PABPC1 RNA-Seq in K562

General Information


RBP	PABPC1
Cell_Line	K562
Method	CRISPR
Exp_Name	PABPC1-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	PABPC1-BGKcLV42-61
Rep2	PABPC1-BGKcLV42-62
CN1	NT-BGKcLV42-1
CN2	NT-BGKcLV42-2
Rep1_qPCR	85.3
Rep2_qPCR	84.0
Rep1_WB	82.1
Rep2_WB	85.7
Antibody Cat#	3505S
Antibody Lot#	lot # 2
Antibody DCC ID
Status	Submitted
Project	ENCORE2
ID	1550

Experiment Information (Status: Submitting)

	BGKcLV42-61	BGKcLV42-62
idx	0	0
TRCN#_or_BGC#	BGC#0001163	BGC#0001163
shRNA_or_gRNA_sequence	TGTGGATGAGATGAACGGAA	TGTGGATGAGATGAACGGAA
PAM	AGG	AGG
Name	PABPC1_74	PABPC1_74
Sample_ID	BGKcLV42-61	BGKcLV42-62
transduction_Date	4/23/24	4/23/24
days	D6	D6
RBP_name	PABPC1	PABPC1
qPCR_result	85.3	84.0
Ave_qPCR	84.6
RT-qPCR_primer-F	CAGGAGTTCGCAATCCTCAG
RT-qPCR_primer-R	GCAGTCAAAGGTTCCTGACC
protein_conc	2259	2359
WB_result	82.1	85.7
Ave_WB	83.9
WB_DONE_date	5/8/24
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	5823	5824

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

	BGKcLV42-61	BGKcLV42-62
Sample_ID	BGKcLV42-61	BGKcLV42-62
Sample Name
Sample Name	PABPC1-BGKcLV42-61	PABPC1-BGKcLV42-62
RBP	PABPC1	PABPC1
Cell_Line	K562	K562
Exp UID
Status	Submitting	Submitting
Status_date	2025-02-13	2025-02-13
Project	ENCORE2	ENCORE2
Note
ID	13094	13095

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV42-61	BGKcLV42-62
Sample #	51	52
Sample Name	PABPC1-BGKcLV42-61	PABPC1-BGKcLV42-62
Sample_Name_Alias
Index Well Position	C07	D07
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	305	306
Peak_Molarity	118.00	109.00
libSampleQC_DNA_Well	DNA_Library_set73/set1/C7.png	DNA_Library_set73/set1/D7.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_set73/set1/C7.png	RNA_Library_set73/set1/D7.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2024-07-15	2024-07-15
Sample_ID	BGKcLV42-61	BGKcLV42-62
RBP	PABPC1	PABPC1
Batch_ID	BGKcLV42	BGKcLV42
WB_result	82.100	85.700
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4320	4321

Sequencing Information

	BGKcLV42-61	BGKcLV42-62
Sample_ID	BGKcLV42-61	BGKcLV42-62
Sample Name	PABPC1-BGKcLV42-61	PABPC1-BGKcLV42-62
Pool ID	Pool-240715	Pool-240715
LocalServer_folder	set73	set73
total_reads	38,779,122	32,130,374
total_aligned_reads	33,999,101	27,302,873
unique_aligned_reads	31,459,377	25,275,529
percent_uniqueAligned	0.81125	0.78666
correlation_replicates	0.999021	0.999021
spikein_reads	426	992
percent_spikeins	0.00001	0.00003
original_ReadLength	101	101
QC_Status	Submitting	Submitting
ID	3187	3188

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-BGKcLV42-61_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set73/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3187	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	30390
PABPC1-BGKcLV42-61_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set73/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3187	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	30480
PABPC1-BGKcLV42-61_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set73/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3187					GRCh38	V40	PABPC1-BGKcLV42-61_L001_R1_001.filtered.trimmed.paired.fastq.gz,PABPC1-BGKcLV42-61_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31322
PABPC1-BGKcLV42-61_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	3187					GRCh38	V40	PABPC1-BGKcLV42-61_Aligned.sortedByCoord.out.bam		ENCORE2	31412
PABPC1-BGKcLV42-61_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	3187					GRCh38	V40	PABPC1-BGKcLV42-61_Aligned.sortedByCoord.out.bam		ENCORE2	31502
PABPC1-BGKcLV42-61_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	3187					GRCh38	V40	PABPC1-BGKcLV42-61_Aligned.sortedByCoord.out.bam		ENCORE2	31592
PABPC1-BGKcLV42-61_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	3187					GRCh38	V40	PABPC1-BGKcLV42-61_Aligned.sortedByCoord.out.bam		ENCORE2	31682
PABPC1-BGKcLV42-61_quant.sf	ENCODE_DATA/set73/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3187					GRCh38	V40	PABPC1-BGKcLV42-61_L001_R1_001.filtered.trimmed.paired.fastq.gz,PABPC1-BGKcLV42-61_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31772
PABPC1-BGKcLV42-62_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set73/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3188	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	30391
PABPC1-BGKcLV42-62_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set73/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3188	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	30481
PABPC1-BGKcLV42-62_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set73/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3188					GRCh38	V40	PABPC1-BGKcLV42-62_L001_R1_001.filtered.trimmed.paired.fastq.gz,PABPC1-BGKcLV42-62_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31323
PABPC1-BGKcLV42-62_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	3188					GRCh38	V40	PABPC1-BGKcLV42-62_Aligned.sortedByCoord.out.bam		ENCORE2	31413
PABPC1-BGKcLV42-62_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	3188					GRCh38	V40	PABPC1-BGKcLV42-62_Aligned.sortedByCoord.out.bam		ENCORE2	31503
PABPC1-BGKcLV42-62_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	3188					GRCh38	V40	PABPC1-BGKcLV42-62_Aligned.sortedByCoord.out.bam		ENCORE2	31593
PABPC1-BGKcLV42-62_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	3188					GRCh38	V40	PABPC1-BGKcLV42-62_Aligned.sortedByCoord.out.bam		ENCORE2	31683
PABPC1-BGKcLV42-62_quant.sf	ENCODE_DATA/set73/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3188					GRCh38	V40	PABPC1-BGKcLV42-62_L001_R1_001.filtered.trimmed.paired.fastq.gz,PABPC1-BGKcLV42-62_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31773