YBX1 RNA-Seq in K562

General Information


RBP	YBX1
Cell_Line	K562
Method	CRISPR
Exp_Name	YBX1-BGKcLV15-K562
ENCODE_series_ID	ENCSR532ZEE
Batch_ID	BGKcLV15
Pool ID	Pool-200102
Local_Set_Name	set43_K
ENCODE_KD_Exp_ID	ENCSR659UXO
ENCODE_CN_Exp_ID	ENCSR404OHQ
Rep1	YBX1-BGKcLV15-63
Rep2	YBX1-BGKcLV15-64
CN1	NT-BGKcLV15-1
CN2	NT-BGKcLV15-2
Rep1_qPCR	48.9
Rep2_qPCR	40.4
Rep1_WB	62.1
Rep2_WB	63.7
Antibody Cat#	PA5-19453
Antibody Lot#	TK2671131
Antibody DCC ID	ENCAB593ZMI
Status	Released
Project	ENCODE4
ID	139

Experiment Information (Status: Released)

	BGKcLV15-63	BGKcLV15-64
idx	605	606
TRCN#_or_BGC#	BGC#0000375	BGC#0000375
shRNA_or_gRNA_sequence	GGACCATACCTGCGGAATCG	GGACCATACCTGCGGAATCG
PAM	AGG	AGG
Name	YBX1-97	YBX1-97
Sample_ID	BGKcLV15-63	BGKcLV15-64
transduction_Date	4/2/19	4/2/19
days	Day 6	Day 6
RBP_name	YBX1	YBX1
qPCR_result	48.9	40.4
Ave_qPCR	44.7
RT-qPCR_primer-F	AGGGTGCAGGAGAACAAGGT
RT-qPCR_primer-R	TCATTGCCGTCCTCTCTAGG
protein_conc	5458	5458
WB_result	62.1	63.7
Ave_WB	62.9	need discussion
WB_DONE_date	4/24/19
MW	36KD
IP	Rabbit / I
antibody_Cat#	PA5-19453
Antibody DCC ID
submitted_to_DCC_date
Rep1_TPM	1200.8	0
Rep2_TPM	1324	0
Action	Ready	Ready
Library_start_date	05/30/19	05/30/19
repeat_library
Note
ID	4717	4718

Western Blot Western Blot info was not avaliable

Experiment Status

	BGKcLV15-63	BGKcLV15-64
Sample_ID	BGKcLV15-63	BGKcLV15-64
Sample Name
Sample Name	YBX1-BGKcLV15-63	YBX1-BGKcLV15-64
RBP	YBX1	YBX1
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2020-12-01	2020-12-01
Project	ENCODE4	ENCODE4
Note
ID	5367	5368

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV15-63	BGKcLV15-64
Sample #	37	38
Sample Name	YBX1-BGKcLV15-63	YBX1-BGKcLV15-64
Sample_Name_Alias
Index Well Position	E05	F05
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2020-08-30	2020-08-30
Lib_ID	Lib-200830	Lib-200830
Tecan_Location	3-E1	3-F1
Tecan	39.34	36.15
Tecan_date	2019-12-10	2019-12-10
Size_bp	266	277
Peak_Molarity	21.40	24.80
libSampleQC_DNA_Well	DNA_Library_set43-44/set1/E5.png	DNA_Library_set43-44/set1/F5.png
RIN	9.9	9.8
libSample_RNA_Well	RNA_Library_set43-44/set1/E5.png	RNA_Library_set43-44/set1/F5.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2019-12-11	2019-12-11
Sample_ID	BGKcLV15-63	BGKcLV15-64
RBP	YBX1	YBX1
Batch_ID	BGKcLV15	BGKcLV15
WB_result	62.100	63.700
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	613	614

Sequencing Information

	BGKcLV15-63	BGKcLV15-64
Sample_ID	BGKcLV15-63	BGKcLV15-64
Sample Name	YBX1-BGKcLV15-63	YBX1-BGKcLV15-64
Pool ID	Pool-200102	Pool-200102
LocalServer_folder	set43_K	set43_K
total_reads	101,490,292	101,947,352
total_aligned_reads	97,035,204	97,085,076
unique_aligned_reads	88,874,466	88,870,230
percent_uniqueAligned	0.87569	0.87173
correlation_replicates	0.995962	0.995962
spikein_reads	47,230	67,292
percent_spikeins	0.00047	0.00066
original_ReadLength	150	150
QC_Status	Submitted	Submitted
ID	119	120

Data Submission Information

	BGKcLV15-63	BGKcLV15-63	BGKcLV15-63	BGKcLV15-63	BGKcLV15-63	BGKcLV15-63	BGKcLV15-64	BGKcLV15-64	BGKcLV15-64	BGKcLV15-64
ENCODE_alias	brenton-graveley:YBX1-BGKcLV15	brenton-graveley:YBX1-BGKcLV15-63	brenton-graveley:L-YBX1-BGKcLV15-63	brenton-graveley:YBX1-BGKcLV15-63_S37_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:YBX1-BGKcLV15-63_S37_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:YBX1-BGKcLV15-K562	brenton-graveley:YBX1-BGKcLV15-64	brenton-graveley:L-YBX1-BGKcLV15-64	brenton-graveley:YBX1-BGKcLV15-64_S38_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:YBX1-BGKcLV15-64_S38_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR659UXO	ENCBS568TBB	ENCLB212CFZ	ENCFF803NZJ	ENCFF573WJT	ENCSR532ZEE	ENCBS446AVJ	ENCLB945CFI	ENCFF301JRH	ENCFF193LXU
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	BGKcLV15-63	BGKcLV15-63	BGKcLV15-63	BGKcLV15-63	BGKcLV15-63	BGKcLV15-63	BGKcLV15-64	BGKcLV15-64	BGKcLV15-64	BGKcLV15-64
Sample Name	YBX1-BGKcLV15-63	YBX1-BGKcLV15-63	YBX1-BGKcLV15-63	YBX1-BGKcLV15-63	YBX1-BGKcLV15-63	YBX1-BGKcLV15-63	YBX1-BGKcLV15-64	YBX1-BGKcLV15-64	YBX1-BGKcLV15-64	YBX1-BGKcLV15-64
Selected	Yes	No	Yes	Yes	Yes	Yes	No	Yes	Yes	Yes
Status	Released	Released	Released	Released	Released	Released	Released	Released	Released	Released
Status_Date	2021-03-18	2021-03-18	2021-03-18	2021-03-18	2021-03-18	2022-03-02	2021-03-18	2021-03-18	2021-03-18	2021-03-18
Project	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4
			LV43K_library_protocol					LV43K_library_protocol
protocol_URL			L-YBX1-BGKcLV15-63.pdf					L-YBX1-BGKcLV15-64.pdf
ID	35	152	316	514	566	7362	153	317	515	567

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-BGKcLV15-63_S37_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set43_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	119	NovaSeq6000	100	paired-ended	1				NT-BGKcLV15-1_S1_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV15-2_S2_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	115
YBX1-BGKcLV15-63_S37_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set43_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	119	NovaSeq6000	100	paired-ended	2				NT-BGKcLV15-1_S1_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV15-2_S2_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	167
YBX1-BGKcLV15-63_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set43_K/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	119					GRCh38	V40	YBX1-BGKcLV15-63_S37_R1_001.filtered.trimmed.paired.fastq.gz,YBX1-BGKcLV15-63_S37_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24406
YBX1-BGKcLV15-63_Signal.Unique.strand+.bw	ENCODE_DATA/set43_K/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	119					GRCh38	V40	YBX1-BGKcLV15-63/Aligned.sortedByCoord.out.bam		ENCORE2	24458
YBX1-BGKcLV15-63_Signal.Unique.strand-.bw	ENCODE_DATA/set43_K/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	119					GRCh38	V40	YBX1-BGKcLV15-63/Aligned.sortedByCoord.out.bam		ENCORE2	24510
YBX1-BGKcLV15-63_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set43_K/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	119					GRCh38	V40	YBX1-BGKcLV15-63/Aligned.sortedByCoord.out.bam		ENCORE2	24562
YBX1-BGKcLV15-63_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set43_K/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	119					GRCh38	V40	YBX1-BGKcLV15-63/Aligned.sortedByCoord.out.bam		ENCORE2	24614
YBX1-BGKcLV15-63_quant.sf	ENCODE_DATA/set43_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	119					GRCh38	V40	YBX1-BGKcLV15-63_S37_R1_001.filtered.trimmed.paired.fastq.gz,YBX1-BGKcLV15-63_S37_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24666
YBX1-BGKcLV15-64_S38_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set43_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	120	NovaSeq6000	100	paired-ended	1				NT-BGKcLV15-1_S1_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV15-2_S2_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	116
YBX1-BGKcLV15-64_S38_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set43_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	120	NovaSeq6000	100	paired-ended	2				NT-BGKcLV15-1_S1_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV15-2_S2_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	168
YBX1-BGKcLV15-64_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set43_K/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	120					GRCh38	V40	YBX1-BGKcLV15-64_S38_R1_001.filtered.trimmed.paired.fastq.gz,YBX1-BGKcLV15-64_S38_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24407
YBX1-BGKcLV15-64_Signal.Unique.strand+.bw	ENCODE_DATA/set43_K/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	120					GRCh38	V40	YBX1-BGKcLV15-64/Aligned.sortedByCoord.out.bam		ENCORE2	24459
YBX1-BGKcLV15-64_Signal.Unique.strand-.bw	ENCODE_DATA/set43_K/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	120					GRCh38	V40	YBX1-BGKcLV15-64/Aligned.sortedByCoord.out.bam		ENCORE2	24511
YBX1-BGKcLV15-64_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set43_K/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	120					GRCh38	V40	YBX1-BGKcLV15-64/Aligned.sortedByCoord.out.bam		ENCORE2	24563
YBX1-BGKcLV15-64_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set43_K/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	120					GRCh38	V40	YBX1-BGKcLV15-64/Aligned.sortedByCoord.out.bam		ENCORE2	24615
YBX1-BGKcLV15-64_quant.sf	ENCODE_DATA/set43_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	120					GRCh38	V40	YBX1-BGKcLV15-64_S38_R1_001.filtered.trimmed.paired.fastq.gz,YBX1-BGKcLV15-64_S38_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24667