KHSRP RNA-Seq in HepG2

General Information


RBP	KHSRP
Cell_Line	HepG2
Method	shRNA
Exp_Name	KHSRP-BGHLV12-HepG2
ENCODE_series_ID	ENCSR355PLU
Batch_ID	BGHLV12
Pool ID	Pool-140701A
Local_Set_Name	set12
ENCODE_KD_Exp_ID	ENCSR850CKU
ENCODE_CN_Exp_ID	ENCSR603TCV
Rep1	KHSRP-BGHLV12-45
Rep2	KHSRP-BGHLV12-46
CN1	NT-BGHLV12-93
CN2	NT-BGHLV12-94
Rep1_qPCR	76.0
Rep2_qPCR	85.9
Rep1_WB	96.3
Rep2_WB	98.3
Antibody Cat#	RN065PW
Antibody Lot#	RN065PW
Antibody DCC ID	ENCAB531WWS
Status	Released
Project	ENCODE3
ID	343

Experiment Information (Status: Released)

	BGHLV12-45	BGHLV12-46
idx	45	46
TRCN#_or_BGC#	TRCN0000013254	TRCN0000013254
shRNA_or_gRNA_sequence	CCCGAGAAGATTGCTCATATA	CCCGAGAAGATTGCTCATATA
PAM
Name	KHSRP	KHSRP
Sample_ID	BGHLV12-45	BGHLV12-46
transduction_Date	5/15/2014	5/15/2014
days
RBP_name	KHSRP	KHSRP
qPCR_result	76.0	85.9
Ave_qPCR	81.0
RT-qPCR_primer-F	aatccgcaaggacgcttt
RT-qPCR_primer-R	tattcactgtcgtggcagcat
protein_conc	2123	2896
WB_result	96.3	98.3
Ave_WB	97.3
WB_DONE_date
MW	73kDa
IP	1	1
antibody_Cat#	RN065PW	RN065PW
Antibody DCC ID	ENCAB531WWS	ENCAB531WWS
submitted_to_DCC_date	4/2/2015
Rep1_TPM	36.4	0
Rep2_TPM	37	0
Action
Library_start_date	6/12/2014	6/12/2014
repeat_library
Note
ID	2092	2093

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
KHSRP	Product_ID: RN065PW Lot_ID: 1 Source: MBLI Target Name: KHSRP-human

Experiment Status

	BGHLV12-45	BGHLV12-46
Sample_ID	BGHLV12-45	BGHLV12-46
Sample Name	KHSRP-BGHLV12-45	KHSRP-BGHLV12-46
Sample Name	KHSRP-BGHLV12-45	KHSRP-BGHLV12-46
RBP	KHSRP	KHSRP
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2014-09-25	2014-09-25
Project	ENCODE3	ENCODE3
Note
ID	400	401

Library-Prep
Sequencing

Library-Prep Information

	BGHLV12-45	BGHLV12-46
Sample #
Sample Name	KHSRP-BGHLV12-45	KHSRP-BGHLV12-46
Sample_Name_Alias	KHSRP-BGHLV12-45	KHSRP-BGHLV12-46
Index Well Position	S09	S10
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2014-06-12	2014-06-12
Lib_ID	Lib-140612	Lib-140612
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV12/set3/A1.png	DNA_Library_LV12/set3/B1.png
RIN	9.3	9.5
libSample_RNA_Well	RNA_Library_LV12/set1/A5.png	RNA_Library_LV12/set1/B5.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date
Sample_ID	BGHLV12-45	BGHLV12-46
RBP	KHSRP	KHSRP
Batch_ID	BGHLV12	BGHLV12
WB_result	96.300	98.300
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2024	2025

Sequencing Information

	BGHLV12-45	BGHLV12-46
Sample_ID	BGHLV12-45	BGHLV12-46
Sample Name	KHSRP-BGHLV12-45	KHSRP-BGHLV12-46
Pool ID	Pool-140701A	Pool-140701A
LocalServer_folder	set12	set12
total_reads	77,470,000	71,560,000
total_aligned_reads	71,276,342	63,909,656
unique_aligned_reads	67,200,122	60,219,716
percent_uniqueAligned	0.86743	0.84153
correlation_replicates	0.992461	0.992461
spikein_reads	477,882	308,234
percent_spikeins	0.00617	0.00431
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	724	725

Data Submission Information

	BGHLV12-45	BGHLV12-45
ENCODE_alias	brenton-graveley:KHSRP-BGHLV12	brenton-graveley:KHSRP-BGHLV12-HepG2
ENCODE_accession	ENCSR850CKU	ENCSR355PLU
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV12-45	BGHLV12-45
Sample Name	KHSRP-BGHLV12-45	KHSRP-BGHLV12-45
Selected	Yes	Yes
Status	Released	Released
Status_Date	2014-09-24	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2749	6789

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
KHSRP-BGHLV12-45_GATCAG_L005_R1_001.fastq.gz	ENCODE_DATA/set12/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	724	HiSeq2000	100	paired-ended	1				NT-BGHLV12-01_ATCACG_L001_R1_001.fastq.gz,NT-BGHLV12-02_CGATGT_L001_R1_001.fastq.gz	ENCODE3	12781
KHSRP-BGHLV12-45_GATCAG_L005_R2_001.fastq.gz	ENCODE_DATA/set12/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	724	HiSeq2000	100	paired-ended	2				NT-BGHLV12-01_ATCACG_L001_R2_001.fastq.gz,NT-BGHLV12-02_CGATGT_L001_R2_001.fastq.gz	ENCODE3	12850
KHSRP-BGHLV12-45_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set12/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	724					GRCh38	V40	KHSRP-BGHLV12-45_GATCAG_L005_R1_001.fastq.gz,KHSRP-BGHLV12-45_GATCAG_L005_R2_001.fastq.gz		ENCORE2	12920
KHSRP-BGHLV12-45_Signal.Unique.strand+.bw	ENCODE_DATA/set12/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	724					GRCh38	V40	KHSRP-BGHLV12-45/Aligned.sortedByCoord.out.bam		ENCORE2	12990
KHSRP-BGHLV12-45_Signal.Unique.strand-.bw	ENCODE_DATA/set12/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	724					GRCh38	V40	KHSRP-BGHLV12-45/Aligned.sortedByCoord.out.bam		ENCORE2	13060
KHSRP-BGHLV12-45_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set12/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	724					GRCh38	V40	KHSRP-BGHLV12-45/Aligned.sortedByCoord.out.bam		ENCORE2	13130
KHSRP-BGHLV12-45_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set12/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	724					GRCh38	V40	KHSRP-BGHLV12-45/Aligned.sortedByCoord.out.bam		ENCORE2	13200
KHSRP-BGHLV12-45_quant.sf	ENCODE_DATA/set12/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	724					GRCh38	V40	KHSRP-BGHLV12-45_GATCAG_L005_R1_001.fastq.gz,KHSRP-BGHLV12-45_GATCAG_L005_R2_001.fastq.gz		ENCORE2	13270
KHSRP-BGHLV12-46_TAGCTT_L005_R1_001.fastq.gz	ENCODE_DATA/set12/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	725	HiSeq2000	100	paired-ended	1				NT-BGHLV12-01_ATCACG_L001_R1_001.fastq.gz,NT-BGHLV12-02_CGATGT_L001_R1_001.fastq.gz	ENCODE3	12782
KHSRP-BGHLV12-46_TAGCTT_L005_R2_001.fastq.gz	ENCODE_DATA/set12/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	725	HiSeq2000	100	paired-ended	2				NT-BGHLV12-01_ATCACG_L001_R2_001.fastq.gz,NT-BGHLV12-02_CGATGT_L001_R2_001.fastq.gz	ENCODE3	12851
KHSRP-BGHLV12-46_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set12/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	725					GRCh38	V40	KHSRP-BGHLV12-46_TAGCTT_L005_R1_001.fastq.gz,KHSRP-BGHLV12-46_TAGCTT_L005_R2_001.fastq.gz		ENCORE2	12921
KHSRP-BGHLV12-46_Signal.Unique.strand+.bw	ENCODE_DATA/set12/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	725					GRCh38	V40	KHSRP-BGHLV12-46/Aligned.sortedByCoord.out.bam		ENCORE2	12991
KHSRP-BGHLV12-46_Signal.Unique.strand-.bw	ENCODE_DATA/set12/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	725					GRCh38	V40	KHSRP-BGHLV12-46/Aligned.sortedByCoord.out.bam		ENCORE2	13061
KHSRP-BGHLV12-46_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set12/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	725					GRCh38	V40	KHSRP-BGHLV12-46/Aligned.sortedByCoord.out.bam		ENCORE2	13131
KHSRP-BGHLV12-46_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set12/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	725					GRCh38	V40	KHSRP-BGHLV12-46/Aligned.sortedByCoord.out.bam		ENCORE2	13201
KHSRP-BGHLV12-46_quant.sf	ENCODE_DATA/set12/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	725					GRCh38	V40	KHSRP-BGHLV12-46_TAGCTT_L005_R1_001.fastq.gz,KHSRP-BGHLV12-46_TAGCTT_L005_R2_001.fastq.gz		ENCORE2	13271