LSM1 RNA-Seq in 293T

Experiment Information (Status: Submitting)

	BG293LV05-21	BG293LV05-22
idx	0	0
TRCN#_or_BGC#	TRCN0000040228	TRCN0000040228
shRNA_or_gRNA_sequence	CCGGGAGCGTATTCATGTGGGCAAACTCGAGTTTGCCCACATGAATACGCTCTTTTTG	CCGGGAGCGTATTCATGTGGGCAAACTCGAGTTTGCCCACATGAATACGCTCTTTTTG
PAM
Name	LSM1	LSM1
Sample_ID	BG293LV05-21	BG293LV05-22
transduction_Date	12/18/23	12/18/23
days	D4	D4
RBP_name	LSM1	LSM1
qPCR_result	74.4	75.2
Ave_qPCR	74.8
RT-qPCR_primer-F	ATTAAGACAGCGGCAGTTGG
RT-qPCR_primer-R	CCTATAAGTGTCCTTCCATCTCG
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	9993	9994

Western Blot Western Blot info was not avaliable

Experiment Status

	BG293LV05-21	BG293LV05-22
Sample_ID	BG293LV05-21	BG293LV05-22
Sample Name
Sample Name	LSM1-BG293LV05-21	LSM1-BG293LV05-22
RBP	LSM1	LSM1
Cell_Line	293T	293T
Exp UID
Status	Submitting	Submitting
Status_date	2024-05-07	2024-05-07
Project	ENCORE2	ENCORE2
Note
ID	12844	12845

Library-Prep
Sequencing

Library-Prep Information

	BG293LV05-21	BG293LV05-22
Sample #	11	12
Sample Name	LSM1-BG293LV05-21	LSM1-BG293LV05-22
Sample_Name_Alias
Index Well Position	C08	D08
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2024-01-16	2024-01-16
Lib_ID	Lib-240116	Lib-240116
Tecan_Location
Tecan
Tecan_date
Size_bp	280	278
Peak_Molarity	98.70	75.10
libSampleQC_DNA_Well	DNA_Library_set69/set1/C2.png	DNA_Library_set69/set1/D2.png
RIN	9.7	9.7
libSample_RNA_Well	RNA_Library_set69/set1/C7.png	RNA_Library_set69/set1/D7.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2024-01-19	2024-01-19
Sample_ID	BG293LV05-21	BG293LV05-22
RBP	LSM1	LSM1
Batch_ID	BG293LV05	BG293LV05
WB_result	0.000	0.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4192	4193

Sequencing Information

	BG293LV05-21	BG293LV05-22
Sample_ID	BG293LV05-21	BG293LV05-22
Sample Name	LSM1-BG293LV05-21	LSM1-BG293LV05-22
Pool ID	Pool-240119	Pool-240119
LocalServer_folder	set69	set69
total_reads	16,107,299	20,139,724
total_aligned_reads	13,780,259	16,055,163
unique_aligned_reads	12,836,692	14,969,203
percent_uniqueAligned	0.79695	0.74327
correlation_replicates	0.990336	0.990336
spikein_reads	7,044	8,894
percent_spikeins	0.00044	0.00044
original_ReadLength	101	101
QC_Status	Submitting	Submitting
ID	2911	2912

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-BG293LV05-21_merged_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set69/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2911	NovaSeq6000	100	paired-ended	1				NT-BG293LV05-1_merged_R1_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV05-2_S134_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	28507
LSM1-BG293LV05-21_merged_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set69/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2911	NovaSeq6000	100	paired-ended	2				NT-BG293LV05-1_merged_R2_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV05-2_S134_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	28551
LSM1-BG293LV05-21_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set69/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2911					GRCh38	V40	LSM1-BG293LV05-21_merged_R1_001.filtered.trimmed.paired.fastq.gz,LSM1-BG293LV05-21_merged_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	28595
LSM1-BG293LV05-21_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set69/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2911					GRCh38	V40	LSM1-BG293LV05-21/Aligned.sortedByCoord.out.bam		ENCORE2	28639
LSM1-BG293LV05-21_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set69/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2911					GRCh38	V40	LSM1-BG293LV05-21/Aligned.sortedByCoord.out.bam		ENCORE2	28683
LSM1-BG293LV05-21_Signal.Unique.strand-.bw	ENCODE_DATA/set69/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2911					GRCh38	V40	LSM1-BG293LV05-21/Aligned.sortedByCoord.out.bam		ENCORE2	28727
LSM1-BG293LV05-21_Signal.Unique.strand+.bw	ENCODE_DATA/set69/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2911					GRCh38	V40	LSM1-BG293LV05-21/Aligned.sortedByCoord.out.bam		ENCORE2	28771
LSM1-BG293LV05-21_quant.sf	ENCODE_DATA/set69/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2911					GRCh38	V40	LSM1-BG293LV05-21_merged_R1_001.filtered.trimmed.paired.fastq.gz,LSM1-BG293LV05-21_merged_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	28815
LSM1-BG293LV05-22_S144_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set69/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2912	NovaSeq6000	100	paired-ended	1				NT-BG293LV05-1_merged_R1_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV05-2_S134_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	28508
LSM1-BG293LV05-22_S144_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set69/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2912	NovaSeq6000	100	paired-ended	2				NT-BG293LV05-1_merged_R2_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV05-2_S134_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	28552
LSM1-BG293LV05-22_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set69/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2912					GRCh38	V40	LSM1-BG293LV05-22_S144_L002_R1_001.filtered.trimmed.paired.fastq.gz,LSM1-BG293LV05-22_S144_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	28596
LSM1-BG293LV05-22_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set69/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2912					GRCh38	V40	LSM1-BG293LV05-22/Aligned.sortedByCoord.out.bam		ENCORE2	28640
LSM1-BG293LV05-22_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set69/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2912					GRCh38	V40	LSM1-BG293LV05-22/Aligned.sortedByCoord.out.bam		ENCORE2	28684
LSM1-BG293LV05-22_Signal.Unique.strand-.bw	ENCODE_DATA/set69/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2912					GRCh38	V40	LSM1-BG293LV05-22/Aligned.sortedByCoord.out.bam		ENCORE2	28728
LSM1-BG293LV05-22_Signal.Unique.strand+.bw	ENCODE_DATA/set69/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2912					GRCh38	V40	LSM1-BG293LV05-22/Aligned.sortedByCoord.out.bam		ENCORE2	28772
LSM1-BG293LV05-22_quant.sf	ENCODE_DATA/set69/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2912					GRCh38	V40	LSM1-BG293LV05-22_S144_L002_R1_001.filtered.trimmed.paired.fastq.gz,LSM1-BG293LV05-22_S144_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	28816