SSR1 RNA-Seq in K562

General Information


RBP	SSR1
Cell_Line	K562
Method	CRISPR
Exp_Name	SSR1-BGKcLV44-K562
ENCODE_series_ID
Batch_ID	BGKcLV44
Pool ID	Pool-241015
Local_Set_Name	set75
ENCODE_KD_Exp_ID
ENCODE_CN_Exp_ID
Rep1	SSR1-BGKcLV44-73
Rep2	SSR1-BGKcLV44-74
CN1	NT-BGKcLV44-1
CN2	NT-BGKcLV44-2
Rep1_qPCR	45.5
Rep2_qPCR	45.0
Rep1_WB	49.8
Rep2_WB	58.3
Antibody Cat#	A304-978A
Antibody Lot#	lot # 1
Antibody DCC ID
Status	Submitted
Project	ENCORE2
ID	1611

Experiment Information (Status: Submitting)

	BGKcLV44-73	BGKcLV44-74
idx	0	0
TRCN#_or_BGC#	BGC#0001219	BGC#0001219
shRNA_or_gRNA_sequence	AGTGGCACAAGATCTTACAG	AGTGGCACAAGATCTTACAG
PAM	AGG	AGG
Name	SSR1_81	SSR1_81
Sample_ID	BGKcLV44-73	BGKcLV44-74
transduction_Date	7/30/24	7/30/24
days	D6	D6
RBP_name	SSR1	SSR1
qPCR_result	45.5	45.0
Ave_qPCR	45.3
RT-qPCR_primer-F	agcttcaccgagtgcagata
RT-qPCR_primer-R	gaccaaaccaaatggtcgtc
protein_conc	4430	4914
WB_result	49.8	58.3
Ave_WB	54.1
WB_DONE_date	8/14/24
MW
IP
antibody_Cat#	A304-978A	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	5956	5957

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
SSR1	Product_ID: A304-978A Lot_ID: 1 Source: Bethyl Labs Target Name: SSR1-human

Experiment Status

	BGKcLV44-73	BGKcLV44-74
Sample_ID	BGKcLV44-73	BGKcLV44-74
Sample Name
Sample Name	SSR1-BGKcLV44-73	SSR1-BGKcLV44-74
RBP	SSR1	SSR1
Cell_Line	K562	K562
Exp UID
Status	Submitting	Submitting
Status_date	2025-02-11	2025-02-11
Project	ENCORE2	ENCORE2
Note
ID	13614	13615

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV44-73	BGKcLV44-74
Sample #	43	44
Sample Name	SSR1-BGKcLV44-73	SSR1-BGKcLV44-74
Sample_Name_Alias
Index Well Position	C11	D11
Index_table	IDT_UniqueDualIndex_96_V2	IDT_UniqueDualIndex_96_V2
LibPrep_date	2024-10-10	2024-10-10
Lib_ID	Lib-241010	Lib-241010
Tecan_Location
Tecan
Tecan_date
Size_bp	288	295
Peak_Molarity	75.40	79.50
libSampleQC_DNA_Well	DNA_Library_set75/set1/C11.png	DNA_Library_set75/set1/D11.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_set75/set1/C5.png	RNA_Library_set75/set1/D5.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2024-10-15	2024-10-15
Sample_ID	BGKcLV44-73	BGKcLV44-74
RBP	SSR1	SSR1
Batch_ID	BGKcLV44	BGKcLV44
WB_result	49.800	58.300
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4602	4603

Sequencing Information

	BGKcLV44-73	BGKcLV44-74
Sample_ID	BGKcLV44-73	BGKcLV44-74
Sample Name	SSR1-BGKcLV44-73	SSR1-BGKcLV44-74
Pool ID	Pool-241015	Pool-241015
LocalServer_folder	set75	set75
total_reads	51,479,701	54,758,083
total_aligned_reads	48,973,276	52,106,225
unique_aligned_reads	45,423,531	48,327,017
percent_uniqueAligned	0.88236	0.88255
correlation_replicates	0.997613	0.997613
spikein_reads	74,034	66,502
percent_spikeins	0.00144	0.00121
original_ReadLength	101	101
QC_Status	Submitting	Submitting
ID	3313	3314

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
SSR1-BGKcLV44-73_S35_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set75/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3313	NovaSeq6000	100	paired-ended	1				NT-BGKcLV44-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV44-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	30972
SSR1-BGKcLV44-73_S35_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set75/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3313	NovaSeq6000	100	paired-ended	2				NT-BGKcLV44-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV44-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	31014
SSR1-BGKcLV44-73_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set75/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3313					GRCh38	V40	SSR1-BGKcLV44-73_S35_L001_R1_001.filtered.trimmed.paired.fastq.gz,SSR1-BGKcLV44-73_S35_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31056
SSR1-BGKcLV44-73_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set75/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3313					GRCh38	V40	SSR1-BGKcLV44-73_Aligned.sortedByCoord.out.bam		ENCORE2	31098
SSR1-BGKcLV44-73_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set75/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3313					GRCh38	V40	SSR1-BGKcLV44-73_Aligned.sortedByCoord.out.bam		ENCORE2	31140
SSR1-BGKcLV44-73_Signal.Unique.strand-.bw	ENCODE_DATA/set75/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3313					GRCh38	V40	SSR1-BGKcLV44-73_Aligned.sortedByCoord.out.bam		ENCORE2	31182
SSR1-BGKcLV44-73_Signal.Unique.strand+.bw	ENCODE_DATA/set75/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3313					GRCh38	V40	SSR1-BGKcLV44-73_Aligned.sortedByCoord.out.bam		ENCORE2	31224
SSR1-BGKcLV44-73_quant.sf	ENCODE_DATA/set75/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3313					GRCh38	V40	SSR1-BGKcLV44-73_S35_L001_R1_001.filtered.trimmed.paired.fastq.gz,SSR1-BGKcLV44-73_S35_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31266
SSR1-BGKcLV44-74_S36_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set75/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3314	NovaSeq6000	100	paired-ended	1				NT-BGKcLV44-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV44-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	30973
SSR1-BGKcLV44-74_S36_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set75/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3314	NovaSeq6000	100	paired-ended	2				NT-BGKcLV44-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV44-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	31015
SSR1-BGKcLV44-74_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set75/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3314					GRCh38	V40	SSR1-BGKcLV44-74_S36_L001_R1_001.filtered.trimmed.paired.fastq.gz,SSR1-BGKcLV44-74_S36_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31057
SSR1-BGKcLV44-74_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set75/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3314					GRCh38	V40	SSR1-BGKcLV44-74_Aligned.sortedByCoord.out.bam		ENCORE2	31099
SSR1-BGKcLV44-74_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set75/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3314					GRCh38	V40	SSR1-BGKcLV44-74_Aligned.sortedByCoord.out.bam		ENCORE2	31141
SSR1-BGKcLV44-74_Signal.Unique.strand-.bw	ENCODE_DATA/set75/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3314					GRCh38	V40	SSR1-BGKcLV44-74_Aligned.sortedByCoord.out.bam		ENCORE2	31183
SSR1-BGKcLV44-74_Signal.Unique.strand+.bw	ENCODE_DATA/set75/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3314					GRCh38	V40	SSR1-BGKcLV44-74_Aligned.sortedByCoord.out.bam		ENCORE2	31225
SSR1-BGKcLV44-74_quant.sf	ENCODE_DATA/set75/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3314					GRCh38	V40	SSR1-BGKcLV44-74_S36_L001_R1_001.filtered.trimmed.paired.fastq.gz,SSR1-BGKcLV44-74_S36_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31267