FXR2 RNA-Seq in HepG2

General Information


RBP	FXR2
Cell_Line	HepG2
Method	CRISPR
Exp_Name	FXR2-BGHcLV05-HepG2
ENCODE_series_ID	ENCSR930RXK
Batch_ID	BGHcLV05
Pool ID	Pool-180316
Local_Set_Name	set40_H
ENCODE_KD_Exp_ID	ENCSR147RTA
ENCODE_CN_Exp_ID	ENCSR834IFU
Rep1	FXR2-BGHcLV05-17
Rep2	FXR2-BGHcLV05-18
CN1	NT-BGHcLV05-1C
CN2	NT-BGHcLV05-2C
Rep1_qPCR	55.5
Rep2_qPCR	32.6
Rep1_WB	99.9
Rep2_WB	99.5
Antibody Cat#	A303-894A
Antibody Lot#	A303-894A
Antibody DCC ID	ENCAB069PGU
Status	Released
Project	ENCODE4
ID	259

Experiment Information (Status: Released)

	BGHcLV05-17	BGHcLV05-17	BGHcLV05-18	BGHcLV05-18
idx	53	92	54	93
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	BGHcLV05-17	BGHcLV05-17	BGHcLV05-18	BGHcLV05-18
transduction_Date	7/12/16	7/12/16	7/12/16	7/12/16
days	DAY 6		DAY 6
RBP_name	FXR2	FXR2	FXR2	FXR2
qPCR_result	55.5		32.6
Ave_qPCR	44.0
RT-qPCR_primer-F	accaaaggcagcttcttcaa
RT-qPCR_primer-R	ccagggctttcttgaactctt
protein_conc	4213	0	4202	0
WB_result	99.9		99.5
Ave_WB	99.7
WB_DONE_date	7/18/16		wes
MW	74 kDa
IP	1
antibody_Cat#	A303-894A		A303-894A
Antibody DCC ID	ENCAB069PGU		ENCAB069PGU
submitted_to_DCC_date	10/26/16
Rep1_TPM	4	0	0	0
Rep2_TPM	5	0	0	0
Action	Ready		Ready
Library_start_date	08/15/16		08/15/16
repeat_library
Note
ID	6196	6233	6197	6234

Western Blot

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

Experiment Status

	BGHcLV05-17	BGHcLV05-18
Sample_ID	BGHcLV05-17	BGHcLV05-18
Sample Name
Sample Name	FXR2-BGHcLV05-17	FXR2-BGHcLV05-18
RBP	FXR2	FXR2
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2021-03-18	2021-03-18
Project	ENCODE4	ENCODE4
Note
ID	6421	6422

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV05-17	BGHcLV05-18
Sample #	5	6
Sample Name	FXR2-BGHcLV05-17C	FXR2-BGHcLV05-18C
Sample_Name_Alias	FXR2-BGHcLV05-17	FXR2-BGHcLV05-18
Index Well Position	S22	S23
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2018-01-02	2018-01-02
Lib_ID	Lib-180102	Lib-180102
Tecan_Location
Tecan
Tecan_date
Size_bp	259	262
Peak_Molarity	15.00	12.80
libSampleQC_DNA_Well	DNA_Library_set40/set3/A1.png	DNA_Library_set40/set3/B1.png
RIN	9.3	9.7
libSample_RNA_Well	RNA_Library_set40/set1/C3.png	RNA_Library_set40/set1/D3.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2018-01-02	2018-01-02
Sample_ID	BGHcLV05-17	BGHcLV05-18
RBP	FXR2	FXR2
Batch_ID	BGHcLV05	BGHcLV05
WB_result	99.900	99.500
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix	C	C
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	928	929

Sequencing Information

	BGHcLV05-17	BGHcLV05-17	BGHcLV05-18
Sample_ID	BGHcLV05-17	BGHcLV05-17	BGHcLV05-18
Sample Name	FXR2-BGHcLV05-17	FXR2-BGHcLV05-17	FXR2-BGHcLV05-18
Pool ID	Pool-180109	Pool-180316	Pool-180109
LocalServer_folder	set40_H	set40_H	set40_H
total_reads	24,818,464	16,654,632	41,040,086
total_aligned_reads	17,173,802	11,628,626	28,500,304
unique_aligned_reads	16,104,426	10,867,252	26,642,708
percent_uniqueAligned	0.64889	0.65251	0.64919
correlation_replicates	0.997953		0.997953
spikein_reads	23,752	15,912	39,852
percent_spikeins	0.00096	0.00096	0.00097
original_ReadLength	100	100	100
QC_Status	Submitted	Submitted	Submitted
ID	331	395	332

Data Submission Information

	BGHcLV05-17	BGHcLV05-17	BGHcLV05-17	BGHcLV05-17	BGHcLV05-17	BGHcLV05-17	BGHcLV05-17	BGHcLV05-17	BGHcLV05-18	BGHcLV05-18	BGHcLV05-18	BGHcLV05-18
ENCODE_alias	brenton-graveley:FXR2-BGHcLV05	brenton-graveley:FXR2-BGHcLV05-17	brenton-graveley:L-FXR2-BGHcLV05-17	brenton-graveley:FXR2-BGHcLV05-17_CGTACG_ACBYWVANXX_L008_001.R1.fastq.gz	brenton-graveley:FXR2-BGHcLV05-17_CGTACG_AHFKCFBCX2_L001_001.R1.fastq.gz	brenton-graveley:FXR2-BGHcLV05-17_CGTACG_ACBYWVANXX_L008_001.R2.fastq.gz	brenton-graveley:FXR2-BGHcLV05-17_CGTACG_AHFKCFBCX2_L001_001.R2.fastq.gz	brenton-graveley:FXR2-BGHcLV05-HepG2	brenton-graveley:FXR2-BGHcLV05-18	brenton-graveley:L-FXR2-BGHcLV05-18	brenton-graveley:FXR2-BGHcLV05-18_GAGTGG_ACBYWVANXX_L008_001.R1.fastq.gz	brenton-graveley:FXR2-BGHcLV05-18_GAGTGG_ACBYWVANXX_L008_001.R2.fastq.gz
ENCODE_accession	ENCSR147RTA	ENCBS752KDK	ENCLB894GPA	ENCFF697TZI	ENCFF700PUE	ENCFF510OBB	ENCFF759MCM	ENCSR930RXK	ENCBS661LCS	ENCLB890LXT	ENCFF564OMO	ENCFF216LRC
object_type	experiment	biosample	library	file_fastq1	file_fastq1	file_fastq2	file_fastq2	gene_silencing_series	biosample	library	file_fastq1	file_fastq2
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHcLV05-17	BGHcLV05-17	BGHcLV05-17	BGHcLV05-17	BGHcLV05-17	BGHcLV05-17	BGHcLV05-17	BGHcLV05-17	BGHcLV05-18	BGHcLV05-18	BGHcLV05-18	BGHcLV05-18
Sample Name	FXR2-BGHcLV05-17	FXR2-BGHcLV05-17	FXR2-BGHcLV05-17	FXR2-BGHcLV05-17	FXR2-BGHcLV05-17	FXR2-BGHcLV05-17	FXR2-BGHcLV05-17	FXR2-BGHcLV05-17	FXR2-BGHcLV05-18	FXR2-BGHcLV05-18	FXR2-BGHcLV05-18	FXR2-BGHcLV05-18
Selected	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes
Status	Released	Released	Released	Released	Released	Released	Released	Released	Released	Released	Released	Released
Status_Date	2021-03-18	2021-03-18	2021-03-18	2021-03-18	2021-03-18	2021-03-18	2021-03-18	2022-03-02	2021-03-18	2021-03-18	2021-03-18	2021-03-18
Project	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4
		LV40_biosample_protocol	LV40_library_protocol						LV40_biosample_protocol	LV40_library_protocol
protocol_URL		FXR2-BGHcLV05-17.pdf	L-FXR2-BGHcLV05-17.pdf						FXR2-BGHcLV05-18.pdf	L-FXR2-BGHcLV05-18.pdf
ID	1436	1470	1526	1580	1581	1617	1618	7225	1471	1527	1582	1619

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-BGHcLV05-17_L001_001.R1.fastq.gz	ENCODE_DATA/set40_H/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	331	HiSeq2500	100	paired-ended	1				NT-BGHcLV05-1C_CGTACG_ACBYWVANXX_L003_001.R1.fastq.gz,NT-BGHcLV05-2C_GAGTGG_ACBYWVANXX_L003_001.R1.fastq.gz	ENCODE4	23232
FXR2-BGHcLV05-17_L001_001.R2.fastq.gz	ENCODE_DATA/set40_H/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	331	HiSeq2500	100	paired-ended	2				NT-BGHcLV05-1C_CGTACG_ACBYWVANXX_L003_001.R2.fastq.gz,NT-BGHcLV05-2C_GAGTGG_ACBYWVANXX_L003_001.R2.fastq.gz	ENCODE4	23240
FXR2-BGHcLV05-17_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set40_H/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	331					GRCh38	V40	FXR2-BGHcLV05-17_L001_001.R1.fastq.gz,FXR2-BGHcLV05-17_L001_001.R2.fastq.gz		ENCORE2	23254
FXR2-BGHcLV05-17_Signal.Unique.strand+.bw	ENCODE_DATA/set40_H/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	331					GRCh38	V40	FXR2-BGHcLV05-17/Aligned.sortedByCoord.out.bam		ENCORE2	23288
FXR2-BGHcLV05-17_Signal.Unique.strand-.bw	ENCODE_DATA/set40_H/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	331					GRCh38	V40	FXR2-BGHcLV05-17/Aligned.sortedByCoord.out.bam		ENCORE2	23322
FXR2-BGHcLV05-17_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set40_H/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	331					GRCh38	V40	FXR2-BGHcLV05-17/Aligned.sortedByCoord.out.bam		ENCORE2	23356
FXR2-BGHcLV05-17_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set40_H/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	331					GRCh38	V40	FXR2-BGHcLV05-17/Aligned.sortedByCoord.out.bam		ENCORE2	23390
FXR2-BGHcLV05-17_quant.sf	ENCODE_DATA/set40_H/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	331					GRCh38	V40	FXR2-BGHcLV05-17_L001_001.R1.fastq.gz,FXR2-BGHcLV05-17_L001_001.R2.fastq.gz		ENCORE2	23424
FXR2-BGHcLV05-18_GAGTGG_ACBYWVANXX_L008_001.R1.fastq.gz	ENCODE_DATA/set40_H/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	332	HiSeq2500	100	paired-ended	1				NT-BGHcLV05-1C_CGTACG_ACBYWVANXX_L003_001.R1.fastq.gz,NT-BGHcLV05-2C_GAGTGG_ACBYWVANXX_L003_001.R1.fastq.gz	ENCODE4	649
FXR2-BGHcLV05-18_GAGTGG_ACBYWVANXX_L008_001.R2.fastq.gz	ENCODE_DATA/set40_H/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	332	HiSeq2500	100	paired-ended	2				NT-BGHcLV05-1C_CGTACG_ACBYWVANXX_L003_001.R2.fastq.gz,NT-BGHcLV05-2C_GAGTGG_ACBYWVANXX_L003_001.R2.fastq.gz	ENCODE4	691
FXR2-BGHcLV05-18_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set40_H/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	332					GRCh38	V40	FXR2-BGHcLV05-18_GAGTGG_ACBYWVANXX_L008_001.R1.fastq.gz,FXR2-BGHcLV05-18_GAGTGG_ACBYWVANXX_L008_001.R2.fastq.gz		ENCORE2	23255
FXR2-BGHcLV05-18_Signal.Unique.strand+.bw	ENCODE_DATA/set40_H/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	332					GRCh38	V40	FXR2-BGHcLV05-18/Aligned.sortedByCoord.out.bam		ENCORE2	23289
FXR2-BGHcLV05-18_Signal.Unique.strand-.bw	ENCODE_DATA/set40_H/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	332					GRCh38	V40	FXR2-BGHcLV05-18/Aligned.sortedByCoord.out.bam		ENCORE2	23323
FXR2-BGHcLV05-18_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set40_H/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	332					GRCh38	V40	FXR2-BGHcLV05-18/Aligned.sortedByCoord.out.bam		ENCORE2	23357
FXR2-BGHcLV05-18_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set40_H/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	332					GRCh38	V40	FXR2-BGHcLV05-18/Aligned.sortedByCoord.out.bam		ENCORE2	23391
FXR2-BGHcLV05-18_quant.sf	ENCODE_DATA/set40_H/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	332					GRCh38	V40	FXR2-BGHcLV05-18_GAGTGG_ACBYWVANXX_L008_001.R1.fastq.gz,FXR2-BGHcLV05-18_GAGTGG_ACBYWVANXX_L008_001.R2.fastq.gz		ENCORE2	23425