RRP9 RNA-Seq in K562

General Information


RBP	RRP9
Cell_Line	K562
Method	shRNA
Exp_Name	RRP9-BGKLV19-K562
ENCODE_series_ID	ENCSR420UVJ
Batch_ID	BGKLV19
Pool ID	Pool-141015
Local_Set_Name	set19
ENCODE_KD_Exp_ID	ENCSR210KJB
ENCODE_CN_Exp_ID	ENCSR661HEL
Rep1	RRP9_BGKLV19_47B
Rep2	RRP9_BGKLV19_48B
CN1	NT_BGKLV19_1B
CN2	NT_BGKLV19_2B
Rep1_qPCR	71.6
Rep2_qPCR	86.8
Rep1_WB	97.8
Rep2_WB	97.9
Antibody Cat#	A303-970A
Antibody Lot#	A303-970A
Antibody DCC ID	ENCAB337GZI
Status	Released
Project	ENCODE3
ID	480

Experiment Information (Status: Released)

	BGKLV19-47	BGKLV19-48
idx	254	255
TRCN#_or_BGC#	TRCN0000180751	TRCN0000180751
shRNA_or_gRNA_sequence	GCTTGACCTTCTCTGTGACAT	GCTTGACCTTCTCTGTGACAT
PAM
Name	RRP9	RRP9
Sample_ID	BGKLV19-47	BGKLV19-48
transduction_Date	9/4/2014	9/4/2014
days
RBP_name	RRP9	RRP9
qPCR_result	71.6	86.8
Ave_qPCR	79.2
RT-qPCR_primer-F	ccctcctcaacacagacctt
RT-qPCR_primer-R	agggggatgtcacagagaag
protein_conc	3628	3071
WB_result	97.8	97.9
Ave_WB	97.9
WB_DONE_date	1/8/2015
MW
IP	1	1
antibody_Cat#	A303-970A	A303-970A
Antibody DCC ID	ENCAB337GZI	ENCAB337GZI
submitted_to_DCC_date	5/4/2015
Rep1_TPM	103.020978	0
Rep2_TPM	133.724882	0
Action
Library_start_date	10/2/2014	10/2/2014
repeat_library
Note
ID	279	280

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
RRP9	Product_ID: A303-970A Lot_ID: 1 Source: Bethyl Labs Target Name: RRP9-human

Experiment Status

	BGKLV19-47	BGKLV19-48
Sample_ID	BGKLV19-47	BGKLV19-48
Sample Name	RRP9_BGKLV19_47B	RRP9_BGKLV19_48B
Sample Name	RRP9_BGKLV19_47B	RRP9_BGKLV19_48B
RBP	RRP9	RRP9
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2014-12-11	2014-12-11
Project	ENCODE3	ENCODE3
Note
ID	694	695

Library-Prep
Sequencing

Library-Prep Information

	BGKLV19-47	BGKLV19-48
Sample #
Sample Name	RRP9-BGKLV19-47B	RRP9-BGKLV19-48B
Sample_Name_Alias	RRP9_BGKLV19_47B	RRP9_BGKLV19_48B
Index Well Position	S07	S08
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2014-10-03	2014-10-03
Lib_ID	Lib-141003	Lib-141003
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV18-19/set1/G10.png	DNA_Library_LV18-19/set1/H10.png
RIN	9.8	9.6
libSample_RNA_Well	RNA_Library_LV19-21-24/set2/E1.png	RNA_Library_LV19-21-24/set1/D5.png
SampleQC_method
SampleQC_date
Sample_ID	BGKLV19-47	BGKLV19-48
RBP	RRP9	RRP9
Batch_ID	BGKLV19	BGKLV19
WB_result	97.800	97.900
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix	B	B
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2378	2379

Sequencing Information

	BGKLV19-47	BGKLV19-48
Sample_ID	BGKLV19-47	BGKLV19-48
Sample Name	RRP9_BGKLV19_47B	RRP9_BGKLV19_48B
Pool ID	Pool-141015	Pool-141015
LocalServer_folder	set19	set19
total_reads	47,330,000	48,280,000
total_aligned_reads	43,979,394	45,611,368
unique_aligned_reads	40,067,696	41,523,452
percent_uniqueAligned	0.84656	0.86005
correlation_replicates	0.997884	0.997884
spikein_reads	969,862	331,808
percent_spikeins	0.02049	0.00687
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1020	1021

Data Submission Information

	BGKLV19-47	BGKLV19-47
ENCODE_alias	brenton-graveley:RRP9_BGKLV19	brenton-graveley:RRP9-BGKLV19-K562
ENCODE_accession	ENCSR210KJB	ENCSR420UVJ
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKLV19-47	BGKLV19-47
Sample Name	RRP9_BGKLV19_47B	RRP9_BGKLV19_47B
Selected	Yes	Yes
Status	Released	Released
Status_Date	2014-12-05	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2895	6924

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
RRP9_BGKLV19_47B_CAGATC_L006_R1_001.fastq.gz	ENCODE_DATA/set19/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1020	HiSeq2000	100	paired-ended	1				NT_BGKLV19_1B_ATCACG_L002_R1_001.fastq.gz,NT_BGKLV19_2B_CGATGT_L002_R1_001.fastq.gz	ENCODE3	15136
RRP9_BGKLV19_47B_CAGATC_L006_R2_001.fastq.gz	ENCODE_DATA/set19/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1020	HiSeq2000	100	paired-ended	2				NT_BGKLV19_1B_ATCACG_L002_R2_001.fastq.gz,NT_BGKLV19_2B_CGATGT_L002_R2_001.fastq.gz	ENCODE3	15194
RRP9_BGKLV19_47B_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1020					GRCh38	V40	RRP9_BGKLV19_47B_CAGATC_L006_R1_001.fastq.gz,RRP9_BGKLV19_47B_CAGATC_L006_R2_001.fastq.gz		ENCORE2	15252
RRP9_BGKLV19_47B_Signal.Unique.strand+.bw	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1020					GRCh38	V40	RRP9_BGKLV19_47B/Aligned.sortedByCoord.out.bam		ENCORE2	15323
RRP9_BGKLV19_47B_Signal.Unique.strand-.bw	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1020					GRCh38	V40	RRP9_BGKLV19_47B/Aligned.sortedByCoord.out.bam		ENCORE2	15381
RRP9_BGKLV19_47B_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1020					GRCh38	V40	RRP9_BGKLV19_47B/Aligned.sortedByCoord.out.bam		ENCORE2	15439
RRP9_BGKLV19_47B_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1020					GRCh38	V40	RRP9_BGKLV19_47B/Aligned.sortedByCoord.out.bam		ENCORE2	15497
RRP9_BGKLV19_47B_quant.sf	ENCODE_DATA/set19/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1020					GRCh38	V40	RRP9_BGKLV19_47B_CAGATC_L006_R1_001.fastq.gz,RRP9_BGKLV19_47B_CAGATC_L006_R2_001.fastq.gz		ENCORE2	16394
RRP9_BGKLV19_48B_ACTTGA_L006_R1_001.fastq.gz	ENCODE_DATA/set19/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1021	HiSeq2000	100	paired-ended	1				NT_BGKLV19_1B_ATCACG_L002_R1_001.fastq.gz,NT_BGKLV19_2B_CGATGT_L002_R1_001.fastq.gz	ENCODE3	15137
RRP9_BGKLV19_48B_ACTTGA_L006_R2_001.fastq.gz	ENCODE_DATA/set19/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1021	HiSeq2000	100	paired-ended	2				NT_BGKLV19_1B_ATCACG_L002_R2_001.fastq.gz,NT_BGKLV19_2B_CGATGT_L002_R2_001.fastq.gz	ENCODE3	15195
RRP9_BGKLV19_48B_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1021					GRCh38	V40	RRP9_BGKLV19_48B_ACTTGA_L006_R1_001.fastq.gz,RRP9_BGKLV19_48B_ACTTGA_L006_R2_001.fastq.gz		ENCORE2	15253
RRP9_BGKLV19_48B_Signal.Unique.strand+.bw	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1021					GRCh38	V40	RRP9_BGKLV19_48B/Aligned.sortedByCoord.out.bam		ENCORE2	15324
RRP9_BGKLV19_48B_Signal.Unique.strand-.bw	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1021					GRCh38	V40	RRP9_BGKLV19_48B/Aligned.sortedByCoord.out.bam		ENCORE2	15382
RRP9_BGKLV19_48B_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1021					GRCh38	V40	RRP9_BGKLV19_48B/Aligned.sortedByCoord.out.bam		ENCORE2	15440
RRP9_BGKLV19_48B_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1021					GRCh38	V40	RRP9_BGKLV19_48B/Aligned.sortedByCoord.out.bam		ENCORE2	15498
RRP9_BGKLV19_48B_quant.sf	ENCODE_DATA/set19/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1021					GRCh38	V40	RRP9_BGKLV19_48B_ACTTGA_L006_R1_001.fastq.gz,RRP9_BGKLV19_48B_ACTTGA_L006_R2_001.fastq.gz		ENCORE2	16395