DNAJC21 RNA-Seq in HepG2

General Information


RBP	DNAJC21
Cell_Line	HepG2
Method	shRNA
Exp_Name	DNAJC21-BGHLV20-HepG2
ENCODE_series_ID	ENCSR855FGM
Batch_ID	BGHLV20
Pool ID	Pool-150705
Local_Set_Name	set20
ENCODE_KD_Exp_ID	ENCSR385KOY
ENCODE_CN_Exp_ID	ENCSR305XWT
Rep1	DNAJC21-46-BGHLV20-23_17718
Rep2	DNAJC21-46-BGHLV20-24_17719
CN1	non-target-BGHLV20-1_17706
CN2	non-target-BGHLV20-2_17707
Rep1_qPCR	79.8
Rep2_qPCR	71.1
Rep1_WB	96.1
Rep2_WB	96.9
Antibody Cat#	A301-884A
Antibody Lot#	A301-884A
Antibody DCC ID	ENCAB534WDJ
Status	Released
Project	ENCODE3
ID	493

Experiment Information (Status: Released)

	BGHLV20-23	BGHLV20-24
idx	387	388
TRCN#_or_BGC#	TRCN0000144746	TRCN0000144746
shRNA_or_gRNA_sequence	GACAAATCGTTCAAGACAGAA	GACAAATCGTTCAAGACAGAA
PAM
Name	DNAJC21_46	DNAJC21_46
Sample_ID	BGHLV20-23	BGHLV20-24
transduction_Date	10/2/2014	10/2/2014
days
RBP_name	DNAJC21	DNAJC21
qPCR_result	79.8	71.1
Ave_qPCR	75.5
RT-qPCR_primer-F	acctgctgaaccacaaacaa
RT-qPCR_primer-R	tgtggcctttagatggtcaa
protein_conc	6193	6299
WB_result	96.1	96.9
Ave_WB	96.5
WB_DONE_date	4/17/2015
MW	62kDa
IP	1	1
antibody_Cat#	A301-884A	A301-884A
Antibody DCC ID	ENCAB534WDJ	ENCAB534WDJ
submitted_to_DCC_date	5/4/2015
Rep1_TPM	16.5	0
Rep2_TPM	15.9	0
Action
Library_start_date	5/29/2015	5/29/2015
repeat_library
Note
ID	2452	2453

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

	BGHLV20-23	BGHLV20-24
Sample_ID	BGHLV20-23	BGHLV20-24
Sample Name	DNAJC21-46-BGHLV20-23_17718	DNAJC21-46-BGHLV20-24_17719
Sample Name	DNAJC21-46-BGHLV20-23_17718	DNAJC21-46-BGHLV20-24_17719
RBP	DNAJC21	DNAJC21
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2015-08-11	2015-08-11
Project	ENCODE3	ENCODE3
Note
ID	716	717

Library-Prep
Sequencing

Library-Prep Information

	BGHLV20-23	BGHLV20-24
Sample #
Sample Name	DNAJC21-BGHLV20-23	DNAJC21-BGHLV20-24
Sample_Name_Alias	DNAJC21-46-BGHLV20-23_17718	DNAJC21-46-BGHLV20-24_17719
Index Well Position	S13	S14
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/E2.png	DNA_Library_LV20-22-23/set1/F2.png
RIN	9.9	9.8
libSample_RNA_Well	RNA_Library_LV20-22-24/set1/G8.png	RNA_Library_LV20-22-24/set1/H8.png
SampleQC_method
SampleQC_date
Sample_ID	BGHLV20-23	BGHLV20-24
RBP	DNAJC21	DNAJC21
Batch_ID	BGHLV20	BGHLV20
WB_result	96.100	96.900
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2402	2403

Sequencing Information

	BGHLV20-23	BGHLV20-24
Sample_ID	BGHLV20-23	BGHLV20-24
Sample Name	DNAJC21-46-BGHLV20-23_17718	DNAJC21-46-BGHLV20-24_17719
Pool ID	Pool-150705	Pool-150705
LocalServer_folder	set20	set20
total_reads	42,140,000	44,360,000
total_aligned_reads	35,703,066	37,853,426
unique_aligned_reads	33,885,320	35,894,688
percent_uniqueAligned	0.80411	0.80917
correlation_replicates	0.998751	0.998751
spikein_reads	178,678	173,624
percent_spikeins	0.00424	0.00391
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1170	1171

Data Submission Information

	BGHLV20-23	BGHLV20-23
ENCODE_alias	brenton-graveley:DNAJC21-46-BGHLV20	brenton-graveley:DNAJC21-BGHLV20-HepG2
ENCODE_accession	ENCSR385KOY	ENCSR855FGM
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV20-23	BGHLV20-23
Sample Name	DNAJC21-46-BGHLV20-23_17718	DNAJC21-46-BGHLV20-23_17718
Selected	Yes	Yes
Status	Released	Released
Status_Date	2015-08-11	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2907	6670

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
DNAJC21-46-BGHLV20-23_17718_AGTCAA_L002_R1_001.fastq.gz	ENCODE_DATA/set20/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1170	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	15594
DNAJC21-46-BGHLV20-23_17718_AGTCAA_L002_R2_001.fastq.gz	ENCODE_DATA/set20/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1170	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	15636
DNAJC21-46-BGHLV20-23_17718_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set20/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1170					GRCh38	V40	DNAJC21-46-BGHLV20-23_17718_AGTCAA_L002_R1_001.fastq.gz,DNAJC21-46-BGHLV20-23_17718_AGTCAA_L002_R2_001.fastq.gz		ENCORE2	15678
DNAJC21-46-BGHLV20-23_17718_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	1170					GRCh38	V40	DNAJC21-46-BGHLV20-23_17718/Aligned.sortedByCoord.out.bam		ENCORE2	15720
DNAJC21-46-BGHLV20-23_17718_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	1170					GRCh38	V40	DNAJC21-46-BGHLV20-23_17718/Aligned.sortedByCoord.out.bam		ENCORE2	15762
DNAJC21-46-BGHLV20-23_17718_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	1170					GRCh38	V40	DNAJC21-46-BGHLV20-23_17718/Aligned.sortedByCoord.out.bam		ENCORE2	15804
DNAJC21-46-BGHLV20-23_17718_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	1170					GRCh38	V40	DNAJC21-46-BGHLV20-23_17718/Aligned.sortedByCoord.out.bam		ENCORE2	15846
DNAJC21-46-BGHLV20-23_17718_quant.sf	ENCODE_DATA/set20/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1170					GRCh38	V40	DNAJC21-46-BGHLV20-23_17718_AGTCAA_L002_R1_001.fastq.gz,DNAJC21-46-BGHLV20-23_17718_AGTCAA_L002_R2_001.fastq.gz		ENCORE2	15888
DNAJC21-46-BGHLV20-24_17719_AGTTCC_L002_R1_001.fastq.gz	ENCODE_DATA/set20/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1171	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	15595
DNAJC21-46-BGHLV20-24_17719_AGTTCC_L002_R2_001.fastq.gz	ENCODE_DATA/set20/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1171	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	15637
DNAJC21-46-BGHLV20-24_17719_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set20/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1171					GRCh38	V40	DNAJC21-46-BGHLV20-24_17719_AGTTCC_L002_R1_001.fastq.gz,DNAJC21-46-BGHLV20-24_17719_AGTTCC_L002_R2_001.fastq.gz		ENCORE2	15679
DNAJC21-46-BGHLV20-24_17719_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	1171					GRCh38	V40	DNAJC21-46-BGHLV20-24_17719/Aligned.sortedByCoord.out.bam		ENCORE2	15721
DNAJC21-46-BGHLV20-24_17719_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	1171					GRCh38	V40	DNAJC21-46-BGHLV20-24_17719/Aligned.sortedByCoord.out.bam		ENCORE2	15763
DNAJC21-46-BGHLV20-24_17719_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	1171					GRCh38	V40	DNAJC21-46-BGHLV20-24_17719/Aligned.sortedByCoord.out.bam		ENCORE2	15805
DNAJC21-46-BGHLV20-24_17719_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	1171					GRCh38	V40	DNAJC21-46-BGHLV20-24_17719/Aligned.sortedByCoord.out.bam		ENCORE2	15847
DNAJC21-46-BGHLV20-24_17719_quant.sf	ENCODE_DATA/set20/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1171					GRCh38	V40	DNAJC21-46-BGHLV20-24_17719_AGTTCC_L002_R1_001.fastq.gz,DNAJC21-46-BGHLV20-24_17719_AGTTCC_L002_R2_001.fastq.gz		ENCORE2	15889