APOBEC3C RNA-Seq in HepG2

General Information


RBP	APOBEC3C
Cell_Line	HepG2
Method	shRNA
Exp_Name	APOBEC3C-BGHLV22-HepG2
ENCODE_series_ID	ENCSR153LWS
Batch_ID	BGHLV22
Pool ID	Pool-150705
Local_Set_Name	set22
ENCODE_KD_Exp_ID	ENCSR012DAF
ENCODE_CN_Exp_ID	ENCSR279HMU
Rep1	APOBE-BGHLV22-3_17748
Rep2	APOBE-BGHLV22-4_17749
CN1	non-target-BGHLV22-1_17746
CN2	non-target-BGHLV22-2_17747
Rep1_qPCR	57.6
Rep2_qPCR	56.8
Rep1_WB	59.0
Rep2_WB	68.1
Antibody Cat#	GTX102164
Antibody Lot#	GTX102164
Antibody DCC ID	ENCAB529HWM
Status	Released
Project	ENCODE3
ID	532

Experiment Information (Status: Released)

	BGHLV22-3	BGHLV22-4
idx	431	432
TRCN#_or_BGC#	TRCN0000052101	TRCN0000052101
shRNA_or_gRNA_sequence	GCACATTCTACTTCCAATTTA	GCACATTCTACTTCCAATTTA
PAM
Name	APOBEC3C	APOBEC3C
Sample_ID	BGHLV22-3	BGHLV22-4
transduction_Date	10/16/2014	10/16/2014
days
RBP_name	APOBEC3C	APOBEC3C
qPCR_result	57.6	56.8
Ave_qPCR	57.2
RT-qPCR_primer-F	TCGCTCTTCCAGACTCTTCC
RT-qPCR_primer-R	GATAGCCATGGAGGCAGAAA
protein_conc	5782	5967
WB_result	59.0	68.1
Ave_WB	63.5
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	15.1	0
Rep2_TPM	6.9	0
Action
Library_start_date	6/5/2015	6/5/2015
repeat_library
Note
ID	2502	2503

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

	BGHLV22-3	BGHLV22-4
Sample_ID	BGHLV22-3	BGHLV22-4
Sample Name	APOBE-BGHLV22-3_17748	APOBE-BGHLV22-4_17749
Sample Name	APOBE-BGHLV22-3_17748	APOBE-BGHLV22-4_17749
RBP	APOBEC3C	APOBEC3C
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2015-08-13	2015-08-13
Project	ENCODE3	ENCODE3
Note
ID	778	779

Library-Prep
Sequencing

Library-Prep Information

	BGHLV22-3	BGHLV22-4
Sample #
Sample Name	APOBEC3C-BGHLV22-3	APOBEC3C-BGHLV22-4
Sample_Name_Alias	APOBE-BGHLV22-3_17748	APOBE-BGHLV22-4_17749
Index Well Position	S03	S04
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2015-06-05	2015-06-05
Lib_ID	Lib-150605	Lib-150605
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV20-22-23/set1/C6.png	DNA_Library_LV20-22-23/set1/D6.png
RIN	9.9	9.9
libSample_RNA_Well	RNA_Library_LV20-22-24/set1/A12.png	RNA_Library_LV19-21-24/set2/A4.png
SampleQC_method
SampleQC_date
Sample_ID	BGHLV22-3	BGHLV22-4
RBP	APOBEC3C	APOBEC3C
Batch_ID	BGHLV22	BGHLV22
WB_result	59.000	68.100
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2464	2465

Sequencing Information

	BGHLV22-3	BGHLV22-4
Sample_ID	BGHLV22-3	BGHLV22-4
Sample Name	APOBE-BGHLV22-3_17748	APOBE-BGHLV22-4_17749
Pool ID	Pool-150705	Pool-150705
LocalServer_folder	set22	set22
total_reads	43,340,000	51,970,000
total_aligned_reads	40,301,716	47,733,936
unique_aligned_reads	38,190,234	44,903,092
percent_uniqueAligned	0.88118	0.86402
correlation_replicates	0.992305	0.992305
spikein_reads	239,906	304,110
percent_spikeins	0.00554	0.00585
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1198	1199

Data Submission Information

	BGHLV22-3	BGHLV22-3
ENCODE_alias	brenton-graveley:APOBE-BGHLV22	brenton-graveley:APOBEC3C-BGHLV22-HepG2
ENCODE_accession	ENCSR012DAF	ENCSR153LWS
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV22-3	BGHLV22-3
Sample Name	APOBE-BGHLV22-3_17748	APOBE-BGHLV22-3_17748
Selected	Yes	Yes
Status	Released	Released
Status_Date	2015-08-11	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2921	6591

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
APOBE-BGHLV22-3_17748_TTAGGC_L007_R1_001.fastq.gz	ENCODE_DATA/set22/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1198	HiSeq2000	100	paired-ended	1				non-target-BGHLV22-1_17746_ATCACG_L006_R1_001.fastq.gz,non-target-BGHLV22-2_17747_CGATGT_L006_R1_001.fastq.gz	ENCODE3	16272
APOBE-BGHLV22-3_17748_TTAGGC_L007_R2_001.fastq.gz	ENCODE_DATA/set22/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1198	HiSeq2000	100	paired-ended	2				non-target-BGHLV22-1_17746_ATCACG_L006_R2_001.fastq.gz,non-target-BGHLV22-2_17747_CGATGT_L006_R2_001.fastq.gz	ENCODE3	16312
APOBE-BGHLV22-3_17748_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set22/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1198					GRCh38	V40	APOBE-BGHLV22-3_17748_TTAGGC_L007_R1_001.fastq.gz,APOBE-BGHLV22-3_17748_TTAGGC_L007_R2_001.fastq.gz		ENCORE2	16410
APOBE-BGHLV22-3_17748_Signal.Unique.strand+.bw	ENCODE_DATA/set22/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1198					GRCh38	V40	APOBE-BGHLV22-3_17748/Aligned.sortedByCoord.out.bam		ENCORE2	16450
APOBE-BGHLV22-3_17748_Signal.Unique.strand-.bw	ENCODE_DATA/set22/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1198					GRCh38	V40	APOBE-BGHLV22-3_17748/Aligned.sortedByCoord.out.bam		ENCORE2	16490
APOBE-BGHLV22-3_17748_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set22/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1198					GRCh38	V40	APOBE-BGHLV22-3_17748/Aligned.sortedByCoord.out.bam		ENCORE2	16530
APOBE-BGHLV22-3_17748_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set22/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1198					GRCh38	V40	APOBE-BGHLV22-3_17748/Aligned.sortedByCoord.out.bam		ENCORE2	16570
APOBE-BGHLV22-3_17748_quant.sf	ENCODE_DATA/set22/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1198					GRCh38	V40	APOBE-BGHLV22-3_17748_TTAGGC_L007_R1_001.fastq.gz,APOBE-BGHLV22-3_17748_TTAGGC_L007_R2_001.fastq.gz		ENCORE2	16610
APOBE-BGHLV22-4_17749_TGACCA_L007_R1_001.fastq.gz	ENCODE_DATA/set22/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1199	HiSeq2000	100	paired-ended	1				non-target-BGHLV22-1_17746_ATCACG_L006_R1_001.fastq.gz,non-target-BGHLV22-2_17747_CGATGT_L006_R1_001.fastq.gz	ENCODE3	16273
APOBE-BGHLV22-4_17749_TGACCA_L007_R2_001.fastq.gz	ENCODE_DATA/set22/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1199	HiSeq2000	100	paired-ended	2				non-target-BGHLV22-1_17746_ATCACG_L006_R2_001.fastq.gz,non-target-BGHLV22-2_17747_CGATGT_L006_R2_001.fastq.gz	ENCODE3	16313
APOBE-BGHLV22-4_17749_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set22/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1199					GRCh38	V40	APOBE-BGHLV22-4_17749_TGACCA_L007_R1_001.fastq.gz,APOBE-BGHLV22-4_17749_TGACCA_L007_R2_001.fastq.gz		ENCORE2	16411
APOBE-BGHLV22-4_17749_Signal.Unique.strand+.bw	ENCODE_DATA/set22/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1199					GRCh38	V40	APOBE-BGHLV22-4_17749/Aligned.sortedByCoord.out.bam		ENCORE2	16451
APOBE-BGHLV22-4_17749_Signal.Unique.strand-.bw	ENCODE_DATA/set22/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1199					GRCh38	V40	APOBE-BGHLV22-4_17749/Aligned.sortedByCoord.out.bam		ENCORE2	16491
APOBE-BGHLV22-4_17749_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set22/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1199					GRCh38	V40	APOBE-BGHLV22-4_17749/Aligned.sortedByCoord.out.bam		ENCORE2	16531
APOBE-BGHLV22-4_17749_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set22/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1199					GRCh38	V40	APOBE-BGHLV22-4_17749/Aligned.sortedByCoord.out.bam		ENCORE2	16571
APOBE-BGHLV22-4_17749_quant.sf	ENCODE_DATA/set22/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1199					GRCh38	V40	APOBE-BGHLV22-4_17749_TGACCA_L007_R1_001.fastq.gz,APOBE-BGHLV22-4_17749_TGACCA_L007_R2_001.fastq.gz		ENCORE2	16611