PABPC1 RNA-Seq in HepG2

General Information


RBP	PABPC1
Cell_Line	HepG2
Method	CRISPR
Exp_Name	PABPC1-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	PABPC1-BGHcLV43-37
Rep2	PABPC1-BGHcLV43-38
CN1	NT-BGHcLV43-1
CN2	NT-BGHcLV43-2
Rep1_qPCR	75.3
Rep2_qPCR	75.2
Rep1_WB	67.7
Rep2_WB	73.7
Antibody Cat#	3505S
Antibody Lot#	lot # 2
Antibody DCC ID
Status	Submitted
Project	ENCORE2
ID	1582

Experiment Information (Status: Submitting)

	BGHcLV43-37	BGHcLV43-38
idx	1405	1406
TRCN#_or_BGC#	BGC#0001164	BGC#0001164
shRNA_or_gRNA_sequence	ATTTGTACACTTTGAGACGC	ATTTGTACACTTTGAGACGC
PAM	AGG	AGG
Name	PABPC1_82	PABPC1_82
Sample_ID	BGHcLV43-37	BGHcLV43-38
transduction_Date	6/6/24	6/6/24
days	D6	D6
RBP_name	PABPC1	PABPC1
qPCR_result	75.3	75.2
Ave_qPCR	75.3
RT-qPCR_primer-F	CAGGAGTTCGCAATCCTCAG
RT-qPCR_primer-R	GCAGTCAAAGGTTCCTGACC
protein_conc	3791	3650
WB_result	67.7	73.7
Ave_WB	70.7
WB_DONE_date	6/21/24
MW	71kd
IP
antibody_Cat#	3505S	lot # 2
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	9658	9659

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
PABPC1	Product_ID: 3505S Lot_ID: 2 Source: Cell Signaling Technology Target Name: PABPC1-human

Experiment Status

	BGHcLV43-37	BGHcLV43-38
Sample_ID	BGHcLV43-37	BGHcLV43-38
Sample Name
Sample Name	PABPC1-BGHcLV43-37	PABPC1-BGHcLV43-38
RBP	PABPC1	PABPC1
Cell_Line	HepG2	HepG2
Exp UID
Status	Submitting	Submitting
Status_date	2025-02-11	2025-02-11
Project	ENCORE2	ENCORE2
Note
ID	13254	13255

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV43-37	BGHcLV43-38
Sample #	27	28
Sample Name	PABPC1-BGHcLV43-37	PABPC1-BGHcLV43-38
Sample_Name_Alias
Index Well Position	C09	D09
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	294	293
Peak_Molarity	110.00	92.40
libSampleQC_DNA_Well	DNA_Library_set74/set1/C4.png	DNA_Library_set74/set1/D4.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_set74/set1/G9.png	RNA_Library_set74/set1/H9.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2024-07-23	2024-07-23
Sample_ID	BGHcLV43-37	BGHcLV43-38
RBP	PABPC1	PABPC1
Batch_ID	BGHcLV43	BGHcLV43
WB_result	67.700	73.700
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4386	4387

Sequencing Information

	BGHcLV43-37	BGHcLV43-38
Sample_ID	BGHcLV43-37	BGHcLV43-38
Sample Name	PABPC1-BGHcLV43-37	PABPC1-BGHcLV43-38
Pool ID	Pool-240723	Pool-240723
LocalServer_folder	set74	set74
total_reads	46,786,171	39,603,503
total_aligned_reads	42,717,695	36,545,212
unique_aligned_reads	40,198,635	34,446,054
percent_uniqueAligned	0.85920	0.86977
correlation_replicates	0.990369	0.990369
spikein_reads	48,930	18,092
percent_spikeins	0.00105	0.00046
original_ReadLength	101	101
QC_Status	Submitting	Submitting
ID	3253	3254

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
PABPC1-BGHcLV43-37_S117_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set74/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3253	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	30546
PABPC1-BGHcLV43-37_S117_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set74/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3253	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	30598
PABPC1-BGHcLV43-37_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set74/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3253					GRCh38	V40	PABPC1-BGHcLV43-37_S117_L003_R1_001.filtered.trimmed.paired.fastq.gz,PABPC1-BGHcLV43-37_S117_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	30650
PABPC1-BGHcLV43-37_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	3253					GRCh38	V40	PABPC1-BGHcLV43-37_Aligned.sortedByCoord.out.bam		ENCORE2	30702
PABPC1-BGHcLV43-37_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	3253					GRCh38	V40	PABPC1-BGHcLV43-37_Aligned.sortedByCoord.out.bam		ENCORE2	30754
PABPC1-BGHcLV43-37_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	3253					GRCh38	V40	PABPC1-BGHcLV43-37_Aligned.sortedByCoord.out.bam		ENCORE2	30806
PABPC1-BGHcLV43-37_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	3253					GRCh38	V40	PABPC1-BGHcLV43-37_Aligned.sortedByCoord.out.bam		ENCORE2	30858
PABPC1-BGHcLV43-37_quant.sf	ENCODE_DATA/set74/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3253					GRCh38	V40	PABPC1-BGHcLV43-37_S117_L003_R1_001.filtered.trimmed.paired.fastq.gz,PABPC1-BGHcLV43-37_S117_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	30910
PABPC1-BGHcLV43-38_S118_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set74/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3254	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	30547
PABPC1-BGHcLV43-38_S118_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set74/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3254	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	30599
PABPC1-BGHcLV43-38_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set74/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3254					GRCh38	V40	PABPC1-BGHcLV43-38_S118_L003_R1_001.filtered.trimmed.paired.fastq.gz,PABPC1-BGHcLV43-38_S118_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	30651
PABPC1-BGHcLV43-38_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	3254					GRCh38	V40	PABPC1-BGHcLV43-38_Aligned.sortedByCoord.out.bam		ENCORE2	30703
PABPC1-BGHcLV43-38_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	3254					GRCh38	V40	PABPC1-BGHcLV43-38_Aligned.sortedByCoord.out.bam		ENCORE2	30755
PABPC1-BGHcLV43-38_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	3254					GRCh38	V40	PABPC1-BGHcLV43-38_Aligned.sortedByCoord.out.bam		ENCORE2	30807
PABPC1-BGHcLV43-38_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	3254					GRCh38	V40	PABPC1-BGHcLV43-38_Aligned.sortedByCoord.out.bam		ENCORE2	30859
PABPC1-BGHcLV43-38_quant.sf	ENCODE_DATA/set74/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3254					GRCh38	V40	PABPC1-BGHcLV43-38_S118_L003_R1_001.filtered.trimmed.paired.fastq.gz,PABPC1-BGHcLV43-38_S118_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	30911