MAK16 RNA-Seq in HepG2

General Information


RBP	MAK16
Cell_Line	HepG2
Method	CRISPR
Exp_Name	MAK16-BGHcLV12-HepG2
ENCODE_series_ID	ENCSR098LIW
Batch_ID	BGHcLV12
Pool ID	Pool-190423
Local_Set_Name	set42
ENCODE_KD_Exp_ID	ENCSR624YDI
ENCODE_CN_Exp_ID	ENCSR827PII
Rep1	MAK16-BGHcLV12-43
Rep2	MAK16-BGHcLV12-44
CN1	NT-BGHcLV12-1
CN2	NT-BGHcLV12-2
Rep1_qPCR	35.5
Rep2_qPCR	19.9
Rep1_WB	97.5
Rep2_WB	96.2
Antibody Cat#	A301-232A
Antibody Lot#
Antibody DCC ID	ENCAB777CMB
Status	Released
Project	ENCODE4
ID	178

Experiment Information (Status: Released)

	BGHcLV12-43	BGHcLV12-44
idx	303	304
TRCN#_or_BGC#	BGC#0000269	BGC#0000269
shRNA_or_gRNA_sequence	GAGTGACTCTTCAGATACTG	GAGTGACTCTTCAGATACTG
PAM	AGG	AGG
Name	MAK16_73	MAK16_73
Sample_ID	BGHcLV12-43	BGHcLV12-44
transduction_Date	8/17/18	8/17/18
days	D6	D6
RBP_name	MAK16	MAK16
qPCR_result	35.5	19.9
Ave_qPCR	27.7
RT-qPCR_primer-F	tttgtcgaagatggtgaggt
RT-qPCR_primer-R	tcttcatcactgctggcatc
protein_conc	3975	4033
WB_result	97.5	96.2
Ave_WB	96.8
WB_DONE_date	2/15/19
MW	35kda
IP
antibody_Cat#	A301-232A
Antibody DCC ID	ENCAB777CMB
submitted_to_DCC_date	2/22/19
Rep1_TPM	10	0
Rep2_TPM	8	0
Action	Ready	Ready
Library_start_date	03/13/19	03/13/19
repeat_library
Note
ID	6446	6447

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
MAK16	Product_ID: A301-232A Lot_ID: 1 Source: Bethyl Labs Target Name: MAK16-human

Experiment Status

	BGHcLV12-43	BGHcLV12-44
Sample_ID	BGHcLV12-43	BGHcLV12-44
Sample Name	MAK16-BGHcLV12-43	MAK16-BGHcLV12-44
Sample Name	MAK16-BGHcLV12-43	MAK16-BGHcLV12-44
RBP	MAK16	MAK16
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2020-11-06	2020-11-06
Project	ENCODE4	ENCODE4
Note
ID	2809	2810

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV12-43	BGHcLV12-44
Sample #	39	40
Sample Name	MAK16-BGHcLV12-43	MAK16-BGHcLV12-44
Sample_Name_Alias
Index Well Position	G05	H05
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2019-03-13	2019-03-13
Lib_ID	Lib-190313	Lib-190313
Tecan_Location	3-G1	3-H1
Tecan	40.23	35.14
Tecan_date	2019-03-13	2019-03-13
Size_bp	293	294
Peak_Molarity	40.40	34.90
libSampleQC_DNA_Well	DNA_Library_set42/set1/G5.png	DNA_Library_set42/set1/H5.png
RIN	10.0	9.8
libSample_RNA_Well	RNA_Library_set42/set1/G5.png	RNA_Library_set42/set1/H5.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2019-03-13	2019-03-13
Sample_ID	BGHcLV12-43	BGHcLV12-44
RBP	MAK16	MAK16
Batch_ID	BGHcLV12	BGHcLV12
WB_result	97.500	96.200
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	39	40

Sequencing Information

	BGHcLV12-43	BGHcLV12-44
Sample_ID	BGHcLV12-43	BGHcLV12-44
Sample Name	MAK16-BGHcLV12-43	MAK16-BGHcLV12-44
Pool ID	Pool-190423	Pool-190423
LocalServer_folder	set42	set42
total_reads	62,954,856	66,555,916
total_aligned_reads	60,078,334	64,116,020
unique_aligned_reads	56,523,222	60,381,858
percent_uniqueAligned	0.89784	0.90724
correlation_replicates	0.995969	0.995969
spikein_reads	56,634	53,824
percent_spikeins	0.00090	0.00081
original_ReadLength	150	150
QC_Status	Submitted	Submitted
ID	35	36

Data Submission Information

	BGHcLV12-43	BGHcLV12-43	BGHcLV12-43	BGHcLV12-43	BGHcLV12-43	BGHcLV12-43	BGHcLV12-44	BGHcLV12-44	BGHcLV12-44	BGHcLV12-44
ENCODE_alias	brenton-graveley:MAK16-BGHcLV12	brenton-graveley:MAK16-BGHcLV12-43	brenton-graveley:L-MAK16-BGHcLV12-43	brenton-graveley:MAK16-BGHcLV12-43_TAAGTGGT+CTTAAGCC_HK3H2DSXX_S39_L004_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:MAK16-BGHcLV12-43_TAAGTGGT+CTTAAGCC_HK3H2DSXX_S39_L004_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:MAK16-BGHcLV12-HepG2	brenton-graveley:MAK16-BGHcLV12-44	brenton-graveley:L-MAK16-BGHcLV12-44	brenton-graveley:MAK16-BGHcLV12-44_CGGACAAC+TCCGGATT_HK3H2DSXX_S40_L004_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:MAK16-BGHcLV12-44_CGGACAAC+TCCGGATT_HK3H2DSXX_S40_L004_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR624YDI	ENCBS656WSC	ENCLB688NYY	ENCFF646NPM	ENCFF553BLJ	ENCSR098LIW	ENCBS833CNT	ENCLB250CUE	ENCFF885PEU	ENCFF449AMX
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	BGHcLV12-43	BGHcLV12-43	BGHcLV12-43	BGHcLV12-43	BGHcLV12-43	BGHcLV12-43	BGHcLV12-44	BGHcLV12-44	BGHcLV12-44	BGHcLV12-44
Sample Name	MAK16-BGHcLV12-43	MAK16-BGHcLV12-43	MAK16-BGHcLV12-43	MAK16-BGHcLV12-43	MAK16-BGHcLV12-43	MAK16-BGHcLV12-43	MAK16-BGHcLV12-44	MAK16-BGHcLV12-44	MAK16-BGHcLV12-44	MAK16-BGHcLV12-44
Selected	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes
Status	Released	Released	Released	Released	Released	Released	Released	Released	Released	Released
Status_Date	2020-11-20	2020-11-20	2020-11-20	2020-11-20	2020-11-20	2022-03-02	2020-11-20	2020-11-20	2020-11-20	2020-11-20
Project	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4
		LV42_biosample_protocol	LV42_library_protocol				LV42_biosample_protocol	LV42_library_protocol
protocol_URL		MAK16-BGHcLV12-43.pdf	L-MAK16-BGHcLV12-43.pdf				MAK16-BGHcLV12-44.pdf	L-MAK16-BGHcLV12-44.pdf
ID	750	795	877	985	1067	7250	796	878	986	1068

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
MAK16-BGHcLV12-43_TAAGTGGT+CTTAAGCC_HK3H2DSXX_S39_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set42/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	35	NovaSeq6000	100	paired-ended	1				NT-BGHcLV12-1_GGCATTCT+CTAGCTTG_HK3H2DSXX_S31_L004_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV12-2_AATGCCTC+TCGATCCA_HK3H2DSXX_S32_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	367
MAK16-BGHcLV12-43_TAAGTGGT+CTTAAGCC_HK3H2DSXX_S39_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set42/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	35	NovaSeq6000	100	paired-ended	2				NT-BGHcLV12-1_GGCATTCT+CTAGCTTG_HK3H2DSXX_S31_L004_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV12-2_AATGCCTC+TCGATCCA_HK3H2DSXX_S32_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	449
MAK16-BGHcLV12-43_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	35					GRCh38	V40	MAK16-BGHcLV12-43_TAAGTGGT+CTTAAGCC_HK3H2DSXX_S39_L004_R1_001.filtered.trimmed.paired.fastq.gz,MAK16-BGHcLV12-43_TAAGTGGT+CTTAAGCC_HK3H2DSXX_S39_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	23706
MAK16-BGHcLV12-43_Signal.Unique.strand+.bw	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	35					GRCh38	V40	MAK16-BGHcLV12-43/Aligned.sortedByCoord.out.bam		ENCORE2	23788
MAK16-BGHcLV12-43_Signal.Unique.strand-.bw	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	35					GRCh38	V40	MAK16-BGHcLV12-43/Aligned.sortedByCoord.out.bam		ENCORE2	23870
MAK16-BGHcLV12-43_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	35					GRCh38	V40	MAK16-BGHcLV12-43/Aligned.sortedByCoord.out.bam		ENCORE2	23952
MAK16-BGHcLV12-43_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	35					GRCh38	V40	MAK16-BGHcLV12-43/Aligned.sortedByCoord.out.bam		ENCORE2	24034
MAK16-BGHcLV12-43_quant.sf	ENCODE_DATA/set42/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	35					GRCh38	V40	MAK16-BGHcLV12-43_TAAGTGGT+CTTAAGCC_HK3H2DSXX_S39_L004_R1_001.filtered.trimmed.paired.fastq.gz,MAK16-BGHcLV12-43_TAAGTGGT+CTTAAGCC_HK3H2DSXX_S39_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24116
MAK16-BGHcLV12-44_CGGACAAC+TCCGGATT_HK3H2DSXX_S40_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set42/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	36	NovaSeq6000	100	paired-ended	1				NT-BGHcLV12-1_GGCATTCT+CTAGCTTG_HK3H2DSXX_S31_L004_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV12-2_AATGCCTC+TCGATCCA_HK3H2DSXX_S32_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	368
MAK16-BGHcLV12-44_CGGACAAC+TCCGGATT_HK3H2DSXX_S40_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set42/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	36	NovaSeq6000	100	paired-ended	2				NT-BGHcLV12-1_GGCATTCT+CTAGCTTG_HK3H2DSXX_S31_L004_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV12-2_AATGCCTC+TCGATCCA_HK3H2DSXX_S32_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	450
MAK16-BGHcLV12-44_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	36					GRCh38	V40	MAK16-BGHcLV12-44_CGGACAAC+TCCGGATT_HK3H2DSXX_S40_L004_R1_001.filtered.trimmed.paired.fastq.gz,MAK16-BGHcLV12-44_CGGACAAC+TCCGGATT_HK3H2DSXX_S40_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	23707
MAK16-BGHcLV12-44_Signal.Unique.strand+.bw	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	36					GRCh38	V40	MAK16-BGHcLV12-44/Aligned.sortedByCoord.out.bam		ENCORE2	23789
MAK16-BGHcLV12-44_Signal.Unique.strand-.bw	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	36					GRCh38	V40	MAK16-BGHcLV12-44/Aligned.sortedByCoord.out.bam		ENCORE2	23871
MAK16-BGHcLV12-44_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	36					GRCh38	V40	MAK16-BGHcLV12-44/Aligned.sortedByCoord.out.bam		ENCORE2	23953
MAK16-BGHcLV12-44_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	36					GRCh38	V40	MAK16-BGHcLV12-44/Aligned.sortedByCoord.out.bam		ENCORE2	24035
MAK16-BGHcLV12-44_quant.sf	ENCODE_DATA/set42/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	36					GRCh38	V40	MAK16-BGHcLV12-44_CGGACAAC+TCCGGATT_HK3H2DSXX_S40_L004_R1_001.filtered.trimmed.paired.fastq.gz,MAK16-BGHcLV12-44_CGGACAAC+TCCGGATT_HK3H2DSXX_S40_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24117