LSM10 RNA-Seq in 293T

Experiment Information (Status: Submitting)

	BG293LV05-31	BG293LV05-32
idx	0	0
TRCN#_or_BGC#	TRCN0000074415	TRCN0000074415
shRNA_or_gRNA_sequence	CCGGCATAGACAATGTCGATGCTTTCTCGAGAAAGCATCGACATTGTCTATGTTTTTG	CCGGCATAGACAATGTCGATGCTTTCTCGAGAAAGCATCGACATTGTCTATGTTTTTG
PAM
Name	LSM10	LSM10
Sample_ID	BG293LV05-31	BG293LV05-32
transduction_Date	12/18/23	12/18/23
days	D4	D4
RBP_name	LSM10	LSM10
qPCR_result	91.8	92
Ave_qPCR	91.9
RT-qPCR_primer-F	gggtaaccactgtggacctg
RT-qPCR_primer-R	cggtccgtgtaggtgacttt
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	10003	10004

Western Blot Western Blot info was not avaliable

Experiment Status

	BG293LV05-31	BG293LV05-32
Sample_ID	BG293LV05-31	BG293LV05-32
Sample Name
Sample Name	LSM10-BG293LV05-31	LSM10-BG293LV05-32
RBP	LSM10	LSM10
Cell_Line	293T	293T
Exp UID
Status	Submitting	Submitting
Status_date	2024-05-07	2024-05-07
Project	ENCORE2	ENCORE2
Note
ID	12848	12849

Library-Prep
Sequencing

Library-Prep Information

	BG293LV05-31	BG293LV05-32
Sample #	15	16
Sample Name	LSM10-BG293LV05-31	LSM10-BG293LV05-32
Sample_Name_Alias
Index Well Position	G08	H08
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	278	281
Peak_Molarity	90.00	69.40
libSampleQC_DNA_Well	DNA_Library_set69/set1/G2.png	DNA_Library_set69/set1/H2.png
RIN	9.6	9.7
libSample_RNA_Well	RNA_Library_set69/set1/G7.png	RNA_Library_set69/set1/H7.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2024-01-19	2024-01-19
Sample_ID	BG293LV05-31	BG293LV05-32
RBP	LSM10	LSM10
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	4196	4197

Sequencing Information

	BG293LV05-31	BG293LV05-32
Sample_ID	BG293LV05-31	BG293LV05-32
Sample Name	LSM10-BG293LV05-31	LSM10-BG293LV05-32
Pool ID	Pool-240119	Pool-240119
LocalServer_folder	set69	set69
total_reads	25,120,475	23,066,149
total_aligned_reads	22,476,203	20,181,510
unique_aligned_reads	20,808,941	18,661,412
percent_uniqueAligned	0.82837	0.80904
correlation_replicates	0.998557	0.998557
spikein_reads	3,552	2,082
percent_spikeins	0.00014	0.00009
original_ReadLength	101	101
QC_Status	Submitting	Submitting
ID	2915	2916

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
LSM10-BG293LV05-31_S147_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set69/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2915	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	28505
LSM10-BG293LV05-31_S147_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set69/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2915	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	28549
LSM10-BG293LV05-31_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set69/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2915					GRCh38	V40	LSM10-BG293LV05-31_S147_L002_R1_001.filtered.trimmed.paired.fastq.gz,LSM10-BG293LV05-31_S147_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	28593
LSM10-BG293LV05-31_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	2915					GRCh38	V40	LSM10-BG293LV05-31/Aligned.sortedByCoord.out.bam		ENCORE2	28637
LSM10-BG293LV05-31_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	2915					GRCh38	V40	LSM10-BG293LV05-31/Aligned.sortedByCoord.out.bam		ENCORE2	28681
LSM10-BG293LV05-31_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	2915					GRCh38	V40	LSM10-BG293LV05-31/Aligned.sortedByCoord.out.bam		ENCORE2	28725
LSM10-BG293LV05-31_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	2915					GRCh38	V40	LSM10-BG293LV05-31/Aligned.sortedByCoord.out.bam		ENCORE2	28769
LSM10-BG293LV05-31_quant.sf	ENCODE_DATA/set69/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2915					GRCh38	V40	LSM10-BG293LV05-31_S147_L002_R1_001.filtered.trimmed.paired.fastq.gz,LSM10-BG293LV05-31_S147_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	28813
LSM10-BG293LV05-32_S148_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set69/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2916	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	28506
LSM10-BG293LV05-32_S148_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set69/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2916	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	28550
LSM10-BG293LV05-32_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set69/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2916					GRCh38	V40	LSM10-BG293LV05-32_S148_L002_R1_001.filtered.trimmed.paired.fastq.gz,LSM10-BG293LV05-32_S148_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	28594
LSM10-BG293LV05-32_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	2916					GRCh38	V40	LSM10-BG293LV05-32/Aligned.sortedByCoord.out.bam		ENCORE2	28638
LSM10-BG293LV05-32_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	2916					GRCh38	V40	LSM10-BG293LV05-32/Aligned.sortedByCoord.out.bam		ENCORE2	28682
LSM10-BG293LV05-32_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	2916					GRCh38	V40	LSM10-BG293LV05-32/Aligned.sortedByCoord.out.bam		ENCORE2	28726
LSM10-BG293LV05-32_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	2916					GRCh38	V40	LSM10-BG293LV05-32/Aligned.sortedByCoord.out.bam		ENCORE2	28770
LSM10-BG293LV05-32_quant.sf	ENCODE_DATA/set69/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2916					GRCh38	V40	LSM10-BG293LV05-32_S148_L002_R1_001.filtered.trimmed.paired.fastq.gz,LSM10-BG293LV05-32_S148_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	28814