NOP2 RNA-Seq in HepG2

General Information


RBP	NOP2
Cell_Line	HepG2
Method	CRISPR
Exp_Name	NOP2-BGHcLV43-HepG2
ENCODE_series_ID
Batch_ID	BGHcLV43
Pool ID	Pool-240723
Local_Set_Name	set74
ENCODE_KD_Exp_ID
ENCODE_CN_Exp_ID
Rep1	NOP2-BGHcLV43-35
Rep2	NOP2-BGHcLV43-36
CN1	NT-BGHcLV43-1
CN2	NT-BGHcLV43-2
Rep1_qPCR	47.1
Rep2_qPCR	33.0
Rep1_WB	94.7
Rep2_WB	82.8
Antibody Cat#	90709S
Antibody Lot#	lot # 1
Antibody DCC ID
Status	Submitted
Project	ENCORE2
ID	1581

Experiment Information (Status: Submitting)

	BGHcLV43-35	BGHcLV43-36
idx	1403	1404
TRCN#_or_BGC#	BGC#0001162	BGC#0001162
shRNA_or_gRNA_sequence	GCGCAAGTTGGACCCTACGA	GCGCAAGTTGGACCCTACGA
PAM	AGG	AGG
Name	NOP2_98	NOP2_98
Sample_ID	BGHcLV43-35	BGHcLV43-36
transduction_Date	6/6/24	6/6/24
days	D6	D6
RBP_name	NOP2	NOP2
qPCR_result	47.1	33.0
Ave_qPCR	40.1
RT-qPCR_primer-F	gagcggctcaagagtgttgt
RT-qPCR_primer-R	catccagcagtactcggtca
protein_conc	3612	3681
WB_result	94.7	82.8
Ave_WB	88.7
WB_DONE_date	6/17/24
MW	110kd
IP
antibody_Cat#	90709S	lot # 1
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	9656	9657

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
NOP2	Product_ID: 90709S Lot_ID: 1 Source: Cell Signaling Technology Target Name: NOP2-human

Experiment Status

	BGHcLV43-35	BGHcLV43-36
Sample_ID	BGHcLV43-35	BGHcLV43-36
Sample Name
Sample Name	NOP2-BGHcLV43-35	NOP2-BGHcLV43-36
RBP	NOP2	NOP2
Cell_Line	HepG2	HepG2
Exp UID
Status	Submitting	Submitting
Status_date	2025-02-11	2025-02-11
Project	ENCORE2	ENCORE2
Note
ID	13252	13253

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV43-35	BGHcLV43-36
Sample #	25	26
Sample Name	NOP2-BGHcLV43-35	NOP2-BGHcLV43-36
Sample_Name_Alias
Index Well Position	A09	B09
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2024-07-22	2024-07-22
Lib_ID	Lib-240722	Lib-240722
Tecan_Location
Tecan
Tecan_date
Size_bp	288	295
Peak_Molarity	112.00	103.00
libSampleQC_DNA_Well	DNA_Library_set74/set1/A4.png	DNA_Library_set74/set1/B4.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_set74/set1/E9.png	RNA_Library_set74/set1/F9.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2024-07-23	2024-07-23
Sample_ID	BGHcLV43-35	BGHcLV43-36
RBP	NOP2	NOP2
Batch_ID	BGHcLV43	BGHcLV43
WB_result	94.700	82.800
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4384	4385

Sequencing Information

	BGHcLV43-35	BGHcLV43-36
Sample_ID	BGHcLV43-35	BGHcLV43-36
Sample Name	NOP2-BGHcLV43-35	NOP2-BGHcLV43-36
Pool ID	Pool-240723	Pool-240723
LocalServer_folder	set74	set74
total_reads	33,559,971	31,465,467
total_aligned_reads	26,104,947	24,926,980
unique_aligned_reads	24,506,891	23,426,464
percent_uniqueAligned	0.73024	0.74451
correlation_replicates	0.999069	0.999069
spikein_reads	23,694	11,160
percent_spikeins	0.00071	0.00035
original_ReadLength	101	101
QC_Status	Submitting	Submitting
ID	3251	3252

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
NOP2-BGHcLV43-35_S115_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set74/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3251	NovaSeq6000	100	paired-ended	1				NT-BGHcLV43-1_S91_L003_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV43-2_S92_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	30542
NOP2-BGHcLV43-35_S115_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set74/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3251	NovaSeq6000	100	paired-ended	2				NT-BGHcLV43-1_S91_L003_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV43-2_S92_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	30594
NOP2-BGHcLV43-35_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set74/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3251					GRCh38	V40	NOP2-BGHcLV43-35_S115_L003_R1_001.filtered.trimmed.paired.fastq.gz,NOP2-BGHcLV43-35_S115_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	30646
NOP2-BGHcLV43-35_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set74/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3251					GRCh38	V40	NOP2-BGHcLV43-35_Aligned.sortedByCoord.out.bam		ENCORE2	30698
NOP2-BGHcLV43-35_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set74/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3251					GRCh38	V40	NOP2-BGHcLV43-35_Aligned.sortedByCoord.out.bam		ENCORE2	30750
NOP2-BGHcLV43-35_Signal.Unique.strand-.bw	ENCODE_DATA/set74/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3251					GRCh38	V40	NOP2-BGHcLV43-35_Aligned.sortedByCoord.out.bam		ENCORE2	30802
NOP2-BGHcLV43-35_Signal.Unique.strand+.bw	ENCODE_DATA/set74/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3251					GRCh38	V40	NOP2-BGHcLV43-35_Aligned.sortedByCoord.out.bam		ENCORE2	30854
NOP2-BGHcLV43-35_quant.sf	ENCODE_DATA/set74/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3251					GRCh38	V40	NOP2-BGHcLV43-35_S115_L003_R1_001.filtered.trimmed.paired.fastq.gz,NOP2-BGHcLV43-35_S115_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	30906
NOP2-BGHcLV43-36_S116_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set74/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3252	NovaSeq6000	100	paired-ended	1				NT-BGHcLV43-1_S91_L003_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV43-2_S92_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	30543
NOP2-BGHcLV43-36_S116_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set74/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3252	NovaSeq6000	100	paired-ended	2				NT-BGHcLV43-1_S91_L003_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV43-2_S92_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	30595
NOP2-BGHcLV43-36_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set74/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3252					GRCh38	V40	NOP2-BGHcLV43-36_S116_L003_R1_001.filtered.trimmed.paired.fastq.gz,NOP2-BGHcLV43-36_S116_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	30647
NOP2-BGHcLV43-36_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set74/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3252					GRCh38	V40	NOP2-BGHcLV43-36_Aligned.sortedByCoord.out.bam		ENCORE2	30699
NOP2-BGHcLV43-36_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set74/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3252					GRCh38	V40	NOP2-BGHcLV43-36_Aligned.sortedByCoord.out.bam		ENCORE2	30751
NOP2-BGHcLV43-36_Signal.Unique.strand-.bw	ENCODE_DATA/set74/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3252					GRCh38	V40	NOP2-BGHcLV43-36_Aligned.sortedByCoord.out.bam		ENCORE2	30803
NOP2-BGHcLV43-36_Signal.Unique.strand+.bw	ENCODE_DATA/set74/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3252					GRCh38	V40	NOP2-BGHcLV43-36_Aligned.sortedByCoord.out.bam		ENCORE2	30855
NOP2-BGHcLV43-36_quant.sf	ENCODE_DATA/set74/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3252					GRCh38	V40	NOP2-BGHcLV43-36_S116_L003_R1_001.filtered.trimmed.paired.fastq.gz,NOP2-BGHcLV43-36_S116_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	30907