IFIT2 RNA-Seq in HepG2

General Information


RBP	IFIT2
Cell_Line	HepG2
Method	CRISPR
Exp_Name	IFIT2-BGHcLV18-HepG2
ENCODE_series_ID	ENCSR158MXJ
Batch_ID	BGHcLV18
Pool ID	Pool-200103
Local_Set_Name	set44_H
ENCODE_KD_Exp_ID	ENCSR144HCM
ENCODE_CN_Exp_ID	ENCSR670KAS
Rep1	IFIT2-BGHcLV18-27
Rep2	IFIT2-BGHcLV18-28
CN1	NT-BGHcLV18-1
CN2	NT-BGHcLV18-2
Rep1_qPCR	0.0
Rep2_qPCR	0.0
Rep1_WB
Rep2_WB
Antibody Cat#	PA5-28800
Antibody Lot#	lot# TK2671326A
Antibody DCC ID	ENCAB688YER
Status	Released
Project	ENCODE4
ID	110

Experiment Information (Status: Released)

	BGHcLV18-27	BGHcLV18-28
idx	520	521
TRCN#_or_BGC#	BGC#0000403	BGC#0000403
shRNA_or_gRNA_sequence	ACTGATCTGCTAGAGCATGG	ACTGATCTGCTAGAGCATGG
PAM	AGG	AGG
Name	IFIT2_81	IFIT2_81
Sample_ID	BGHcLV18-27	BGHcLV18-28
transduction_Date	8/13/19	8/13/19
days	D6	D6
RBP_name	IFIT2	IFIT2
qPCR_result	0.0	0.0
Ave_qPCR	0.0
RT-qPCR_primer-F	aagcaacaaaacgtgggaac
RT-qPCR_primer-R	gggaaaaccccaccatctat
protein_conc	3854	3852
WB_result
Ave_WB		No clear band on the position
WB_DONE_date	8/21/19,8/28/19,9/16	Licor, wes
MW	55KD
IP	Rabbit / I	Polyclonal
antibody_Cat#	PA5-28800	lot# TK2671326A
Antibody DCC ID
submitted_to_DCC_date
Rep1_TPM	0	0
Rep2_TPM	0	0
Action	Ready	Ready
Library_start_date	12/11/19	12/11/19
repeat_library
Note
ID	6673	6674

Western Blot Western Blot info was not avaliable

Experiment Status

	BGHcLV18-27	BGHcLV18-28
Sample_ID	BGHcLV18-27	BGHcLV18-28
Sample Name
Sample Name	IFIT2-BGHcLV18-27	IFIT2-BGHcLV18-28
RBP	IFIT2	IFIT2
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2020-12-01	2020-12-01
Project	ENCODE4	ENCODE4
Note
ID	5637	5638

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV18-27	BGHcLV18-28
Sample #	143	144
Sample Name	IFIT2-BGHcLV18-27	IFIT2-BGHcLV18-28
Sample_Name_Alias
Index Well Position	G06	H06
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2020-01-02	2020-01-02
Lib_ID	Lib-200102	Lib-200102
Tecan_Location	4-C2	4-D2
Tecan	38.53	35.86
Tecan_date	2019-12-16	2019-12-16
Size_bp	274	278
Peak_Molarity	29.90	28.90
libSampleQC_DNA_Well	DNA_Library_set43-44/set2/G10.png	DNA_Library_set43-44/set2/H10.png
RIN	9.8	9.8
libSample_RNA_Well	RNA_Library_set43-44/set4/C12.png	RNA_Library_set43-44/set4/D12.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2019-12-13	2019-12-13
Sample_ID	BGHcLV18-27	BGHcLV18-28
RBP	IFIT2	IFIT2
Batch_ID	BGHcLV18	BGHcLV18
WB_result	0.000	0.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	719	720

Sequencing Information

	BGHcLV18-27	BGHcLV18-28
Sample_ID	BGHcLV18-27	BGHcLV18-28
Sample Name	IFIT2-BGHcLV18-27	IFIT2-BGHcLV18-28
Pool ID	Pool-200103	Pool-200103
LocalServer_folder	set44_H	set44_H
total_reads	190,672,950	181,677,128
total_aligned_reads	183,683,450	173,268,562
unique_aligned_reads	172,221,190	162,221,814
percent_uniqueAligned	0.90323	0.89291
correlation_replicates	0.999098	0.999098
spikein_reads	335,370	310,686
percent_spikeins	0.00176	0.00171
original_ReadLength	150	150
QC_Status	Submitted	Submitted
ID	225	226

Data Submission Information

	BGHcLV18-27	BGHcLV18-27	BGHcLV18-27	BGHcLV18-27	BGHcLV18-27	BGHcLV18-27	BGHcLV18-28	BGHcLV18-28	BGHcLV18-28	BGHcLV18-28
ENCODE_alias	brenton-graveley:IFIT2-BGHcLV18	brenton-graveley:IFIT2-BGHcLV18-27	brenton-graveley:L-IFIT2-BGHcLV18-27	brenton-graveley:IFIT2-BGHcLV18-27_S81_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:IFIT2-BGHcLV18-27_S81_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:IFIT2-BGHcLV18-HepG2	brenton-graveley:IFIT2-BGHcLV18-28	brenton-graveley:L-IFIT2-BGHcLV18-28	brenton-graveley:IFIT2-BGHcLV18-28_S82_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:IFIT2-BGHcLV18-28_S82_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR144HCM	ENCBS131LVO	ENCLB782KSD	ENCFF056ZZS	ENCFF074PFU	ENCSR158MXJ	ENCBS518VOZ	ENCLB373DJP	ENCFF967LBC	ENCFF192MUI
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	BGHcLV18-27	BGHcLV18-27	BGHcLV18-27	BGHcLV18-27	BGHcLV18-27	BGHcLV18-27	BGHcLV18-28	BGHcLV18-28	BGHcLV18-28	BGHcLV18-28
Sample Name	IFIT2-BGHcLV18-27	IFIT2-BGHcLV18-27	IFIT2-BGHcLV18-27	IFIT2-BGHcLV18-27	IFIT2-BGHcLV18-27	IFIT2-BGHcLV18-27	IFIT2-BGHcLV18-28	IFIT2-BGHcLV18-28	IFIT2-BGHcLV18-28	IFIT2-BGHcLV18-28
Selected	Yes	No	Yes	Yes	Yes	Yes	No	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
			LV44H_library_protocol					LV44H_library_protocol
protocol_URL			L-IFIT2-BGHcLV18-27.pdf					L-IFIT2-BGHcLV18-28.pdf
ID	57	194	360	610	662	7242	195	361	611	663

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-BGHcLV18-27_S81_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set44_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	225	NovaSeq6000	100	paired-ended	1				NT-BGHcLV18-1_S35_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV18-2_S36_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	193
IFIT2-BGHcLV18-27_S81_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set44_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	225	NovaSeq6000	100	paired-ended	2				NT-BGHcLV18-1_S35_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV18-2_S36_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	245
IFIT2-BGHcLV18-27_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set44_H/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	225					GRCh38	V40	IFIT2-BGHcLV18-27_S81_R1_001.filtered.trimmed.paired.fastq.gz,IFIT2-BGHcLV18-27_S81_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24913
IFIT2-BGHcLV18-27_Signal.Unique.strand+.bw	ENCODE_DATA/set44_H/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	225					GRCh38	V40	IFIT2-BGHcLV18-27/Aligned.sortedByCoord.out.bam		ENCORE2	24965
IFIT2-BGHcLV18-27_Signal.Unique.strand-.bw	ENCODE_DATA/set44_H/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	225					GRCh38	V40	IFIT2-BGHcLV18-27/Aligned.sortedByCoord.out.bam		ENCORE2	25017
IFIT2-BGHcLV18-27_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set44_H/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	225					GRCh38	V40	IFIT2-BGHcLV18-27/Aligned.sortedByCoord.out.bam		ENCORE2	25069
IFIT2-BGHcLV18-27_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set44_H/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	225					GRCh38	V40	IFIT2-BGHcLV18-27/Aligned.sortedByCoord.out.bam		ENCORE2	25121
IFIT2-BGHcLV18-27_quant.sf	ENCODE_DATA/set44_H/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	225					GRCh38	V40	IFIT2-BGHcLV18-27_S81_R1_001.filtered.trimmed.paired.fastq.gz,IFIT2-BGHcLV18-27_S81_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25173
IFIT2-BGHcLV18-28_S82_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set44_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	226	NovaSeq6000	100	paired-ended	1				NT-BGHcLV18-1_S35_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV18-2_S36_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	194
IFIT2-BGHcLV18-28_S82_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set44_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	226	NovaSeq6000	100	paired-ended	2				NT-BGHcLV18-1_S35_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV18-2_S36_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	246
IFIT2-BGHcLV18-28_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set44_H/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	226					GRCh38	V40	IFIT2-BGHcLV18-28_S82_R1_001.filtered.trimmed.paired.fastq.gz,IFIT2-BGHcLV18-28_S82_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24914
IFIT2-BGHcLV18-28_Signal.Unique.strand+.bw	ENCODE_DATA/set44_H/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	226					GRCh38	V40	IFIT2-BGHcLV18-28/Aligned.sortedByCoord.out.bam		ENCORE2	24966
IFIT2-BGHcLV18-28_Signal.Unique.strand-.bw	ENCODE_DATA/set44_H/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	226					GRCh38	V40	IFIT2-BGHcLV18-28/Aligned.sortedByCoord.out.bam		ENCORE2	25018
IFIT2-BGHcLV18-28_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set44_H/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	226					GRCh38	V40	IFIT2-BGHcLV18-28/Aligned.sortedByCoord.out.bam		ENCORE2	25070
IFIT2-BGHcLV18-28_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set44_H/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	226					GRCh38	V40	IFIT2-BGHcLV18-28/Aligned.sortedByCoord.out.bam		ENCORE2	25122
IFIT2-BGHcLV18-28_quant.sf	ENCODE_DATA/set44_H/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	226					GRCh38	V40	IFIT2-BGHcLV18-28_S82_R1_001.filtered.trimmed.paired.fastq.gz,IFIT2-BGHcLV18-28_S82_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25174