FBL RNA-Seq in K562

General Information


RBP	FBL
Cell_Line	K562
Method	CRISPR
Exp_Name	FBL-BGKcLV17-K562
ENCODE_series_ID	ENCSR848QFN
Batch_ID	BGKcLV17
Pool ID	Pool-200103
Local_Set_Name	set44_K
ENCODE_KD_Exp_ID	ENCSR635RAB
ENCODE_CN_Exp_ID	ENCSR516TLX
Rep1	FBL-BGKcLV17-19
Rep2	FBL-BGKcLV17-20
CN1	NT-BGKcLV17-1
CN2	NT-BGKcLV17-2
Rep1_qPCR	65.6
Rep2_qPCR	68.6
Rep1_WB	65.8
Rep2_WB	73.1
Antibody Cat#	PA5-27529
Antibody Lot#	lot# TL2692996
Antibody DCC ID	ENCAB364WTO
Status	Released
Project	ENCODE4
ID	85

Experiment Information (Status: Released)

	BGKcLV17-19	BGKcLV17-20
idx	626	627
TRCN#_or_BGC#	BGC#0000396	BGC#0000396
shRNA_or_gRNA_sequence	ATGTGATGGTGGAGCCGCAT	ATGTGATGGTGGAGCCGCAT
PAM	CGG	CGG
Name	FBL_90	FBL_90
Sample_ID	BGKcLV17-19	BGKcLV17-20
transduction_Date	7/2/19	7/2/19
days	Day 6	Day 6
RBP_name	FBL	FBL
qPCR_result	65.6	68.6
Ave_qPCR	67.1
RT-qPCR_primer-F	TGTCGAGGAAAGGAAGATGC
RT-qPCR_primer-R	GTTCCAGGCTCGGTACTCAA
protein_conc	3268	3604
WB_result	65.8	73.1
Ave_WB	69.4
WB_DONE_date	7/9/19
MW	34KD
IP	Rabbit / I	Polyclonal
antibody_Cat#	PA5-27529	lot# TL2692996
Antibody DCC ID	ENCAB364WTO
submitted_to_DCC_date
Rep1_TPM	1135.9	0
Rep2_TPM	1146.2	0
Action	Ready	Ready
Library_start_date	12/05/19	12/05/19
repeat_library
Note
ID	4742	4743

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
FBL	Product_ID: PA5-27529 Lot_ID: TL2692996 Source: Thermo Fisher Target Name: FBL-human

Experiment Status

	BGKcLV17-19	BGKcLV17-20
Sample_ID	BGKcLV17-19	BGKcLV17-20
Sample Name
Sample Name	FBL-BGKcLV17-19	FBL-BGKcLV17-20
RBP	FBL	FBL
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2020-12-01	2020-12-01
Project	ENCODE4	ENCODE4
Note
ID	5503	5504

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV17-19	BGKcLV17-20
Sample #	93	94
Sample Name	FBL-BGKcLV17-19	FBL-BGKcLV17-20
Sample_Name_Alias
Index Well Position	C12	D12
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2020-01-02	2020-01-02
Lib_ID	Lib-200102	Lib-200102
Tecan_Location	1-A2	1-B2
Tecan	43.45	36.42
Tecan_date	2019-12-16	2019-12-16
Size_bp	279	282
Peak_Molarity	35.50	28.60
libSampleQC_DNA_Well	DNA_Library_set43-44/set1/C8.png	DNA_Library_set43-44/set1/D8.png
RIN	9.0	9.3
libSample_RNA_Well	RNA_Library_set43-44/set4/C3.png	RNA_Library_set43-44/set4/D3.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2019-12-11	2019-12-11
Sample_ID	BGKcLV17-19	BGKcLV17-20
RBP	FBL	FBL
Batch_ID	BGKcLV17	BGKcLV17
WB_result	65.800	73.100
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	669	670

Sequencing Information

	BGKcLV17-19	BGKcLV17-20
Sample_ID	BGKcLV17-19	BGKcLV17-20
Sample Name	FBL-BGKcLV17-19	FBL-BGKcLV17-20
Pool ID	Pool-200103	Pool-200103
LocalServer_folder	set44_K	set44_K
total_reads	253,343,586	271,059,194
total_aligned_reads	243,896,808	261,241,340
unique_aligned_reads	221,094,360	237,727,396
percent_uniqueAligned	0.87271	0.87703
correlation_replicates	0.998767	0.998767
spikein_reads	50,956	63,422
percent_spikeins	0.00020	0.00023
original_ReadLength	150	150
QC_Status	Submitted	Submitted
ID	175	176

Data Submission Information

	BGKcLV17-19	BGKcLV17-19	BGKcLV17-19	BGKcLV17-19	BGKcLV17-19	BGKcLV17-19	BGKcLV17-20	BGKcLV17-20	BGKcLV17-20	BGKcLV17-20
ENCODE_alias	brenton-graveley:FBL-BGKcLV17	brenton-graveley:FBL-BGKcLV17-19	brenton-graveley:L-FBL-BGKcLV17-19	brenton-graveley:FBL-BGKcLV17-19_S5_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:FBL-BGKcLV17-19_S5_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:FBL-BGKcLV17-K562	brenton-graveley:FBL-BGKcLV17-20	brenton-graveley:L-FBL-BGKcLV17-20	brenton-graveley:FBL-BGKcLV17-20_S6_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:FBL-BGKcLV17-20_S6_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR635RAB	ENCBS642JRY	ENCLB253RUF	ENCFF773IFG	ENCFF363LVG	ENCSR848QFN	ENCBS923WNC	ENCLB284HVU	ENCFF406WYY	ENCFF757JUK
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	BGKcLV17-19	BGKcLV17-19	BGKcLV17-19	BGKcLV17-19	BGKcLV17-19	BGKcLV17-19	BGKcLV17-20	BGKcLV17-20	BGKcLV17-20	BGKcLV17-20
Sample Name	FBL-BGKcLV17-19	FBL-BGKcLV17-19	FBL-BGKcLV17-19	FBL-BGKcLV17-19	FBL-BGKcLV17-19	FBL-BGKcLV17-19	FBL-BGKcLV17-20	FBL-BGKcLV17-20	FBL-BGKcLV17-20	FBL-BGKcLV17-20
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		FBL-BGKcLV17-19.pdf	L-FBL-BGKcLV17-19.pdf				FBL-BGKcLV17-20.pdf	L-FBL-BGKcLV17-20.pdf
ID	71	222	388	690	720	7221	223	389	691	721

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-BGKcLV17-19_S5_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set44_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	175	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	277
FBL-BGKcLV17-19_S5_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set44_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	175	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	307
FBL-BGKcLV17-19_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set44_K/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	175					GRCh38	V40	FBL-BGKcLV17-19_S5_R1_001.filtered.trimmed.paired.fastq.gz,FBL-BGKcLV17-19_S5_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24673
FBL-BGKcLV17-19_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	175					GRCh38	V40	FBL-BGKcLV17-19/Aligned.sortedByCoord.out.bam		ENCORE2	24703
FBL-BGKcLV17-19_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	175					GRCh38	V40	FBL-BGKcLV17-19/Aligned.sortedByCoord.out.bam		ENCORE2	24733
FBL-BGKcLV17-19_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	175					GRCh38	V40	FBL-BGKcLV17-19/Aligned.sortedByCoord.out.bam		ENCORE2	24763
FBL-BGKcLV17-19_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	175					GRCh38	V40	FBL-BGKcLV17-19/Aligned.sortedByCoord.out.bam		ENCORE2	24793
FBL-BGKcLV17-19_quant.sf	ENCODE_DATA/set44_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	175					GRCh38	V40	FBL-BGKcLV17-19_S5_R1_001.filtered.trimmed.paired.fastq.gz,FBL-BGKcLV17-19_S5_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24823
FBL-BGKcLV17-20_S6_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set44_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	176	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	278
FBL-BGKcLV17-20_S6_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set44_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	176	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	308
FBL-BGKcLV17-20_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set44_K/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	176					GRCh38	V40	FBL-BGKcLV17-20_S6_R1_001.filtered.trimmed.paired.fastq.gz,FBL-BGKcLV17-20_S6_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24674
FBL-BGKcLV17-20_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	176					GRCh38	V40	FBL-BGKcLV17-20/Aligned.sortedByCoord.out.bam		ENCORE2	24704
FBL-BGKcLV17-20_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	176					GRCh38	V40	FBL-BGKcLV17-20/Aligned.sortedByCoord.out.bam		ENCORE2	24734
FBL-BGKcLV17-20_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	176					GRCh38	V40	FBL-BGKcLV17-20/Aligned.sortedByCoord.out.bam		ENCORE2	24764
FBL-BGKcLV17-20_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	176					GRCh38	V40	FBL-BGKcLV17-20/Aligned.sortedByCoord.out.bam		ENCORE2	24794
FBL-BGKcLV17-20_quant.sf	ENCODE_DATA/set44_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	176					GRCh38	V40	FBL-BGKcLV17-20_S6_R1_001.filtered.trimmed.paired.fastq.gz,FBL-BGKcLV17-20_S6_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24824