SSRP1 RNA-Seq in K562

General Information


RBP	SSRP1
Cell_Line	K562
Method	shRNA
Exp_Name	SSRP1-BGKLV29-K562
ENCODE_series_ID	ENCSR096NLA
Batch_ID	BGKLV29
Pool ID	Pool-151215C
Local_Set_Name	set29
ENCODE_KD_Exp_ID	ENCSR902WSK
ENCODE_CN_Exp_ID	ENCSR032YMP
Rep1	SSRP1_BGKLV29-55
Rep2	SSRP1_BGKLV29-56
CN1	NT_BGKLV29-1
CN2	NT_BGKLV29-2
Rep1_qPCR	87.3
Rep2_qPCR	82.9
Rep1_WB	90.0
Rep2_WB	87.8
Antibody Cat#	GTX111816
Antibody Lot#	GTX111816
Antibody DCC ID	ENCAB983GBT
Status	Released
Project	ENCODE3
ID	666

Experiment Information (Status: Released)

	BGKLV29-55	BGKLV29-56
idx	590	591
TRCN#_or_BGC#	TRCN0000019272	TRCN0000019272
shRNA_or_gRNA_sequence	CGCTTCGATGAGATCTCCTTT	CGCTTCGATGAGATCTCCTTT
PAM
Name	SSRP1	SSRP1
Sample_ID	BGKLV29-55	BGKLV29-56
transduction_Date	8/11/2015	8/11/2015
days
RBP_name	SSRP1	SSRP1
qPCR_result	87.3	82.9
Ave_qPCR	85.1
RT-qPCR_primer-F	acagctcaaaaaggccaaga
RT-qPCR_primer-R	gtatgcagacatgggcctct
protein_conc	3085	3294
WB_result	90.0	87.8
Ave_WB	88.9
WB_DONE_date	9/9/2015
MW	81kDa
IP	1MB	1MB
antibody_Cat#	GTX111816	GTX111816
Antibody DCC ID	ENCAB983GBT	ENCAB983GBT
submitted_to_DCC_date	12/7/2015
Rep1_TPM	85.3454743	0
Rep2_TPM	60.3851571	0
Action
Library_start_date	11/2/2015	11/2/2015
repeat_library
Note	x	x
ID	669	670

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
SSRP1	Product_ID: GTX111816 Lot_ID: 40079 Source: GeneTex Target Name: SSRP1-human

Experiment Status

	BGKLV29-55	BGKLV29-56
Sample_ID	BGKLV29-55	BGKLV29-56
Sample Name	SSRP1_BGKLV29-55	SSRP1_BGKLV29-56
Sample Name	SSRP1_BGKLV29-55	SSRP1_BGKLV29-56
RBP	SSRP1	SSRP1
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2016-03-03	2016-03-03
Project	ENCODE3	ENCODE3
Note
ID	1036	1037

Library-Prep
Sequencing

Library-Prep Information

	BGKLV29-55	BGKLV29-56
Sample #
Sample Name	SSRP1-BGKLV29-55	SSRP1-BGKLV29-56
Sample_Name_Alias	SSRP1_BGKLV29-55	SSRP1_BGKLV29-56
Index Well Position	S07	S08
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2015-11-02	2015-11-02
Lib_ID	Lib-151102	Lib-151102
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV28-29-30/set1/G7.png	DNA_Library_LV28-29-30/set1/H7.png
RIN	9.8	9.8
libSample_RNA_Well	RNA_Library_LV29-30-31-32/set1/C3.png	RNA_Library_LV29-30-31-32/set1/D3.png
SampleQC_method
SampleQC_date
Sample_ID	BGKLV29-55	BGKLV29-56
RBP	SSRP1	SSRP1
Batch_ID	BGKLV29	BGKLV29
WB_result	90.000	87.800
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2720	2721

Sequencing Information

	BGKLV29-55	BGKLV29-56
Sample_ID	BGKLV29-55	BGKLV29-56
Sample Name	SSRP1_BGKLV29-55	SSRP1_BGKLV29-56
Pool ID	Pool-151215C	Pool-151215C
LocalServer_folder	set29	set29
total_reads	94,043,620	107,939,516
total_aligned_reads	84,549,150	97,981,568
unique_aligned_reads	77,361,262	89,651,358
percent_uniqueAligned	0.82261	0.83057
correlation_replicates	0.997830	0.997830
spikein_reads	411,104	510,528
percent_spikeins	0.00437	0.00473
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1354	1355

Data Submission Information

	BGKLV29-55	BGKLV29-55
ENCODE_alias	brenton-graveley:SSRP1_BGKLV29	brenton-graveley:SSRP1-BGKLV29-K562
ENCODE_accession	ENCSR902WSK	ENCSR096NLA
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKLV29-55	BGKLV29-55
Sample Name	SSRP1_BGKLV29-55	SSRP1_BGKLV29-55
Selected	Yes	Yes
Status	Released	Released
Status_Date	2016-03-03	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	3067	6983

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
SSRP1_BGKLV29-55_CAGATC_L007_001.R1.fastq.gz	ENCODE_DATA/set29/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1354	HiSeq2500	100	paired-ended	1				NT_BGKLV29-1_GATCAG_L005_001.R1.fastq.gz,NT_BGKLV29-2_TAGCTT_L005_001.R1.fastq.gz	ENCODE3	20438
SSRP1_BGKLV29-55_CAGATC_L007_001.R2.fastq.gz	ENCODE_DATA/set29/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1354	HiSeq2500	100	paired-ended	2				NT_BGKLV29-1_GATCAG_L005_001.R2.fastq.gz,NT_BGKLV29-2_TAGCTT_L005_001.R2.fastq.gz	ENCODE3	20468
SSRP1_BGKLV29-55_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set29/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1354					GRCh38	V40	SSRP1_BGKLV29-55_CAGATC_L007_001.R1.fastq.gz,SSRP1_BGKLV29-55_CAGATC_L007_001.R2.fastq.gz		ENCORE2	20498
SSRP1_BGKLV29-55_Signal.Unique.strand+.bw	ENCODE_DATA/set29/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1354					GRCh38	V40	SSRP1_BGKLV29-55/Aligned.sortedByCoord.out.bam		ENCORE2	20528
SSRP1_BGKLV29-55_Signal.Unique.strand-.bw	ENCODE_DATA/set29/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1354					GRCh38	V40	SSRP1_BGKLV29-55/Aligned.sortedByCoord.out.bam		ENCORE2	20558
SSRP1_BGKLV29-55_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set29/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1354					GRCh38	V40	SSRP1_BGKLV29-55/Aligned.sortedByCoord.out.bam		ENCORE2	20588
SSRP1_BGKLV29-55_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set29/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1354					GRCh38	V40	SSRP1_BGKLV29-55/Aligned.sortedByCoord.out.bam		ENCORE2	20618
SSRP1_BGKLV29-55_quant.sf	ENCODE_DATA/set29/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1354					GRCh38	V40	SSRP1_BGKLV29-55_CAGATC_L007_001.R1.fastq.gz,SSRP1_BGKLV29-55_CAGATC_L007_001.R2.fastq.gz		ENCORE2	20648
SSRP1_BGKLV29-56_ACTTGA_L007_001.R1.fastq.gz	ENCODE_DATA/set29/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1355	HiSeq2500	100	paired-ended	1				NT_BGKLV29-1_GATCAG_L005_001.R1.fastq.gz,NT_BGKLV29-2_TAGCTT_L005_001.R1.fastq.gz	ENCODE3	20439
SSRP1_BGKLV29-56_ACTTGA_L007_001.R2.fastq.gz	ENCODE_DATA/set29/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1355	HiSeq2500	100	paired-ended	2				NT_BGKLV29-1_GATCAG_L005_001.R2.fastq.gz,NT_BGKLV29-2_TAGCTT_L005_001.R2.fastq.gz	ENCODE3	20469
SSRP1_BGKLV29-56_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set29/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1355					GRCh38	V40	SSRP1_BGKLV29-56_ACTTGA_L007_001.R1.fastq.gz,SSRP1_BGKLV29-56_ACTTGA_L007_001.R2.fastq.gz		ENCORE2	20499
SSRP1_BGKLV29-56_Signal.Unique.strand+.bw	ENCODE_DATA/set29/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1355					GRCh38	V40	SSRP1_BGKLV29-56/Aligned.sortedByCoord.out.bam		ENCORE2	20529
SSRP1_BGKLV29-56_Signal.Unique.strand-.bw	ENCODE_DATA/set29/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1355					GRCh38	V40	SSRP1_BGKLV29-56/Aligned.sortedByCoord.out.bam		ENCORE2	20559
SSRP1_BGKLV29-56_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set29/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1355					GRCh38	V40	SSRP1_BGKLV29-56/Aligned.sortedByCoord.out.bam		ENCORE2	20589
SSRP1_BGKLV29-56_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set29/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1355					GRCh38	V40	SSRP1_BGKLV29-56/Aligned.sortedByCoord.out.bam		ENCORE2	20619
SSRP1_BGKLV29-56_quant.sf	ENCODE_DATA/set29/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1355					GRCh38	V40	SSRP1_BGKLV29-56_ACTTGA_L007_001.R1.fastq.gz,SSRP1_BGKLV29-56_ACTTGA_L007_001.R2.fastq.gz		ENCORE2	20649