SRP9 RNA-Seq in K562

Experiment Information (Status: Sequenced)

	BGKcLV48-73	BGKcLV48-74
idx	0	0
TRCN#_or_BGC#	BGC#0001052	BGC#0001052
shRNA_or_gRNA_sequence	TTACCTTCATAGGGTCAGCG	TTACCTTCATAGGGTCAGCG
PAM	AGG	AGG
Name	SRP9_89	SRP9_89
Sample_ID	BGKcLV48-73	BGKcLV48-74
transduction_Date	4/15/25	4/15/25
days	D6	D6
RBP_name	SRP9	SRP9
qPCR_result	0.0	0.0
Ave_qPCR	0.0
RT-qPCR_primer-F	GGTGGTCTCTGCCTTCCTAAAG
RT-qPCR_primer-R	CGAGGAGTTGAAAGCCTTCTGC
protein_conc	2256	2338
WB_result	65.1	60.9
Ave_WB
WB_DONE_date	5/8/25
MW	10kd
IP
antibody_Cat#	A305-455A	lot# 1
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	6221	6222

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
SRP9	Product_ID: A305-455A Lot_ID: 1 Source: Bethyl Labs Target Name: SRP9-human

Experiment Status

	BGKcLV48-73	BGKcLV48-74
Sample_ID	BGKcLV48-73	BGKcLV48-74
Sample Name
Sample Name	SRP9-BGKcLV48-73	SRP9-BGKcLV48-74
RBP	SRP9	SRP9
Cell_Line	K562	K562
Exp UID
Status	Sequenced	Sequenced
Status_date	2025-10-02	2025-10-02
Project	ENCORE2	ENCORE2
Note
ID	14256	14257

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV48-73	BGKcLV48-74
Sample #	19	20
Sample Name	SRP9-BGKcLV48-73	SRP9-BGKcLV48-74
Sample_Name_Alias
Index Well Position	C03	D03
Index_table	IDT_UniqueDualIndex_96_V2	IDT_UniqueDualIndex_96_V2
LibPrep_date	2025-08-18	2025-08-18
Lib_ID	Lib-250818	Lib-250818
Tecan_Location
Tecan
Tecan_date
Size_bp	264	265
Peak_Molarity	112.00	89.50
libSampleQC_DNA_Well	DNA_Library_set79/set1/C3.png	DNA_Library_set79/set1/D3.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_set79/set1/C12.png	RNA_Library_set79/set1/D12.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2025-08-19	2025-08-19
Sample_ID	BGKcLV48-73	BGKcLV48-74
RBP	SRP9	SRP9
Batch_ID	BGKcLV48	BGKcLV48
WB_result	65.100	60.900
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4764	4765

Sequencing Information

	BGKcLV48-73	BGKcLV48-74
Sample_ID	BGKcLV48-73	BGKcLV48-74
Sample Name	SRP9-BGKcLV48-73	SRP9-BGKcLV48-74
Pool ID	Pool-250822	Pool-250822
LocalServer_folder	set79	set79
total_reads	19,853,519	22,471,335
total_aligned_reads	17,305,877	20,079,332
unique_aligned_reads	16,004,938	18,581,498
percent_uniqueAligned	0.80615	0.82690
correlation_replicates	0.995978	0.995978
spikein_reads	62,256	68,912
percent_spikeins	0.00314	0.00307
original_ReadLength	151	151
QC_Status	ReadyToSubmit	ReadyToSubmit
ID	3467	3468

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
SRP9-BGKcLV48-73_S183_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set79/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3467	NovaSeq6000	100	paired-ended	1				NT-BGKcLV48-1_S165_L002_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV48-2_S166_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	32838
SRP9-BGKcLV48-73_S183_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set79/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3467	NovaSeq6000	100	paired-ended	2				NT-BGKcLV48-1_S165_L002_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV48-2_S166_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	32860
SRP9-BGKcLV48-73_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set79/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3467					GRCh38	V40	SRP9-BGKcLV48-73_S183_L002_R1_001.filtered.trimmed.paired.fastq.gz,SRP9-BGKcLV48-73_S183_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	32882
SRP9-BGKcLV48-73_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set79/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3467					GRCh38	V40	SRP9-BGKcLV48-73_Aligned.sortedByCoord.out.bam		ENCORE2	32904
SRP9-BGKcLV48-73_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set79/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3467					GRCh38	V40	SRP9-BGKcLV48-73_Aligned.sortedByCoord.out.bam		ENCORE2	32926
SRP9-BGKcLV48-73_Signal.Unique.strand-.bw	ENCODE_DATA/set79/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3467					GRCh38	V40	SRP9-BGKcLV48-73_Aligned.sortedByCoord.out.bam		ENCORE2	32948
SRP9-BGKcLV48-73_Signal.Unique.strand+.bw	ENCODE_DATA/set79/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3467					GRCh38	V40	SRP9-BGKcLV48-73_Aligned.sortedByCoord.out.bam		ENCORE2	32970
SRP9-BGKcLV48-74_S184_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set79/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3468	NovaSeq6000	100	paired-ended	1				NT-BGKcLV48-1_S165_L002_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV48-2_S166_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	32839
SRP9-BGKcLV48-74_S184_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set79/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3468	NovaSeq6000	100	paired-ended	2				NT-BGKcLV48-1_S165_L002_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV48-2_S166_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	32861
SRP9-BGKcLV48-74_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set79/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3468					GRCh38	V40	SRP9-BGKcLV48-74_S184_L002_R1_001.filtered.trimmed.paired.fastq.gz,SRP9-BGKcLV48-74_S184_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	32883
SRP9-BGKcLV48-74_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set79/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3468					GRCh38	V40	SRP9-BGKcLV48-74_Aligned.sortedByCoord.out.bam		ENCORE2	32905
SRP9-BGKcLV48-74_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set79/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3468					GRCh38	V40	SRP9-BGKcLV48-74_Aligned.sortedByCoord.out.bam		ENCORE2	32927
SRP9-BGKcLV48-74_Signal.Unique.strand-.bw	ENCODE_DATA/set79/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3468					GRCh38	V40	SRP9-BGKcLV48-74_Aligned.sortedByCoord.out.bam		ENCORE2	32949
SRP9-BGKcLV48-74_Signal.Unique.strand+.bw	ENCODE_DATA/set79/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3468					GRCh38	V40	SRP9-BGKcLV48-74_Aligned.sortedByCoord.out.bam		ENCORE2	32971