CNOT4 RNA-Seq in 293T

Experiment Information (Status: Revoked)

	BG293LV02-5	BG293LV02-6
idx	0	0
TRCN#_or_BGC#	TRCN0000015215	TRCN0000015215
shRNA_or_gRNA_sequence	GCCTCTTCACATCAGAAACAACTCGAGTTGTTTCTGATGTGAAGAGGC	GCCTCTTCACATCAGAAACAACTCGAGTTGTTTCTGATGTGAAGAGGC
PAM
Name	CNOT4	CNOT4
Sample_ID	BG293LV02-5	BG293LV02-6
transduction_Date	3/20/23	3/20/23
days	D4	D4
RBP_name	CNOT4	CNOT4
qPCR_result	68.0	72.0
Ave_qPCR	70.0
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	9800	9801

Western Blot Western Blot info was not avaliable

Experiment Status

	BG293LV02-5	BG293LV02-6
Sample_ID	BG293LV02-5	BG293LV02-6
Sample Name
Sample Name	CNOT4-BG293LV02-5	CNOT4-BG293LV02-6
RBP	CNOT4	CNOT4
Cell_Line	293T	293T
Exp UID
Status	Revoked	Revoked
Status_date	2023-09-20	2023-09-20
Project	ENCORE2	ENCORE2
Note
ID	11562	11563

Library-Prep
Sequencing

Library-Prep Information

	BG293LV02-5	BG293LV02-6
Sample #	5	6
Sample Name	CNOT4-BG293LV02-5	CNOT4-BG293LV02-6
Sample_Name_Alias
Index Well Position	E01	F01
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2023-04-12	2023-04-12
Lib_ID	Lib-230412	Lib-230412
Tecan_Location
Tecan
Tecan_date
Size_bp	291	290
Peak_Molarity	79.60	87.10
libSampleQC_DNA_Well	DNA_Library_set60-62/set2/E1.png	DNA_Library_set60-62/set2/F1.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_set60-62/set1/E1.png	RNA_Library_set60-62/set1/F1.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-04-17	2023-04-17
Sample_ID	BG293LV02-5	BG293LV02-6
RBP	CNOT4	CNOT4
Batch_ID	BG293LV02	BG293LV02
WB_result	0.000	0.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	3592	3593

Sequencing Information

	BG293LV02-5	BG293LV02-6
Sample_ID	BG293LV02-5	BG293LV02-6
Sample Name	CNOT4-BG293LV02-5	CNOT4-BG293LV02-6
Pool ID	Pool-230417	Pool-230417
LocalServer_folder	set60	set60
total_reads	44,094,430	25,296,535
total_aligned_reads	35,498,869	16,733,174
unique_aligned_reads	32,998,396	15,590,672
percent_uniqueAligned	0.74836	0.61632
correlation_replicates	0.978044	0.978044
spikein_reads	79,782	50,458
percent_spikeins	0.00181	0.00199
original_ReadLength	101	101
QC_Status	Submitting	Submitting
ID	2463	2464

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-BG293LV02-5_S5_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set60/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2463	NovaSeq6000	100	paired-ended	1				NT-BG293LV02-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV02-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	7964
CNOT4-BG293LV02-5_S5_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set60/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2463	NovaSeq6000	100	paired-ended	2				NT-BG293LV02-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV02-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8008
CNOT4-BG293LV02-5_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set60/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2463					GRCh38	V40	CNOT4-BG293LV02-5_S5_L001_R1_001.filtered.trimmed.paired.fastq.gz,CNOT4-BG293LV02-5_S5_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10757
CNOT4-BG293LV02-5_Signal.Unique.strand+.bw	ENCODE_DATA/set60/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2463					GRCh38	V40	CNOT4-BG293LV02-5/Aligned.sortedByCoord.out.bam		ENCORE2	10801
CNOT4-BG293LV02-5_Signal.Unique.strand-.bw	ENCODE_DATA/set60/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2463					GRCh38	V40	CNOT4-BG293LV02-5/Aligned.sortedByCoord.out.bam		ENCORE2	10845
CNOT4-BG293LV02-5_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set60/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2463					GRCh38	V40	CNOT4-BG293LV02-5/Aligned.sortedByCoord.out.bam		ENCORE2	10889
CNOT4-BG293LV02-5_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set60/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2463					GRCh38	V40	CNOT4-BG293LV02-5/Aligned.sortedByCoord.out.bam		ENCORE2	10933
CNOT4-BG293LV02-5_quant.sf	ENCODE_DATA/set60/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2463					GRCh38	V40	CNOT4-BG293LV02-5_S5_L001_R1_001.filtered.trimmed.paired.fastq.gz,CNOT4-BG293LV02-5_S5_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10977
CNOT4-BG293LV02-6_S6_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set60/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2464	NovaSeq6000	100	paired-ended	1				NT-BG293LV02-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV02-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	7965
CNOT4-BG293LV02-6_S6_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set60/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2464	NovaSeq6000	100	paired-ended	2				NT-BG293LV02-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV02-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8009
CNOT4-BG293LV02-6_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set60/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2464					GRCh38	V40	CNOT4-BG293LV02-6_S6_L001_R1_001.filtered.trimmed.paired.fastq.gz,CNOT4-BG293LV02-6_S6_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10758
CNOT4-BG293LV02-6_Signal.Unique.strand+.bw	ENCODE_DATA/set60/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2464					GRCh38	V40	CNOT4-BG293LV02-6/Aligned.sortedByCoord.out.bam		ENCORE2	10802
CNOT4-BG293LV02-6_Signal.Unique.strand-.bw	ENCODE_DATA/set60/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2464					GRCh38	V40	CNOT4-BG293LV02-6/Aligned.sortedByCoord.out.bam		ENCORE2	10846
CNOT4-BG293LV02-6_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set60/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2464					GRCh38	V40	CNOT4-BG293LV02-6/Aligned.sortedByCoord.out.bam		ENCORE2	10890
CNOT4-BG293LV02-6_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set60/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2464					GRCh38	V40	CNOT4-BG293LV02-6/Aligned.sortedByCoord.out.bam		ENCORE2	10934
CNOT4-BG293LV02-6_quant.sf	ENCODE_DATA/set60/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2464					GRCh38	V40	CNOT4-BG293LV02-6_S6_L001_R1_001.filtered.trimmed.paired.fastq.gz,CNOT4-BG293LV02-6_S6_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10978