PKM RNA-Seq in HepG2

General Information


RBP	PKM
Cell_Line	HepG2
Method	CRISPR
Exp_Name	PKM-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	PKM-BGHcLV43-41
Rep2	PKM-BGHcLV43-42
CN1	NT-BGHcLV43-1
CN2	NT-BGHcLV43-2
Rep1_qPCR	82.9
Rep2_qPCR	81.2
Rep1_WB	83.5
Rep2_WB	91.8
Antibody Cat#	4053S
Antibody Lot#	lot # 6
Antibody DCC ID
Status	Submitted
Project	ENCORE2
ID	1584

Experiment Information (Status: Submitting)

	BGHcLV43-41	BGHcLV43-42
idx	1409	1410
TRCN#_or_BGC#	BGC#0001169	BGC#0001169
shRNA_or_gRNA_sequence	TTGGACGGTGCAACCGAGCT	TTGGACGGTGCAACCGAGCT
PAM	GGG	GGG
Name	PKM_96	PKM_96
Sample_ID	BGHcLV43-41	BGHcLV43-42
transduction_Date	6/6/24	6/6/24
days	D6	D6
RBP_name	PKM	PKM
qPCR_result	82.9	81.2
Ave_qPCR	82.0
RT-qPCR_primer-F	cgtggatgatgggcttattt
RT-qPCR_primer-R	ggttcacacccttcttgctg
protein_conc	3825	3470
WB_result	83.5	91.8
Ave_WB	87.6
WB_DONE_date	6/17/24
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	9662	9663

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

	BGHcLV43-41	BGHcLV43-42
Sample_ID	BGHcLV43-41	BGHcLV43-42
Sample Name
Sample Name	PKM-BGHcLV43-41	PKM-BGHcLV43-42
RBP	PKM	PKM
Cell_Line	HepG2	HepG2
Exp UID
Status	Submitting	Submitting
Status_date	2025-02-11	2025-02-11
Project	ENCORE2	ENCORE2
Note
ID	13258	13259

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV43-41	BGHcLV43-42
Sample #	31	32
Sample Name	PKM-BGHcLV43-41	PKM-BGHcLV43-42
Sample_Name_Alias
Index Well Position	G09	H09
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	282	280
Peak_Molarity	89.80	73.00
libSampleQC_DNA_Well	DNA_Library_set74/set1/G4.png	DNA_Library_set74/set1/H4.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_set74/set1/C10.png	RNA_Library_set74/set1/D10.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2024-07-23	2024-07-23
Sample_ID	BGHcLV43-41	BGHcLV43-42
RBP	PKM	PKM
Batch_ID	BGHcLV43	BGHcLV43
WB_result	83.500	91.800
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4390	4391

Sequencing Information

	BGHcLV43-41	BGHcLV43-42
Sample_ID	BGHcLV43-41	BGHcLV43-42
Sample Name	PKM-BGHcLV43-41	PKM-BGHcLV43-42
Pool ID	Pool-240723	Pool-240723
LocalServer_folder	set74	set74
total_reads	59,237,610	50,565,586
total_aligned_reads	53,771,072	46,141,652
unique_aligned_reads	50,596,334	43,298,363
percent_uniqueAligned	0.85413	0.85628
correlation_replicates	0.995789	0.995789
spikein_reads	53,604	42,140
percent_spikeins	0.00090	0.00083
original_ReadLength	101	101
QC_Status	Submitting	Submitting
ID	3257	3258

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-BGHcLV43-41_S121_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set74/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3257	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	30550
PKM-BGHcLV43-41_S121_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set74/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3257	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	30602
PKM-BGHcLV43-41_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set74/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3257					GRCh38	V40	PKM-BGHcLV43-41_S121_L003_R1_001.filtered.trimmed.paired.fastq.gz,PKM-BGHcLV43-41_S121_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	30654
PKM-BGHcLV43-41_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	3257					GRCh38	V40	PKM-BGHcLV43-41_Aligned.sortedByCoord.out.bam		ENCORE2	30706
PKM-BGHcLV43-41_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	3257					GRCh38	V40	PKM-BGHcLV43-41_Aligned.sortedByCoord.out.bam		ENCORE2	30758
PKM-BGHcLV43-41_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	3257					GRCh38	V40	PKM-BGHcLV43-41_Aligned.sortedByCoord.out.bam		ENCORE2	30810
PKM-BGHcLV43-41_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	3257					GRCh38	V40	PKM-BGHcLV43-41_Aligned.sortedByCoord.out.bam		ENCORE2	30862
PKM-BGHcLV43-41_quant.sf	ENCODE_DATA/set74/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3257					GRCh38	V40	PKM-BGHcLV43-41_S121_L003_R1_001.filtered.trimmed.paired.fastq.gz,PKM-BGHcLV43-41_S121_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	30914
PKM-BGHcLV43-42_S122_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set74/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3258	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	30551
PKM-BGHcLV43-42_S122_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set74/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3258	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	30603
PKM-BGHcLV43-42_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set74/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3258					GRCh38	V40	PKM-BGHcLV43-42_S122_L003_R1_001.filtered.trimmed.paired.fastq.gz,PKM-BGHcLV43-42_S122_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	30655
PKM-BGHcLV43-42_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	3258					GRCh38	V40	PKM-BGHcLV43-42_Aligned.sortedByCoord.out.bam		ENCORE2	30707
PKM-BGHcLV43-42_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	3258					GRCh38	V40	PKM-BGHcLV43-42_Aligned.sortedByCoord.out.bam		ENCORE2	30759
PKM-BGHcLV43-42_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	3258					GRCh38	V40	PKM-BGHcLV43-42_Aligned.sortedByCoord.out.bam		ENCORE2	30811
PKM-BGHcLV43-42_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	3258					GRCh38	V40	PKM-BGHcLV43-42_Aligned.sortedByCoord.out.bam		ENCORE2	30863
PKM-BGHcLV43-42_quant.sf	ENCODE_DATA/set74/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3258					GRCh38	V40	PKM-BGHcLV43-42_S122_L003_R1_001.filtered.trimmed.paired.fastq.gz,PKM-BGHcLV43-42_S122_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	30915