MECP2 RNA-Seq in K562

General Information


RBP	MECP2
Cell_Line	K562
Method	CRISPR
Exp_Name	MECP2-BGKcLV15-K562
ENCODE_series_ID	ENCSR269CKX
Batch_ID	BGKcLV15
Pool ID	Pool-200102
Local_Set_Name	set43_K
ENCODE_KD_Exp_ID	ENCSR665DMA
ENCODE_CN_Exp_ID	ENCSR404OHQ
Rep1	MECP2-BGKcLV15-39
Rep2	MECP2-BGKcLV15-40
CN1	NT-BGKcLV15-1
CN2	NT-BGKcLV15-2
Rep1_qPCR	47.0
Rep2_qPCR	43.6
Rep1_WB	55.2
Rep2_WB	54.7
Antibody Cat#	49-1029
Antibody Lot#	LOT# A200042181226
Antibody DCC ID	ENCAB380QZE
Status	Released
Project	ENCODE4
ID	129

Experiment Information (Status: Released)

	BGKcLV15-39	BGKcLV15-40
idx	577	578
TRCN#_or_BGC#	BGC#0000355	BGC#0000355
shRNA_or_gRNA_sequence	CATACATGGGTCCCCGGTCA	CATACATGGGTCCCCGGTCA
PAM	CGG	CGG
Name	MECP2-90	MECP2-90
Sample_ID	BGKcLV15-39	BGKcLV15-40
transduction_Date	4/2/19	4/2/19
days	Day 6	Day 6
RBP_name	MECP2	MECP2
qPCR_result	47.0	43.6
Ave_qPCR	45.3
RT-qPCR_primer-F	gatcaatccccagggaaaag
RT-qPCR_primer-R	cattagggtccagggatgtg
protein_conc	5757	5448
WB_result	55.2	54.7
Ave_WB	55.0
WB_DONE_date	4/29/19
MW	52KD
IP	Rabbit / I
antibody_Cat#	49-1029	LOT# A200042181226
Antibody DCC ID	ENCAB380QZE
submitted_to_DCC_date
Rep1_TPM	18.7	0
Rep2_TPM	15.2	0
Action	Ready	Ready
Library_start_date	05/30/19	05/30/19
repeat_library
Note
ID	4689	4690

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
MECP2	Product_ID: 49-1029 Lot_ID: A200042181226 Source: Thermo Fisher Target Name: MECP2-human

Experiment Status

	BGKcLV15-39	BGKcLV15-40
Sample_ID	BGKcLV15-39	BGKcLV15-40
Sample Name
Sample Name	MECP2-BGKcLV15-39	MECP2-BGKcLV15-40
RBP	MECP2	MECP2
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2020-12-01	2020-12-01
Project	ENCODE4	ENCODE4
Note
ID	5347	5348

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV15-39	BGKcLV15-40
Sample #	17	18
Sample Name	MECP2-BGKcLV15-39	MECP2-BGKcLV15-40
Sample_Name_Alias
Index Well Position	A03	B03
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2020-08-30	2020-08-30
Lib_ID	Lib-200830	Lib-200830
Tecan_Location	2-A1	2-B1
Tecan	37.84	38.07
Tecan_date	2019-12-10	2019-12-10
Size_bp	262	270
Peak_Molarity	20.00	21.60
libSampleQC_DNA_Well	DNA_Library_set43-44/set1/A3.png	DNA_Library_set43-44/set1/B3.png
RIN	9.6	9.6
libSample_RNA_Well	RNA_Library_set43-44/set1/A3.png	RNA_Library_set43-44/set1/B3.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2019-12-11	2019-12-11
Sample_ID	BGKcLV15-39	BGKcLV15-40
RBP	MECP2	MECP2
Batch_ID	BGKcLV15	BGKcLV15
WB_result	55.200	54.700
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	593	594

Sequencing Information

	BGKcLV15-39	BGKcLV15-40
Sample_ID	BGKcLV15-39	BGKcLV15-40
Sample Name	MECP2-BGKcLV15-39	MECP2-BGKcLV15-40
Pool ID	Pool-200102	Pool-200102
LocalServer_folder	set43_K	set43_K
total_reads	122,936,862	94,393,514
total_aligned_reads	117,534,762	92,241,886
unique_aligned_reads	107,650,184	84,529,026
percent_uniqueAligned	0.87565	0.89550
correlation_replicates	0.997881	0.997881
spikein_reads	61,676	57,632
percent_spikeins	0.00050	0.00061
original_ReadLength	150	150
QC_Status	Submitted	Submitted
ID	99	100

Data Submission Information

	BGKcLV15-39	BGKcLV15-39	BGKcLV15-39	BGKcLV15-39	BGKcLV15-39	BGKcLV15-39	BGKcLV15-40	BGKcLV15-40	BGKcLV15-40	BGKcLV15-40
ENCODE_alias	brenton-graveley:MECP2-BGKcLV15	brenton-graveley:MECP2-BGKcLV15-39	brenton-graveley:L-MECP2-BGKcLV15-39	brenton-graveley:MECP2-BGKcLV15-39_S17_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:MECP2-BGKcLV15-39_S17_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:MECP2-BGKcLV15-K562	brenton-graveley:MECP2-BGKcLV15-40	brenton-graveley:L-MECP2-BGKcLV15-40	brenton-graveley:MECP2-BGKcLV15-40_S18_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:MECP2-BGKcLV15-40_S18_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR665DMA	ENCBS691RCG	ENCLB322DGZ	ENCFF135VUI	ENCFF612ORU	ENCSR269CKX	ENCBS786QAW	ENCLB213UQE	ENCFF831TST	ENCFF201MYS
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	BGKcLV15-39	BGKcLV15-39	BGKcLV15-39	BGKcLV15-39	BGKcLV15-39	BGKcLV15-39	BGKcLV15-40	BGKcLV15-40	BGKcLV15-40	BGKcLV15-40
Sample Name	MECP2-BGKcLV15-39	MECP2-BGKcLV15-39	MECP2-BGKcLV15-39	MECP2-BGKcLV15-39	MECP2-BGKcLV15-39	MECP2-BGKcLV15-39	MECP2-BGKcLV15-40	MECP2-BGKcLV15-40	MECP2-BGKcLV15-40	MECP2-BGKcLV15-40
Selected	Yes	Yes	Yes	Yes	Yes	Yes	Yes	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_biosample_protocol	LV43K_library_protocol				LV43K_biosample_protocol	LV43K_library_protocol
protocol_URL		MECP2-BGKcLV15-39.pdf	L-GSK3B-BGKcLV15-37.pdf				MECP2-BGKcLV15-40.pdf	L-GSK3B-BGKcLV15-38.pdf
ID	25	132	296	494	546	7254	133	297	495	547

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
MECP2-BGKcLV15-39_S17_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set43_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	99	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	93
MECP2-BGKcLV15-39_S17_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set43_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	99	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	145
MECP2-BGKcLV15-39_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set43_K/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	99					GRCh38	V40	MECP2-BGKcLV15-39_S17_R1_001.filtered.trimmed.paired.fastq.gz,MECP2-BGKcLV15-39_S17_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24384
MECP2-BGKcLV15-39_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	99					GRCh38	V40	MECP2-BGKcLV15-39/Aligned.sortedByCoord.out.bam		ENCORE2	24436
MECP2-BGKcLV15-39_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	99					GRCh38	V40	MECP2-BGKcLV15-39/Aligned.sortedByCoord.out.bam		ENCORE2	24488
MECP2-BGKcLV15-39_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	99					GRCh38	V40	MECP2-BGKcLV15-39/Aligned.sortedByCoord.out.bam		ENCORE2	24540
MECP2-BGKcLV15-39_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	99					GRCh38	V40	MECP2-BGKcLV15-39/Aligned.sortedByCoord.out.bam		ENCORE2	24592
MECP2-BGKcLV15-39_quant.sf	ENCODE_DATA/set43_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	99					GRCh38	V40	MECP2-BGKcLV15-39_S17_R1_001.filtered.trimmed.paired.fastq.gz,MECP2-BGKcLV15-39_S17_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24644
MECP2-BGKcLV15-40_S18_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set43_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	100	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	94
MECP2-BGKcLV15-40_S18_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set43_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	100	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	146
MECP2-BGKcLV15-40_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set43_K/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	100					GRCh38	V40	MECP2-BGKcLV15-40_S18_R1_001.filtered.trimmed.paired.fastq.gz,MECP2-BGKcLV15-40_S18_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24385
MECP2-BGKcLV15-40_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	100					GRCh38	V40	MECP2-BGKcLV15-40/Aligned.sortedByCoord.out.bam		ENCORE2	24437
MECP2-BGKcLV15-40_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	100					GRCh38	V40	MECP2-BGKcLV15-40/Aligned.sortedByCoord.out.bam		ENCORE2	24489
MECP2-BGKcLV15-40_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	100					GRCh38	V40	MECP2-BGKcLV15-40/Aligned.sortedByCoord.out.bam		ENCORE2	24541
MECP2-BGKcLV15-40_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	100					GRCh38	V40	MECP2-BGKcLV15-40/Aligned.sortedByCoord.out.bam		ENCORE2	24593
MECP2-BGKcLV15-40_quant.sf	ENCODE_DATA/set43_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	100					GRCh38	V40	MECP2-BGKcLV15-40_S18_R1_001.filtered.trimmed.paired.fastq.gz,MECP2-BGKcLV15-40_S18_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24645