SRP68 RNA-Seq in K562

General Information


RBP	SRP68
Cell_Line	K562
Method	shRNA
Exp_Name	SRP68-BGKLV19-K562
ENCODE_series_ID	ENCSR552QKE
Batch_ID	BGKLV19
Pool ID	Pool-141015
Local_Set_Name	set19
ENCODE_KD_Exp_ID	ENCSR312SRB
ENCODE_CN_Exp_ID	ENCSR661HEL
Rep1	SRP68_BGKLV19_51B
Rep2	SRP68_BGKLV19_52B
CN1	NT_BGKLV19_1B
CN2	NT_BGKLV19_2B
Rep1_qPCR	57.7
Rep2_qPCR	61.8
Rep1_WB	68.9
Rep2_WB	47.2
Antibody Cat#	A303-955A
Antibody Lot#	A303-955A
Antibody DCC ID	ENCAB434DUK
Status	Released
Project	ENCODE3
ID	482

Experiment Information (Status: Released)

	BGKLV19-51	BGKLV19-52
idx	258	259
TRCN#_or_BGC#	TRCN0000075080	TRCN0000075080
shRNA_or_gRNA_sequence	CCGACTCTATGACATCATCTT	CCGACTCTATGACATCATCTT
PAM
Name	SRP68	SRP68
Sample_ID	BGKLV19-51	BGKLV19-52
transduction_Date	9/4/2014	9/4/2014
days
RBP_name	SRP68	SRP68
qPCR_result	57.7	61.8
Ave_qPCR	59.8
RT-qPCR_primer-F	gagagccagggaaggtgtct
RT-qPCR_primer-R	cctttggccatgttctcatt
protein_conc	2466	3107
WB_result	68.9	47.2
Ave_WB	58.1
WB_DONE_date	2/24/2015
MW	71kDa
IP	1	1
antibody_Cat#	A303-955A	A303-955A
Antibody DCC ID	ENCAB434DUK	ENCAB434DUK
submitted_to_DCC_date	4/2/2015
Rep1_TPM	69.7291611	0
Rep2_TPM	62.9683557	0
Action
Library_start_date	10/2/2014	10/2/2014
repeat_library
Note
ID	283	284

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
SRP68	Product_ID: A303-955A Lot_ID: 1 Source: Bethyl Labs Target Name: SRP68-human

Experiment Status

	BGKLV19-51	BGKLV19-52
Sample_ID	BGKLV19-51	BGKLV19-52
Sample Name	SRP68_BGKLV19_51B	SRP68_BGKLV19_52B
Sample Name	SRP68_BGKLV19_51B	SRP68_BGKLV19_52B
RBP	SRP68	SRP68
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2014-12-11	2014-12-11
Project	ENCODE3	ENCODE3
Note
ID	698	699

Library-Prep
Sequencing

Library-Prep Information

	BGKLV19-51	BGKLV19-52
Sample #
Sample Name	SRP68-BGKLV19-51B	SRP68-BGKLV19-52B
Sample_Name_Alias	SRP68_BGKLV19_51B	SRP68_BGKLV19_52B
Index Well Position	S11	S12
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2014-10-03	2014-10-03
Lib_ID	Lib-141003	Lib-141003
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV18-19/set1/C11.png	DNA_Library_LV18-19/set1/D11.png
RIN	10.0	9.9
libSample_RNA_Well	RNA_Library_LV19-21-24/set1/G5.png	RNA_Library_LV35_LV36/set1/C11.png
SampleQC_method
SampleQC_date
Sample_ID	BGKLV19-51	BGKLV19-52
RBP	SRP68	SRP68
Batch_ID	BGKLV19	BGKLV19
WB_result	68.900	47.200
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix	B	B
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2382	2383

Sequencing Information

	BGKLV19-51	BGKLV19-52
Sample_ID	BGKLV19-51	BGKLV19-52
Sample Name	SRP68_BGKLV19_51B	SRP68_BGKLV19_52B
Pool ID	Pool-141015	Pool-141015
LocalServer_folder	set19	set19
total_reads	43,430,000	46,540,000
total_aligned_reads	40,447,640	43,666,040
unique_aligned_reads	37,071,892	40,037,652
percent_uniqueAligned	0.85360	0.86028
correlation_replicates	0.997133	0.997133
spikein_reads	197,622	154,446
percent_spikeins	0.00455	0.00332
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1024	1025

Data Submission Information

	BGKLV19-51	BGKLV19-51
ENCODE_alias	brenton-graveley:SRP68_BGKLV19	brenton-graveley:SRP68-BGKLV19-K562
ENCODE_accession	ENCSR312SRB	ENCSR552QKE
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKLV19-51	BGKLV19-51
Sample Name	SRP68_BGKLV19_51B	SRP68_BGKLV19_51B
Selected	Yes	Yes
Status	Released	Released
Status_Date	2014-12-05	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2897	6964

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
SRP68_BGKLV19_51B_GGCTAC_L006_R1_001.fastq.gz	ENCODE_DATA/set19/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1024	HiSeq2000	100	paired-ended	1				NT_BGKLV19_1B_ATCACG_L002_R1_001.fastq.gz,NT_BGKLV19_2B_CGATGT_L002_R1_001.fastq.gz	ENCODE3	15140
SRP68_BGKLV19_51B_GGCTAC_L006_R2_001.fastq.gz	ENCODE_DATA/set19/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1024	HiSeq2000	100	paired-ended	2				NT_BGKLV19_1B_ATCACG_L002_R2_001.fastq.gz,NT_BGKLV19_2B_CGATGT_L002_R2_001.fastq.gz	ENCODE3	15198
SRP68_BGKLV19_51B_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1024					GRCh38	V40	SRP68_BGKLV19_51B_GGCTAC_L006_R1_001.fastq.gz,SRP68_BGKLV19_51B_GGCTAC_L006_R2_001.fastq.gz		ENCORE2	15256
SRP68_BGKLV19_51B_Signal.Unique.strand+.bw	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1024					GRCh38	V40	SRP68_BGKLV19_51B/Aligned.sortedByCoord.out.bam		ENCORE2	15327
SRP68_BGKLV19_51B_Signal.Unique.strand-.bw	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1024					GRCh38	V40	SRP68_BGKLV19_51B/Aligned.sortedByCoord.out.bam		ENCORE2	15385
SRP68_BGKLV19_51B_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1024					GRCh38	V40	SRP68_BGKLV19_51B/Aligned.sortedByCoord.out.bam		ENCORE2	15443
SRP68_BGKLV19_51B_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1024					GRCh38	V40	SRP68_BGKLV19_51B/Aligned.sortedByCoord.out.bam		ENCORE2	15501
SRP68_BGKLV19_51B_quant.sf	ENCODE_DATA/set19/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1024					GRCh38	V40	SRP68_BGKLV19_51B_GGCTAC_L006_R1_001.fastq.gz,SRP68_BGKLV19_51B_GGCTAC_L006_R2_001.fastq.gz		ENCORE2	16398
SRP68_BGKLV19_52B_CTTGTA_L006_R1_001.fastq.gz	ENCODE_DATA/set19/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1025	HiSeq2000	100	paired-ended	1				NT_BGKLV19_1B_ATCACG_L002_R1_001.fastq.gz,NT_BGKLV19_2B_CGATGT_L002_R1_001.fastq.gz	ENCODE3	15141
SRP68_BGKLV19_52B_CTTGTA_L006_R2_001.fastq.gz	ENCODE_DATA/set19/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1025	HiSeq2000	100	paired-ended	2				NT_BGKLV19_1B_ATCACG_L002_R2_001.fastq.gz,NT_BGKLV19_2B_CGATGT_L002_R2_001.fastq.gz	ENCODE3	15199
SRP68_BGKLV19_52B_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1025					GRCh38	V40	SRP68_BGKLV19_52B_CTTGTA_L006_R1_001.fastq.gz,SRP68_BGKLV19_52B_CTTGTA_L006_R2_001.fastq.gz		ENCORE2	15257
SRP68_BGKLV19_52B_Signal.Unique.strand+.bw	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1025					GRCh38	V40	SRP68_BGKLV19_52B/Aligned.sortedByCoord.out.bam		ENCORE2	15328
SRP68_BGKLV19_52B_Signal.Unique.strand-.bw	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1025					GRCh38	V40	SRP68_BGKLV19_52B/Aligned.sortedByCoord.out.bam		ENCORE2	15386
SRP68_BGKLV19_52B_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1025					GRCh38	V40	SRP68_BGKLV19_52B/Aligned.sortedByCoord.out.bam		ENCORE2	15444
SRP68_BGKLV19_52B_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1025					GRCh38	V40	SRP68_BGKLV19_52B/Aligned.sortedByCoord.out.bam		ENCORE2	15502
SRP68_BGKLV19_52B_quant.sf	ENCODE_DATA/set19/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1025					GRCh38	V40	SRP68_BGKLV19_52B_CTTGTA_L006_R1_001.fastq.gz,SRP68_BGKLV19_52B_CTTGTA_L006_R2_001.fastq.gz		ENCORE2	16399