SUGP2 RNA-Seq in K562

General Information


RBP	SUGP2
Cell_Line	K562
Method	shRNA
Exp_Name	SUGP2-BGKLV28-K562
ENCODE_series_ID	ENCSR615MJH
Batch_ID	BGKLV28
Pool ID	Pool-151215
Local_Set_Name	set28
ENCODE_KD_Exp_ID	ENCSR192BPV
ENCODE_CN_Exp_ID	ENCSR164MUK
Rep1	SUGP2_BGKLV28-55
Rep2	SUGP2_BGKLV28-56
CN1	non-target_BGKLV28-1
CN2	non-target_BGKLV28-2
Rep1_qPCR	42.6
Rep2_qPCR	52.2
Rep1_WB	95.9
Rep2_WB	96.7
Antibody Cat#	A301-607A
Antibody Lot#	A301-607A
Antibody DCC ID	ENCAB433XTU
Status	Released
Project	ENCODE3
ID	659

Experiment Information (Status: Released)

	BGKLV28-55	BGKLV28-56
idx	524	525
TRCN#_or_BGC#	TRCN0000152597	TRCN0000152597
shRNA_or_gRNA_sequence	GTCATTGAAGGTTGGCATGAT	GTCATTGAAGGTTGGCATGAT
PAM
Name	SUGP2	SUGP2
Sample_ID	BGKLV28-55	BGKLV28-56
transduction_Date	6/16/2015	6/16/2015
days
RBP_name	SUGP2	SUGP2
qPCR_result	42.6	52.2
Ave_qPCR	47.4
RT-qPCR_primer-F	TGTGTTCCGACAGAGGATGA
RT-qPCR_primer-R	CAATTGCTGCTTCAAGGCTTA
protein_conc	2806	2590
WB_result	95.9	96.7
Ave_WB	96.3
WB_DONE_date	7/24/2015
MW	120kDa
IP	1	1
antibody_Cat#	A301-607A	A301-607A
Antibody DCC ID	ENCAB433XTU	ENCAB433XTU
submitted_to_DCC_date	3/8/2016
Rep1_TPM	25.1183253	0
Rep2_TPM	30.0139197	0
Action
Library_start_date	10/28/2015	10/28/2015
repeat_library
Note	x	x
ID	601	602

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
SUGP2	Product_ID: A301-607A Lot_ID: 1 Source: Bethyl Labs Target Name: SUGP2-human

Experiment Status

	BGKLV28-55	BGKLV28-56
Sample_ID	BGKLV28-55	BGKLV28-56
Sample Name	SUGP2_BGKLV28-55	SUGP2_BGKLV28-56
Sample Name	SUGP2_BGKLV28-55	SUGP2_BGKLV28-56
RBP	SUGP2	SUGP2
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2016-03-03	2016-03-03
Project	ENCODE3	ENCODE3
Note
ID	1004	1005

Library-Prep
Sequencing

Library-Prep Information

	BGKLV28-55	BGKLV28-56
Sample #
Sample Name	SUGP2-BGKLV28-55	SUGP2-BGKLV28-56
Sample_Name_Alias	SUGP2_BGKLV28-55	SUGP2_BGKLV28-56
Index Well Position	S01	S02
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/A4.png	DNA_Library_LV28-29-30/set1/B4.png
RIN	9.8	10.0
libSample_RNA_Well	RNA_Library_LV26-27-28-29/set1/E9.png	RNA_Library_LV26-27-28-29/set1/F9.png
SampleQC_method
SampleQC_date
Sample_ID	BGKLV28-55	BGKLV28-56
RBP	SUGP2	SUGP2
Batch_ID	BGKLV28	BGKLV28
WB_result	95.900	96.700
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2696	2697

Sequencing Information

	BGKLV28-55	BGKLV28-56
Sample_ID	BGKLV28-55	BGKLV28-56
Sample Name	SUGP2_BGKLV28-55	SUGP2_BGKLV28-56
Pool ID	Pool-151215	Pool-151215
LocalServer_folder	set28	set28
total_reads	96,541,914	113,809,490
total_aligned_reads	76,002,670	90,622,920
unique_aligned_reads	69,299,642	82,164,220
percent_uniqueAligned	0.71782	0.72195
correlation_replicates	0.965150	0.965150
spikein_reads	320,070	351,118
percent_spikeins	0.00332	0.00309
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1338	1339

Data Submission Information

	BGKLV28-55	BGKLV28-55
ENCODE_alias	brenton-graveley:SUGP2_BGKLV28	brenton-graveley:SUGP2-BGKLV28-K562
ENCODE_accession	ENCSR192BPV	ENCSR615MJH
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKLV28-55	BGKLV28-55
Sample Name	SUGP2_BGKLV28-55	SUGP2_BGKLV28-55
Selected	Yes	Yes
Status	Released	Released
Status_Date	2016-03-03	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	3051	6993

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
SUGP2_BGKLV28-55_ATCACG_L004_001.R1.fastq.gz	ENCODE_DATA/set28/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1338	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	20182
SUGP2_BGKLV28-55_ATCACG_L004_001.R2.fastq.gz	ENCODE_DATA/set28/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1338	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	20214
SUGP2_BGKLV28-55_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set28/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1338					GRCh38	V40	SUGP2_BGKLV28-55_ATCACG_L004_001.R1.fastq.gz,SUGP2_BGKLV28-55_ATCACG_L004_001.R2.fastq.gz		ENCORE2	20246
SUGP2_BGKLV28-55_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	1338					GRCh38	V40	SUGP2_BGKLV28-55/Aligned.sortedByCoord.out.bam		ENCORE2	20278
SUGP2_BGKLV28-55_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	1338					GRCh38	V40	SUGP2_BGKLV28-55/Aligned.sortedByCoord.out.bam		ENCORE2	20310
SUGP2_BGKLV28-55_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	1338					GRCh38	V40	SUGP2_BGKLV28-55/Aligned.sortedByCoord.out.bam		ENCORE2	20342
SUGP2_BGKLV28-55_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	1338					GRCh38	V40	SUGP2_BGKLV28-55/Aligned.sortedByCoord.out.bam		ENCORE2	20374
SUGP2_BGKLV28-55_quant.sf	ENCODE_DATA/set28/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1338					GRCh38	V40	SUGP2_BGKLV28-55_ATCACG_L004_001.R1.fastq.gz,SUGP2_BGKLV28-55_ATCACG_L004_001.R2.fastq.gz		ENCORE2	20406
SUGP2_BGKLV28-56_CGATGT_L004_001.R1.fastq.gz	ENCODE_DATA/set28/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1339	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	20183
SUGP2_BGKLV28-56_CGATGT_L004_001.R2.fastq.gz	ENCODE_DATA/set28/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1339	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	20215
SUGP2_BGKLV28-56_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set28/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1339					GRCh38	V40	SUGP2_BGKLV28-56_CGATGT_L004_001.R1.fastq.gz,SUGP2_BGKLV28-56_CGATGT_L004_001.R2.fastq.gz		ENCORE2	20247
SUGP2_BGKLV28-56_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	1339					GRCh38	V40	SUGP2_BGKLV28-56/Aligned.sortedByCoord.out.bam		ENCORE2	20279
SUGP2_BGKLV28-56_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	1339					GRCh38	V40	SUGP2_BGKLV28-56/Aligned.sortedByCoord.out.bam		ENCORE2	20311
SUGP2_BGKLV28-56_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	1339					GRCh38	V40	SUGP2_BGKLV28-56/Aligned.sortedByCoord.out.bam		ENCORE2	20343
SUGP2_BGKLV28-56_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	1339					GRCh38	V40	SUGP2_BGKLV28-56/Aligned.sortedByCoord.out.bam		ENCORE2	20375
SUGP2_BGKLV28-56_quant.sf	ENCODE_DATA/set28/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1339					GRCh38	V40	SUGP2_BGKLV28-56_CGATGT_L004_001.R1.fastq.gz,SUGP2_BGKLV28-56_CGATGT_L004_001.R2.fastq.gz		ENCORE2	20407