FBL RNA-Seq in HepG2

General Information


RBP	FBL
Cell_Line	HepG2
Method	CRISPR
Exp_Name	FBL-BGHcLV18-HepG2
ENCODE_series_ID	ENCSR407XDO
Batch_ID	BGHcLV18
Pool ID	Pool-200103
Local_Set_Name	set44_H
ENCODE_KD_Exp_ID	ENCSR796HOP
ENCODE_CN_Exp_ID	ENCSR670KAS
Rep1	FBL-BGHcLV18-19
Rep2	FBL-BGHcLV18-20
CN1	NT-BGHcLV18-1
CN2	NT-BGHcLV18-2
Rep1_qPCR	68.9
Rep2_qPCR	60.2
Rep1_WB	53.6
Rep2_WB	50.7
Antibody Cat#	PA5-27529
Antibody Lot#	lot# TL2692996
Antibody DCC ID	ENCAB364WTO
Status	Released
Project	ENCODE4
ID	107

Experiment Information (Status: Released)

	BGHcLV18-19	BGHcLV18-20
idx	512	513
TRCN#_or_BGC#	BGC#0000396	BGC#0000396
shRNA_or_gRNA_sequence	ATGTGATGGTGGAGCCGCAT	ATGTGATGGTGGAGCCGCAT
PAM	CGG	CGG
Name	FBL_90	FBL_90
Sample_ID	BGHcLV18-19	BGHcLV18-20
transduction_Date	8/13/19	8/13/19
days	D6	D6
RBP_name	FBL	FBL
qPCR_result	68.9	60.2
Ave_qPCR	64.6
RT-qPCR_primer-F	TGTCGAGGAAAGGAAGATGC
RT-qPCR_primer-R	GTTCCAGGCTCGGTACTCAA
protein_conc	3199	3825
WB_result	53.6	50.7
Ave_WB	52.1
WB_DONE_date	10/3/19
MW	34KD
IP	Rabbit / I	Polyclonal
antibody_Cat#	PA5-27529	lot# TL2692996
Antibody DCC ID	ENCAB364WTO
submitted_to_DCC_date
Rep1_TPM	666	0
Rep2_TPM	541	0
Action	Ready	Ready
Library_start_date	12/11/19	12/11/19
repeat_library
Note
ID	6665	6666

Western Blot Western Blot info was not avaliable

Experiment Status

	BGHcLV18-19	BGHcLV18-20
Sample_ID	BGHcLV18-19	BGHcLV18-20
Sample Name
Sample Name	FBL-BGHcLV18-19	FBL-BGHcLV18-20
RBP	FBL	FBL
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2020-12-01	2020-12-01
Project	ENCODE4	ENCODE4
Note
ID	5631	5632

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV18-19	BGHcLV18-20
Sample #	137	138
Sample Name	FBL-BGHcLV18-19	FBL-BGHcLV18-20
Sample_Name_Alias
Index Well Position	C06	D06
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-E1	4-F1
Tecan	40.73	33.05
Tecan_date	2019-12-16	2019-12-16
Size_bp	273	277
Peak_Molarity	32.10	30.10
libSampleQC_DNA_Well	DNA_Library_set43-44/set2/C7.png	DNA_Library_set43-44/set2/D7.png
RIN	9.0	9.6
libSample_RNA_Well	RNA_Library_set43-44/set4/G8.png	RNA_Library_set43-44/set4/H8.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2019-12-13	2019-12-13
Sample_ID	BGHcLV18-19	BGHcLV18-20
RBP	FBL	FBL
Batch_ID	BGHcLV18	BGHcLV18
WB_result	53.600	50.700
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	713	714

Sequencing Information

	BGHcLV18-19	BGHcLV18-20
Sample_ID	BGHcLV18-19	BGHcLV18-20
Sample Name	FBL-BGHcLV18-19	FBL-BGHcLV18-20
Pool ID	Pool-200103	Pool-200103
LocalServer_folder	set44_H	set44_H
total_reads	173,231,188	148,827,114
total_aligned_reads	168,516,074	143,082,726
unique_aligned_reads	157,933,868	134,088,814
percent_uniqueAligned	0.91169	0.90097
correlation_replicates	0.998580	0.998580
spikein_reads	304,518	234,304
percent_spikeins	0.00176	0.00157
original_ReadLength	150	150
QC_Status	Submitted	Submitted
ID	219	220

Data Submission Information

	BGHcLV18-19	BGHcLV18-19	BGHcLV18-19	BGHcLV18-19	BGHcLV18-19	BGHcLV18-19	BGHcLV18-20	BGHcLV18-20	BGHcLV18-20	BGHcLV18-20
ENCODE_alias	brenton-graveley:FBL-BGHcLV18	brenton-graveley:FBL-BGHcLV18-19	brenton-graveley:L-FBL-BGHcLV18-19	brenton-graveley:FBL-BGHcLV18-19_S53_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:FBL-BGHcLV18-19_S53_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:FBL-BGHcLV18-HepG2	brenton-graveley:FBL-BGHcLV18-20	brenton-graveley:L-FBL-BGHcLV18-20	brenton-graveley:FBL-BGHcLV18-20_S54_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:FBL-BGHcLV18-20_S54_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR796HOP	ENCBS141JHO	ENCLB135EOF	ENCFF937LWR	ENCFF188XIP	ENCSR407XDO	ENCBS145TEI	ENCLB381VPB	ENCFF205YLI	ENCFF028LFD
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	BGHcLV18-19	BGHcLV18-19	BGHcLV18-19	BGHcLV18-19	BGHcLV18-19	BGHcLV18-19	BGHcLV18-20	BGHcLV18-20	BGHcLV18-20	BGHcLV18-20
Sample Name	FBL-BGHcLV18-19	FBL-BGHcLV18-19	FBL-BGHcLV18-19	FBL-BGHcLV18-19	FBL-BGHcLV18-19	FBL-BGHcLV18-19	FBL-BGHcLV18-20	FBL-BGHcLV18-20	FBL-BGHcLV18-20	FBL-BGHcLV18-20
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-FBL-BGHcLV18-19.pdf					L-FBL-BGHcLV18-20.pdf
ID	54	188	354	604	656	7220	189	355	605	657

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
FBL-BGHcLV18-19_S53_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set44_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	219	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	185
FBL-BGHcLV18-19_S53_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set44_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	219	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	237
FBL-BGHcLV18-19_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set44_H/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	219					GRCh38	V40	FBL-BGHcLV18-19_S53_R1_001.filtered.trimmed.paired.fastq.gz,FBL-BGHcLV18-19_S53_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24905
FBL-BGHcLV18-19_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	219					GRCh38	V40	FBL-BGHcLV18-19/Aligned.sortedByCoord.out.bam		ENCORE2	24957
FBL-BGHcLV18-19_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	219					GRCh38	V40	FBL-BGHcLV18-19/Aligned.sortedByCoord.out.bam		ENCORE2	25009
FBL-BGHcLV18-19_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	219					GRCh38	V40	FBL-BGHcLV18-19/Aligned.sortedByCoord.out.bam		ENCORE2	25061
FBL-BGHcLV18-19_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	219					GRCh38	V40	FBL-BGHcLV18-19/Aligned.sortedByCoord.out.bam		ENCORE2	25113
FBL-BGHcLV18-19_quant.sf	ENCODE_DATA/set44_H/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	219					GRCh38	V40	FBL-BGHcLV18-19_S53_R1_001.filtered.trimmed.paired.fastq.gz,FBL-BGHcLV18-19_S53_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25165
FBL-BGHcLV18-20_S54_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set44_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	220	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	186
FBL-BGHcLV18-20_S54_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set44_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	220	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	238
FBL-BGHcLV18-20_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set44_H/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	220					GRCh38	V40	FBL-BGHcLV18-20_S54_R1_001.filtered.trimmed.paired.fastq.gz,FBL-BGHcLV18-20_S54_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24906
FBL-BGHcLV18-20_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	220					GRCh38	V40	FBL-BGHcLV18-20/Aligned.sortedByCoord.out.bam		ENCORE2	24958
FBL-BGHcLV18-20_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	220					GRCh38	V40	FBL-BGHcLV18-20/Aligned.sortedByCoord.out.bam		ENCORE2	25010
FBL-BGHcLV18-20_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	220					GRCh38	V40	FBL-BGHcLV18-20/Aligned.sortedByCoord.out.bam		ENCORE2	25062
FBL-BGHcLV18-20_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	220					GRCh38	V40	FBL-BGHcLV18-20/Aligned.sortedByCoord.out.bam		ENCORE2	25114
FBL-BGHcLV18-20_quant.sf	ENCODE_DATA/set44_H/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	220					GRCh38	V40	FBL-BGHcLV18-20_S54_R1_001.filtered.trimmed.paired.fastq.gz,FBL-BGHcLV18-20_S54_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25166