SRA1 RNA-Seq in K562

General Information


RBP	SRA1
Cell_Line	K562
Method	CRISPR
Exp_Name	SRA1-BGKcLV33-K562
ENCODE_series_ID	ENCSR458NFA
Batch_ID	BGKcLV33
Pool ID	Pool-220418
Local_Set_Name	set53
ENCODE_KD_Exp_ID	ENCSR033MIV
ENCODE_CN_Exp_ID	ENCSR271ZAB
Rep1	SRA1-BGKcLV33-73
Rep2	SRA1-BGKcLV33-74
CN1	NT-BGKcLV33-1
CN2	NT-BGKcLV33-2
Rep1_qPCR	35.7
Rep2_qPCR	43.4
Rep1_WB	82.7
Rep2_WB	80.6
Antibody Cat#	A300-743A
Antibody Lot#	LOT #1
Antibody DCC ID	NO ID
Status	Submitted
Project	ENCODE4
ID	916

Experiment Information (Status: Released)

	BGKcLV33-73	BGKcLV33-74
idx	1272	1273
TRCN#_or_BGC#	BGC#0000887	BGC#0000887
shRNA_or_gRNA_sequence	GCGCTCGCTGCTTACCAAGA	GCGCTCGCTGCTTACCAAGA
PAM	GGG	GGG
Name	SRA1_93	SRA1_93
Sample_ID	BGKcLV33-73	BGKcLV33-74
transduction_Date	2/22/22	2/22/22
days	D6	D6
RBP_name	SRA1	SRA1
qPCR_result	35.7	43.4
Ave_qPCR	39.6
RT-qPCR_primer-F	atggaggatgtgctgagacc
RT-qPCR_primer-R	actttcctccagcccactgt
protein_conc	2297	2363
WB_result	82.7	80.6
Ave_WB	81.6
WB_DONE_date	3/10/22
MW	26kd
IP
antibody_Cat#	A300-743A	LOT #1
Antibody DCC ID	NO ID	8/4/22
submitted_to_DCC_date
Rep1_TPM	0	0
Rep2_TPM	0	0
Action	Ready	Ready
Library_start_date	04/13/22	04/13/22
repeat_library
Note
ID	5414	5415

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
SRA1	Product_ID: A300-743A Lot_ID: 1 Source: Bethyl Labs Target Name: SRA1-human

Experiment Status

	BGKcLV33-73	BGKcLV33-74
Sample_ID	BGKcLV33-73	BGKcLV33-74
Sample Name
Sample Name	SRA1-BGKcLV33-73	SRA1-BGKcLV33-74
RBP	SRA1	SRA1
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2022-10-28	2022-10-28
Project	ENCODE4	ENCODE4
Note
ID	10685	10686

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV33-73	BGKcLV33-74
Sample #	55	56
Sample Name	SRA1-BGKcLV33-73	SRA1-BGKcLV33-74
Sample_Name_Alias
Index Well Position	G07	H07
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2022-04-06	2022-04-06
Lib_ID	Lib-220406	Lib-220406
Tecan_Location
Tecan
Tecan_date
Size_bp	299	297
Peak_Molarity	72.10	73.00
libSampleQC_DNA_Well	DNA_Library_set53/set1/G11.png	DNA_Library_set53/set1/H11.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_set53/set1/G7.png	RNA_Library_set53/set1/H7.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2022-04-18	2022-04-18
Sample_ID	BGKcLV33-73	BGKcLV33-74
RBP	SRA1	SRA1
Batch_ID	BGKcLV33	BGKcLV33
WB_result	82.700	80.600
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	3316	3317

Sequencing Information

	BGKcLV33-73	BGKcLV33-74
Sample_ID	BGKcLV33-73	BGKcLV33-74
Sample Name	SRA1-BGKcLV33-73	SRA1-BGKcLV33-74
Pool ID	Pool-220418	Pool-220418
LocalServer_folder	set53	set53
total_reads	94,813,502	96,869,606
total_aligned_reads	88,933,722	88,440,416
unique_aligned_reads	81,816,248	81,214,874
percent_uniqueAligned	0.86292	0.83839
correlation_replicates	0.994002	0.994002
spikein_reads	5,996	7,200
percent_spikeins	0.00006	0.00007
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	2083	2084

Data Submission Information

	BGKcLV33-73	BGKcLV33-73	BGKcLV33-73	BGKcLV33-73	BGKcLV33-73	BGKcLV33-73	BGKcLV33-74	BGKcLV33-74	BGKcLV33-74	BGKcLV33-74
ENCODE_alias	brenton-graveley:SRA1-BGKcLV33	brenton-graveley:SRA1-BGKcLV33-73	brenton-graveley:L-SRA1-BGKcLV33-73	brenton-graveley:SRA1-BGKcLV33-73_S109_L002_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:SRA1-BGKcLV33-73_S109_L002_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:SRA1-BGKcLV33-K562	brenton-graveley:SRA1-BGKcLV33-74	brenton-graveley:L-SRA1-BGKcLV33-74	brenton-graveley:SRA1-BGKcLV33-74_S110_L002_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:SRA1-BGKcLV33-74_S110_L002_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR033MIV	ENCBS234IIM	ENCLB535ZXW	ENCFF070AIC	ENCFF552DUS	ENCSR458NFA	ENCBS885CJQ	ENCLB478PHH	ENCFF073UMJ	ENCFF691BGL
object_type	experiment	biosample	library	file_fastq1	file_fastq2	gene_silencing_series	biosample	library	file_fastq1	file_fastq2
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKcLV33-73	BGKcLV33-73	BGKcLV33-73	BGKcLV33-73	BGKcLV33-73	BGKcLV33-73	BGKcLV33-74	BGKcLV33-74	BGKcLV33-74	BGKcLV33-74
Sample Name	SRA1-BGKcLV33-73	SRA1-BGKcLV33-73	SRA1-BGKcLV33-73	SRA1-BGKcLV33-73	SRA1-BGKcLV33-73	SRA1-BGKcLV33-73	SRA1-BGKcLV33-74	SRA1-BGKcLV33-74	SRA1-BGKcLV33-74	SRA1-BGKcLV33-74
Selected	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes
Status	Released	Released	Released	Released	Released	Released	Released	Released	Released	Released
Status_Date	2022-10-28	2022-10-28	2022-10-28	2022-10-28	2022-10-28	2022-10-28	2022-10-28	2022-10-28	2022-10-28	2022-10-28
Project	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4
		LV53_biosample_protocol	LV53_library_protocol				LV53_biosample_protocol	LV53_library_protocol
protocol_URL		SRA1-BGKcLV33-73.pdf	L-SRA1-BGKcLV33-73.pdf				SRA1-BGKcLV33-74.pdf	L-SRA1-BGKcLV33-74.pdf
ID	7497	7603	7713	7825	7935	7987	7604	7714	7826	7936

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
SRA1-BGKcLV33-73_S109_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set53/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2083	NovaSeq6000	100	paired-ended	1				NT-BGKcLV33-1_S55_L002_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV33-2_S56_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	6663
SRA1-BGKcLV33-73_S109_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set53/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2083	NovaSeq6000	100	paired-ended	2				NT-BGKcLV33-1_S55_L002_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV33-2_S56_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	6719
SRA1-BGKcLV33-73_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set53/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2083					GRCh38	V40	SRA1-BGKcLV33-73_S109_L002_R1_001.filtered.trimmed.paired.fastq.gz,SRA1-BGKcLV33-73_S109_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18140
SRA1-BGKcLV33-73_Signal.Unique.strand+.bw	ENCODE_DATA/set53/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2083					GRCh38	V40	SRA1-BGKcLV33-73/Aligned.sortedByCoord.out.bam		ENCORE2	18196
SRA1-BGKcLV33-73_Signal.Unique.strand-.bw	ENCODE_DATA/set53/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2083					GRCh38	V40	SRA1-BGKcLV33-73/Aligned.sortedByCoord.out.bam		ENCORE2	18252
SRA1-BGKcLV33-73_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set53/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2083					GRCh38	V40	SRA1-BGKcLV33-73/Aligned.sortedByCoord.out.bam		ENCORE2	18308
SRA1-BGKcLV33-73_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set53/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2083					GRCh38	V40	SRA1-BGKcLV33-73/Aligned.sortedByCoord.out.bam		ENCORE2	18364
SRA1-BGKcLV33-73_quant.sf	ENCODE_DATA/set53/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2083					GRCh38	V40	SRA1-BGKcLV33-73_S109_L002_R1_001.filtered.trimmed.paired.fastq.gz,SRA1-BGKcLV33-73_S109_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18420
SRA1-BGKcLV33-74_S110_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set53/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2084	NovaSeq6000	100	paired-ended	1				NT-BGKcLV33-1_S55_L002_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV33-2_S56_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	6664
SRA1-BGKcLV33-74_S110_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set53/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2084	NovaSeq6000	100	paired-ended	2				NT-BGKcLV33-1_S55_L002_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV33-2_S56_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	6720
SRA1-BGKcLV33-74_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set53/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2084					GRCh38	V40	SRA1-BGKcLV33-74_S110_L002_R1_001.filtered.trimmed.paired.fastq.gz,SRA1-BGKcLV33-74_S110_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18141
SRA1-BGKcLV33-74_Signal.Unique.strand+.bw	ENCODE_DATA/set53/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2084					GRCh38	V40	SRA1-BGKcLV33-74/Aligned.sortedByCoord.out.bam		ENCORE2	18197
SRA1-BGKcLV33-74_Signal.Unique.strand-.bw	ENCODE_DATA/set53/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2084					GRCh38	V40	SRA1-BGKcLV33-74/Aligned.sortedByCoord.out.bam		ENCORE2	18253
SRA1-BGKcLV33-74_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set53/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2084					GRCh38	V40	SRA1-BGKcLV33-74/Aligned.sortedByCoord.out.bam		ENCORE2	18309
SRA1-BGKcLV33-74_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set53/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2084					GRCh38	V40	SRA1-BGKcLV33-74/Aligned.sortedByCoord.out.bam		ENCORE2	18365
SRA1-BGKcLV33-74_quant.sf	ENCODE_DATA/set53/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2084					GRCh38	V40	SRA1-BGKcLV33-74_S110_L002_R1_001.filtered.trimmed.paired.fastq.gz,SRA1-BGKcLV33-74_S110_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18421