ADAR RNA-Seq in K562

General Information


RBP	ADAR
Cell_Line	K562
Method	shRNA
Exp_Name	ADAR-BGKLV24-K562
ENCODE_series_ID	ENCSR415ETS
Batch_ID	BGKLV24
Pool ID	Pool-150615
Local_Set_Name	set24
ENCODE_KD_Exp_ID	ENCSR164TLB
ENCODE_CN_Exp_ID	ENCSR667PLJ
Rep1	ADAR_BGKLV24_3_17596
Rep2	ADAR_BGKLV24_4_17597
CN1	non-target_BGKLV24_1_17594
CN2	non-target_BGKLV24_2_17595
Rep1_qPCR	99.5
Rep2_qPCR	99.3
Rep1_WB	81.0
Rep2_WB	71.7
Antibody Cat#	A303-883A
Antibody Lot#	A303-883A
Antibody DCC ID	ENCAB202TNA
Status	Released
Project	ENCODE3
ID	555

Experiment Information (Status: Released)

	BGKLV24-3	BGKLV24-3	BGKLV24-3	BGKLV24-4	BGKLV24-4	BGKLV24-4
idx	340	0	0	341	0	0
TRCN#_or_BGC#	TRCN0000050788	TRCN0000050788	TRCN0000050788	TRCN0000050788	TRCN0000050788	TRCN0000050788
shRNA_or_gRNA_sequence	GCCCACTGTTATCTTCACTTT	GCCCACTGTTATCTTCACTTT	GCCCACTGTTATCTTCACTTT	GCCCACTGTTATCTTCACTTT	GCCCACTGTTATCTTCACTTT	GCCCACTGTTATCTTCACTTT
PAM
Name	ADAR	ADAR	ADAR	ADAR	ADAR	ADAR
Sample_ID	BGKLV24-3	BGKLV24-3	BGKLV24-3	BGKLV24-4	BGKLV24-4	BGKLV24-4
transduction_Date	2/27/2015	2/27/2015	2/27/2015	2/27/2015	2/27/2015	2/27/2015
days
RBP_name	ADAR	ADAR	ADAR	ADAR	ADAR	ADAR
qPCR_result	99.5	99.5	99.5	99.3	99.3	99.3
Ave_qPCR	99.4	99.4	99.4
RT-qPCR_primer-F	CGAGAATCCCAAACAAGGAA	CGAGAATCCCAAACAAGGAA	CGAGAATCCCAAACAAGGAA
RT-qPCR_primer-R	CCACGTAGGCACAATGTCAC	CCACGTAGGCACAATGTCAC	CCACGTAGGCACAATGTCAC
protein_conc	3664	3664	3664	4351	4351	4351
WB_result	81.0	87.9	91.0	71.7	89.1	91.1
Ave_WB	76.3	88.5
WB_DONE_date	4/17/2015	2/22/2022	5/2/2024
MW	136KD	136KD	136kd
IP	1MB			1MB
antibody_Cat#	A303-883A	A303-883A	81284S	A303-883A	LOT# 3	LOT# 1
Antibody DCC ID	ENCAB202TNA	ENCAB047LUR		ENCAB202TNA	8/4/22
submitted_to_DCC_date	5/4/2015	8/16/2022
Rep1_TPM	23.3294016	0	0	0	0	0
Rep2_TPM	22.6178686	0	0	0	0	0
Action
Library_start_date	5/22/2015			5/22/2015
repeat_library
Note
ID	381	383	385	382	384	386

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
ADAR	Product_ID: 81284S Lot_ID: 1 Source: Cell Signaling Technology Target Name: ADAR-human

Experiment Status

	BGKLV24-3	BGKLV24-4
Sample_ID	BGKLV24-3	BGKLV24-4
Sample Name	ADAR_BGKLV24_3_17596	ADAR_BGKLV24_4_17597
Sample Name	ADAR_BGKLV24_3_17596	ADAR_BGKLV24_4_17597
RBP	ADAR	ADAR
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2015-08-14	2015-08-14
Project	ENCODE3	ENCODE3
Note
ID	848	849

Library-Prep
Sequencing

Library-Prep Information

	BGKLV24-3	BGKLV24-4
Sample #
Sample Name	ADAR-BGKLV24-3	ADAR-BGKLV24-4
Sample_Name_Alias	ADAR_BGKLV24_3_17596	ADAR_BGKLV24_4_17597
Index Well Position	S20	S21
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2015-05-22	2015-05-22
Lib_ID	Lib-150522	Lib-150522
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV21-24/set1/D1.png	DNA_Library_LV21-24/set1/E1.png
RIN	9.8	9.5
libSample_RNA_Well	RNA_Library_LV19-21-24/set1/G12.png	RNA_Library_LV19-21-24/set1/H12.png
SampleQC_method
SampleQC_date
Sample_ID	BGKLV24-3	BGKLV24-4
RBP	ADAR	ADAR
Batch_ID	BGKLV24	BGKLV24
WB_result	81.000	71.700
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2536	2537

Sequencing Information

	BGKLV24-3	BGKLV24-4
Sample_ID	BGKLV24-3	BGKLV24-4
Sample Name	ADAR_BGKLV24_3_17596	ADAR_BGKLV24_4_17597
Pool ID	Pool-150615	Pool-150615
LocalServer_folder	set24	set24
total_reads	37,940,000	34,550,000
total_aligned_reads	35,326,292	32,127,784
unique_aligned_reads	32,285,172	29,372,406
percent_uniqueAligned	0.85095	0.85014
correlation_replicates	0.895805	0.895805
spikein_reads	125,354	170,372
percent_spikeins	0.00330	0.00493
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1070	1071

Data Submission Information

	BGKLV24-3	BGKLV24-3
ENCODE_alias	brenton-graveley:ADAR_BGKLV24	brenton-graveley:ADAR-BGKLV24-K562
ENCODE_accession	ENCSR164TLB	ENCSR415ETS
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKLV24-3	BGKLV24-3
Sample Name	ADAR_BGKLV24_3_17596	ADAR_BGKLV24_3_17596
Selected	Yes	Yes
Status	Released	Released
Status_Date	2015-08-13	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2975	6580

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_BGKLV24_3_17596_GTGGCC_L005_R1_001.fastq.gz	ENCODE_DATA/set24/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1070	HiSeq2000	100	paired-ended	1				non-target_BGKLV24_1_17594_GTCCGC_L005_R1_001.fastq.gz,non-target_BGKLV24_2_17595_GTGAAA_L005_R1_001.fastq.gz	ENCODE3	17182
ADAR_BGKLV24_3_17596_GTGGCC_L005_R2_001.fastq.gz	ENCODE_DATA/set24/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1070	HiSeq2000	100	paired-ended	2				non-target_BGKLV24_1_17594_GTCCGC_L005_R2_001.fastq.gz,non-target_BGKLV24_2_17595_GTGAAA_L005_R2_001.fastq.gz	ENCODE3	17218
ADAR_BGKLV24_3_17596_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set24/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1070					GRCh38	V40	ADAR_BGKLV24_3_17596_GTGGCC_L005_R1_001.fastq.gz,ADAR_BGKLV24_3_17596_GTGGCC_L005_R2_001.fastq.gz		ENCORE2	17254
ADAR_BGKLV24_3_17596_Signal.Unique.strand+.bw	ENCODE_DATA/set24/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1070					GRCh38	V40	ADAR_BGKLV24_3_17596/Aligned.sortedByCoord.out.bam		ENCORE2	17290
ADAR_BGKLV24_3_17596_Signal.Unique.strand-.bw	ENCODE_DATA/set24/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1070					GRCh38	V40	ADAR_BGKLV24_3_17596/Aligned.sortedByCoord.out.bam		ENCORE2	17326
ADAR_BGKLV24_3_17596_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set24/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1070					GRCh38	V40	ADAR_BGKLV24_3_17596/Aligned.sortedByCoord.out.bam		ENCORE2	17362
ADAR_BGKLV24_3_17596_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set24/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1070					GRCh38	V40	ADAR_BGKLV24_3_17596/Aligned.sortedByCoord.out.bam		ENCORE2	17398
ADAR_BGKLV24_3_17596_quant.sf	ENCODE_DATA/set24/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1070					GRCh38	V40	ADAR_BGKLV24_3_17596_GTGGCC_L005_R1_001.fastq.gz,ADAR_BGKLV24_3_17596_GTGGCC_L005_R2_001.fastq.gz		ENCORE2	17434
ADAR_BGKLV24_4_17597_GTTTCG_L005_R1_001.fastq.gz	ENCODE_DATA/set24/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1071	HiSeq2000	100	paired-ended	1				non-target_BGKLV24_1_17594_GTCCGC_L005_R1_001.fastq.gz,non-target_BGKLV24_2_17595_GTGAAA_L005_R1_001.fastq.gz	ENCODE3	17183
ADAR_BGKLV24_4_17597_GTTTCG_L005_R2_001.fastq.gz	ENCODE_DATA/set24/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1071	HiSeq2000	100	paired-ended	2				non-target_BGKLV24_1_17594_GTCCGC_L005_R2_001.fastq.gz,non-target_BGKLV24_2_17595_GTGAAA_L005_R2_001.fastq.gz	ENCODE3	17219
ADAR_BGKLV24_4_17597_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set24/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1071					GRCh38	V40	ADAR_BGKLV24_4_17597_GTTTCG_L005_R1_001.fastq.gz,ADAR_BGKLV24_4_17597_GTTTCG_L005_R2_001.fastq.gz		ENCORE2	17255
ADAR_BGKLV24_4_17597_Signal.Unique.strand+.bw	ENCODE_DATA/set24/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1071					GRCh38	V40	ADAR_BGKLV24_4_17597/Aligned.sortedByCoord.out.bam		ENCORE2	17291
ADAR_BGKLV24_4_17597_Signal.Unique.strand-.bw	ENCODE_DATA/set24/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1071					GRCh38	V40	ADAR_BGKLV24_4_17597/Aligned.sortedByCoord.out.bam		ENCORE2	17327
ADAR_BGKLV24_4_17597_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set24/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1071					GRCh38	V40	ADAR_BGKLV24_4_17597/Aligned.sortedByCoord.out.bam		ENCORE2	17363
ADAR_BGKLV24_4_17597_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set24/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1071					GRCh38	V40	ADAR_BGKLV24_4_17597/Aligned.sortedByCoord.out.bam		ENCORE2	17399
ADAR_BGKLV24_4_17597_quant.sf	ENCODE_DATA/set24/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1071					GRCh38	V40	ADAR_BGKLV24_4_17597_GTTTCG_L005_R1_001.fastq.gz,ADAR_BGKLV24_4_17597_GTTTCG_L005_R2_001.fastq.gz		ENCORE2	17435