FXR2 RNA-Seq in K562

General Information


RBP	FXR2
Cell_Line	K562
Method	shRNA
Exp_Name	FXR2-BGKLV08-K562
ENCODE_series_ID	ENCSR373JYP
Batch_ID	BGKLV08
Pool ID	Pool-140601
Local_Set_Name	set10
ENCODE_KD_Exp_ID	ENCSR577XBW
ENCODE_CN_Exp_ID	ENCSR913CAE
Rep1	FXR2-LV08-31
Rep2	FXR2-LV08-32
CN1	Nontarget-LV08-1_00003527
CN2	nontarget-LV08-2_00003527
Rep1_qPCR	59.0
Rep2_qPCR	47.8
Rep1_WB	24.1
Rep2_WB	35.8
Antibody Cat#	A303-894A
Antibody Lot#	LOT# 1
Antibody DCC ID	ENCAB069PGU
Status	Archived
Project	ENCODE3
ID	292

Experiment Information (Status: Released)

	BGKLV08-31	BGKLV08-32
idx	32	33
TRCN#_or_BGC#	TRCN0000013455	TRCN0000013455
shRNA_or_gRNA_sequence	GCGCACCAAACTGCTACTTAT	GCGCACCAAACTGCTACTTAT
PAM
Name	FXR2	FXR2
Sample_ID	BGKLV08-31	BGKLV08-32
transduction_Date	4/4/2014	4/4/2014
days
RBP_name	FXR2	FXR2
qPCR_result	59.0	47.8
Ave_qPCR	53.4
RT-qPCR_primer-F	accaaaggcagcttcttcaa
RT-qPCR_primer-R	ccagggctttcttgaactctt
protein_conc	2987	3124
WB_result	24.1	35.8
Ave_WB	30.0
WB_DONE_date	6/24/2015
MW	74kDa
IP	1	1
antibody_Cat#	A303-894A	A303-894A
Antibody DCC ID
submitted_to_DCC_date
Rep1_TPM	9.91338509	0
Rep2_TPM	9.46116981	0
Action	Ready	Ready
Library_start_date	5/5/2014	5/5/2014
repeat_library
Note
ID	33	34

Western Blot Western Blot info was not avaliable

Experiment Status

	BGKLV08-31	BGKLV08-32
Sample_ID	BGKLV08-31	BGKLV08-32
Sample Name	FXR2-LV08-31	FXR2-LV08-32
Sample Name	FXR2-LV08-31	FXR2-LV08-32
RBP	FXR2	FXR2
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2014-09-16	2014-09-16
Project	ENCODE3	ENCODE3
Note
ID	292	293

Library-Prep
Sequencing

Library-Prep Information

	BGKLV08-31	BGKLV08-32
Sample #
Sample Name	FXR2-BGKLV08-31	FXR2-BGKLV08-32
Sample_Name_Alias	FXR2-LV08-31	FXR2-LV08-32
Index Well Position	S03	S04
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2014-05-05	2014-05-05
Lib_ID	Lib-140505	Lib-140505
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV08/set2/E2.png	DNA_Library_LV08/set2/F2.png
RIN	9.4	8.8
libSample_RNA_Well	RNA_Library_LV08/set2/G2.png	RNA_Library_LV08/set2/H2.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date
Sample_ID	BGKLV08-31	BGKLV08-32
RBP	FXR2	FXR2
Batch_ID	BGKLV08	BGKLV08
WB_result	24.100	35.800
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	1914	1915

Sequencing Information

	BGKLV08-31	BGKLV08-32
Sample_ID	BGKLV08-31	BGKLV08-32
Sample Name	FXR2-LV08-31	FXR2-LV08-32
Pool ID	Pool-140601	Pool-140601
LocalServer_folder	set10	set10
total_reads	52,660,000	47,270,000
total_aligned_reads	46,174,800	40,808,742
unique_aligned_reads	42,203,156	37,281,230
percent_uniqueAligned	0.80143	0.78869
correlation_replicates	0.999112	0.999112
spikein_reads	443,986	338,918
percent_spikeins	0.00843	0.00717
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	614	615

Data Submission Information

	BGKLV08-31	BGKLV08-31
ENCODE_alias	brenton-graveley:FXR2-LV08	brenton-graveley:FXR2-BGKLV08-K562
ENCODE_accession	ENCSR577XBW	ENCSR373JYP
object_type	experiment	experiment
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKLV08-31	BGKLV08-31
Sample Name	FXR2-LV08-31	FXR2-LV08-31
Selected	Yes	No
Status	Released	Archived
Status_Date	2014-08-13	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2695	6726

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
FXR2-LV08-31_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set10/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	614					GRCh38	V40	FXR2-LV08-31_TTAGGC_L004_R1_001.fastq.gz,FXR2-LV08-31_TTAGGC_L004_R2_001.fastq.gz		ENCORE2	11999
FXR2-LV08-31_TTAGGC_L004_R1_001.fastq.gz	ENCODE_DATA/set10/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	614	HiSeq2000	100	paired-ended	1				Nontarget-LV08-1_00003527_ATCACG_L001_R1_001.fastq.gz,nontarget-LV08-2_00003527_CGATGT_L001_R1_001.fastq.gz	ENCODE3	12055
FXR2-LV08-31_TTAGGC_L004_R2_001.fastq.gz	ENCODE_DATA/set10/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	614	HiSeq2000	100	paired-ended	2				Nontarget-LV08-1_00003527_ATCACG_L001_R2_001.fastq.gz,nontarget-LV08-2_00003527_CGATGT_L001_R2_001.fastq.gz	ENCODE3	12111
FXR2-LV08-31_Signal.Unique.strand+.bw	ENCODE_DATA/set10/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	614					GRCh38	V40	FXR2-LV08-31/Aligned.sortedByCoord.out.bam		ENCORE2	12167
FXR2-LV08-31_Signal.Unique.strand-.bw	ENCODE_DATA/set10/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	614					GRCh38	V40	FXR2-LV08-31/Aligned.sortedByCoord.out.bam		ENCORE2	12223
FXR2-LV08-31_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set10/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	614					GRCh38	V40	FXR2-LV08-31/Aligned.sortedByCoord.out.bam		ENCORE2	12279
FXR2-LV08-31_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set10/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	614					GRCh38	V40	FXR2-LV08-31/Aligned.sortedByCoord.out.bam		ENCORE2	12335
FXR2-LV08-31_quant.sf	ENCODE_DATA/set10/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	614					GRCh38	V40	FXR2-LV08-31_TTAGGC_L004_R1_001.fastq.gz,FXR2-LV08-31_TTAGGC_L004_R2_001.fastq.gz		ENCORE2	13334
FXR2-LV08-32_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set10/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	615					GRCh38	V40	FXR2-LV08-32_TGACCA_L004_R1_001.fastq.gz,FXR2-LV08-32_TGACCA_L004_R2_001.fastq.gz		ENCORE2	12000
FXR2-LV08-32_TGACCA_L004_R1_001.fastq.gz	ENCODE_DATA/set10/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	615	HiSeq2000	100	paired-ended	1				Nontarget-LV08-1_00003527_ATCACG_L001_R1_001.fastq.gz,nontarget-LV08-2_00003527_CGATGT_L001_R1_001.fastq.gz	ENCODE3	12056
FXR2-LV08-32_TGACCA_L004_R2_001.fastq.gz	ENCODE_DATA/set10/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	615	HiSeq2000	100	paired-ended	2				Nontarget-LV08-1_00003527_ATCACG_L001_R2_001.fastq.gz,nontarget-LV08-2_00003527_CGATGT_L001_R2_001.fastq.gz	ENCODE3	12112
FXR2-LV08-32_Signal.Unique.strand+.bw	ENCODE_DATA/set10/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	615					GRCh38	V40	FXR2-LV08-32/Aligned.sortedByCoord.out.bam		ENCORE2	12168
FXR2-LV08-32_Signal.Unique.strand-.bw	ENCODE_DATA/set10/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	615					GRCh38	V40	FXR2-LV08-32/Aligned.sortedByCoord.out.bam		ENCORE2	12224
FXR2-LV08-32_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set10/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	615					GRCh38	V40	FXR2-LV08-32/Aligned.sortedByCoord.out.bam		ENCORE2	12280
FXR2-LV08-32_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set10/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	615					GRCh38	V40	FXR2-LV08-32/Aligned.sortedByCoord.out.bam		ENCORE2	12336
FXR2-LV08-32_quant.sf	ENCODE_DATA/set10/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	615					GRCh38	V40	FXR2-LV08-32_TGACCA_L004_R1_001.fastq.gz,FXR2-LV08-32_TGACCA_L004_R2_001.fastq.gz		ENCORE2	13335