SSB RNA-Seq in K562

General Information


RBP	SSB
Cell_Line	K562
Method	CRISPR
Exp_Name	SSB-BGKcLV53-K562
ENCODE_series_ID
Batch_ID	BGKcLV53
Pool ID	Pool-260528
Local_Set_Name	set82
ENCODE_KD_Exp_ID
ENCODE_CN_Exp_ID
Rep1	SSB-BGKcLV53-133
Rep2	SSB-BGKcLV53-134
CN1	NT-BGKcLV53-1
CN2	NT-BGKcLV53-2
Rep1_qPCR	51.7
Rep2_qPCR	55.3
Rep1_WB	49.1
Rep2_WB	51.4
Antibody Cat#	RN074PW
Antibody Lot#	lot #1
Antibody DCC ID
Status	Submitted
Project	ENCORE2
ID	1741

Experiment Information (Status: Submitting)

	BGKcLV53-133	BGKcLV53-134
idx	0	0
TRCN#_or_BGC#	BGC#0001383	BGC#0001383
shRNA_or_gRNA_sequence	TTGGCGACTTCAATTTGCCA	TTGGCGACTTCAATTTGCCA
PAM	CGG	CGG
Name	SSB-69	SSB-69
Sample_ID	BGKcLV53-133	BGKcLV53-134
transduction_Date	2/24/26	2/24/26
days	D6	D6
RBP_name	SSB	SSB
qPCR_result	51.7	55.3
Ave_qPCR	53.5
RT-qPCR_primer-F	TTCTCAAATCATGGTGAAATAAA
RT-qPCR_primer-R	CCAATGCTTCCTTGGCTTT
protein_conc	4048	4099
WB_result	49.1	51.4
Ave_WB
WB_DONE_date	4/6/26
MW	47kd	#47
IP
antibody_Cat#	RN074PW	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	6497	6498

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
SSB	Product_ID: RN074PW Lot_ID: 001 Source: MBLI Target Name: SSB-human

Experiment Status

	BGKcLV53-133	BGKcLV53-134
Sample_ID	BGKcLV53-133	BGKcLV53-134
Sample Name
Sample Name	SSB-BGKcLV53-133	SSB-BGKcLV53-134
RBP	SSB	SSB
Cell_Line	K562	K562
Exp UID
Status	Submitting	Submitting
Status_date	2026-10-30	2026-10-30
Project	ENCORE2	ENCORE2
Note
ID	14806	14807

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV53-133	BGKcLV53-134
Sample #	57	58
Sample Name	SSB-BGKcLV53-133	SSB-BGKcLV53-134
Sample_Name_Alias
Index Well Position	G08	H08
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	293	309
Peak_Molarity	65.20	54.20
libSampleQC_DNA_Well	DNA_Library_set82/set2/G11.png	DNA_Library_set82/set2/H11.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_set82/set2/G8.png	RNA_Library_set82/set2/H8.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2026-05-27	2026-05-27
Sample_ID	BGKcLV53-133	BGKcLV53-134
RBP	SSB	SSB
Batch_ID	BGKcLV53	BGKcLV53
WB_result	49.100	51.400
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4896	4897

Sequencing Information

	BGKcLV53-133	BGKcLV53-134
Sample_ID	BGKcLV53-133	BGKcLV53-134
Sample Name	SSB-BGKcLV53-133	SSB-BGKcLV53-134
Pool ID	Pool-260528	Pool-260528
LocalServer_folder	set82	set82
total_reads	33,133,247	38,370,084
total_aligned_reads	30,109,432	36,049,223
unique_aligned_reads	27,862,246	33,417,581
percent_uniqueAligned	0.84092	0.87093
correlation_replicates	0.997688	0.997688
spikein_reads	40,686	65,700
percent_spikeins	0.00123	0.00171
original_ReadLength	151	151
QC_Status	Submitting	Submitting
ID	3597	3598

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
SSB-BGKcLV53-133_R1.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set82/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3597	NovaSeq6000	100	paired-ended	1				NT-BGKcLV53-1_R1.filtered.trimmed.paired.fastq.gz,NT-BGKcLV53-2_R1.filtered.trimmed.paired.fastq.gz	ENCORE2	33704
SSB-BGKcLV53-133_R2.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set82/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3597	NovaSeq6000	100	paired-ended	2				NT-BGKcLV53-1_R2.filtered.trimmed.paired.fastq.gz,NT-BGKcLV53-2_R2.filtered.trimmed.paired.fastq.gz	ENCORE2	33762
SSB-BGKcLV53-133_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set82/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3597					GRCh38	V40	SSB-BGKcLV53-133_R1.filtered.trimmed.paired.fastq.gz,SSB-BGKcLV53-133_R2.filtered.trimmed.paired.fastq.gz		ENCORE2	33822
SSB-BGKcLV53-133_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	3597					GRCh38	V40	SSB-BGKcLV53-133_Aligned.sortedByCoord.out.bam		ENCORE2	33880
SSB-BGKcLV53-133_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	3597					GRCh38	V40	SSB-BGKcLV53-133_Aligned.sortedByCoord.out.bam		ENCORE2	33938
SSB-BGKcLV53-133_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	3597					GRCh38	V40	SSB-BGKcLV53-133_Aligned.sortedByCoord.out.bam		ENCORE2	33996
SSB-BGKcLV53-133_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	3597					GRCh38	V40	SSB-BGKcLV53-133_Aligned.sortedByCoord.out.bam		ENCORE2	34054
SSB-BGKcLV53-133_quant.sf	ENCODE_DATA/set82/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3597					GRCh38	V40	SSB-BGKcLV53-133_R1.filtered.trimmed.paired.fastq.gz,SSB-BGKcLV53-133_R2.filtered.trimmed.paired.fastq.gz		ENCORE2	34112
SSB-BGKcLV53-134_R1.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set82/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3598	NovaSeq6000	100	paired-ended	1				NT-BGKcLV53-1_R1.filtered.trimmed.paired.fastq.gz,NT-BGKcLV53-2_R1.filtered.trimmed.paired.fastq.gz	ENCORE2	33705
SSB-BGKcLV53-134_R2.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set82/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3598	NovaSeq6000	100	paired-ended	2				NT-BGKcLV53-1_R2.filtered.trimmed.paired.fastq.gz,NT-BGKcLV53-2_R2.filtered.trimmed.paired.fastq.gz	ENCORE2	33763
SSB-BGKcLV53-134_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set82/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3598					GRCh38	V40	SSB-BGKcLV53-134_R1.filtered.trimmed.paired.fastq.gz,SSB-BGKcLV53-134_R2.filtered.trimmed.paired.fastq.gz		ENCORE2	33823
SSB-BGKcLV53-134_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	3598					GRCh38	V40	SSB-BGKcLV53-134_Aligned.sortedByCoord.out.bam		ENCORE2	33881
SSB-BGKcLV53-134_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	3598					GRCh38	V40	SSB-BGKcLV53-134_Aligned.sortedByCoord.out.bam		ENCORE2	33939
SSB-BGKcLV53-134_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	3598					GRCh38	V40	SSB-BGKcLV53-134_Aligned.sortedByCoord.out.bam		ENCORE2	33997
SSB-BGKcLV53-134_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	3598					GRCh38	V40	SSB-BGKcLV53-134_Aligned.sortedByCoord.out.bam		ENCORE2	34055
SSB-BGKcLV53-134_quant.sf	ENCODE_DATA/set82/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3598					GRCh38	V40	SSB-BGKcLV53-134_R1.filtered.trimmed.paired.fastq.gz,SSB-BGKcLV53-134_R2.filtered.trimmed.paired.fastq.gz		ENCORE2	34113