SLBP RNA-Seq in K562

General Information


RBP	SLBP
Cell_Line	K562
Method	shRNA
Exp_Name	SLBP-BGKLV24-K562
ENCODE_series_ID	ENCSR027WCW
Batch_ID	BGKLV24
Pool ID	Pool-150615
Local_Set_Name	set24
ENCODE_KD_Exp_ID	ENCSR112YTD
ENCODE_CN_Exp_ID	ENCSR667PLJ
Rep1	SLBP_BGKLV24_57_17626
Rep2	SLBP_BGKLV24_58_17627
CN1	non-target_BGKLV24_1_17594
CN2	non-target_BGKLV24_2_17595
Rep1_qPCR	52.1
Rep2_qPCR	85.6
Rep1_WB	96.5
Rep2_WB	95.2
Antibody Cat#	RN045P
Antibody Lot#	RN045P
Antibody DCC ID	ENCAB000BGB
Status	Released
Project	ENCODE3
ID	569

Experiment Information (Status: Released)

	BGKLV24-57	BGKLV24-58
idx	394	395
TRCN#_or_BGC#	TRCN0000106680	TRCN0000106680
shRNA_or_gRNA_sequence	CCAGCGAGCTTAATTGCGTAA	CCAGCGAGCTTAATTGCGTAA
PAM
Name	SLBP	SLBP
Sample_ID	BGKLV24-57	BGKLV24-58
transduction_Date	2/27/2015	2/27/2015
days
RBP_name	SLBP	SLBP
qPCR_result	52.1	85.6
Ave_qPCR	68.9
RT-qPCR_primer-F	AGACCTTGAATCTGCAGAAAGC
RT-qPCR_primer-R	ACTGTCCATGTGTCTCACCTTG
protein_conc	3909	3989
WB_result	96.5	95.2
Ave_WB	95.9
WB_DONE_date	5/11/2015
MW	32kDa
IP	1	1
antibody_Cat#	RN045P	RN045P
Antibody DCC ID	ENCAB000BGB	ENCAB000BGB
submitted_to_DCC_date	8/6/2015
Rep1_TPM	92.9440271	0
Rep2_TPM	63.8117504	0
Action
Library_start_date	5/22/2015	5/22/2015
repeat_library
Note
ID	453	454

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
SLBP	Product_ID: RN045P Lot_ID: 1 Source: MBLI Target Name: SLBP-human

Experiment Status

	BGKLV24-57	BGKLV24-58
Sample_ID	BGKLV24-57	BGKLV24-58
Sample Name	SLBP_BGKLV24_57_17626	SLBP_BGKLV24_58_17627
Sample Name	SLBP_BGKLV24_57_17626	SLBP_BGKLV24_58_17627
RBP	SLBP	SLBP
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2015-08-14	2015-08-14
Project	ENCODE3	ENCODE3
Note
ID	878	879

Library-Prep
Sequencing

Library-Prep Information

	BGKLV24-57	BGKLV24-58
Sample #
Sample Name	SLBP-BGKLV24-57	SLBP-BGKLV24-58
Sample_Name_Alias	SLBP_BGKLV24_57_17626	SLBP_BGKLV24_58_17627
Index Well Position	S25	S27
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2015-05-22	2015-05-22
Lib_ID	Lib-150522	Lib-150522
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV21-24/set1/G4.png	DNA_Library_LV21-24/set1/H4.png
RIN	9.7	9.5
libSample_RNA_Well	RNA_Library_LV19-21-24/set2/E3.png	RNA_Library_LV20-22-24/set1/F6.png
SampleQC_method
SampleQC_date
Sample_ID	BGKLV24-57	BGKLV24-58
RBP	SLBP	SLBP
Batch_ID	BGKLV24	BGKLV24
WB_result	96.500	95.200
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2566	2567

Sequencing Information

	BGKLV24-57	BGKLV24-58
Sample_ID	BGKLV24-57	BGKLV24-58
Sample Name	SLBP_BGKLV24_57_17626	SLBP_BGKLV24_58_17627
Pool ID	Pool-150615	Pool-150615
LocalServer_folder	set24	set24
total_reads	40,540,000	38,090,000
total_aligned_reads	38,125,992	36,008,948
unique_aligned_reads	34,893,302	33,026,830
percent_uniqueAligned	0.86071	0.86707
correlation_replicates	0.997810	0.997810
spikein_reads	199,520	206,008
percent_spikeins	0.00492	0.00541
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1100	1101

Data Submission Information

	BGKLV24-57	BGKLV24-57
ENCODE_alias	brenton-graveley:SLBP_BGKLV24	brenton-graveley:SLBP-BGKLV24-K562
ENCODE_accession	ENCSR112YTD	ENCSR027WCW
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKLV24-57	BGKLV24-57
Sample Name	SLBP_BGKLV24_57_17626	SLBP_BGKLV24_57_17626
Selected	Yes	Yes
Status	Released	Released
Status_Date	2015-08-13	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2990	6949

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
SLBP_BGKLV24_57_17626_ACTGAT_L008_R1_001.fastq.gz	ENCODE_DATA/set24/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1100	HiSeq2000	100	paired-ended	1				non-target_BGKLV24_1_17594_GTCCGC_L005_R1_001.fastq.gz,non-target_BGKLV24_2_17595_GTGAAA_L005_R1_001.fastq.gz	ENCODE3	17216
SLBP_BGKLV24_57_17626_ACTGAT_L008_R2_001.fastq.gz	ENCODE_DATA/set24/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1100	HiSeq2000	100	paired-ended	2				non-target_BGKLV24_1_17594_GTCCGC_L005_R2_001.fastq.gz,non-target_BGKLV24_2_17595_GTGAAA_L005_R2_001.fastq.gz	ENCODE3	17252
SLBP_BGKLV24_57_17626_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set24/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1100					GRCh38	V40	SLBP_BGKLV24_57_17626_ACTGAT_L008_R1_001.fastq.gz,SLBP_BGKLV24_57_17626_ACTGAT_L008_R2_001.fastq.gz		ENCORE2	17288
SLBP_BGKLV24_57_17626_Signal.Unique.strand+.bw	ENCODE_DATA/set24/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1100					GRCh38	V40	SLBP_BGKLV24_57_17626/Aligned.sortedByCoord.out.bam		ENCORE2	17324
SLBP_BGKLV24_57_17626_Signal.Unique.strand-.bw	ENCODE_DATA/set24/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1100					GRCh38	V40	SLBP_BGKLV24_57_17626/Aligned.sortedByCoord.out.bam		ENCORE2	17360
SLBP_BGKLV24_57_17626_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set24/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1100					GRCh38	V40	SLBP_BGKLV24_57_17626/Aligned.sortedByCoord.out.bam		ENCORE2	17396
SLBP_BGKLV24_57_17626_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set24/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1100					GRCh38	V40	SLBP_BGKLV24_57_17626/Aligned.sortedByCoord.out.bam		ENCORE2	17432
SLBP_BGKLV24_57_17626_quant.sf	ENCODE_DATA/set24/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1100					GRCh38	V40	SLBP_BGKLV24_57_17626_ACTGAT_L008_R1_001.fastq.gz,SLBP_BGKLV24_57_17626_ACTGAT_L008_R2_001.fastq.gz		ENCORE2	17468
SLBP_BGKLV24_58_17627_ATTCCT_L008_R1_001.fastq.gz	ENCODE_DATA/set24/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1101	HiSeq2000	100	paired-ended	1				non-target_BGKLV24_1_17594_GTCCGC_L005_R1_001.fastq.gz,non-target_BGKLV24_2_17595_GTGAAA_L005_R1_001.fastq.gz	ENCODE3	17217
SLBP_BGKLV24_58_17627_ATTCCT_L008_R2_001.fastq.gz	ENCODE_DATA/set24/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1101	HiSeq2000	100	paired-ended	2				non-target_BGKLV24_1_17594_GTCCGC_L005_R2_001.fastq.gz,non-target_BGKLV24_2_17595_GTGAAA_L005_R2_001.fastq.gz	ENCODE3	17253
SLBP_BGKLV24_58_17627_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set24/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1101					GRCh38	V40	SLBP_BGKLV24_58_17627_ATTCCT_L008_R1_001.fastq.gz,SLBP_BGKLV24_58_17627_ATTCCT_L008_R2_001.fastq.gz		ENCORE2	17289
SLBP_BGKLV24_58_17627_Signal.Unique.strand+.bw	ENCODE_DATA/set24/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1101					GRCh38	V40	SLBP_BGKLV24_58_17627/Aligned.sortedByCoord.out.bam		ENCORE2	17325
SLBP_BGKLV24_58_17627_Signal.Unique.strand-.bw	ENCODE_DATA/set24/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1101					GRCh38	V40	SLBP_BGKLV24_58_17627/Aligned.sortedByCoord.out.bam		ENCORE2	17361
SLBP_BGKLV24_58_17627_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set24/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1101					GRCh38	V40	SLBP_BGKLV24_58_17627/Aligned.sortedByCoord.out.bam		ENCORE2	17397
SLBP_BGKLV24_58_17627_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set24/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1101					GRCh38	V40	SLBP_BGKLV24_58_17627/Aligned.sortedByCoord.out.bam		ENCORE2	17433
SLBP_BGKLV24_58_17627_quant.sf	ENCODE_DATA/set24/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1101					GRCh38	V40	SLBP_BGKLV24_58_17627_ATTCCT_L008_R1_001.fastq.gz,SLBP_BGKLV24_58_17627_ATTCCT_L008_R2_001.fastq.gz		ENCORE2	17469