SRPRA RNA-Seq in K562

General Information


RBP	SRPRA
Cell_Line	K562
Method	CRISPR
Exp_Name	SRPRA-BGKcLV37-K562
ENCODE_series_ID
Batch_ID	BGKcLV37
Pool ID	Pool-230130
Local_Set_Name	set55
ENCODE_KD_Exp_ID
ENCODE_CN_Exp_ID
Rep1	SRPRA-BGKcLV37-41
Rep2	SRPRA-BGKcLV37-42
CN1	NT-BGKcLV37-1
CN2	NT-BGKcLV37-2
Rep1_qPCR	52.5
Rep2_qPCR	46.9
Rep1_WB	68.0
Rep2_WB	50.7
Antibody Cat#	A305-141A
Antibody Lot#	lot # 1
Antibody DCC ID	NO ID
Status	Submitted
Project	ENCORE2
ID	1059

Experiment Information (Status: Submitting)

	BGKcLV37-41	BGKcLV37-41	BGKcLV37-42	BGKcLV37-42
idx	1393	0	1394	0
TRCN#_or_BGC#	BGC#0001056	BGC#0001056	BGC#0001056	BGC#0001056
shRNA_or_gRNA_sequence	AATCAACGCGTTAACGGGTC	AATCAACGCGTTAACGGGTC	AATCAACGCGTTAACGGGTC	AATCAACGCGTTAACGGGTC
PAM	CGG	CGG	CGG	CGG
Name	SRPRA_100	SRPRA_100	SRPRA_100	SRPRA_100
Sample_ID	BGKcLV37-41	BGKcLV37-41	BGKcLV37-42	BGKcLV37-42
transduction_Date	9/20/22	9/20/22	9/20/22	9/20/22
days	D6	D6	D6	D6
RBP_name	SRPRA	SRPRA	SRPRA	SRPRA
qPCR_result	52.5	52.5	46.9	46.9
Ave_qPCR	49.7	49.7
RT-qPCR_primer-F	gcacagagatccaacagcaa	gcacagagatccaacagcaa
RT-qPCR_primer-R	tcttcatggtagtgggagca	tcttcatggtagtgggagca
protein_conc	1745	1745	1608	1608
WB_result	68.0	60.6	50.7	58.7776
Ave_WB	59.3	59.7
WB_DONE_date	10/12/22	10/18/22	Licor
MW	70kd	70kd
IP
antibody_Cat#	A305-141A	A305-140A	lot # 1	lot # 1
Antibody DCC ID	NO ID	NO ID
submitted_to_DCC_date	8/29/23	8/29/23
Rep1_TPM	0	0	0	0
Rep2_TPM	0	0	0	0
Action	Ready		Ready
Library_start_date
repeat_library
Note
ID	5547	5549	5548	5550

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
SRPRA	Product_ID: A305-140A Lot_ID: 1 Source: Bethyl Labs Target Name: SRPRA-human
SRPRA	Product_ID: A305-141A Lot_ID: 1 Source: Bethyl Labs Target Name: SRPRA-human

Experiment Status

	BGKcLV37-41	BGKcLV37-41	BGKcLV37-42	BGKcLV37-42
Sample_ID	BGKcLV37-41	BGKcLV37-41	BGKcLV37-42	BGKcLV37-42
Sample Name
Sample Name	SRPRA-BGKcLV37-41		SRPRA-BGKcLV37-42
RBP	SRPRA	SRPRA	SRPRA	SRPRA
Cell_Line	K562	K562	K562	K562
Exp UID
Status	Submitting	NotSatisfied	Submitting	NotSatisfied
Status_date	2023-04-14	2023-01-03	2023-04-14	2023-01-03
Project	ENCORE2	ENCORE2	ENCORE2	ENCORE2
Note
ID	11102	11132	11103	11133

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV37-41	BGKcLV37-42
Sample #	41	42
Sample Name	SRPRA-BGKcLV37-41	SRPRA-BGKcLV37-42
Sample_Name_Alias
Index Well Position	A06	B06
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2023-01-13	2023-01-13
Lib_ID	Lib-230113	Lib-230113
Tecan_Location
Tecan
Tecan_date
Size_bp	302	303
Peak_Molarity	67.40	53.40
libSampleQC_DNA_Well	DNA_Library_set54-56/set1/A6.png	DNA_Library_set54-56/set1/B6.png
RIN	9.8	9.8
libSample_RNA_Well	RNA_Library_set54-56/set1/A6.png	RNA_Library_set54-56/set1/B6.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-01-27	2023-01-27
Sample_ID	BGKcLV37-41	BGKcLV37-42
RBP	SRPRA	SRPRA
Batch_ID	BGKcLV37	BGKcLV37
WB_result	68.000	50.700
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	3412	3413

Sequencing Information

	BGKcLV37-41	BGKcLV37-42
Sample_ID	BGKcLV37-41	BGKcLV37-42
Sample Name	SRPRA-BGKcLV37-41	SRPRA-BGKcLV37-42
Pool ID	Pool-230130	Pool-230130
LocalServer_folder	set55	set55
total_reads	50,917,988	35,979,923
total_aligned_reads	48,603,730	34,248,638
unique_aligned_reads	45,202,522	31,821,091
percent_uniqueAligned	0.88775	0.88441
correlation_replicates	0.999399	0.999399
spikein_reads	10,802	4,836
percent_spikeins	0.00021	0.00013
original_ReadLength	101	101
QC_Status	Submitting	Submitting
ID	2285	2286

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
SRPRA-BGKcLV37-41_S41_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set55/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2285	NovaSeq6000	100	paired-ended	1				NT-BGKcLV37-1_S21_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV37-2_S22_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8412
SRPRA-BGKcLV37-41_S41_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set55/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2285	NovaSeq6000	100	paired-ended	2				NT-BGKcLV37-1_S21_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV37-2_S22_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8462
SRPRA-BGKcLV37-41_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set55/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2285					GRCh38	V40	SRPRA-BGKcLV37-41_S41_L001_R1_001.filtered.trimmed.paired.fastq.gz,SRPRA-BGKcLV37-41_S41_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25653
SRPRA-BGKcLV37-41_Signal.Unique.strand+.bw	ENCODE_DATA/set55/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2285					GRCh38	V40	SRPRA-BGKcLV37-41/Aligned.sortedByCoord.out.bam		ENCORE2	25703
SRPRA-BGKcLV37-41_Signal.Unique.strand-.bw	ENCODE_DATA/set55/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2285					GRCh38	V40	SRPRA-BGKcLV37-41/Aligned.sortedByCoord.out.bam		ENCORE2	25753
SRPRA-BGKcLV37-41_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set55/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2285					GRCh38	V40	SRPRA-BGKcLV37-41/Aligned.sortedByCoord.out.bam		ENCORE2	25803
SRPRA-BGKcLV37-41_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set55/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2285					GRCh38	V40	SRPRA-BGKcLV37-41/Aligned.sortedByCoord.out.bam		ENCORE2	25853
SRPRA-BGKcLV37-41_quant.sf	ENCODE_DATA/set55/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2285					GRCh38	V40	SRPRA-BGKcLV37-41_S41_L001_R1_001.filtered.trimmed.paired.fastq.gz,SRPRA-BGKcLV37-41_S41_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25903
SRPRA-BGKcLV37-42_S42_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set55/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2286	NovaSeq6000	100	paired-ended	1				NT-BGKcLV37-1_S21_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV37-2_S22_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8413
SRPRA-BGKcLV37-42_S42_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set55/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2286	NovaSeq6000	100	paired-ended	2				NT-BGKcLV37-1_S21_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV37-2_S22_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8463
SRPRA-BGKcLV37-42_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set55/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2286					GRCh38	V40	SRPRA-BGKcLV37-42_S42_L001_R1_001.filtered.trimmed.paired.fastq.gz,SRPRA-BGKcLV37-42_S42_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25654
SRPRA-BGKcLV37-42_Signal.Unique.strand+.bw	ENCODE_DATA/set55/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2286					GRCh38	V40	SRPRA-BGKcLV37-42/Aligned.sortedByCoord.out.bam		ENCORE2	25704
SRPRA-BGKcLV37-42_Signal.Unique.strand-.bw	ENCODE_DATA/set55/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2286					GRCh38	V40	SRPRA-BGKcLV37-42/Aligned.sortedByCoord.out.bam		ENCORE2	25754
SRPRA-BGKcLV37-42_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set55/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2286					GRCh38	V40	SRPRA-BGKcLV37-42/Aligned.sortedByCoord.out.bam		ENCORE2	25804
SRPRA-BGKcLV37-42_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set55/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2286					GRCh38	V40	SRPRA-BGKcLV37-42/Aligned.sortedByCoord.out.bam		ENCORE2	25854
SRPRA-BGKcLV37-42_quant.sf	ENCODE_DATA/set55/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2286					GRCh38	V40	SRPRA-BGKcLV37-42_S42_L001_R1_001.filtered.trimmed.paired.fastq.gz,SRPRA-BGKcLV37-42_S42_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25904