PCBP1 RNA-Seq in 293T

Experiment Information (Status: Released)

	BG293LV06-67	BG293LV06-68
idx	0	0
TRCN#_or_BGC#	TRCN0000074668	TRCN0000074668
shRNA_or_gRNA_sequence	CCGGCCCATGATCCAACTGTGTAATCTCGAGATTACACAGTTGGATCATGGGTTTTTG	CCGGCCCATGATCCAACTGTGTAATCTCGAGATTACACAGTTGGATCATGGGTTTTTG
PAM
Name	PCBP1	PCBP1
Sample_ID	BG293LV06-67	BG293LV06-68
transduction_Date	9/5/24	9/5/24
days	D4	D4
RBP_name	PCBP1	PCBP1
qPCR_result	81.6	81.2
Ave_qPCR	81.4
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	12202	12203

Western Blot Western Blot info was not avaliable

Experiment Status

	BG293LV06-67	BG293LV06-68
Sample_ID	BG293LV06-67	BG293LV06-68
Sample Name
Sample Name	PCBP1-BG293LV06-67B	PCBP1-BG293LV06-68B
RBP	PCBP1	PCBP1
Cell_Line	293T	293T
Exp UID
Status	Released	Released
Status_date	2025-04-21	2025-04-21
Project	ENCORE2	ENCORE2
Note
ID	13504	13505

Library-Prep
Sequencing

Library-Prep Information

	BG293LV06-67	BG293LV06-68
Sample #	69	70
Sample Name	PCBP1-BG293LV06-67B	PCBP1-BG293LV06-68B
Sample_Name_Alias
Index Well Position	E02	F02
Index_table	IDT_UniqueDualIndex_96_V2	IDT_UniqueDualIndex_96_V2
LibPrep_date	2024-10-02	2024-10-02
Lib_ID	Lib-241002	Lib-241002
Tecan_Location
Tecan
Tecan_date
Size_bp	277	280
Peak_Molarity	88.80	86.60
libSampleQC_DNA_Well	DNA_Library_set72/set1/E2.png	DNA_Library_set72/set1/F2.png
RIN	9.9	9.9
libSample_RNA_Well	RNA_Library_set72/set1/E2.png	RNA_Library_set72/set1/F2.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2024-10-04	2024-10-04
Sample_ID	BG293LV06-67	BG293LV06-68
RBP	PCBP1	PCBP1
Batch_ID	BG293LV06	BG293LV06
WB_result	0.000	0.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix	B	B
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4494	4495

Sequencing Information

	BG293LV06-67	BG293LV06-68
Sample_ID	BG293LV06-67	BG293LV06-68
Sample Name	PCBP1-BG293LV06-67B	PCBP1-BG293LV06-68B
Pool ID	Pool-241004	Pool-241004
LocalServer_folder	set72	set72
total_reads	72,274,876	26,436,526
total_aligned_reads	64,672,370	24,139,633
unique_aligned_reads	60,215,990	22,500,258
percent_uniqueAligned	0.83315	0.85110
correlation_replicates	0.998407	0.998407
spikein_reads	212,056	89,014
percent_spikeins	0.00293	0.00337
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	3063	3064

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-BG293LV06-67B_S21_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set72/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3063	NovaSeq6000	100	paired-ended	1				NT-BG293LV06-1Bmerged_S9_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV06-2Bmerged_S10_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	29802
PCBP1-BG293LV06-67B_S21_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set72/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3063	NovaSeq6000	100	paired-ended	2				NT-BG293LV06-1Bmerged_S9_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV06-2Bmerged_S10_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	29874
PCBP1-BG293LV06-67B_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set72/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3063					GRCh38	V40	PCBP1-BG293LV06-67B_S21_L001_R1_001.filtered.trimmed.paired.fastq.gz,PCBP1-BG293LV06-67B_S21_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	29946
PCBP1-BG293LV06-67B_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set72/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3063					GRCh38	V40	PCBP1-BG293LV06-67B_Aligned.sortedByCoord.out.bam		ENCORE2	30018
PCBP1-BG293LV06-67B_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set72/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3063					GRCh38	V40	PCBP1-BG293LV06-67B_Aligned.sortedByCoord.out.bam		ENCORE2	30090
PCBP1-BG293LV06-67B_Signal.Unique.strand-.bw	ENCODE_DATA/set72/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3063					GRCh38	V40	PCBP1-BG293LV06-67B_Aligned.sortedByCoord.out.bam		ENCORE2	30162
PCBP1-BG293LV06-67B_Signal.Unique.strand+.bw	ENCODE_DATA/set72/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3063					GRCh38	V40	PCBP1-BG293LV06-67B_Aligned.sortedByCoord.out.bam		ENCORE2	30234
PCBP1-BG293LV06-67B_quant.sf	ENCODE_DATA/set72/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3063					GRCh38	V40	PCBP1-BG293LV06-67B_S21_L001_R1_001.filtered.trimmed.paired.fastq.gz,PCBP1-BG293LV06-67B_S21_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	30306
PCBP1-BG293LV06-68B_S22_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set72/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3064	NovaSeq6000	100	paired-ended	1				NT-BG293LV06-1Bmerged_S9_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV06-2Bmerged_S10_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	29803
PCBP1-BG293LV06-68B_S22_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set72/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3064	NovaSeq6000	100	paired-ended	2				NT-BG293LV06-1Bmerged_S9_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV06-2Bmerged_S10_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	29875
PCBP1-BG293LV06-68B_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set72/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3064					GRCh38	V40	PCBP1-BG293LV06-68B_S22_L001_R1_001.filtered.trimmed.paired.fastq.gz,PCBP1-BG293LV06-68B_S22_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	29947
PCBP1-BG293LV06-68B_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set72/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3064					GRCh38	V40	PCBP1-BG293LV06-68B_Aligned.sortedByCoord.out.bam		ENCORE2	30019
PCBP1-BG293LV06-68B_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set72/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3064					GRCh38	V40	PCBP1-BG293LV06-68B_Aligned.sortedByCoord.out.bam		ENCORE2	30091
PCBP1-BG293LV06-68B_Signal.Unique.strand-.bw	ENCODE_DATA/set72/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3064					GRCh38	V40	PCBP1-BG293LV06-68B_Aligned.sortedByCoord.out.bam		ENCORE2	30163
PCBP1-BG293LV06-68B_Signal.Unique.strand+.bw	ENCODE_DATA/set72/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3064					GRCh38	V40	PCBP1-BG293LV06-68B_Aligned.sortedByCoord.out.bam		ENCORE2	30235
PCBP1-BG293LV06-68B_quant.sf	ENCODE_DATA/set72/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3064					GRCh38	V40	PCBP1-BG293LV06-68B_S22_L001_R1_001.filtered.trimmed.paired.fastq.gz,PCBP1-BG293LV06-68B_S22_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	30307