DNAJC21 RNA-Seq in K562

General Information


RBP	DNAJC21
Cell_Line	K562
Method	shRNA
Exp_Name	DNAJC21-BGKLV24-K562
ENCODE_series_ID	ENCSR569UZZ
Batch_ID	BGKLV24
Pool ID	Pool-150615
Local_Set_Name	set24
ENCODE_KD_Exp_ID	ENCSR079LMZ
ENCODE_CN_Exp_ID	ENCSR667PLJ
Rep1	DNAJC21_BGKLV24_19_17611
Rep2	DNAJC21_BGKLV24_20_17612
CN1	non-target_BGKLV24_1_17594
CN2	non-target_BGKLV24_2_17595
Rep1_qPCR	69.0
Rep2_qPCR	60.2
Rep1_WB	88.8
Rep2_WB	88.8
Antibody Cat#	A301-884A
Antibody Lot#	A301-884A
Antibody DCC ID	ENCAB534WDJ
Status	Released
Project	ENCODE3
ID	561

Experiment Information (Status: Released)

	BGKLV24-19	BGKLV24-20
idx	356	357
TRCN#_or_BGC#	TRCN0000144746	TRCN0000144746
shRNA_or_gRNA_sequence	GACAAATCGTTCAAGACAGAA	GACAAATCGTTCAAGACAGAA
PAM
Name	DNAJC21_46	DNAJC21_46
Sample_ID	BGKLV24-19	BGKLV24-20
transduction_Date	2/27/2015	2/27/2015
days
RBP_name	DNAJC21	DNAJC21
qPCR_result	69.0	60.2
Ave_qPCR	64.6
RT-qPCR_primer-F	acctgctgaaccacaaacaa
RT-qPCR_primer-R	tgtggcctttagatggtcaa
protein_conc	3734	3581
WB_result	88.8	88.8
Ave_WB	88.8
WB_DONE_date	4/17/2015
MW
IP	1	1
antibody_Cat#	A301-884A	A301-884A
Antibody DCC ID	ENCAB534WDJ	ENCAB534WDJ
submitted_to_DCC_date	5/4/2015
Rep1_TPM	39.2990824	0
Rep2_TPM	32.9499153	0
Action
Library_start_date	5/22/2015	5/22/2015
repeat_library
Note
ID	405	406

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
DNAJC21	Product_ID: A301-884A Lot_ID: 1 Source: Bethyl Labs Target Name: DNAJC21-human

Experiment Status

	BGKLV24-19	BGKLV24-20
Sample_ID	BGKLV24-19	BGKLV24-20
Sample Name	DNAJC21_BGKLV24_19_17611	DNAJC21_BGKLV24_20_17612
Sample Name	DNAJC21_BGKLV24_19_17611	DNAJC21_BGKLV24_20_17612
RBP	DNAJC21	DNAJC21
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2015-08-14	2015-08-14
Project	ENCODE3	ENCODE3
Note
ID	860	861

Library-Prep
Sequencing

Library-Prep Information

	BGKLV24-19	BGKLV24-20
Sample #
Sample Name	DNAJC21-BGKLV24-19	DNAJC21-BGKLV24-20
Sample_Name_Alias	DNAJC21_BGKLV24_19_17611	DNAJC21_BGKLV24_20_17612
Index Well Position	S09	S10
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/B3.png	DNA_Library_LV21-24/set1/C3.png
RIN	9.8	9.5
libSample_RNA_Well	RNA_Library_LV20-22-24/set1/G2.png	RNA_Library_LV20-22-24/set1/H2.png
SampleQC_method
SampleQC_date
Sample_ID	BGKLV24-19	BGKLV24-20
RBP	DNAJC21	DNAJC21
Batch_ID	BGKLV24	BGKLV24
WB_result	88.800	88.800
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2548	2549

Sequencing Information

	BGKLV24-19	BGKLV24-20
Sample_ID	BGKLV24-19	BGKLV24-20
Sample Name	DNAJC21_BGKLV24_19_17611	DNAJC21_BGKLV24_20_17612
Pool ID	Pool-150615	Pool-150615
LocalServer_folder	set24	set24
total_reads	37,080,000	37,310,000
total_aligned_reads	34,969,790	35,467,736
unique_aligned_reads	32,162,296	32,678,212
percent_uniqueAligned	0.86738	0.87586
correlation_replicates	0.999314	0.999314
spikein_reads	162,124	169,808
percent_spikeins	0.00437	0.00455
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1082	1083

Data Submission Information

	BGKLV24-19	BGKLV24-19
ENCODE_alias	brenton-graveley:DNAJC21_BGKLV24	brenton-graveley:DNAJC21-BGKLV24-K562
ENCODE_accession	ENCSR079LMZ	ENCSR569UZZ
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKLV24-19	BGKLV24-19
Sample Name	DNAJC21_BGKLV24_19_17611	DNAJC21_BGKLV24_19_17611
Selected	Yes	Yes
Status	Released	Released
Status_Date	2015-08-13	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2981	6671

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
DNAJC21_BGKLV24_19_17611_GATCAG_L007_R1_001.fastq.gz	ENCODE_DATA/set24/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1082	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	17194
DNAJC21_BGKLV24_19_17611_GATCAG_L007_R2_001.fastq.gz	ENCODE_DATA/set24/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1082	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	17230
DNAJC21_BGKLV24_19_17611_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set24/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1082					GRCh38	V40	DNAJC21_BGKLV24_19_17611_GATCAG_L007_R1_001.fastq.gz,DNAJC21_BGKLV24_19_17611_GATCAG_L007_R2_001.fastq.gz		ENCORE2	17266
DNAJC21_BGKLV24_19_17611_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	1082					GRCh38	V40	DNAJC21_BGKLV24_19_17611/Aligned.sortedByCoord.out.bam		ENCORE2	17302
DNAJC21_BGKLV24_19_17611_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	1082					GRCh38	V40	DNAJC21_BGKLV24_19_17611/Aligned.sortedByCoord.out.bam		ENCORE2	17338
DNAJC21_BGKLV24_19_17611_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	1082					GRCh38	V40	DNAJC21_BGKLV24_19_17611/Aligned.sortedByCoord.out.bam		ENCORE2	17374
DNAJC21_BGKLV24_19_17611_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	1082					GRCh38	V40	DNAJC21_BGKLV24_19_17611/Aligned.sortedByCoord.out.bam		ENCORE2	17410
DNAJC21_BGKLV24_19_17611_quant.sf	ENCODE_DATA/set24/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1082					GRCh38	V40	DNAJC21_BGKLV24_19_17611_GATCAG_L007_R1_001.fastq.gz,DNAJC21_BGKLV24_19_17611_GATCAG_L007_R2_001.fastq.gz		ENCORE2	17446
DNAJC21_BGKLV24_20_17612_TAGCTT_L007_R1_001.fastq.gz	ENCODE_DATA/set24/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1083	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	17195
DNAJC21_BGKLV24_20_17612_TAGCTT_L007_R2_001.fastq.gz	ENCODE_DATA/set24/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1083	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	17231
DNAJC21_BGKLV24_20_17612_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set24/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1083					GRCh38	V40	DNAJC21_BGKLV24_20_17612_TAGCTT_L007_R1_001.fastq.gz,DNAJC21_BGKLV24_20_17612_TAGCTT_L007_R2_001.fastq.gz		ENCORE2	17267
DNAJC21_BGKLV24_20_17612_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	1083					GRCh38	V40	DNAJC21_BGKLV24_20_17612/Aligned.sortedByCoord.out.bam		ENCORE2	17303
DNAJC21_BGKLV24_20_17612_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	1083					GRCh38	V40	DNAJC21_BGKLV24_20_17612/Aligned.sortedByCoord.out.bam		ENCORE2	17339
DNAJC21_BGKLV24_20_17612_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	1083					GRCh38	V40	DNAJC21_BGKLV24_20_17612/Aligned.sortedByCoord.out.bam		ENCORE2	17375
DNAJC21_BGKLV24_20_17612_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	1083					GRCh38	V40	DNAJC21_BGKLV24_20_17612/Aligned.sortedByCoord.out.bam		ENCORE2	17411
DNAJC21_BGKLV24_20_17612_quant.sf	ENCODE_DATA/set24/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1083					GRCh38	V40	DNAJC21_BGKLV24_20_17612_TAGCTT_L007_R1_001.fastq.gz,DNAJC21_BGKLV24_20_17612_TAGCTT_L007_R2_001.fastq.gz		ENCORE2	17447