CNOT4 RNA-Seq in Ribo-STAMP-293T

Experiment Information (Status: Submitted)

	BGRSLV02-69	BGRSLV02-70
idx	0	0
TRCN#_or_BGC#	TRCN0000015215	TRCN0000015215
shRNA_or_gRNA_sequence	GCCTCTTCACATCAGAAACAACTCGAGTTGTTTCTGATGTGAAGAGGC	GCCTCTTCACATCAGAAACAACTCGAGTTGTTTCTGATGTGAAGAGGC
PAM
Name	CNOT4	CNOT4
Sample_ID	BGRSLV02-69	BGRSLV02-70
transduction_Date	12/5/22	12/5/22
days	D4	D4
RBP_name	CNOT4	CNOT4
qPCR_result	60.2	60.7
Ave_qPCR	60.4
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	8306	8307

Western Blot Western Blot info was not avaliable

Experiment Status

	BGRSLV02-69	BGRSLV02-70
Sample_ID	BGRSLV02-69	BGRSLV02-70
Sample Name
Sample Name	CNOT4-BGRSLV02-69	CNOT4-BGRSLV02-70
RBP	CNOT4	CNOT4
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	11342	11343

Library-Prep
Sequencing

Library-Prep Information

	BGRSLV02-69	BGRSLV02-70
Sample #	45	46
Sample Name	CNOT4-BGRSLV02-69	CNOT4-BGRSLV02-70
Sample_Name_Alias
Index Well Position	E06	F06
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2023-02-07	2023-02-07
Lib_ID	Lib-230207	Lib-230207
Tecan_Location
Tecan
Tecan_date
Size_bp	294	292
Peak_Molarity	56.70	21.40
libSampleQC_DNA_Well	DNA_Library_set57/set1/E12.png	DNA_Library_set57/set1/F12.png
RIN	9.6	9.9
libSample_RNA_Well	RNA_Library_set57/set1/E6.png	RNA_Library_set57/set1/F6.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-02-07	2023-02-07
Sample_ID	BGRSLV02-69	BGRSLV02-70
RBP	CNOT4	CNOT4
Batch_ID	BGRSLV02	BGRSLV02
WB_result	0.000	0.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	3506	3507

Sequencing Information

	BGRSLV02-69	BGRSLV02-70
Sample_ID	BGRSLV02-69	BGRSLV02-70
Sample Name	CNOT4-BGRSLV02-69	CNOT4-BGRSLV02-70
Pool ID	Pool-230207	Pool-230207
LocalServer_folder	set57	set57
total_reads	43,011,732	99,952,553
total_aligned_reads	40,013,620	94,296,850
unique_aligned_reads	37,407,785	88,310,659
percent_uniqueAligned	0.86971	0.88353
correlation_replicates	0.997606	0.997606
spikein_reads	20,100	48,162
percent_spikeins	0.00047	0.00048
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	2377	2378

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-BGRSLV02-69_S133_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set57/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2377	NovaSeq6000	100	paired-ended	1				NT-BGRSLV02-1_S89_L003_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV02-2_S90_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8212
CNOT4-BGRSLV02-69_S133_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set57/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2377	NovaSeq6000	100	paired-ended	2				NT-BGRSLV02-1_S89_L003_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV02-2_S90_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8258
CNOT4-BGRSLV02-69_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set57/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2377					GRCh38	V40	CNOT4-BGRSLV02-69_S133_L003_R1_001.filtered.trimmed.paired.fastq.gz,CNOT4-BGRSLV02-69_S133_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	11501
CNOT4-BGRSLV02-69_Signal.Unique.strand+.bw	ENCODE_DATA/set57/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2377					GRCh38	V40	CNOT4-BGRSLV02-69/Aligned.sortedByCoord.out.bam		ENCORE2	11547
CNOT4-BGRSLV02-69_Signal.Unique.strand-.bw	ENCODE_DATA/set57/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2377					GRCh38	V40	CNOT4-BGRSLV02-69/Aligned.sortedByCoord.out.bam		ENCORE2	11593
CNOT4-BGRSLV02-69_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set57/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2377					GRCh38	V40	CNOT4-BGRSLV02-69/Aligned.sortedByCoord.out.bam		ENCORE2	11639
CNOT4-BGRSLV02-69_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set57/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2377					GRCh38	V40	CNOT4-BGRSLV02-69/Aligned.sortedByCoord.out.bam		ENCORE2	11685
CNOT4-BGRSLV02-69_quant.sf	ENCODE_DATA/set57/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2377					GRCh38	V40	CNOT4-BGRSLV02-69_S133_L003_R1_001.filtered.trimmed.paired.fastq.gz,CNOT4-BGRSLV02-69_S133_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	11731
CNOT4-BGRSLV02-70_S134_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set57/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2378	NovaSeq6000	100	paired-ended	1				NT-BGRSLV02-1_S89_L003_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV02-2_S90_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8213
CNOT4-BGRSLV02-70_S134_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set57/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2378	NovaSeq6000	100	paired-ended	2				NT-BGRSLV02-1_S89_L003_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV02-2_S90_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8259
CNOT4-BGRSLV02-70_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set57/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2378					GRCh38	V40	CNOT4-BGRSLV02-70_S134_L003_R1_001.filtered.trimmed.paired.fastq.gz,CNOT4-BGRSLV02-70_S134_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	11502
CNOT4-BGRSLV02-70_Signal.Unique.strand+.bw	ENCODE_DATA/set57/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2378					GRCh38	V40	CNOT4-BGRSLV02-70/Aligned.sortedByCoord.out.bam		ENCORE2	11548
CNOT4-BGRSLV02-70_Signal.Unique.strand-.bw	ENCODE_DATA/set57/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2378					GRCh38	V40	CNOT4-BGRSLV02-70/Aligned.sortedByCoord.out.bam		ENCORE2	11594
CNOT4-BGRSLV02-70_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set57/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2378					GRCh38	V40	CNOT4-BGRSLV02-70/Aligned.sortedByCoord.out.bam		ENCORE2	11640
CNOT4-BGRSLV02-70_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set57/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2378					GRCh38	V40	CNOT4-BGRSLV02-70/Aligned.sortedByCoord.out.bam		ENCORE2	11686
CNOT4-BGRSLV02-70_quant.sf	ENCODE_DATA/set57/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2378					GRCh38	V40	CNOT4-BGRSLV02-70_S134_L003_R1_001.filtered.trimmed.paired.fastq.gz,CNOT4-BGRSLV02-70_S134_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	11732