APOBEC3C RNA-Seq in K562

General Information


RBP	APOBEC3C
Cell_Line	K562
Method	shRNA
Exp_Name	APOBEC3C-BGKLV25-K562
ENCODE_series_ID	ENCSR628KJM
Batch_ID	BGKLV25
Pool ID	Pool-151101
Local_Set_Name	set25
ENCODE_KD_Exp_ID	ENCSR963RLK
ENCODE_CN_Exp_ID	ENCSR620PUP
Rep1	APOBEC3C_BGKLV25-3
Rep2	APOBEC3C_BGKLV25-4
CN1	NT_BGKLV25-1
CN2	NT_BGKLV25-2
Rep1_qPCR	85.2
Rep2_qPCR	86.3
Rep1_WB	100.0
Rep2_WB	100.0
Antibody Cat#	GTX102164
Antibody Lot#	GTX102164
Antibody DCC ID	ENCAB529HWM
Status	Released
Project	ENCODE3
ID	613

Experiment Information (Status: Released)

	BGKLV25-3	BGKLV25-4
idx	404	405
TRCN#_or_BGC#	TRCN0000052101	TRCN0000052101
shRNA_or_gRNA_sequence	GCACATTCTACTTCCAATTTA	GCACATTCTACTTCCAATTTA
PAM
Name	APOBEC3C	APOBEC3C
Sample_ID	BGKLV25-3	BGKLV25-4
transduction_Date	3/17/2015	3/17/2015
days
RBP_name	APOBEC3C	APOBEC3C
qPCR_result	85.2	86.3
Ave_qPCR	85.7
RT-qPCR_primer-F	TCGCTCTTCCAGACTCTTCC
RT-qPCR_primer-R	GATAGCCATGGAGGCAGAAA
protein_conc	2613	3111
WB_result	100.0	100.0
Ave_WB	100.0
WB_DONE_date	5/11/2015
MW	23kDa
IP	1	1
antibody_Cat#	GTX102164	GTX102164
Antibody DCC ID	ENCAB529HWM	ENCAB529HWM
submitted_to_DCC_date	8/6/2015
Rep1_TPM	34.9865066	0
Rep2_TPM	24.410743	0
Action
Library_start_date	6/23/2015	6/23/2015
repeat_library
Note
ID	463	464

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
APOBEC3C	Product_ID: GTX102164 Lot_ID: 40968 Source: GeneTex Target Name: APOBEC3C-human

Experiment Status

	BGKLV25-3	BGKLV25-4
Sample_ID	BGKLV25-3	BGKLV25-4
Sample Name	APOBEC3C_BGKLV25-3	APOBEC3C_BGKLV25-4
Sample Name	APOBEC3C_BGKLV25-3	APOBEC3C_BGKLV25-4
RBP	APOBEC3C	APOBEC3C
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2015-12-08	2015-12-08
Project	ENCODE3	ENCODE3
Note
ID	908	909

Library-Prep
Sequencing

Library-Prep Information

	BGKLV25-3	BGKLV25-4
Sample #
Sample Name	APOBEC3C-BGKLV25-3	APOBEC3C-BGKLV25-4
Sample_Name_Alias	APOBEC3C_BGKLV25-3	APOBEC3C_BGKLV25-4
Index Well Position	S11	S12
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2015-06-23	2015-06-23
Lib_ID	Lib-150623	Lib-150623
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV24-25-26/set1/D1.png	DNA_Library_LV24-25-26/set1/E1.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_LV22-23-25/set1/C9.png	RNA_Library_LV22-23-25/set1/D9.png
SampleQC_method
SampleQC_date
Sample_ID	BGKLV25-3	BGKLV25-4
RBP	APOBEC3C	APOBEC3C
Batch_ID	BGKLV25	BGKLV25
WB_result	100.000	100.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2596	2597

Sequencing Information

	BGKLV25-3	BGKLV25-4
Sample_ID	BGKLV25-3	BGKLV25-4
Sample Name	APOBEC3C_BGKLV25-3	APOBEC3C_BGKLV25-4
Pool ID	Pool-151101	Pool-151101
LocalServer_folder	set25	set25
total_reads	47,937,168	83,508,164
total_aligned_reads	48,644,844	84,710,910
unique_aligned_reads	44,411,504	77,318,924
percent_uniqueAligned	0.92645	0.92588
correlation_replicates	0.988002	0.988002
spikein_reads	264,560	384,706
percent_spikeins	0.00552	0.00461
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1238	1239

Data Submission Information

	BGKLV25-3	BGKLV25-3
ENCODE_alias	brenton-graveley:APOBEC3C_BGKLV25	brenton-graveley:APOBEC3C-BGKLV25-K562
ENCODE_accession	ENCSR963RLK	ENCSR628KJM
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKLV25-3	BGKLV25-3
Sample Name	APOBEC3C_BGKLV25-3	APOBEC3C_BGKLV25-3
Selected	Yes	Yes
Status	Released	Released
Status_Date	2015-12-02	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	3003	6592

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
APOBEC3C_BGKLV25-3_GGCTAC_L004_001.R1.fastq.gz	ENCODE_DATA/set25/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1238	HiSeq2000	100	paired-ended	1				NT_BGKLV25-1_GATCAG_L004_001.R1.fastq.gz,NT_BGKLV25-2_TAGCTT_L004_001.R1.fastq.gz	ENCODE3	19562
APOBEC3C_BGKLV25-3_GGCTAC_L004_001.R2.fastq.gz	ENCODE_DATA/set25/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1238	HiSeq2000	100	paired-ended	2				NT_BGKLV25-1_GATCAG_L004_001.R2.fastq.gz,NT_BGKLV25-2_TAGCTT_L004_001.R2.fastq.gz	ENCODE3	19598
APOBEC3C_BGKLV25-3_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set25/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1238					GRCh38	V40	APOBEC3C_BGKLV25-3_GGCTAC_L004_001.R1.fastq.gz,APOBEC3C_BGKLV25-3_GGCTAC_L004_001.R2.fastq.gz		ENCORE2	19634
APOBEC3C_BGKLV25-3_Signal.Unique.strand+.bw	ENCODE_DATA/set25/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1238					GRCh38	V40	APOBEC3C_BGKLV25-3/Aligned.sortedByCoord.out.bam		ENCORE2	19670
APOBEC3C_BGKLV25-3_Signal.Unique.strand-.bw	ENCODE_DATA/set25/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1238					GRCh38	V40	APOBEC3C_BGKLV25-3/Aligned.sortedByCoord.out.bam		ENCORE2	19706
APOBEC3C_BGKLV25-3_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set25/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1238					GRCh38	V40	APOBEC3C_BGKLV25-3/Aligned.sortedByCoord.out.bam		ENCORE2	19742
APOBEC3C_BGKLV25-3_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set25/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1238					GRCh38	V40	APOBEC3C_BGKLV25-3/Aligned.sortedByCoord.out.bam		ENCORE2	19778
APOBEC3C_BGKLV25-3_quant.sf	ENCODE_DATA/set25/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1238					GRCh38	V40	APOBEC3C_BGKLV25-3_GGCTAC_L004_001.R1.fastq.gz,APOBEC3C_BGKLV25-3_GGCTAC_L004_001.R2.fastq.gz		ENCORE2	19968
APOBEC3C_BGKLV25-4_CTTGTA_L004_001.R1.fastq.gz	ENCODE_DATA/set25/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1239	HiSeq2000	100	paired-ended	1				NT_BGKLV25-1_GATCAG_L004_001.R1.fastq.gz,NT_BGKLV25-2_TAGCTT_L004_001.R1.fastq.gz	ENCODE3	19563
APOBEC3C_BGKLV25-4_CTTGTA_L004_001.R2.fastq.gz	ENCODE_DATA/set25/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1239	HiSeq2000	100	paired-ended	2				NT_BGKLV25-1_GATCAG_L004_001.R2.fastq.gz,NT_BGKLV25-2_TAGCTT_L004_001.R2.fastq.gz	ENCODE3	19599
APOBEC3C_BGKLV25-4_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set25/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1239					GRCh38	V40	APOBEC3C_BGKLV25-4_CTTGTA_L004_001.R1.fastq.gz,APOBEC3C_BGKLV25-4_CTTGTA_L004_001.R2.fastq.gz		ENCORE2	19635
APOBEC3C_BGKLV25-4_Signal.Unique.strand+.bw	ENCODE_DATA/set25/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1239					GRCh38	V40	APOBEC3C_BGKLV25-4/Aligned.sortedByCoord.out.bam		ENCORE2	19671
APOBEC3C_BGKLV25-4_Signal.Unique.strand-.bw	ENCODE_DATA/set25/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1239					GRCh38	V40	APOBEC3C_BGKLV25-4/Aligned.sortedByCoord.out.bam		ENCORE2	19707
APOBEC3C_BGKLV25-4_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set25/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1239					GRCh38	V40	APOBEC3C_BGKLV25-4/Aligned.sortedByCoord.out.bam		ENCORE2	19743
APOBEC3C_BGKLV25-4_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set25/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1239					GRCh38	V40	APOBEC3C_BGKLV25-4/Aligned.sortedByCoord.out.bam		ENCORE2	19779
APOBEC3C_BGKLV25-4_quant.sf	ENCODE_DATA/set25/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1239					GRCh38	V40	APOBEC3C_BGKLV25-4_CTTGTA_L004_001.R1.fastq.gz,APOBEC3C_BGKLV25-4_CTTGTA_L004_001.R2.fastq.gz		ENCORE2	19969