HSPD1 RNA-Seq in K562

General Information


RBP	HSPD1
Cell_Line	K562
Method	shRNA
Exp_Name	HSPD1-BGKLV29-K562
ENCODE_series_ID	ENCSR777FQO
Batch_ID	BGKLV29
Pool ID	Pool-151215B
Local_Set_Name	set29
ENCODE_KD_Exp_ID	ENCSR222ABK
ENCODE_CN_Exp_ID	ENCSR032YMP
Rep1	HSPD1_BGKLV29-41
Rep2	HSPD1_BGKLV29-42
CN1	NT_BGKLV29-1
CN2	NT_BGKLV29-2
Rep1_qPCR	87.8
Rep2_qPCR	86.7
Rep1_WB	61.7
Rep2_WB	66.3
Antibody Cat#	A302-845A
Antibody Lot#	A302-845A
Antibody DCC ID	ENCAB679PIU
Status	Released
Project	ENCODE3
ID	671

Experiment Information (Status: Released)

	BGKLV29-41	BGKLV29-42
idx	576	577
TRCN#_or_BGC#	TRCN0000029445	TRCN0000029445
shRNA_or_gRNA_sequence	CAGTGATTATTGAGCAGAGTT	CAGTGATTATTGAGCAGAGTT
PAM
Name	HSPD1	HSPD1
Sample_ID	BGKLV29-41	BGKLV29-42
transduction_Date	8/11/2015	8/11/2015
days
RBP_name	HSPD1	HSPD1
qPCR_result	87.8	86.7
Ave_qPCR	87.2
RT-qPCR_primer-F	cagatgcccgagccttaat
RT-qPCR_primer-R	acttccccaactctgctcaa
protein_conc	2758	2502
WB_result	61.7	66.3
Ave_WB	64.0
WB_DONE_date	9/22/2015
MW	61kDa
IP	1	1
antibody_Cat#	A302-845A	A302-845A
Antibody DCC ID	ENCAB679PIU	ENCAB679PIU
submitted_to_DCC_date	12/7/2015
Rep1_TPM	226.383808	0
Rep2_TPM	136.766751	0
Action
Library_start_date	11/2/2015	11/2/2015
repeat_library
Note	x	x
ID	657	658

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

	BGKLV29-41	BGKLV29-42
Sample_ID	BGKLV29-41	BGKLV29-42
Sample Name	HSPD1_BGKLV29-41	HSPD1_BGKLV29-42
Sample Name	HSPD1_BGKLV29-41	HSPD1_BGKLV29-42
RBP	HSPD1	HSPD1
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2016-03-03	2016-03-03
Project	ENCODE3	ENCODE3
Note
ID	1026	1027

Library-Prep
Sequencing

Library-Prep Information

	BGKLV29-41	BGKLV29-42
Sample #
Sample Name	HSPD1-BGKLV29-41	HSPD1-BGKLV29-42
Sample_Name_Alias	HSPD1_BGKLV29-41	HSPD1_BGKLV29-42
Index Well Position	S01	S02
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2015-11-02	2015-11-02
Lib_ID	Lib-151102	Lib-151102
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV28-29-30/set1/A7.png	DNA_Library_LV28-29-30/set1/B7.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_LV29-30-31-32/set1/E2.png	RNA_Library_LV29-30-31-32/set1/F2.png
SampleQC_method
SampleQC_date
Sample_ID	BGKLV29-41	BGKLV29-42
RBP	HSPD1	HSPD1
Batch_ID	BGKLV29	BGKLV29
WB_result	61.700	66.300
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2714	2715

Sequencing Information

	BGKLV29-41	BGKLV29-42
Sample_ID	BGKLV29-41	BGKLV29-42
Sample Name	HSPD1_BGKLV29-41	HSPD1_BGKLV29-42
Pool ID	Pool-151215B	Pool-151215B
LocalServer_folder	set29	set29
total_reads	86,231,638	105,837,996
total_aligned_reads	77,330,262	97,009,216
unique_aligned_reads	70,504,910	88,417,398
percent_uniqueAligned	0.81762	0.83540
correlation_replicates	0.997522	0.997522
spikein_reads	510,378	508,076
percent_spikeins	0.00592	0.00480
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1385	1386

Data Submission Information

	BGKLV29-41	BGKLV29-41
ENCODE_alias	brenton-graveley:HSPD1_BGKLV29	brenton-graveley:HSPD1-BGKLV29-K562
ENCODE_accession	ENCSR222ABK	ENCSR777FQO
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKLV29-41	BGKLV29-41
Sample Name	HSPD1_BGKLV29-41	HSPD1_BGKLV29-41
Selected	Yes	Yes
Status	Released	Released
Status_Date	2016-03-03	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	3062	6774

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_BGKLV29-41_ATCACG_L002_001.R1.fastq.gz	ENCODE_DATA/set29/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1385	HiSeq2500	100	paired-ended	1				NT_BGKLV29-1_GATCAG_L005_001.R1.fastq.gz,NT_BGKLV29-2_TAGCTT_L005_001.R1.fastq.gz	ENCODE3	20428
HSPD1_BGKLV29-41_ATCACG_L002_001.R2.fastq.gz	ENCODE_DATA/set29/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1385	HiSeq2500	100	paired-ended	2				NT_BGKLV29-1_GATCAG_L005_001.R2.fastq.gz,NT_BGKLV29-2_TAGCTT_L005_001.R2.fastq.gz	ENCODE3	20458
HSPD1_BGKLV29-41_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set29/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1385					GRCh38	V40	HSPD1_BGKLV29-41_ATCACG_L002_001.R1.fastq.gz,HSPD1_BGKLV29-41_ATCACG_L002_001.R2.fastq.gz		ENCORE2	20488
HSPD1_BGKLV29-41_Signal.Unique.strand+.bw	ENCODE_DATA/set29/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1385					GRCh38	V40	HSPD1_BGKLV29-41/Aligned.sortedByCoord.out.bam		ENCORE2	20518
HSPD1_BGKLV29-41_Signal.Unique.strand-.bw	ENCODE_DATA/set29/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1385					GRCh38	V40	HSPD1_BGKLV29-41/Aligned.sortedByCoord.out.bam		ENCORE2	20548
HSPD1_BGKLV29-41_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set29/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1385					GRCh38	V40	HSPD1_BGKLV29-41/Aligned.sortedByCoord.out.bam		ENCORE2	20578
HSPD1_BGKLV29-41_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set29/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1385					GRCh38	V40	HSPD1_BGKLV29-41/Aligned.sortedByCoord.out.bam		ENCORE2	20608
HSPD1_BGKLV29-41_quant.sf	ENCODE_DATA/set29/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1385					GRCh38	V40	HSPD1_BGKLV29-41_ATCACG_L002_001.R1.fastq.gz,HSPD1_BGKLV29-41_ATCACG_L002_001.R2.fastq.gz		ENCORE2	20638
HSPD1_BGKLV29-42_CGATGT_L002_001.R1.fastq.gz	ENCODE_DATA/set29/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1386	HiSeq2500	100	paired-ended	1				NT_BGKLV29-1_GATCAG_L005_001.R1.fastq.gz,NT_BGKLV29-2_TAGCTT_L005_001.R1.fastq.gz	ENCODE3	20429
HSPD1_BGKLV29-42_CGATGT_L002_001.R2.fastq.gz	ENCODE_DATA/set29/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1386	HiSeq2500	100	paired-ended	2				NT_BGKLV29-1_GATCAG_L005_001.R2.fastq.gz,NT_BGKLV29-2_TAGCTT_L005_001.R2.fastq.gz	ENCODE3	20459
HSPD1_BGKLV29-42_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set29/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1386					GRCh38	V40	HSPD1_BGKLV29-42_CGATGT_L002_001.R1.fastq.gz,HSPD1_BGKLV29-42_CGATGT_L002_001.R2.fastq.gz		ENCORE2	20489
HSPD1_BGKLV29-42_Signal.Unique.strand+.bw	ENCODE_DATA/set29/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1386					GRCh38	V40	HSPD1_BGKLV29-42/Aligned.sortedByCoord.out.bam		ENCORE2	20519
HSPD1_BGKLV29-42_Signal.Unique.strand-.bw	ENCODE_DATA/set29/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1386					GRCh38	V40	HSPD1_BGKLV29-42/Aligned.sortedByCoord.out.bam		ENCORE2	20549
HSPD1_BGKLV29-42_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set29/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1386					GRCh38	V40	HSPD1_BGKLV29-42/Aligned.sortedByCoord.out.bam		ENCORE2	20579
HSPD1_BGKLV29-42_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set29/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1386					GRCh38	V40	HSPD1_BGKLV29-42/Aligned.sortedByCoord.out.bam		ENCORE2	20609
HSPD1_BGKLV29-42_quant.sf	ENCODE_DATA/set29/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1386					GRCh38	V40	HSPD1_BGKLV29-42_CGATGT_L002_001.R1.fastq.gz,HSPD1_BGKLV29-42_CGATGT_L002_001.R2.fastq.gz		ENCORE2	20639