LSM1 RNA-Seq in 293T

Experiment Information (Status: Released)

	BG293LV06-61	BG293LV06-62
idx	0	0
TRCN#_or_BGC#	TRCN0000040228	TRCN0000040228
shRNA_or_gRNA_sequence	CCGGGAGCGTATTCATGTGGGCAAACTCGAGTTTGCCCACATGAATACGCTCTTTTTG	CCGGGAGCGTATTCATGTGGGCAAACTCGAGTTTGCCCACATGAATACGCTCTTTTTG
PAM
Name	LSM1	LSM1
Sample_ID	BG293LV06-61	BG293LV06-62
transduction_Date	9/5/24	9/5/24
days	D4	D4
RBP_name	LSM1	LSM1
qPCR_result	54.7	77.5
Ave_qPCR	66.1
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	12196	12197

Western Blot Western Blot info was not avaliable

Experiment Status

	BG293LV06-61	BG293LV06-62
Sample_ID	BG293LV06-61	BG293LV06-62
Sample Name
Sample Name	LSM1-BG293LV06-61	LSM1-BG293LV06-62
RBP	LSM1	LSM1
Cell_Line	293T	293T
Exp UID
Status	Released	Released
Status_date	2025-04-21	2025-04-21
Project	ENCORE2	ENCORE2
Note
ID	13498	13499

Library-Prep
Sequencing

Library-Prep Information

	BG293LV06-61	BG293LV06-62
Sample #	63	64
Sample Name	LSM1-BG293LV06-61	LSM1-BG293LV06-62
Sample_Name_Alias
Index Well Position	G08	H08
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	276	281
Peak_Molarity	81.20	56.30
libSampleQC_DNA_Well	DNA_Library_set71/set1/G8.png	DNA_Library_set71/set1/H8.png
RIN	10.0	9.9
libSample_RNA_Well	RNA_Library_set71/set1/G8.png	RNA_Library_set71/set1/H8.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2024-09-30	2024-09-30
Sample_ID	BG293LV06-61	BG293LV06-62
RBP	LSM1	LSM1
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	4488	4489

Sequencing Information

	BG293LV06-61	BG293LV06-62
Sample_ID	BG293LV06-61	BG293LV06-62
Sample Name	LSM1-BG293LV06-61	LSM1-BG293LV06-62
Pool ID	Pool-240930	Pool-240930
LocalServer_folder	set71	set71
total_reads	44,330,038	47,016,212
total_aligned_reads	41,174,335	43,626,128
unique_aligned_reads	38,545,443	40,829,409
percent_uniqueAligned	0.86951	0.86841
correlation_replicates	0.943409	0.943409
spikein_reads	86,250	182,956
percent_spikeins	0.00195	0.00389
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	3057	3058

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
LSM1-BG293LV06-61_S63_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set71/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3057	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	29331
LSM1-BG293LV06-61_S63_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set71/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3057	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	29395
LSM1-BG293LV06-61_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set71/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3057					GRCh38	V40	LSM1-BG293LV06-61_S63_L002_R1_001.filtered.trimmed.paired.fastq.gz,LSM1-BG293LV06-61_S63_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	29460
LSM1-BG293LV06-61_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	3057					GRCh38	V40	LSM1-BG293LV06-61_Aligned.sortedByCoord.out.bam		ENCORE2	29524
LSM1-BG293LV06-61_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	3057					GRCh38	V40	LSM1-BG293LV06-61_Aligned.sortedByCoord.out.bam		ENCORE2	29588
LSM1-BG293LV06-61_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	3057					GRCh38	V40	LSM1-BG293LV06-61_Aligned.sortedByCoord.out.bam		ENCORE2	29652
LSM1-BG293LV06-61_quant.sf	ENCODE_DATA/set71/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3057					GRCh38	V40	LSM1-BG293LV06-61_S63_L002_R1_001.filtered.trimmed.paired.fastq.gz,LSM1-BG293LV06-61_S63_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	29716
LSM1-BG293LV06-62_S64_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set71/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3058	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	29332
LSM1-BG293LV06-62_S64_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set71/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3058	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	29396
LSM1-BG293LV06-62_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set71/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3058					GRCh38	V40	LSM1-BG293LV06-62_S64_L002_R1_001.filtered.trimmed.paired.fastq.gz,LSM1-BG293LV06-62_S64_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	29461
LSM1-BG293LV06-62_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	3058					GRCh38	V40	LSM1-BG293LV06-62_Aligned.sortedByCoord.out.bam		ENCORE2	29525
LSM1-BG293LV06-62_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	3058					GRCh38	V40	LSM1-BG293LV06-62_Aligned.sortedByCoord.out.bam		ENCORE2	29589
LSM1-BG293LV06-62_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	3058					GRCh38	V40	LSM1-BG293LV06-62_Aligned.sortedByCoord.out.bam		ENCORE2	29653
LSM1-BG293LV06-62_quant.sf	ENCODE_DATA/set71/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3058					GRCh38	V40	LSM1-BG293LV06-62_S64_L002_R1_001.filtered.trimmed.paired.fastq.gz,LSM1-BG293LV06-62_S64_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	29717