DNAJC2 RNA-Seq in K562

General Information


RBP	DNAJC2
Cell_Line	K562
Method	shRNA
Exp_Name	DNAJC2-BGKLV24-K562
ENCODE_series_ID	ENCSR756GCR
Batch_ID	BGKLV24
Pool ID	Pool-150615
Local_Set_Name	set24
ENCODE_KD_Exp_ID	ENCSR577OVP
ENCODE_CN_Exp_ID	ENCSR667PLJ
Rep1	DNAJC2_BGKLV24_17_17608
Rep2	DNAJC2_BGKLV24_18_17609
CN1	non-target_BGKLV24_1_17594
CN2	non-target_BGKLV24_2_17595
Rep1_qPCR	43.0
Rep2_qPCR	52.0
Rep1_WB	71.4
Rep2_WB	59.8
Antibody Cat#	A303-721A
Antibody Lot#	A303-721A
Antibody DCC ID	ENCAB425OIO
Status	Released
Project	ENCODE3
ID	562

Experiment Information (Status: Released)

	BGKLV24-17	BGKLV24-18
idx	354	355
TRCN#_or_BGC#	TRCN0000254057	TRCN0000254057
shRNA_or_gRNA_sequence	TACTTCACTTGCATAACTAAA	TACTTCACTTGCATAACTAAA
PAM
Name	DNAJC2_57	DNAJC2_57
Sample_ID	BGKLV24-17	BGKLV24-18
transduction_Date	2/27/2015	2/27/2015
days
RBP_name	DNAJC2	DNAJC2
qPCR_result	43.0	52.0
Ave_qPCR	47.5
RT-qPCR_primer-F	tccttctaaaagtgaagcaaagg
RT-qPCR_primer-R	gaccatctggaattcctttca
protein_conc	3274	3441
WB_result	71.4	59.8
Ave_WB	65.6
WB_DONE_date	4/6/2015
MW
IP	1	1
antibody_Cat#	A303-721A	A303-721A
Antibody DCC ID	ENCAB425OIO	ENCAB425OIO
submitted_to_DCC_date	5/4/2015
Rep1_TPM	219.191764	0
Rep2_TPM	116.976054	0
Action
Library_start_date	5/22/2015	5/22/2015
repeat_library
Note
ID	403	404

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
DNAJC2	Product_ID: A303-721A Lot_ID: 1 Source: Bethyl Labs Target Name: DNAJC2-human

Experiment Status

	BGKLV24-17	BGKLV24-18
Sample_ID	BGKLV24-17	BGKLV24-18
Sample Name	DNAJC2_BGKLV24_17_17608	DNAJC2_BGKLV24_18_17609
Sample Name	DNAJC2_BGKLV24_17_17608	DNAJC2_BGKLV24_18_17609
RBP	DNAJC2	DNAJC2
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2015-08-14	2015-08-14
Project	ENCODE3	ENCODE3
Note
ID	862	863

Library-Prep
Sequencing

Library-Prep Information

	BGKLV24-17	BGKLV24-18
Sample #
Sample Name	DNAJC2-BGKLV24-17	DNAJC2-BGKLV24-18
Sample_Name_Alias	DNAJC2_BGKLV24_17_17608	DNAJC2_BGKLV24_18_17609
Index Well Position	S07	S08
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/H2.png	DNA_Library_LV21-24/set1/A3.png
RIN	9.4	9.7
libSample_RNA_Well	RNA_Library_LV20-22-24/set1/E2.png	RNA_Library_LV20-22-24/set1/F2.png
SampleQC_method
SampleQC_date
Sample_ID	BGKLV24-17	BGKLV24-18
RBP	DNAJC2	DNAJC2
Batch_ID	BGKLV24	BGKLV24
WB_result	71.400	59.800
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2550	2551

Sequencing Information

	BGKLV24-17	BGKLV24-18
Sample_ID	BGKLV24-17	BGKLV24-18
Sample Name	DNAJC2_BGKLV24_17_17608	DNAJC2_BGKLV24_18_17609
Pool ID	Pool-150615	Pool-150615
LocalServer_folder	set24	set24
total_reads	42,170,000	44,360,000
total_aligned_reads	39,516,050	41,389,250
unique_aligned_reads	36,264,946	37,792,468
percent_uniqueAligned	0.85997	0.85195
correlation_replicates	0.972380	0.972380
spikein_reads	228,424	180,378
percent_spikeins	0.00542	0.00407
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1084	1085

Data Submission Information

	BGKLV24-17	BGKLV24-17
ENCODE_alias	brenton-graveley:DNAJC2_BGKLV24	brenton-graveley:DNAJC2-BGKLV24-K562
ENCODE_accession	ENCSR577OVP	ENCSR756GCR
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKLV24-17	BGKLV24-17
Sample Name	DNAJC2_BGKLV24_17_17608	DNAJC2_BGKLV24_17_17608
Selected	Yes	Yes
Status	Released	Released
Status_Date	2015-08-13	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2982	6669

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
DNAJC2_BGKLV24_17_17608_CAGATC_L006_R1_001.fastq.gz	ENCODE_DATA/set24/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1084	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	17196
DNAJC2_BGKLV24_17_17608_CAGATC_L006_R2_001.fastq.gz	ENCODE_DATA/set24/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1084	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	17232
DNAJC2_BGKLV24_17_17608_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set24/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1084					GRCh38	V40	DNAJC2_BGKLV24_17_17608_CAGATC_L006_R1_001.fastq.gz,DNAJC2_BGKLV24_17_17608_CAGATC_L006_R2_001.fastq.gz		ENCORE2	17268
DNAJC2_BGKLV24_17_17608_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	1084					GRCh38	V40	DNAJC2_BGKLV24_17_17608/Aligned.sortedByCoord.out.bam		ENCORE2	17304
DNAJC2_BGKLV24_17_17608_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	1084					GRCh38	V40	DNAJC2_BGKLV24_17_17608/Aligned.sortedByCoord.out.bam		ENCORE2	17340
DNAJC2_BGKLV24_17_17608_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	1084					GRCh38	V40	DNAJC2_BGKLV24_17_17608/Aligned.sortedByCoord.out.bam		ENCORE2	17376
DNAJC2_BGKLV24_17_17608_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	1084					GRCh38	V40	DNAJC2_BGKLV24_17_17608/Aligned.sortedByCoord.out.bam		ENCORE2	17412
DNAJC2_BGKLV24_17_17608_quant.sf	ENCODE_DATA/set24/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1084					GRCh38	V40	DNAJC2_BGKLV24_17_17608_CAGATC_L006_R1_001.fastq.gz,DNAJC2_BGKLV24_17_17608_CAGATC_L006_R2_001.fastq.gz		ENCORE2	17448
DNAJC2_BGKLV24_18_17609_ACTTGA_L006_R1_001.fastq.gz	ENCODE_DATA/set24/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1085	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	17197
DNAJC2_BGKLV24_18_17609_ACTTGA_L006_R2_001.fastq.gz	ENCODE_DATA/set24/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1085	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	17233
DNAJC2_BGKLV24_18_17609_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set24/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1085					GRCh38	V40	DNAJC2_BGKLV24_18_17609_ACTTGA_L006_R1_001.fastq.gz,DNAJC2_BGKLV24_18_17609_ACTTGA_L006_R2_001.fastq.gz		ENCORE2	17269
DNAJC2_BGKLV24_18_17609_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	1085					GRCh38	V40	DNAJC2_BGKLV24_18_17609/Aligned.sortedByCoord.out.bam		ENCORE2	17305
DNAJC2_BGKLV24_18_17609_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	1085					GRCh38	V40	DNAJC2_BGKLV24_18_17609/Aligned.sortedByCoord.out.bam		ENCORE2	17341
DNAJC2_BGKLV24_18_17609_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	1085					GRCh38	V40	DNAJC2_BGKLV24_18_17609/Aligned.sortedByCoord.out.bam		ENCORE2	17377
DNAJC2_BGKLV24_18_17609_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	1085					GRCh38	V40	DNAJC2_BGKLV24_18_17609/Aligned.sortedByCoord.out.bam		ENCORE2	17413
DNAJC2_BGKLV24_18_17609_quant.sf	ENCODE_DATA/set24/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1085					GRCh38	V40	DNAJC2_BGKLV24_18_17609_ACTTGA_L006_R1_001.fastq.gz,DNAJC2_BGKLV24_18_17609_ACTTGA_L006_R2_001.fastq.gz		ENCORE2	17449