PCBP3 RNA-Seq in 293T

Experiment Information (Status: Submitting)

	BG293LV04-43	BG293LV04-44
idx	0	0
TRCN#_or_BGC#	TRCN0000074698	TRCN0000074698
shRNA_or_gRNA_sequence	CCGGCCTGCCTCACAGATACCAATACTCGAGTATTGGTATCTGTGAGGCAGGTTTTTG	CCGGCCTGCCTCACAGATACCAATACTCGAGTATTGGTATCTGTGAGGCAGGTTTTTG
PAM
Name	PCBP3	PCBP3
Sample_ID	BG293LV04-43	BG293LV04-44
transduction_Date	9/7/23	9/7/23
days	D4	D4
RBP_name	PCBP3	PCBP3
qPCR_result	80.0	78.9
Ave_qPCR	79.4
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	9930	9931

Western Blot Western Blot info was not avaliable

Experiment Status

	BG293LV04-43	BG293LV04-44
Sample_ID	BG293LV04-43	BG293LV04-44
Sample Name
Sample Name	PCBP3-BG293LV04-43	PCBP3-BG293LV04-44
RBP	PCBP3	PCBP3
Cell_Line	293T	293T
Exp UID
Status	Submitting	Submitting
Status_date	2023-12-30	2023-12-30
Project	ENCORE2	ENCORE2
Note
ID	12528	12529

Library-Prep
Sequencing

Library-Prep Information

	BG293LV04-43	BG293LV04-44
Sample #	15	16
Sample Name	PCBP3-BG293LV04-43	PCBP3-BG293LV04-44
Sample_Name_Alias
Index Well Position	G02	H02
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2023-10-10	2023-10-10
Lib_ID	Lib-231010	Lib-231010
Tecan_Location
Tecan
Tecan_date
Size_bp	275	271
Peak_Molarity	52.80	67.30
libSampleQC_DNA_Well	DNA_Library_set64/set1/G10.png	DNA_Library_set64/set1/H10.png
RIN	9.5	9.8
libSample_RNA_Well	RNA_Library_set64/set1/G6.png	RNA_Library_set64/set1/H6.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-10-12	2023-10-12
Sample_ID	BG293LV04-43	BG293LV04-44
RBP	PCBP3	PCBP3
Batch_ID	BG293LV04	BG293LV04
WB_result	0.000	0.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4020	4021

Sequencing Information

	BG293LV04-43	BG293LV04-44
Sample_ID	BG293LV04-43	BG293LV04-44
Sample Name	PCBP3-BG293LV04-43	PCBP3-BG293LV04-44
Pool ID	Pool-231012	Pool-231012
LocalServer_folder	set64	set64
total_reads	22,958,620	30,094,017
total_aligned_reads	20,338,233	28,400,770
unique_aligned_reads	18,932,474	26,595,538
percent_uniqueAligned	0.82463	0.88375
correlation_replicates	0.992623	0.992623
spikein_reads	10,978	11,696
percent_spikeins	0.00048	0.00039
original_ReadLength	100	100
QC_Status	Submitting	Submitting
ID	2629	2630

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-BG293LV04-43_S15_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set64/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2629	NextSeq2000	100	paired-ended	1				NT-BG293LV04-1_S1_R1_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV04-2_S2_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8694
PCBP3-BG293LV04-43_S15_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set64/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2629	NextSeq2000	100	paired-ended	2				NT-BG293LV04-1_S1_R2_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV04-2_S2_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8722
PCBP3-BG293LV04-43_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set64/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2629					GRCh38	V40	PCBP3-BG293LV04-43_S15_R1_001.filtered.trimmed.paired.fastq.gz,PCBP3-BG293LV04-43_S15_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9771
PCBP3-BG293LV04-43_Signal.Unique.strand+.bw	ENCODE_DATA/set64/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2629					GRCh38	V40	PCBP3-BG293LV04-43/Aligned.sortedByCoord.out.bam		ENCORE2	9799
PCBP3-BG293LV04-43_Signal.Unique.strand-.bw	ENCODE_DATA/set64/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2629					GRCh38	V40	PCBP3-BG293LV04-43/Aligned.sortedByCoord.out.bam		ENCORE2	9827
PCBP3-BG293LV04-43_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set64/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2629					GRCh38	V40	PCBP3-BG293LV04-43/Aligned.sortedByCoord.out.bam		ENCORE2	9855
PCBP3-BG293LV04-43_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set64/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2629					GRCh38	V40	PCBP3-BG293LV04-43/Aligned.sortedByCoord.out.bam		ENCORE2	9883
PCBP3-BG293LV04-43_quant.sf	ENCODE_DATA/set64/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2629					GRCh38	V40	PCBP3-BG293LV04-43_S15_R1_001.filtered.trimmed.paired.fastq.gz,PCBP3-BG293LV04-43_S15_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9911
PCBP3-BG293LV04-44_S16_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set64/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2630	NextSeq2000	100	paired-ended	1				NT-BG293LV04-1_S1_R1_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV04-2_S2_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8695
PCBP3-BG293LV04-44_S16_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set64/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2630	NextSeq2000	100	paired-ended	2				NT-BG293LV04-1_S1_R2_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV04-2_S2_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8723
PCBP3-BG293LV04-44_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set64/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2630					GRCh38	V40	PCBP3-BG293LV04-44_S16_R1_001.filtered.trimmed.paired.fastq.gz,PCBP3-BG293LV04-44_S16_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9772
PCBP3-BG293LV04-44_Signal.Unique.strand+.bw	ENCODE_DATA/set64/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2630					GRCh38	V40	PCBP3-BG293LV04-44/Aligned.sortedByCoord.out.bam		ENCORE2	9800
PCBP3-BG293LV04-44_Signal.Unique.strand-.bw	ENCODE_DATA/set64/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2630					GRCh38	V40	PCBP3-BG293LV04-44/Aligned.sortedByCoord.out.bam		ENCORE2	9828
PCBP3-BG293LV04-44_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set64/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2630					GRCh38	V40	PCBP3-BG293LV04-44/Aligned.sortedByCoord.out.bam		ENCORE2	9856
PCBP3-BG293LV04-44_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set64/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2630					GRCh38	V40	PCBP3-BG293LV04-44/Aligned.sortedByCoord.out.bam		ENCORE2	9884
PCBP3-BG293LV04-44_quant.sf	ENCODE_DATA/set64/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2630					GRCh38	V40	PCBP3-BG293LV04-44_S16_R1_001.filtered.trimmed.paired.fastq.gz,PCBP3-BG293LV04-44_S16_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9912