PKM RNA-Seq in K562

General Information


RBP	PKM
Cell_Line	K562
Method	CRISPR
Exp_Name	PKM-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	PKM-BGKcLV42-65
Rep2	PKM-BGKcLV42-66
CN1	NT-BGKcLV42-1
CN2	NT-BGKcLV42-2
Rep1_qPCR	42.0
Rep2_qPCR	52.6
Rep1_WB	98.6
Rep2_WB	94.7
Antibody Cat#	4053S
Antibody Lot#	lot # 6
Antibody DCC ID
Status	Submitted
Project	ENCORE2
ID	1552

Experiment Information (Status: Submitting)

	BGKcLV42-65	BGKcLV42-66
idx	0	0
TRCN#_or_BGC#	BGC#0001166	BGC#0001166
shRNA_or_gRNA_sequence	GTGGTGAATCAATGTCCAGG	GTGGTGAATCAATGTCCAGG
PAM	CGG	CGG
Name	PKM_75	PKM_75
Sample_ID	BGKcLV42-65	BGKcLV42-66
transduction_Date	4/23/24	4/23/24
days	D6	D6
RBP_name	PKM	PKM
qPCR_result	42.0	52.6
Ave_qPCR	47.3
RT-qPCR_primer-F	cgtggatgatgggcttattt
RT-qPCR_primer-R	ggttcacacccttcttgctg
protein_conc	2492	2528
WB_result	98.6	94.7
Ave_WB	96.7
WB_DONE_date	5/8/24
MW	60kd
IP
antibody_Cat#	4053S	lot # 6
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	5829	5830

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
PKM	Product_ID: 4053S Lot_ID: 6 Source: Cell Signaling Technology Target Name: PKM-human

Experiment Status

	BGKcLV42-65	BGKcLV42-66
Sample_ID	BGKcLV42-65	BGKcLV42-66
Sample Name
Sample Name	PKM-BGKcLV42-65	PKM-BGKcLV42-66
RBP	PKM	PKM
Cell_Line	K562	K562
Exp UID
Status	Submitting	Submitting
Status_date	2025-02-13	2025-02-13
Project	ENCORE2	ENCORE2
Note
ID	13098	13099

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV42-65	BGKcLV42-66
Sample #	55	56
Sample Name	PKM-BGKcLV42-65	PKM-BGKcLV42-66
Sample_Name_Alias
Index Well Position	G07	H07
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	298	303
Peak_Molarity	73.40	68.60
libSampleQC_DNA_Well	DNA_Library_set73/set1/G7.png	DNA_Library_set73/set1/H7.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_set73/set1/G7.png	RNA_Library_set73/set1/H7.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2024-07-15	2024-07-15
Sample_ID	BGKcLV42-65	BGKcLV42-66
RBP	PKM	PKM
Batch_ID	BGKcLV42	BGKcLV42
WB_result	98.600	94.700
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4324	4325

Sequencing Information

	BGKcLV42-65	BGKcLV42-66
Sample_ID	BGKcLV42-65	BGKcLV42-66
Sample Name	PKM-BGKcLV42-65	PKM-BGKcLV42-66
Pool ID	Pool-240715	Pool-240715
LocalServer_folder	set73	set73
total_reads	49,573,358	50,961,950
total_aligned_reads	44,885,793	46,681,964
unique_aligned_reads	41,425,752	43,148,050
percent_uniqueAligned	0.83565	0.84667
correlation_replicates	0.995079	0.995079
spikein_reads	5,076	6,044
percent_spikeins	0.00010	0.00012
original_ReadLength	101	101
QC_Status	Submitting	Submitting
ID	3191	3192

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
PKM-BGKcLV42-65_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set73/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3191	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	30394
PKM-BGKcLV42-65_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set73/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3191	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	30484
PKM-BGKcLV42-65_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set73/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3191					GRCh38	V40	PKM-BGKcLV42-65_L001_R1_001.filtered.trimmed.paired.fastq.gz,PKM-BGKcLV42-65_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31326
PKM-BGKcLV42-65_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	3191					GRCh38	V40	PKM-BGKcLV42-65_Aligned.sortedByCoord.out.bam		ENCORE2	31416
PKM-BGKcLV42-65_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	3191					GRCh38	V40	PKM-BGKcLV42-65_Aligned.sortedByCoord.out.bam		ENCORE2	31506
PKM-BGKcLV42-65_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	3191					GRCh38	V40	PKM-BGKcLV42-65_Aligned.sortedByCoord.out.bam		ENCORE2	31596
PKM-BGKcLV42-65_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	3191					GRCh38	V40	PKM-BGKcLV42-65_Aligned.sortedByCoord.out.bam		ENCORE2	31686
PKM-BGKcLV42-65_quant.sf	ENCODE_DATA/set73/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3191					GRCh38	V40	PKM-BGKcLV42-65_L001_R1_001.filtered.trimmed.paired.fastq.gz,PKM-BGKcLV42-65_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31776
PKM-BGKcLV42-66_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set73/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3192	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	30395
PKM-BGKcLV42-66_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set73/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3192	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	30485
PKM-BGKcLV42-66_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set73/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3192					GRCh38	V40	PKM-BGKcLV42-66_L001_R1_001.filtered.trimmed.paired.fastq.gz,PKM-BGKcLV42-66_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31327
PKM-BGKcLV42-66_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	3192					GRCh38	V40	PKM-BGKcLV42-66_Aligned.sortedByCoord.out.bam		ENCORE2	31417
PKM-BGKcLV42-66_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	3192					GRCh38	V40	PKM-BGKcLV42-66_Aligned.sortedByCoord.out.bam		ENCORE2	31507
PKM-BGKcLV42-66_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	3192					GRCh38	V40	PKM-BGKcLV42-66_Aligned.sortedByCoord.out.bam		ENCORE2	31597
PKM-BGKcLV42-66_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	3192					GRCh38	V40	PKM-BGKcLV42-66_Aligned.sortedByCoord.out.bam		ENCORE2	31687
PKM-BGKcLV42-66_quant.sf	ENCODE_DATA/set73/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3192					GRCh38	V40	PKM-BGKcLV42-66_L001_R1_001.filtered.trimmed.paired.fastq.gz,PKM-BGKcLV42-66_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31777