NOP2 RNA-Seq in K562

General Information


RBP	NOP2
Cell_Line	K562
Method	CRISPR
Exp_Name	NOP2-BGKcLV42-K562
ENCODE_series_ID
Batch_ID	BGKcLV42
Pool ID	Pool-240715
Local_Set_Name	set73
ENCODE_KD_Exp_ID
ENCODE_CN_Exp_ID
Rep1	NOP2-BGKcLV42-59
Rep2	NOP2-BGKcLV42-60
CN1	NT-BGKcLV42-1
CN2	NT-BGKcLV42-2
Rep1_qPCR	0.0
Rep2_qPCR	0.0
Rep1_WB	89.7
Rep2_WB	89.1
Antibody Cat#	90709S
Antibody Lot#	lot # 1
Antibody DCC ID
Status	Submitted
Project	ENCORE2
ID	1549

Experiment Information (Status: Submitting)

	BGKcLV42-59	BGKcLV42-60
idx	0	0
TRCN#_or_BGC#	BGC#0001161	BGC#0001161
shRNA_or_gRNA_sequence	ACCCTACGAAGGAGAAGCGG	ACCCTACGAAGGAGAAGCGG
PAM	GGG	GGG
Name	NOP2_88	NOP2_88
Sample_ID	BGKcLV42-59	BGKcLV42-60
transduction_Date	4/23/24	4/23/24
days	D6	D6
RBP_name	NOP2	NOP2
qPCR_result	0.0	0.0
Ave_qPCR	0.0
RT-qPCR_primer-F	gagcggctcaagagtgttgt
RT-qPCR_primer-R	catccagcagtactcggtca
protein_conc	667	773
WB_result	89.7	89.1
Ave_WB	89.4
WB_DONE_date	4/30/24
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	5821	5822

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

	BGKcLV42-59	BGKcLV42-60
Sample_ID	BGKcLV42-59	BGKcLV42-60
Sample Name
Sample Name	NOP2-BGKcLV42-59	NOP2-BGKcLV42-60
RBP	NOP2	NOP2
Cell_Line	K562	K562
Exp UID
Status	Submitting	Submitting
Status_date	2025-02-13	2025-02-13
Project	ENCORE2	ENCORE2
Note
ID	13092	13093

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV42-59	BGKcLV42-60
Sample #	49	50
Sample Name	NOP2-BGKcLV42-59	NOP2-BGKcLV42-60
Sample_Name_Alias
Index Well Position	A07	B07
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2024-06-21	2024-06-21
Lib_ID	Lib-240621	Lib-240621
Tecan_Location
Tecan
Tecan_date
Size_bp	309	306
Peak_Molarity	126.00	99.80
libSampleQC_DNA_Well	DNA_Library_set73/set1/A7.png	DNA_Library_set73/set1/B7.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_set73/set1/A7.png	RNA_Library_set73/set1/B7.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2024-07-15	2024-07-15
Sample_ID	BGKcLV42-59	BGKcLV42-60
RBP	NOP2	NOP2
Batch_ID	BGKcLV42	BGKcLV42
WB_result	89.700	89.100
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4318	4319

Sequencing Information

	BGKcLV42-59	BGKcLV42-60
Sample_ID	BGKcLV42-59	BGKcLV42-60
Sample Name	NOP2-BGKcLV42-59	NOP2-BGKcLV42-60
Pool ID	Pool-240715	Pool-240715
LocalServer_folder	set73	set73
total_reads	64,054,468	43,552,092
total_aligned_reads	59,643,075	39,154,567
unique_aligned_reads	54,778,851	35,920,062
percent_uniqueAligned	0.85519	0.82476
correlation_replicates	0.996934	0.996934
spikein_reads	13,836	1,586
percent_spikeins	0.00022	0.00004
original_ReadLength	101	101
QC_Status	Submitting	Submitting
ID	3185	3186

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-BGKcLV42-59_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set73/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3185	NovaSeq6000	100	paired-ended	1				NT-BGKcLV42-1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV42-2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	30386
NOP2-BGKcLV42-59_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set73/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3185	NovaSeq6000	100	paired-ended	2				NT-BGKcLV42-1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV42-2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	30476
NOP2-BGKcLV42-59_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set73/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3185					GRCh38	V40	NOP2-BGKcLV42-59_L001_R1_001.filtered.trimmed.paired.fastq.gz,NOP2-BGKcLV42-59_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31318
NOP2-BGKcLV42-59_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set73/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3185					GRCh38	V40	NOP2-BGKcLV42-59_Aligned.sortedByCoord.out.bam		ENCORE2	31408
NOP2-BGKcLV42-59_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set73/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3185					GRCh38	V40	NOP2-BGKcLV42-59_Aligned.sortedByCoord.out.bam		ENCORE2	31498
NOP2-BGKcLV42-59_Signal.Unique.strand-.bw	ENCODE_DATA/set73/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3185					GRCh38	V40	NOP2-BGKcLV42-59_Aligned.sortedByCoord.out.bam		ENCORE2	31588
NOP2-BGKcLV42-59_Signal.Unique.strand+.bw	ENCODE_DATA/set73/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3185					GRCh38	V40	NOP2-BGKcLV42-59_Aligned.sortedByCoord.out.bam		ENCORE2	31678
NOP2-BGKcLV42-59_quant.sf	ENCODE_DATA/set73/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3185					GRCh38	V40	NOP2-BGKcLV42-59_L001_R1_001.filtered.trimmed.paired.fastq.gz,NOP2-BGKcLV42-59_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31768
NOP2-BGKcLV42-60_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set73/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3186	NovaSeq6000	100	paired-ended	1				NT-BGKcLV42-1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV42-2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	30387
NOP2-BGKcLV42-60_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set73/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3186	NovaSeq6000	100	paired-ended	2				NT-BGKcLV42-1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV42-2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	30477
NOP2-BGKcLV42-60_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set73/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3186					GRCh38	V40	NOP2-BGKcLV42-60_L001_R1_001.filtered.trimmed.paired.fastq.gz,NOP2-BGKcLV42-60_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31319
NOP2-BGKcLV42-60_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set73/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3186					GRCh38	V40	NOP2-BGKcLV42-60_Aligned.sortedByCoord.out.bam		ENCORE2	31409
NOP2-BGKcLV42-60_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set73/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3186					GRCh38	V40	NOP2-BGKcLV42-60_Aligned.sortedByCoord.out.bam		ENCORE2	31499
NOP2-BGKcLV42-60_Signal.Unique.strand-.bw	ENCODE_DATA/set73/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3186					GRCh38	V40	NOP2-BGKcLV42-60_Aligned.sortedByCoord.out.bam		ENCORE2	31589
NOP2-BGKcLV42-60_Signal.Unique.strand+.bw	ENCODE_DATA/set73/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3186					GRCh38	V40	NOP2-BGKcLV42-60_Aligned.sortedByCoord.out.bam		ENCORE2	31679
NOP2-BGKcLV42-60_quant.sf	ENCODE_DATA/set73/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3186					GRCh38	V40	NOP2-BGKcLV42-60_L001_R1_001.filtered.trimmed.paired.fastq.gz,NOP2-BGKcLV42-60_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31769