PCBP1 RNA-Seq in 293T

Experiment Information (Status: Submitting)

	BG293LV05-33	BG293LV05-34
idx	0	0
TRCN#_or_BGC#	TRCN0000074668	TRCN0000074668
shRNA_or_gRNA_sequence	CCGGCCCATGATCCAACTGTGTAATCTCGAGATTACACAGTTGGATCATGGGTTTTTG	CCGGCCCATGATCCAACTGTGTAATCTCGAGATTACACAGTTGGATCATGGGTTTTTG
PAM
Name	PCBP1	PCBP1
Sample_ID	BG293LV05-33	BG293LV05-34
transduction_Date	12/18/23	12/18/23
days	D4	D4
RBP_name	PCBP1	PCBP1
qPCR_result	88	84
Ave_qPCR	86
RT-qPCR_primer-F	ACCACCCATGAACTCACCAT
RT-qPCR_primer-R	GACATCTGGCGGATCTCATT
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	10005	10006

Western Blot Western Blot info was not avaliable

Experiment Status

	BG293LV05-33	BG293LV05-34
Sample_ID	BG293LV05-33	BG293LV05-34
Sample Name
Sample Name	PCBP1-BG293LV05-33	PCBP1-BG293LV05-34
RBP	PCBP1	PCBP1
Cell_Line	293T	293T
Exp UID
Status	Submitting	Submitting
Status_date	2024-05-07	2024-05-07
Project	ENCORE2	ENCORE2
Note
ID	12850	12851

Library-Prep
Sequencing

Library-Prep Information

	BG293LV05-33	BG293LV05-34
Sample #	17	18
Sample Name	PCBP1-BG293LV05-33	PCBP1-BG293LV05-34
Sample_Name_Alias
Index Well Position	A09	B09
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2024-01-16	2024-01-16
Lib_ID	Lib-240116	Lib-240116
Tecan_Location
Tecan
Tecan_date
Size_bp	275	274
Peak_Molarity	77.50	82.60
libSampleQC_DNA_Well	DNA_Library_set69/set1/A3.png	DNA_Library_set69/set1/B3.png
RIN	9.7	9.9
libSample_RNA_Well	RNA_Library_set69/set1/B8.png	RNA_Library_set69/set1/C8.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2024-01-19	2024-01-19
Sample_ID	BG293LV05-33	BG293LV05-34
RBP	PCBP1	PCBP1
Batch_ID	BG293LV05	BG293LV05
WB_result	0.000	0.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4198	4199

Sequencing Information

	BG293LV05-33	BG293LV05-34
Sample_ID	BG293LV05-33	BG293LV05-34
Sample Name	PCBP1-BG293LV05-33	PCBP1-BG293LV05-34
Pool ID	Pool-240119	Pool-240119
LocalServer_folder	set69	set69
total_reads	18,897,128	15,637,563
total_aligned_reads	16,446,395	13,193,278
unique_aligned_reads	15,277,981	12,197,258
percent_uniqueAligned	0.80848	0.78000
correlation_replicates	0.989713	0.989713
spikein_reads	5,218	1,392
percent_spikeins	0.00028	0.00009
original_ReadLength	101	101
QC_Status	Submitting	Submitting
ID	2917	2918

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
PCBP1-BG293LV05-33_S149_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set69/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2917	NovaSeq6000	100	paired-ended	1				NT-BG293LV05-1_merged_R1_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV05-2_S134_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	28513
PCBP1-BG293LV05-33_S149_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set69/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2917	NovaSeq6000	100	paired-ended	2				NT-BG293LV05-1_merged_R2_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV05-2_S134_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	28557
PCBP1-BG293LV05-33_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set69/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2917					GRCh38	V40	PCBP1-BG293LV05-33_S149_L002_R1_001.filtered.trimmed.paired.fastq.gz,PCBP1-BG293LV05-33_S149_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	28601
PCBP1-BG293LV05-33_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set69/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2917					GRCh38	V40	PCBP1-BG293LV05-33/Aligned.sortedByCoord.out.bam		ENCORE2	28645
PCBP1-BG293LV05-33_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set69/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2917					GRCh38	V40	PCBP1-BG293LV05-33/Aligned.sortedByCoord.out.bam		ENCORE2	28689
PCBP1-BG293LV05-33_Signal.Unique.strand-.bw	ENCODE_DATA/set69/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2917					GRCh38	V40	PCBP1-BG293LV05-33/Aligned.sortedByCoord.out.bam		ENCORE2	28733
PCBP1-BG293LV05-33_Signal.Unique.strand+.bw	ENCODE_DATA/set69/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2917					GRCh38	V40	PCBP1-BG293LV05-33/Aligned.sortedByCoord.out.bam		ENCORE2	28777
PCBP1-BG293LV05-33_quant.sf	ENCODE_DATA/set69/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2917					GRCh38	V40	PCBP1-BG293LV05-33_S149_L002_R1_001.filtered.trimmed.paired.fastq.gz,PCBP1-BG293LV05-33_S149_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	28821
PCBP1-BG293LV05-34_S150_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set69/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2918	NovaSeq6000	100	paired-ended	1				NT-BG293LV05-1_merged_R1_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV05-2_S134_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	28514
PCBP1-BG293LV05-34_S150_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set69/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2918	NovaSeq6000	100	paired-ended	2				NT-BG293LV05-1_merged_R2_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV05-2_S134_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	28558
PCBP1-BG293LV05-34_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set69/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2918					GRCh38	V40	PCBP1-BG293LV05-34_S150_L002_R1_001.filtered.trimmed.paired.fastq.gz,PCBP1-BG293LV05-34_S150_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	28602
PCBP1-BG293LV05-34_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set69/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2918					GRCh38	V40	PCBP1-BG293LV05-34/Aligned.sortedByCoord.out.bam		ENCORE2	28646
PCBP1-BG293LV05-34_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set69/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2918					GRCh38	V40	PCBP1-BG293LV05-34/Aligned.sortedByCoord.out.bam		ENCORE2	28690
PCBP1-BG293LV05-34_Signal.Unique.strand-.bw	ENCODE_DATA/set69/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2918					GRCh38	V40	PCBP1-BG293LV05-34/Aligned.sortedByCoord.out.bam		ENCORE2	28734
PCBP1-BG293LV05-34_Signal.Unique.strand+.bw	ENCODE_DATA/set69/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2918					GRCh38	V40	PCBP1-BG293LV05-34/Aligned.sortedByCoord.out.bam		ENCORE2	28778
PCBP1-BG293LV05-34_quant.sf	ENCODE_DATA/set69/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2918					GRCh38	V40	PCBP1-BG293LV05-34_S150_L002_R1_001.filtered.trimmed.paired.fastq.gz,PCBP1-BG293LV05-34_S150_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	28822