MECP2 RNA-Seq in HepG2

General Information


RBP	MECP2
Cell_Line	HepG2
Method	CRISPR
Exp_Name	MECP2-BGHcLV16-HepG2
ENCODE_series_ID	ENCSR046NIJ
Batch_ID	BGHcLV16
Pool ID	Pool-200102
Local_Set_Name	set43_H
ENCODE_KD_Exp_ID	ENCSR266XKN
ENCODE_CN_Exp_ID	ENCSR964HKT
Rep1	MECP2-BGHcLV16-33
Rep2	MECP2-BGHcLV16-34
CN1	NT-BGHcLV16-1
CN2	NT-BGHcLV16-2
Rep1_qPCR	0.0
Rep2_qPCR	0.0
Rep1_WB	58.4
Rep2_WB	58.2
Antibody Cat#	49-1029
Antibody Lot#	LOT# A200042181226
Antibody DCC ID	ENCAB380QZE
Status	Released
Project	ENCODE4
ID	152

Experiment Information (Status: Released)

	BGHcLV16-33	BGHcLV16-34
idx	463	464
TRCN#_or_BGC#	BGC#0000356	BGC#0000356
shRNA_or_gRNA_sequence	GGACACGGAAGCTTAAGCAA	GGACACGGAAGCTTAAGCAA
PAM	AGG	AGG
Name	MECP2-82	MECP2-82
Sample_ID	BGHcLV16-33	BGHcLV16-34
transduction_Date	4/16/19	4/16/19
days	D6	D6
RBP_name	MECP2	MECP2
qPCR_result	0.0	0.0
Ave_qPCR	0.0
RT-qPCR_primer-F	gatcaatccccagggaaaag
RT-qPCR_primer-R	cattagggtccagggatgtg
protein_conc	4902	4830
WB_result	58.4	58.2
Ave_WB	58.3
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	9	0
Rep2_TPM	6	0
Action	Ready	Ready
Library_start_date	12/03/19	12/03/19
repeat_library
Note
ID	6612	6613

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

	BGHcLV16-33	BGHcLV16-34
Sample_ID	BGHcLV16-33	BGHcLV16-34
Sample Name
Sample Name	MECP2-BGHcLV16-33	MECP2-BGHcLV16-34
RBP	MECP2	MECP2
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2020-12-01	2020-12-01
Project	ENCODE4	ENCODE4
Note
ID	5423	5424

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV16-33	BGHcLV16-34
Sample #	57	58
Sample Name	MECP2-BGHcLV16-33	MECP2-BGHcLV16-34
Sample_Name_Alias
Index Well Position	E07	F07
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2020-08-31	2020-08-31
Lib_ID	Lib-200831	Lib-200831
Tecan_Location	1-G2	1-H2
Tecan	34.13	38.31
Tecan_date	2019-12-10	2019-12-10
Size_bp	274	278
Peak_Molarity	26.60	31.80
libSampleQC_DNA_Well	DNA_Library_set43-44/set2/G2.png	DNA_Library_set43-44/set2/H2.png
RIN	9.6	9.7
libSample_RNA_Well	RNA_Library_set43-44/set1/G7.png	RNA_Library_set43-44/set1/H7.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2019-12-13	2019-12-13
Sample_ID	BGHcLV16-33	BGHcLV16-34
RBP	MECP2	MECP2
Batch_ID	BGHcLV16	BGHcLV16
WB_result	58.400	58.200
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	633	634

Sequencing Information

	BGHcLV16-33	BGHcLV16-34
Sample_ID	BGHcLV16-33	BGHcLV16-34
Sample Name	MECP2-BGHcLV16-33	MECP2-BGHcLV16-34
Pool ID	Pool-200102	Pool-200102
LocalServer_folder	set43_H	set43_H
total_reads	148,481,698	151,143,060
total_aligned_reads	140,241,660	143,485,776
unique_aligned_reads	131,528,206	134,391,782
percent_uniqueAligned	0.88582	0.88917
correlation_replicates	0.999407	0.999407
spikein_reads	224,236	251,238
percent_spikeins	0.00151	0.00166
original_ReadLength	150	150
QC_Status	Submitted	Submitted
ID	135	136

Data Submission Information

	BGHcLV16-33	BGHcLV16-33	BGHcLV16-33	BGHcLV16-33	BGHcLV16-33	BGHcLV16-33	BGHcLV16-34	BGHcLV16-34	BGHcLV16-34	BGHcLV16-34
ENCODE_alias	brenton-graveley:MECP2-BGHcLV16	brenton-graveley:MECP2-BGHcLV16-33	brenton-graveley:L-MECP2-BGHcLV16-33	brenton-graveley:MECP2-BGHcLV16-33_S53_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:MECP2-BGHcLV16-33_S53_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:MECP2-BGHcLV16-HepG2	brenton-graveley:MECP2-BGHcLV16-34	brenton-graveley:L-MECP2-BGHcLV16-34	brenton-graveley:MECP2-BGHcLV16-34_S54_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:MECP2-BGHcLV16-34_S54_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR266XKN	ENCBS355HDT	ENCLB245OWS	ENCFF890FAL	ENCFF708AZO	ENCSR046NIJ	ENCBS007KVT	ENCLB433SNT	ENCFF999KCZ	ENCFF616IUR
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	BGHcLV16-33	BGHcLV16-33	BGHcLV16-33	BGHcLV16-33	BGHcLV16-33	BGHcLV16-33	BGHcLV16-34	BGHcLV16-34	BGHcLV16-34	BGHcLV16-34
Sample Name	MECP2-BGHcLV16-33	MECP2-BGHcLV16-33	MECP2-BGHcLV16-33	MECP2-BGHcLV16-33	MECP2-BGHcLV16-33	MECP2-BGHcLV16-33	MECP2-BGHcLV16-34	MECP2-BGHcLV16-34	MECP2-BGHcLV16-34	MECP2-BGHcLV16-34
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
		LV43H_biosample_protocol	LV43H_library_protocol				LV43H_biosample_protocol	LV43H_library_protocol
protocol_URL		MECP2-BGHcLV16-33.pdf	L-MECP2-BGHcLV16-33.pdf				MECP2-BGHcLV16-34.pdf	L-MECP2-BGHcLV16-34.pdf
ID	8	98	262	428	460	7253	99	263	429	461

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-BGHcLV16-33_S53_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set43_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	135	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	15
MECP2-BGHcLV16-33_S53_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set43_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	135	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	47
MECP2-BGHcLV16-33_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set43_H/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	135					GRCh38	V40	MECP2-BGHcLV16-33_S53_R1_001.filtered.trimmed.paired.fastq.gz,MECP2-BGHcLV16-33_S53_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24178
MECP2-BGHcLV16-33_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	135					GRCh38	V40	MECP2-BGHcLV16-33/Aligned.sortedByCoord.out.bam		ENCORE2	24210
MECP2-BGHcLV16-33_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	135					GRCh38	V40	MECP2-BGHcLV16-33/Aligned.sortedByCoord.out.bam		ENCORE2	24242
MECP2-BGHcLV16-33_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	135					GRCh38	V40	MECP2-BGHcLV16-33/Aligned.sortedByCoord.out.bam		ENCORE2	24274
MECP2-BGHcLV16-33_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	135					GRCh38	V40	MECP2-BGHcLV16-33/Aligned.sortedByCoord.out.bam		ENCORE2	24306
MECP2-BGHcLV16-33_quant.sf	ENCODE_DATA/set43_H/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	135					GRCh38	V40	MECP2-BGHcLV16-33_S53_R1_001.filtered.trimmed.paired.fastq.gz,MECP2-BGHcLV16-33_S53_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24338
MECP2-BGHcLV16-34_S54_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set43_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	136	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	16
MECP2-BGHcLV16-34_S54_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set43_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	136	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	48
MECP2-BGHcLV16-34_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set43_H/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	136					GRCh38	V40	MECP2-BGHcLV16-34_S54_R1_001.filtered.trimmed.paired.fastq.gz,MECP2-BGHcLV16-34_S54_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24179
MECP2-BGHcLV16-34_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	136					GRCh38	V40	MECP2-BGHcLV16-34/Aligned.sortedByCoord.out.bam		ENCORE2	24211
MECP2-BGHcLV16-34_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	136					GRCh38	V40	MECP2-BGHcLV16-34/Aligned.sortedByCoord.out.bam		ENCORE2	24243
MECP2-BGHcLV16-34_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	136					GRCh38	V40	MECP2-BGHcLV16-34/Aligned.sortedByCoord.out.bam		ENCORE2	24275
MECP2-BGHcLV16-34_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	136					GRCh38	V40	MECP2-BGHcLV16-34/Aligned.sortedByCoord.out.bam		ENCORE2	24307
MECP2-BGHcLV16-34_quant.sf	ENCODE_DATA/set43_H/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	136					GRCh38	V40	MECP2-BGHcLV16-34_S54_R1_001.filtered.trimmed.paired.fastq.gz,MECP2-BGHcLV16-34_S54_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24339