CNOT2 RNA-Seq in HepG2

General Information


RBP	CNOT2
Cell_Line	HepG2
Method	CRISPR
Exp_Name	CNOT2-BGHcLV24-HepG2
ENCODE_series_ID	ENCSR834DVP
Batch_ID	BGHcLV24
Pool ID	Pool-210622
Local_Set_Name	set47
ENCODE_KD_Exp_ID	ENCSR918MUU
ENCODE_CN_Exp_ID	ENCSR671FDZ
Rep1	CNOT2-BGHcLV24-21
Rep2	CNOT2-BGHcLV24-22
CN1	NT-BGHcLV24-1
CN2	NT-BGHcLV24-2
Rep1_qPCR	0.0
Rep2_qPCR	0.0
Rep1_WB	73.0
Rep2_WB	73.0
Antibody Cat#	A302-562A
Antibody Lot#
Antibody DCC ID
Status	Released
Project	ENCODE4
ID	5

Experiment Information (Status: Released)

	BGHcLV24-21	BGHcLV24-22
idx	679	680
TRCN#_or_BGC#	BGC#0000501	BGC#0000501
shRNA_or_gRNA_sequence	GGGTTACTAACATTCCTCAA	GGGTTACTAACATTCCTCAA
PAM	GGG	GGG
Name	CNOT2_84	CNOT2_84
Sample_ID	BGHcLV24-21	BGHcLV24-22
transduction_Date	10/30/20	10/30/20
days	D6	D6
RBP_name	CNOT2	CNOT2
qPCR_result	0.0	0.0
Ave_qPCR	0.0
RT-qPCR_primer-F	TTATCAGGGCAGCAGAGACAG
RT-qPCR_primer-R	CGCAAATTTGGGGTAGAGATT
protein_conc	4493	3575
WB_result	73.0	73.0
Ave_WB	73.0
WB_DONE_date	9/2/20,11/12/20,
MW	59.7KD
IP	Rabbit / I
antibody_Cat#	A302-562A
Antibody DCC ID
submitted_to_DCC_date
Rep1_TPM	0	0
Rep2_TPM	0	0
Action	Ready	Ready
Library_start_date	06/16/21	06/16/21
repeat_library
Note
ID	6834	6835

Western Blot Western Blot info was not avaliable

Experiment Status

	BGHcLV24-21	BGHcLV24-22
Sample_ID	BGHcLV24-21	BGHcLV24-22
Sample Name
Sample Name	CNOT2-BGHcLV24-21	CNOT2-BGHcLV24-22
RBP	CNOT2	CNOT2
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2021-11-04	2021-11-04
Project	ENCODE4	ENCODE4
Note
ID	7789	7790

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV24-21	BGHcLV24-22
Sample #	11	12
Sample Name	CNOT2-BGHcLV24-21	CNOT2-BGHcLV24-22
Sample_Name_Alias
Index Well Position	C08	D08
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2021-06-04	2021-06-04
Lib_ID	Lib-210604	Lib-210604
Tecan_Location
Tecan
Tecan_date
Size_bp	300	305
Peak_Molarity	73.50	74.20
libSampleQC_DNA_Well	DNA_Library_set47/set1/C5.png	DNA_Library_set47/set1/D5.png
RIN	9.6	9.8
libSample_RNA_Well	RNA_Library_set47/set1/C2.png	RNA_Library_set47/set1/D2.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2021-06-22	2021-06-22
Sample_ID	BGHcLV24-21	BGHcLV24-22
RBP	CNOT2	CNOT2
Batch_ID	BGHcLV24	BGHcLV24
WB_result	73.000	73.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	1474	1475

Sequencing Information

	BGHcLV24-21	BGHcLV24-22
Sample_ID	BGHcLV24-21	BGHcLV24-22
Sample Name	CNOT2-BGHcLV24-21	CNOT2-BGHcLV24-22
Pool ID	Pool-210622	Pool-210622
LocalServer_folder	set47	set47
total_reads	131,717,990	114,946,278
total_aligned_reads	120,206,996	104,553,444
unique_aligned_reads	113,497,890	98,770,178
percent_uniqueAligned	0.86167	0.85927
correlation_replicates	0.988608	0.988608
spikein_reads	64,412	27,846
percent_spikeins	0.00049	0.00024
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	556	557

Data Submission Information

	BGHcLV24-21	BGHcLV24-21	BGHcLV24-21	BGHcLV24-21	BGHcLV24-21	BGHcLV24-21	BGHcLV24-22	BGHcLV24-22	BGHcLV24-22	BGHcLV24-22
ENCODE_alias	brenton-graveley:CNOT2-BGHcLV24	brenton-graveley:CNOT2-BGHcLV24-21	brenton-graveley:L-CNOT2-BGHcLV24-21	brenton-graveley:CNOT2-BGHcLV24-21_S71_L002_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:CNOT2-BGHcLV24-21_S71_L002_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:CNOT2-BGHcLV24-HepG2	brenton-graveley:CNOT2-BGHcLV24-22	brenton-graveley:L-CNOT2-BGHcLV24-22	brenton-graveley:CNOT2-BGHcLV24-22_S72_L002_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:CNOT2-BGHcLV24-22_S72_L002_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR918MUU	ENCBS429YTL	ENCLB351QKE	ENCFF379YWQ	ENCFF006NJF	ENCSR834DVP	ENCBS068UAP	ENCLB156YES	ENCFF333TOF	ENCFF093UMS
object_type	experiment	biosample	library	file_fastq1	file_fastq2	gene_silencing_series	biosample	library	file_fastq1	file_fastq2
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHcLV24-21	BGHcLV24-21	BGHcLV24-21	BGHcLV24-21	BGHcLV24-21	BGHcLV24-21	BGHcLV24-22	BGHcLV24-22	BGHcLV24-22	BGHcLV24-22
Sample Name	CNOT2-BGHcLV24-21	CNOT2-BGHcLV24-21	CNOT2-BGHcLV24-21	CNOT2-BGHcLV24-21	CNOT2-BGHcLV24-21	CNOT2-BGHcLV24-21	CNOT2-BGHcLV24-22	CNOT2-BGHcLV24-22	CNOT2-BGHcLV24-22	CNOT2-BGHcLV24-22
Selected	Yes	No	Yes	Yes	Yes	Yes	No	Yes	Yes	Yes
Status	Released	Released	Released	Released	Released	Released	Released	Released	Released	Released
Status_Date	2021-11-04	2021-11-04	2021-11-04	2021-11-04	2021-11-04	2022-03-02	2021-11-04	2021-11-04	2021-11-04	2021-11-04
Project	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4
			LV47_library_protocol					LV47_library_protocol
protocol_URL			L-CNOT2-BGHcLV24-21.pdf					L-CNOT2-BGHcLV24-22.pdf
ID	3240	3267	3311	3355	3399	7149	3268	3312	3356	3400

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-BGHcLV24-21_S71_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set47/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	556	NovaSeq6000	100	paired-ended	1				NT-BGHcLV24-1_S61_L002_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV24-2_S62_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	3714
CNOT2-BGHcLV24-21_S71_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set47/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	556	NovaSeq6000	100	paired-ended	2				NT-BGHcLV24-1_S61_L002_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV24-2_S62_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	3760
CNOT2-BGHcLV24-21_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set47/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	556					GRCh38	V40	CNOT2-BGHcLV24-21_S71_L002_R1_001.filtered.trimmed.paired.fastq.gz,CNOT2-BGHcLV24-21_S71_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25403
CNOT2-BGHcLV24-21_quant.sf	ENCODE_DATA/set47/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	556					GRCh38	V40	CNOT2-BGHcLV24-21_S71_L002_R1_001.filtered.trimmed.paired.fastq.gz,CNOT2-BGHcLV24-21_S71_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25447
CNOT2-BGHcLV24-21_Signal.Unique.strand+.bw	ENCODE_DATA/set47/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	556					GRCh38	V40	CNOT2-BGHcLV24-21/Aligned.sortedByCoord.out.bam		ENCORE2	26279
CNOT2-BGHcLV24-21_Signal.Unique.strand-.bw	ENCODE_DATA/set47/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	556					GRCh38	V40	CNOT2-BGHcLV24-21/Aligned.sortedByCoord.out.bam		ENCORE2	26323
CNOT2-BGHcLV24-21_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set47/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	556					GRCh38	V40	CNOT2-BGHcLV24-21/Aligned.sortedByCoord.out.bam		ENCORE2	26367
CNOT2-BGHcLV24-21_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set47/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	556					GRCh38	V40	CNOT2-BGHcLV24-21/Aligned.sortedByCoord.out.bam		ENCORE2	26411
CNOT2-BGHcLV24-22_S72_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set47/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	557	NovaSeq6000	100	paired-ended	1				NT-BGHcLV24-1_S61_L002_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV24-2_S62_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	3715
CNOT2-BGHcLV24-22_S72_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set47/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	557	NovaSeq6000	100	paired-ended	2				NT-BGHcLV24-1_S61_L002_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV24-2_S62_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	3761
CNOT2-BGHcLV24-22_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set47/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	557					GRCh38	V40	CNOT2-BGHcLV24-22_S72_L002_R1_001.filtered.trimmed.paired.fastq.gz,CNOT2-BGHcLV24-22_S72_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25404
CNOT2-BGHcLV24-22_quant.sf	ENCODE_DATA/set47/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	557					GRCh38	V40	CNOT2-BGHcLV24-22_S72_L002_R1_001.filtered.trimmed.paired.fastq.gz,CNOT2-BGHcLV24-22_S72_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25448
CNOT2-BGHcLV24-22_Signal.Unique.strand+.bw	ENCODE_DATA/set47/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	557					GRCh38	V40	CNOT2-BGHcLV24-22/Aligned.sortedByCoord.out.bam		ENCORE2	26280
CNOT2-BGHcLV24-22_Signal.Unique.strand-.bw	ENCODE_DATA/set47/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	557					GRCh38	V40	CNOT2-BGHcLV24-22/Aligned.sortedByCoord.out.bam		ENCORE2	26324
CNOT2-BGHcLV24-22_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set47/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	557					GRCh38	V40	CNOT2-BGHcLV24-22/Aligned.sortedByCoord.out.bam		ENCORE2	26368
CNOT2-BGHcLV24-22_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set47/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	557					GRCh38	V40	CNOT2-BGHcLV24-22/Aligned.sortedByCoord.out.bam		ENCORE2	26412