KHDRBS1 RNA-Seq in HepG2

General Information


RBP	KHDRBS1
Cell_Line	HepG2
Method	shRNA
Exp_Name	KHDRBS1-BGHLV22-HepG2
ENCODE_series_ID	ENCSR787JDA
Batch_ID	BGHLV22
Pool ID	Pool-150701
Local_Set_Name	set22
ENCODE_KD_Exp_ID	ENCSR784FTX
ENCODE_CN_Exp_ID	ENCSR279HMU
Rep1	KHDRBS1-BGHLV22-31
Rep2	KHDRBS1-BGHLV22-32
CN1	non-target-BGHLV22-1_17746
CN2	non-target-BGHLV22-2_17747
Rep1_qPCR	70.1
Rep2_qPCR	78.6
Rep1_WB	62.0
Rep2_WB	58.9
Antibody Cat#	A302-110A
Antibody Lot#	A302-110A
Antibody DCC ID	ENCAB974QUZ
Status	Released
Project	ENCODE3
ID	523

Experiment Information (Status: Released)

	BGHLV22-31	BGHLV22-32
idx	459	460
TRCN#_or_BGC#	TRCN0000000046	TRCN0000000046
shRNA_or_gRNA_sequence	GACGGCAGAAATTGAGAAGAT	GACGGCAGAAATTGAGAAGAT
PAM
Name	KHDRBS1	KHDRBS1
Sample_ID	BGHLV22-31	BGHLV22-32
transduction_Date	10/16/2014	10/16/2014
days
RBP_name	KHDRBS1	KHDRBS1
qPCR_result	70.1	78.6
Ave_qPCR	74.3
RT-qPCR_primer-F	ctgtattgggaaagggctca
RT-qPCR_primer-R	agtgggcatatttggggtct
protein_conc	7075	7718
WB_result	62.0	58.9
Ave_WB	60.5
WB_DONE_date	4/6/2015
MW
IP	1	1
antibody_Cat#	A302-110A	A302-110A
Antibody DCC ID	ENCAB974QUZ	ENCAB974QUZ
submitted_to_DCC_date	5/6/2015
Rep1_TPM	70.1	0
Rep2_TPM	52.9	0
Action
Library_start_date	6/5/2015	6/5/2015
repeat_library
Note
ID	2530	2531

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
KHDRBS1	Product_ID: A302-110A Lot_ID: 1 Source: Bethyl Labs Target Name: KHDRBS1-human

Experiment Status

	BGHLV22-31	BGHLV22-32
Sample_ID	BGHLV22-31	BGHLV22-32
Sample Name	KHDRBS1-BGHLV22-31	KHDRBS1-BGHLV22-32
Sample Name	KHDRBS1-BGHLV22-31	KHDRBS1-BGHLV22-32
RBP	KHDRBS1	KHDRBS1
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2015-08-13	2015-08-13
Project	ENCODE3	ENCODE3
Note
ID	794	795

Library-Prep
Sequencing

Library-Prep Information

	BGHLV22-31	BGHLV22-32
Sample #
Sample Name	KHDRBS1-BGHLV22-31	KHDRBS1-BGHLV22-32
Sample_Name_Alias	KHDRBS1-BGHLV22-31	KHDRBS1-BGHLV22-32
Index Well Position	S20	S21
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2015-06-05	2015-06-05
Lib_ID	Lib-150605	Lib-150605
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV20-22-23/set2/E1.png	DNA_Library_LV20-22-23/set2/F1.png
RIN	9.8	9.8
libSample_RNA_Well	RNA_Library_LV22-23-25/set1/C2.png	RNA_Library_LV22-23-25/set1/D2.png
SampleQC_method
SampleQC_date
Sample_ID	BGHLV22-31	BGHLV22-32
RBP	KHDRBS1	KHDRBS1
Batch_ID	BGHLV22	BGHLV22
WB_result	62.000	58.900
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2480	2481

Sequencing Information

	BGHLV22-31	BGHLV22-32
Sample_ID	BGHLV22-31	BGHLV22-32
Sample Name	KHDRBS1-BGHLV22-31	KHDRBS1-BGHLV22-32
Pool ID	Pool-150701	Pool-150701
LocalServer_folder	set22	set22
total_reads	54,980,000	51,710,000
total_aligned_reads	50,814,404	47,867,342
unique_aligned_reads	47,805,680	45,048,152
percent_uniqueAligned	0.86951	0.87117
correlation_replicates	0.998548	0.998548
spikein_reads	268,278	249,764
percent_spikeins	0.00488	0.00483
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1104	1105

Data Submission Information

	BGHLV22-31	BGHLV22-31
ENCODE_alias	brenton-graveley:KHDRBS1-BGHLV22	brenton-graveley:KHDRBS1-BGHLV22-HepG2
ENCODE_accession	ENCSR784FTX	ENCSR787JDA
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV22-31	BGHLV22-31
Sample Name	KHDRBS1-BGHLV22-31	KHDRBS1-BGHLV22-31
Selected	Yes	Yes
Status	Released	Released
Status_Date	2015-08-11	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2929	6787

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
KHDRBS1-BGHLV22-31_GTGGCC_L001_R1_001.fastq.gz	ENCODE_DATA/set22/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1104	HiSeq2000	100	paired-ended	1				non-target-BGHLV22-1_17746_ATCACG_L006_R1_001.fastq.gz,non-target-BGHLV22-2_17747_CGATGT_L006_R1_001.fastq.gz	ENCODE3	16290
KHDRBS1-BGHLV22-31_GTGGCC_L001_R2_001.fastq.gz	ENCODE_DATA/set22/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1104	HiSeq2000	100	paired-ended	2				non-target-BGHLV22-1_17746_ATCACG_L006_R2_001.fastq.gz,non-target-BGHLV22-2_17747_CGATGT_L006_R2_001.fastq.gz	ENCODE3	16330
KHDRBS1-BGHLV22-31_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set22/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1104					GRCh38	V40	KHDRBS1-BGHLV22-31_GTGGCC_L001_R1_001.fastq.gz,KHDRBS1-BGHLV22-31_GTGGCC_L001_R2_001.fastq.gz		ENCORE2	16428
KHDRBS1-BGHLV22-31_Signal.Unique.strand+.bw	ENCODE_DATA/set22/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1104					GRCh38	V40	KHDRBS1-BGHLV22-31/Aligned.sortedByCoord.out.bam		ENCORE2	16468
KHDRBS1-BGHLV22-31_Signal.Unique.strand-.bw	ENCODE_DATA/set22/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1104					GRCh38	V40	KHDRBS1-BGHLV22-31/Aligned.sortedByCoord.out.bam		ENCORE2	16508
KHDRBS1-BGHLV22-31_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set22/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1104					GRCh38	V40	KHDRBS1-BGHLV22-31/Aligned.sortedByCoord.out.bam		ENCORE2	16548
KHDRBS1-BGHLV22-31_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set22/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1104					GRCh38	V40	KHDRBS1-BGHLV22-31/Aligned.sortedByCoord.out.bam		ENCORE2	16588
KHDRBS1-BGHLV22-31_quant.sf	ENCODE_DATA/set22/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1104					GRCh38	V40	KHDRBS1-BGHLV22-31_GTGGCC_L001_R1_001.fastq.gz,KHDRBS1-BGHLV22-31_GTGGCC_L001_R2_001.fastq.gz		ENCORE2	16628
KHDRBS1-BGHLV22-32_GTTTCG_L001_R1_001.fastq.gz	ENCODE_DATA/set22/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1105	HiSeq2000	100	paired-ended	1				non-target-BGHLV22-1_17746_ATCACG_L006_R1_001.fastq.gz,non-target-BGHLV22-2_17747_CGATGT_L006_R1_001.fastq.gz	ENCODE3	16291
KHDRBS1-BGHLV22-32_GTTTCG_L001_R2_001.fastq.gz	ENCODE_DATA/set22/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1105	HiSeq2000	100	paired-ended	2				non-target-BGHLV22-1_17746_ATCACG_L006_R2_001.fastq.gz,non-target-BGHLV22-2_17747_CGATGT_L006_R2_001.fastq.gz	ENCODE3	16331
KHDRBS1-BGHLV22-32_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set22/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1105					GRCh38	V40	KHDRBS1-BGHLV22-32_GTTTCG_L001_R1_001.fastq.gz,KHDRBS1-BGHLV22-32_GTTTCG_L001_R2_001.fastq.gz		ENCORE2	16429
KHDRBS1-BGHLV22-32_Signal.Unique.strand+.bw	ENCODE_DATA/set22/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1105					GRCh38	V40	KHDRBS1-BGHLV22-32/Aligned.sortedByCoord.out.bam		ENCORE2	16469
KHDRBS1-BGHLV22-32_Signal.Unique.strand-.bw	ENCODE_DATA/set22/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1105					GRCh38	V40	KHDRBS1-BGHLV22-32/Aligned.sortedByCoord.out.bam		ENCORE2	16509
KHDRBS1-BGHLV22-32_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set22/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1105					GRCh38	V40	KHDRBS1-BGHLV22-32/Aligned.sortedByCoord.out.bam		ENCORE2	16549
KHDRBS1-BGHLV22-32_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set22/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1105					GRCh38	V40	KHDRBS1-BGHLV22-32/Aligned.sortedByCoord.out.bam		ENCORE2	16589
KHDRBS1-BGHLV22-32_quant.sf	ENCODE_DATA/set22/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1105					GRCh38	V40	KHDRBS1-BGHLV22-32_GTTTCG_L001_R1_001.fastq.gz,KHDRBS1-BGHLV22-32_GTTTCG_L001_R2_001.fastq.gz		ENCORE2	16629