KRR1 RNA-Seq in HepG2

General Information


RBP	KRR1
Cell_Line	HepG2
Method	shRNA
Exp_Name	KRR1-BGHLV27-HepG2
ENCODE_series_ID	ENCSR597NVC
Batch_ID	BGHLV27
Pool ID	Pool-151201
Local_Set_Name	set27
ENCODE_KD_Exp_ID	ENCSR542ESY
ENCODE_CN_Exp_ID	ENCSR246RRQ
Rep1	KRR1_BGHLV27-27
Rep2	KRR1_BGHLV27-28
CN1	non-target_BGHLV27-1
CN2	non-target_BGHLV27-2
Rep1_qPCR	54.2
Rep2_qPCR	45.3
Rep1_WB	93.3
Rep2_WB	91.4
Antibody Cat#	A303-898A
Antibody Lot#	A303-898A
Antibody DCC ID	ENCAB458ZFO
Status	Released
Project	ENCODE3
ID	641

Experiment Information (Status: Released)

	BGHLV27-27	BGHLV27-28
idx	647	648
TRCN#_or_BGC#	TRCN0000072295	TRCN0000072295
shRNA_or_gRNA_sequence	GCATTGGAACTCTTAACTAAT	GCATTGGAACTCTTAACTAAT
PAM
Name	KRR1	KRR1
Sample_ID	BGHLV27-27	BGHLV27-28
transduction_Date	6/9/2015	6/9/2015
days
RBP_name	KRR1	KRR1
qPCR_result	54.2	45.3
Ave_qPCR	49.8
RT-qPCR_primer-F	cgaagacaacggcttattgg
RT-qPCR_primer-R	ggtccaatggctgaaactgt
protein_conc	4394	4556
WB_result	93.3	91.4
Ave_WB	92.4
WB_DONE_date	9/2/2015
MW	44kDa
IP	1	1
antibody_Cat#	A303-898A	A303-898A
Antibody DCC ID	ENCAB458ZFO	ENCAB458ZFO
submitted_to_DCC_date	12/7/2015
Rep1_TPM	33.8	0
Rep2_TPM	28.1	0
Action
Library_start_date	9/28/2015	9/28/2015
repeat_library
Note	?	?
ID	2734	2735

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
KRR1	Product_ID: A303-898A Lot_ID: 1 Source: Bethyl Labs Target Name: KRR1-human

Experiment Status

	BGHLV27-27	BGHLV27-28
Sample_ID	BGHLV27-27	BGHLV27-28
Sample Name	KRR1_BGHLV27-27	KRR1_BGHLV27-28
Sample Name	KRR1_BGHLV27-27	KRR1_BGHLV27-28
RBP	KRR1	KRR1
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2016-01-16	2016-01-16
Project	ENCODE3	ENCODE3
Note
ID	966	967

Library-Prep
Sequencing

Library-Prep Information

	BGHLV27-27	BGHLV27-28
Sample #
Sample Name	KRR1-BGHLV27-27	KRR1-BGHLV27-28
Sample_Name_Alias	KRR1_BGHLV27-27	KRR1_BGHLV27-28
Index Well Position	S07	S08
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2015-09-28	2015-09-28
Lib_ID	Lib-150928	Lib-150928
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV27/set1/G1.png	DNA_Library_LV27/set1/H1.png
RIN	10.0	9.8
libSample_RNA_Well	RNA_Library_LV26-27-28-29/set1/G4.png	RNA_Library_LV26-27-28-29/set1/H4.png
SampleQC_method
SampleQC_date
Sample_ID	BGHLV27-27	BGHLV27-28
RBP	KRR1	KRR1
Batch_ID	BGHLV27	BGHLV27
WB_result	93.300	91.400
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2658	2659

Sequencing Information

	BGHLV27-27	BGHLV27-28
Sample_ID	BGHLV27-27	BGHLV27-28
Sample Name	KRR1_BGHLV27-27	KRR1_BGHLV27-28
Pool ID	Pool-151201	Pool-151201
LocalServer_folder	set27	set27
total_reads	69,622,158	93,353,600
total_aligned_reads	63,560,762	84,954,714
unique_aligned_reads	59,844,760	79,850,168
percent_uniqueAligned	0.85956	0.85535
correlation_replicates	0.997506	0.997506
spikein_reads	278,730	335,906
percent_spikeins	0.00400	0.00360
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	1300	1301

Data Submission Information

	BGHLV27-27	BGHLV27-27
ENCODE_alias	brenton-graveley:KRR1_BGHLV27	brenton-graveley:KRR1-BGHLV27-HepG2
ENCODE_accession	ENCSR542ESY	ENCSR597NVC
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV27-27	BGHLV27-27
Sample Name	KRR1_BGHLV27-27	KRR1_BGHLV27-27
Selected	Yes	Yes
Status	Released	Released
Status_Date	2016-01-14	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	3030	6793

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
KRR1_BGHLV27-27_1.fastq.gz	ENCODE_DATA/set27/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1300	HiSeq2500	100	paired-ended	1	GRCh38	V40		non-target_BGHLV27-1_1.fastq.gz,non-target_BGHLV27-2_1.fastq.gz	ENCODE3	20008
KRR1_BGHLV27-27_2.fastq.gz	ENCODE_DATA/set27/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1300	HiSeq2500	100	paired-ended	2				non-target_BGHLV27-1_2.fastq.gz,non-target_BGHLV27-2_2.fastq.gz	ENCODE3	20030
KRR1_BGHLV27-27_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set27/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1300					GRCh38	V40	KRR1_BGHLV27-27_1.fastq.gz,KRR1_BGHLV27-27_2.fastq.gz		ENCORE2	20052
KRR1_BGHLV27-27_Signal.Unique.strand+.bw	ENCODE_DATA/set27/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1300					GRCh38	V40	KRR1_BGHLV27-27/Aligned.sortedByCoord.out.bam		ENCORE2	20074
KRR1_BGHLV27-27_Signal.Unique.strand-.bw	ENCODE_DATA/set27/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1300					GRCh38	V40	KRR1_BGHLV27-27/Aligned.sortedByCoord.out.bam		ENCORE2	20096
KRR1_BGHLV27-27_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set27/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1300					GRCh38	V40	KRR1_BGHLV27-27/Aligned.sortedByCoord.out.bam		ENCORE2	20118
KRR1_BGHLV27-27_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set27/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1300					GRCh38	V40	KRR1_BGHLV27-27/Aligned.sortedByCoord.out.bam		ENCORE2	20140
KRR1_BGHLV27-27_quant.sf	ENCODE_DATA/set27/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1300					GRCh38	V40	KRR1_BGHLV27-27_1.fastq.gz,KRR1_BGHLV27-27_2.fastq.gz		ENCORE2	20680
KRR1_BGHLV27-28_1.fastq.gz	ENCODE_DATA/set27/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1301	HiSeq2500	100	paired-ended	1	GRCh38	V40		non-target_BGHLV27-1_1.fastq.gz,non-target_BGHLV27-2_1.fastq.gz	ENCODE3	20009
KRR1_BGHLV27-28_2.fastq.gz	ENCODE_DATA/set27/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1301	HiSeq2500	100	paired-ended	2				non-target_BGHLV27-1_2.fastq.gz,non-target_BGHLV27-2_2.fastq.gz	ENCODE3	20031
KRR1_BGHLV27-28_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set27/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1301					GRCh38	V40	KRR1_BGHLV27-28_1.fastq.gz,KRR1_BGHLV27-28_2.fastq.gz		ENCORE2	20053
KRR1_BGHLV27-28_Signal.Unique.strand+.bw	ENCODE_DATA/set27/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1301					GRCh38	V40	KRR1_BGHLV27-28/Aligned.sortedByCoord.out.bam		ENCORE2	20075
KRR1_BGHLV27-28_Signal.Unique.strand-.bw	ENCODE_DATA/set27/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1301					GRCh38	V40	KRR1_BGHLV27-28/Aligned.sortedByCoord.out.bam		ENCORE2	20097
KRR1_BGHLV27-28_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set27/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1301					GRCh38	V40	KRR1_BGHLV27-28/Aligned.sortedByCoord.out.bam		ENCORE2	20119
KRR1_BGHLV27-28_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set27/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1301					GRCh38	V40	KRR1_BGHLV27-28/Aligned.sortedByCoord.out.bam		ENCORE2	20141
KRR1_BGHLV27-28_quant.sf	ENCODE_DATA/set27/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1301					GRCh38	V40	KRR1_BGHLV27-28_1.fastq.gz,KRR1_BGHLV27-28_2.fastq.gz		ENCORE2	20681