IFIT2 RNA-Seq in K562

General Information


RBP	IFIT2
Cell_Line	K562
Method	CRISPR
Exp_Name	IFIT2-BGKcLV17-K562
ENCODE_series_ID	ENCSR781IDA
Batch_ID	BGKcLV17
Pool ID	Pool-200103
Local_Set_Name	set44_K
ENCODE_KD_Exp_ID	ENCSR671OGO
ENCODE_CN_Exp_ID	ENCSR516TLX
Rep1	IFIT2-BGKcLV17-31
Rep2	IFIT2-BGKcLV17-32
CN1	NT-BGKcLV17-1
CN2	NT-BGKcLV17-2
Rep1_qPCR	44.8
Rep2_qPCR	58.8
Rep1_WB	49.6
Rep2_WB	50.6
Antibody Cat#	PA5-28800
Antibody Lot#	lot# TK2671326A
Antibody DCC ID	ENCAB688YER
Status	Released
Project	ENCODE4
ID	89

Experiment Information (Status: Released)

	BGKcLV17-31	BGKcLV17-32
idx	638	639
TRCN#_or_BGC#	BGC#0000402	BGC#0000402
shRNA_or_gRNA_sequence	AATGGCATTTTAGTTGCCGT	AATGGCATTTTAGTTGCCGT
PAM	tgg	tgg
Name	IFIT2_90	IFIT2_90
Sample_ID	BGKcLV17-31	BGKcLV17-32
transduction_Date	7/2/19	7/2/19
days	Day 6	Day 6
RBP_name	IFIT2	IFIT2
qPCR_result	44.8	58.8
Ave_qPCR	51.8
RT-qPCR_primer-F	aagcaacaaaacgtgggaac
RT-qPCR_primer-R	gggaaaaccccaccatctat
protein_conc	4928	4775
WB_result	49.6	50.6
Ave_WB	50.1
WB_DONE_date	7/25/19
MW	55KD
IP	Rabbit / I	Polyclonal
antibody_Cat#	PA5-28800	lot# TK2671326A
Antibody DCC ID	ENCAB688YER
submitted_to_DCC_date	8/20/19
Rep1_TPM	0.1	0
Rep2_TPM	0	0
Action	Ready	Ready
Library_start_date	12/05/19	12/05/19
repeat_library
Note
ID	4754	4755

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
IFIT2	Product_ID: PA5-28800 Lot_ID: TK2671326A Source: Thermo Fisher Target Name: IFIT2-human

Experiment Status

	BGKcLV17-31	BGKcLV17-32
Sample_ID	BGKcLV17-31	BGKcLV17-32
Sample Name
Sample Name	IFIT2-BGKcLV17-31	IFIT2-BGKcLV17-32
RBP	IFIT2	IFIT2
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2020-12-01	2020-12-01
Project	ENCODE4	ENCODE4
Note
ID	5511	5512

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV17-31	BGKcLV17-32
Sample #	101	102
Sample Name	IFIT2-BGKcLV17-31	IFIT2-BGKcLV17-32
Sample_Name_Alias
Index Well Position	A01	B01
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2020-01-02	2020-01-02
Lib_ID	Lib-200102	Lib-200102
Tecan_Location	2-A1	2-B1
Tecan	15.07	43.19
Tecan_date	2019-12-16	2019-12-16
Size_bp	278	276
Peak_Molarity	10.40	19.30
libSampleQC_DNA_Well	DNA_Library_set43-44/set1/A9.png	DNA_Library_set43-44/set1/B9.png
RIN	9.5	9.4
libSample_RNA_Well	RNA_Library_set43-44/set4/A4.png	RNA_Library_set43-44/set4/B4.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2019-12-11	2019-12-11
Sample_ID	BGKcLV17-31	BGKcLV17-32
RBP	IFIT2	IFIT2
Batch_ID	BGKcLV17	BGKcLV17
WB_result	49.600	50.600
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	677	678

Sequencing Information

	BGKcLV17-31	BGKcLV17-32
Sample_ID	BGKcLV17-31	BGKcLV17-32
Sample Name	IFIT2-BGKcLV17-31	IFIT2-BGKcLV17-32
Pool ID	Pool-200103	Pool-200103
LocalServer_folder	set44_K	set44_K
total_reads	293,884,258	107,508,308
total_aligned_reads	262,243,608	95,324,138
unique_aligned_reads	237,853,546	86,751,932
percent_uniqueAligned	0.80934	0.80693
correlation_replicates	0.997452	0.997452
spikein_reads	95,366	14,548
percent_spikeins	0.00032	0.00014
original_ReadLength	150	150
QC_Status	Submitted	Submitted
ID	183	184

Data Submission Information

	BGKcLV17-31	BGKcLV17-31	BGKcLV17-31	BGKcLV17-31	BGKcLV17-31	BGKcLV17-31	BGKcLV17-32	BGKcLV17-32	BGKcLV17-32	BGKcLV17-32
ENCODE_alias	brenton-graveley:IFIT2-BGKcLV17	brenton-graveley:IFIT2-BGKcLV17-31	brenton-graveley:L-IFIT2-BGKcLV17-31	brenton-graveley:IFIT2-BGKcLV17-31_S11_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:IFIT2-BGKcLV17-31_S11_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:IFIT2-BGKcLV17-K562	brenton-graveley:IFIT2-BGKcLV17-32	brenton-graveley:L-IFIT2-BGKcLV17-32	brenton-graveley:IFIT2-BGKcLV17-32_S12_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:IFIT2-BGKcLV17-32_S12_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR671OGO	ENCBS101PEX	ENCLB719ENY	ENCFF169FIG	ENCFF398OTD	ENCSR781IDA	ENCBS662ZVC	ENCLB512NHN	ENCFF385MXH	ENCFF025KBG
object_type	experiment	biosample	library	file_fastq1	file_fastq2	gene_silencing_series	biosample	library	file_fastq1	file_fastq2
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKcLV17-31	BGKcLV17-31	BGKcLV17-31	BGKcLV17-31	BGKcLV17-31	BGKcLV17-31	BGKcLV17-32	BGKcLV17-32	BGKcLV17-32	BGKcLV17-32
Sample Name	IFIT2-BGKcLV17-31	IFIT2-BGKcLV17-31	IFIT2-BGKcLV17-31	IFIT2-BGKcLV17-31	IFIT2-BGKcLV17-31	IFIT2-BGKcLV17-31	IFIT2-BGKcLV17-32	IFIT2-BGKcLV17-32	IFIT2-BGKcLV17-32	IFIT2-BGKcLV17-32
Selected	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes
Status	Released	Released	Released	Released	Released	Released	Released	Released	Released	Released
Status_Date	2020-12-01	2020-12-01	2020-12-01	2020-12-01	2020-12-01	2022-03-02	2020-12-01	2020-12-01	2020-12-01	2020-12-01
Project	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4
		LV44K_biosample_protocol	LV44K_library_protocol				LV44K_biosample_protocol	LV44K_library_protocol
protocol_URL		IFIT2-BGKcLV17-31.pdf	L-IFIT2-BGKcLV17-31.pdf				IFIT2-BGKcLV17-32.pdf	L-IFIT2-BGKcLV17-32.pdf
ID	75	230	396	698	728	7243	231	397	699	729

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
IFIT2-BGKcLV17-31_S11_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set44_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	183	NovaSeq6000	100	paired-ended	1				NT-BGKcLV17-1_S71_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV17-2_S72_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	285
IFIT2-BGKcLV17-31_S11_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set44_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	183	NovaSeq6000	100	paired-ended	2				NT-BGKcLV17-1_S71_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV17-2_S72_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	315
IFIT2-BGKcLV17-31_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set44_K/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	183					GRCh38	V40	IFIT2-BGKcLV17-31_S11_R1_001.filtered.trimmed.paired.fastq.gz,IFIT2-BGKcLV17-31_S11_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24681
IFIT2-BGKcLV17-31_Signal.Unique.strand+.bw	ENCODE_DATA/set44_K/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	183					GRCh38	V40	IFIT2-BGKcLV17-31/Aligned.sortedByCoord.out.bam		ENCORE2	24711
IFIT2-BGKcLV17-31_Signal.Unique.strand-.bw	ENCODE_DATA/set44_K/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	183					GRCh38	V40	IFIT2-BGKcLV17-31/Aligned.sortedByCoord.out.bam		ENCORE2	24741
IFIT2-BGKcLV17-31_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set44_K/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	183					GRCh38	V40	IFIT2-BGKcLV17-31/Aligned.sortedByCoord.out.bam		ENCORE2	24771
IFIT2-BGKcLV17-31_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set44_K/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	183					GRCh38	V40	IFIT2-BGKcLV17-31/Aligned.sortedByCoord.out.bam		ENCORE2	24801
IFIT2-BGKcLV17-31_quant.sf	ENCODE_DATA/set44_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	183					GRCh38	V40	IFIT2-BGKcLV17-31_S11_R1_001.filtered.trimmed.paired.fastq.gz,IFIT2-BGKcLV17-31_S11_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24831
IFIT2-BGKcLV17-32_S12_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set44_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	184	NovaSeq6000	100	paired-ended	1				NT-BGKcLV17-1_S71_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV17-2_S72_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	286
IFIT2-BGKcLV17-32_S12_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set44_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	184	NovaSeq6000	100	paired-ended	2				NT-BGKcLV17-1_S71_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV17-2_S72_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	316
IFIT2-BGKcLV17-32_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set44_K/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	184					GRCh38	V40	IFIT2-BGKcLV17-32_S12_R1_001.filtered.trimmed.paired.fastq.gz,IFIT2-BGKcLV17-32_S12_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24682
IFIT2-BGKcLV17-32_Signal.Unique.strand+.bw	ENCODE_DATA/set44_K/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	184					GRCh38	V40	IFIT2-BGKcLV17-32/Aligned.sortedByCoord.out.bam		ENCORE2	24712
IFIT2-BGKcLV17-32_Signal.Unique.strand-.bw	ENCODE_DATA/set44_K/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	184					GRCh38	V40	IFIT2-BGKcLV17-32/Aligned.sortedByCoord.out.bam		ENCORE2	24742
IFIT2-BGKcLV17-32_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set44_K/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	184					GRCh38	V40	IFIT2-BGKcLV17-32/Aligned.sortedByCoord.out.bam		ENCORE2	24772
IFIT2-BGKcLV17-32_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set44_K/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	184					GRCh38	V40	IFIT2-BGKcLV17-32/Aligned.sortedByCoord.out.bam		ENCORE2	24802
IFIT2-BGKcLV17-32_quant.sf	ENCODE_DATA/set44_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	184					GRCh38	V40	IFIT2-BGKcLV17-32_S12_R1_001.filtered.trimmed.paired.fastq.gz,IFIT2-BGKcLV17-32_S12_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24832