PARN RNA-Seq in 293T

Experiment Information (Status: Released)

	BG293LV06-27	BG293LV06-28
idx	0	0
TRCN#_or_BGC#	TRCN0000049744	TRCN0000049744
shRNA_or_gRNA_sequence	CCCAGACTCTTGGATACTAAACTCGAGTTTAGTATCCAAGAGTCTGGG	CCCAGACTCTTGGATACTAAACTCGAGTTTAGTATCCAAGAGTCTGGG
PAM
Name	PARN	PARN
Sample_ID	BG293LV06-27	BG293LV06-28
transduction_Date	9/5/24	9/5/24
days	D4	D4
RBP_name	PARN	PARN
qPCR_result	66.5	61.5
Ave_qPCR	64.0
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	12162	12163

Western Blot Western Blot info was not avaliable

Experiment Status

	BG293LV06-27	BG293LV06-28
Sample_ID	BG293LV06-27	BG293LV06-28
Sample Name
Sample Name	PARN-BG293LV06-27	PARN-BG293LV06-28
RBP	PARN	PARN
Cell_Line	293T	293T
Exp UID
Status	Released	Released
Status_date	2025-04-21	2025-04-21
Project	ENCORE2	ENCORE2
Note
ID	13464	13465

Library-Prep
Sequencing

Library-Prep Information

	BG293LV06-27	BG293LV06-28
Sample #	31	32
Sample Name	PARN-BG293LV06-27	PARN-BG293LV06-28
Sample_Name_Alias
Index Well Position	G04	H04
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	274
Peak_Molarity	82.80	65.50
libSampleQC_DNA_Well	DNA_Library_set71/set1/G4.png	DNA_Library_set71/set1/H4.png
RIN	9.9	10.0
libSample_RNA_Well	RNA_Library_set71/set1/G4.png	RNA_Library_set71/set1/H4.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2024-09-30	2024-09-30
Sample_ID	BG293LV06-27	BG293LV06-28
RBP	PARN	PARN
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	4456	4457

Sequencing Information

	BG293LV06-27	BG293LV06-28
Sample_ID	BG293LV06-27	BG293LV06-28
Sample Name	PARN-BG293LV06-27	PARN-BG293LV06-28
Pool ID	Pool-240930	Pool-240930
LocalServer_folder	set71	set71
total_reads	35,313,034	43,476,492
total_aligned_reads	32,476,567	39,295,379
unique_aligned_reads	30,282,677	36,613,507
percent_uniqueAligned	0.85755	0.84214
correlation_replicates	0.994564	0.994564
spikein_reads	73,718	131,904
percent_spikeins	0.00209	0.00303
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	3025	3026

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
PARN-BG293LV06-27_S31_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set71/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3025	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	29347
PARN-BG293LV06-27_S31_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set71/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3025	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	29411
PARN-BG293LV06-27_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set71/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3025					GRCh38	V40	PARN-BG293LV06-27_S31_L002_R1_001.filtered.trimmed.paired.fastq.gz,PARN-BG293LV06-27_S31_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	29476
PARN-BG293LV06-27_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	3025					GRCh38	V40	PARN-BG293LV06-27_Aligned.sortedByCoord.out.bam		ENCORE2	29540
PARN-BG293LV06-27_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	3025					GRCh38	V40	PARN-BG293LV06-27_Aligned.sortedByCoord.out.bam		ENCORE2	29604
PARN-BG293LV06-27_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	3025					GRCh38	V40	PARN-BG293LV06-27_Aligned.sortedByCoord.out.bam		ENCORE2	29668
PARN-BG293LV06-27_quant.sf	ENCODE_DATA/set71/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3025					GRCh38	V40	PARN-BG293LV06-27_S31_L002_R1_001.filtered.trimmed.paired.fastq.gz,PARN-BG293LV06-27_S31_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	29732
PARN-BG293LV06-28_S32_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set71/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3026	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	29348
PARN-BG293LV06-28_S32_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set71/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3026	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	29412
PARN-BG293LV06-28_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set71/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3026					GRCh38	V40	PARN-BG293LV06-28_S32_L002_R1_001.filtered.trimmed.paired.fastq.gz,PARN-BG293LV06-28_S32_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	29477
PARN-BG293LV06-28_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	3026					GRCh38	V40	PARN-BG293LV06-28_Aligned.sortedByCoord.out.bam		ENCORE2	29541
PARN-BG293LV06-28_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	3026					GRCh38	V40	PARN-BG293LV06-28_Aligned.sortedByCoord.out.bam		ENCORE2	29605
PARN-BG293LV06-28_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	3026					GRCh38	V40	PARN-BG293LV06-28_Aligned.sortedByCoord.out.bam		ENCORE2	29669
PARN-BG293LV06-28_quant.sf	ENCODE_DATA/set71/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3026					GRCh38	V40	PARN-BG293LV06-28_S32_L002_R1_001.filtered.trimmed.paired.fastq.gz,PARN-BG293LV06-28_S32_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	29733