RRP9 RNA-Seq in HepG2

General Information


RBP	RRP9
Cell_Line	HepG2
Method	shRNA
Exp_Name	RRP9-BGHLV17-HepG2
ENCODE_series_ID	ENCSR793FHF
Batch_ID	BGHLV17
Pool ID	Pool-141001
Local_Set_Name	set17
ENCODE_KD_Exp_ID	ENCSR471GIS
ENCODE_CN_Exp_ID	ENCSR856ZRV
Rep1	RRP9_BGHLV17_25
Rep2	RRP9_BGHLV17_26
CN1	NT_BGHLV17_63
CN2	NT_BGHLV17_64
Rep1_qPCR	71.7
Rep2_qPCR	78.8
Rep1_WB	99.9
Rep2_WB	99.9
Antibody Cat#	A303-970A
Antibody Lot#	A303-970A
Antibody DCC ID	ENCAB337GZI
Status	Released
Project	ENCODE3
ID	437

Experiment Information (Status: Released)

	BGHLV17-25	BGHLV17-26
idx	261	262
TRCN#_or_BGC#	TRCN0000180751	TRCN0000180751
shRNA_or_gRNA_sequence	GCTTGACCTTCTCTGTGACAT	GCTTGACCTTCTCTGTGACAT
PAM
Name	RRP9	RRP9
Sample_ID	BGHLV17-25	BGHLV17-26
transduction_Date	8/19/2014	8/19/2014
days
RBP_name	RRP9	RRP9
qPCR_result	71.7	78.8
Ave_qPCR	75.3
RT-qPCR_primer-F	ccctcctcaacacagacctt
RT-qPCR_primer-R	agggggatgtcacagagaag
protein_conc	1742	2940
WB_result	99.9	99.9
Ave_WB	99.9
WB_DONE_date	2/5/2015
MW	52kDa
IP	1	1
antibody_Cat#	A303-970A	A303-970A
Antibody DCC ID	ENCAB337GZI	ENCAB337GZI
submitted_to_DCC_date	5/6/2015
Rep1_TPM	56.8	0
Rep2_TPM	66.9	0
Action
Library_start_date	9/26/2014	9/26/2014
repeat_library
Note
ID	2326	2327

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

	BGHLV17-25	BGHLV17-26
Sample_ID	BGHLV17-25	BGHLV17-26
Sample Name	RRP9_BGHLV17_25	RRP9_BGHLV17_26
Sample Name	RRP9_BGHLV17_25	RRP9_BGHLV17_26
RBP	RRP9	RRP9
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2014-12-11	2014-12-11
Project	ENCODE3	ENCODE3
Note
ID	602	603

Library-Prep
Sequencing

Library-Prep Information

	BGHLV17-25	BGHLV17-26
Sample #
Sample Name	RRP9-BGHLV17-25	RRP9-BGHLV17-26
Sample_Name_Alias	RRP9_BGHLV17_25	RRP9_BGHLV17_26
Index Well Position	S15	S16
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2014-09-26	2014-09-26
Lib_ID	Lib-140926	Lib-140926
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV16-17/set2/E1.png	DNA_Library_LV16-17/set2/F1.png
RIN	9.6	9.6
libSample_RNA_Well	RNA_Library_LV16-17-18/set1/G4.png	RNA_Library_LV16-17-18/set1/H4.png
SampleQC_method
SampleQC_date
Sample_ID	BGHLV17-25	BGHLV17-26
RBP	RRP9	RRP9
Batch_ID	BGHLV17	BGHLV17
WB_result	99.900	99.900
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2286	2287

Sequencing Information

	BGHLV17-25	BGHLV17-26
Sample_ID	BGHLV17-25	BGHLV17-26
Sample Name	RRP9_BGHLV17_25	RRP9_BGHLV17_26
Pool ID	Pool-141001	Pool-141001
LocalServer_folder	set17	set17
total_reads	40,410,000	38,360,000
total_aligned_reads	36,182,036	34,610,084
unique_aligned_reads	34,215,692	32,741,988
percent_uniqueAligned	0.84671	0.85355
correlation_replicates	0.996651	0.996651
spikein_reads	73,770	98,210
percent_spikeins	0.00183	0.00256
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	928	929

Data Submission Information

	BGHLV17-25	BGHLV17-25
ENCODE_alias	brenton-graveley:RRP9_BGHLV17	brenton-graveley:RRP9-BGHLV17-HepG2
ENCODE_accession	ENCSR471GIS	ENCSR793FHF
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV17-25	BGHLV17-25
Sample Name	RRP9_BGHLV17_25	RRP9_BGHLV17_25
Selected	Yes	Yes
Status	Released	Released
Status_Date	2014-12-08	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2868	6923

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_BGHLV17_25_ATGTCA_L002_R1_001.fastq.gz	ENCODE_DATA/set17/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	928	HiSeq2000	100	paired-ended	1				NT_BGHLV17_63_ATCACG_L001_R1_001.merged.fastq.gz,NT_BGHLV17_64_CGATGT_L001_R1_001.fastq.gz	ENCODE3	14510
RRP9_BGHLV17_25_ATGTCA_L002_R2_001.fastq.gz	ENCODE_DATA/set17/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	928	HiSeq2000	100	paired-ended	2				NT_BGHLV17_63_ATCACG_L001_R2_001.merged.fastq.gz,NT_BGHLV17_64_CGATGT_L001_R2_001.fastq.gz	ENCODE3	14548
RRP9_BGHLV17_25_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set17/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	928					GRCh38	V40	RRP9_BGHLV17_25_ATGTCA_L002_R1_001.fastq.gz,RRP9_BGHLV17_25_ATGTCA_L002_R2_001.fastq.gz		ENCORE2	14586
RRP9_BGHLV17_25_Signal.Unique.strand+.bw	ENCODE_DATA/set17/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	928					GRCh38	V40	RRP9_BGHLV17_25/Aligned.sortedByCoord.out.bam		ENCORE2	14624
RRP9_BGHLV17_25_Signal.Unique.strand-.bw	ENCODE_DATA/set17/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	928					GRCh38	V40	RRP9_BGHLV17_25/Aligned.sortedByCoord.out.bam		ENCORE2	14662
RRP9_BGHLV17_25_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set17/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	928					GRCh38	V40	RRP9_BGHLV17_25/Aligned.sortedByCoord.out.bam		ENCORE2	14700
RRP9_BGHLV17_25_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set17/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	928					GRCh38	V40	RRP9_BGHLV17_25/Aligned.sortedByCoord.out.bam		ENCORE2	14738
RRP9_BGHLV17_25_quant.sf	ENCODE_DATA/set17/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	928					GRCh38	V40	RRP9_BGHLV17_25_ATGTCA_L002_R1_001.fastq.gz,RRP9_BGHLV17_25_ATGTCA_L002_R2_001.fastq.gz		ENCORE2	14776
RRP9_BGHLV17_26_CCGTCC_L002_R1_001.fastq.gz	ENCODE_DATA/set17/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	929	HiSeq2000	100	paired-ended	1				NT_BGHLV17_63_ATCACG_L001_R1_001.merged.fastq.gz,NT_BGHLV17_64_CGATGT_L001_R1_001.fastq.gz	ENCODE3	14511
RRP9_BGHLV17_26_CCGTCC_L002_R2_001.fastq.gz	ENCODE_DATA/set17/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	929	HiSeq2000	100	paired-ended	2				NT_BGHLV17_63_ATCACG_L001_R2_001.merged.fastq.gz,NT_BGHLV17_64_CGATGT_L001_R2_001.fastq.gz	ENCODE3	14549
RRP9_BGHLV17_26_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set17/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	929					GRCh38	V40	RRP9_BGHLV17_26_CCGTCC_L002_R1_001.fastq.gz,RRP9_BGHLV17_26_CCGTCC_L002_R2_001.fastq.gz		ENCORE2	14587
RRP9_BGHLV17_26_Signal.Unique.strand+.bw	ENCODE_DATA/set17/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	929					GRCh38	V40	RRP9_BGHLV17_26/Aligned.sortedByCoord.out.bam		ENCORE2	14625
RRP9_BGHLV17_26_Signal.Unique.strand-.bw	ENCODE_DATA/set17/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	929					GRCh38	V40	RRP9_BGHLV17_26/Aligned.sortedByCoord.out.bam		ENCORE2	14663
RRP9_BGHLV17_26_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set17/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	929					GRCh38	V40	RRP9_BGHLV17_26/Aligned.sortedByCoord.out.bam		ENCORE2	14701
RRP9_BGHLV17_26_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set17/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	929					GRCh38	V40	RRP9_BGHLV17_26/Aligned.sortedByCoord.out.bam		ENCORE2	14739
RRP9_BGHLV17_26_quant.sf	ENCODE_DATA/set17/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	929					GRCh38	V40	RRP9_BGHLV17_26_CCGTCC_L002_R1_001.fastq.gz,RRP9_BGHLV17_26_CCGTCC_L002_R2_001.fastq.gz		ENCORE2	14777