FMR1 RNA-Seq in HepG2

General Information


RBP	FMR1
Cell_Line	HepG2
Method	shRNA
Exp_Name	FMR1-BGHLV23-HepG2
ENCODE_series_ID	ENCSR560IJH
Batch_ID	BGHLV23
Pool ID	Pool-150701
Local_Set_Name	set23
ENCODE_KD_Exp_ID	ENCSR905HID
ENCODE_CN_Exp_ID	ENCSR042QTH
Rep1	FMR1-BGHLV23-17
Rep2	FMR1-BGHLV23-18
CN1	non-target-BGHLV23-1
CN2	non-target-BGHLV23-2
Rep1_qPCR	67.5
Rep2_qPCR	73.2
Rep1_WB	83.7
Rep2_WB	84.5
Antibody Cat#	RN016P
Antibody Lot#	RN016P
Antibody DCC ID	ENCAB000BFK
Status	Released
Project	ENCODE3
ID	543

Experiment Information (Status: Released)

	BGHLV23-17	BGHLV23-17	BGHLV23-18	BGHLV23-18
idx	509	509	510	510
TRCN#_or_BGC#	TRCN0000059758	TRCN0000059758	TRCN0000059758	TRCN0000059758
shRNA_or_gRNA_sequence	GCCAGAAGACTTACGGCAAAT	GCCAGAAGACTTACGGCAAAT	GCCAGAAGACTTACGGCAAAT	GCCAGAAGACTTACGGCAAAT
PAM
Name	FMR1	FMRP/FMR1	FMR1	FMRP/FMR1
Sample_ID	BGHLV23-17	BGHLV23-17	BGHLV23-18	BGHLV23-18
transduction_Date	10/29/2014	10/29/2014	10/29/2014	10/29/2014
days
RBP_name	FMR1	FMR1	FMR1	FMR1
qPCR_result	67.5	67.5	73.2	73.2
Ave_qPCR	70.4	70.4
RT-qPCR_primer-F	ctgcgcactaagttgtctctg	ctgcgcactaagttgtctctg
RT-qPCR_primer-R	catgaaatctcgaggcaagc	catgaaatctcgaggcaagc
protein_conc	5588	5588	5203	5203
WB_result	83.7	95.6	84.5	95.2
Ave_WB	84.1	95.4
WB_DONE_date	2/15/2016	1/14/2021
MW	71kDa	71kDa	WES
IP	1		1
antibody_Cat#	RN016P	PA5-34584	RN016P	TK2671134
Antibody DCC ID	ENCAB000BFK	ENCAB650WPE		11/24/20
submitted_to_DCC_date	3/8/2016
Rep1_TPM	53.5	0	0	0
Rep2_TPM	42.8	0	0	0
Action
Library_start_date	6/10/2015		6/10/2015
repeat_library
Note
ID	2586	2588	2587	2589

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
FMR1	Product_ID: RN016P Lot_ID: 1 Source: MBLI Target Name: FMR1-human
FMR1	Product_ID: PA5-34584 Lot_ID: TK2671134 Source: Thermo Fisher Target Name: FMR1-human

Experiment Status

	BGHLV23-17	BGHLV23-18
Sample_ID	BGHLV23-17	BGHLV23-18
Sample Name	FMR1-BGHLV23-17	FMR1-BGHLV23-18
Sample Name	FMR1-BGHLV23-17	FMR1-BGHLV23-18
RBP	FMR1	FMR1
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2015-08-13	2015-08-13
Project	ENCODE3	ENCODE3
Note
ID	822	823

Library-Prep
Sequencing

Library-Prep Information

	BGHLV23-17	BGHLV23-18
Sample #
Sample Name	FMR1-BGHLV23-17	FMR1-BGHLV23-18
Sample_Name_Alias	FMR1-BGHLV23-17	FMR1-BGHLV23-18
Index Well Position	S05	S06
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2015-06-10	2015-06-10
Lib_ID	Lib-150610	Lib-150610
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV20-22-23/set1/E12.png	DNA_Library_LV20-22-23/set1/F12.png
RIN	9.6	9.6
libSample_RNA_Well	RNA_Library_LV19-21-24/set2/G5.png	RNA_Library_LV19-21-24/set2/H5.png
SampleQC_method
SampleQC_date
Sample_ID	BGHLV23-17	BGHLV23-18
RBP	FMR1	FMR1
Batch_ID	BGHLV23	BGHLV23
WB_result	83.700	84.500
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2510	2511

Sequencing Information

	BGHLV23-17	BGHLV23-18
Sample_ID	BGHLV23-17	BGHLV23-18
Sample Name	FMR1-BGHLV23-17	FMR1-BGHLV23-18
Pool ID	Pool-150701	Pool-150701
LocalServer_folder	set23	set23
total_reads	47,420,000	59,690,000
total_aligned_reads	42,306,876	53,817,438
unique_aligned_reads	39,876,878	50,811,210
percent_uniqueAligned	0.84093	0.85125
correlation_replicates	0.983236	0.983236
spikein_reads	285,894	343,634
percent_spikeins	0.00603	0.00576
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1132	1133

Data Submission Information

	BGHLV23-17	BGHLV23-17
ENCODE_alias	brenton-graveley:FMR1-BGHLV23	brenton-graveley:FMR1-BGHLV23-HepG2
ENCODE_accession	ENCSR905HID	ENCSR560IJH
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV23-17	BGHLV23-17
Sample Name	FMR1-BGHLV23-17	FMR1-BGHLV23-17
Selected	Yes	Yes
Status	Released	Released
Status_Date	2015-08-11	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2943	6715

File Information

Search:

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
FMR1-BGHLV23-17_ACAGTG_L005_R1_001.fastq.gz	ENCODE_DATA/set23/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1132	HiSeq2000	100	paired-ended	1				non-target-BGHLV23-1_GTCCGC_L003_R1_001.fastq.gz,non-target-BGHLV23-2_GTGAAA_L004_R1_001.fastq.gz	ENCODE3	16660
FMR1-BGHLV23-17_ACAGTG_L005_R2_001.fastq.gz	ENCODE_DATA/set23/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1132	HiSeq2000	100	paired-ended	2				non-target-BGHLV23-1_GTCCGC_L003_R2_001.fastq.gz,non-target-BGHLV23-2_GTGAAA_L004_R2_001.fastq.gz	ENCODE3	16698
FMR1-BGHLV23-17_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set23/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1132					GRCh38	V40	FMR1-BGHLV23-17_ACAGTG_L005_R1_001.fastq.gz,FMR1-BGHLV23-17_ACAGTG_L005_R2_001.fastq.gz		ENCORE2	16736
FMR1-BGHLV23-17_quant.sf	ENCODE_DATA/set23/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1132					GRCh38	V40	FMR1-BGHLV23-17_ACAGTG_L005_R1_001.fastq.gz,FMR1-BGHLV23-17_ACAGTG_L005_R2_001.fastq.gz		ENCORE2	16926
FMR1-BGHLV23-17_Signal.Unique.strand+.bw	ENCODE_DATA/set23/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1132					GRCh38	V40	FMR1-BGHLV23-17/Aligned.sortedByCoord.out.bam		ENCORE2	16774
FMR1-BGHLV23-17_Signal.Unique.strand-.bw	ENCODE_DATA/set23/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1132					GRCh38	V40	FMR1-BGHLV23-17/Aligned.sortedByCoord.out.bam		ENCORE2	16812
FMR1-BGHLV23-17_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set23/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1132					GRCh38	V40	FMR1-BGHLV23-17/Aligned.sortedByCoord.out.bam		ENCORE2	16850
FMR1-BGHLV23-17_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set23/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1132					GRCh38	V40	FMR1-BGHLV23-17/Aligned.sortedByCoord.out.bam		ENCORE2	16888
FMR1-BGHLV23-18_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set23/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1133					GRCh38	V40	FMR1-BGHLV23-18_GCCAAT_L005_R1_001.fastq.gz,FMR1-BGHLV23-18_GCCAAT_L005_R2_001.fastq.gz		ENCORE2	16737
FMR1-BGHLV23-18_GCCAAT_L005_R1_001.fastq.gz	ENCODE_DATA/set23/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1133	HiSeq2000	100	paired-ended	1				non-target-BGHLV23-1_GTCCGC_L003_R1_001.fastq.gz,non-target-BGHLV23-2_GTGAAA_L004_R1_001.fastq.gz	ENCODE3	16661
FMR1-BGHLV23-18_GCCAAT_L005_R2_001.fastq.gz	ENCODE_DATA/set23/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1133	HiSeq2000	100	paired-ended	2				non-target-BGHLV23-1_GTCCGC_L003_R2_001.fastq.gz,non-target-BGHLV23-2_GTGAAA_L004_R2_001.fastq.gz	ENCODE3	16699
FMR1-BGHLV23-18_quant.sf	ENCODE_DATA/set23/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1133					GRCh38	V40	FMR1-BGHLV23-18_GCCAAT_L005_R1_001.fastq.gz,FMR1-BGHLV23-18_GCCAAT_L005_R2_001.fastq.gz		ENCORE2	16927
FMR1-BGHLV23-18_Signal.Unique.strand+.bw	ENCODE_DATA/set23/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1133					GRCh38	V40	FMR1-BGHLV23-18/Aligned.sortedByCoord.out.bam		ENCORE2	16775
FMR1-BGHLV23-18_Signal.Unique.strand-.bw	ENCODE_DATA/set23/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1133					GRCh38	V40	FMR1-BGHLV23-18/Aligned.sortedByCoord.out.bam		ENCORE2	16813
FMR1-BGHLV23-18_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set23/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1133					GRCh38	V40	FMR1-BGHLV23-18/Aligned.sortedByCoord.out.bam		ENCORE2	16851
FMR1-BGHLV23-18_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set23/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1133					GRCh38	V40	FMR1-BGHLV23-18/Aligned.sortedByCoord.out.bam		ENCORE2	16889

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