SBDS RNA-Seq in K562

General Information


RBP	SBDS
Cell_Line	K562
Method	shRNA
Exp_Name	SBDS-BGKLV24-K562
ENCODE_series_ID	ENCSR818WLG
Batch_ID	BGKLV24
Pool ID	Pool-151101
Local_Set_Name	set24_2
ENCODE_KD_Exp_ID	ENCSR219DXZ
ENCODE_CN_Exp_ID	ENCSR419JMU
Rep1	SBDS_BGKLV24_55B
Rep2	SBDS_BGKLV24_56B
CN1	non-target_BGKLV24_1B
CN2	non-target_BGKLV24_2B
Rep1_qPCR	78.7
Rep2_qPCR	74.7
Rep1_WB	75.6
Rep2_WB	82.6
Antibody Cat#	GTX109168
Antibody Lot#	GTX109168
Antibody DCC ID	ENCAB894TLT
Status	Released
Project	ENCODE3
ID	610

Experiment Information (Status: Released)

	BGKLV24-55	BGKLV24-56
idx	392	393
TRCN#_or_BGC#	TRCN0000119047	TRCN0000119047
shRNA_or_gRNA_sequence	GCCAAATACTTGCTTAAACTA	GCCAAATACTTGCTTAAACTA
PAM
Name	SBDS	SBDS
Sample_ID	BGKLV24-55	BGKLV24-56
transduction_Date	2/27/2015	2/27/2015
days
RBP_name	SBDS	SBDS
qPCR_result	78.7	74.7
Ave_qPCR	76.7
RT-qPCR_primer-F	aacagcaggctttggaagtg
RT-qPCR_primer-R	gatgaaccgaagcctcatgt
protein_conc	3893	3864
WB_result	75.6	82.6
Ave_WB	79.1
WB_DONE_date	5/4/2015
MW
IP	1	1
antibody_Cat#	GTX109168	GTX109168
Antibody DCC ID	ENCAB894TLT	ENCAB894TLT
submitted_to_DCC_date	5/4/2015
Rep1_TPM	95.9367377	0
Rep2_TPM	91.8436432	0
Action
Library_start_date	9/2/2015	9/2/2015
repeat_library
Note	x	x
ID	453	454

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
SBDS	Product_ID: GTX109168 Lot_ID: 40023 Source: GeneTex Target Name: SBDS-human

Experiment Status

	BGKLV24-55	BGKLV24-56
Sample_ID	BGKLV24-55	BGKLV24-56
Sample Name	SBDS_BGKLV24_55B	SBDS_BGKLV24_56B
Sample Name	SBDS_BGKLV24_55B	SBDS_BGKLV24_56B
RBP	SBDS	SBDS
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2015-12-08	2015-12-08
Project	ENCODE3	ENCODE3
Note
ID	902	903

Library-Prep
Sequencing

Library-Prep Information

	BGKLV24-55	BGKLV24-56
Sample #
Sample Name	SBDS-BGKLV24-55B	SBDS-BGKLV24-56B
Sample_Name_Alias	SBDS_BGKLV24_55B	SBDS_BGKLV24_56B
Index Well Position	S20	S21
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2015-09-02	2015-09-02
Lib_ID	Lib-150902	Lib-150902
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV24-25-26/set1/C7.png	DNA_Library_LV24-25-26/set2/E2.png
RIN	9.4	9.5
libSample_RNA_Well	RNA_Library_LV20-22-24/set1/C6.png	RNA_Library_LV20-22-24/set1/D6.png
SampleQC_method
SampleQC_date
Sample_ID	BGKLV24-55	BGKLV24-56
RBP	SBDS	SBDS
Batch_ID	BGKLV24	BGKLV24
WB_result	75.600	82.600
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix	B	B
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2590	2591

Sequencing Information

	BGKLV24-55	BGKLV24-56
Sample_ID	BGKLV24-55	BGKLV24-56
Sample Name	SBDS_BGKLV24_55B	SBDS_BGKLV24_56B
Pool ID	Pool-151101	Pool-151101
LocalServer_folder	set24_2	set24_2
total_reads	83,587,380	67,431,406
total_aligned_reads	81,630,830	64,481,258
unique_aligned_reads	73,943,828	58,800,334
percent_uniqueAligned	0.88463	0.87200
correlation_replicates	0.992190	0.992190
spikein_reads	382,368	251,388
percent_spikeins	0.00457	0.00373
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1232	1233

Data Submission Information

	BGKLV24-55	BGKLV24-55
ENCODE_alias	brenton-graveley:SBDS_BGKLV24_B	brenton-graveley:SBDS-BGKLV24-K562
ENCODE_accession	ENCSR219DXZ	ENCSR818WLG
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKLV24-55	BGKLV24-55
Sample Name	SBDS_BGKLV24_55B	SBDS_BGKLV24_55B
Selected	Yes	Yes
Status	Released	Released
Status_Date	2015-12-02	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	3000	6933

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
SBDS_BGKLV24_55B_GTGGCC_L003_001.R1.fastq.gz	ENCODE_DATA/set24_2/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1232	HiSeq2000	100	paired-ended	1				non-target_BGKLV24_1B_ATCACG_L001_001.R1.fastq.gz,non-target_BGKLV24_2B_CGATGT_L001_001.R1.fastq.gz	ENCODE3	17488
SBDS_BGKLV24_55B_GTGGCC_L003_001.R2.fastq.gz	ENCODE_DATA/set24_2/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1232	HiSeq2000	100	paired-ended	2				non-target_BGKLV24_1B_ATCACG_L001_001.R2.fastq.gz,non-target_BGKLV24_2B_CGATGT_L001_001.R2.fastq.gz	ENCODE3	17512
SBDS_BGKLV24_55B_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set24_2/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1232					GRCh38	V40	SBDS_BGKLV24_55B_GTGGCC_L003_001.R1.fastq.gz,SBDS_BGKLV24_55B_GTGGCC_L003_001.R2.fastq.gz		ENCORE2	17536
SBDS_BGKLV24_55B_Signal.Unique.strand+.bw	ENCODE_DATA/set24_2/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1232					GRCh38	V40	SBDS_BGKLV24_55B/Aligned.sortedByCoord.out.bam		ENCORE2	17560
SBDS_BGKLV24_55B_Signal.Unique.strand-.bw	ENCODE_DATA/set24_2/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1232					GRCh38	V40	SBDS_BGKLV24_55B/Aligned.sortedByCoord.out.bam		ENCORE2	17584
SBDS_BGKLV24_55B_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set24_2/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1232					GRCh38	V40	SBDS_BGKLV24_55B/Aligned.sortedByCoord.out.bam		ENCORE2	17608
SBDS_BGKLV24_55B_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set24_2/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1232					GRCh38	V40	SBDS_BGKLV24_55B/Aligned.sortedByCoord.out.bam		ENCORE2	17632
SBDS_BGKLV24_55B_quant.sf	ENCODE_DATA/set24_2/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1232					GRCh38	V40	SBDS_BGKLV24_55B_GTGGCC_L003_001.R1.fastq.gz,SBDS_BGKLV24_55B_GTGGCC_L003_001.R2.fastq.gz		ENCORE2	17656
SBDS_BGKLV24_56B_GTTTCG_L003_001.R1.fastq.gz	ENCODE_DATA/set24_2/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1233	HiSeq2000	100	paired-ended	1				non-target_BGKLV24_1B_ATCACG_L001_001.R1.fastq.gz,non-target_BGKLV24_2B_CGATGT_L001_001.R1.fastq.gz	ENCODE3	17489
SBDS_BGKLV24_56B_GTTTCG_L003_001.R2.fastq.gz	ENCODE_DATA/set24_2/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1233	HiSeq2000	100	paired-ended	2				non-target_BGKLV24_1B_ATCACG_L001_001.R2.fastq.gz,non-target_BGKLV24_2B_CGATGT_L001_001.R2.fastq.gz	ENCODE3	17513
SBDS_BGKLV24_56B_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set24_2/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1233					GRCh38	V40	SBDS_BGKLV24_56B_GTTTCG_L003_001.R1.fastq.gz,SBDS_BGKLV24_56B_GTTTCG_L003_001.R2.fastq.gz		ENCORE2	17537
SBDS_BGKLV24_56B_Signal.Unique.strand+.bw	ENCODE_DATA/set24_2/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1233					GRCh38	V40	SBDS_BGKLV24_56B/Aligned.sortedByCoord.out.bam		ENCORE2	17561
SBDS_BGKLV24_56B_Signal.Unique.strand-.bw	ENCODE_DATA/set24_2/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1233					GRCh38	V40	SBDS_BGKLV24_56B/Aligned.sortedByCoord.out.bam		ENCORE2	17585
SBDS_BGKLV24_56B_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set24_2/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1233					GRCh38	V40	SBDS_BGKLV24_56B/Aligned.sortedByCoord.out.bam		ENCORE2	17609
SBDS_BGKLV24_56B_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set24_2/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1233					GRCh38	V40	SBDS_BGKLV24_56B/Aligned.sortedByCoord.out.bam		ENCORE2	17633
SBDS_BGKLV24_56B_quant.sf	ENCODE_DATA/set24_2/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1233					GRCh38	V40	SBDS_BGKLV24_56B_GTTTCG_L003_001.R1.fastq.gz,SBDS_BGKLV24_56B_GTTTCG_L003_001.R2.fastq.gz		ENCORE2	17657