KIF1C RNA-Seq in K562

General Information


RBP	KIF1C
Cell_Line	K562
Method	shRNA
Exp_Name	KIF1C-BGKLV32-K562
ENCODE_series_ID	ENCSR183RYM
Batch_ID	BGKLV32
Pool ID	Pool-160425
Local_Set_Name	set32
ENCODE_KD_Exp_ID	ENCSR823WTA
ENCODE_CN_Exp_ID	ENCSR143COQ
Rep1	KIF1C_BGKLV32-33
Rep2	KIF1C_BGKLV32-34
CN1	NT_BGKLV32-1
CN2	NT_BGKLV32-2
Rep1_qPCR	86.5
Rep2_qPCR	89.2
Rep1_WB	70.9
Rep2_WB	79.0
Antibody Cat#	A301-069A
Antibody Lot#	A301-069A
Antibody DCC ID	ENCAB630KUK
Status	Released
Project	ENCODE3
ID	709

Experiment Information (Status: Released)

	BGKLV32-33	BGKLV32-34
idx	632	633
TRCN#_or_BGC#	TRCN0000116589	TRCN0000116589
shRNA_or_gRNA_sequence	CTGGAGAATCAGTACCGGAAA	CTGGAGAATCAGTACCGGAAA
PAM
Name	KIF1C	KIF1C
Sample_ID	BGKLV32-33	BGKLV32-34
transduction_Date	10/1/2015	10/1/2015
days
RBP_name	KIF1C	KIF1C
qPCR_result	86.5	89.2
Ave_qPCR	87.8
RT-qPCR_primer-F	aggtgaagctgcagaacagc
RT-qPCR_primer-R	ggacctcaccaccttcttca
protein_conc	3582	3211
WB_result	70.9	79.0
Ave_WB	75.0
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	20.79146021	0
Rep2_TPM	14.42907382	0
Action
Library_start_date	3/7/2016	3/7/2016
repeat_library
Note
ID	715	716

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

	BGKLV32-33	BGKLV32-34
Sample_ID	BGKLV32-33	BGKLV32-34
Sample Name	KIF1C_BGKLV32-33	KIF1C_BGKLV32-34
Sample Name	KIF1C_BGKLV32-33	KIF1C_BGKLV32-34
RBP	KIF1C	KIF1C
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2016-09-24	2016-09-24
Project	ENCODE3	ENCODE3
Note
ID	1167	1168

Library-Prep
Sequencing

Library-Prep Information

	BGKLV32-33	BGKLV32-34
Sample #
Sample Name	KIF1C-BGKLV32-33	KIF1C-BGKLV32-34
Sample_Name_Alias	KIF1C_BGKLV32-33	KIF1C_BGKLV32-34
Index Well Position	S18	S19
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2016-03-07	2016-03-07
Lib_ID	Lib-160307	Lib-160307
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV33-34-25B-32/set1/A8.png	DNA_Library_LV33-34-25B-32/set1/B8.png
RIN	9.6	9.6
libSample_RNA_Well	RNA_Library_LV32-33-34/set1/A1.png	RNA_Library_LV32-33-34/set1/B1.png
SampleQC_method
SampleQC_date
Sample_ID	BGKLV32-33	BGKLV32-34
RBP	KIF1C	KIF1C
Batch_ID	BGKLV32	BGKLV32
WB_result	70.900	79.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2852	2853

Sequencing Information

	BGKLV32-33	BGKLV32-34
Sample_ID	BGKLV32-33	BGKLV32-34
Sample Name	KIF1C_BGKLV32-33	KIF1C_BGKLV32-34
Pool ID	Pool-160425	Pool-160425
LocalServer_folder	set32	set32
total_reads	75,243,866	132,000,000
total_aligned_reads	55,615,802	111,497,860
unique_aligned_reads	50,835,992	101,490,180
percent_uniqueAligned	0.67562	0.76887
correlation_replicates	0.993924	0.993924
spikein_reads	322,068	611,466
percent_spikeins	0.00428	0.00463
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1501	1502

Data Submission Information

	BGKLV32-33	BGKLV32-33
ENCODE_alias	brenton-graveley:KIF1C_BGKLV32	brenton-graveley:KIF1C-BGKLV32-K562
ENCODE_accession	ENCSR823WTA	ENCSR183RYM
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKLV32-33	BGKLV32-33
Sample Name	KIF1C_BGKLV32-33	KIF1C_BGKLV32-33
Selected	Yes	Yes
Status	Released	Released
Status_Date	2016-05-25	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	3123	6792

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_BGKLV32-33_GTCCGC_L003_001.R1.fastq.gz	ENCODE_DATA/set32/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1501	HiSeq2500	100	paired-ended	1				NT_BGKLV32-1_ATCACG_L001_001.R1.fastq.gz,NT_BGKLV32-2_CGATGT_L001_001.R1.fastq.gz	ENCODE3	21200
KIF1C_BGKLV32-33_GTCCGC_L003_001.R2.fastq.gz	ENCODE_DATA/set32/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1501	HiSeq2500	100	paired-ended	2				NT_BGKLV32-1_ATCACG_L001_001.R2.fastq.gz,NT_BGKLV32-2_CGATGT_L001_001.R2.fastq.gz	ENCODE3	21230
KIF1C_BGKLV32-33_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set32/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1501					GRCh38	V40	KIF1C_BGKLV32-33_GTCCGC_L003_001.R1.fastq.gz,KIF1C_BGKLV32-33_GTCCGC_L003_001.R2.fastq.gz		ENCORE2	21260
KIF1C_BGKLV32-33_Signal.Unique.strand+.bw	ENCODE_DATA/set32/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1501					GRCh38	V40	KIF1C_BGKLV32-33/Aligned.sortedByCoord.out.bam		ENCORE2	21290
KIF1C_BGKLV32-33_Signal.Unique.strand-.bw	ENCODE_DATA/set32/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1501					GRCh38	V40	KIF1C_BGKLV32-33/Aligned.sortedByCoord.out.bam		ENCORE2	21320
KIF1C_BGKLV32-33_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set32/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1501					GRCh38	V40	KIF1C_BGKLV32-33/Aligned.sortedByCoord.out.bam		ENCORE2	21350
KIF1C_BGKLV32-33_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set32/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1501					GRCh38	V40	KIF1C_BGKLV32-33/Aligned.sortedByCoord.out.bam		ENCORE2	21380
KIF1C_BGKLV32-33_quant.sf	ENCODE_DATA/set32/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1501					GRCh38	V40	KIF1C_BGKLV32-33_GTCCGC_L003_001.R1.fastq.gz,KIF1C_BGKLV32-33_GTCCGC_L003_001.R2.fastq.gz		ENCORE2	21410
KIF1C_BGKLV32-34_GTGAAA_L003_001.R1.fastq.gz	ENCODE_DATA/set32/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1502	HiSeq2500	100	paired-ended	1				NT_BGKLV32-1_ATCACG_L001_001.R1.fastq.gz,NT_BGKLV32-2_CGATGT_L001_001.R1.fastq.gz	ENCODE3	21201
KIF1C_BGKLV32-34_GTGAAA_L003_001.R2.fastq.gz	ENCODE_DATA/set32/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1502	HiSeq2500	100	paired-ended	2				NT_BGKLV32-1_ATCACG_L001_001.R2.fastq.gz,NT_BGKLV32-2_CGATGT_L001_001.R2.fastq.gz	ENCODE3	21231
KIF1C_BGKLV32-34_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set32/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1502					GRCh38	V40	KIF1C_BGKLV32-34_GTGAAA_L003_001.R1.fastq.gz,KIF1C_BGKLV32-34_GTGAAA_L003_001.R2.fastq.gz		ENCORE2	21261
KIF1C_BGKLV32-34_Signal.Unique.strand+.bw	ENCODE_DATA/set32/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1502					GRCh38	V40	KIF1C_BGKLV32-34/Aligned.sortedByCoord.out.bam		ENCORE2	21291
KIF1C_BGKLV32-34_Signal.Unique.strand-.bw	ENCODE_DATA/set32/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1502					GRCh38	V40	KIF1C_BGKLV32-34/Aligned.sortedByCoord.out.bam		ENCORE2	21321
KIF1C_BGKLV32-34_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set32/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1502					GRCh38	V40	KIF1C_BGKLV32-34/Aligned.sortedByCoord.out.bam		ENCORE2	21351
KIF1C_BGKLV32-34_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set32/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1502					GRCh38	V40	KIF1C_BGKLV32-34/Aligned.sortedByCoord.out.bam		ENCORE2	21381
KIF1C_BGKLV32-34_quant.sf	ENCODE_DATA/set32/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1502					GRCh38	V40	KIF1C_BGKLV32-34_GTGAAA_L003_001.R1.fastq.gz,KIF1C_BGKLV32-34_GTGAAA_L003_001.R2.fastq.gz		ENCORE2	21411