SRP68 RNA-Seq in 293T

Experiment Information (Status: Released)

	BG293LV06-53	BG293LV06-54
idx	0	0
TRCN#_or_BGC#	TRCN0000075078	TRCN0000075078
shRNA_or_gRNA_sequence	CCGGCCCAGCAAGTTCCATGATATTCTCGAGAATATCATGGAACTTGCTGGGTTTTTG	CCGGCCCAGCAAGTTCCATGATATTCTCGAGAATATCATGGAACTTGCTGGGTTTTTG
PAM
Name	SRP68	SRP68
Sample_ID	BG293LV06-53	BG293LV06-54
transduction_Date	9/5/24	9/5/24
days	D4	D4
RBP_name	SRP68	SRP68
qPCR_result	72.2	64.9
Ave_qPCR	68.5
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	12188	12189

Western Blot Western Blot info was not avaliable

Experiment Status

	BG293LV06-53	BG293LV06-54
Sample_ID	BG293LV06-53	BG293LV06-54
Sample Name
Sample Name	SRP68-BG293LV06-53	SRP68-BG293LV06-54
RBP	SRP68	SRP68
Cell_Line	293T	293T
Exp UID
Status	Released	Released
Status_date	2025-04-21	2025-04-21
Project	ENCORE2	ENCORE2
Note
ID	13490	13491

Library-Prep
Sequencing

Library-Prep Information

	BG293LV06-53	BG293LV06-54
Sample #	55	56
Sample Name	SRP68-BG293LV06-53	SRP68-BG293LV06-54
Sample_Name_Alias
Index Well Position	G07	H07
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	269	267
Peak_Molarity	88.50	82.90
libSampleQC_DNA_Well	DNA_Library_set71/set1/G7.png	DNA_Library_set71/set1/H7.png
RIN	9.9	10.0
libSample_RNA_Well	RNA_Library_set71/set1/G7.png	RNA_Library_set71/set1/H7.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2024-09-30	2024-09-30
Sample_ID	BG293LV06-53	BG293LV06-54
RBP	SRP68	SRP68
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	4480	4481

Sequencing Information

	BG293LV06-53	BG293LV06-54
Sample_ID	BG293LV06-53	BG293LV06-54
Sample Name	SRP68-BG293LV06-53	SRP68-BG293LV06-54
Pool ID	Pool-240930	Pool-240930
LocalServer_folder	set71	set71
total_reads	38,441,443	41,648,076
total_aligned_reads	34,988,952	38,244,053
unique_aligned_reads	32,854,284	35,905,673
percent_uniqueAligned	0.85466	0.86212
correlation_replicates	0.997809	0.997809
spikein_reads	106,500	170,840
percent_spikeins	0.00277	0.00410
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	3049	3050

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
SRP68-BG293LV06-53_S141_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set71/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3049	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	29373
SRP68-BG293LV06-53_S141_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set71/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3049	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	29437
SRP68-BG293LV06-53_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set71/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3049					GRCh38	V40	SRP68-BG293LV06-53_S141_L002_R1_001.filtered.trimmed.paired.fastq.gz,SRP68-BG293LV06-53_S141_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	29502
SRP68-BG293LV06-53_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	3049					GRCh38	V40	SRP68-BG293LV06-53_Aligned.sortedByCoord.out.bam		ENCORE2	29566
SRP68-BG293LV06-53_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	3049					GRCh38	V40	SRP68-BG293LV06-53_Aligned.sortedByCoord.out.bam		ENCORE2	29630
SRP68-BG293LV06-53_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	3049					GRCh38	V40	SRP68-BG293LV06-53_Aligned.sortedByCoord.out.bam		ENCORE2	29694
SRP68-BG293LV06-53_quant.sf	ENCODE_DATA/set71/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3049					GRCh38	V40	SRP68-BG293LV06-53_S141_L002_R1_001.filtered.trimmed.paired.fastq.gz,SRP68-BG293LV06-53_S141_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	29758
SRP68-BG293LV06-54_S142_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set71/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3050	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	29374
SRP68-BG293LV06-54_S142_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set71/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3050	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	29438
SRP68-BG293LV06-54_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set71/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3050					GRCh38	V40	SRP68-BG293LV06-54_S142_L002_R1_001.filtered.trimmed.paired.fastq.gz,SRP68-BG293LV06-54_S142_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	29503
SRP68-BG293LV06-54_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	3050					GRCh38	V40	SRP68-BG293LV06-54_Aligned.sortedByCoord.out.bam		ENCORE2	29567
SRP68-BG293LV06-54_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	3050					GRCh38	V40	SRP68-BG293LV06-54_Aligned.sortedByCoord.out.bam		ENCORE2	29631
SRP68-BG293LV06-54_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	3050					GRCh38	V40	SRP68-BG293LV06-54_Aligned.sortedByCoord.out.bam		ENCORE2	29695
SRP68-BG293LV06-54_quant.sf	ENCODE_DATA/set71/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3050					GRCh38	V40	SRP68-BG293LV06-54_S142_L002_R1_001.filtered.trimmed.paired.fastq.gz,SRP68-BG293LV06-54_S142_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	29759