RCC2 RNA-Seq in K562

General Information


RBP	RCC2
Cell_Line	K562
Method	shRNA
Exp_Name	RCC2-BGKLV21-K562
ENCODE_series_ID	ENCSR100GIZ
Batch_ID	BGKLV21
Pool ID	Pool-150615
Local_Set_Name	set21
ENCODE_KD_Exp_ID	ENCSR921KDS
ENCODE_CN_Exp_ID	ENCSR572FFX
Rep1	RCC2_BGKLV21_49_17584
Rep2	RCC2_BGKLV21_50_17585
CN1	non-target_BGKLV21_1
CN2	non-target_BGKLV21_2
Rep1_qPCR	83.3
Rep2_qPCR	84.2
Rep1_WB	80.5
Rep2_WB	82.0
Antibody Cat#	A300-873A
Antibody Lot#	A300-873A
Antibody DCC ID	ENCAB827PVH
Status	Released
Project	ENCODE3
ID	518

Experiment Information (Status: Released)

	BGKLV21-49	BGKLV21-49	BGKLV21-50	BGKLV21-50
idx	320	320	321	321
TRCN#_or_BGC#	TRCN0000153686	TRCN0000153686	TRCN0000153686	TRCN0000153686
shRNA_or_gRNA_sequence	CAACTCAGATGGGAAGTTCAT	CAACTCAGATGGGAAGTTCAT	CAACTCAGATGGGAAGTTCAT	CAACTCAGATGGGAAGTTCAT
PAM
Name	RCC2	RCC2	RCC2	RCC2
Sample_ID	BGKLV21-49	BGKLV21-49	BGKLV21-50	BGKLV21-50
transduction_Date	10/9/2014	10/9/2014	10/9/2014	10/9/2014
days
RBP_name	RCC2	RCC2	RCC2	RCC2
qPCR_result	83.3	83.3	84.2	84.2
Ave_qPCR	83.8	83.8
RT-qPCR_primer-F	gcaaccaactgggacttgat	gcaaccaactgggacttgat
RT-qPCR_primer-R	cccacaaattctgaccgaga	cccacaaattctgaccgaga
protein_conc	3000	3000	2906	2906
WB_result	80.5	70.6	82.0	64.5
Ave_WB	81.3	67.5
WB_DONE_date	3/3/2015	6/28/2022
MW	56kDa	56kDa
IP	1		1
antibody_Cat#	A300-873A	A300-872A	A300-873A	lot # 1
Antibody DCC ID	ENCAB827PVH	ENCAB304XFE	ENCAB827PVH
submitted_to_DCC_date	4/2/2015	8/16/22
Rep1_TPM	23.8024624	0	0	0
Rep2_TPM	27.6011968	0	0	0
Action
Library_start_date	5/19/2015		5/19/2015
repeat_library
Note
ID	357	359	358	360

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
RCC2	Product_ID: A300-872A Lot_ID: 1 Source: Bethyl Labs Target Name: RCC2-human

Experiment Status

	BGKLV21-49	BGKLV21-50
Sample_ID	BGKLV21-49	BGKLV21-50
Sample Name	RCC2_BGKLV21_49_17584	RCC2_BGKLV21_50_17585
Sample Name	RCC2_BGKLV21_49_17584	RCC2_BGKLV21_50_17585
RBP	RCC2	RCC2
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2015-08-14	2015-08-14
Project	ENCODE3	ENCODE3
Note
ID	770	771

Library-Prep
Sequencing

Library-Prep Information

	BGKLV21-49	BGKLV21-50
Sample #
Sample Name	RCC2-BGKLV21-49	RCC2-BGKLV21-50
Sample_Name_Alias	RCC2_BGKLV21_49_17584	RCC2_BGKLV21_50_17585
Index Well Position	S03	S04
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2015-05-19	2015-05-19
Lib_ID	Lib-150519	Lib-150519
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV21-24/set1/C8.png	DNA_Library_LV21-24/set1/D8.png
RIN	7.1	9.5
libSample_RNA_Well	RNA_Library_LV19-21-24/set1/C11.png	RNA_Library_LV19-21-24/set1/D11.png
SampleQC_method
SampleQC_date
Sample_ID	BGKLV21-49	BGKLV21-50
RBP	RCC2	RCC2
Batch_ID	BGKLV21	BGKLV21
WB_result	80.500	82.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2456	2457

Sequencing Information

	BGKLV21-49	BGKLV21-50
Sample_ID	BGKLV21-49	BGKLV21-50
Sample Name	RCC2_BGKLV21_49_17584	RCC2_BGKLV21_50_17585
Pool ID	Pool-150615	Pool-150615
LocalServer_folder	set21	set21
total_reads	30,030,000	37,940,000
total_aligned_reads	27,393,468	34,598,518
unique_aligned_reads	25,183,256	31,770,128
percent_uniqueAligned	0.83860	0.83738
correlation_replicates	0.998675	0.998675
spikein_reads	143,592	197,576
percent_spikeins	0.00478	0.00521
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1062	1063

Data Submission Information

	BGKLV21-49	BGKLV21-49
ENCODE_alias	brenton-graveley:RCC2_BGKLV21	brenton-graveley:RCC2-BGKLV21-K562
ENCODE_accession	ENCSR921KDS	ENCSR100GIZ
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKLV21-49	BGKLV21-49
Sample Name	RCC2_BGKLV21_49_17584	RCC2_BGKLV21_49_17584
Selected	Yes	Yes
Status	Released	Released
Status_Date	2015-08-13	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2971	6908

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_BGKLV21_49_17584_TTAGGC_L004_R1_001.fastq.gz	ENCODE_DATA/set21/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1062	HiSeq2000	100	paired-ended	1				non-target_BGKLV21_1_ATCACG_R1_001.fastq.gz,non-target_BGKLV21_2_CGATGT_R1_001.fastq.gz	ENCODE3	15954
RCC2_BGKLV21_49_17584_TTAGGC_L004_R2_001.fastq.gz	ENCODE_DATA/set21/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1062	HiSeq2000	100	paired-ended	2				non-target_BGKLV21_1_ATCACG_R2_001.fastq.gz,non-target_BGKLV21_2_CGATGT_R2_001.fastq.gz	ENCODE3	15998
RCC2_BGKLV21_49_17584_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set21/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1062					GRCh38	V40	RCC2_BGKLV21_49_17584_TTAGGC_L004_R1_001.fastq.gz,RCC2_BGKLV21_49_17584_TTAGGC_L004_R2_001.fastq.gz		ENCORE2	16042
RCC2_BGKLV21_49_17584_Signal.Unique.strand+.bw	ENCODE_DATA/set21/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1062					GRCh38	V40	RCC2_BGKLV21_49_17584/Aligned.sortedByCoord.out.bam		ENCORE2	16086
RCC2_BGKLV21_49_17584_Signal.Unique.strand-.bw	ENCODE_DATA/set21/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1062					GRCh38	V40	RCC2_BGKLV21_49_17584/Aligned.sortedByCoord.out.bam		ENCORE2	16130
RCC2_BGKLV21_49_17584_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set21/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1062					GRCh38	V40	RCC2_BGKLV21_49_17584/Aligned.sortedByCoord.out.bam		ENCORE2	16174
RCC2_BGKLV21_49_17584_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set21/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1062					GRCh38	V40	RCC2_BGKLV21_49_17584/Aligned.sortedByCoord.out.bam		ENCORE2	16218
RCC2_BGKLV21_49_17584_quant.sf	ENCODE_DATA/set21/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1062					GRCh38	V40	RCC2_BGKLV21_49_17584_TTAGGC_L004_R1_001.fastq.gz,RCC2_BGKLV21_49_17584_TTAGGC_L004_R2_001.fastq.gz		ENCORE2	16262
RCC2_BGKLV21_50_17585_TGACCA_L004_R1_001.fastq.gz	ENCODE_DATA/set21/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1063	HiSeq2000	100	paired-ended	1				non-target_BGKLV21_1_ATCACG_R1_001.fastq.gz,non-target_BGKLV21_2_CGATGT_R1_001.fastq.gz	ENCODE3	15955
RCC2_BGKLV21_50_17585_TGACCA_L004_R2_001.fastq.gz	ENCODE_DATA/set21/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1063	HiSeq2000	100	paired-ended	2				non-target_BGKLV21_1_ATCACG_R2_001.fastq.gz,non-target_BGKLV21_2_CGATGT_R2_001.fastq.gz	ENCODE3	15999
RCC2_BGKLV21_50_17585_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set21/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1063					GRCh38	V40	RCC2_BGKLV21_50_17585_TGACCA_L004_R1_001.fastq.gz,RCC2_BGKLV21_50_17585_TGACCA_L004_R2_001.fastq.gz		ENCORE2	16043
RCC2_BGKLV21_50_17585_Signal.Unique.strand+.bw	ENCODE_DATA/set21/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1063					GRCh38	V40	RCC2_BGKLV21_50_17585/Aligned.sortedByCoord.out.bam		ENCORE2	16087
RCC2_BGKLV21_50_17585_Signal.Unique.strand-.bw	ENCODE_DATA/set21/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1063					GRCh38	V40	RCC2_BGKLV21_50_17585/Aligned.sortedByCoord.out.bam		ENCORE2	16131
RCC2_BGKLV21_50_17585_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set21/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1063					GRCh38	V40	RCC2_BGKLV21_50_17585/Aligned.sortedByCoord.out.bam		ENCORE2	16175
RCC2_BGKLV21_50_17585_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set21/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1063					GRCh38	V40	RCC2_BGKLV21_50_17585/Aligned.sortedByCoord.out.bam		ENCORE2	16219
RCC2_BGKLV21_50_17585_quant.sf	ENCODE_DATA/set21/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1063					GRCh38	V40	RCC2_BGKLV21_50_17585_TGACCA_L004_R1_001.fastq.gz,RCC2_BGKLV21_50_17585_TGACCA_L004_R2_001.fastq.gz		ENCORE2	16263