RCC2 RNA-Seq in HepG2

General Information


RBP	RCC2
Cell_Line	HepG2
Method	shRNA
Exp_Name	RCC2-BGHLV18-HepG2
ENCODE_series_ID	ENCSR754FNO
Batch_ID	BGHLV18
Pool ID	Pool-141010
Local_Set_Name	set18
ENCODE_KD_Exp_ID	ENCSR685JXU
ENCODE_CN_Exp_ID	ENCSR674KEK
Rep1	RCC2_BGHLV18_49
Rep2	RCC2_BGHLV18_50
CN1	NT_BGHLV18_1
CN2	NT_BGHLV18_2
Rep1_qPCR	76.8
Rep2_qPCR	77.6
Rep1_WB	69.8
Rep2_WB	61.5
Antibody Cat#	A300-873A
Antibody Lot#	A300-873A
Antibody DCC ID	ENCAB827PVH
Status	Released
Project	ENCODE3
ID	457

Experiment Information (Status: Released)

	BGHLV18-49	BGHLV18-50
idx	349	350
TRCN#_or_BGC#	TRCN0000153686	TRCN0000153686
shRNA_or_gRNA_sequence	CAACTCAGATGGGAAGTTCAT	CAACTCAGATGGGAAGTTCAT
PAM
Name	RCC2	RCC2
Sample_ID	BGHLV18-49	BGHLV18-50
transduction_Date	8/28/2014	8/28/2014
days
RBP_name	RCC2	RCC2
qPCR_result	76.8	77.6
Ave_qPCR	77.2
RT-qPCR_primer-F	gcaaccaactgggacttgat
RT-qPCR_primer-R	cccacaaattctgaccgaga
protein_conc	3639	3915
WB_result	69.8	61.5
Ave_WB	65.7
WB_DONE_date	3/3/2015
MW	52kDa
IP	1	1
antibody_Cat#	A300-873A	A300-873A
Antibody DCC ID	ENCAB827PVH	ENCAB827PVH
submitted_to_DCC_date	4/2/2015
Rep1_TPM	3.5	0
Rep2_TPM	3.9	0
Action
Library_start_date	10/2/2014	10/2/2014
repeat_library
Note
ID	2414	2415

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
RCC2	Product_ID: A300-873A Lot_ID: 1 Source: Bethyl Labs Target Name: RCC2-human

Experiment Status

	BGHLV18-49	BGHLV18-50
Sample_ID	BGHLV18-49	BGHLV18-50
Sample Name	RCC2_BGHLV18_49	RCC2_BGHLV18_50
Sample Name	RCC2_BGHLV18_49	RCC2_BGHLV18_50
RBP	RCC2	RCC2
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2014-12-11	2014-12-11
Project	ENCODE3	ENCODE3
Note
ID	644	645

Library-Prep
Sequencing

Library-Prep Information

	BGHLV18-49	BGHLV18-50
Sample #
Sample Name	RCC2-BGHLV18-49	RCC2-BGHLV18-50
Sample_Name_Alias	RCC2_BGHLV18_49	RCC2_BGHLV18_50
Index Well Position	S05	S06
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2014-10-02	2014-10-02
Lib_ID	Lib-141002	Lib-141002
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV18-19/set1/E4.png	DNA_Library_LV18-19/set1/F4.png
RIN	9.3	8.8
libSample_RNA_Well	RNA_Library_LV18-19/set1/C11.png	RNA_Library_LV18-19/set1/D11.png
SampleQC_method
SampleQC_date
Sample_ID	BGHLV18-49	BGHLV18-50
RBP	RCC2	RCC2
Batch_ID	BGHLV18	BGHLV18
WB_result	69.800	61.500
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2328	2329

Sequencing Information

	BGHLV18-49	BGHLV18-50
Sample_ID	BGHLV18-49	BGHLV18-50
Sample Name	RCC2_BGHLV18_49	RCC2_BGHLV18_50
Pool ID	Pool-141010	Pool-141010
LocalServer_folder	set18	set18
total_reads	73,320,000	27,900,000
total_aligned_reads	67,089,056	23,758,742
unique_aligned_reads	63,172,520	22,383,826
percent_uniqueAligned	0.86160	0.80229
correlation_replicates	0.996738	0.996738
spikein_reads	207,424	54,664
percent_spikeins	0.00283	0.00196
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	970	971

Data Submission Information

	BGHLV18-49	BGHLV18-49
ENCODE_alias	brenton-graveley:RCC2_BGHLV18	brenton-graveley:RCC2-BGHLV18-HepG2
ENCODE_accession	ENCSR685JXU	ENCSR754FNO
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV18-49	BGHLV18-49
Sample Name	RCC2_BGHLV18_49	RCC2_BGHLV18_49
Selected	Yes	Yes
Status	Released	Released
Status_Date	2014-12-08	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2839	6907

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
RCC2_BGHLV18_49_ACAGTG_L004_R1_001.fastq.gz	ENCODE_DATA/set18/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	970	HiSeq2000	100	paired-ended	1				NT_BGHLV18_1_ATCACG_L008_R1_001.fastq.gz,NT_BGHLV18_2_CGATGT_L008_R1_001.fastq.gz	ENCODE3	14818
RCC2_BGHLV18_49_ACAGTG_L004_R2_001.fastq.gz	ENCODE_DATA/set18/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	970	HiSeq2000	100	paired-ended	2				NT_BGHLV18_1_ATCACG_L008_R2_001.fastq.gz,NT_BGHLV18_2_CGATGT_L008_R2_001.fastq.gz	ENCODE3	14856
RCC2_BGHLV18_49_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set18/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	970					GRCh38	V40	RCC2_BGHLV18_49_ACAGTG_L004_R1_001.fastq.gz,RCC2_BGHLV18_49_ACAGTG_L004_R2_001.fastq.gz		ENCORE2	14894
RCC2_BGHLV18_49_Signal.Unique.strand+.bw	ENCODE_DATA/set18/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	970					GRCh38	V40	RCC2_BGHLV18_49/Aligned.sortedByCoord.out.bam		ENCORE2	14932
RCC2_BGHLV18_49_Signal.Unique.strand-.bw	ENCODE_DATA/set18/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	970					GRCh38	V40	RCC2_BGHLV18_49/Aligned.sortedByCoord.out.bam		ENCORE2	14970
RCC2_BGHLV18_49_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set18/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	970					GRCh38	V40	RCC2_BGHLV18_49/Aligned.sortedByCoord.out.bam		ENCORE2	15008
RCC2_BGHLV18_49_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set18/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	970					GRCh38	V40	RCC2_BGHLV18_49/Aligned.sortedByCoord.out.bam		ENCORE2	15046
RCC2_BGHLV18_49_quant.sf	ENCODE_DATA/set18/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	970					GRCh38	V40	RCC2_BGHLV18_49_ACAGTG_L004_R1_001.fastq.gz,RCC2_BGHLV18_49_ACAGTG_L004_R2_001.fastq.gz		ENCORE2	15084
RCC2_BGHLV18_50_GCCAAT_L004_R1_001.fastq.gz	ENCODE_DATA/set18/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	971	HiSeq2000	100	paired-ended	1				NT_BGHLV18_1_ATCACG_L008_R1_001.fastq.gz,NT_BGHLV18_2_CGATGT_L008_R1_001.fastq.gz	ENCODE3	14819
RCC2_BGHLV18_50_GCCAAT_L004_R2_001.fastq.gz	ENCODE_DATA/set18/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	971	HiSeq2000	100	paired-ended	2				NT_BGHLV18_1_ATCACG_L008_R2_001.fastq.gz,NT_BGHLV18_2_CGATGT_L008_R2_001.fastq.gz	ENCODE3	14857
RCC2_BGHLV18_50_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set18/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	971					GRCh38	V40	RCC2_BGHLV18_50_GCCAAT_L004_R1_001.fastq.gz,RCC2_BGHLV18_50_GCCAAT_L004_R2_001.fastq.gz		ENCORE2	14895
RCC2_BGHLV18_50_Signal.Unique.strand+.bw	ENCODE_DATA/set18/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	971					GRCh38	V40	RCC2_BGHLV18_50/Aligned.sortedByCoord.out.bam		ENCORE2	14933
RCC2_BGHLV18_50_Signal.Unique.strand-.bw	ENCODE_DATA/set18/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	971					GRCh38	V40	RCC2_BGHLV18_50/Aligned.sortedByCoord.out.bam		ENCORE2	14971
RCC2_BGHLV18_50_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set18/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	971					GRCh38	V40	RCC2_BGHLV18_50/Aligned.sortedByCoord.out.bam		ENCORE2	15009
RCC2_BGHLV18_50_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set18/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	971					GRCh38	V40	RCC2_BGHLV18_50/Aligned.sortedByCoord.out.bam		ENCORE2	15047
RCC2_BGHLV18_50_quant.sf	ENCODE_DATA/set18/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	971					GRCh38	V40	RCC2_BGHLV18_50_GCCAAT_L004_R1_001.fastq.gz,RCC2_BGHLV18_50_GCCAAT_L004_R2_001.fastq.gz		ENCORE2	15085