PCBP3 RNA-Seq in 293T

Experiment Information (Status: Released)

	BG293LV06-41	BG293LV06-42
idx	0	0
TRCN#_or_BGC#	TRCN0000074700	TRCN0000074700
shRNA_or_gRNA_sequence	CCGGCCTTGCCCAGTATCTCATCAACTCGAGTTGATGAGATACTGGGCAAGGTTTTTG	CCGGCCTTGCCCAGTATCTCATCAACTCGAGTTGATGAGATACTGGGCAAGGTTTTTG
PAM
Name	PCBP3	PCBP3
Sample_ID	BG293LV06-41	BG293LV06-42
transduction_Date	9/5/24	9/5/24
days	D4	D4
RBP_name	PCBP3	PCBP3
qPCR_result	88.9	87.6
Ave_qPCR	88.2
RT-qPCR_primer-F
RT-qPCR_primer-R
protein_conc	0	0
WB_result
Ave_WB
WB_DONE_date
MW
IP
antibody_Cat#
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	12176	12177

Western Blot Western Blot info was not avaliable

Experiment Status

	BG293LV06-41	BG293LV06-42
Sample_ID	BG293LV06-41	BG293LV06-42
Sample Name
Sample Name	PCBP3-BG293LV06-41	PCBP3-BG293LV06-42
RBP	PCBP3	PCBP3
Cell_Line	293T	293T
Exp UID
Status	Released	Released
Status_date	2025-04-21	2025-04-21
Project	ENCORE2	ENCORE2
Note
ID	13478	13479

Library-Prep
Sequencing

Library-Prep Information

	BG293LV06-41	BG293LV06-42
Sample #	43	44
Sample Name	PCBP3-BG293LV06-41	PCBP3-BG293LV06-42
Sample_Name_Alias
Index Well Position	C06	D06
Index_table	IDT_UniqueDualIndex_96_V2	IDT_UniqueDualIndex_96_V2
LibPrep_date	2024-09-25	2024-09-25
Lib_ID	Lib-240925B	Lib-240925B
Tecan_Location
Tecan
Tecan_date
Size_bp	274	278
Peak_Molarity	70.80	78.60
libSampleQC_DNA_Well	DNA_Library_set71/set1/C6.png	DNA_Library_set71/set1/D6.png
RIN	9.9	9.9
libSample_RNA_Well	RNA_Library_set71/set1/C6.png	RNA_Library_set71/set1/D6.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2024-09-30	2024-09-30
Sample_ID	BG293LV06-41	BG293LV06-42
RBP	PCBP3	PCBP3
Batch_ID	BG293LV06	BG293LV06
WB_result	0.000	0.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4468	4469

Sequencing Information

	BG293LV06-41	BG293LV06-42
Sample_ID	BG293LV06-41	BG293LV06-42
Sample Name	PCBP3-BG293LV06-41	PCBP3-BG293LV06-42
Pool ID	Pool-240930	Pool-240930
LocalServer_folder	set71	set71
total_reads	39,071,991	35,401,746
total_aligned_reads	36,159,465	32,633,364
unique_aligned_reads	33,804,837	30,491,931
percent_uniqueAligned	0.86519	0.86131
correlation_replicates	0.982730	0.982730
spikein_reads	83,314	77,192
percent_spikeins	0.00213	0.00218
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	3037	3038

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
PCBP3-BG293LV06-41_S43_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set71/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3037	NovaSeq6000	100	paired-ended	1				NT-BG293LV06-1merged_S1_L002_R1_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV06-2merged_S2_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	29349
PCBP3-BG293LV06-41_S43_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set71/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3037	NovaSeq6000	100	paired-ended	2				NT-BG293LV06-1merged_S1_L002_R2_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV06-2merged_S2_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	29413
PCBP3-BG293LV06-41_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set71/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3037					GRCh38	V40	PCBP3-BG293LV06-41_S43_L002_R1_001.filtered.trimmed.paired.fastq.gz,PCBP3-BG293LV06-41_S43_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	29478
PCBP3-BG293LV06-41_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set71/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3037					GRCh38	V40	PCBP3-BG293LV06-41_Aligned.sortedByCoord.out.bam		ENCORE2	29542
PCBP3-BG293LV06-41_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set71/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3037					GRCh38	V40	PCBP3-BG293LV06-41_Aligned.sortedByCoord.out.bam		ENCORE2	29606
PCBP3-BG293LV06-41_Signal.Unique.strand-.bw	ENCODE_DATA/set71/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3037					GRCh38	V40	PCBP3-BG293LV06-41_Aligned.sortedByCoord.out.bam		ENCORE2	29670
PCBP3-BG293LV06-41_quant.sf	ENCODE_DATA/set71/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3037					GRCh38	V40	PCBP3-BG293LV06-41_S43_L002_R1_001.filtered.trimmed.paired.fastq.gz,PCBP3-BG293LV06-41_S43_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	29734
PCBP3-BG293LV06-42_S44_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set71/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3038	NovaSeq6000	100	paired-ended	1				NT-BG293LV06-1merged_S1_L002_R1_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV06-2merged_S2_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	29350
PCBP3-BG293LV06-42_S44_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set71/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3038	NovaSeq6000	100	paired-ended	2				NT-BG293LV06-1merged_S1_L002_R2_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV06-2merged_S2_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	29414
PCBP3-BG293LV06-42_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set71/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3038					GRCh38	V40	PCBP3-BG293LV06-42_S44_L002_R1_001.filtered.trimmed.paired.fastq.gz,PCBP3-BG293LV06-42_S44_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	29479
PCBP3-BG293LV06-42_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set71/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3038					GRCh38	V40	PCBP3-BG293LV06-42_Aligned.sortedByCoord.out.bam		ENCORE2	29543
PCBP3-BG293LV06-42_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set71/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3038					GRCh38	V40	PCBP3-BG293LV06-42_Aligned.sortedByCoord.out.bam		ENCORE2	29607
PCBP3-BG293LV06-42_Signal.Unique.strand-.bw	ENCODE_DATA/set71/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3038					GRCh38	V40	PCBP3-BG293LV06-42_Aligned.sortedByCoord.out.bam		ENCORE2	29671
PCBP3-BG293LV06-42_quant.sf	ENCODE_DATA/set71/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3038					GRCh38	V40	PCBP3-BG293LV06-42_S44_L002_R1_001.filtered.trimmed.paired.fastq.gz,PCBP3-BG293LV06-42_S44_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	29735