HDGF RNA-Seq in K562

General Information


RBP	HDGF
Cell_Line	K562
Method	shRNA
Exp_Name	HDGF-BGKLV36-K562
ENCODE_series_ID	ENCSR033XRC
Batch_ID	BGKLV36
Pool ID	Pool-180109
Local_Set_Name	set40_K
ENCODE_KD_Exp_ID	ENCSR793QPX
ENCODE_CN_Exp_ID	ENCSR619PCR
Rep1	HDGF-BGKLV36-29
Rep2	HDGF-BGKLV36-30
CN1	NT-BGKLV36-1C
CN2	NT-BGKLV36-2C
Rep1_qPCR	89.8
Rep2_qPCR	91.6
Rep1_WB	82.9
Rep2_WB	80.8
Antibody Cat#	A303-170A
Antibody Lot#	A303-170A
Antibody DCC ID	ENCAB173GGB
Status	Released
Project	ENCODE4
ID	271

Experiment Information (Status: Released)

	BGKLV36-29	BGKLV36-29	BGKLV36-30	BGKLV36-30
idx	752	752	753	753
TRCN#_or_BGC#	TRCN0000118159	TRCN0000118159	TRCN0000118159	TRCN0000118159
shRNA_or_gRNA_sequence	GAACGAGAAAGGAGCGTTGAA	GAACGAGAAAGGAGCGTTGAA	GAACGAGAAAGGAGCGTTGAA	GAACGAGAAAGGAGCGTTGAA
PAM
Name	HDGF	HDGF	HDGF	HDGF
Sample_ID	BGKLV36-29	BGKLV36-29	BGKLV36-30	BGKLV36-30
transduction_Date	5/19/2016	5/19/2016	5/19/2016	5/19/2016
days
RBP_name	HDGF	HDGF	HDGF	HDGF
qPCR_result	89.8	89.8	91.6	91.6
Ave_qPCR	90.7	90.7
RT-qPCR_primer-F	cctccccaagaggaagaaga	cctccccaagaggaagaaga
RT-qPCR_primer-R	cattggtggctacaggctct	cattggtggctacaggctct
protein_conc	4108	4108	4207	4207
WB_result	82.9	87.2	80.8	86.3
Ave_WB	81.9	86.8
WB_DONE_date	6/21/16	6/13/23
MW	27kDa	27kDa
IP	1MW		1MW
antibody_Cat#	A303-170A	42105S	A303-170A	LOT # 1
Antibody DCC ID	ENCAB173GGB		ENCAB173GGB
submitted_to_DCC_date	11/16/17	1/8/24
Rep1_TPM	94.1	0	0	0
Rep2_TPM	59	0	0	0
Action
Library_start_date	07/28/16		07/28/16
repeat_library
Note
ID	843	845	844	846

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
HDGF	Product_ID: A303-170A Lot_ID: 1 Source: Bethyl Labs Target Name: HDGF-human
HDGF	Product_ID: 42105S Lot_ID: 1 Source: Cell Signaling Technology Target Name: HDGF-human

Experiment Status

	BGKLV36-29	BGKLV36-30
Sample_ID	BGKLV36-29	BGKLV36-30
Sample Name
Sample Name	HDGF-BGKLV36-29	HDGF-BGKLV36-30
RBP	HDGF	HDGF
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2021-03-18	2021-03-18
Project	ENCODE4	ENCODE4
Note
ID	6465	6466

Library-Prep
Sequencing

Library-Prep Information

	BGKLV36-29	BGKLV36-30
Sample #	49	50
Sample Name	HDGF-BGKLV36-29C	HDGF-BGKLV36-30C
Sample_Name_Alias	HDGF-BGKLV36-29	HDGF-BGKLV36-30
Index Well Position	S22	S23
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2018-01-02	2018-01-02
Lib_ID	Lib-180102	Lib-180102
Tecan_Location
Tecan
Tecan_date
Size_bp	263	275
Peak_Molarity	11.40	12.10
libSampleQC_DNA_Well	DNA_Library_LV36/set1/E2.png	DNA_Library_LV36/set1/F2.png
RIN	9.9	9.9
libSample_RNA_Well	RNA_Library_LV35_LV36/set1/G5.png	RNA_Library_LV35_LV36/set1/H5.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2016-07-29	2016-07-29
Sample_ID	BGKLV36-29	BGKLV36-30
RBP	HDGF	HDGF
Batch_ID	BGKLV36	BGKLV36
WB_result	82.900	80.800
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix	C	C
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	972	973

Sequencing Information

	BGKLV36-29	BGKLV36-30
Sample_ID	BGKLV36-29	BGKLV36-30
Sample Name	HDGF-BGKLV36-29	HDGF-BGKLV36-30
Pool ID	Pool-180109	Pool-180109
LocalServer_folder	set40_K	set40_K
total_reads	29,647,438	38,110,156
total_aligned_reads	25,837,134	33,243,114
unique_aligned_reads	23,539,750	30,448,700
percent_uniqueAligned	0.79399	0.79897
correlation_replicates	0.999201	0.999201
spikein_reads	48,482	67,484
percent_spikeins	0.00164	0.00177
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	375	376

Data Submission Information

	BGKLV36-29	BGKLV36-29	BGKLV36-29	BGKLV36-29	BGKLV36-29	BGKLV36-29	BGKLV36-30	BGKLV36-30	BGKLV36-30	BGKLV36-30
ENCODE_alias	brenton-graveley:HDGF-BGKLV36-C	brenton-graveley:HDGF-BGKLV36-29	brenton-graveley:L-HDGF-BGKLV36-29	brenton-graveley:HDGF-BGKLV36-29_CGTACG_ACBYWVANXX_L007_001.R1.fastq.gz	brenton-graveley:HDGF-BGKLV36-29_CGTACG_ACBYWVANXX_L007_001.R2.fastq.gz	brenton-graveley:HDGF-BGKLV36-K562	brenton-graveley:HDGF-BGKLV36-30	brenton-graveley:L-HDGF-BGKLV36-30	brenton-graveley:HDGF-BGKLV36-30_GAGTGG_ACBYWVANXX_L007_001.R1.fastq.gz	brenton-graveley:HDGF-BGKLV36-30_GAGTGG_ACBYWVANXX_L007_001.R2.fastq.gz
ENCODE_accession	ENCSR793QPX	ENCBS663QKK	ENCLB112BHZ	ENCFF401KAG	ENCFF921QQD	ENCSR033XRC	ENCBS882LEE	ENCLB975QGI	ENCFF022KNC	ENCFF421URY
object_type	experiment	biosample	library	file_fastq1	file_fastq2	gene_silencing_series	biosample	library	file_fastq1	file_fastq2
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKLV36-29	BGKLV36-29	BGKLV36-29	BGKLV36-29	BGKLV36-29	BGKLV36-29	BGKLV36-30	BGKLV36-30	BGKLV36-30	BGKLV36-30
Sample Name	HDGF-BGKLV36-29	HDGF-BGKLV36-29	HDGF-BGKLV36-29	HDGF-BGKLV36-29	HDGF-BGKLV36-29	HDGF-BGKLV36-29	HDGF-BGKLV36-30	HDGF-BGKLV36-30	HDGF-BGKLV36-30	HDGF-BGKLV36-30
Selected	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes
Status	Released	Released	Released	Released	Released	Released	Released	Released	Released	Released
Status_Date	2021-03-18	2021-03-18	2021-03-18	2021-03-18	2021-03-18	2022-03-02	2021-03-18	2021-03-18	2021-03-18	2021-03-18
Project	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4
		LV40_biosample_protocol	LV40_library_protocol				LV40_biosample_protocol	LV40_library_protocol
protocol_URL		HDGF-BGKLV36-29.pdf	L-HDGF-BGKLV36-29.pdf				HDGF-BGKLV36-30.pdf	L-HDGF-BGKLV36-30.pdf
ID	1437	1472	1528	1649	1682	7240	1473	1529	1650	1683

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
HDGF-BGKLV36-29_CGTACG_ACBYWVANXX_L007_001.R1.fastq.gz	ENCODE_DATA/set40_K/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	375	HiSeq2500	100	paired-ended	1				NT-BGKLV36-1C_L001_001.R1.fastq.gz,NT-BGKLV36-2C_L001_001.R1.fastq.gz	ENCODE4	728
HDGF-BGKLV36-29_CGTACG_ACBYWVANXX_L007_001.R2.fastq.gz	ENCODE_DATA/set40_K/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	375	HiSeq2500	100	paired-ended	2				NT-BGKLV36-1C_L001_001.R2.fastq.gz,NT-BGKLV36-2C_L001_001.R2.fastq.gz	ENCODE4	771
HDGF-BGKLV36-29_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set40_K/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	375					GRCh38	V40	HDGF-BGKLV36-29_CGTACG_ACBYWVANXX_L007_001.R1.fastq.gz,HDGF-BGKLV36-29_CGTACG_ACBYWVANXX_L007_001.R2.fastq.gz		ENCORE2	23474
HDGF-BGKLV36-29_Signal.Unique.strand+.bw	ENCODE_DATA/set40_K/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	375					GRCh38	V40	HDGF-BGKLV36-29/Aligned.sortedByCoord.out.bam		ENCORE2	23508
HDGF-BGKLV36-29_Signal.Unique.strand-.bw	ENCODE_DATA/set40_K/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	375					GRCh38	V40	HDGF-BGKLV36-29/Aligned.sortedByCoord.out.bam		ENCORE2	23542
HDGF-BGKLV36-29_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set40_K/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	375					GRCh38	V40	HDGF-BGKLV36-29/Aligned.sortedByCoord.out.bam		ENCORE2	23576
HDGF-BGKLV36-29_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set40_K/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	375					GRCh38	V40	HDGF-BGKLV36-29/Aligned.sortedByCoord.out.bam		ENCORE2	23610
HDGF-BGKLV36-29_quant.sf	ENCODE_DATA/set40_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	375					GRCh38	V40	HDGF-BGKLV36-29_CGTACG_ACBYWVANXX_L007_001.R1.fastq.gz,HDGF-BGKLV36-29_CGTACG_ACBYWVANXX_L007_001.R2.fastq.gz		ENCORE2	23644
HDGF-BGKLV36-30_GAGTGG_ACBYWVANXX_L007_001.R1.fastq.gz	ENCODE_DATA/set40_K/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	376	HiSeq2500	100	paired-ended	1				NT-BGKLV36-1C_L001_001.R1.fastq.gz,NT-BGKLV36-2C_L001_001.R1.fastq.gz	ENCODE4	729
HDGF-BGKLV36-30_GAGTGG_ACBYWVANXX_L007_001.R2.fastq.gz	ENCODE_DATA/set40_K/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	376	HiSeq2500	100	paired-ended	2				NT-BGKLV36-1C_L001_001.R2.fastq.gz,NT-BGKLV36-2C_L001_001.R2.fastq.gz	ENCODE4	772
HDGF-BGKLV36-30_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set40_K/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	376					GRCh38	V40	HDGF-BGKLV36-30_GAGTGG_ACBYWVANXX_L007_001.R1.fastq.gz,HDGF-BGKLV36-30_GAGTGG_ACBYWVANXX_L007_001.R2.fastq.gz		ENCORE2	23475
HDGF-BGKLV36-30_Signal.Unique.strand+.bw	ENCODE_DATA/set40_K/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	376					GRCh38	V40	HDGF-BGKLV36-30/Aligned.sortedByCoord.out.bam		ENCORE2	23509
HDGF-BGKLV36-30_Signal.Unique.strand-.bw	ENCODE_DATA/set40_K/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	376					GRCh38	V40	HDGF-BGKLV36-30/Aligned.sortedByCoord.out.bam		ENCORE2	23543
HDGF-BGKLV36-30_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set40_K/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	376					GRCh38	V40	HDGF-BGKLV36-30/Aligned.sortedByCoord.out.bam		ENCORE2	23577
HDGF-BGKLV36-30_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set40_K/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	376					GRCh38	V40	HDGF-BGKLV36-30/Aligned.sortedByCoord.out.bam		ENCORE2	23611
HDGF-BGKLV36-30_quant.sf	ENCODE_DATA/set40_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	376					GRCh38	V40	HDGF-BGKLV36-30_GAGTGG_ACBYWVANXX_L007_001.R1.fastq.gz,HDGF-BGKLV36-30_GAGTGG_ACBYWVANXX_L007_001.R2.fastq.gz		ENCORE2	23645