HSPD1 RNA-Seq in HepG2

General Information


RBP	HSPD1
Cell_Line	HepG2
Method	shRNA
Exp_Name	HSPD1-BGHLV27-HepG2
ENCODE_series_ID	ENCSR610MSU
Batch_ID	BGHLV27
Pool ID	Pool-151201
Local_Set_Name	set27
ENCODE_KD_Exp_ID	ENCSR243IGA
ENCODE_CN_Exp_ID	ENCSR246RRQ
Rep1	HSPD1_BGHLV27-25
Rep2	HSPD1_BGHLV27-26
CN1	non-target_BGHLV27-1
CN2	non-target_BGHLV27-2
Rep1_qPCR	87.0
Rep2_qPCR	86.7
Rep1_WB	44.3
Rep2_WB	47.6
Antibody Cat#	A302-845A
Antibody Lot#	A302-845A
Antibody DCC ID	ENCAB679PIU
Status	Released
Project	ENCODE3
ID	640

Experiment Information (Status: Released)

	BGHLV27-25	BGHLV27-26
idx	645	646
TRCN#_or_BGC#	TRCN0000029445	TRCN0000029445
shRNA_or_gRNA_sequence	CAGTGATTATTGAGCAGAGTT	CAGTGATTATTGAGCAGAGTT
PAM
Name	HSPD1	HSPD1
Sample_ID	BGHLV27-25	BGHLV27-26
transduction_Date	6/9/2015	6/9/2015
days
RBP_name	HSPD1	HSPD1
qPCR_result	87.0	86.7
Ave_qPCR	86.8
RT-qPCR_primer-F	cagatgcccgagccttaat
RT-qPCR_primer-R	acttccccaactctgctcaa
protein_conc	4775	4045
WB_result	44.3	47.6
Ave_WB	45.9
WB_DONE_date	7/24/2015
MW	61kDa
IP	1	1
antibody_Cat#	A302-845A	A302-845A
Antibody DCC ID	ENCAB679PIU	ENCAB679PIU
submitted_to_DCC_date	8/6/2015
Rep1_TPM	788.3	0
Rep2_TPM	659.1	0
Action
Library_start_date	9/28/2015	9/28/2015
repeat_library
Note	x	x
ID	2732	2733

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
HSPD1	Product_ID: A302-845A Lot_ID: 1 Source: Bethyl Labs Target Name: HSPD1-human

Experiment Status

	BGHLV27-25	BGHLV27-26
Sample_ID	BGHLV27-25	BGHLV27-26
Sample Name	HSPD1_BGHLV27-25	HSPD1_BGHLV27-26
Sample Name	HSPD1_BGHLV27-25	HSPD1_BGHLV27-26
RBP	HSPD1	HSPD1
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2016-01-16	2016-01-16
Project	ENCODE3	ENCODE3
Note
ID	964	965

Library-Prep
Sequencing

Library-Prep Information

	BGHLV27-25	BGHLV27-26
Sample #
Sample Name	HSPD1-BGHLV27-25	HSPD1-BGHLV27-26
Sample_Name_Alias	HSPD1_BGHLV27-25	HSPD1_BGHLV27-26
Index Well Position	S05	S06
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2015-09-28	2015-09-28
Lib_ID	Lib-150928	Lib-150928
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV27/set1/E1.png	DNA_Library_LV27/set1/F1.png
RIN	9.9	9.7
libSample_RNA_Well	RNA_Library_LV26-27-28-29/set1/E4.png	RNA_Library_LV26-27-28-29/set1/F4.png
SampleQC_method
SampleQC_date
Sample_ID	BGHLV27-25	BGHLV27-26
RBP	HSPD1	HSPD1
Batch_ID	BGHLV27	BGHLV27
WB_result	44.300	47.600
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2656	2657

Sequencing Information

	BGHLV27-25	BGHLV27-26
Sample_ID	BGHLV27-25	BGHLV27-26
Sample Name	HSPD1_BGHLV27-25	HSPD1_BGHLV27-26
Pool ID	Pool-151201	Pool-151201
LocalServer_folder	set27	set27
total_reads	92,936,570	75,142,438
total_aligned_reads	85,457,098	68,869,002
unique_aligned_reads	80,348,586	64,799,900
percent_uniqueAligned	0.86455	0.86236
correlation_replicates	0.996441	0.996441
spikein_reads	364,626	280,556
percent_spikeins	0.00392	0.00373
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	1298	1299

Data Submission Information

	BGHLV27-25	BGHLV27-25
ENCODE_alias	brenton-graveley:HSPD1_BGHLV27	brenton-graveley:HSPD1-BGHLV27-HepG2
ENCODE_accession	ENCSR243IGA	ENCSR610MSU
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV27-25	BGHLV27-25
Sample Name	HSPD1_BGHLV27-25	HSPD1_BGHLV27-25
Selected	Yes	Yes
Status	Released	Released
Status_Date	2016-01-14	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	3029	6773

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
HSPD1_BGHLV27-25_1.fastq.gz	ENCODE_DATA/set27/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1298	HiSeq2500	100	paired-ended	1	GRCh38	V40		non-target_BGHLV27-1_1.fastq.gz,non-target_BGHLV27-2_1.fastq.gz	ENCODE3	20006
HSPD1_BGHLV27-25_2.fastq.gz	ENCODE_DATA/set27/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1298	HiSeq2500	100	paired-ended	2				non-target_BGHLV27-1_2.fastq.gz,non-target_BGHLV27-2_2.fastq.gz	ENCODE3	20028
HSPD1_BGHLV27-25_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set27/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1298					GRCh38	V40	HSPD1_BGHLV27-25_1.fastq.gz,HSPD1_BGHLV27-25_2.fastq.gz		ENCORE2	20050
HSPD1_BGHLV27-25_Signal.Unique.strand+.bw	ENCODE_DATA/set27/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1298					GRCh38	V40	HSPD1_BGHLV27-25/Aligned.sortedByCoord.out.bam		ENCORE2	20072
HSPD1_BGHLV27-25_Signal.Unique.strand-.bw	ENCODE_DATA/set27/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1298					GRCh38	V40	HSPD1_BGHLV27-25/Aligned.sortedByCoord.out.bam		ENCORE2	20094
HSPD1_BGHLV27-25_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set27/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1298					GRCh38	V40	HSPD1_BGHLV27-25/Aligned.sortedByCoord.out.bam		ENCORE2	20116
HSPD1_BGHLV27-25_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set27/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1298					GRCh38	V40	HSPD1_BGHLV27-25/Aligned.sortedByCoord.out.bam		ENCORE2	20138
HSPD1_BGHLV27-25_quant.sf	ENCODE_DATA/set27/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1298					GRCh38	V40	HSPD1_BGHLV27-25_1.fastq.gz,HSPD1_BGHLV27-25_2.fastq.gz		ENCORE2	20678
HSPD1_BGHLV27-26_1.fastq.gz	ENCODE_DATA/set27/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1299	HiSeq2500	100	paired-ended	1	GRCh38	V40		non-target_BGHLV27-1_1.fastq.gz,non-target_BGHLV27-2_1.fastq.gz	ENCODE3	20007
HSPD1_BGHLV27-26_2.fastq.gz	ENCODE_DATA/set27/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1299	HiSeq2500	100	paired-ended	2				non-target_BGHLV27-1_2.fastq.gz,non-target_BGHLV27-2_2.fastq.gz	ENCODE3	20029
HSPD1_BGHLV27-26_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set27/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1299					GRCh38	V40	HSPD1_BGHLV27-26_1.fastq.gz,HSPD1_BGHLV27-26_2.fastq.gz		ENCORE2	20051
HSPD1_BGHLV27-26_Signal.Unique.strand+.bw	ENCODE_DATA/set27/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1299					GRCh38	V40	HSPD1_BGHLV27-26/Aligned.sortedByCoord.out.bam		ENCORE2	20073
HSPD1_BGHLV27-26_Signal.Unique.strand-.bw	ENCODE_DATA/set27/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1299					GRCh38	V40	HSPD1_BGHLV27-26/Aligned.sortedByCoord.out.bam		ENCORE2	20095
HSPD1_BGHLV27-26_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set27/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1299					GRCh38	V40	HSPD1_BGHLV27-26/Aligned.sortedByCoord.out.bam		ENCORE2	20117
HSPD1_BGHLV27-26_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set27/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1299					GRCh38	V40	HSPD1_BGHLV27-26/Aligned.sortedByCoord.out.bam		ENCORE2	20139
HSPD1_BGHLV27-26_quant.sf	ENCODE_DATA/set27/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1299					GRCh38	V40	HSPD1_BGHLV27-26_1.fastq.gz,HSPD1_BGHLV27-26_2.fastq.gz		ENCORE2	20679