PABPN1 RNA-Seq in K562

General Information


RBP	PABPN1
Cell_Line	K562
Method	CRISPR
Exp_Name	PABPN1-BGKcLV44-K562
ENCODE_series_ID
Batch_ID	BGKcLV44
Pool ID	Pool-241015
Local_Set_Name	set75
ENCODE_KD_Exp_ID
ENCODE_CN_Exp_ID
Rep1	PABPN1-BGKcLV44-41
Rep2	PABPN1-BGKcLV44-42
CN1	NT-BGKcLV44-1
CN2	NT-BGKcLV44-2
Rep1_qPCR	73.1
Rep2_qPCR	77.1
Rep1_WB	96.9
Rep2_WB	96.9
Antibody Cat#	14154S
Antibody Lot#	lot # 1
Antibody DCC ID
Status	Submitted
Project	ENCORE2
ID	1603

Experiment Information (Status: Submitting)

	BGKcLV44-41	BGKcLV44-42
idx	0	0
TRCN#_or_BGC#	BGC#0001040	BGC#0001040
shRNA_or_gRNA_sequence	AGTTACTCACCATTGCCTGG	AGTTACTCACCATTGCCTGG
PAM	AGG	AGG
Name	PABPN1-70	PABPN1-70
Sample_ID	BGKcLV44-41	BGKcLV44-42
transduction_Date	7/30/24	7/30/24
days	D6	D6
RBP_name	PABPN1	PABPN1
qPCR_result	73.1	77.1
Ave_qPCR	75.1
RT-qPCR_primer-F	cggtgatcatgtccattgag
RT-qPCR_primer-R	agcttccagctcttctgctg
protein_conc	3904	3926
WB_result	96.9	96.9
Ave_WB	96.9
WB_DONE_date	8/12/24
MW	33/50kd/
IP
antibody_Cat#	14154S	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	done on BGKLV28-35
ID	5920	5921

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
PABPN1	Product_ID: 14154S Lot_ID: 1 Source: Cell Signaling Technology Target Name: PABPN1-human

Experiment Status

	BGKcLV44-41	BGKcLV44-42
Sample_ID	BGKcLV44-41	BGKcLV44-42
Sample Name
Sample Name	PABPN1-BGKcLV44-41	PABPN1-BGKcLV44-42
RBP	PABPN1	PABPN1
Cell_Line	K562	K562
Exp UID
Status	Submitting	Submitting
Status_date	2025-02-11	2025-02-11
Project	ENCORE2	ENCORE2
Note
ID	13598	13599

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV44-41	BGKcLV44-42
Sample #	27	28
Sample Name	PABPN1-BGKcLV44-41	PABPN1-BGKcLV44-42
Sample_Name_Alias
Index Well Position	C09	D09
Index_table	IDT_UniqueDualIndex_96_V2	IDT_UniqueDualIndex_96_V2
LibPrep_date	2024-10-10	2024-10-10
Lib_ID	Lib-241010	Lib-241010
Tecan_Location
Tecan
Tecan_date
Size_bp	291	289
Peak_Molarity	72.00	93.20
libSampleQC_DNA_Well	DNA_Library_set75/set1/C9.png	DNA_Library_set75/set1/D9.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_set75/set1/C3.png	RNA_Library_set75/set1/D3.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2024-10-15	2024-10-15
Sample_ID	BGKcLV44-41	BGKcLV44-42
RBP	PABPN1	PABPN1
Batch_ID	BGKcLV44	BGKcLV44
WB_result	96.900	96.900
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4586	4587

Sequencing Information

	BGKcLV44-41	BGKcLV44-42
Sample_ID	BGKcLV44-41	BGKcLV44-42
Sample Name	PABPN1-BGKcLV44-41	PABPN1-BGKcLV44-42
Pool ID	Pool-241015	Pool-241015
LocalServer_folder	set75	set75
total_reads	95,907,695	33,445,382
total_aligned_reads	90,985,247	31,853,112
unique_aligned_reads	83,411,137	29,280,780
percent_uniqueAligned	0.86970	0.87548
correlation_replicates	0.999395	0.999395
spikein_reads	206,750	70,960
percent_spikeins	0.00216	0.00212
original_ReadLength	101	101
QC_Status	Submitting	Submitting
ID	3297	3298

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
PABPN1-BGKcLV44-41_S19_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set75/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3297	NovaSeq6000	100	paired-ended	1				NT-BGKcLV44-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV44-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	30954
PABPN1-BGKcLV44-41_S19_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set75/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3297	NovaSeq6000	100	paired-ended	2				NT-BGKcLV44-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV44-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	30996
PABPN1-BGKcLV44-41_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set75/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3297					GRCh38	V40	PABPN1-BGKcLV44-41_S19_L001_R1_001.filtered.trimmed.paired.fastq.gz,PABPN1-BGKcLV44-41_S19_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31038
PABPN1-BGKcLV44-41_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set75/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3297					GRCh38	V40	PABPN1-BGKcLV44-41_Aligned.sortedByCoord.out.bam		ENCORE2	31080
PABPN1-BGKcLV44-41_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set75/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3297					GRCh38	V40	PABPN1-BGKcLV44-41_Aligned.sortedByCoord.out.bam		ENCORE2	31122
PABPN1-BGKcLV44-41_Signal.Unique.strand-.bw	ENCODE_DATA/set75/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3297					GRCh38	V40	PABPN1-BGKcLV44-41_Aligned.sortedByCoord.out.bam		ENCORE2	31164
PABPN1-BGKcLV44-41_Signal.Unique.strand+.bw	ENCODE_DATA/set75/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3297					GRCh38	V40	PABPN1-BGKcLV44-41_Aligned.sortedByCoord.out.bam		ENCORE2	31206
PABPN1-BGKcLV44-41_quant.sf	ENCODE_DATA/set75/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3297					GRCh38	V40	PABPN1-BGKcLV44-41_S19_L001_R1_001.filtered.trimmed.paired.fastq.gz,PABPN1-BGKcLV44-41_S19_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31248
PABPN1-BGKcLV44-42_S20_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set75/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3298	NovaSeq6000	100	paired-ended	1				NT-BGKcLV44-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV44-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	30955
PABPN1-BGKcLV44-42_S20_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set75/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3298	NovaSeq6000	100	paired-ended	2				NT-BGKcLV44-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV44-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	30997
PABPN1-BGKcLV44-42_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set75/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3298					GRCh38	V40	PABPN1-BGKcLV44-42_S20_L001_R1_001.filtered.trimmed.paired.fastq.gz,PABPN1-BGKcLV44-42_S20_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31039
PABPN1-BGKcLV44-42_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set75/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3298					GRCh38	V40	PABPN1-BGKcLV44-42_Aligned.sortedByCoord.out.bam		ENCORE2	31081
PABPN1-BGKcLV44-42_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set75/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3298					GRCh38	V40	PABPN1-BGKcLV44-42_Aligned.sortedByCoord.out.bam		ENCORE2	31123
PABPN1-BGKcLV44-42_Signal.Unique.strand-.bw	ENCODE_DATA/set75/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3298					GRCh38	V40	PABPN1-BGKcLV44-42_Aligned.sortedByCoord.out.bam		ENCORE2	31165
PABPN1-BGKcLV44-42_Signal.Unique.strand+.bw	ENCODE_DATA/set75/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3298					GRCh38	V40	PABPN1-BGKcLV44-42_Aligned.sortedByCoord.out.bam		ENCORE2	31207
PABPN1-BGKcLV44-42_quant.sf	ENCODE_DATA/set75/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3298					GRCh38	V40	PABPN1-BGKcLV44-42_S20_L001_R1_001.filtered.trimmed.paired.fastq.gz,PABPN1-BGKcLV44-42_S20_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31249