CNOT2 RNA-Seq in 293T

Experiment Information (Status: Released)

	BG293LV06-21	BG293LV06-22
idx	0	0
TRCN#_or_BGC#	TRCN0000234898	TRCN0000234898
shRNA_or_gRNA_sequence	CCGGATGAATGGAGGAGACGTATTACTCGAGTAATACGTCTCCTCCATTCATTTTTTG	CCGGATGAATGGAGGAGACGTATTACTCGAGTAATACGTCTCCTCCATTCATTTTTTG
PAM
Name	CNOT2	CNOT2
Sample_ID	BG293LV06-21	BG293LV06-22
transduction_Date	9/5/24	9/5/24
days	D4	D4
RBP_name	CNOT2	CNOT2
qPCR_result	88.0	84.2
Ave_qPCR	86.1
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	12156	12157

Western Blot Western Blot info was not avaliable

Experiment Status

	BG293LV06-21	BG293LV06-22
Sample_ID	BG293LV06-21	BG293LV06-22
Sample Name
Sample Name	CNOT2-BG293LV06-21	CNOT2-BG293LV06-22
RBP	CNOT2	CNOT2
Cell_Line	293T	293T
Exp UID
Status	Released	Released
Status_date	2025-04-21	2025-04-21
Project	ENCORE2	ENCORE2
Note
ID	13458	13459

Library-Prep
Sequencing

Library-Prep Information

	BG293LV06-21	BG293LV06-22
Sample #	25	26
Sample Name	CNOT2-BG293LV06-21	CNOT2-BG293LV06-22
Sample_Name_Alias
Index Well Position	A04	B04
Index_table	IDT_UniqueDualIndex_96_V2	IDT_UniqueDualIndex_96_V2
LibPrep_date	2024-09-25	2024-09-25
Lib_ID	Lib-240925B	Lib-240925B
Tecan_Location
Tecan
Tecan_date
Size_bp	287	289
Peak_Molarity	75.10	98.60
libSampleQC_DNA_Well	DNA_Library_set71/set1/A4.png	DNA_Library_set71/set1/B4.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_set71/set1/A4.png	RNA_Library_set71/set1/B4.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2024-09-30	2024-09-30
Sample_ID	BG293LV06-21	BG293LV06-22
RBP	CNOT2	CNOT2
Batch_ID	BG293LV06	BG293LV06
WB_result	0.000	0.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4450	4451

Sequencing Information

	BG293LV06-21	BG293LV06-22
Sample_ID	BG293LV06-21	BG293LV06-22
Sample Name	CNOT2-BG293LV06-21	CNOT2-BG293LV06-22
Pool ID	Pool-240930	Pool-240930
LocalServer_folder	set71	set71
total_reads	27,957,605	27,889,486
total_aligned_reads	24,368,012	25,545,339
unique_aligned_reads	22,683,340	23,900,768
percent_uniqueAligned	0.81135	0.85698
correlation_replicates	0.974899	0.974899
spikein_reads	100,702	82,488
percent_spikeins	0.00360	0.00296
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	3019	3020

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
CNOT2-BG293LV06-21_S25_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set71/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3019	NovaSeq6000	100	paired-ended	1				NT-BG293LV06-1merged_S1_L002_R1_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV06-2merged_S2_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	29315
CNOT2-BG293LV06-21_S25_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set71/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3019	NovaSeq6000	100	paired-ended	2				NT-BG293LV06-1merged_S1_L002_R2_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV06-2merged_S2_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	29379
CNOT2-BG293LV06-21_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set71/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3019					GRCh38	V40	CNOT2-BG293LV06-21_S25_L002_R1_001.filtered.trimmed.paired.fastq.gz,CNOT2-BG293LV06-21_S25_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	29444
CNOT2-BG293LV06-21_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set71/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3019					GRCh38	V40	CNOT2-BG293LV06-21_Aligned.sortedByCoord.out.bam		ENCORE2	29508
CNOT2-BG293LV06-21_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set71/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3019					GRCh38	V40	CNOT2-BG293LV06-21_Aligned.sortedByCoord.out.bam		ENCORE2	29572
CNOT2-BG293LV06-21_Signal.Unique.strand-.bw	ENCODE_DATA/set71/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3019					GRCh38	V40	CNOT2-BG293LV06-21_Aligned.sortedByCoord.out.bam		ENCORE2	29636
CNOT2-BG293LV06-21_quant.sf	ENCODE_DATA/set71/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3019					GRCh38	V40	CNOT2-BG293LV06-21_S25_L002_R1_001.filtered.trimmed.paired.fastq.gz,CNOT2-BG293LV06-21_S25_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	29700
CNOT2-BG293LV06-22_S26_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set71/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3020	NovaSeq6000	100	paired-ended	1				NT-BG293LV06-1merged_S1_L002_R1_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV06-2merged_S2_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	29316
CNOT2-BG293LV06-22_S26_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set71/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3020	NovaSeq6000	100	paired-ended	2				NT-BG293LV06-1merged_S1_L002_R2_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV06-2merged_S2_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	29380
CNOT2-BG293LV06-22_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set71/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3020					GRCh38	V40	CNOT2-BG293LV06-22_S26_L002_R1_001.filtered.trimmed.paired.fastq.gz,CNOT2-BG293LV06-22_S26_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	29445
CNOT2-BG293LV06-22_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set71/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3020					GRCh38	V40	CNOT2-BG293LV06-22_Aligned.sortedByCoord.out.bam		ENCORE2	29509
CNOT2-BG293LV06-22_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set71/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3020					GRCh38	V40	CNOT2-BG293LV06-22_Aligned.sortedByCoord.out.bam		ENCORE2	29573
CNOT2-BG293LV06-22_Signal.Unique.strand-.bw	ENCODE_DATA/set71/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3020					GRCh38	V40	CNOT2-BG293LV06-22_Aligned.sortedByCoord.out.bam		ENCORE2	29637
CNOT2-BG293LV06-22_quant.sf	ENCODE_DATA/set71/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3020					GRCh38	V40	CNOT2-BG293LV06-22_S26_L002_R1_001.filtered.trimmed.paired.fastq.gz,CNOT2-BG293LV06-22_S26_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	29701