NGRN RNA-Seq in 293T

Experiment Information (Status: Revoked)

	BG293LV02-31	BG293LV02-32
idx	0	0
TRCN#_or_BGC#	TRCN0000219779	TRCN0000219779
shRNA_or_gRNA_sequence	CCGGGCTGCGTGGATAGATTCAAACCTCGAGGTTTGAATCTATCCACGCAGCTTTTTG	CCGGGCTGCGTGGATAGATTCAAACCTCGAGGTTTGAATCTATCCACGCAGCTTTTTG
PAM
Name	NGRN	NGRN
Sample_ID	BG293LV02-31	BG293LV02-32
transduction_Date	3/20/23	3/20/23
days	D4	D4
RBP_name	NGRN	NGRN
qPCR_result	88.7	88.0
Ave_qPCR	88.4
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	9826	9827

Western Blot Western Blot info was not avaliable

Experiment Status

	BG293LV02-31	BG293LV02-32
Sample_ID	BG293LV02-31	BG293LV02-32
Sample Name
Sample Name	NGRN-BG293LV02-31	NGRN-BG293LV02-32
RBP	NGRN	NGRN
Cell_Line	293T	293T
Exp UID
Status	Revoked	Revoked
Status_date	2023-09-20	2023-09-20
Project	ENCORE2	ENCORE2
Note
ID	11584	11585

Library-Prep
Sequencing

Library-Prep Information

	BG293LV02-31	BG293LV02-32
Sample #	27	28
Sample Name	NGRN-BG293LV02-31	NGRN-BG293LV02-32
Sample_Name_Alias
Index Well Position	C04	D04
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	285	284
Peak_Molarity	99.90	106.00
libSampleQC_DNA_Well	DNA_Library_set60-62/set2/C4.png	DNA_Library_set60-62/set2/D4.png
RIN	9.7	9.7
libSample_RNA_Well	RNA_Library_set60-62/set1/C4.png	RNA_Library_set60-62/set1/D4.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-04-17	2023-04-17
Sample_ID	BG293LV02-31	BG293LV02-32
RBP	NGRN	NGRN
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	3614	3615

Sequencing Information

	BG293LV02-31	BG293LV02-32
Sample_ID	BG293LV02-31	BG293LV02-32
Sample Name	NGRN-BG293LV02-31	NGRN-BG293LV02-32
Pool ID	Pool-230417	Pool-230417
LocalServer_folder	set60	set60
total_reads	48,697,462	39,096,861
total_aligned_reads	42,033,445	33,549,705
unique_aligned_reads	39,134,577	31,283,003
percent_uniqueAligned	0.80363	0.80014
correlation_replicates	0.997141	0.997141
spikein_reads	152,170	81,518
percent_spikeins	0.00312	0.00209
original_ReadLength	101	101
QC_Status	Submitting	Submitting
ID	2485	2486

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
NGRN-BG293LV02-31_S27_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set60/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2485	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	7986
NGRN-BG293LV02-31_S27_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set60/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2485	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	8030
NGRN-BG293LV02-31_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set60/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2485					GRCh38	V40	NGRN-BG293LV02-31_S27_L001_R1_001.filtered.trimmed.paired.fastq.gz,NGRN-BG293LV02-31_S27_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10779
NGRN-BG293LV02-31_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	2485					GRCh38	V40	NGRN-BG293LV02-31/Aligned.sortedByCoord.out.bam		ENCORE2	10823
NGRN-BG293LV02-31_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	2485					GRCh38	V40	NGRN-BG293LV02-31/Aligned.sortedByCoord.out.bam		ENCORE2	10867
NGRN-BG293LV02-31_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	2485					GRCh38	V40	NGRN-BG293LV02-31/Aligned.sortedByCoord.out.bam		ENCORE2	10911
NGRN-BG293LV02-31_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	2485					GRCh38	V40	NGRN-BG293LV02-31/Aligned.sortedByCoord.out.bam		ENCORE2	10955
NGRN-BG293LV02-31_quant.sf	ENCODE_DATA/set60/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2485					GRCh38	V40	NGRN-BG293LV02-31_S27_L001_R1_001.filtered.trimmed.paired.fastq.gz,NGRN-BG293LV02-31_S27_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10999
NGRN-BG293LV02-32_S28_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set60/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2486	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	7987
NGRN-BG293LV02-32_S28_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set60/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2486	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	8031
NGRN-BG293LV02-32_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set60/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2486					GRCh38	V40	NGRN-BG293LV02-32_S28_L001_R1_001.filtered.trimmed.paired.fastq.gz,NGRN-BG293LV02-32_S28_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10780
NGRN-BG293LV02-32_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	2486					GRCh38	V40	NGRN-BG293LV02-32/Aligned.sortedByCoord.out.bam		ENCORE2	10824
NGRN-BG293LV02-32_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	2486					GRCh38	V40	NGRN-BG293LV02-32/Aligned.sortedByCoord.out.bam		ENCORE2	10868
NGRN-BG293LV02-32_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	2486					GRCh38	V40	NGRN-BG293LV02-32/Aligned.sortedByCoord.out.bam		ENCORE2	10912
NGRN-BG293LV02-32_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	2486					GRCh38	V40	NGRN-BG293LV02-32/Aligned.sortedByCoord.out.bam		ENCORE2	10956
NGRN-BG293LV02-32_quant.sf	ENCODE_DATA/set60/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2486					GRCh38	V40	NGRN-BG293LV02-32_S28_L001_R1_001.filtered.trimmed.paired.fastq.gz,NGRN-BG293LV02-32_S28_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	11000