CNOT4-BGRSDLV03-7dox_S7_L001_R1_001.filtered.trimmed.paired.fastq.gz,CNOT4-BGRSDLV03-7dox_S7_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	8988
CNOT4-BGRSDLV03-7dox_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	2759					GRCh38	V40	CNOT4-BGRSDLV03-7dox/Aligned.sortedByCoord.out.bam		ENCORE2	9028
CNOT4-BGRSDLV03-7dox_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	2759					GRCh38	V40	CNOT4-BGRSDLV03-7dox/Aligned.sortedByCoord.out.bam		ENCORE2	9068
CNOT4-BGRSDLV03-7dox_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	2759					GRCh38	V40	CNOT4-BGRSDLV03-7dox/Aligned.sortedByCoord.out.bam		ENCORE2	9108
CNOT4-BGRSDLV03-7dox_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	2759					GRCh38	V40	CNOT4-BGRSDLV03-7dox/Aligned.sortedByCoord.out.bam		ENCORE2	9148
CNOT4-BGRSDLV03-7dox_quant.sf	ENCODE_DATA/set66/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2759					GRCh38	V40	CNOT4-BGRSDLV03-7dox_S7_L001_R1_001.filtered.trimmed.paired.fastq.gz,CNOT4-BGRSDLV03-7dox_S7_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9188
CNOT4-BGRSDLV03-8dox_S8_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set66/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2760	NovaSeq6000	100	paired-ended	1				NT-BGRSDLV03-3dox_S3_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDLV03-4dox_merged_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8909
CNOT4-BGRSDLV03-8dox_S8_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set66/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2760	NovaSeq6000	100	paired-ended	2				NT-BGRSDLV03-3dox_S3_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDLV03-4dox_merged_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8949
CNOT4-BGRSDLV03-8dox_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set66/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2760					GRCh38	V40	CNOT4-BGRSDLV03-8dox_S8_L001_R1_001.filtered.trimmed.paired.fastq.gz,CNOT4-BGRSDLV03-8dox_S8_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	8989
CNOT4-BGRSDLV03-8dox_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	2760					GRCh38	V40	CNOT4-BGRSDLV03-8dox/Aligned.sortedByCoord.out.bam		ENCORE2	9029
CNOT4-BGRSDLV03-8dox_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	2760					GRCh38	V40	CNOT4-BGRSDLV03-8dox/Aligned.sortedByCoord.out.bam		ENCORE2	9069
CNOT4-BGRSDLV03-8dox_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	2760					GRCh38	V40	CNOT4-BGRSDLV03-8dox/Aligned.sortedByCoord.out.bam		ENCORE2	9109
CNOT4-BGRSDLV03-8dox_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	2760					GRCh38	V40	CNOT4-BGRSDLV03-8dox/Aligned.sortedByCoord.out.bam		ENCORE2	9149
CNOT4-BGRSDLV03-8dox_quant.sf	ENCODE_DATA/set66/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2760					GRCh38	V40	CNOT4-BGRSDLV03-8dox_S8_L001_R1_001.filtered.trimmed.paired.fastq.gz,CNOT4-BGRSDLV03-8dox_S8_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9189