DNAJC2 RNA-Seq in HepG2

General Information


RBP	DNAJC2
Cell_Line	HepG2
Method	shRNA
Exp_Name	DNAJC2-BGHLV20-HepG2
ENCODE_series_ID	ENCSR795ZKR
Batch_ID	BGHLV20
Pool ID	Pool-150705
Local_Set_Name	set20
ENCODE_KD_Exp_ID	ENCSR004OSI
ENCODE_CN_Exp_ID	ENCSR305XWT
Rep1	DNAJC2-57-BGHLV20-21_17716
Rep2	DNAJC2-57-BGHLV20-22_17717
CN1	non-target-BGHLV20-1_17706
CN2	non-target-BGHLV20-2_17707
Rep1_qPCR	72.1
Rep2_qPCR	58.0
Rep1_WB	54.6
Rep2_WB	50.8
Antibody Cat#	A303-721A
Antibody Lot#	A303-721A
Antibody DCC ID	ENCAB425OIO
Status	Released
Project	ENCODE3
ID	494

Experiment Information (Status: Released)

	BGHLV20-21	BGHLV20-22
idx	385	386
TRCN#_or_BGC#	TRCN0000254057	TRCN0000254057
shRNA_or_gRNA_sequence	TACTTCACTTGCATAACTAAA	TACTTCACTTGCATAACTAAA
PAM
Name	DNAJC2_57	DNAJC2_57
Sample_ID	BGHLV20-21	BGHLV20-22
transduction_Date	10/2/2014	10/2/2014
days
RBP_name	DNAJC2	DNAJC2
qPCR_result	72.1	58.0
Ave_qPCR	65.0
RT-qPCR_primer-F	tccttctaaaagtgaagcaaagg
RT-qPCR_primer-R	gaccatctggaattcctttca
protein_conc	5885	5860
WB_result	54.6	50.8
Ave_WB	52.7
WB_DONE_date	4/13/2015
MW	72kDa
IP	1	1
antibody_Cat#	A303-721A	A303-721A
Antibody DCC ID	ENCAB425OIO	ENCAB425OIO
submitted_to_DCC_date	5/4/2015
Rep1_TPM	44.1	0
Rep2_TPM	39	0
Action
Library_start_date	5/29/2015	5/29/2015
repeat_library
Note
ID	2450	2451

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

	BGHLV20-21	BGHLV20-22
Sample_ID	BGHLV20-21	BGHLV20-22
Sample Name	DNAJC2-57-BGHLV20-21_17716	DNAJC2-57-BGHLV20-22_17717
Sample Name	DNAJC2-57-BGHLV20-21_17716	DNAJC2-57-BGHLV20-22_17717
RBP	DNAJC2	DNAJC2
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2015-08-11	2015-08-11
Project	ENCODE3	ENCODE3
Note
ID	718	719

Library-Prep
Sequencing

Library-Prep Information

	BGHLV20-21	BGHLV20-22
Sample #
Sample Name	DNAJC2-BGHLV20-21	DNAJC2-BGHLV20-22
Sample_Name_Alias	DNAJC2-57-BGHLV20-21_17716	DNAJC2-57-BGHLV20-22_17717
Index Well Position	S11	S12
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/C2.png	DNA_Library_LV20-22-23/set1/D2.png
RIN	9.8	9.7
libSample_RNA_Well	RNA_Library_LV20-22-24/set1/E8.png	RNA_Library_LV20-22-24/set1/F8.png
SampleQC_method
SampleQC_date
Sample_ID	BGHLV20-21	BGHLV20-22
RBP	DNAJC2	DNAJC2
Batch_ID	BGHLV20	BGHLV20
WB_result	54.600	50.800
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2404	2405

Sequencing Information

	BGHLV20-21	BGHLV20-22
Sample_ID	BGHLV20-21	BGHLV20-22
Sample Name	DNAJC2-57-BGHLV20-21_17716	DNAJC2-57-BGHLV20-22_17717
Pool ID	Pool-150705	Pool-150705
LocalServer_folder	set20	set20
total_reads	39,830,000	42,700,000
total_aligned_reads	33,667,794	36,601,964
unique_aligned_reads	31,821,458	34,596,372
percent_uniqueAligned	0.79893	0.81022
correlation_replicates	0.999331	0.999331
spikein_reads	166,564	177,958
percent_spikeins	0.00418	0.00417
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1172	1173

Data Submission Information

	BGHLV20-21	BGHLV20-21
ENCODE_alias	brenton-graveley:DNAJC2-57-BGHLV20	brenton-graveley:DNAJC2-BGHLV20-HepG2
ENCODE_accession	ENCSR004OSI	ENCSR795ZKR
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV20-21	BGHLV20-21
Sample Name	DNAJC2-57-BGHLV20-21_17716	DNAJC2-57-BGHLV20-21_17716
Selected	Yes	Yes
Status	Released	Released
Status_Date	2015-08-11	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2908	6668

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
DNAJC2-57-BGHLV20-21_17716_GGCTAC_L002_R1_001.fastq.gz	ENCODE_DATA/set20/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1172	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	15596
DNAJC2-57-BGHLV20-21_17716_GGCTAC_L002_R2_001.fastq.gz	ENCODE_DATA/set20/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1172	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	15638
DNAJC2-57-BGHLV20-21_17716_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set20/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1172					GRCh38	V40	DNAJC2-57-BGHLV20-21_17716_GGCTAC_L002_R1_001.fastq.gz,DNAJC2-57-BGHLV20-21_17716_GGCTAC_L002_R2_001.fastq.gz		ENCORE2	15680
DNAJC2-57-BGHLV20-21_17716_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	1172					GRCh38	V40	DNAJC2-57-BGHLV20-21_17716/Aligned.sortedByCoord.out.bam		ENCORE2	15722
DNAJC2-57-BGHLV20-21_17716_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	1172					GRCh38	V40	DNAJC2-57-BGHLV20-21_17716/Aligned.sortedByCoord.out.bam		ENCORE2	15764
DNAJC2-57-BGHLV20-21_17716_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	1172					GRCh38	V40	DNAJC2-57-BGHLV20-21_17716/Aligned.sortedByCoord.out.bam		ENCORE2	15806
DNAJC2-57-BGHLV20-21_17716_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	1172					GRCh38	V40	DNAJC2-57-BGHLV20-21_17716/Aligned.sortedByCoord.out.bam		ENCORE2	15848
DNAJC2-57-BGHLV20-21_17716_quant.sf	ENCODE_DATA/set20/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1172					GRCh38	V40	DNAJC2-57-BGHLV20-21_17716_GGCTAC_L002_R1_001.fastq.gz,DNAJC2-57-BGHLV20-21_17716_GGCTAC_L002_R2_001.fastq.gz		ENCORE2	15890
DNAJC2-57-BGHLV20-22_17717_CTTGTA_L002_R1_001.fastq.gz	ENCODE_DATA/set20/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1173	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	15597
DNAJC2-57-BGHLV20-22_17717_CTTGTA_L002_R2_001.fastq.gz	ENCODE_DATA/set20/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1173	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	15639
DNAJC2-57-BGHLV20-22_17717_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set20/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1173					GRCh38	V40	DNAJC2-57-BGHLV20-22_17717_CTTGTA_L002_R1_001.fastq.gz,DNAJC2-57-BGHLV20-22_17717_CTTGTA_L002_R2_001.fastq.gz		ENCORE2	15681
DNAJC2-57-BGHLV20-22_17717_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	1173					GRCh38	V40	DNAJC2-57-BGHLV20-22_17717/Aligned.sortedByCoord.out.bam		ENCORE2	15723
DNAJC2-57-BGHLV20-22_17717_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	1173					GRCh38	V40	DNAJC2-57-BGHLV20-22_17717/Aligned.sortedByCoord.out.bam		ENCORE2	15765
DNAJC2-57-BGHLV20-22_17717_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	1173					GRCh38	V40	DNAJC2-57-BGHLV20-22_17717/Aligned.sortedByCoord.out.bam		ENCORE2	15807
DNAJC2-57-BGHLV20-22_17717_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	1173					GRCh38	V40	DNAJC2-57-BGHLV20-22_17717/Aligned.sortedByCoord.out.bam		ENCORE2	15849
DNAJC2-57-BGHLV20-22_17717_quant.sf	ENCODE_DATA/set20/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1173					GRCh38	V40	DNAJC2-57-BGHLV20-22_17717_CTTGTA_L002_R1_001.fastq.gz,DNAJC2-57-BGHLV20-22_17717_CTTGTA_L002_R2_001.fastq.gz		ENCORE2	15891