FTO RNA-Seq in HepG2

General Information


RBP	FTO
Cell_Line	HepG2
Method	shRNA
Exp_Name	FTO-BGHLV35-HepG2
ENCODE_series_ID	ENCSR100DSP
Batch_ID	BGHLV35
Pool ID	Pool-160912
Local_Set_Name	set35
ENCODE_KD_Exp_ID	ENCSR389HFU
ENCODE_CN_Exp_ID	ENCSR264TUE
Rep1	FTO_BGHLV35-17
Rep2	FTO_BGHLV35-18
CN1	NT_BGHLV35-1
CN2	NT_BGHLV35-2
Rep1_qPCR	60.1
Rep2_qPCR	59.9
Rep1_WB	94.8
Rep2_WB	96.7
Antibody Cat#	RN121PW
Antibody Lot#	RN121PW
Antibody DCC ID	ENCAB377UYD
Status	Released
Project	ENCODE3
ID	733

Experiment Information (Status: Released)

	BGHLV35-17	BGHLV35-18
idx	873	874
TRCN#_or_BGC#	TRCN0000246247	TRCN0000246247
shRNA_or_gRNA_sequence	TCACGAATTGCCCGAACATTA	TCACGAATTGCCCGAACATTA
PAM
Name	FTO	FTO
Sample_ID	BGHLV35-17	BGHLV35-18
transduction_Date	4/29/16	4/29/16
days
RBP_name	FTO	FTO
qPCR_result	60.1	59.9
Ave_qPCR	60.0
RT-qPCR_primer-F	GGCTCAACTGGAAGCACTGT
RT-qPCR_primer-R	GGGGAGCCCCTCTCTTTTA
protein_conc	2998	2624
WB_result	94.8	96.7
Ave_WB	95.7
WB_DONE_date	5/9/2016	WES
MW	58kDa
IP
antibody_Cat#	RN121PW	RN121PW
Antibody DCC ID	ENCAB377UYD	ENCAB377UYD
submitted_to_DCC_date	10/26/16
Rep1_TPM	0	0
Rep2_TPM	0	0
Action
Library_start_date	07/18/16	07/18/16
repeat_library
Note
ID	2962	2963

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
FTO	Product_ID: RN121PW Lot_ID: 1 Source: MBLI Target Name: FTO-human

Experiment Status

	BGHLV35-17	BGHLV35-18
Sample_ID	BGHLV35-17	BGHLV35-18
Sample Name	FTO_BGHLV35-17	FTO_BGHLV35-18
Sample Name	FTO_BGHLV35-17	FTO_BGHLV35-18
RBP	FTO	FTO
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2016-09-24	2016-09-24
Project	ENCODE3	ENCODE3
Note
ID	1255	1256

Library-Prep
Sequencing

Library-Prep Information

	BGHLV35-17	BGHLV35-18
Sample #
Sample Name	FTO-BGHLV35-17	FTO-BGHLV35-18
Sample_Name_Alias	FTO_BGHLV35-17	FTO_BGHLV35-18
Index Well Position	S09	S10
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2016-07-18	2016-07-18
Lib_ID	Lib-160718	Lib-160718
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV35/set2/A2.png	DNA_Library_LV35/set2/B2.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_LV35_LV36/set1/A2.png	RNA_Library_LV35_LV36/set1/B2.png
SampleQC_method
SampleQC_date
Sample_ID	BGHLV35-17	BGHLV35-18
RBP	FTO	FTO
Batch_ID	BGHLV35	BGHLV35
WB_result	94.800	96.700
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2940	2941

Sequencing Information

	BGHLV35-17	BGHLV35-18
Sample_ID	BGHLV35-17	BGHLV35-18
Sample Name	FTO_BGHLV35-17	FTO_BGHLV35-18
Pool ID	Pool-160912	Pool-160912
LocalServer_folder	set35	set35
total_reads	79,625,504	71,655,948
total_aligned_reads	61,808,604	54,066,098
unique_aligned_reads	58,271,678	50,954,210
percent_uniqueAligned	0.73182	0.71110
correlation_replicates	0.991807	0.991807
spikein_reads	200,222	144,544
percent_spikeins	0.00251	0.00202
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1589	1590

Data Submission Information

	BGHLV35-17	BGHLV35-17
ENCODE_alias	brenton-graveley:FTO_BGHLV35	brenton-graveley:FTO-BGHLV35-HepG2
ENCODE_accession	ENCSR389HFU	ENCSR100DSP
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV35-17	BGHLV35-17
Sample Name	FTO_BGHLV35-17	FTO_BGHLV35-17
Selected	Yes	Yes
Status	Released	Released
Status_Date	2016-09-23	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	3167	6717

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
FTO_BGHLV35-17_GATCAG_L006_001.R1.fastq.gz	ENCODE_DATA/set35/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1589	HiSeq2500	100	paired-ended	1				NT_BGHLV35-1_ATCACG_L005_001.R1.fastq.gz,NT_BGHLV35-2_CGATGT_L005_001.R1.fastq.gz	ENCODE3	21688
FTO_BGHLV35-17_GATCAG_L006_001.R2.fastq.gz	ENCODE_DATA/set35/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1589	HiSeq2500	100	paired-ended	2				NT_BGHLV35-1_ATCACG_L005_001.R2.fastq.gz,NT_BGHLV35-2_CGATGT_L005_001.R2.fastq.gz	ENCODE3	21714
FTO_BGHLV35-17_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set35/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1589					GRCh38	V40	FTO_BGHLV35-17_GATCAG_L006_001.R1.fastq.gz,FTO_BGHLV35-17_GATCAG_L006_001.R2.fastq.gz		ENCORE2	21740
FTO_BGHLV35-17_Signal.Unique.strand+.bw	ENCODE_DATA/set35/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1589					GRCh38	V40	FTO_BGHLV35-17/Aligned.sortedByCoord.out.bam		ENCORE2	21766
FTO_BGHLV35-17_Signal.Unique.strand-.bw	ENCODE_DATA/set35/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1589					GRCh38	V40	FTO_BGHLV35-17/Aligned.sortedByCoord.out.bam		ENCORE2	21792
FTO_BGHLV35-17_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set35/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1589					GRCh38	V40	FTO_BGHLV35-17/Aligned.sortedByCoord.out.bam		ENCORE2	21818
FTO_BGHLV35-17_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set35/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1589					GRCh38	V40	FTO_BGHLV35-17/Aligned.sortedByCoord.out.bam		ENCORE2	21844
FTO_BGHLV35-17_quant.sf	ENCODE_DATA/set35/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1589					GRCh38	V40	FTO_BGHLV35-17_GATCAG_L006_001.R1.fastq.gz,FTO_BGHLV35-17_GATCAG_L006_001.R2.fastq.gz		ENCORE2	21870
FTO_BGHLV35-18_TAGCTT_L006_001.R1.fastq.gz	ENCODE_DATA/set35/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1590	HiSeq2500	100	paired-ended	1				NT_BGHLV35-1_ATCACG_L005_001.R1.fastq.gz,NT_BGHLV35-2_CGATGT_L005_001.R1.fastq.gz	ENCODE3	21689
FTO_BGHLV35-18_TAGCTT_L006_001.R2.fastq.gz	ENCODE_DATA/set35/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1590	HiSeq2500	100	paired-ended	2				NT_BGHLV35-1_ATCACG_L005_001.R2.fastq.gz,NT_BGHLV35-2_CGATGT_L005_001.R2.fastq.gz	ENCODE3	21715
FTO_BGHLV35-18_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set35/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1590					GRCh38	V40	FTO_BGHLV35-18_TAGCTT_L006_001.R1.fastq.gz,FTO_BGHLV35-18_TAGCTT_L006_001.R2.fastq.gz		ENCORE2	21741
FTO_BGHLV35-18_Signal.Unique.strand+.bw	ENCODE_DATA/set35/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1590					GRCh38	V40	FTO_BGHLV35-18/Aligned.sortedByCoord.out.bam		ENCORE2	21767
FTO_BGHLV35-18_Signal.Unique.strand-.bw	ENCODE_DATA/set35/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1590					GRCh38	V40	FTO_BGHLV35-18/Aligned.sortedByCoord.out.bam		ENCORE2	21793
FTO_BGHLV35-18_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set35/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1590					GRCh38	V40	FTO_BGHLV35-18/Aligned.sortedByCoord.out.bam		ENCORE2	21819
FTO_BGHLV35-18_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set35/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1590					GRCh38	V40	FTO_BGHLV35-18/Aligned.sortedByCoord.out.bam		ENCORE2	21845
FTO_BGHLV35-18_quant.sf	ENCODE_DATA/set35/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1590					GRCh38	V40	FTO_BGHLV35-18_TAGCTT_L006_001.R1.fastq.gz,FTO_BGHLV35-18_TAGCTT_L006_001.R2.fastq.gz		ENCORE2	21871