KIF1C RNA-Seq in HepG2

General Information


RBP	KIF1C
Cell_Line	HepG2
Method	shRNA
Exp_Name	KIF1C-BGHLV31-HepG2
ENCODE_series_ID	ENCSR514ALV
Batch_ID	BGHLV31
Pool ID	Pool-160229
Local_Set_Name	set31
ENCODE_KD_Exp_ID	ENCSR182GKG
ENCODE_CN_Exp_ID	ENCSR538QOG
Rep1	KIF1C_BGHLV31-41
Rep2	KIF1C_BGHLV31-42
CN1	NT-BGHLV31-1
CN2	NT-BGHLV31-2
Rep1_qPCR	83.9
Rep2_qPCR	84.4
Rep1_WB	78.4
Rep2_WB	77.4
Antibody Cat#	A301-069A
Antibody Lot#	A301-069A
Antibody DCC ID	ENCAB630KUK
Status	Released
Project	ENCODE3
ID	698

Experiment Information (Status: Released)

	BGHLV31-41	BGHLV31-42
idx	789	790
TRCN#_or_BGC#	TRCN0000116589	TRCN0000116589
shRNA_or_gRNA_sequence	CTGGAGAATCAGTACCGGAAA	CTGGAGAATCAGTACCGGAAA
PAM
Name	KIF1C	KIF1C
Sample_ID	BGHLV31-41	BGHLV31-42
transduction_Date	9/24/2015	9/24/2015
days
RBP_name	KIF1C	KIF1C
qPCR_result	83.9	84.4
Ave_qPCR	84.1
RT-qPCR_primer-F	aggtgaagctgcagaacagc
RT-qPCR_primer-R	ggacctcaccaccttcttca
protein_conc	4692	4021
WB_result	78.4	77.4
Ave_WB	77.9
WB_DONE_date	12/2/2015
MW	123kDa
IP	1IP	1IP
antibody_Cat#	A301-069A	A301-069A
Antibody DCC ID	ENCAB630KUK	ENCAB630KUK
submitted_to_DCC_date	12/7/2015
Rep1_TPM	43.5	0
Rep2_TPM	51.7	0
Action
Library_start_date	2/4/2016	2/4/2016
repeat_library
Note
ID	2878	2879

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
KIF1C	Product_ID: A301-069A Lot_ID: 1 Source: Bethyl Labs Target Name: KIF1C-human

Experiment Status

	BGHLV31-41	BGHLV31-42
Sample_ID	BGHLV31-41	BGHLV31-42
Sample Name	KIF1C_BGHLV31-41	KIF1C_BGHLV31-42
Sample Name	KIF1C_BGHLV31-41	KIF1C_BGHLV31-42
RBP	KIF1C	KIF1C
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2016-03-07	2016-03-07
Project	ENCODE3	ENCODE3
Note
ID	1123	1124

Library-Prep
Sequencing

Library-Prep Information

	BGHLV31-41	BGHLV31-42
Sample #
Sample Name	KIF1C-BGHLV31-41	KIF1C-BGHLV31-42
Sample_Name_Alias	KIF1C_BGHLV31-41	KIF1C_BGHLV31-42
Index Well Position	S01	S02
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2016-02-04	2016-02-04
Lib_ID	Lib-160204	Lib-160204
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV31-21B/set1/A7.png	DNA_Library_LV31-21B/set1/B7.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_LV29-30-31-32/set1/A10.png	RNA_Library_LV29-30-31-32/set1/B10.png
SampleQC_method
SampleQC_date
Sample_ID	BGHLV31-41	BGHLV31-42
RBP	KIF1C	KIF1C
Batch_ID	BGHLV31	BGHLV31
WB_result	78.400	77.400
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2820	2821

Sequencing Information

	BGHLV31-41	BGHLV31-42
Sample_ID	BGHLV31-41	BGHLV31-42
Sample Name	KIF1C_BGHLV31-41	KIF1C_BGHLV31-42
Pool ID	Pool-160229	Pool-160229
LocalServer_folder	set31	set31
total_reads	55,454,930	57,667,996
total_aligned_reads	49,276,852	50,945,196
unique_aligned_reads	46,363,766	47,965,868
percent_uniqueAligned	0.83606	0.83176
correlation_replicates	0.998519	0.998519
spikein_reads	258,622	283,494
percent_spikeins	0.00466	0.00492
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1469	1470

Data Submission Information

	BGHLV31-41	BGHLV31-41
ENCODE_alias	brenton-graveley:KIF1C_BGHLV31	brenton-graveley:KIF1C-BGHLV31-HepG2
ENCODE_accession	ENCSR182GKG	ENCSR514ALV
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV31-41	BGHLV31-41
Sample Name	KIF1C_BGHLV31-41	KIF1C_BGHLV31-41
Selected	Yes	Yes
Status	Released	Released
Status_Date	2016-03-07	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	3094	6791

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
KIF1C_BGHLV31-41_ATCACG_L007_001.R1.fastq.gz	ENCODE_DATA/set31/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1469	HiSeq2500	100	paired-ended	1				NT-BGHLV31-1_GATCAG_L005_001.R1.fastq.gz,NT-BGHLV31-2_TAGCTT_L005_001.R1.fastq.gz	ENCODE3	20984
KIF1C_BGHLV31-41_ATCACG_L007_001.R2.fastq.gz	ENCODE_DATA/set31/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1469	HiSeq2500	100	paired-ended	2				NT-BGHLV31-1_GATCAG_L005_001.R2.fastq.gz,NT-BGHLV31-2_TAGCTT_L005_001.R2.fastq.gz	ENCODE3	21010
KIF1C_BGHLV31-41_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set31/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1469					GRCh38	V40	KIF1C_BGHLV31-41_ATCACG_L007_001.R1.fastq.gz,KIF1C_BGHLV31-41_ATCACG_L007_001.R2.fastq.gz		ENCORE2	21044
KIF1C_BGHLV31-41_Signal.Unique.strand+.bw	ENCODE_DATA/set31/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1469					GRCh38	V40	KIF1C_BGHLV31-41/Aligned.sortedByCoord.out.bam		ENCORE2	21070
KIF1C_BGHLV31-41_Signal.Unique.strand-.bw	ENCODE_DATA/set31/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1469					GRCh38	V40	KIF1C_BGHLV31-41/Aligned.sortedByCoord.out.bam		ENCORE2	21096
KIF1C_BGHLV31-41_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set31/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1469					GRCh38	V40	KIF1C_BGHLV31-41/Aligned.sortedByCoord.out.bam		ENCORE2	21122
KIF1C_BGHLV31-41_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set31/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1469					GRCh38	V40	KIF1C_BGHLV31-41/Aligned.sortedByCoord.out.bam		ENCORE2	21148
KIF1C_BGHLV31-41_quant.sf	ENCODE_DATA/set31/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1469					GRCh38	V40	KIF1C_BGHLV31-41_ATCACG_L007_001.R1.fastq.gz,KIF1C_BGHLV31-41_ATCACG_L007_001.R2.fastq.gz		ENCORE2	21174
KIF1C_BGHLV31-42_CGATGT_L007_001.R1.fastq.gz	ENCODE_DATA/set31/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1470	HiSeq2500	100	paired-ended	1				NT-BGHLV31-1_GATCAG_L005_001.R1.fastq.gz,NT-BGHLV31-2_TAGCTT_L005_001.R1.fastq.gz	ENCODE3	20985
KIF1C_BGHLV31-42_CGATGT_L007_001.R2.fastq.gz	ENCODE_DATA/set31/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1470	HiSeq2500	100	paired-ended	2				NT-BGHLV31-1_GATCAG_L005_001.R2.fastq.gz,NT-BGHLV31-2_TAGCTT_L005_001.R2.fastq.gz	ENCODE3	21011
KIF1C_BGHLV31-42_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set31/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1470					GRCh38	V40	KIF1C_BGHLV31-42_CGATGT_L007_001.R1.fastq.gz,KIF1C_BGHLV31-42_CGATGT_L007_001.R2.fastq.gz		ENCORE2	21045
KIF1C_BGHLV31-42_Signal.Unique.strand+.bw	ENCODE_DATA/set31/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1470					GRCh38	V40	KIF1C_BGHLV31-42/Aligned.sortedByCoord.out.bam		ENCORE2	21071
KIF1C_BGHLV31-42_Signal.Unique.strand-.bw	ENCODE_DATA/set31/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1470					GRCh38	V40	KIF1C_BGHLV31-42/Aligned.sortedByCoord.out.bam		ENCORE2	21097
KIF1C_BGHLV31-42_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set31/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1470					GRCh38	V40	KIF1C_BGHLV31-42/Aligned.sortedByCoord.out.bam		ENCORE2	21123
KIF1C_BGHLV31-42_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set31/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1470					GRCh38	V40	KIF1C_BGHLV31-42/Aligned.sortedByCoord.out.bam		ENCORE2	21149
KIF1C_BGHLV31-42_quant.sf	ENCODE_DATA/set31/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1470					GRCh38	V40	KIF1C_BGHLV31-42_CGATGT_L007_001.R1.fastq.gz,KIF1C_BGHLV31-42_CGATGT_L007_001.R2.fastq.gz		ENCORE2	21175