LSM4 RNA-Seq in K562

Experiment Information (Status: Sequenced)

	BGKcLV53-79	BGKcLV53-80
idx	0	0
TRCN#_or_BGC#	BGC#0001520	BGC#0001520
shRNA_or_gRNA_sequence	CCCCGCCGGCACCATGGTGA	CCCCGCCGGCACCATGGTGA
PAM	GGG	GGG
Name	LSM4_77U	LSM4_77U
Sample_ID	BGKcLV53-79	BGKcLV53-80
transduction_Date	2/24/26	2/24/26
days	D6	D6
RBP_name	LSM4	LSM4
qPCR_result	96.1	94.9
Ave_qPCR	95.5
RT-qPCR_primer-F	TGGATGAACATTAACCTGCG
RT-qPCR_primer-R	GATGTAGCACTCGGGCATC
protein_conc	2323	1858
WB_result	84.1	89.0
Ave_WB
WB_DONE_date	3/20/26
MW	15kd
IP
antibody_Cat#	GTX117766
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	6441	6442

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
LSM4	Product_ID: GTX117766 Lot_ID: 40429 Source: GeneTex Target Name: LSM4-human

Experiment Status

	BGKcLV53-79	BGKcLV53-80
Sample_ID	BGKcLV53-79	BGKcLV53-80
Sample Name
Sample Name	LSM4-BGKcLV53-79	LSM4-BGKcLV53-80
RBP	LSM4	LSM4
Cell_Line	K562	K562
Exp UID
Status	Sequenced	Sequenced
Status_date	2026-09-16	2026-09-16
Project	ENCORE2	ENCORE2
Note
ID	14798	14799

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV53-79	BGKcLV53-80
Sample #	49	50
Sample Name	LSM4-BGKcLV53-79	LSM4-BGKcLV53-80
Sample_Name_Alias
Index Well Position	G07	H07
Index_table	IDT_UniqueDualIndex_96_V2	IDT_UniqueDualIndex_96_V2
LibPrep_date	2026-05-26	2026-05-26
Lib_ID	Lib-260526	Lib-260526
Tecan_Location
Tecan
Tecan_date
Size_bp	300	306
Peak_Molarity	60.00	53.80
libSampleQC_DNA_Well	DNA_Library_set82/set2/G10.png	DNA_Library_set82/set2/H10.png
RIN	10.0	9.9
libSample_RNA_Well	RNA_Library_set82/set2/G7.png	RNA_Library_set82/set2/H7.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2026-05-27	2026-05-27
Sample_ID	BGKcLV53-79	BGKcLV53-80
RBP	LSM4	LSM4
Batch_ID	BGKcLV53	BGKcLV53
WB_result	84.100	89.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4888	4889

Sequencing Information

	BGKcLV53-79	BGKcLV53-80
Sample_ID	BGKcLV53-79	BGKcLV53-80
Sample Name	LSM4-BGKcLV53-79	LSM4-BGKcLV53-80
Pool ID	Pool-260528	Pool-260528
LocalServer_folder	set82	set82
total_reads	16,457,511	14,073,996
total_aligned_reads	15,166,081	13,305,360
unique_aligned_reads	14,098,560	12,294,468
percent_uniqueAligned	0.85666	0.87356
correlation_replicates	0.998959	0.998959
spikein_reads	29,984	37,834
percent_spikeins	0.00182	0.00269
original_ReadLength	151	151
QC_Status	ReadyToSubmit	ReadyToSubmit
ID	3589	3590

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
LSM4-BGKcLV53-79_R1.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set82/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3589	NovaSeq6000	100	paired-ended	1				NT-BGKcLV53-1_R1.filtered.trimmed.paired.fastq.gz,NT-BGKcLV53-2_R1.filtered.trimmed.paired.fastq.gz	ENCORE2	33672
LSM4-BGKcLV53-79_R2.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set82/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3589	NovaSeq6000	100	paired-ended	2				NT-BGKcLV53-1_R2.filtered.trimmed.paired.fastq.gz,NT-BGKcLV53-2_R2.filtered.trimmed.paired.fastq.gz	ENCORE2	33730
LSM4-BGKcLV53-79_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set82/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3589					GRCh38	V40	LSM4-BGKcLV53-79_R1.filtered.trimmed.paired.fastq.gz,LSM4-BGKcLV53-79_R2.filtered.trimmed.paired.fastq.gz		ENCORE2	33788
LSM4-BGKcLV53-79_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set82/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3589					GRCh38	V40	LSM4-BGKcLV53-79_Aligned.sortedByCoord.out.bam		ENCORE2	33846
LSM4-BGKcLV53-79_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set82/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3589					GRCh38	V40	LSM4-BGKcLV53-79_Aligned.sortedByCoord.out.bam		ENCORE2	33904
LSM4-BGKcLV53-79_Signal.Unique.strand-.bw	ENCODE_DATA/set82/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3589					GRCh38	V40	LSM4-BGKcLV53-79_Aligned.sortedByCoord.out.bam		ENCORE2	33962
LSM4-BGKcLV53-79_Signal.Unique.strand+.bw	ENCODE_DATA/set82/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3589					GRCh38	V40	LSM4-BGKcLV53-79_Aligned.sortedByCoord.out.bam		ENCORE2	34020
LSM4-BGKcLV53-79_quant.sf	ENCODE_DATA/set82/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3589					GRCh38	V40	LSM4-BGKcLV53-79_R1.filtered.trimmed.paired.fastq.gz,LSM4-BGKcLV53-79_R2.filtered.trimmed.paired.fastq.gz		ENCORE2	34078
LSM4-BGKcLV53-80_R1.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set82/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3590	NovaSeq6000	100	paired-ended	1				NT-BGKcLV53-1_R1.filtered.trimmed.paired.fastq.gz,NT-BGKcLV53-2_R1.filtered.trimmed.paired.fastq.gz	ENCORE2	33673
LSM4-BGKcLV53-80_R2.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set82/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3590	NovaSeq6000	100	paired-ended	2				NT-BGKcLV53-1_R2.filtered.trimmed.paired.fastq.gz,NT-BGKcLV53-2_R2.filtered.trimmed.paired.fastq.gz	ENCORE2	33731
LSM4-BGKcLV53-80_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set82/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3590					GRCh38	V40	LSM4-BGKcLV53-80_R1.filtered.trimmed.paired.fastq.gz,LSM4-BGKcLV53-80_R2.filtered.trimmed.paired.fastq.gz		ENCORE2	33789
LSM4-BGKcLV53-80_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set82/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3590					GRCh38	V40	LSM4-BGKcLV53-80_Aligned.sortedByCoord.out.bam		ENCORE2	33847
LSM4-BGKcLV53-80_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set82/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3590					GRCh38	V40	LSM4-BGKcLV53-80_Aligned.sortedByCoord.out.bam		ENCORE2	33905
LSM4-BGKcLV53-80_Signal.Unique.strand-.bw	ENCODE_DATA/set82/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3590					GRCh38	V40	LSM4-BGKcLV53-80_Aligned.sortedByCoord.out.bam		ENCORE2	33963
LSM4-BGKcLV53-80_Signal.Unique.strand+.bw	ENCODE_DATA/set82/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3590					GRCh38	V40	LSM4-BGKcLV53-80_Aligned.sortedByCoord.out.bam		ENCORE2	34021
LSM4-BGKcLV53-80_quant.sf	ENCODE_DATA/set82/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3590					GRCh38	V40	LSM4-BGKcLV53-80_R1.filtered.trimmed.paired.fastq.gz,LSM4-BGKcLV53-80_R2.filtered.trimmed.paired.fastq.gz		ENCORE2	34079