YBX1 RNA-Seq in HepG2

General Information


RBP	YBX1
Cell_Line	HepG2
Method	CRISPR
Exp_Name	YBX1-BGHcLV16-HepG2
ENCODE_series_ID	ENCSR816NLN
Batch_ID	BGHcLV16
Pool ID	Pool-200102
Local_Set_Name	set43_H
ENCODE_KD_Exp_ID	ENCSR548OTL
ENCODE_CN_Exp_ID	ENCSR964HKT
Rep1	YBX1-BGHcLV16-61
Rep2	YBX1-BGHcLV16-62
CN1	NT-BGHcLV16-1
CN2	NT-BGHcLV16-2
Rep1_qPCR	60.1
Rep2_qPCR	69.3
Rep1_WB	86.3
Rep2_WB	72.1
Antibody Cat#	PA5-19453
Antibody Lot#	TK2671131
Antibody DCC ID	ENCAB593ZMI
Status	Released
Project	ENCODE4
ID	160

Experiment Information (Status: Released)

	BGHcLV16-61	BGHcLV16-62
idx	491	492
TRCN#_or_BGC#	BGC#0000375	BGC#0000375
shRNA_or_gRNA_sequence	GGACCATACCTGCGGAATCG	GGACCATACCTGCGGAATCG
PAM	AGG	AGG
Name	YBX1-97	YBX1-97
Sample_ID	BGHcLV16-61	BGHcLV16-62
transduction_Date	4/16/19	4/16/19
days	D6	D6
RBP_name	YBX1	YBX1
qPCR_result	60.1	69.3
Ave_qPCR	64.7
RT-qPCR_primer-F	AGGGTGCAGGAGAACAAGGT
RT-qPCR_primer-R	TCATTGCCGTCCTCTCTAGG
protein_conc	3385	4490
WB_result	86.3	72.1
Ave_WB	79.2
WB_DONE_date	4/24/19
MW	36KD
IP	Rabbit / I
antibody_Cat#	PA5-19453
Antibody DCC ID	no ID
submitted_to_DCC_date
Rep1_TPM	918	0
Rep2_TPM	843	0
Action	Question	Question
Library_start_date	12/03/19	12/03/19
repeat_library
Note
ID	6642	6643

Western Blot Western Blot info was not avaliable

Experiment Status

	BGHcLV16-61	BGHcLV16-62
Sample_ID	BGHcLV16-61	BGHcLV16-62
Sample Name
Sample Name	YBX1-BGHcLV16-61	YBX1-BGHcLV16-62
RBP	YBX1	YBX1
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2020-12-01	2020-12-01
Project	ENCODE4	ENCODE4
Note
ID	5439	5440

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV16-61	BGHcLV16-62
Sample #	73	74
Sample Name	YBX1-BGHcLV16-61	YBX1-BGHcLV16-62
Sample_Name_Alias
Index Well Position	E09	F09
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2020-08-31	2020-08-31
Lib_ID	Lib-200831	Lib-200831
Tecan_Location	2-G2	2-H2
Tecan	34.41	33.02
Tecan_date	2019-12-10	2019-12-10
Size_bp	285	279
Peak_Molarity	57.40	70.00
libSampleQC_DNA_Well	DNA_Library_set43-44/set2/G4.png	DNA_Library_set43-44/set2/H4.png
RIN	9.6	9.5
libSample_RNA_Well	RNA_Library_set43-44/set1/G9.png	RNA_Library_set43-44/set1/H9.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2019-12-13	2019-12-13
Sample_ID	BGHcLV16-61	BGHcLV16-62
RBP	YBX1	YBX1
Batch_ID	BGHcLV16	BGHcLV16
WB_result	86.300	72.100
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	649	650

Sequencing Information

	BGHcLV16-61	BGHcLV16-62
Sample_ID	BGHcLV16-61	BGHcLV16-62
Sample Name	YBX1-BGHcLV16-61	YBX1-BGHcLV16-62
Pool ID	Pool-200102	Pool-200102
LocalServer_folder	set43_H	set43_H
total_reads	293,032,984	278,986,666
total_aligned_reads	279,733,314	251,235,002
unique_aligned_reads	261,928,352	235,168,208
percent_uniqueAligned	0.89385	0.84294
correlation_replicates	0.998646	0.998646
spikein_reads	380,590	365,982
percent_spikeins	0.00130	0.00131
original_ReadLength	150	150
QC_Status	Submitted	Submitted
ID	151	152

Data Submission Information

	BGHcLV16-61	BGHcLV16-61	BGHcLV16-61	BGHcLV16-61	BGHcLV16-61	BGHcLV16-61	BGHcLV16-62	BGHcLV16-62	BGHcLV16-62	BGHcLV16-62
ENCODE_alias	brenton-graveley:YBX1-BGHcLV16	brenton-graveley:YBX1-BGHcLV16-61	brenton-graveley:L-YBX1-BGHcLV16-61	brenton-graveley:YBX1-BGHcLV16-61_S69_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:YBX1-BGHcLV16-61_S69_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:YBX1-BGHcLV16-HepG2	brenton-graveley:YBX1-BGHcLV16-62	brenton-graveley:L-YBX1-BGHcLV16-62	brenton-graveley:YBX1-BGHcLV16-62_S70_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:YBX1-BGHcLV16-62_S70_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR548OTL	ENCBS970PIQ	ENCLB616UED	ENCFF268GVX	ENCFF723GPA	ENCSR816NLN	ENCBS856DYN	ENCLB769MQL	ENCFF782UJV	ENCFF667WMF
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	BGHcLV16-61	BGHcLV16-61	BGHcLV16-61	BGHcLV16-61	BGHcLV16-61	BGHcLV16-61	BGHcLV16-62	BGHcLV16-62	BGHcLV16-62	BGHcLV16-62
Sample Name	YBX1-BGHcLV16-61	YBX1-BGHcLV16-61	YBX1-BGHcLV16-61	YBX1-BGHcLV16-61	YBX1-BGHcLV16-61	YBX1-BGHcLV16-61	YBX1-BGHcLV16-62	YBX1-BGHcLV16-62	YBX1-BGHcLV16-62	YBX1-BGHcLV16-62
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
			LV43H_library_protocol					LV43H_library_protocol
protocol_URL			L-YBX1-BGHcLV16-61.pdf					L-YBX1-BGHcLV16-62.pdf
ID	16	114	278	444	476	7361	115	279	445	477

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
YBX1-BGHcLV16-61_S69_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set43_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	151	NovaSeq6000	100	paired-ended	1				NT-BGHcLV16-1_S39_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV16-2_S40_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	31
YBX1-BGHcLV16-61_S69_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set43_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	151	NovaSeq6000	100	paired-ended	2				NT-BGHcLV16-1_S39_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV16-2_S40_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	63
YBX1-BGHcLV16-61_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set43_H/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	151					GRCh38	V40	YBX1-BGHcLV16-61_S69_R1_001.filtered.trimmed.paired.fastq.gz,YBX1-BGHcLV16-61_S69_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24194
YBX1-BGHcLV16-61_Signal.Unique.strand+.bw	ENCODE_DATA/set43_H/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	151					GRCh38	V40	YBX1-BGHcLV16-61/Aligned.sortedByCoord.out.bam		ENCORE2	24226
YBX1-BGHcLV16-61_Signal.Unique.strand-.bw	ENCODE_DATA/set43_H/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	151					GRCh38	V40	YBX1-BGHcLV16-61/Aligned.sortedByCoord.out.bam		ENCORE2	24258
YBX1-BGHcLV16-61_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set43_H/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	151					GRCh38	V40	YBX1-BGHcLV16-61/Aligned.sortedByCoord.out.bam		ENCORE2	24290
YBX1-BGHcLV16-61_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set43_H/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	151					GRCh38	V40	YBX1-BGHcLV16-61/Aligned.sortedByCoord.out.bam		ENCORE2	24322
YBX1-BGHcLV16-61_quant.sf	ENCODE_DATA/set43_H/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	151					GRCh38	V40	YBX1-BGHcLV16-61_S69_R1_001.filtered.trimmed.paired.fastq.gz,YBX1-BGHcLV16-61_S69_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24354
YBX1-BGHcLV16-62_S70_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set43_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	152	NovaSeq6000	100	paired-ended	1				NT-BGHcLV16-1_S39_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV16-2_S40_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	32
YBX1-BGHcLV16-62_S70_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set43_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	152	NovaSeq6000	100	paired-ended	2				NT-BGHcLV16-1_S39_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV16-2_S40_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	64
YBX1-BGHcLV16-62_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set43_H/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	152					GRCh38	V40	YBX1-BGHcLV16-62_S70_R1_001.filtered.trimmed.paired.fastq.gz,YBX1-BGHcLV16-62_S70_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24195
YBX1-BGHcLV16-62_Signal.Unique.strand+.bw	ENCODE_DATA/set43_H/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	152					GRCh38	V40	YBX1-BGHcLV16-62/Aligned.sortedByCoord.out.bam		ENCORE2	24227
YBX1-BGHcLV16-62_Signal.Unique.strand-.bw	ENCODE_DATA/set43_H/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	152					GRCh38	V40	YBX1-BGHcLV16-62/Aligned.sortedByCoord.out.bam		ENCORE2	24259
YBX1-BGHcLV16-62_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set43_H/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	152					GRCh38	V40	YBX1-BGHcLV16-62/Aligned.sortedByCoord.out.bam		ENCORE2	24291
YBX1-BGHcLV16-62_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set43_H/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	152					GRCh38	V40	YBX1-BGHcLV16-62/Aligned.sortedByCoord.out.bam		ENCORE2	24323
YBX1-BGHcLV16-62_quant.sf	ENCODE_DATA/set43_H/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	152					GRCh38	V40	YBX1-BGHcLV16-62_S70_R1_001.filtered.trimmed.paired.fastq.gz,YBX1-BGHcLV16-62_S70_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24355