HLTF RNA-Seq in K562

General Information


RBP	HLTF
Cell_Line	K562
Method	shRNA
Exp_Name	HLTF-BGKLV13-K562
ENCODE_series_ID	ENCSR230SKS
Batch_ID	BGKLV13
Pool ID	Pool-140901
Local_Set_Name	set13
ENCODE_KD_Exp_ID	ENCSR958NDU
ENCODE_CN_Exp_ID	ENCSR815CVQ
Rep1	HLTF_BGKLV13_3
Rep2	HLTF_BGKLV13_4
CN1	NT_BGKLV13_1
CN2	NT_BGKLV13_2
Rep1_qPCR	70.9
Rep2_qPCR	70.8
Rep1_WB	84.5
Rep2_WB	84.6
Antibody Cat#	A300-230A
Antibody Lot#	A300-230A
Antibody DCC ID	ENCAB902OZZ
Status	Released
Project	ENCODE3
ID	360

Experiment Information (Status: Released)

	BGKLV13-3	BGKLV13-4
idx	136	137
TRCN#_or_BGC#	TRCN0000010836	TRCN0000010836
shRNA_or_gRNA_sequence	GCAGGTGGAGTTGGTTTGAAT	GCAGGTGGAGTTGGTTTGAAT
PAM
Name	HLTF	HLTF
Sample_ID	BGKLV13-3	BGKLV13-4
transduction_Date	6/13/2014	6/13/2014
days
RBP_name	HLTF	HLTF
qPCR_result	70.9	70.8
Ave_qPCR	70.9
RT-qPCR_primer-F	tgtcctccagaagaattagca
RT-qPCR_primer-R	cgtgcattagcgcattaatct
protein_conc	2104	1952
WB_result	84.5	84.6
Ave_WB	84.6
WB_DONE_date	7/30/2014
MW	114kDa
IP	1	1
antibody_Cat#	A300-230A	A300-230A
Antibody DCC ID	ENCAB902OZZ	ENCAB902OZZ
submitted_to_DCC_date	5/4/2015
Rep1_TPM	24.3640623	0
Rep2_TPM	27.9726298	0
Action
Library_start_date	7/27/2014	7/27/2014
repeat_library
Note
ID	151	152

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
HLTF	Product_ID: A300-230A Lot_ID: 2 Source: Bethyl Labs Target Name: HLTF-human

Experiment Status

	BGKLV13-3	BGKLV13-4
Sample_ID	BGKLV13-3	BGKLV13-4
Sample Name	HLTF_BGKLV13_3	HLTF_BGKLV13_4
Sample Name	HLTF_BGKLV13_3	HLTF_BGKLV13_4
RBP	HLTF	HLTF
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2014-10-29	2014-10-29
Project	ENCODE3	ENCODE3
Note
ID	456	457

Library-Prep
Sequencing

Library-Prep Information

	BGKLV13-3	BGKLV13-4
Sample #
Sample Name	HLTF-BGKLV13-3	HLTF-BGKLV13-4
Sample_Name_Alias	HLTF_BGKLV13_3	HLTF_BGKLV13_4
Index Well Position	S03	S04
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2014-07-27	2014-07-27
Lib_ID	Lib-140727	Lib-140727
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV13-14/set1/D1.png	DNA_Library_LV13-14/set1/E1.png
RIN	9.5	9.4
libSample_RNA_Well	RNA_Library_LV12/set1/G9.png	RNA_Library_LV12/set1/H9.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date
Sample_ID	BGKLV13-3	BGKLV13-4
RBP	HLTF	HLTF
Batch_ID	BGKLV13	BGKLV13
WB_result	84.500	84.600
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2122	2123

Sequencing Information

	BGKLV13-3	BGKLV13-4
Sample_ID	BGKLV13-3	BGKLV13-4
Sample Name	HLTF_BGKLV13_3	HLTF_BGKLV13_4
Pool ID	Pool-140901	Pool-140901
LocalServer_folder	set13	set13
total_reads	42,980,000	44,100,000
total_aligned_reads	39,076,370	40,757,192
unique_aligned_reads	35,892,832	37,453,450
percent_uniqueAligned	0.83511	0.84928
correlation_replicates	0.998387	0.998387
spikein_reads	109,988	174,524
percent_spikeins	0.00256	0.00396
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	764	765

Data Submission Information

	BGKLV13-3	BGKLV13-3
ENCODE_alias	brenton-graveley:HLTF_BGKLV13	brenton-graveley:HLTF-BGKLV13-K562
ENCODE_accession	ENCSR958NDU	ENCSR230SKS
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKLV13-3	BGKLV13-3
Sample Name	HLTF_BGKLV13_3	HLTF_BGKLV13_3
Selected	Yes	Yes
Status	Released	Released
Status_Date	2014-10-15	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2777	6745

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
HLTF_BGKLV13_3_TTAGGC_L001_R1_001.fastq.gz	ENCODE_DATA/set13/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	764	HiSeq2000	100	paired-ended	1				NT_BGKLV13_1_ATCACG_L001_R1_001.fastq.gz,NT_BGKLV13_2_CGATGT_L001_R1_001.fastq.gz	ENCODE3	13384
HLTF_BGKLV13_3_TTAGGC_L001_R2_001.fastq.gz	ENCODE_DATA/set13/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	764	HiSeq2000	100	paired-ended	2				NT_BGKLV13_1_ATCACG_L001_R2_001.fastq.gz,NT_BGKLV13_2_CGATGT_L001_R2_001.fastq.gz	ENCODE3	13436
HLTF_BGKLV13_3_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set13/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	764					GRCh38	V40	HLTF_BGKLV13_3_TTAGGC_L001_R1_001.fastq.gz,HLTF_BGKLV13_3_TTAGGC_L001_R2_001.fastq.gz		ENCORE2	13488
HLTF_BGKLV13_3_Signal.Unique.strand+.bw	ENCODE_DATA/set13/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	764					GRCh38	V40	HLTF_BGKLV13_3/Aligned.sortedByCoord.out.bam		ENCORE2	13540
HLTF_BGKLV13_3_Signal.Unique.strand-.bw	ENCODE_DATA/set13/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	764					GRCh38	V40	HLTF_BGKLV13_3/Aligned.sortedByCoord.out.bam		ENCORE2	13592
HLTF_BGKLV13_3_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set13/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	764					GRCh38	V40	HLTF_BGKLV13_3/Aligned.sortedByCoord.out.bam		ENCORE2	13644
HLTF_BGKLV13_3_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set13/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	764					GRCh38	V40	HLTF_BGKLV13_3/Aligned.sortedByCoord.out.bam		ENCORE2	13696
HLTF_BGKLV13_3_quant.sf	ENCODE_DATA/set13/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	764					GRCh38	V40	HLTF_BGKLV13_3_TTAGGC_L001_R1_001.fastq.gz,HLTF_BGKLV13_3_TTAGGC_L001_R2_001.fastq.gz		ENCORE2	13748
HLTF_BGKLV13_4_TGACCA_L001_R1_001.fastq.gz	ENCODE_DATA/set13/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	765	HiSeq2000	100	paired-ended	1				NT_BGKLV13_1_ATCACG_L001_R1_001.fastq.gz,NT_BGKLV13_2_CGATGT_L001_R1_001.fastq.gz	ENCODE3	13385
HLTF_BGKLV13_4_TGACCA_L001_R2_001.fastq.gz	ENCODE_DATA/set13/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	765	HiSeq2000	100	paired-ended	2				NT_BGKLV13_1_ATCACG_L001_R2_001.fastq.gz,NT_BGKLV13_2_CGATGT_L001_R2_001.fastq.gz	ENCODE3	13437
HLTF_BGKLV13_4_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set13/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	765					GRCh38	V40	HLTF_BGKLV13_4_TGACCA_L001_R1_001.fastq.gz,HLTF_BGKLV13_4_TGACCA_L001_R2_001.fastq.gz		ENCORE2	13489
HLTF_BGKLV13_4_Signal.Unique.strand+.bw	ENCODE_DATA/set13/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	765					GRCh38	V40	HLTF_BGKLV13_4/Aligned.sortedByCoord.out.bam		ENCORE2	13541
HLTF_BGKLV13_4_Signal.Unique.strand-.bw	ENCODE_DATA/set13/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	765					GRCh38	V40	HLTF_BGKLV13_4/Aligned.sortedByCoord.out.bam		ENCORE2	13593
HLTF_BGKLV13_4_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set13/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	765					GRCh38	V40	HLTF_BGKLV13_4/Aligned.sortedByCoord.out.bam		ENCORE2	13645
HLTF_BGKLV13_4_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set13/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	765					GRCh38	V40	HLTF_BGKLV13_4/Aligned.sortedByCoord.out.bam		ENCORE2	13697
HLTF_BGKLV13_4_quant.sf	ENCODE_DATA/set13/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	765					GRCh38	V40	HLTF_BGKLV13_4_TGACCA_L001_R1_001.fastq.gz,HLTF_BGKLV13_4_TGACCA_L001_R2_001.fastq.gz		ENCORE2	13749