CNOT4 RNA-Seq in 293T

Experiment Information (Status: Released)

	BG293LV06-95	BG293LV06-96
idx	0	0
TRCN#_or_BGC#	TRCN0000015215	TRCN0000015215
shRNA_or_gRNA_sequence	GCCTCTTCACATCAGAAACAACTCGAGTTGTTTCTGATGTGAAGAGGC	GCCTCTTCACATCAGAAACAACTCGAGTTGTTTCTGATGTGAAGAGGC
PAM
Name	CNOT4	CNOT4
Sample_ID	BG293LV06-95	BG293LV06-96
transduction_Date	9/5/24	9/5/24
days	D4	D4
RBP_name	CNOT4	CNOT4
qPCR_result	83.6	80.6
Ave_qPCR	82.1
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	12230	12231

Western Blot Western Blot info was not avaliable

Experiment Status

	BG293LV06-95	BG293LV06-96
Sample_ID	BG293LV06-95	BG293LV06-96
Sample Name
Sample Name	CNOT4-BG293LV06-95B	CNOT4-BG293LV06-96B
RBP	CNOT4	CNOT4
Cell_Line	293T	293T
Exp UID
Status	Released	Released
Status_date	2025-04-21	2025-04-21
Project	ENCORE2	ENCORE2
Note
ID	13532	13533

Library-Prep
Sequencing

Library-Prep Information

	BG293LV06-95	BG293LV06-96
Sample #	95	96
Sample Name	CNOT4-BG293LV06-95B	CNOT4-BG293LV06-96B
Sample_Name_Alias
Index Well Position	G05	H05
Index_table	IDT_UniqueDualIndex_96_V2	IDT_UniqueDualIndex_96_V2
LibPrep_date	2024-10-02	2024-10-02
Lib_ID	Lib-241002	Lib-241002
Tecan_Location
Tecan
Tecan_date
Size_bp	276	279
Peak_Molarity	86.90	62.10
libSampleQC_DNA_Well	DNA_Library_set72/set1/G5.png	DNA_Library_set72/set1/H5.png
RIN	9.6	9.7
libSample_RNA_Well	RNA_Library_set72/set1/G5.png	RNA_Library_set72/set1/H5.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2024-10-04	2024-10-04
Sample_ID	BG293LV06-95	BG293LV06-96
RBP	CNOT4	CNOT4
Batch_ID	BG293LV06	BG293LV06
WB_result	0.000	0.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix	B	B
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4520	4521

Sequencing Information

	BG293LV06-95	BG293LV06-96
Sample_ID	BG293LV06-95	BG293LV06-96
Sample Name	CNOT4-BG293LV06-95B	CNOT4-BG293LV06-96B
Pool ID	Pool-241004	Pool-241004
LocalServer_folder	set72	set72
total_reads	24,330,504	32,222,897
total_aligned_reads	22,143,354	29,312,442
unique_aligned_reads	20,872,578	27,586,072
percent_uniqueAligned	0.85788	0.85610
correlation_replicates	0.996692	0.996692
spikein_reads	94,104	155,546
percent_spikeins	0.00387	0.00483
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	3089	3090

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-BG293LV06-95B_S47_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set72/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3089	NovaSeq6000	100	paired-ended	1				NT-BG293LV06-1Bmerged_S9_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV06-2Bmerged_S10_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	29768
CNOT4-BG293LV06-95B_S47_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set72/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3089	NovaSeq6000	100	paired-ended	2				NT-BG293LV06-1Bmerged_S9_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV06-2Bmerged_S10_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	29840
CNOT4-BG293LV06-95B_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set72/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3089					GRCh38	V40	CNOT4-BG293LV06-95B_S47_L001_R1_001.filtered.trimmed.paired.fastq.gz,CNOT4-BG293LV06-95B_S47_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	29912
CNOT4-BG293LV06-95B_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set72/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3089					GRCh38	V40	CNOT4-BG293LV06-95B_Aligned.sortedByCoord.out.bam		ENCORE2	29984
CNOT4-BG293LV06-95B_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set72/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3089					GRCh38	V40	CNOT4-BG293LV06-95B_Aligned.sortedByCoord.out.bam		ENCORE2	30056
CNOT4-BG293LV06-95B_Signal.Unique.strand-.bw	ENCODE_DATA/set72/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3089					GRCh38	V40	CNOT4-BG293LV06-95B_Aligned.sortedByCoord.out.bam		ENCORE2	30128
CNOT4-BG293LV06-95B_Signal.Unique.strand+.bw	ENCODE_DATA/set72/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3089					GRCh38	V40	CNOT4-BG293LV06-95B_Aligned.sortedByCoord.out.bam		ENCORE2	30200
CNOT4-BG293LV06-95B_quant.sf	ENCODE_DATA/set72/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3089					GRCh38	V40	CNOT4-BG293LV06-95B_S47_L001_R1_001.filtered.trimmed.paired.fastq.gz,CNOT4-BG293LV06-95B_S47_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	30272
CNOT4-BG293LV06-96B_S48_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set72/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3090	NovaSeq6000	100	paired-ended	1				NT-BG293LV06-1Bmerged_S9_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV06-2Bmerged_S10_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	29769
CNOT4-BG293LV06-96B_S48_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set72/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3090	NovaSeq6000	100	paired-ended	2				NT-BG293LV06-1Bmerged_S9_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV06-2Bmerged_S10_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	29841
CNOT4-BG293LV06-96B_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set72/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3090					GRCh38	V40	CNOT4-BG293LV06-96B_S48_L001_R1_001.filtered.trimmed.paired.fastq.gz,CNOT4-BG293LV06-96B_S48_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	29913
CNOT4-BG293LV06-96B_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set72/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3090					GRCh38	V40	CNOT4-BG293LV06-96B_Aligned.sortedByCoord.out.bam		ENCORE2	29985
CNOT4-BG293LV06-96B_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set72/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3090					GRCh38	V40	CNOT4-BG293LV06-96B_Aligned.sortedByCoord.out.bam		ENCORE2	30057
CNOT4-BG293LV06-96B_Signal.Unique.strand-.bw	ENCODE_DATA/set72/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3090					GRCh38	V40	CNOT4-BG293LV06-96B_Aligned.sortedByCoord.out.bam		ENCORE2	30129
CNOT4-BG293LV06-96B_Signal.Unique.strand+.bw	ENCODE_DATA/set72/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3090					GRCh38	V40	CNOT4-BG293LV06-96B_Aligned.sortedByCoord.out.bam		ENCORE2	30201
CNOT4-BG293LV06-96B_quant.sf	ENCODE_DATA/set72/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3090					GRCh38	V40	CNOT4-BG293LV06-96B_S48_L001_R1_001.filtered.trimmed.paired.fastq.gz,CNOT4-BG293LV06-96B_S48_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	30273