FXR1 RNA-Seq in HepG2

General Information


RBP	FXR1
Cell_Line	HepG2
Method	shRNA
Exp_Name	FXR1-BGHLV12-HepG2
ENCODE_series_ID	ENCSR180ZGG
Batch_ID	BGHLV12
Pool ID	Pool-140701A
Local_Set_Name	set12
ENCODE_KD_Exp_ID	ENCSR009PPI
ENCODE_CN_Exp_ID	ENCSR237YZT
Rep1	FXR1-BGHLV12-29
Rep2	FXR1-BGHLV12-30
CN1	NT-BGHLV12-01
CN2	NT-BGHLV12-02
Rep1_qPCR	75.5
Rep2_qPCR	88.3
Rep1_WB
Rep2_WB
Antibody Cat#	A303-892A
Antibody Lot#	LOT# 1
Antibody DCC ID	ENCAB712TFO
Status	Released
Project	ENCODE3
ID	337

Experiment Information (Status: Released)

	BGHLV12-29	BGHLV12-30
idx	29	30
TRCN#_or_BGC#	TRCN0000159153	TRCN0000159153
shRNA_or_gRNA_sequence	GACGCTACTTACAATGAAATA	GACGCTACTTACAATGAAATA
PAM
Name	FXR1	FXR1
Sample_ID	BGHLV12-29	BGHLV12-30
transduction_Date	5/15/2014	5/15/2014
days
RBP_name	FXR1	FXR1
qPCR_result	75.5	88.3
Ave_qPCR	81.9
RT-qPCR_primer-F	GTCGAGGTCGTGGTGGAC
RT-qPCR_primer-R	CAAGTAAGCTGTATGGATTGCTG
protein_conc	2200	1761
WB_result
Ave_WB
WB_DONE_date
MW	70kDa
IP	1	1
antibody_Cat#	A303-892A	A303-892A
Antibody DCC ID
submitted_to_DCC_date
Rep1_TPM	68.4	0
Rep2_TPM	70.5	0
Action
Library_start_date	6/9/2014	6/9/2014
repeat_library
Note
ID	2076	2077

Western Blot Western Blot info was not avaliable

Experiment Status

	BGHLV12-29	BGHLV12-30
Sample_ID	BGHLV12-29	BGHLV12-30
Sample Name	FXR1-BGHLV12-29	FXR1-BGHLV12-30
Sample Name	FXR1-BGHLV12-29	FXR1-BGHLV12-30
RBP	FXR1	FXR1
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2014-09-25	2014-09-25
Project	ENCODE3	ENCODE3
Note
ID	388	389

Library-Prep
Sequencing

Library-Prep Information

	BGHLV12-29	BGHLV12-30
Sample #
Sample Name	FXR1-BGHLV12-29	FXR1-BGHLV12-30
Sample_Name_Alias	FXR1-BGHLV12-29	FXR1-BGHLV12-30
Index Well Position	S22	S23
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2014-06-09	2014-06-09
Lib_ID	Lib-140609	Lib-140609
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV12/set2/F1.png	DNA_Library_LV12/set2/G1.png
RIN	9.3	9.4
libSample_RNA_Well	RNA_Library_LV12/set1/E3.png	RNA_Library_LV12/set1/F3.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date
Sample_ID	BGHLV12-29	BGHLV12-30
RBP	FXR1	FXR1
Batch_ID	BGHLV12	BGHLV12
WB_result	0.000	0.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2012	2013

Sequencing Information

	BGHLV12-29	BGHLV12-30
Sample_ID	BGHLV12-29	BGHLV12-30
Sample Name	FXR1-BGHLV12-29	FXR1-BGHLV12-30
Pool ID	Pool-140701A	Pool-140701A
LocalServer_folder	set12	set12
total_reads	67,310,000	58,870,000
total_aligned_reads	62,795,804	54,516,276
unique_aligned_reads	59,384,788	51,583,208
percent_uniqueAligned	0.88226	0.87622
correlation_replicates	0.997841	0.997841
spikein_reads	506,234	402,084
percent_spikeins	0.00752	0.00683
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	712	713

Data Submission Information

	BGHLV12-29	BGHLV12-29
ENCODE_alias	brenton-graveley:FXR1-BGHLV12	brenton-graveley:FXR1-BGHLV12-HepG2
ENCODE_accession	ENCSR009PPI	ENCSR180ZGG
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV12-29	BGHLV12-29
Sample Name	FXR1-BGHLV12-29	FXR1-BGHLV12-29
Selected	Yes	Yes
Status	Released	Released
Status_Date	2014-09-24	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2743	6723

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
FXR1-BGHLV12-29_CGTACG_L003_R1_001.fastq.gz	ENCODE_DATA/set12/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	712	HiSeq2000	100	paired-ended	1				NT-BGHLV12-01_ATCACG_L001_R1_001.fastq.gz,NT-BGHLV12-02_CGATGT_L001_R1_001.fastq.gz	ENCODE3	12769
FXR1-BGHLV12-29_CGTACG_L003_R2_001.fastq.gz	ENCODE_DATA/set12/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	712	HiSeq2000	100	paired-ended	2				NT-BGHLV12-01_ATCACG_L001_R2_001.fastq.gz,NT-BGHLV12-02_CGATGT_L001_R2_001.fastq.gz	ENCODE3	12838
FXR1-BGHLV12-29_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set12/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	712					GRCh38	V40	FXR1-BGHLV12-29_CGTACG_L003_R1_001.fastq.gz,FXR1-BGHLV12-29_CGTACG_L003_R2_001.fastq.gz		ENCORE2	12908
FXR1-BGHLV12-29_Signal.Unique.strand+.bw	ENCODE_DATA/set12/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	712					GRCh38	V40	FXR1-BGHLV12-29/Aligned.sortedByCoord.out.bam		ENCORE2	12978
FXR1-BGHLV12-29_Signal.Unique.strand-.bw	ENCODE_DATA/set12/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	712					GRCh38	V40	FXR1-BGHLV12-29/Aligned.sortedByCoord.out.bam		ENCORE2	13048
FXR1-BGHLV12-29_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set12/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	712					GRCh38	V40	FXR1-BGHLV12-29/Aligned.sortedByCoord.out.bam		ENCORE2	13118
FXR1-BGHLV12-29_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set12/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	712					GRCh38	V40	FXR1-BGHLV12-29/Aligned.sortedByCoord.out.bam		ENCORE2	13188
FXR1-BGHLV12-29_quant.sf	ENCODE_DATA/set12/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	712					GRCh38	V40	FXR1-BGHLV12-29_CGTACG_L003_R1_001.fastq.gz,FXR1-BGHLV12-29_CGTACG_L003_R2_001.fastq.gz		ENCORE2	13258
FXR1-BGHLV12-30_GAGTGG_L004_R1_001.fastq.gz	ENCODE_DATA/set12/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	713	HiSeq2000	100	paired-ended	1				NT-BGHLV12-01_ATCACG_L001_R1_001.fastq.gz,NT-BGHLV12-02_CGATGT_L001_R1_001.fastq.gz	ENCODE3	12770
FXR1-BGHLV12-30_GAGTGG_L004_R2_001.fastq.gz	ENCODE_DATA/set12/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	713	HiSeq2000	100	paired-ended	2				NT-BGHLV12-01_ATCACG_L001_R2_001.fastq.gz,NT-BGHLV12-02_CGATGT_L001_R2_001.fastq.gz	ENCODE3	12839
FXR1-BGHLV12-30_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set12/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	713					GRCh38	V40	FXR1-BGHLV12-30_GAGTGG_L004_R1_001.fastq.gz,FXR1-BGHLV12-30_GAGTGG_L004_R2_001.fastq.gz		ENCORE2	12909
FXR1-BGHLV12-30_Signal.Unique.strand+.bw	ENCODE_DATA/set12/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	713					GRCh38	V40	FXR1-BGHLV12-30/Aligned.sortedByCoord.out.bam		ENCORE2	12979
FXR1-BGHLV12-30_Signal.Unique.strand-.bw	ENCODE_DATA/set12/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	713					GRCh38	V40	FXR1-BGHLV12-30/Aligned.sortedByCoord.out.bam		ENCORE2	13049
FXR1-BGHLV12-30_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set12/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	713					GRCh38	V40	FXR1-BGHLV12-30/Aligned.sortedByCoord.out.bam		ENCORE2	13119
FXR1-BGHLV12-30_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set12/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	713					GRCh38	V40	FXR1-BGHLV12-30/Aligned.sortedByCoord.out.bam		ENCORE2	13189
FXR1-BGHLV12-30_quant.sf	ENCODE_DATA/set12/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	713					GRCh38	V40	FXR1-BGHLV12-30_GAGTGG_L004_R1_001.fastq.gz,FXR1-BGHLV12-30_GAGTGG_L004_R2_001.fastq.gz		ENCORE2	13259