NGRN RNA-Seq in 293T

Experiment Information (Status: Released)

	BG293LV06-105	BG293LV06-106
idx	0	0
TRCN#_or_BGC#	TRCN0000219779	TRCN0000219779
shRNA_or_gRNA_sequence	CCGGGCTGCGTGGATAGATTCAAACCTCGAGGTTTGAATCTATCCACGCAGCTTTTTG	CCGGGCTGCGTGGATAGATTCAAACCTCGAGGTTTGAATCTATCCACGCAGCTTTTTG
PAM
Name	NGRN	NGRN
Sample_ID	BG293LV06-105	BG293LV06-106
transduction_Date	9/5/24	9/5/24
days	D4	D4
RBP_name	NGRN	NGRN
qPCR_result	60.1	65.6
Ave_qPCR	62.8
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	12240	12241

Western Blot Western Blot info was not avaliable

Experiment Status

	BG293LV06-105	BG293LV06-106
Sample_ID	BG293LV06-105	BG293LV06-106
Sample Name
Sample Name	NGRN-BG293LV06-105B	NGRN-BG293LV06-106B
RBP	NGRN	NGRN
Cell_Line	293T	293T
Exp UID
Status	Released	Released
Status_date	2025-04-21	2025-04-21
Project	ENCORE2	ENCORE2
Note
ID	13542	13543

Library-Prep
Sequencing

Library-Prep Information

	BG293LV06-105	BG293LV06-106
Sample #	105	106
Sample Name	NGRN-BG293LV06-105B	NGRN-BG293LV06-106B
Sample_Name_Alias
Index Well Position	A07	B07
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	274	270
Peak_Molarity	69.30	83.80
libSampleQC_DNA_Well	DNA_Library_set72/set1/A7.png	DNA_Library_set72/set1/B7.png
RIN	9.9	10.0
libSample_RNA_Well	RNA_Library_set72/set1/A7.png	RNA_Library_set72/set1/B7.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2024-10-04	2024-10-04
Sample_ID	BG293LV06-105	BG293LV06-106
RBP	NGRN	NGRN
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	4530	4531

Sequencing Information

	BG293LV06-105	BG293LV06-106
Sample_ID	BG293LV06-105	BG293LV06-106
Sample Name	NGRN-BG293LV06-105B	NGRN-BG293LV06-106B
Pool ID	Pool-241004	Pool-241004
LocalServer_folder	set72	set72
total_reads	55,337,619	40,670,635
total_aligned_reads	51,477,874	37,648,332
unique_aligned_reads	48,140,980	35,271,587
percent_uniqueAligned	0.86995	0.86725
correlation_replicates	0.996281	0.996281
spikein_reads	310,958	220,480
percent_spikeins	0.00562	0.00542
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	3099	3100

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-BG293LV06-105B_S57_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set72/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3099	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	29792
NGRN-BG293LV06-105B_S57_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set72/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3099	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	29864
NGRN-BG293LV06-105B_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set72/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3099					GRCh38	V40	NGRN-BG293LV06-105B_S57_L001_R1_001.filtered.trimmed.paired.fastq.gz,NGRN-BG293LV06-105B_S57_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	29936
NGRN-BG293LV06-105B_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	3099					GRCh38	V40	NGRN-BG293LV06-105B_Aligned.sortedByCoord.out.bam		ENCORE2	30008
NGRN-BG293LV06-105B_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	3099					GRCh38	V40	NGRN-BG293LV06-105B_Aligned.sortedByCoord.out.bam		ENCORE2	30080
NGRN-BG293LV06-105B_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	3099					GRCh38	V40	NGRN-BG293LV06-105B_Aligned.sortedByCoord.out.bam		ENCORE2	30152
NGRN-BG293LV06-105B_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	3099					GRCh38	V40	NGRN-BG293LV06-105B_Aligned.sortedByCoord.out.bam		ENCORE2	30224
NGRN-BG293LV06-105B_quant.sf	ENCODE_DATA/set72/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3099					GRCh38	V40	NGRN-BG293LV06-105B_S57_L001_R1_001.filtered.trimmed.paired.fastq.gz,NGRN-BG293LV06-105B_S57_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	30296
NGRN-BG293LV06-106B_S58_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set72/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3100	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	29793
NGRN-BG293LV06-106B_S58_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set72/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3100	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	29865
NGRN-BG293LV06-106B_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set72/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3100					GRCh38	V40	NGRN-BG293LV06-106B_S58_L001_R1_001.filtered.trimmed.paired.fastq.gz,NGRN-BG293LV06-106B_S58_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	29937
NGRN-BG293LV06-106B_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	3100					GRCh38	V40	NGRN-BG293LV06-106B_Aligned.sortedByCoord.out.bam		ENCORE2	30009
NGRN-BG293LV06-106B_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	3100					GRCh38	V40	NGRN-BG293LV06-106B_Aligned.sortedByCoord.out.bam		ENCORE2	30081
NGRN-BG293LV06-106B_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	3100					GRCh38	V40	NGRN-BG293LV06-106B_Aligned.sortedByCoord.out.bam		ENCORE2	30153
NGRN-BG293LV06-106B_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	3100					GRCh38	V40	NGRN-BG293LV06-106B_Aligned.sortedByCoord.out.bam		ENCORE2	30225
NGRN-BG293LV06-106B_quant.sf	ENCODE_DATA/set72/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3100					GRCh38	V40	NGRN-BG293LV06-106B_S58_L001_R1_001.filtered.trimmed.paired.fastq.gz,NGRN-BG293LV06-106B_S58_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	30297