SNRNP200 RNA-Seq in K562

General Information


RBP	SNRNP200
Cell_Line	K562
Method	shRNA
Exp_Name	SNRNP200-BGKLV28-K562
ENCODE_series_ID	ENCSR565WQW
Batch_ID	BGKLV28
Pool ID	Pool-151215
Local_Set_Name	set28
ENCODE_KD_Exp_ID	ENCSR943LIB
ENCODE_CN_Exp_ID	ENCSR164MUK
Rep1	SNRNP200_BGKLV28-53
Rep2	SNRNP200_BGKLV28-54
CN1	non-target_BGKLV28-1
CN2	non-target_BGKLV28-2
Rep1_qPCR	62.5
Rep2_qPCR	60.7
Rep1_WB	63.5
Rep2_WB	73.3
Antibody Cat#	A303-453A
Antibody Lot#	A303-453A
Antibody DCC ID	ENCAB770ROF
Status	Released
Project	ENCODE3
ID	658

Experiment Information (Status: Released)

	BGKLV28-53	BGKLV28-54
idx	522	523
TRCN#_or_BGC#	TRCN0000051832	TRCN0000051832
shRNA_or_gRNA_sequence	CCAATGATACAGTGCAGACTT	CCAATGATACAGTGCAGACTT
PAM
Name	SNRNP200-32	SNRNP200-32
Sample_ID	BGKLV28-53	BGKLV28-54
transduction_Date	6/16/2015	6/16/2015
days
RBP_name	SNRNP200	SNRNP200
qPCR_result	62.5	60.7
Ave_qPCR	61.6
RT-qPCR_primer-F	CTGCCCACCTGGTAATCATC
RT-qPCR_primer-R	CACCATCTGAAGCACGTCAT
protein_conc	2752	2780
WB_result	63.5	73.3
Ave_WB	68.4
WB_DONE_date	7/6/2015
MW	244kDa
IP	1	1
antibody_Cat#	A303-453A	A303-453A
Antibody DCC ID	ENCAB770ROF	ENCAB770ROF
submitted_to_DCC_date	8/6/2015
Rep1_TPM	120.372227	0
Rep2_TPM	88.143828	0
Action
Library_start_date	10/28/2015	10/28/2015
repeat_library
Note	x	x
ID	599	600

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
SNRNP200	Product_ID: A303-453A Lot_ID: 1 Source: Bethyl Labs Target Name: SNRNP200-human

Experiment Status

	BGKLV28-53	BGKLV28-54
Sample_ID	BGKLV28-53	BGKLV28-54
Sample Name	SNRNP200_BGKLV28-53	SNRNP200_BGKLV28-54
Sample Name	SNRNP200_BGKLV28-53	SNRNP200_BGKLV28-54
RBP	SNRNP200	SNRNP200
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2016-03-03	2016-03-03
Project	ENCODE3	ENCODE3
Note
ID	1002	1003

Library-Prep
Sequencing

Library-Prep Information

	BGKLV28-53	BGKLV28-54
Sample #
Sample Name	SNRNP200-BGKLV28-53	SNRNP200-BGKLV28-54
Sample_Name_Alias	SNRNP200_BGKLV28-53	SNRNP200_BGKLV28-54
Index Well Position	S25	S27
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2015-10-28	2015-10-28
Lib_ID	Lib-151028	Lib-151028
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV28-29-30/set1/G3.png	DNA_Library_LV28-29-30/set1/H3.png
RIN	9.5	9.7
libSample_RNA_Well	RNA_Library_LV26-27-28-29/set1/C9.png	RNA_Library_LV26-27-28-29/set1/D9.png
SampleQC_method
SampleQC_date
Sample_ID	BGKLV28-53	BGKLV28-54
RBP	SNRNP200	SNRNP200
Batch_ID	BGKLV28	BGKLV28
WB_result	63.500	73.300
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2694	2695

Sequencing Information

	BGKLV28-53	BGKLV28-54
Sample_ID	BGKLV28-53	BGKLV28-54
Sample Name	SNRNP200_BGKLV28-53	SNRNP200_BGKLV28-54
Pool ID	Pool-151215	Pool-151215
LocalServer_folder	set28	set28
total_reads	65,789,936	84,541,604
total_aligned_reads	59,431,642	74,399,678
unique_aligned_reads	54,310,992	68,132,204
percent_uniqueAligned	0.82552	0.80590
correlation_replicates	0.991031	0.991031
spikein_reads	212,098	258,248
percent_spikeins	0.00322	0.00305
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1336	1337

Data Submission Information

	BGKLV28-53	BGKLV28-53
ENCODE_alias	brenton-graveley:SNRNP200_BGKLV28	brenton-graveley:SNRNP200-BGKLV28-K562
ENCODE_accession	ENCSR943LIB	ENCSR565WQW
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKLV28-53	BGKLV28-53
Sample Name	SNRNP200_BGKLV28-53	SNRNP200_BGKLV28-53
Selected	Yes	Yes
Status	Released	Released
Status_Date	2016-03-03	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	3050	6959

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
SNRNP200_BGKLV28-53_ACTGAT_L001_001.R1.fastq.gz	ENCODE_DATA/set28/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1336	HiSeq2500	100	paired-ended	1				non-target_BGKLV28-1_ATCACG_L001_001.R1.fastq.gz,non-target_BGKLV28-2_CGATGT_L001_001.R1.fastq.gz	ENCODE3	20180
SNRNP200_BGKLV28-53_ACTGAT_L001_001.R2.fastq.gz	ENCODE_DATA/set28/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1336	HiSeq2500	100	paired-ended	2				non-target_BGKLV28-1_ATCACG_L001_001.R2.fastq.gz,non-target_BGKLV28-2_CGATGT_L001_001.R2.fastq.gz	ENCODE3	20212
SNRNP200_BGKLV28-53_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set28/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1336					GRCh38	V40	SNRNP200_BGKLV28-53_ACTGAT_L001_001.R1.fastq.gz,SNRNP200_BGKLV28-53_ACTGAT_L001_001.R2.fastq.gz		ENCORE2	20244
SNRNP200_BGKLV28-53_Signal.Unique.strand+.bw	ENCODE_DATA/set28/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1336					GRCh38	V40	SNRNP200_BGKLV28-53/Aligned.sortedByCoord.out.bam		ENCORE2	20276
SNRNP200_BGKLV28-53_Signal.Unique.strand-.bw	ENCODE_DATA/set28/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1336					GRCh38	V40	SNRNP200_BGKLV28-53/Aligned.sortedByCoord.out.bam		ENCORE2	20308
SNRNP200_BGKLV28-53_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set28/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1336					GRCh38	V40	SNRNP200_BGKLV28-53/Aligned.sortedByCoord.out.bam		ENCORE2	20340
SNRNP200_BGKLV28-53_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set28/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1336					GRCh38	V40	SNRNP200_BGKLV28-53/Aligned.sortedByCoord.out.bam		ENCORE2	20372
SNRNP200_BGKLV28-53_quant.sf	ENCODE_DATA/set28/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1336					GRCh38	V40	SNRNP200_BGKLV28-53_ACTGAT_L001_001.R1.fastq.gz,SNRNP200_BGKLV28-53_ACTGAT_L001_001.R2.fastq.gz		ENCORE2	20404
SNRNP200_BGKLV28-54_ATTCCT_L001_001.R1.fastq.gz	ENCODE_DATA/set28/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1337	HiSeq2500	100	paired-ended	1				non-target_BGKLV28-1_ATCACG_L001_001.R1.fastq.gz,non-target_BGKLV28-2_CGATGT_L001_001.R1.fastq.gz	ENCODE3	20181
SNRNP200_BGKLV28-54_ATTCCT_L001_001.R2.fastq.gz	ENCODE_DATA/set28/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1337	HiSeq2500	100	paired-ended	2				non-target_BGKLV28-1_ATCACG_L001_001.R2.fastq.gz,non-target_BGKLV28-2_CGATGT_L001_001.R2.fastq.gz	ENCODE3	20213
SNRNP200_BGKLV28-54_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set28/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1337					GRCh38	V40	SNRNP200_BGKLV28-54_ATTCCT_L001_001.R1.fastq.gz,SNRNP200_BGKLV28-54_ATTCCT_L001_001.R2.fastq.gz		ENCORE2	20245
SNRNP200_BGKLV28-54_Signal.Unique.strand+.bw	ENCODE_DATA/set28/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1337					GRCh38	V40	SNRNP200_BGKLV28-54/Aligned.sortedByCoord.out.bam		ENCORE2	20277
SNRNP200_BGKLV28-54_Signal.Unique.strand-.bw	ENCODE_DATA/set28/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1337					GRCh38	V40	SNRNP200_BGKLV28-54/Aligned.sortedByCoord.out.bam		ENCORE2	20309
SNRNP200_BGKLV28-54_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set28/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1337					GRCh38	V40	SNRNP200_BGKLV28-54/Aligned.sortedByCoord.out.bam		ENCORE2	20341
SNRNP200_BGKLV28-54_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set28/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1337					GRCh38	V40	SNRNP200_BGKLV28-54/Aligned.sortedByCoord.out.bam		ENCORE2	20373
SNRNP200_BGKLV28-54_quant.sf	ENCODE_DATA/set28/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1337					GRCh38	V40	SNRNP200_BGKLV28-54_ATTCCT_L001_001.R1.fastq.gz,SNRNP200_BGKLV28-54_ATTCCT_L001_001.R2.fastq.gz		ENCORE2	20405