FXR2 RNA-Seq in K562

General Information


RBP	FXR2
Cell_Line	K562
Method	CRISPR
Exp_Name	FXR2-BGKcLV04-K562
ENCODE_series_ID	ENCSR621SBF
Batch_ID	BGKcLV04
Pool ID	Pool-161129
Local_Set_Name	BGKcLV04
ENCODE_KD_Exp_ID	ENCSR376GHG
ENCODE_CN_Exp_ID	ENCSR828YEB
Rep1	FXR2_BGKcLV04_13
Rep2	FXR2_BGKcLV04_14
CN1	NT_BGKcLV04-1
CN2	NT_BGKcLV04-2
Rep1_qPCR	65.6
Rep2_qPCR	53.9
Rep1_WB	78.5
Rep2_WB	82.3
Antibody Cat#	A303-894A
Antibody Lot#	A303-894A
Antibody DCC ID	ENCAB069PGU
Status	Released
Project	ENCODE3
ID	590

Experiment Information (Status: Released)

	BGKcLV04-13	BGKcLV04-13	BGKcLV04-14	BGKcLV04-14
idx	61	63	62	64
TRCN#_or_BGC#	BGC#0000035	BGC#0000035	BGC#0000035	BGC#0000035
shRNA_or_gRNA_sequence	GGACTGCCCGTCGAGGTGCG	GGACTGCCCGTCGAGGTGCG	GGACTGCCCGTCGAGGTGCG	GGACTGCCCGTCGAGGTGCG
PAM
Name	FXR2_3	FXR2_3	FXR2_3	FXR2_3
Sample_ID	BGKcLV04-13	BGKcLV04-13	BGKcLV04-14	BGKcLV04-14
transduction_Date	6/22/16	6/22/16	6/22/16	6/22/16
days	day 6	day 6	day 6	day 6
RBP_name	FXR2	FXR2	FXR2	FXR2
qPCR_result	65.6	65.6	53.9	53.9
Ave_qPCR	59.8	59.8
RT-qPCR_primer-F	accaaaggcagcttcttcaa	accaaaggcagcttcttcaa
RT-qPCR_primer-R	ccagggctttcttgaactctt	ccagggctttcttgaactctt
protein_conc	2196	2196	2185	2185
WB_result	78.5	96.9	82.3	94.7
Ave_WB	80.4	95.8
WB_DONE_date	7/1/16	10/23/18	WES	wes
MW	74	74
IP	1
antibody_Cat#	A303-894A	MA1-16767	A303-894A	Lot# SD251451
Antibody DCC ID	ENCAB069PGU	ENCAB479NSE	ENCAB069PGU
submitted_to_DCC_date	10/26/16	3/11/19
Rep1_TPM	9.9	0	0	0
Rep2_TPM	9.5	0	0	0
Action	Ready		Ready
Library_start_date	08/15/16		08/15/16
repeat_library
Note
ID	4159	4161	4160	4162

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
FXR2	Product_ID: MA1-16767 Lot_ID: SD251451 Source: Thermo Fisher Target Name: FXR2-human
FXR2	Product_ID: A303-894A Lot_ID: 1 Source: Bethyl Labs Target Name: FXR2-human

Experiment Status

	BGKcLV04-13	BGKcLV04-14
Sample_ID	BGKcLV04-13	BGKcLV04-14
Sample Name	FXR2_BGKcLV04_13	FXR2_BGKcLV04_14
Sample Name	FXR2_BGKcLV04_13	FXR2_BGKcLV04_14
RBP	FXR2	FXR2
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2016-12-12	2016-12-12
Project	ENCODE3	ENCODE3
Note
ID	1317	1318

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV04-13	BGKcLV04-14
Sample #
Sample Name	FXR2-BGKcLV04-13	FXR2-BGKcLV04-14
Sample_Name_Alias	FXR2_BGKcLV04_13	FXR2_BGKcLV04_14
Index Well Position	S09	S10
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2016-08-15	2016-08-15
Lib_ID	Lib-160815	Lib-160815
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV37-38/set1/F2.png	DNA_Library_LV37-38/set1/G2.png
RIN	9.2	9.0
libSample_RNA_Well	RNA_Library_cLV04-05/set1/G8.png	RNA_Library_cLV04-05/set1/H8.png
SampleQC_method
SampleQC_date
Sample_ID	BGKcLV04-13	BGKcLV04-14
RBP	FXR2	FXR2
Batch_ID	BGKcLV04	BGKcLV04
WB_result	78.500	82.300
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	3006	3007

Sequencing Information

	BGKcLV04-13	BGKcLV04-14
Sample_ID	BGKcLV04-13	BGKcLV04-14
Sample Name	FXR2_BGKcLV04_13	FXR2_BGKcLV04_14
Pool ID	Pool-161129	Pool-161129
LocalServer_folder	BGKcLV04	BGKcLV04
total_reads	70,741,412	70,943,342
total_aligned_reads	57,251,384	59,866,328
unique_aligned_reads	52,673,456	55,055,990
percent_uniqueAligned	0.74459	0.77606
correlation_replicates	0.993224	0.993224
spikein_reads	82,662	141,126
percent_spikeins	0.00117	0.00199
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1655	1656

Data Submission Information

	BGKcLV04-13	BGKcLV04-13
ENCODE_alias	brenton-graveley:FXR2_BGKcLV04	brenton-graveley:FXR2-BGKcLV04-K562
ENCODE_accession	ENCSR376GHG	ENCSR621SBF
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKcLV04-13	BGKcLV04-13
Sample Name	FXR2_BGKcLV04_13	FXR2_BGKcLV04_13
Selected	Yes	Yes
Status	Released	Released
Status_Date	2016-12-12	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	3198	6725

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_BGKcLV04_13_GATCAG_L004_001.R1.fastq.gz	ENCODE_DATA/BGKcLV04/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1655	HiSeq2500	100	paired-ended	1				NT_BGKcLV04-1_ACAGTG_L004_001.R1.fastq.gz,NT_BGKcLV04-2_GCCAAT_L004_001.R1.fastq.gz	ENCODE3	23056
FXR2_BGKcLV04_13_GATCAG_L004_001.R2.fastq.gz	ENCODE_DATA/BGKcLV04/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1655	HiSeq2500	100	paired-ended	2				NT_BGKcLV04-1_ACAGTG_L004_001.R2.fastq.gz,NT_BGKcLV04-2_GCCAAT_L004_001.R2.fastq.gz	ENCODE3	23066
FXR2_BGKcLV04_13_Aligned.sortedByCoord.out.bam	ENCODE_DATA/BGKcLV04/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1655					GRCh38	V40	FXR2_BGKcLV04_13_GATCAG_L004_001.R1.fastq.gz,FXR2_BGKcLV04_13_GATCAG_L004_001.R2.fastq.gz		ENCORE2	23076
FXR2_BGKcLV04_13_Signal.Unique.strand+.bw	ENCODE_DATA/BGKcLV04/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1655					GRCh38	V40	FXR2_BGKcLV04_13/Aligned.sortedByCoord.out.bam		ENCORE2	23086
FXR2_BGKcLV04_13_Signal.Unique.strand-.bw	ENCODE_DATA/BGKcLV04/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1655					GRCh38	V40	FXR2_BGKcLV04_13/Aligned.sortedByCoord.out.bam		ENCORE2	23096
FXR2_BGKcLV04_13_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/BGKcLV04/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1655					GRCh38	V40	FXR2_BGKcLV04_13/Aligned.sortedByCoord.out.bam		ENCORE2	23106
FXR2_BGKcLV04_13_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/BGKcLV04/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1655					GRCh38	V40	FXR2_BGKcLV04_13/Aligned.sortedByCoord.out.bam		ENCORE2	23116
FXR2_BGKcLV04_13_quant.sf	ENCODE_DATA/BGKcLV04/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1655					GRCh38	V40	FXR2_BGKcLV04_13_GATCAG_L004_001.R1.fastq.gz,FXR2_BGKcLV04_13_GATCAG_L004_001.R2.fastq.gz		ENCORE2	23126
FXR2_BGKcLV04_14_TAGCTT_L004_001.R1.fastq.gz	ENCODE_DATA/BGKcLV04/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1656	HiSeq2500	100	paired-ended	1				NT_BGKcLV04-1_ACAGTG_L004_001.R1.fastq.gz,NT_BGKcLV04-2_GCCAAT_L004_001.R1.fastq.gz	ENCODE3	23057
FXR2_BGKcLV04_14_TAGCTT_L004_001.R2.fastq.gz	ENCODE_DATA/BGKcLV04/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1656	HiSeq2500	100	paired-ended	2				NT_BGKcLV04-1_ACAGTG_L004_001.R2.fastq.gz,NT_BGKcLV04-2_GCCAAT_L004_001.R2.fastq.gz	ENCODE3	23067
FXR2_BGKcLV04_14_Aligned.sortedByCoord.out.bam	ENCODE_DATA/BGKcLV04/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1656					GRCh38	V40	FXR2_BGKcLV04_14_TAGCTT_L004_001.R1.fastq.gz,FXR2_BGKcLV04_14_TAGCTT_L004_001.R2.fastq.gz		ENCORE2	23077
FXR2_BGKcLV04_14_Signal.Unique.strand+.bw	ENCODE_DATA/BGKcLV04/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1656					GRCh38	V40	FXR2_BGKcLV04_14/Aligned.sortedByCoord.out.bam		ENCORE2	23087
FXR2_BGKcLV04_14_Signal.Unique.strand-.bw	ENCODE_DATA/BGKcLV04/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1656					GRCh38	V40	FXR2_BGKcLV04_14/Aligned.sortedByCoord.out.bam		ENCORE2	23097
FXR2_BGKcLV04_14_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/BGKcLV04/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1656					GRCh38	V40	FXR2_BGKcLV04_14/Aligned.sortedByCoord.out.bam		ENCORE2	23107
FXR2_BGKcLV04_14_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/BGKcLV04/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1656					GRCh38	V40	FXR2_BGKcLV04_14/Aligned.sortedByCoord.out.bam		ENCORE2	23117
FXR2_BGKcLV04_14_quant.sf	ENCODE_DATA/BGKcLV04/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1656					GRCh38	V40	FXR2_BGKcLV04_14_TAGCTT_L004_001.R1.fastq.gz,FXR2_BGKcLV04_14_TAGCTT_L004_001.R2.fastq.gz		ENCORE2	23127