FTO RNA-Seq in K562

General Information


RBP	FTO
Cell_Line	K562
Method	shRNA
Exp_Name	FTO-BGKLV36-K562
ENCODE_series_ID	ENCSR753TVZ
Batch_ID	BGKLV36
Pool ID	Pool-161129
Local_Set_Name	set36
ENCODE_KD_Exp_ID	ENCSR688GVV
ENCODE_CN_Exp_ID	ENCSR424QCW
Rep1	FTO_BGKLV36-25
Rep2	FTO_BGKLV36-26
CN1	NT_BGKLV36-1
CN2	NT_BGKLV36-2
Rep1_qPCR	60.1
Rep2_qPCR	66.5
Rep1_WB	86.4
Rep2_WB	84.6
Antibody Cat#	RN121PW
Antibody Lot#	RN121PW
Antibody DCC ID	ENCAB377UYD
Status	Released
Project	ENCODE3
ID	745

Experiment Information (Status: Released)

	BGKLV36-25	BGKLV36-26
idx	748	749
TRCN#_or_BGC#	TRCN0000246247	TRCN0000246247
shRNA_or_gRNA_sequence	TCACGAATTGCCCGAACATTA	TCACGAATTGCCCGAACATTA
PAM
Name	FTO	FTO
Sample_ID	BGKLV36-25	BGKLV36-26
transduction_Date	5/19/2016	5/19/2016
days
RBP_name	FTO	FTO
qPCR_result	60.1	66.5
Ave_qPCR	63.3
RT-qPCR_primer-F	GGCTCAACTGGAAGCACTGT
RT-qPCR_primer-R	GGGGAGCCCCTCTCTTTTA
protein_conc	3907	4227
WB_result	86.4	84.6
Ave_WB	85.5
WB_DONE_date	6/23/16	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	07/28/16	07/28/16
repeat_library
Note
ID	839	840

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

	BGKLV36-25	BGKLV36-26
Sample_ID	BGKLV36-25	BGKLV36-26
Sample Name	FTO_BGKLV36-25	FTO_BGKLV36-26
Sample Name	FTO_BGKLV36-25	FTO_BGKLV36-26
RBP	FTO	FTO
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2016-12-12	2016-12-12
Project	ENCODE3	ENCODE3
Note
ID	1283	1284

Library-Prep
Sequencing

Library-Prep Information

	BGKLV36-25	BGKLV36-26
Sample #
Sample Name	FTO-BGKLV36-25	FTO-BGKLV36-26
Sample_Name_Alias	FTO_BGKLV36-25	FTO_BGKLV36-26
Index Well Position	S18	S19
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2016-07-28	2016-07-28
Lib_ID	Lib-160728	Lib-160728
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV36/set1/A2.png	DNA_Library_LV36/set1/B2.png
RIN	9.7	9.8
libSample_RNA_Well	RNA_Library_LV35_LV36/set1/C5.png	RNA_Library_LV35_LV36/set1/D5.png
SampleQC_method
SampleQC_date
Sample_ID	BGKLV36-25	BGKLV36-26
RBP	FTO	FTO
Batch_ID	BGKLV36	BGKLV36
WB_result	86.400	84.600
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2968	2969

Sequencing Information

	BGKLV36-25	BGKLV36-26
Sample_ID	BGKLV36-25	BGKLV36-26
Sample Name	FTO_BGKLV36-25	FTO_BGKLV36-26
Pool ID	Pool-161129	Pool-161129
LocalServer_folder	set36	set36
total_reads	57,270,398	59,016,578
total_aligned_reads	47,069,660	52,072,848
unique_aligned_reads	43,148,042	47,665,740
percent_uniqueAligned	0.75341	0.80767
correlation_replicates	0.990751	0.990751
spikein_reads	131,962	162,218
percent_spikeins	0.00230	0.00275
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1617	1618

Data Submission Information

	BGKLV36-25	BGKLV36-25
ENCODE_alias	brenton-graveley:FTO_BGKLV36	brenton-graveley:FTO-BGKLV36-K562
ENCODE_accession	ENCSR688GVV	ENCSR753TVZ
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKLV36-25	BGKLV36-25
Sample Name	FTO_BGKLV36-25	FTO_BGKLV36-25
Selected	Yes	Yes
Status	Released	Released
Status_Date	2016-09-23	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	3181	6718

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_BGKLV36-25_GTCCGC_L001_001.R1.fastq.gz	ENCODE_DATA/set36/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1617	HiSeq2500	100	paired-ended	1				NT_BGKLV36-1_GATCAG_L008_001.R1.fastq.gz,NT_BGKLV36-2_TAGCTT_L008_001.R1.fastq.gz	ENCODE3	21896
FTO_BGKLV36-25_GTCCGC_L001_001.R2.fastq.gz	ENCODE_DATA/set36/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1617	HiSeq2500	100	paired-ended	2				NT_BGKLV36-1_GATCAG_L008_001.R2.fastq.gz,NT_BGKLV36-2_TAGCTT_L008_001.R2.fastq.gz	ENCODE3	21914
FTO_BGKLV36-25_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set36/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1617					GRCh38	V40	FTO_BGKLV36-25_GTCCGC_L001_001.R1.fastq.gz,FTO_BGKLV36-25_GTCCGC_L001_001.R2.fastq.gz		ENCORE2	21932
FTO_BGKLV36-25_Signal.Unique.strand+.bw	ENCODE_DATA/set36/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1617					GRCh38	V40	FTO_BGKLV36-25/Aligned.sortedByCoord.out.bam		ENCORE2	21950
FTO_BGKLV36-25_Signal.Unique.strand-.bw	ENCODE_DATA/set36/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1617					GRCh38	V40	FTO_BGKLV36-25/Aligned.sortedByCoord.out.bam		ENCORE2	21968
FTO_BGKLV36-25_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set36/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1617					GRCh38	V40	FTO_BGKLV36-25/Aligned.sortedByCoord.out.bam		ENCORE2	21986
FTO_BGKLV36-25_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set36/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1617					GRCh38	V40	FTO_BGKLV36-25/Aligned.sortedByCoord.out.bam		ENCORE2	22004
FTO_BGKLV36-25_quant.sf	ENCODE_DATA/set36/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1617					GRCh38	V40	FTO_BGKLV36-25_GTCCGC_L001_001.R1.fastq.gz,FTO_BGKLV36-25_GTCCGC_L001_001.R2.fastq.gz		ENCORE2	22022
FTO_BGKLV36-26_GTGAAA_L001_001.R1.fastq.gz	ENCODE_DATA/set36/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1618	HiSeq2500	100	paired-ended	1				NT_BGKLV36-1_GATCAG_L008_001.R1.fastq.gz,NT_BGKLV36-2_TAGCTT_L008_001.R1.fastq.gz	ENCODE3	21897
FTO_BGKLV36-26_GTGAAA_L001_001.R2.fastq.gz	ENCODE_DATA/set36/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1618	HiSeq2500	100	paired-ended	2				NT_BGKLV36-1_GATCAG_L008_001.R2.fastq.gz,NT_BGKLV36-2_TAGCTT_L008_001.R2.fastq.gz	ENCODE3	21915
FTO_BGKLV36-26_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set36/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1618					GRCh38	V40	FTO_BGKLV36-26_GTGAAA_L001_001.R1.fastq.gz,FTO_BGKLV36-26_GTGAAA_L001_001.R2.fastq.gz		ENCORE2	21933
FTO_BGKLV36-26_Signal.Unique.strand+.bw	ENCODE_DATA/set36/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1618					GRCh38	V40	FTO_BGKLV36-26/Aligned.sortedByCoord.out.bam		ENCORE2	21951
FTO_BGKLV36-26_Signal.Unique.strand-.bw	ENCODE_DATA/set36/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1618					GRCh38	V40	FTO_BGKLV36-26/Aligned.sortedByCoord.out.bam		ENCORE2	21969
FTO_BGKLV36-26_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set36/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1618					GRCh38	V40	FTO_BGKLV36-26/Aligned.sortedByCoord.out.bam		ENCORE2	21987
FTO_BGKLV36-26_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set36/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1618					GRCh38	V40	FTO_BGKLV36-26/Aligned.sortedByCoord.out.bam		ENCORE2	22005
FTO_BGKLV36-26_quant.sf	ENCODE_DATA/set36/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1618					GRCh38	V40	FTO_BGKLV36-26_GTGAAA_L001_001.R1.fastq.gz,FTO_BGKLV36-26_GTGAAA_L001_001.R2.fastq.gz		ENCORE2	22023