SMNDC1 RNA-Seq in 293T

Experiment Information (Status: Released)

	BG293LV06-91	BG293LV06-92
idx	0	0
TRCN#_or_BGC#	TRCN0000369078	TRCN0000369078
shRNA_or_gRNA_sequence	CCGGGAAAGTGAAATGGCAACAATTCTCGAGAATTGTTGCCATTTCACTTTCTTTTTG	CCGGGAAAGTGAAATGGCAACAATTCTCGAGAATTGTTGCCATTTCACTTTCTTTTTG
PAM
Name	SMNDC1	SMNDC1
Sample_ID	BG293LV06-91	BG293LV06-92
transduction_Date	9/5/24	9/5/24
days	D4	D4
RBP_name	SMNDC1	SMNDC1
qPCR_result	74.3	67.9
Ave_qPCR	71.1
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	12226	12227

Western Blot Western Blot info was not avaliable

Experiment Status

	BG293LV06-91	BG293LV06-92
Sample_ID	BG293LV06-91	BG293LV06-92
Sample Name
Sample Name	SMNDC1-BG293LV06-91B	SMNDC1-BG293LV06-92B
RBP	SMNDC1	SMNDC1
Cell_Line	293T	293T
Exp UID
Status	Released	Released
Status_date	2025-04-21	2025-04-21
Project	ENCORE2	ENCORE2
Note
ID	13528	13529

Library-Prep
Sequencing

Library-Prep Information

	BG293LV06-91	BG293LV06-92
Sample #	91	92
Sample Name	SMNDC1-BG293LV06-91B	SMNDC1-BG293LV06-92B
Sample_Name_Alias
Index Well Position	C05	D05
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	275	276
Peak_Molarity	102.00	90.20
libSampleQC_DNA_Well	DNA_Library_set72/set1/C5.png	DNA_Library_set72/set1/D5.png
RIN	9.8	9.9
libSample_RNA_Well	RNA_Library_set72/set1/C5.png	RNA_Library_set72/set1/D5.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2024-10-04	2024-10-04
Sample_ID	BG293LV06-91	BG293LV06-92
RBP	SMNDC1	SMNDC1
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	4516	4517

Sequencing Information

	BG293LV06-91	BG293LV06-92
Sample_ID	BG293LV06-91	BG293LV06-92
Sample Name	SMNDC1-BG293LV06-91B	SMNDC1-BG293LV06-92B
Pool ID	Pool-241004	Pool-241004
LocalServer_folder	set72	set72
total_reads	94,288,197	37,445,492
total_aligned_reads	84,861,005	33,967,262
unique_aligned_reads	79,378,362	31,813,901
percent_uniqueAligned	0.84187	0.84961
correlation_replicates	0.971385	0.971385
spikein_reads	344,980	121,638
percent_spikeins	0.00366	0.00325
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	3085	3086

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
SMNDC1-BG293LV06-91B_S43_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set72/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3085	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	29812
SMNDC1-BG293LV06-91B_S43_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set72/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3085	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	29884
SMNDC1-BG293LV06-91B_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set72/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3085					GRCh38	V40	SMNDC1-BG293LV06-91B_S43_L001_R1_001.filtered.trimmed.paired.fastq.gz,SMNDC1-BG293LV06-91B_S43_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	29956
SMNDC1-BG293LV06-91B_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	3085					GRCh38	V40	SMNDC1-BG293LV06-91B_Aligned.sortedByCoord.out.bam		ENCORE2	30028
SMNDC1-BG293LV06-91B_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	3085					GRCh38	V40	SMNDC1-BG293LV06-91B_Aligned.sortedByCoord.out.bam		ENCORE2	30100
SMNDC1-BG293LV06-91B_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	3085					GRCh38	V40	SMNDC1-BG293LV06-91B_Aligned.sortedByCoord.out.bam		ENCORE2	30172
SMNDC1-BG293LV06-91B_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	3085					GRCh38	V40	SMNDC1-BG293LV06-91B_Aligned.sortedByCoord.out.bam		ENCORE2	30244
SMNDC1-BG293LV06-91B_quant.sf	ENCODE_DATA/set72/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3085					GRCh38	V40	SMNDC1-BG293LV06-91B_S43_L001_R1_001.filtered.trimmed.paired.fastq.gz,SMNDC1-BG293LV06-91B_S43_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	30316
SMNDC1-BG293LV06-92B_S44_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set72/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3086	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	29813
SMNDC1-BG293LV06-92B_S44_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set72/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3086	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	29885
SMNDC1-BG293LV06-92B_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set72/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3086					GRCh38	V40	SMNDC1-BG293LV06-92B_S44_L001_R1_001.filtered.trimmed.paired.fastq.gz,SMNDC1-BG293LV06-92B_S44_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	29957
SMNDC1-BG293LV06-92B_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	3086					GRCh38	V40	SMNDC1-BG293LV06-92B_Aligned.sortedByCoord.out.bam		ENCORE2	30029
SMNDC1-BG293LV06-92B_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	3086					GRCh38	V40	SMNDC1-BG293LV06-92B_Aligned.sortedByCoord.out.bam		ENCORE2	30101
SMNDC1-BG293LV06-92B_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	3086					GRCh38	V40	SMNDC1-BG293LV06-92B_Aligned.sortedByCoord.out.bam		ENCORE2	30173
SMNDC1-BG293LV06-92B_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	3086					GRCh38	V40	SMNDC1-BG293LV06-92B_Aligned.sortedByCoord.out.bam		ENCORE2	30245
SMNDC1-BG293LV06-92B_quant.sf	ENCODE_DATA/set72/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3086					GRCh38	V40	SMNDC1-BG293LV06-92B_S44_L001_R1_001.filtered.trimmed.paired.fastq.gz,SMNDC1-BG293LV06-92B_S44_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	30317