ZC3H8 RNA-Seq in HepG2


RBP	ZC3H8
Cell_Line	HepG2
Method	shRNA
Exp_Name	ZC3H8-BGHLV37-HepG2
ENCODE_series_ID	ENCSR123ZDP
Batch_ID	BGHLV37
Pool ID	Pool-181119
Local_Set_Name	set41_spikeins
ENCODE_KD_Exp_ID	ENCSR184YDW
ENCODE_CN_Exp_ID	ENCSR093ERJ
Rep1	ZC3H8-BGHLV37-115D
Rep2	ZC3H8-BGHLV37-116D
CN1	NT-BGHLV37-1D
CN2	NT-BGHLV37-2D
Rep1_qPCR	66.8
Rep2_qPCR	64.0
Rep1_WB	54.3
Rep2_WB	58.8
Antibody Cat#	A303-089A
Antibody Lot#	A303-089A
Antibody DCC ID	ENCAB192ZJZ
Status	Released
Project	ENCODE4
ID	883

	BGHLV37-115	BGHLV37-116
idx	1027	1028
TRCN#_or_BGC#	TRCN0000163082	TRCN0000163082
shRNA_or_gRNA_sequence	GCAGCATTTGAGTCAGGCATT	GCAGCATTTGAGTCAGGCATT
PAM
Name	ZC3H8	ZC3H8
Sample_ID	BGHLV37-115	BGHLV37-116
transduction_Date	9/1/16	9/1/16
days
RBP_name	ZC3H8	ZC3H8
qPCR_result	66.8	64.0
Ave_qPCR	65.4
RT-qPCR_primer-F	ccctggaaacaaaggatcaa
RT-qPCR_primer-R	tgaatgcctgactcaaatgc
protein_conc	3619	3973
WB_result	54.3	58.8
Ave_WB	56.6
WB_DONE_date	9/15/16
MW	34kd
IP	1	1
antibody_Cat#	A303-089A	A303-089A
Antibody DCC ID	ENCAB192ZJZ	ENCAB192ZJZ
submitted_to_DCC_date	10/26/16
Rep1_TPM	19.2	0
Rep2_TPM	17.5	0
Action
Library_start_date	11/3/16	11/3/16
repeat_library	5/11/17	5/11/17
Note
ID	3122	3123

Library-Prep
Sequencing

Library-Prep Information

	BGHLV37-115	BGHLV37-115	BGHLV37-115	BGHLV37-116	BGHLV37-116	BGHLV37-116
Sample #			65			66
Sample Name	ZC3H8-BGHLV37-115	ZC3H8-BGHLV37-115B	ZC3H8-BGHLV37-115D	ZC3H8-BGHLV37-116	ZC3H8-BGHLV37-116B	ZC3H8-BGHLV37-116D
Sample_Name_Alias	ZC3H8_BGHLV37-115	ZC3H8-BGHLV37-115B		ZC3H8_BGHLV37-116	ZC3H8-BGHLV37-116B
Index Well Position	S07	S09	S09	S08	S10	S10
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2016-11-03	2017-05-11	2018-11-19	2016-11-03	2017-05-11	2018-11-19
Lib_ID	Lib-161103	Lib-170511	Lib-181119	Lib-161103	Lib-170511	Lib-181119
Tecan_Location
Tecan
Tecan_date
Size_bp			290			290
Peak_Molarity			41.30			51.50
libSampleQC_DNA_Well	DNA_Library_LV37-38/set1/G4.png	DNA_Library_set39/set2/A6.png	DNA_Library_set41/set1/A8.png	DNA_Library_LV37-38/set1/H4.png	DNA_Library_set39/set2/B6.png	DNA_Library_set41/set1/B8.png
RIN	9.8	9.8	9.8	9.7	9.7	9.7
libSample_RNA_Well	RNA_Library_LV37_38/set1/G2.png	RNA_Library_LV37_38/set1/G2.png	RNA_Library_LV37_38/set1/G2.png	RNA_Library_LV37_38/set1/H2.png	RNA_Library_LV37_38/set1/H2.png	RNA_Library_LV37_38/set1/H2.png
SampleQC_method			TapeStation			TapeStation
SampleQC_date			2022-03-01			2022-03-01
Sample_ID	BGHLV37-115	BGHLV37-115	BGHLV37-115	BGHLV37-116	BGHLV37-116	BGHLV37-116
RBP	ZC3H8	ZC3H8	ZC3H8	ZC3H8	ZC3H8	ZC3H8
Batch_ID	BGHLV37	BGHLV37	BGHLV37	BGHLV37	BGHLV37	BGHLV37
WB_result	54.300	54.300	54.300	58.800	58.800	58.800
Library Description	TruSeq mRNA	TruSeq mRNA	TruSeq mRNA	TruSeq mRNA	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix		B	D		B	D
Lib_Status	SendToSequence	SendToSequence	SendToSequence	SendToSequence	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3	ENCODE4	ENCODE3	ENCODE3	ENCODE4
ID	2992	3036	3242	2993	3037	3243

Sequencing Information

	BGHLV37-115	BGHLV37-115	BGHLV37-115	BGHLV37-116	BGHLV37-116	BGHLV37-116
Sample_ID	BGHLV37-115	BGHLV37-115	BGHLV37-115	BGHLV37-116	BGHLV37-116	BGHLV37-116
Sample Name	ZC3H8_BGHLV37-115	ZC3H8-BGHLV37-115B	ZC3H8-BGHLV37-115D	ZC3H8_BGHLV37-116	ZC3H8-BGHLV37-116B	ZC3H8-BGHLV37-116D
Pool ID	Pool-161129	Pool-170911	Pool-181119	Pool-161129	Pool-170911	Pool-181119
LocalServer_folder	set37	set39_H	set41_spikeins	set37	set39_H	set41_spikeins
total_reads	65,756,378	57,147,040	30,904,740	26,901,560	56,330,148	44,638,562
total_aligned_reads	61,486,502	49,129,086	29,042,258	24,343,742	48,944,536	42,231,824
unique_aligned_reads	57,894,076	46,077,008	27,226,106	22,621,402	45,820,978	39,570,048
percent_uniqueAligned	0.88043	0.80629	0.88097	0.84090	0.81344	0.88645
correlation_replicates	0.592470	0.993662	0.999060	0.592470	0.993662	0.999060
spikein_reads	216,394	110	116,864	648	56	143,158
percent_spikeins	0.00329		0.00378	0.00002		0.00321
original_ReadLength	100	100	100	100	100	100
QC_Status	BadCorrelation	Submitted	Submitted	BadCorrelation	Submitted	Submitted
ID	1641	1691	1955	1642	1692	1956

	BGHLV37-115	BGHLV37-115	BGHLV37-115	BGHLV37-115	BGHLV37-115	BGHLV37-115	BGHLV37-116	BGHLV37-116
ENCODE_alias	brenton-graveley:ZC3H8-BGHLV37-B	brenton-graveley:ZC3H8-BGHLV37-HepG2_A	brenton-graveley:ZC3H8-BGHLV37-D	brenton-graveley:L-ZC3H8-BGHLV37-115D	brenton-graveley:ZC3H8-BGHLV37-HepG2	brenton-graveley:ZC3H8-BGHLV37-115B	brenton-graveley:L-ZC3H8-BGHLV37-116D	brenton-graveley:ZC3H8-BGHLV37-116B
ENCODE_accession	ENCSR696JWA	ENCSR102PLQ	ENCSR184YDW	ENCLB426NWV	ENCSR123ZDP	ENCBS699OQY	ENCLB551FBN	ENCBS112RBO
object_type	experiment	experiment	experiment	library	gene_silencing_series	biosample	library	biosample
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
Sample_ID	BGHLV37-115	BGHLV37-115	BGHLV37-115	BGHLV37-115	BGHLV37-115	BGHLV37-115	BGHLV37-116	BGHLV37-116
Sample Name	ZC3H8-BGHLV37-115B	ZC3H8-BGHLV37-115B	ZC3H8-BGHLV37-115D	ZC3H8-BGHLV37-115D	ZC3H8-BGHLV37-115D	ZC3H8-BGHLV37-115B	ZC3H8-BGHLV37-116D	ZC3H8-BGHLV37-116B
Selected	Yes	No	Yes	Yes	Yes	Yes	Yes	Yes
Status	Released	Released	Released	Released	Released	Released	Released	Released
Status_Date	2022-03-07	2022-03-07	2022-03-07	2022-03-07	2022-03-07	2019-03-13	2022-03-07	2019-03-13
Project	ENCODE3	ENCODE3	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4
				LV41_library_protocol_spikeins		LV39_biosample_protocol	LV41_library_protocol_spikeins	LV39_biosample_protocol
protocol_URL				L-ZC3H8-BGHLV37-115D.pdf		ZC3H8-BGHLV37-115B.pdf	L-ZC3H8-BGHLV37-116D.pdf	ZC3H8-BGHLV37-116B.pdf
ID	3209	7052	7379	7399	7423	7430	7400	7431

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
ZC3H8_BGHLV37-115_CAGATC_L007_001.R1.fastq.gz	ENCODE_DATA/set37/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1641	HiSeq2500	100	paired-ended	1				NT_BGHLV37-1_GTCCGC_L005_001.R1.fastq.gz,NT_BGHLV37-2_GTGAAA_L005_001.R1.fastq.gz	ENCODE3	22048
ZC3H8_BGHLV37-115_CAGATC_L007_001.R2.fastq.gz	ENCODE_DATA/set37/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1641	HiSeq2500	100	paired-ended	2				NT_BGHLV37-1_GTCCGC_L005_001.R2.fastq.gz,NT_BGHLV37-2_GTGAAA_L005_001.R2.fastq.gz	ENCODE3	22064
ZC3H8_BGHLV37-115_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set37/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1641					GRCh38	V40	ZC3H8_BGHLV37-115_CAGATC_L007_001.R1.fastq.gz,ZC3H8_BGHLV37-115_CAGATC_L007_001.R2.fastq.gz		ENCORE2	22080
ZC3H8_BGHLV37-115_Signal.Unique.strand+.bw	ENCODE_DATA/set37/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1641					GRCh38	V40	ZC3H8_BGHLV37-115/Aligned.sortedByCoord.out.bam		ENCORE2	22096
ZC3H8_BGHLV37-115_Signal.Unique.strand-.bw	ENCODE_DATA/set37/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1641					GRCh38	V40	ZC3H8_BGHLV37-115/Aligned.sortedByCoord.out.bam		ENCORE2	22112
ZC3H8_BGHLV37-115_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set37/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1641					GRCh38	V40	ZC3H8_BGHLV37-115/Aligned.sortedByCoord.out.bam		ENCORE2	22128
ZC3H8_BGHLV37-115_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set37/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1641					GRCh38	V40	ZC3H8_BGHLV37-115/Aligned.sortedByCoord.out.bam		ENCORE2	22144
ZC3H8_BGHLV37-115_quant.sf	ENCODE_DATA/set37/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1641					GRCh38	V40	ZC3H8_BGHLV37-115_CAGATC_L007_001.R1.fastq.gz,ZC3H8_BGHLV37-115_CAGATC_L007_001.R2.fastq.gz		ENCORE2	22160
ZC3H8-BGHLV37-115B_GATCAG_ACBE67ANXX_L002_001.R1.fastq.gz	ENCODE_DATA/set39_H/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1691	HiSeq2500	100	paired-ended	1				NT-BGHLV37-1B_ACAGTG_ACBE67ANXX_L001_001.R1.fastq.gz,NT-BGHLV37-2B_GCCAAT_ACBE67ANXX_L001_001.R1.fastq.gz	ENCODE3	22292
ZC3H8-BGHLV37-115B_GATCAG_ACBE67ANXX_L002_001.R2.fastq.gz	ENCODE_DATA/set39_H/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1691	HiSeq2500	100	paired-ended	2				NT-BGHLV37-1B_ACAGTG_ACBE67ANXX_L001_001.R2.fastq.gz,NT-BGHLV37-2B_GCCAAT_ACBE67ANXX_L001_001.R2.fastq.gz	ENCODE3	22316
ZC3H8-BGHLV37-115B_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set39_H/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1691					GRCh38	V40	ZC3H8-BGHLV37-115B_GATCAG_ACBE67ANXX_L002_001.R1.fastq.gz,ZC3H8-BGHLV37-115B_GATCAG_ACBE67ANXX_L002_001.R2.fastq.gz		ENCORE2	22340
ZC3H8-BGHLV37-115B_Signal.Unique.strand+.bw	ENCODE_DATA/set39_H/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1691					GRCh38	V40	ZC3H8-BGHLV37-115B/Aligned.sortedByCoord.out.bam		ENCORE2	22364
ZC3H8-BGHLV37-115B_Signal.Unique.strand-.bw	ENCODE_DATA/set39_H/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1691					GRCh38	V40	ZC3H8-BGHLV37-115B/Aligned.sortedByCoord.out.bam		ENCORE2	22388
ZC3H8-BGHLV37-115B_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set39_H/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1691					GRCh38	V40	ZC3H8-BGHLV37-115B/Aligned.sortedByCoord.out.bam		ENCORE2	22412
ZC3H8-BGHLV37-115B_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set39_H/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1691					GRCh38	V40	ZC3H8-BGHLV37-115B/Aligned.sortedByCoord.out.bam		ENCORE2	22436
ZC3H8-BGHLV37-115B_quant.sf	ENCODE_DATA/set39_H/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1691					GRCh38	V40	ZC3H8-BGHLV37-115B_GATCAG_ACBE67ANXX_L002_001.R1.fastq.gz,ZC3H8-BGHLV37-115B_GATCAG_ACBE67ANXX_L002_001.R2.fastq.gz		ENCORE2	22460
ZC3H8-BGHLV37-115D_GATCAG_HJMK5BCX2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set41_spikeins/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1955	HiSeq2500	100	paired-ended	1				NT-BGHLV37-1D_ACAGTG_HJMK5BCX2_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHLV37-2D_GCCAAT_HJMK5BCX2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	27431
ZC3H8-BGHLV37-115D_GATCAG_HJMK5BCX2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set41_spikeins/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1955	HiSeq2500	100	paired-ended	2				NT-BGHLV37-1D_ACAGTG_HJMK5BCX2_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHLV37-2D_GCCAAT_HJMK5BCX2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	27459
ZC3H8-BGHLV37-115D_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set41_spikeins/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1955					GRCh38	V40	ZC3H8-BGHLV37-115D_GATCAG_HJMK5BCX2_L001_R1_001.filtered.trimmed.paired.fastq.gz,ZC3H8-BGHLV37-115D_GATCAG_HJMK5BCX2_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	27487
ZC3H8-BGHLV37-115D_Signal.Unique.strand+.bw	ENCODE_DATA/set41_spikeins/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1955					GRCh38	V40	ZC3H8-BGHLV37-115D/Aligned.sortedByCoord.out.bam		ENCORE2	27515
ZC3H8-BGHLV37-115D_Signal.Unique.strand-.bw	ENCODE_DATA/set41_spikeins/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1955					GRCh38	V40	ZC3H8-BGHLV37-115D/Aligned.sortedByCoord.out.bam		ENCORE2	27543
ZC3H8-BGHLV37-115D_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set41_spikeins/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1955					GRCh38	V40	ZC3H8-BGHLV37-115D/Aligned.sortedByCoord.out.bam		ENCORE2	27571
ZC3H8-BGHLV37-115D_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set41_spikeins/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1955					GRCh38	V40	ZC3H8-BGHLV37-115D/Aligned.sortedByCoord.out.bam		ENCORE2	27599
ZC3H8-BGHLV37-115D_quant.sf	ENCODE_DATA/set41_spikeins/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1955					GRCh38	V40	ZC3H8-BGHLV37-115D_GATCAG_HJMK5BCX2_L001_R1_001.filtered.trimmed.paired.fastq.gz,ZC3H8-BGHLV37-115D_GATCAG_HJMK5BCX2_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	27627
ZC3H8_BGHLV37-116_ACTTGA_L007_001.R1.fastq.gz	ENCODE_DATA/set37/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1642	HiSeq2500	100	paired-ended	1				NT_BGHLV37-1_GTCCGC_L005_001.R1.fastq.gz,NT_BGHLV37-2_GTGAAA_L005_001.R1.fastq.gz	ENCODE3	22049
ZC3H8_BGHLV37-116_ACTTGA_L007_001.R2.fastq.gz	ENCODE_DATA/set37/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1642	HiSeq2500	100	paired-ended	2				NT_BGHLV37-1_GTCCGC_L005_001.R2.fastq.gz,NT_BGHLV37-2_GTGAAA_L005_001.R2.fastq.gz	ENCODE3	22065
ZC3H8_BGHLV37-116_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set37/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1642					GRCh38	V40	ZC3H8_BGHLV37-116_ACTTGA_L007_001.R1.fastq.gz,ZC3H8_BGHLV37-116_ACTTGA_L007_001.R2.fastq.gz		ENCORE2	22081
ZC3H8_BGHLV37-116_Signal.Unique.strand+.bw	ENCODE_DATA/set37/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1642					GRCh38	V40	ZC3H8_BGHLV37-116/Aligned.sortedByCoord.out.bam		ENCORE2	22097
ZC3H8_BGHLV37-116_Signal.Unique.strand-.bw	ENCODE_DATA/set37/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1642					GRCh38	V40	ZC3H8_BGHLV37-116/Aligned.sortedByCoord.out.bam		ENCORE2	22113
ZC3H8_BGHLV37-116_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set37/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1642					GRCh38	V40	ZC3H8_BGHLV37-116/Aligned.sortedByCoord.out.bam		ENCORE2	22129
ZC3H8_BGHLV37-116_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set37/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1642					GRCh38	V40	ZC3H8_BGHLV37-116/Aligned.sortedByCoord.out.bam		ENCORE2	22145
ZC3H8_BGHLV37-116_quant.sf	ENCODE_DATA/set37/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1642					GRCh38	V40	ZC3H8_BGHLV37-116_ACTTGA_L007_001.R1.fastq.gz,ZC3H8_BGHLV37-116_ACTTGA_L007_001.R2.fastq.gz		ENCORE2	22161
ZC3H8-BGHLV37-116B_TAGCTT_ACBE67ANXX_L002_001.R1.fastq.gz	ENCODE_DATA/set39_H/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1692	HiSeq2500	100	paired-ended	1				NT-BGHLV37-1B_ACAGTG_ACBE67ANXX_L001_001.R1.fastq.gz,NT-BGHLV37-2B_GCCAAT_ACBE67ANXX_L001_001.R1.fastq.gz	ENCODE3	22293
ZC3H8-BGHLV37-116B_TAGCTT_ACBE67ANXX_L002_001.R2.fastq.gz	ENCODE_DATA/set39_H/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1692	HiSeq2500	100	paired-ended	2				NT-BGHLV37-1B_ACAGTG_ACBE67ANXX_L001_001.R2.fastq.gz,NT-BGHLV37-2B_GCCAAT_ACBE67ANXX_L001_001.R2.fastq.gz	ENCODE3	22317
ZC3H8-BGHLV37-116B_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set39_H/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1692					GRCh38	V40	ZC3H8-BGHLV37-116B_TAGCTT_ACBE67ANXX_L002_001.R1.fastq.gz,ZC3H8-BGHLV37-116B_TAGCTT_ACBE67ANXX_L002_001.R2.fastq.gz		ENCORE2	22341
ZC3H8-BGHLV37-116B_Signal.Unique.strand+.bw	ENCODE_DATA/set39_H/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1692					GRCh38	V40	ZC3H8-BGHLV37-116B/Aligned.sortedByCoord.out.bam		ENCORE2	22365
ZC3H8-BGHLV37-116B_Signal.Unique.strand-.bw	ENCODE_DATA/set39_H/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1692					GRCh38	V40	ZC3H8-BGHLV37-116B/Aligned.sortedByCoord.out.bam		ENCORE2	22389
ZC3H8-BGHLV37-116B_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set39_H/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1692					GRCh38	V40	ZC3H8-BGHLV37-116B/Aligned.sortedByCoord.out.bam		ENCORE2	22413
ZC3H8-BGHLV37-116B_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set39_H/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1692					GRCh38	V40	ZC3H8-BGHLV37-116B/Aligned.sortedByCoord.out.bam		ENCORE2	22437
ZC3H8-BGHLV37-116B_quant.sf	ENCODE_DATA/set39_H/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1692					GRCh38	V40	ZC3H8-BGHLV37-116B_TAGCTT_ACBE67ANXX_L002_001.R1.fastq.gz,ZC3H8-BGHLV37-116B_TAGCTT_ACBE67ANXX_L002_001.R2.fastq.gz		ENCORE2	22461
ZC3H8-BGHLV37-116D_TAGCTT_HJMK5BCX2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set41_spikeins/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1956	HiSeq2500	100	paired-ended	1				NT-BGHLV37-1D_ACAGTG_HJMK5BCX2_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHLV37-2D_GCCAAT_HJMK5BCX2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	27432
ZC3H8-BGHLV37-116D_TAGCTT_HJMK5BCX2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set41_spikeins/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1956	HiSeq2500	100	paired-ended	2				NT-BGHLV37-1D_ACAGTG_HJMK5BCX2_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHLV37-2D_GCCAAT_HJMK5BCX2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	27460
ZC3H8-BGHLV37-116D_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set41_spikeins/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1956					GRCh38	V40	ZC3H8-BGHLV37-116D_TAGCTT_HJMK5BCX2_L001_R1_001.filtered.trimmed.paired.fastq.gz,ZC3H8-BGHLV37-116D_TAGCTT_HJMK5BCX2_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	27488
ZC3H8-BGHLV37-116D_Signal.Unique.strand+.bw	ENCODE_DATA/set41_spikeins/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1956					GRCh38	V40	ZC3H8-BGHLV37-116D/Aligned.sortedByCoord.out.bam		ENCORE2	27516
ZC3H8-BGHLV37-116D_Signal.Unique.strand-.bw	ENCODE_DATA/set41_spikeins/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1956					GRCh38	V40	ZC3H8-BGHLV37-116D/Aligned.sortedByCoord.out.bam		ENCORE2	27544
ZC3H8-BGHLV37-116D_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set41_spikeins/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1956					GRCh38	V40	ZC3H8-BGHLV37-116D/Aligned.sortedByCoord.out.bam		ENCORE2	27572
ZC3H8-BGHLV37-116D_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set41_spikeins/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1956					GRCh38	V40	ZC3H8-BGHLV37-116D/Aligned.sortedByCoord.out.bam		ENCORE2	27600
ZC3H8-BGHLV37-116D_quant.sf	ENCODE_DATA/set41_spikeins/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1956					GRCh38	V40	ZC3H8-BGHLV37-116D_TAGCTT_HJMK5BCX2_L001_R1_001.filtered.trimmed.paired.fastq.gz,ZC3H8-BGHLV37-116D_TAGCTT_HJMK5BCX2_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	27628