PARN RNA-Seq in 293T

Experiment Information (Status: Revoked)

	BG293LV02-33	BG293LV02-34
idx	0	0
TRCN#_or_BGC#	TRCN0000049744	TRCN0000049744
shRNA_or_gRNA_sequence	CCCAGACTCTTGGATACTAAACTCGAGTTTAGTATCCAAGAGTCTGGG	CCCAGACTCTTGGATACTAAACTCGAGTTTAGTATCCAAGAGTCTGGG
PAM
Name	PARN	PARN
Sample_ID	BG293LV02-33	BG293LV02-34
transduction_Date	3/20/23	3/20/23
days	D4	D4
RBP_name	PARN	PARN
qPCR_result	51.2	54.3
Ave_qPCR	52.7
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	9828	9829

Western Blot Western Blot info was not avaliable

Experiment Status

	BG293LV02-33	BG293LV02-34
Sample_ID	BG293LV02-33	BG293LV02-34
Sample Name
Sample Name	PARN-BG293LV02-33	PARN-BG293LV02-34
RBP	PARN	PARN
Cell_Line	293T	293T
Exp UID
Status	Revoked	Revoked
Status_date	2023-09-20	2023-09-20
Project	ENCORE2	ENCORE2
Note
ID	11586	11587

Library-Prep
Sequencing

Library-Prep Information

	BG293LV02-33	BG293LV02-34
Sample #	29	30
Sample Name	PARN-BG293LV02-33	PARN-BG293LV02-34
Sample_Name_Alias
Index Well Position	E04	F04
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2023-04-12	2023-04-12
Lib_ID	Lib-230412	Lib-230412
Tecan_Location
Tecan
Tecan_date
Size_bp	275	286
Peak_Molarity	107.00	88.90
libSampleQC_DNA_Well	DNA_Library_set60-62/set2/E4.png	DNA_Library_set60-62/set2/F4.png
RIN	9.8	9.8
libSample_RNA_Well	RNA_Library_set60-62/set1/E4.png	RNA_Library_set60-62/set1/F4.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-04-17	2023-04-17
Sample_ID	BG293LV02-33	BG293LV02-34
RBP	PARN	PARN
Batch_ID	BG293LV02	BG293LV02
WB_result	0.000	0.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	3616	3617

Sequencing Information

	BG293LV02-33	BG293LV02-34
Sample_ID	BG293LV02-33	BG293LV02-34
Sample Name	PARN-BG293LV02-33	PARN-BG293LV02-34
Pool ID	Pool-230417	Pool-230417
LocalServer_folder	set60	set60
total_reads	50,636,270	46,600,987
total_aligned_reads	42,871,644	41,500,669
unique_aligned_reads	39,984,666	38,642,368
percent_uniqueAligned	0.78964	0.82922
correlation_replicates	0.958318	0.958318
spikein_reads	96,334	79,476
percent_spikeins	0.00190	0.00171
original_ReadLength	101	101
QC_Status	Submitting	Submitting
ID	2487	2488

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-BG293LV02-33_S29_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set60/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2487	NovaSeq6000	100	paired-ended	1				NT-BG293LV02-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV02-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	7990
PARN-BG293LV02-33_S29_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set60/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2487	NovaSeq6000	100	paired-ended	2				NT-BG293LV02-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV02-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8034
PARN-BG293LV02-33_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set60/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2487					GRCh38	V40	PARN-BG293LV02-33_S29_L001_R1_001.filtered.trimmed.paired.fastq.gz,PARN-BG293LV02-33_S29_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10783
PARN-BG293LV02-33_Signal.Unique.strand+.bw	ENCODE_DATA/set60/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2487					GRCh38	V40	PARN-BG293LV02-33/Aligned.sortedByCoord.out.bam		ENCORE2	10827
PARN-BG293LV02-33_Signal.Unique.strand-.bw	ENCODE_DATA/set60/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2487					GRCh38	V40	PARN-BG293LV02-33/Aligned.sortedByCoord.out.bam		ENCORE2	10871
PARN-BG293LV02-33_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set60/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2487					GRCh38	V40	PARN-BG293LV02-33/Aligned.sortedByCoord.out.bam		ENCORE2	10915
PARN-BG293LV02-33_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set60/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2487					GRCh38	V40	PARN-BG293LV02-33/Aligned.sortedByCoord.out.bam		ENCORE2	10959
PARN-BG293LV02-33_quant.sf	ENCODE_DATA/set60/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2487					GRCh38	V40	PARN-BG293LV02-33_S29_L001_R1_001.filtered.trimmed.paired.fastq.gz,PARN-BG293LV02-33_S29_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	11003
PARN-BG293LV02-34_S30_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set60/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2488	NovaSeq6000	100	paired-ended	1				NT-BG293LV02-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV02-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	7991
PARN-BG293LV02-34_S30_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set60/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2488	NovaSeq6000	100	paired-ended	2				NT-BG293LV02-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV02-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8035
PARN-BG293LV02-34_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set60/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2488					GRCh38	V40	PARN-BG293LV02-34_S30_L001_R1_001.filtered.trimmed.paired.fastq.gz,PARN-BG293LV02-34_S30_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10784
PARN-BG293LV02-34_Signal.Unique.strand+.bw	ENCODE_DATA/set60/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2488					GRCh38	V40	PARN-BG293LV02-34/Aligned.sortedByCoord.out.bam		ENCORE2	10828
PARN-BG293LV02-34_Signal.Unique.strand-.bw	ENCODE_DATA/set60/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2488					GRCh38	V40	PARN-BG293LV02-34/Aligned.sortedByCoord.out.bam		ENCORE2	10872
PARN-BG293LV02-34_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set60/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2488					GRCh38	V40	PARN-BG293LV02-34/Aligned.sortedByCoord.out.bam		ENCORE2	10916
PARN-BG293LV02-34_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set60/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2488					GRCh38	V40	PARN-BG293LV02-34/Aligned.sortedByCoord.out.bam		ENCORE2	10960
PARN-BG293LV02-34_quant.sf	ENCODE_DATA/set60/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2488					GRCh38	V40	PARN-BG293LV02-34_S30_L001_R1_001.filtered.trimmed.paired.fastq.gz,PARN-BG293LV02-34_S30_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	11004