PPIA RNA-Seq in 293T

Experiment Information (Status: Submitting)

	BG293LV04-49	BG293LV04-50
idx	0	0
TRCN#_or_BGC#	TRCN0000049230	TRCN0000049230
shRNA_or_gRNA_sequence	CCGGTGGTGACTTCACACGCCATAACTCGAGTTATGGCGTGTGAAGTCACCATTTTTG	CCGGTGGTGACTTCACACGCCATAACTCGAGTTATGGCGTGTGAAGTCACCATTTTTG
PAM
Name	PPIA	PPIA
Sample_ID	BG293LV04-49	BG293LV04-50
transduction_Date	9/7/23	9/7/23
days	D4	D4
RBP_name	PPIA	PPIA
qPCR_result	98.2	98.3
Ave_qPCR	98.3
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	9936	9937

Western Blot Western Blot info was not avaliable

Experiment Status

	BG293LV04-49	BG293LV04-50
Sample_ID	BG293LV04-49	BG293LV04-50
Sample Name
Sample Name	PPIA-BG293LV04-49	PPIA-BG293LV04-50
RBP	PPIA	PPIA
Cell_Line	293T	293T
Exp UID
Status	Submitting	Submitting
Status_date	2023-12-30	2023-12-30
Project	ENCORE2	ENCORE2
Note
ID	12530	12531

Library-Prep
Sequencing

Library-Prep Information

	BG293LV04-49	BG293LV04-50
Sample #	17	18
Sample Name	PPIA-BG293LV04-49	PPIA-BG293LV04-50
Sample_Name_Alias
Index Well Position	A03	B03
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	281	273
Peak_Molarity	66.20	60.70
libSampleQC_DNA_Well	DNA_Library_set64/set1/A11.png	DNA_Library_set64/set1/B11.png
RIN	9.6	9.5
libSample_RNA_Well	RNA_Library_set64/set1/A7.png	RNA_Library_set64/set1/B7.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-10-12	2023-10-12
Sample_ID	BG293LV04-49	BG293LV04-50
RBP	PPIA	PPIA
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	4022	4023

Sequencing Information

	BG293LV04-49	BG293LV04-50
Sample_ID	BG293LV04-49	BG293LV04-50
Sample Name	PPIA-BG293LV04-49	PPIA-BG293LV04-50
Pool ID	Pool-231012	Pool-231012
LocalServer_folder	set64	set64
total_reads	30,355,111	28,159,860
total_aligned_reads	27,442,647	26,033,260
unique_aligned_reads	25,589,774	24,161,276
percent_uniqueAligned	0.84301	0.85800
correlation_replicates	0.995754	0.995754
spikein_reads	9,912	3,104
percent_spikeins	0.00033	0.00011
original_ReadLength	100	100
QC_Status	Submitting	Submitting
ID	2631	2632

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
PPIA-BG293LV04-49_S17_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set64/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2631	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	8696
PPIA-BG293LV04-49_S17_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set64/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2631	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	8724
PPIA-BG293LV04-49_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set64/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2631					GRCh38	V40	PPIA-BG293LV04-49_S17_R1_001.filtered.trimmed.paired.fastq.gz,PPIA-BG293LV04-49_S17_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9773
PPIA-BG293LV04-49_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	2631					GRCh38	V40	PPIA-BG293LV04-49/Aligned.sortedByCoord.out.bam		ENCORE2	9801
PPIA-BG293LV04-49_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	2631					GRCh38	V40	PPIA-BG293LV04-49/Aligned.sortedByCoord.out.bam		ENCORE2	9829
PPIA-BG293LV04-49_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	2631					GRCh38	V40	PPIA-BG293LV04-49/Aligned.sortedByCoord.out.bam		ENCORE2	9857
PPIA-BG293LV04-49_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	2631					GRCh38	V40	PPIA-BG293LV04-49/Aligned.sortedByCoord.out.bam		ENCORE2	9885
PPIA-BG293LV04-49_quant.sf	ENCODE_DATA/set64/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2631					GRCh38	V40	PPIA-BG293LV04-49_S17_R1_001.filtered.trimmed.paired.fastq.gz,PPIA-BG293LV04-49_S17_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9913
PPIA-BG293LV04-50_S18_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set64/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2632	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	8697
PPIA-BG293LV04-50_S18_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set64/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2632	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	8725
PPIA-BG293LV04-50_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set64/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2632					GRCh38	V40	PPIA-BG293LV04-50_S18_R1_001.filtered.trimmed.paired.fastq.gz,PPIA-BG293LV04-50_S18_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9774
PPIA-BG293LV04-50_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	2632					GRCh38	V40	PPIA-BG293LV04-50/Aligned.sortedByCoord.out.bam		ENCORE2	9802
PPIA-BG293LV04-50_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	2632					GRCh38	V40	PPIA-BG293LV04-50/Aligned.sortedByCoord.out.bam		ENCORE2	9830
PPIA-BG293LV04-50_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	2632					GRCh38	V40	PPIA-BG293LV04-50/Aligned.sortedByCoord.out.bam		ENCORE2	9858
PPIA-BG293LV04-50_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	2632					GRCh38	V40	PPIA-BG293LV04-50/Aligned.sortedByCoord.out.bam		ENCORE2	9886
PPIA-BG293LV04-50_quant.sf	ENCODE_DATA/set64/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2632					GRCh38	V40	PPIA-BG293LV04-50_S18_R1_001.filtered.trimmed.paired.fastq.gz,PPIA-BG293LV04-50_S18_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9914