ADAR RNA-Seq in HepG2

General Information


RBP	ADAR
Cell_Line	HepG2
Method	shRNA
Exp_Name	ADAR-BGHLV20-HepG2
ENCODE_series_ID	ENCSR553SDV
Batch_ID	BGHLV20
Pool ID	Pool-150705
Local_Set_Name	set20
ENCODE_KD_Exp_ID	ENCSR104OLN
ENCODE_CN_Exp_ID	ENCSR305XWT
Rep1	ADAR-BGHLV20-3_17708
Rep2	ADAR-BGHLV20-4_17709
CN1	non-target-BGHLV20-1_17706
CN2	non-target-BGHLV20-2_17707
Rep1_qPCR	81.1
Rep2_qPCR	76.7
Rep1_WB	77.0
Rep2_WB	68.8
Antibody Cat#	A303-883A
Antibody Lot#	A303-883A
Antibody DCC ID	ENCAB202TNA
Status	Released
Project	ENCODE3
ID	489

Experiment Information (Status: Released)

	BGHLV20-3	BGHLV20-4
idx	367	368
TRCN#_or_BGC#	TRCN0000050788	TRCN0000050788
shRNA_or_gRNA_sequence	GCCCACTGTTATCTTCACTTT	GCCCACTGTTATCTTCACTTT
PAM
Name	ADAR	ADAR
Sample_ID	BGHLV20-3	BGHLV20-4
transduction_Date	10/2/2014	10/2/2014
days
RBP_name	ADAR	ADAR
qPCR_result	81.1	76.7
Ave_qPCR	78.9
RT-qPCR_primer-F	CGAGAATCCCAAACAAGGAA
RT-qPCR_primer-R	CCACGTAGGCACAATGTCAC
protein_conc	4752	4055
WB_result	77.0	68.8
Ave_WB	72.9
WB_DONE_date	4/17/2015
MW	136kDa
IP	1MB	1MB
antibody_Cat#	A303-883A	A303-883A
Antibody DCC ID	ENCAB202TNA	ENCAB202TNA
submitted_to_DCC_date	5/4/2015
Rep1_TPM	15.2	0
Rep2_TPM	14.5	0
Action
Library_start_date	5/29/2015	5/29/2015
repeat_library
Note
ID	2432	2433

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
ADAR	Product_ID: A303-883A Lot_ID: 1 Source: Bethyl Labs Target Name: ADAR-human

Experiment Status

	BGHLV20-3	BGHLV20-4
Sample_ID	BGHLV20-3	BGHLV20-4
Sample Name	ADAR-BGHLV20-3_17708	ADAR-BGHLV20-4_17709
Sample Name	ADAR-BGHLV20-3_17708	ADAR-BGHLV20-4_17709
RBP	ADAR	ADAR
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2015-08-11	2015-08-11
Project	ENCODE3	ENCODE3
Note
ID	708	709

Library-Prep
Sequencing

Library-Prep Information

	BGHLV20-3	BGHLV20-4
Sample #
Sample Name	ADAR-BGHLV20-3	ADAR-BGHLV20-4
Sample_Name_Alias	ADAR-BGHLV20-3_17708	ADAR-BGHLV20-4_17709
Index Well Position	S03	S04
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2015-05-29	2015-05-29
Lib_ID	Lib-150529	Lib-150529
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV20-22-23/set1/C1.png	DNA_Library_LV20-22-23/set1/D1.png
RIN	9.8	9.9
libSample_RNA_Well	RNA_Library_LV20-22-24/set1/E7.png	RNA_Library_LV20-22-24/set1/F7.png
SampleQC_method
SampleQC_date
Sample_ID	BGHLV20-3	BGHLV20-4
RBP	ADAR	ADAR
Batch_ID	BGHLV20	BGHLV20
WB_result	77.000	68.800
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2394	2395

Sequencing Information

	BGHLV20-3	BGHLV20-4
Sample_ID	BGHLV20-3	BGHLV20-4
Sample Name	ADAR-BGHLV20-3_17708	ADAR-BGHLV20-4_17709
Pool ID	Pool-150705	Pool-150705
LocalServer_folder	set20	set20
total_reads	42,320,000	43,680,000
total_aligned_reads	37,934,318	38,486,598
unique_aligned_reads	35,716,330	36,197,374
percent_uniqueAligned	0.84396	0.82869
correlation_replicates	0.996108	0.996108
spikein_reads	178,134	177,154
percent_spikeins	0.00421	0.00406
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1162	1163

Data Submission Information

	BGHLV20-3	BGHLV20-3
ENCODE_alias	brenton-graveley:ADAR-BGHLV20	brenton-graveley:ADAR-BGHLV20-HepG2
ENCODE_accession	ENCSR104OLN	ENCSR553SDV
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV20-3	BGHLV20-3
Sample Name	ADAR-BGHLV20-3_17708	ADAR-BGHLV20-3_17708
Selected	Yes	Yes
Status	Released	Released
Status_Date	2015-08-11	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2903	6579

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
ADAR-BGHLV20-3_17708_TTAGGC_L001_R1_001.fastq.gz	ENCODE_DATA/set20/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1162	HiSeq2000	100	paired-ended	1				non-target-BGHLV20-1_17706_ATCACG_L001_R1_001.fastq.gz,non-target-BGHLV20-2_17707_CGATGT_L001_R1_001.fastq.gz	ENCODE3	15584
ADAR-BGHLV20-3_17708_TTAGGC_L001_R2_001.fastq.gz	ENCODE_DATA/set20/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1162	HiSeq2000	100	paired-ended	2				non-target-BGHLV20-1_17706_ATCACG_L001_R2_001.fastq.gz,non-target-BGHLV20-2_17707_CGATGT_L001_R2_001.fastq.gz	ENCODE3	15626
ADAR-BGHLV20-3_17708_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set20/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1162					GRCh38	V40	ADAR-BGHLV20-3_17708_TTAGGC_L001_R1_001.fastq.gz,ADAR-BGHLV20-3_17708_TTAGGC_L001_R2_001.fastq.gz		ENCORE2	15668
ADAR-BGHLV20-3_17708_Signal.Unique.strand+.bw	ENCODE_DATA/set20/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1162					GRCh38	V40	ADAR-BGHLV20-3_17708/Aligned.sortedByCoord.out.bam		ENCORE2	15710
ADAR-BGHLV20-3_17708_Signal.Unique.strand-.bw	ENCODE_DATA/set20/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1162					GRCh38	V40	ADAR-BGHLV20-3_17708/Aligned.sortedByCoord.out.bam		ENCORE2	15752
ADAR-BGHLV20-3_17708_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set20/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1162					GRCh38	V40	ADAR-BGHLV20-3_17708/Aligned.sortedByCoord.out.bam		ENCORE2	15794
ADAR-BGHLV20-3_17708_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set20/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1162					GRCh38	V40	ADAR-BGHLV20-3_17708/Aligned.sortedByCoord.out.bam		ENCORE2	15836
ADAR-BGHLV20-3_17708_quant.sf	ENCODE_DATA/set20/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1162					GRCh38	V40	ADAR-BGHLV20-3_17708_TTAGGC_L001_R1_001.fastq.gz,ADAR-BGHLV20-3_17708_TTAGGC_L001_R2_001.fastq.gz		ENCORE2	15878
ADAR-BGHLV20-4_17709_TGACCA_L001_R1_001.fastq.gz	ENCODE_DATA/set20/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1163	HiSeq2000	100	paired-ended	1				non-target-BGHLV20-1_17706_ATCACG_L001_R1_001.fastq.gz,non-target-BGHLV20-2_17707_CGATGT_L001_R1_001.fastq.gz	ENCODE3	15585
ADAR-BGHLV20-4_17709_TGACCA_L001_R2_001.fastq.gz	ENCODE_DATA/set20/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1163	HiSeq2000	100	paired-ended	2				non-target-BGHLV20-1_17706_ATCACG_L001_R2_001.fastq.gz,non-target-BGHLV20-2_17707_CGATGT_L001_R2_001.fastq.gz	ENCODE3	15627
ADAR-BGHLV20-4_17709_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set20/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1163					GRCh38	V40	ADAR-BGHLV20-4_17709_TGACCA_L001_R1_001.fastq.gz,ADAR-BGHLV20-4_17709_TGACCA_L001_R2_001.fastq.gz		ENCORE2	15669
ADAR-BGHLV20-4_17709_Signal.Unique.strand+.bw	ENCODE_DATA/set20/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1163					GRCh38	V40	ADAR-BGHLV20-4_17709/Aligned.sortedByCoord.out.bam		ENCORE2	15711
ADAR-BGHLV20-4_17709_Signal.Unique.strand-.bw	ENCODE_DATA/set20/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1163					GRCh38	V40	ADAR-BGHLV20-4_17709/Aligned.sortedByCoord.out.bam		ENCORE2	15753
ADAR-BGHLV20-4_17709_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set20/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1163					GRCh38	V40	ADAR-BGHLV20-4_17709/Aligned.sortedByCoord.out.bam		ENCORE2	15795
ADAR-BGHLV20-4_17709_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set20/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1163					GRCh38	V40	ADAR-BGHLV20-4_17709/Aligned.sortedByCoord.out.bam		ENCORE2	15837
ADAR-BGHLV20-4_17709_quant.sf	ENCODE_DATA/set20/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1163					GRCh38	V40	ADAR-BGHLV20-4_17709_TGACCA_L001_R1_001.fastq.gz,ADAR-BGHLV20-4_17709_TGACCA_L001_R2_001.fastq.gz		ENCORE2	15879