SNRPA RNA-Seq in 293T

Experiment Information (Status: Revoked)

	BG293LV02-45	BG293LV02-46
idx	0	0
TRCN#_or_BGC#	TRCN0000006610	TRCN0000006610
shRNA_or_gRNA_sequence	CCGGCCTCAATGAGAAGATCAAGAACTCGAGTTCTTGATCTTCTCATTGAGGTTTTT	CCGGCCTCAATGAGAAGATCAAGAACTCGAGTTCTTGATCTTCTCATTGAGGTTTTT
PAM
Name	SNRPA	SNRPA
Sample_ID	BG293LV02-45	BG293LV02-46
transduction_Date	3/20/23	3/20/23
days	D4	D4
RBP_name	SNRPA	SNRPA
qPCR_result	89.4	88.8
Ave_qPCR	89.1
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	9840	9841

Western Blot Western Blot info was not avaliable

Experiment Status

	BG293LV02-45	BG293LV02-46
Sample_ID	BG293LV02-45	BG293LV02-46
Sample Name
Sample Name	SNRPA-BG293LV02-45	SNRPA-BG293LV02-46
RBP	SNRPA	SNRPA
Cell_Line	293T	293T
Exp UID
Status	Revoked	Revoked
Status_date	2023-09-20	2023-09-20
Project	ENCORE2	ENCORE2
Note
ID	11596	11597

Library-Prep
Sequencing

Library-Prep Information

	BG293LV02-45	BG293LV02-46
Sample #	39	40
Sample Name	SNRPA-BG293LV02-45	SNRPA-BG293LV02-46
Sample_Name_Alias
Index Well Position	G05	H05
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2023-04-12	2023-04-12
Lib_ID	Lib-230412	Lib-230412
Tecan_Location
Tecan
Tecan_date
Size_bp	279	283
Peak_Molarity	80.60	91.00
libSampleQC_DNA_Well	DNA_Library_set60-62/set2/G5.png	DNA_Library_set60-62/set2/H5.png
RIN	9.8	9.8
libSample_RNA_Well	RNA_Library_set60-62/set1/G5.png	RNA_Library_set60-62/set1/H5.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-04-17	2023-04-17
Sample_ID	BG293LV02-45	BG293LV02-46
RBP	SNRPA	SNRPA
Batch_ID	BG293LV02	BG293LV02
WB_result	0.000	0.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	3626	3627

Sequencing Information

	BG293LV02-45	BG293LV02-46
Sample_ID	BG293LV02-45	BG293LV02-46
Sample Name	SNRPA-BG293LV02-45	SNRPA-BG293LV02-46
Pool ID	Pool-230417	Pool-230417
LocalServer_folder	set60	set60
total_reads	29,112,037	39,690,919
total_aligned_reads	18,705,086	34,049,853
unique_aligned_reads	17,385,477	31,678,392
percent_uniqueAligned	0.59719	0.79813
correlation_replicates	0.974746	0.974746
spikein_reads	35,608	66,026
percent_spikeins	0.00122	0.00166
original_ReadLength	101	101
QC_Status	Submitting	Submitting
ID	2497	2498

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
SNRPA-BG293LV02-45_S39_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set60/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2497	NovaSeq6000	100	paired-ended	1				NT-BG293LV02-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV02-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8000
SNRPA-BG293LV02-45_S39_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set60/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2497	NovaSeq6000	100	paired-ended	2				NT-BG293LV02-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV02-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8044
SNRPA-BG293LV02-45_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set60/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2497					GRCh38	V40	SNRPA-BG293LV02-45_S39_L001_R1_001.filtered.trimmed.paired.fastq.gz,SNRPA-BG293LV02-45_S39_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10793
SNRPA-BG293LV02-45_Signal.Unique.strand+.bw	ENCODE_DATA/set60/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2497					GRCh38	V40	SNRPA-BG293LV02-45/Aligned.sortedByCoord.out.bam		ENCORE2	10837
SNRPA-BG293LV02-45_Signal.Unique.strand-.bw	ENCODE_DATA/set60/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2497					GRCh38	V40	SNRPA-BG293LV02-45/Aligned.sortedByCoord.out.bam		ENCORE2	10881
SNRPA-BG293LV02-45_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set60/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2497					GRCh38	V40	SNRPA-BG293LV02-45/Aligned.sortedByCoord.out.bam		ENCORE2	10925
SNRPA-BG293LV02-45_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set60/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2497					GRCh38	V40	SNRPA-BG293LV02-45/Aligned.sortedByCoord.out.bam		ENCORE2	10969
SNRPA-BG293LV02-45_quant.sf	ENCODE_DATA/set60/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2497					GRCh38	V40	SNRPA-BG293LV02-45_S39_L001_R1_001.filtered.trimmed.paired.fastq.gz,SNRPA-BG293LV02-45_S39_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	11013
SNRPA-BG293LV02-46_S40_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set60/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2498	NovaSeq6000	100	paired-ended	1				NT-BG293LV02-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV02-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8001
SNRPA-BG293LV02-46_S40_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set60/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2498	NovaSeq6000	100	paired-ended	2				NT-BG293LV02-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV02-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8045
SNRPA-BG293LV02-46_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set60/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2498					GRCh38	V40	SNRPA-BG293LV02-46_S40_L001_R1_001.filtered.trimmed.paired.fastq.gz,SNRPA-BG293LV02-46_S40_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10794
SNRPA-BG293LV02-46_Signal.Unique.strand+.bw	ENCODE_DATA/set60/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2498					GRCh38	V40	SNRPA-BG293LV02-46/Aligned.sortedByCoord.out.bam		ENCORE2	10838
SNRPA-BG293LV02-46_Signal.Unique.strand-.bw	ENCODE_DATA/set60/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2498					GRCh38	V40	SNRPA-BG293LV02-46/Aligned.sortedByCoord.out.bam		ENCORE2	10882
SNRPA-BG293LV02-46_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set60/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2498					GRCh38	V40	SNRPA-BG293LV02-46/Aligned.sortedByCoord.out.bam		ENCORE2	10926
SNRPA-BG293LV02-46_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set60/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2498					GRCh38	V40	SNRPA-BG293LV02-46/Aligned.sortedByCoord.out.bam		ENCORE2	10970
SNRPA-BG293LV02-46_quant.sf	ENCODE_DATA/set60/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2498					GRCh38	V40	SNRPA-BG293LV02-46_S40_L001_R1_001.filtered.trimmed.paired.fastq.gz,SNRPA-BG293LV02-46_S40_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	11014