AGGF1 RNA-Seq in K562

General Information


RBP	AGGF1
Cell_Line	K562
Method	shRNA
Exp_Name	AGGF1-BGKLV32-K562
ENCODE_series_ID	ENCSR708JGT
Batch_ID	BGKLV32
Pool ID	Pool-160425
Local_Set_Name	set32
ENCODE_KD_Exp_ID	ENCSR812TLY
ENCODE_CN_Exp_ID	ENCSR143COQ
Rep1	AGGF1_BGKLV32-5
Rep2	AGGF1_BGKLV32-6
CN1	NT_BGKLV32-1
CN2	NT_BGKLV32-2
Rep1_qPCR	91.7
Rep2_qPCR	89.4
Rep1_WB	78.7
Rep2_WB	81.8
Antibody Cat#	A303-634A
Antibody Lot#	A303-634A
Antibody DCC ID	ENCAB191KLA
Status	Released
Project	ENCODE3
ID	702

Experiment Information (Status: Released)

	BGKLV32-5	BGKLV32-6
idx	604	605
TRCN#_or_BGC#	TRCN0000129956	TRCN0000129956
shRNA_or_gRNA_sequence	GCTCATCATTAGCTGAAAGTT	GCTCATCATTAGCTGAAAGTT
PAM
Name	AGGF1	AGGF1
Sample_ID	BGKLV32-5	BGKLV32-6
transduction_Date	10/1/2015	10/1/2015
days
RBP_name	AGGF1	AGGF1
qPCR_result	91.7	89.4
Ave_qPCR	90.5
RT-qPCR_primer-F	GGTTGGAAGAAAGGAGAGGG
RT-qPCR_primer-R	CAAGCCTGCATGTGTTCG
protein_conc	3161	3250
WB_result	78.7	81.8
Ave_WB	80.2
WB_DONE_date	11/12/2015
MW	81kDa
IP	1IP	1IP
antibody_Cat#	A303-634A	A303-634A
Antibody DCC ID	ENCAB191KLA	ENCAB191KLA
submitted_to_DCC_date	12/7/2015
Rep1_TPM	9.543992321	0
Rep2_TPM	9.435691791	0
Action
Library_start_date	3/7/2016	3/7/2016
repeat_library
Note
ID	685	686

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
AGGF1	Product_ID: A303-634A Lot_ID: 1 Source: Bethyl Labs Target Name: AGGF1-human

Experiment Status

	BGKLV32-5	BGKLV32-6
Sample_ID	BGKLV32-5	BGKLV32-6
Sample Name	AGGF1_BGKLV32-5	AGGF1_BGKLV32-6
Sample Name	AGGF1_BGKLV32-5	AGGF1_BGKLV32-6
RBP	AGGF1	AGGF1
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2016-09-24	2016-09-24
Project	ENCODE3	ENCODE3
Note
ID	1153	1154

Library-Prep
Sequencing

Library-Prep Information

	BGKLV32-5	BGKLV32-6
Sample #
Sample Name	AGGF1-BGKLV32-5	AGGF1-BGKLV32-6
Sample_Name_Alias	AGGF1_BGKLV32-5	AGGF1_BGKLV32-6
Index Well Position	S03	S04
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2016-03-07	2016-03-07
Lib_ID	Lib-160307	Lib-160307
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV33-34-25B-32/set1/C6.png	DNA_Library_LV33-34-25B-32/set1/D6.png
RIN	9.7	9.7
libSample_RNA_Well	RNA_Library_LV29-30-31-32/set1/C11.png	RNA_Library_LV19-21-24/set2/B10.png
SampleQC_method
SampleQC_date
Sample_ID	BGKLV32-5	BGKLV32-6
RBP	AGGF1	AGGF1
Batch_ID	BGKLV32	BGKLV32
WB_result	78.700	81.800
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2838	2839

Sequencing Information

	BGKLV32-5	BGKLV32-6
Sample_ID	BGKLV32-5	BGKLV32-6
Sample Name	AGGF1_BGKLV32-5	AGGF1_BGKLV32-6
Pool ID	Pool-160425	Pool-160425
LocalServer_folder	set32	set32
total_reads	81,397,000	78,146,504
total_aligned_reads	68,965,242	67,277,092
unique_aligned_reads	63,111,490	61,412,462
percent_uniqueAligned	0.77535	0.78586
correlation_replicates	0.999538	0.999538
spikein_reads	336,060	345,664
percent_spikeins	0.00413	0.00442
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1487	1488

Data Submission Information

	BGKLV32-5	BGKLV32-5
ENCODE_alias	brenton-graveley:AGGF1_BGKLV32	brenton-graveley:AGGF1-BGKLV32-K562
ENCODE_accession	ENCSR812TLY	ENCSR708JGT
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKLV32-5	BGKLV32-5
Sample Name	AGGF1_BGKLV32-5	AGGF1_BGKLV32-5
Selected	Yes	Yes
Status	Released	Released
Status_Date	2016-05-25	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	3116	6582

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
AGGF1_BGKLV32-5_TTAGGC_L001_001.R1.fastq.gz	ENCODE_DATA/set32/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1487	HiSeq2500	100	paired-ended	1				NT_BGKLV32-1_ATCACG_L001_001.R1.fastq.gz,NT_BGKLV32-2_CGATGT_L001_001.R1.fastq.gz	ENCODE3	21186
AGGF1_BGKLV32-5_TTAGGC_L001_001.R2.fastq.gz	ENCODE_DATA/set32/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1487	HiSeq2500	100	paired-ended	2				NT_BGKLV32-1_ATCACG_L001_001.R2.fastq.gz,NT_BGKLV32-2_CGATGT_L001_001.R2.fastq.gz	ENCODE3	21216
AGGF1_BGKLV32-5_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set32/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1487					GRCh38	V40	AGGF1_BGKLV32-5_TTAGGC_L001_001.R1.fastq.gz,AGGF1_BGKLV32-5_TTAGGC_L001_001.R2.fastq.gz		ENCORE2	21246
AGGF1_BGKLV32-5_Signal.Unique.strand+.bw	ENCODE_DATA/set32/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1487					GRCh38	V40	AGGF1_BGKLV32-5/Aligned.sortedByCoord.out.bam		ENCORE2	21276
AGGF1_BGKLV32-5_Signal.Unique.strand-.bw	ENCODE_DATA/set32/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1487					GRCh38	V40	AGGF1_BGKLV32-5/Aligned.sortedByCoord.out.bam		ENCORE2	21306
AGGF1_BGKLV32-5_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set32/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1487					GRCh38	V40	AGGF1_BGKLV32-5/Aligned.sortedByCoord.out.bam		ENCORE2	21336
AGGF1_BGKLV32-5_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set32/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1487					GRCh38	V40	AGGF1_BGKLV32-5/Aligned.sortedByCoord.out.bam		ENCORE2	21366
AGGF1_BGKLV32-5_quant.sf	ENCODE_DATA/set32/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1487					GRCh38	V40	AGGF1_BGKLV32-5_TTAGGC_L001_001.R1.fastq.gz,AGGF1_BGKLV32-5_TTAGGC_L001_001.R2.fastq.gz		ENCORE2	21396
AGGF1_BGKLV32-6_TGACCA_L001_001.R1.fastq.gz	ENCODE_DATA/set32/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1488	HiSeq2500	100	paired-ended	1				NT_BGKLV32-1_ATCACG_L001_001.R1.fastq.gz,NT_BGKLV32-2_CGATGT_L001_001.R1.fastq.gz	ENCODE3	21187
AGGF1_BGKLV32-6_TGACCA_L001_001.R2.fastq.gz	ENCODE_DATA/set32/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1488	HiSeq2500	100	paired-ended	2				NT_BGKLV32-1_ATCACG_L001_001.R2.fastq.gz,NT_BGKLV32-2_CGATGT_L001_001.R2.fastq.gz	ENCODE3	21217
AGGF1_BGKLV32-6_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set32/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1488					GRCh38	V40	AGGF1_BGKLV32-6_TGACCA_L001_001.R1.fastq.gz,AGGF1_BGKLV32-6_TGACCA_L001_001.R2.fastq.gz		ENCORE2	21247
AGGF1_BGKLV32-6_Signal.Unique.strand+.bw	ENCODE_DATA/set32/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1488					GRCh38	V40	AGGF1_BGKLV32-6/Aligned.sortedByCoord.out.bam		ENCORE2	21277
AGGF1_BGKLV32-6_Signal.Unique.strand-.bw	ENCODE_DATA/set32/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1488					GRCh38	V40	AGGF1_BGKLV32-6/Aligned.sortedByCoord.out.bam		ENCORE2	21307
AGGF1_BGKLV32-6_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set32/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1488					GRCh38	V40	AGGF1_BGKLV32-6/Aligned.sortedByCoord.out.bam		ENCORE2	21337
AGGF1_BGKLV32-6_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set32/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1488					GRCh38	V40	AGGF1_BGKLV32-6/Aligned.sortedByCoord.out.bam		ENCORE2	21367
AGGF1_BGKLV32-6_quant.sf	ENCODE_DATA/set32/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1488					GRCh38	V40	AGGF1_BGKLV32-6_TGACCA_L001_001.R1.fastq.gz,AGGF1_BGKLV32-6_TGACCA_L001_001.R2.fastq.gz		ENCORE2	21397