title: pre-MBT rep1

description:
Exp1_512_1
Paired-end S sample
processed data file: pre_MBT_average.txt (processed from two repeats)

source_name: whole embryos_pre-MBT

value: 512-cell embryos


title: pre-MBT rep2

status: Public on Apr 13 2017

type: SRA

city: Oklahoma

first: Christopher

middle: Lee

last: Sansam

state: OK

address: 825 NE 13th Street

department: Cell Cycle and Cancer Biology Program

country: USA

institute: Oklahoma Medical Research Foundation

description:
Exp1_512_2
Paired-end S sample
processed data file: pre_MBT_average.txt (processed from two repeats)

library_source: genomic

data_processing:
Basecalls performed using bcl2fastq
Sequencing reads were aligned to the GRCz10 genome build using BWA-mem with standard parameters, and PCR duplicates were marked with PiCard
Data were filtered to removed 100bp regions with greater than 5 standard deviations from the genome median (chromosome 4 excluded).
200 read count G1 windows of varying sizes were defined and S-phase reads counted in the same windows
Data was normalized by setting the genome mean (excluding chromosome 4) replication timing value to 0, and standard deviation to 1.
Genome_build: GRCz10/danRer10
Supplementary_files_format_and_content: txt files were generated using Matlab and contain a genomic coordinate (chromosome number in column 1 and chromosomal location in column 2), and replication timing value in column 3.  Timing value represents S-phase copy number relative to G1 sample, normalized to a genome mean of 0 and standard deviation of 1 (excluding chromosome 4)

molecule: genomic DNA

organism: Danio rerio

growth_protocol: For whole embryos, timed matings were performed between dozens of adults and hundres of embryos were collected in 10 minute intervals.  Embryos were allowed to develop in a 28.5C incubator until appropriate developmental stage was reached.  Developmental stage was visually assessed, embryos were dechorionated, deyolked, and cells were fixed in 70% ethanol and stored at -20C.  Primary ZTF cells were generated from adult zebrafish tailfin clip.  Tail clips were washed extensively with PBS/pen/strep then grown in Amniomax-II complete medium, with twice weekly media changes, in a 96-well coated tissue culture plate, at 28.5C and 5%CO2.  As fibroblasts migrated out of the tissue and filled the well, cells were trypsinized to remove from plate and transferred to progressively larger coated cell culture plates.  Once cells filled a 6 cell plate, they were transferred to 6cm coated cell culture plates and the medium was changed to DMEM with 15% serum and added L-glutamine.

extract_protocol:
FACS purified cell pellets were removed from -20C and briefly thawed on ice.  Cells were resuspended in SDS buffer and then proteinase K was added.  Solution was quickly vortexed and incubated at 56C for 2hrs with periodic vortexing.  After 2 hours of cell lysis, DNA was isolated by phenol-chloroform extraction and ethanol precipitation.  Briefly, a 1:1 ratio of phenol-chloroform was added to cell lysate, vortexed vigorously for 15sec, centrifuged at 14,000g and 4C for 10 minutes, and top aqueous layer containing DNA was transferred to a new tube.  A 1/10 volume of sodium acetate and 2.5x volume of ethanol was added to precipitate DNA, along with glycogen as a carrier.   Solution was placed at -80C for 20 minutes, centrifuged at 14,000g for 15 minutes, pellet was washed with 70% ethanol and centrifuged as before, pellet was resuspended in water.  Solution was RNAse treated by adding 4ul of 2mg/ml DNAse-free RNAse A (Genelink) and placing at 37C for 1hr.  DNA was then purified by phenol-choloroform extraction and ethanol precipitation as before, quantified using a Qubit dsDNA High Sensitivity assay, and solution stored at -20C.
Purified DNA solution was thawed and 1ug of DNA was sheared on a Covaris S220 Focused-ultrasonicator optimized to produce 300bp fragments.  Quality of sheared DNA was analyzed using an Agilent TapeStation 2200 with High Sensitivity D1000 ScreenTape.  Libraries were prepared using NEBNext DNA Library Prep Kit for Illumina with NEBNext Multiplex Oligos for Illumina according to manufacturer’s instructions.  Briefly, DNA fragment ends are prepared for adapter ligation, adapters are ligated onto DNA, adapter-ligated DNA is size-selected and cleaned up,  5 cycles of PCR amplification of adapter-ligated DNA was performed with different multiplex primers for each sample, and PCR was cleaned up.  Quality of library prep was analyzed on Agilent 2200 TapeStation and quantified using Qubit.  DNA libraries were pooled and sequenced at a depth of 300 million total reads per lane in 100bp paired-end read fragments on Illumina HiSeq 2500.

treatment_protocol: Ethanol-fixed 28hpf embryos and ZTF cells were removed from -20C, centrifuged at 1400g and 4C, and placed on ice.  The supernatant was removed and cell pellet was resuspended in PBS with 1%BSA to wash cells.  Cells were centrifuged as before and cells were resuspended in cold propidium iodide solution to stain DNA and incubated on ice for 5 minutes.  The cells were then filtered through a 40um mesh then sorted on a FACSAria at a flowrate of 1.0ml/min.  Cells are first gated by FCS/SSC to removed cell debris, then by FSC/PI to removed cell doublets.  Cells are then sorted based on DNA content, sorting the left side of a G1 peak of 2N DNA content to prevent S-phase contamination, and cells in S-phase between the 2N and 4N DNA content peaks were sorted.  More than 500,000 total cells were sorted for all G1 and S-phase samples and cells were kept at 4C or on ice during sorting.  Sorted cells were then centrifuged at 1400g, washed in PBS-BSA, centrifuged again as before, and the dry pellet was frozen at -20C.

tag: strain

tag: developmental stage

tag: tissue

value: Whole embryos


title: K562 dCas9-KRAB, Lenti-sgRNA set C pooled infection, batch 16

city: Dallas

first: Gary

middle: Chung

last: Hon

state: TX

address: 5323 Harry Hines Blvd.

department: OB/GYN

institute: UT Southwestern

description: sgrnas and barcodes: listed in supplementary document

library_source: transcriptomic

data_processing:
Basecalls performed by Picard ExtractIlluminaBarcodes v1.117.
Drop-Seq data were mapped using Drop-Seq Tools to the human genome augmented with a sequence representing the sgRNA-containing plasmid with a fully degenerate 12-bp barcode sequence. Uniquely mapping reads with mapping quality ≥ 10 were subjected to PCR duplicate removal by examining the unique molecular identifiers (UMI) for each read. Reads were then partitioned to individual cells based on cell barcodes.
Read counts were tabulated with featureCounts v1.5.0.
Genome build: hg19
Supplementary_files_format_and_content: read counts for all genes

molecule: total RNA

organism: Homo sapiens

source_name: K562 cells

growth_protocol: K562 were cultured in IMDM plus 10% FBS and pen/strep at 37C and 5% CO2.

extract_protocol: Single cell RNA sequencing was performed using the Drop-Seq method. Briefly, single cells, polyA-containing barcoded beads (ChemGenes), and droplet generation oil (Bio-Rad) were each flowed into individual input ports on a microfluidic device (NanoShift). Cells in droplets were lysed and hybridized to beads. Beads were isolated and subjected to reverse transcription (Thermo Fisher) and exonuclease I (NEB) treatment, followed by PCR of full length transcripts (Kapa). Final libraries were created by Tn5-mediated tagmentation of cDNA, and amplified by PCR (Kapa) and purified by SPRI beads.

treatment_protocol: HEK293T cells were cultured in DMEM with 10% FBS and pen/strep. For lentiviral packaging, 3X106 293T cells were seeded in a 6 cm dish one day before transfection. The indicated viral plasmid(s) were co-transfected with lentivirus packaging plasmids pMD2.G and psPAX2 (Addgene ID 12259 and 12260) with 4:2:3 ratio by using Lipofectamine 3000 (Thermo Fisher) according to the manufacturer's protocol. Twelve hours after transfection, media was changed to fresh DMEM with 10% FBS plus Pen/Strep. Seventy-two hours after transfection, virus-containing media was collected, passed through a 45 um filter, and aliquoted into 1.5ml tubes. Viruses were stored in -80°C before infection or titration. For virus infection, 2X105 K562 cells were seeded in 24 well plate per well with 500 µl complete medium plus 1µg/ml polybrene. Titrated virus aliquot(s) were thawed to room temperature, combined as a pool, and added to the plates. The plate was then centrifuged at 1000xg at 36 °C and returned to the incubator. The following day, the media was changed to fresh complete medium with antibiotics to screen for infected cells. Cells were kept at ~30% confluence during antibiotic selection.

tag: cell line


title: 28hpf rep1

description:
Exp1_S/G1_repeat_1
Paired-end G1 and S samples
processed data file: Exp1_S_G1_average.txt (processed from two repeats)
processed data file: Exp1_and_2_S_G1_average.txt (processed from three repeats)

source_name: whole embryos_28hpf

value: 28hpf embryos


title: 28hpf Exp2

description:
Exp2_S/G1
processed from two repeats
processed data file: Exp1_and_2_S_G1_average.txt (processed from three repeats)

source_name: whole embryos_28hpf Exp2


title: K562 dCas9-KRAB, Lenti-sgRNA set A pooled infection, batch 11


title: K562 dCas9-KRAB, Lenti-sgRNA set C pooled infection, batch 15


title: 28hpf rep2

description:
Exp1_S/G1_repeat_2
Paired-end G1 and S samples
processed data file: Exp1_S_G1_average.txt (processed from two repeats)
processed data file: Exp1_and_2_S_G1_average.txt (processed from three repeats)


title: K562 dCas9-KRAB, Lenti-sgRNA set B pooled infection, batch 2


title: K562 dCas9-KRAB, Lenti-sgRNA set C pooled infection, batch 12


title: K562 dCas9-KRAB, Lenti-sgRNA set C pooled infection, batch 14


title: K562 dCas9-KRAB, Lenti-sgRNA set C pooled infection, batch 13


title: Shield rep1

description:
Exp1_Shield
Paired-end S sample
processed data file: Shield_average.txt (processed from two repeats)

source_name: whole embryos_Shield

value: Shield stage embryos


title: K562 dCas9-KRAB, Lenti-sgRNA set B pooled infection, batch 8


title: K562 dCas9-KRAB, Lenti-sgRNA set B pooled infection, batch 7


title: K562 dCas9-KRAB, Lenti-sgRNA set A pooled infection, batch 10


title: K562 dCas9-KRAB, Lenti-sgRNA set B pooled infection, batch 10


title: K562 dCas9-KRAB, Lenti-sgRNA set A pooled infection, batch 8


title: K562 dCas9-KRAB, Lenti-sgRNA set B pooled infection, batch 1


title: K562 dCas9-KRAB, Lenti-sgRNA set B pooled infection, batch 5


title: K562 dCas9-KRAB, Lenti-sgRNA set B pooled infection, batch 6


title: K562 dCas9-KRAB, WT vs TNFA treatment, biorep1, batch 10

treatment_protocol: HEK293T cells were cultured in DMEM with 10% FBS and pen/strep. For lentiviral packaging, 3X106 293T cells were seeded in a 6 cm dish one day before transfection. The indicated viral plasmid(s) were co-transfected with lentivirus packaging plasmids pMD2.G and psPAX2 (Addgene ID 12259 and 12260) with 4:2:3 ratio by using Lipofectamine 3000 (Thermo Fisher) according to the manufacturer's protocol. Twelve hours after transfection, media was changed to fresh DMEM with 10% FBS plus Pen/Strep. Seventy-two hours after transfection, virus-containing media was collected, passed through a 45 um filter, and aliquoted into 1.5ml tubes. Viruses were stored in -80°C before infection or titration. For virus infection, 2X105 K562 cells were seeded in 24 well plate per well with 500 µl complete medium plus 1µg/ml polybrene. Titrated virus aliquot(s) were thawed to room temperature and one virus was added to each well. The plate was then centrifuged at 1000xg at 36 °C and returned to the incubator. The following day, the media was changed to fresh complete medium with antibiotics to screen for infected cells. Cells were kept at ~30% confluence during antibiotic selection. One batch of cells were treated with TNF-alpha for 1 hour. Immediately prior to library construction, the TNF-alpha treated cells (labeled with sgRNA64) and mock treated cells (labeled with sgRNA63) were combined to a single tube in PBS/BSA.


title: K562 dCas9-KRAB, WT vs TNFA treatment, biorep1, batch 9


title: K562 dCas9-KRAB, Lenti-sgRNA set C pooled infection, batch 11


title: K562 dCas9-KRAB, Lenti-sgRNA set C pooled infection, batch 10


title: K562 dCas9-KRAB, Lenti-sgRNA set C pooled infection, batch 8


title: K562 dCas9-KRAB, Lenti-sgRNA set C pooled infection, batch 9


title: K562 dCas9-KRAB, WT vs TNFA treatment, biorep2, batch 2


title: K562 dCas9-KRAB, WT vs TNFA treatment, biorep2, batch 5


title: K562 dCas9-KRAB, WT vs TNFA treatment, biorep2, batch 3


title: K562 dCas9-KRAB, WT vs TNFA treatment, biorep1, batch 4


title: K562 dCas9-KRAB, Lenti-sgRNA set A pooled infection, batch 9


title: K562 dCas9-KRAB, Lenti-sgRNA set B pooled infection, batch 9


title: K562 dCas9-KRAB, WT vs TNFA treatment, biorep1, batch 6


title: K562 dCas9-KRAB, WT vs TNFA treatment, biorep1, batch 1


title: K562 dCas9-KRAB, Lenti-sgRNA separate infection, beta-globin pilot, batch 5

treatment_protocol: HEK293T cells were cultured in DMEM with 10% FBS and pen/strep. For lentiviral packaging, 3X106 293T cells were seeded in a 6 cm dish one day before transfection. The indicated viral plasmid(s) were co-transfected with lentivirus packaging plasmids pMD2.G and psPAX2 (Addgene ID 12259 and 12260) with 4:2:3 ratio by using Lipofectamine 3000 (Thermo Fisher) according to the manufacturer's protocol. Twelve hours after transfection, media was changed to fresh DMEM with 10% FBS plus Pen/Strep. Seventy-two hours after transfection, virus-containing media was collected, passed through a 45 um filter, and aliquoted into 1.5ml tubes. Viruses were stored in -80°C before infection or titration. For virus infection, 2X105 K562 cells were seeded in 24 well plate per well with 500 µl complete medium plus 1µg/ml polybrene. Titrated virus aliquot(s) were thawed to room temperature and one virus was added to each well. The plate was then centrifuged at 1000xg at 36 °C and returned to the incubator. The following day, the media was changed to fresh complete medium with antibiotics to screen for infected cells. Cells were kept at ~30% confluence during antibiotic selection. Immediately prior to library construction, the separately infected cells were combined to a single tube.


title: K562 dCas9-KRAB, WT vs TNFA treatment, biorep1, batch 7


title: K562 dCas9-KRAB, WT vs TNFA treatment, biorep2, batch 1


title: K562 dCas9-KRAB, Lenti-sgRNA separate infection, beta-globin pilot, batch 3


title: K562 dCas9-KRAB, WT vs TNFA treatment, biorep1, batch 5


title: K562 dCas9-KRAB, WT vs TNFA treatment, biorep1, batch 3


title: K562 dCas9-KRAB, Lenti-sgRNA separate infection, beta-globin pilot, batch 2


title: K562 dCas9-KRAB, WT vs TNFA treatment, biorep1, batch 2


title: K562 dCas9-KRAB, Lenti-sgRNA pooled infection, beta-globin pilot, batch 6


title: K562 dCas9-KRAB, Lenti-sgRNA pooled infection, beta-globin pilot, batch 7


title: K562 dCas9-KRAB, Lenti-sgRNA pooled infection, beta-globin pilot, batch 8


title: K562 dCas9-KRAB, Lenti-sgRNA set A pooled infection, batch 7


title: K562 dCas9-KRAB, Lenti-sgRNA separate infection, beta-globin pilot, batch 7


title: K562 dCas9-KRAB, Lenti-sgRNA separate infection, beta-globin pilot, batch 6


title: K562 dCas9-KRAB, WT vs TNFA treatment, biorep2, batch 4


title: K562 dCas9-KRAB, WT vs TNFA treatment, biorep1, batch 8


title: K562 dCas9-KRAB, Lenti-sgRNA pooled infection, beta-globin pilot, batch 3


title: K562 dCas9-KRAB, Lenti-sgRNA pooled infection, beta-globin pilot, batch 4


title: K562 dCas9-KRAB, Lenti-sgRNA pooled infection, beta-globin pilot, batch 1


title: K562 dCas9-KRAB, Lenti-sgRNA62_bc37

description:
sgrna barcode id: bc37
sgrna id: sgRNA62
sgrna sequence: CTGTGTTTGTGAGCGGTGC
sgrna target: HSBP1 enhancer

data_processing:
Basecalls performed bcl2fastq v2.17.1.14.
RNA-seq reads were aligned using the STAR aligner v2.4.2a with default parameters to the hg19 genome assembly augmented with a sequence representing the sgRNA-containing plasmid with a fully degenerate 12-bp barcode sequence.
10, and PCR duplicates were removed with Picard v1.117.
Read counts were tabulated with featureCounts v1.5.0.
Genome_build: hg19
Supplementary_files_format_and_content: read counts for all genes

extract_protocol:
total RNA was extracted from cells using Trizol Reagent (Thermo), and were subjected to enrichment of polyA+ RNA using the NEBNext Poly(A) kit (NEB).
Strand-specific polyA+ RNA-Seq was performed using the LM-Seq method, as described previously. Briefly, PolyA+ RNA was fragmented at 85Â°C in SmartScribe first-strand buffer (CloneTech) supplemented with a 3â sequencing adapter containing a random hexamer sequence.  The fragmented RNA were subjected to first strand cDNA synthesis, followed by RNase A/H treatment.  The remaining single-stranded DNA were ligated to a 5â sequencing adapter.  The libraries were then amplified by PCR using Illumina TruSeq-compatible primers and purified using SPRI purification beads.

treatment_protocol: HEK293T cells were cultured in DMEM with 10% FBS and pen/strep. For lentiviral packaging, 3X106 293T cells were seeded in a 6 cm dish one day before transfection. The indicated viral plasmid(s) were co-transfected with lentivirus packaging plasmids pMD2.G and psPAX2 (Addgene ID 12259 and 12260) with 4:2:3 ratio by using Lipofectamine 3000 (Thermo Fisher) according to the manufacturer's protocol. Twelve hours after transfection, media was changed to fresh DMEM with 10% FBS plus Pen/Strep. Seventy-two hours after transfection, virus-containing media was collected, passed through a 45 um filter, and aliquoted into 1.5ml tubes. Viruses were stored in -80Â°C before infection or titration. For virus infection, 2X105 K562 cells were seeded in 24 well plate per well with 500 Âµl complete medium plus 1Âµg/ml polybrene. Virus aliquot(s) were thawed to room temperature and added to the plates. The plate was then centrifuged at 1000xg at 36 Â°C and returned to the incubator. The following day, the media was changed to fresh complete medium with antibiotics to screen for infected cells. Cells were kept at ~30% confluence during antibiotic selection.


title: K562 dCas9-KRAB, Lenti-sgRNA63_bc38

description:
sgrna barcode id: bc38
sgrna id: sgRNA63
sgrna sequence: gtcattgtttaaccctatc
sgrna target: HSBP1 enhancer


title: K562 dCas9-KRAB, Lenti-sgRNA80_bc24

description:
sgrna barcode id: bc24
sgrna id: sgRNA80
sgrna sequence: GAGATTTGCTCCTTTATATG
sgrna target: HBE1 promoter


title: K562 dCas9-KRAB, Lenti-sgRNA59_bc33

description:
sgrna barcode id: bc33
sgrna id: sgRNA59
sgrna sequence: AAGTGAGACCAACTCAGAAA
sgrna target: HSBP1 promoter


title: K562 dCas9-KRAB, Lenti-sgRNA separate infection, beta-globin pilot, batch 4


title: K562 dCas9-KRAB, Lenti-sgRNA57_bc19

description:
sgrna barcode id: bc19
sgrna id: sgRNA57
sgrna sequence: GCTATTGGTCAAGGCAAGGC
sgrna target: HBG1/2 promoter


title: K562 dCas9-KRAB, Lenti-sgRNA46_bc17

description:
sgrna barcode id: bc17
sgrna id: sgRNA46
sgrna sequence: gccctgtaagcatcctgctg
sgrna target: beta globin HS2


title: K562 dCas9-KRAB, Lenti-sgRNA separate infection, beta-globin pilot, batch 1


title: K562 dCas9-KRAB, Lenti-sgRNA56_bc18

description:
sgrna barcode id: bc18
sgrna id: sgRNA56
sgrna sequence: GCTAAACTCCACCCATGGGT
sgrna target: HBG1/2 promoter


title: K562 dCas9-KRAB, Lenti-sgRNA44_bc15

description:
sgrna barcode id: bc15
sgrna id: sgRNA44
sgrna sequence: ggactatgggaggtcactaa
sgrna target: beta globin HS2


title: K562 dCas9-KRAB, not infected

description:
sgrna barcode id: none
sgrna id: none


title: K562 dCas9-KRAB, Lenti-sgRNA82_bc29

description:
sgrna barcode id: bc29
sgrna id: sgRNA82
sgrna sequence: TGTCACTGTCACCACCTTTA
sgrna target: HBE1 promoter


title: K562 + MEF, 11 PCR1 cycles, 300 cells per ul, two-thirds beads for RT

data_processing:
Basecalls performed by Picard ExtractIlluminaBarcodes v1.117.
Drop-Seq data were mapped using Drop-Seq Tools to a combined human and mouse genome. Uniquely mapping reads with mapping quality ≥ 10 were subjected to PCR duplicate removal by examining the unique molecular identifiers (UMI) for each read. Reads were then partitioned to individual cells based on cell barcodes.
Read counts were tabulated with featureCounts v1.5.0.
Genome_build: hg19
Genome_build: mm9
Supplementary_files_format_and_content: read counts for all genes

organism:
Homo sapiens
Mus musculus

source_name: K562 cells, mouse embryonic fibroblasts

extract_protocol: K562 and MEF cells were mixed and single cell RNA sequencing was performed using the Drop-Seq method. Briefly, single cells, polyA-containing barcoded beads (ChemGenes), and droplet generation oil (Bio-Rad) were each flowed into individual input ports on a microfluidic device (NanoShift). Cells in droplets were lysed and hybridized to beads. Beads were isolated and subjected to reverse transcription (Thermo Fisher) and exonuclease I (NEB) treatment, followed by PCR of full length transcripts (Kapa). Final libraries were created by Tn5-mediated tagmentation of cDNA, and amplified by PCR (Kapa) and purified by SPRI beads.

tag: cell type

value: human K562 cells and mouse embryonic fibroblasts


title: K562 dCas9-KRAB, Lenti-sgRNA pooled infection, beta-globin pilot, batch 5


title: K562 + MEF, 13 PCR1 cycles, 300 cells per ul, two-thirds beads for RT


title: K562 + MEF, 11 PCR1 cycles, 100 cells per ul, two-thirds beads for RT


title: K562 + MEF, 11 PCR1 cycles, 300 cells per ul, one-third beads for RT


title: K562 + MEF, 11 PCR1 cycles, 200 cells per ul, two-thirds beads for RT


title: K562 + MEF, 13 PCR1 cycles, 200 cells per ul, one-third beads for RT


title: K562 + MEF, 13 PCR1 cycles, 200 cells per ul, two-thirds beads for RT


title: K562 + MEF, 13 PCR1 cycles, 300 cells per ul, one-third beads for RT


title: K562 + MEF, 11 PCR1 cycles, 200 cells per ul, one-third beads for RT


title: K562 + MEF, 13 PCR1 cycles, 100 cells per ul, two-thirds beads for RT


title: K562 dCas9-KRAB, Lenti-sgRNA pooled infection, beta-globin pilot, batch 2


title: K562 dCas9-KRAB, Lenti-sgRNA60_bc35

description:
sgrna barcode id: bc35
sgrna id: sgRNA60
sgrna sequence: ACGGCGCGCTGCGTGAGGGG
sgrna target: HSBP1 promoter


title: K562 + MEF, 13 PCR1 cycles, 100 cells per ul, one-third beads for RT


title: K562 + MEF, 11 PCR1 cycles, 100 cells per ul, one-third beads for RT


title: Input DNA

city: Pittsburgh

first: Cecilia

middle: W

last: Lo

state: PA

address: 530 45th St., 8120 Rangos Research Center

department: Developmental Biology

institute: University of Pittsburgh

data_processing:
Reads were mapped to the mouse reference genome (GRCm38 from Illumina iGenomes website) using Bowtie1 (Version: 1.1.2) with the commandline options: bowtie -v 2 -t -k 2 -m 1
Peaks were called using MACS2 (Model-based Analysis for ChIP-Seq, version: MACS-2.1.0.20140616) with the command-line options: macs2 callpeak -t sap130File -c ctrlFile -f BOWTIE -g mm -B -q 0.01. (FDR cutoff of 0.01).
Genome_build: mm10
Supplementary_files_format_and_content: Chromosome-wise wig files (tar) for each of Sap130 and Input and a BED file with peaks found by comparing Sap130 to Input.

organism: Mus musculus

source_name: Mouse heart

extract_protocol:
Chromatin immunoprecipitation of Sap130 was performed with rabbit anti-Sap130 antibody (A302-491A: Bethyl laboratories, 2ug) and iDeal ChIP-seq Kit for Transcription Factors (Diagenode) following the manufacturer’s protocol
ChIP-seq libraries were generated using NEBNext Ultra DNA Library Prep Kit for Illumina (NEB) following the manufacturer’s protocol.

tag: Stage

value: Heart

tag: chip antibody


title: Sap130_ChIPSeq

value: Sap130 (A302-491A:Bethyl laboratories)


title: unstimulated_control_1

city: Philadelphia

first: Kristen

last: Lynch

state: Pennsylvania

address: 906 Stellar Chance Labs 422 Curie Blvd

department: Biochemistry and Molecular Biophysics

institute: University of Pennsylvania

description:
processed data file:
JSL1unstim_Control_v_shCELF2.deltapsi.txt

data_processing:
RNA-Seq reads mapped to the reference human genome (hg19) using STAR (version 2.5.1b_modified) with the option --alignSJoverhangMin 8
Aligned reads were analyzed with MAJIQ (version 0.9.2a; http://majiq.biociphers.org/) for quantification of splicing changes between control and knockdown samples
Genome_build: hg19
Supplementary_files_format_and_content: tab-seperated text files containing information relating to splicing quantifications for all events (Local Splicing Variations or LSVs) detected when comparing control and knockdown experiments

molecule: polyA RNA

growth_protocol: JSL1 cells were cultured in RPMI supplemented with 5% heat-inactivated fetal bovine serum (FBS) at 37°C in 5% CO2.

extract_protocol:
Total RNA extracted with TRIzol using manufacturer's instructions
RNA QC and TruSeq stranded library construction were carried out by  the Genomics Division of the Iowa Institute of Human Genetics which is supported, in part, by the University of Iowa Carver College of Medicine.

value: Jurkat-derived monoclonal (JSL1)

value: T lymphocyte


title: stimulated_shCELF2_2

description:
processed data file:
JSL1stim_Control_v_shCELF2.deltapsi.txt

treatment_protocol: For stimulation growth medium was supplemented with the phorbol ester PMA (Sigma- Aldrich) for 48 hours (at a concentration of 20 ng/mL). Depletion of CELF2 was achieved via stable lentiviral integration of a doxycycline-inducible shRNAs against CELF2.

tag: genotype/variation

value: Depletion of CELF2

tag: stimulated with

value: 20 ng/mL phorbol ester PMA for 48 h


title: stimulated_control_2

treatment_protocol: For stimulation growth medium was supplemented with the phorbol ester PMA (Sigma- Aldrich) for 48 hours (at a concentration of 20 ng/mL)


title: WT_3AT, replicate 2

city: Cork

first: Audrey

middle: M

last: Michel

state: Cork

address: Western Gateway, Western Road

department: School of Biochemistry and Cell Biology

country: Ireland

institute: University College Cork

description:
processed data file:
NCU04050T1_RB15.xlsx, NCU04050T1_RB17_3AT.xlsx

data_processing:
Raw Ribo-seq reads were trimmed to remove the CTGTAGGCACCATCAAT adapter sequence with cutadapt-1.2.1 (options -n 1 -M 28)
Trimmed reads of length 28-31 were mapped to Neurospora transcripts with Bowtie version 0.12.9 (options -n 0 -l 25 -a –norc)
Counts of reads at each framing position were generated with Python scripts.
Genome_build: Neurospora crassa genome assembly 10, Gene annotation 10.6
Supplementary_files_format_and_content: The NCU* files contain the ribosome footprint alignment counts and the reading frame position that the count maps to. The extra data in the unlabeled columns corresponds to the sum of counts for certain  coordinates in the mRNA.

organism: Neurospora crassa

growth_protocol: N. crassa cultures were grown for 24 hr in the dark and, following the breakage procedure used for the preparation of N. crassa cell-free translation extracts described in Wu et al., (2012) J Mol Biol. but using the buffers described in Ingolia et al (2012), Nature Protocols.

extract_protocol: Ribosome-protected mRNA fragments were prepared for sequencing essentially as described in Ingolia et al (2012),Nature Protocols, except that 50 A260 units of lysate was used, nucleic acid pellets recovered from each step were washed with 80% ethanol, and the rRNA depletion step was omitted.

treatment_protocol: N. crassa wild type cells and N. crassa cells grown in the presence of 3-Amino-1,2,4-triazole (3AT)

value: wild type

tag: treated with

value: 3-Amino-1,2,4-triazole (3AT)

value: mycelium

tag: rna type

value: Ribosome protected fragment


title: Second wild type, replicate 2

description:
processed data file:
NCU04050T1_RB14.xlsx, NCU04050T1_RB16_wt.xlsx

source_name: Second wild type_mycelium


title: Wild type, replicate 1

description:
processed data file:
NCU00366-1.csv, NCU04050_counts.csv, NCU07732-1.csv

source_name: Wild type_mycelium


title: stimulated_shCELF2_1


title: Human hepatic macrophages rep.1

city: New York

first: Panagiotis

last: Douvaras

state: New York

address: 619 West 54th Street

institute: The New York Stem Cell Foundation

data_processing:
Single-ended RNA-seq data was generated with the Illumina HiSeq 2500 platform following the Illumina protocol. The raw sequencing reads were aligned to human hg19 genome using star aligner (version 2.5.0b).
Following read alignment, featureCounts (v1.5.0-p1) was used to quantify the gene expression at the gene level based on Ensembl gene model GRCh37.70.
Genes with at least 1 count per million (CPM) in at least one sample were considered expressed and hence retained for further analysis, otherwise removed.
The gene level read counts data was normalized using trimmed mean of M-values normalization (TMM) method to adjust for sequencing library size difference. Hierarchical cluster analysis was performed using R programming language.
Genome_build: hg19
Supplementary_files_format_and_content: expression.log2.CPM.txt.gz

source_name: Human hepatic macrophages

growth_protocol: Primary hepatic macrophages were cultured in Macrophage Medium (ScienCell)

extract_protocol:
RNA extraction was performed using the RNeasy Plus Mini Kit (Qiagen) with QIAshredder (Qiagen). Cells were enzymatically detached after treatment with Accutase for 5 min and using a cell lifter. After centrifuging, cells were washed with PBS and resuspended in lysis buffer. Samples were then stored at -80oC until processed further according to manufacturer’s instructions. RNA was eluted in 30μl RNase free ddH2O.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Fetal liver

value: Hepatic macrophage


title: Second wild type, replicate 1


title: unstimulated_shCELF2_1

treatment_protocol: Depletion of CELF2 was achieved via stable lentiviral integration of a doxycycline-inducible shRNAs against CELF2.


title: WT_3AT, replicate 1


title: iPSC3-derived microglia rep.2

source_name: iPSC3-derived microglia

growth_protocol: 4 days mTeSR Custom medium with 80ng/ml BMP4. 2 days in STEM-Pro34 with 2mM GutaMAX-I, 25ng/ml bFGF, 100ng/ml SCF and 80ng/ml VEGF. 8 days in StemPro-34 containing 50ng/ml SCF, 50ng/ml IL-3, 5ng/ml TPO, 50ng/ml M-CSF and 50ng/ml Flt3 ligand. 10-20 days in StemPro-34 containing 50ng/ml M-CSF, 50ng/ml Flt3 ligand and 25ng/ml GM-CSF until CD14+ and/or CX3CR1+ progenitors were isolated. Finally cells were cultured in RPMI-1640 supplemented with 2mM GlutaMAX-I, 10ng/ml GM-CSF and 100ng/ml IL-34 for 2 weeks.

value: iPSC-derived microglia


title: stimulated_control_1


title: unstimulated_shCELF2_2


title: unstimulated_control_2


title: iPSC4-derived microglia rep.1

source_name: iPSC4-derived microglia


title: iPSC2-derived microglia rep.2

source_name: iPSC2-derived microglia


title: iPSC1-derived microglia rep.1

source_name: iPSC1-derived microglia


title: iPSC1-derived microglia rep.2


title: iPSC2-derived microglia rep.1


title: Human primary microglia Serum Free rep.2

source_name: Human primary microglia Serum Free

growth_protocol: Primary microglia were cultured in serum-free medium consiting of RPMI-1640 supplemented with 2mM GlutaMAX-I, 10ng/ml GM-CSF and 100ng/ml IL-34

value: Fetal brain

value: Primary microglia


title: Human primary microglia Serum Free rep.1


title: Human hepatic macrophages rep.2


title: iPSC7-derived microglia rep.1

source_name: iPSC7-derived microglia


title: iPSC5-derived microglia rep.2

source_name: iPSC5-derived microglia


title: Wild type, replicate 2


title: Human primary microglia rep.1

source_name: Human primary microglia

growth_protocol: Primary microglia were cultured in Microglial Medium (ScienCell)


title: Human primary microglia rep.2


title: iPSC6-derived microglia rep.1

source_name: iPSC6-derived microglia


title: Macrophages polarized with IL-4 and IL-13 rep.2

growth_protocol: CD14+ cells isolated from peripheral blood were cultured for 5 days in ultra-low attachment in RPMI-1640 with 2mM GlutaMAX-I, 10% heat-inactivated human serum and 20ng/ml M-CSF.

value: Peripheral blood

value: Circulating macrophage

tag: treatment

value: Extra 2 days in  IL-4 and IL-13


title: iPSC3-derived microglia rep.1


title: Non-polarized macrophages rep.1

source_name: Non-polarized macrophages

growth_protocol: CD14+ cells isolated from peripheral blood were cultured for 7 days in ultra-low attachment in RPMI-1640 with 2mM GlutaMAX-I, 10% heat-inactivated human serum and 20ng/ml M-CSF.


title: Macrophages polarized with IFN-γ and LPS rep.1

value: Extra 2 days in IFN-γ and LPS


title: Non-polarized macrophages rep.2


title: Macrophages polarized with IFN-γ and LPS rep.2


title: Macrophages polarized with IL-10 rep.2

source_name: Macrophages polarized with IL-10

value: Extra 2 days in IL-10


title: 4KLF1_CAGATC_L002_K1ER

city: Sydney

first: Jon

last: Burdach

state: NSW

address: UNSW

department: BABS

country: Australia

institute: University of New South Wales

data_processing:
Quality control was performed using FastQC v0.10.1
Reads were quality filtered, trimmed and adapter sequences were removed using Trimmomatic v0.3.214
Reads were aligned to the hg19 or mm9 genomes using Bowtie v2.2.115 set to --very-sensitive
Resulting alignments were sorted, merged and indexed using Samtools v0.1.1816
Pseudoreplicates were created using homer-idr v0.118 for individual and combined IP samples. Peaks were  then  called  using  Homer  v4.7.219 using  the  permissive  settings  (-P  .1  -LP.1  -poisson  .1)  on individual  replicates,  combined  replicates,  individual  pseudoreplicates  and  combined pseudoreplicates against the combined input control. Peaks lists were then supplied to homer-idr to determine the IDR statistic for each peak generating a final peak list satisfying the thresholds set by homer-idr
Genome_build: mm9, hg19
Supplementary_files_format_and_content: HOMER IDR output peak files

source_name: K1ER cells

growth_protocol: K1ER cells were cultured in high-glucose DMEM supplemented with 10% FCS  and 1% penicillin/streptomycin. HuDEP cells were cultured in cultured in DMEM supplemented with 7.5% fetal bovine serum.

extract_protocol:
ChIP experiments were performed as previously described (Schmidt D, Wilson MD, Spyrou C, Brown GD, Hadfield J, Odom DT. ChIP-seq: using highthroughput  sequencing to discover protein-DNA interactions. Methods. Jul 2009;48(3):240-248). Approximately 5 x 107 cells were used for each IP. ChIP-Seq experiments were conducted on two replicates of K1ER cells induced with 200 nM Tamoxifen for 2 hrs, and two replicates of HUDEP-2 cells. The antibodies  used  were  α-KLF1  (PIEPA5-18031,  Thermo  Scientific),  anti-goat  IgG  (SCZSC-2028,  Santa Cruz) as a negative control.
Library  preparation  was  performed  using  the  TruSeq  DNA  Sample  Preparation  Kit  (FC-121-2001, Illumina) according to the manufacturer’s instructions with minor modifications. Adapter sequences were diluted 1/40 before use and following adapter ligation, the library size extracted from the gel was 100-280 bp (excluding adapters) in line with the size of sonicated fragments. Libraries (2 inputs and 2 IP samples) were multiplexed into 2 lanes such that there were 2 samples per lane. Samples were  sequenced  using  50  bp  single  read  chemistry  on  the  HiSeq  2500  (Illumina).

value: Immortalised Fetal Liver Cell Line

value: K1ER cells


title: 4KLF1_CAGATC_L001_K1ER


title: Macrophages polarized with IL-10 rep.1


title: Macrophages polarized with IL-4 and IL-13 rep.1


title: 3KLF1_CGATGT_L002_K1ER


title: 3KLF1_CGATGT_L001_K1ER


title: 4Input_CCGTCC_L001_K1ER


title: HuDEP-6-IP_S4_L004

source_name: HuDEP cells

value: Immortalized Human Erythroid Progenitor Cell Line

value: HuDEP cells


title: HuDEP-6-IP_S4_L001


title: HuDEP-6-IN_S3_L004


title: 4Input_CCGTCC_L002_K1ER


title: 3Input_TGACCA_L001_K1ER


title: 3Input_TGACCA_L002_K1ER


title: 2KLF1_CTTGTA_L002_K1ER


title: HuDEP-6-IN_S3_L002


title: HuDEP-6-IN_S3_L003


title: HuDEP-6-IN_S3_L001


title: HuDEP-6-IP_S4_L003


title: 2KLF1_CTTGTA_L001_K1ER


title: HuDEP-5-IP_S2_L004


title: HuDEP-5-IP_S2_L003


title: 2Input_GTGAAA_L001_K1ER


title: HuDEP-5-IP_S2_L002


title: 1KLF1_ACAGTG_L002_K1ER


title: HuDEP-5-IP_S2_L001


title: HuDEP-6-IP_S4_L002


title: HuDEP-5-IN_S1_L003


title: 1Input_GCCAAT_L001_K1ER


title: HuDEP-5-IN_S1_L002


title: 1KLF1_ACAGTG_L001_K1ER


title: HuDEP-5-IN_S1_L001


title: HuDEP-5-IN_S1_L004


title: MDA-IBC3

city: Houston

first: Edward

middle: S.

last: Chen

address: 1 Baylor Plz

department: Molecular and Human Genetics

institute: Baylor College of Medicine

description:
LZ32423
LZ32423_NoIndex_L005
Human/Mouse
Patient-derived breast cancer xenograft (PDX).
Processed data file: xeno.exp.txt

data_processing:
Xenome was used to qualify gene grouping by species.
STAR, with a hg19 reference, was used for alignment of human sequences.
R's Rsubread (default settings) package was used to estimate gene counts.
R's edgeR:::rpkm was then used to quantify gene expression.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: xeno.exp.txt: Tab-delimited text file includes RPKM values.

source_name: Human breast cancer xenograft

extract_protocol:
Total RNA was extracted from PDX samples and 10ng was used to generate and amplify whole transcriptome cDNA (NuGen Ovation v2, NuGen Technologies).
Illumina TruSeq DNA-Seq library was quantified with the Kapa qPCR Library Quantitation Kit (Kapa).

treatment_protocol: PDX tumour fragments were transplanted into the cleared fat pad of 3- to 4-week-old SCID/Beige mice treated either with vehicle, IPI926 (40mg/kg, oral gavage) or GANT61 (50mg/kg, subcutaneous injection) once a day for two weeks.

value: breast cancer xenograft


title: MC1

description:
LZ39532
LZ39532_NoIndex_L007
Human/Mouse
Patient-derived breast cancer xenograft (PDX).
Processed data file: xeno.exp.txt


title: shKdm5b_mES

city: Detroit

first: Benjamin

middle: L

last: Kidder

state: MI

address: 4100 John R St

department: Oncology

institute: Wayne State University

description:
mES_shKdm5b
Poly-A RNA

data_processing:
Basecalls performed using GAPipeline or CASAVA.
Sequence reads were obtained and mapped to the mouse (mm9) genome with Bowtie2.
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: BedGraph files.

source_name: R1 ES cells, shKdm5b

growth_protocol: ES cells were cultured on irradiated MEFs in DMEM, 15% FBS media containing LIF (ESGRO) at 37oC with 5% CO2. For RNA-Seq experiments, ES cells were cultured on gelatin-coated dishes in ES cell media containing 1.5 µM CHIR9901 (GSK3 inhibitor) for several passages to remove feeder cells. ES cells were passed by washing with PBS, and dissociating with trypsin.

extract_protocol:
RNA was harvested using RNeasy and miRNeasy Qiagen kits.
Double-stranded cDNA was sonicated and end-repaired using the End-It DNA End-Repair kit (Epicentre), followed by addition of a single A nucleotide, and ligation of PE adapters (Illumina) or custom indexed adapters. PCR was performed using Phusion High Fidelity PCR master mix.

value: embryonic stem cell line

tag: shRNA


title: 8563

description:
LZ37250
LZML_37250_NoIndex
Human/Mouse
Patient-derived breast cancer xenograft (PDX).
Processed data file: xeno.exp.txt


title: 6257

description:
LZ37388
LZML_37388_NoIndex
Human/Mouse
Patient-derived breast cancer xenograft (PDX).
Processed data file: xeno.exp.txt


title: 5156

description:
LZ32179
LZ32179_NoIndex_L008
Human/Mouse
Patient-derived breast cancer xenograft (PDX).
Processed data file: xeno.exp.txt


title: 5998

description:
LZ32181
LZ32181_NoIndex_L002
Human/Mouse
Patient-derived breast cancer xenograft (PDX).
Processed data file: xeno.exp.txt


title: 9161

description:
LZ37143
LZML_37143_NoIndex
Human/Mouse
Patient-derived breast cancer xenograft (PDX).
Processed data file: xeno.exp.txt


title: shLuc_ctrl_mES

description:
mES_shLuc_ctrl
Poly-A RNA

source_name: R1 ES cells, shLuc

value: shLuc


title: shKdm5b_Input_mESC, rep1

description: Direct sequencing following sonication of x-linked chromatin.

data_processing:
Basecalls performed using GAPipeline or CASAVA.
Sequence reads were obtained and mapped to the mouse (mm9) genome with Bowtie2.
The RBPM measure (reads per base per million reads) was used to generate graph files.
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: BedGraph files.

source_name: R1 ES cells, shKdm5b, input

growth_protocol: shLuc and shKdm5b ES cells were cultured on irradiated MEFs in DMEM, 15% FBS media containing LIF (ESGRO) at 37oC with 5% CO2. For ChIP experiments, ES cells were cultured on gelatin-coated dishes in ES cell media containing 1.5 µM CHIR9901 (GSK3 inhibitor) for several passages to remove feeder cells. ES cells were passed by washing with PBS, and dissociating with trypsin.

extract_protocol:
ES cells were crosslinked with formaldehyde and subsequently sonicated. Sonicated cell extracts were used for ChIP assays.
ChIP-enriched DNA was end-repaired using the End-It DNA End-Repair kit (Epicentre), followed by addition of a single A nucleotide, and ligation of PE adapters (Illumina) or custom indexed adapters. PCR was performed using Phusion High Fidelity PCR master mix.


title: 5471

description:
LZ32180
LZ32180_NoIndex_L001
Human/Mouse
Patient-derived breast cancer xenograft (PDX).
Processed data file: xeno.exp.txt


title: shLuc_Input_mESC, rep1

source_name: R1 ES cells, shLuc, input


title: 2Input_GTGAAA_L002_K1ER


title: 5097

description:
LZ32178
LZ32178_NoIndex_L007
Human/Mouse
Patient-derived breast cancer xenograft (PDX).
Processed data file: xeno.exp.txt


title: shKdm5b_RNAPII-Ser2P_mESC

description: Chromatin IP against RNAPII-Ser2P.

source_name: R1 ES cells, shKdm5b, RNAPII-Ser2P ChIP

value: Anti-RNAPII-Ser2P antibody (Abcam; ab5095)


title: 4888

description:
LZ32422
LZ32422_NoIndex_L006
Human/Mouse
Patient-derived breast cancer xenograft (PDX).
Processed data file: xeno.exp.txt


title: 4913

description:
LZ32468
LZ32468_NoIndex_L008
Human/Mouse
Patient-derived breast cancer xenograft (PDX).
Processed data file: xeno.exp.txt


title: 1Input_GCCAAT_L002_K1ER


title: shLuc_RNAPII-Ser2P_mESC

description: Chromatin IP against RNAPII-Ser2P.

source_name: R1 ES cells, shLuc, RNAPII-Ser2P ChIP


title: shKdm5b_Input_mESC, rep2


title: 4272

description:
LZ32420
LZ32420_NoIndex_L005
Human/Mouse
Patient-derived breast cancer xenograft (PDX).
Processed data file: xeno.exp.txt


title: shLuc_Input_mESC, rep2


title: shKdm5b_RNAPII-Ser5P_mESC

description: Chromatin IP against RNAPII-Ser5P.

source_name: R1 ES cells, shKdm5b, RNAPII-Ser5P ChIP

value: Anti-RNAPII-Ser5P antibody (Abcam; ab5131)


title: 4664

description:
LZ32084
LZ32084_NoIndex_L008
Human/Mouse
Patient-derived breast cancer xenograft (PDX).
Processed data file: xeno.exp.txt


title: 4195

description:
LZ32177
LZ32177_NoIndex_L006
Human/Mouse
Patient-derived breast cancer xenograft (PDX).
Processed data file: xeno.exp.txt


title: 4189

description:
LZ32094
LZ32094_NoIndex_L002
Human/Mouse
Patient-derived breast cancer xenograft (PDX).
Processed data file: xeno.exp.txt


title: 4175

description:
LZ32176
LZ32176_NoIndex_L005
Human/Mouse
Patient-derived breast cancer xenograft (PDX).
Processed data file: xeno.exp.txt


title: shKdm5b_RNAPII_mESC

description: Chromatin IP against RNAPII.

source_name: R1 ES cells, shKdm5b, RNAPII ChIP

value: Anti-RNAPII antibody (Abcam; ab817)


title: shLuc_RNAPII_mESC

description: Chromatin IP against RNAPII.

source_name: R1 ES cells, shLuc, RNAPII ChIP


title: PARE_Diana 12hpi with Bremia

city: St. Louis

first: Blake

middle: C.

last: Meyers

state: MO

address: 975 N Warson Road

institute: Donald Danforth Plant Science Center

description: Text containing distinct PARE RNAs with their raw abundance after removing the adapter sequences

data_processing:
Small RNA-seq: the adapter sequences were trimmed from raw sequence reads, and then the small RNA sequences were trimmed to the lengths between 15 and 34 nucleotides. Small RNA reads were mapped to the lettuce genome (Lettuce Genome Database).
PARE-seq: the adapter sequences were trimmed from raw sequence reads, and then the PARE sequences were trimmed to the lengths between 18 and 21 nucleotides. PARE reads were mapped to the lettuce genome (Lettuce Genome Database).
Genome_build: Lettuce Genome Database

organism: Lactuca sativa

source_name: leaf tissue

extract_protocol: Small RNA libraries were constructed from total RNA isolated from leaf tissues of Lactuca sativa using Plant RNA Reagent (Invitrogen, Life Technologies, USA). The sRNA library preparation protocol is based on Illumina’s sRNA Sequencing Sample Preparation Guide (Illumina, San Diego, CA). The libraries were sequenced on an Illumina HiSeq at the Delaware Biotechnology Institute (Newark, DE). Degradome libraries (PARE) constructed from total RNA isolated from the same tissues using Plant RNA Reagent (Invitrogen, Life Technologies, USA). The libraries were constructed as previously described (Zhai et al. 2014 PMID: 23810899). The libraries were sequenced on an Illumina HiSeq at the Delaware Biotechnology Institute (Newark, DE)."

tag: population

value: Diana

tag: innoculation

value: 12hpi with Bremia


title: 4013

description:
LZ32081
LZ32081_NoIndex_L007
Human/Mouse
Patient-derived breast cancer xenograft (PDX).
Processed data file: xeno.exp.txt


title: PARE_Diana 12dpi mock

value: 12dpi mock


title: 3963

description:
LZ32078
LZ32078_NoIndex_L006
Human/Mouse
Patient-derived breast cancer xenograft (PDX).
Processed data file: xeno.exp.txt


title: PARE_Cobham Green 5dpi mock

value: Cobham Green

value: 5dpi mock


title: 7441

description:
LZ39533
LZ39533_NoIndex_L008
Human/Mouse
Patient-derived breast cancer xenograft (PDX).
Processed data file: xeno.exp.txt


title: 3936

description:
LZ32073
LZ32073_NoIndex_L004
Human/Mouse
Patient-derived breast cancer xenograft (PDX).
Processed data file: xeno.exp.txt


title: PARE_Cobham Green 12hpi mock

value: 12hpi mock


title: 3904

description:
LZ32076
LZ32076_NoIndex_L005
Human/Mouse
Patient-derived breast cancer xenograft (PDX).
Processed data file: xeno.exp.txt


title: HLHS_635AP-121-1-RV

description:
HLHS_121-1-RV
Processed data file: counts.txt
Processed data file: deResults.xlsx

data_processing:
Reads were aligned using TopHat2 (v2.0.9) with the following options: --segment-length 25 --segment-mismatches 2 --no-novel-juncs --min-achor=8 --splice-mismatches 0 --max-intron-length 500000 --microexon-search --no-mixed --no-coverage-search and values for the inner mate distance estimated using RSeQC (v2.3.6).
PCR duplicates were removed using the MarkDuplicates utility from the Picard suite of tools (v1.96).
Gene-level counts were calculated by HTSeq-count (v0.5.4p5) using "union" mode and Ensembl GTF file as retrieved from iGenomes (ftp://igenome:G3nom3s4u@ussd-ftp.illumina.com/README.txt; Ensembl release 66) for mm9.
Differential expression analyses were performed using the R package edgeR (v3.4.2). Genes with low expression (counts-per-million < 1 in all samples) were discarded. Dispersion parameters were estimated accounting for side (LV and RV), stage (E13.5, E14.5, and E17.5), disease (HLHS and control), and their pairwise interactions. For each gene, the maximum of common, trended and tag-wise dispersion estimate was used for subsequent analyses. Linear contrasts were used to compare HLHS to control in LV and RV, respectively, using likelihood ratio tests. Genes with an FDR <=0.05 and a fold-change >= 1.5 were considered significantly differentially expressed.
Genome_build: MGSCv37 (mm9)
Supplementary_files_format_and_content: counts.txt: Tab-delimited text file with raw gene-level counts for all samples.
Supplementary_files_format_and_content: deResults.xlsx: Excel spreadsheets for results of the differential expression analyses in LV (HLHS vs. Control) and RV (HLHS vs. Control), respectively. These additionally include the counts-per-million (cpm) values (log2 with pseudocount 1) for all analyzed genes.

source_name: right ventricle, HLHS, E14.5

extract_protocol:
Total RNA was isolated from mouse embryonic hearts using the miRNeasy micro Kit (QIAGEN) with on-column DNase I digestion method (QIAGEN).
Libraries were constructed using TruSeq RNA Sample Preparation Lit v2 (Illumina).

tag: strain/background

tag: phenotype

value: hypoplastic left heart syndrome (HLHS)

value: heart ventricle

tag: side

value: right


title: HLHS_635-333-1-LV

description:
HLHS_333-1-LV
Processed data file: counts.txt
Processed data file: deResults.xlsx

source_name: left ventricle, HLHS, E17.5

tag: developmental stage

value: left


title: PARE_Cobham Green 5dpi with Bremia

value: 5dpi with Bremia


title: HLHS_635AP-121-1-LV

description:
HLHS_121-1-LV
Processed data file: counts.txt
Processed data file: deResults.xlsx

source_name: left ventricle, HLHS, E14.5

tag: tissue


title: HLHS_635-333-1-RV

description:
HLHS_333-1-RV
Processed data file: counts.txt
Processed data file: deResults.xlsx

source_name: right ventricle, HLHS, E17.5


title: 3887

description:
LZ32072
LZ32072_NoIndex_L003
Human/Mouse
Patient-derived breast cancer xenograft (PDX).
Processed data file: xeno.exp.txt

value: breast cancer xenograft


title: HLHS_635-260-1-RV

description:
HLHS_260-1-RV
Processed data file: counts.txt
Processed data file: deResults.xlsx

source_name: right ventricle, HLHS, E13.5


title: PARE_Cobham Green 12hpi with Bremia


title: shLuc_RNAPII-Ser5P_mESC

description: Chromatin IP against RNAPII-Ser5P.

source_name: R1 ES cells, shLuc, RNAPII-Ser5P ChIP

tag: cell line

value: embryonic stem cell line


title: 3613

description:
LZ32182
LZ32182_NoIndex_L003
Human/Mouse
Patient-derived breast cancer xenograft (PDX).
Processed data file: xeno.exp.txt

source_name: Human breast cancer xenograft


title: HLHS_635-260-1-LV

description:
HLHS_260-1-LV
Processed data file: counts.txt
Processed data file: deResults.xlsx

source_name: left ventricle, HLHS, E13.5


title: CTRL_635-333-3-RV

description:
CTRL_333-3-RV
Processed data file: counts.txt
Processed data file: deResults.xlsx

source_name: right ventricle, control, E17.5

value: control


title: 3807

description:
LZ32467
LZ32467_NoIndex_L007
Human/Mouse
Patient-derived breast cancer xenograft (PDX).
Processed data file: xeno.exp.txt


title: PARE_Salinas 12hpi mock

value: Salinas


title: PARE_Salinas 5dpi mock


title: 3611

description:
LZ32070
LZ32070_NoIndex_L002
Human/Mouse
Patient-derived breast cancer xenograft (PDX).
Processed data file: xeno.exp.txt


title: 3561

description:
LZ32093
LZ32093_NoIndex_L001
Human/Mouse
Patient-derived breast cancer xenograft (PDX).
Processed data file: xeno.exp.txt


title: PARE_Salinas 12hpi with Bremia

description: Text containing distinct PARE RNAs with their raw abundance after removing the adapter sequences


title: 3469

description:
LZ37139
LZML_37139_NoIndex
Human/Mouse
Patient-derived breast cancer xenograft (PDX).
Processed data file: xeno.exp.txt


title: CTRL_635-333-3-LV

description:
CTRL_333-3-LV
Processed data file: counts.txt
Processed data file: deResults.xlsx

source_name: left ventricle, control, E17.5


title: CTRL_635-333-2-LV

description:
CTRL_333-2-LV
Processed data file: counts.txt
Processed data file: deResults.xlsx


title: CTRL_635-333-2-RV

description:
CTRL_333-2-RV
Processed data file: counts.txt
Processed data file: deResults.xlsx


title: sRNA_Diana 12dpi mock

description: Text containing distinct small RNAs with their raw abundance after removing the adapter sequences


title: 3277

description:
LZ37140
LZML_37140_NoIndex
Human/Mouse
Patient-derived breast cancer xenograft (PDX).
Processed data file: xeno.exp.txt


title: CTRL_635AP-121-3-RV

description:
CTRL_121-3-RV
Processed data file: counts.txt
Processed data file: deResults.xlsx

source_name: right ventricle, control, E14.5


title: 3204

description:
LZ32419
LZ32419_NoIndex_L004
Human/Mouse
Patient-derived breast cancer xenograft (PDX).
Processed data file: xeno.exp.txt


title: sRNA_Diana 12hpi with Bremia


title: sRNA_Cobham Green 5dpi mock


title: CTRL_635AP-121-2-RV

description:
CTRL_121-2-RV
Processed data file: counts.txt
Processed data file: deResults.xlsx


title: 3107

description:
LZ32175
LZ32175_NoIndex_L004
Human/Mouse
Patient-derived breast cancer xenograft (PDX).
Processed data file: xeno.exp.txt


title: 3143

description:
LZ32067
LZ32067_NoIndex_L001
Human/Mouse
Patient-derived breast cancer xenograft (PDX).
Processed data file: xeno.exp.txt


title: sRNA_Cobham Green 12hpi mock


title: CTRL_635AP-121-2-LV

description:
CTRL_121-2-LV
Processed data file: counts.txt
Processed data file: deResults.xlsx

source_name: left ventricle, control, E14.5


title: sRNA_Cobham Green 5dpi with Bremia


title: 2665

description:
LZ32174
LZ32174_NoIndex_L003
Human/Mouse
Patient-derived breast cancer xenograft (PDX).
Processed data file: xeno.exp.txt


title: CTRL_635AP-121-3-LV

description:
CTRL_121-3-LV
Processed data file: counts.txt
Processed data file: deResults.xlsx


title: sRNA_Cobham Green 12hpi with Bremia


title: 2147

description:
LZ32290
LZ32290_NoIndex_L001
Human/Mouse
Patient-derived breast cancer xenograft (PDX).
Processed data file: xeno.exp.txt


title: CTRL_635-260-2-RV

description:
CTRL_260-2-RV
Processed data file: counts.txt
Processed data file: deResults.xlsx

source_name: right ventricle, control, E13.5


title: PARE_Salinas 5dpi with Bremia

description: Text containing distinct PARE RNAs with their raw abundance after removing the adapter sequences


title: 0049

description:
LZ37138
LZML_37138_NoIndex
Human/Mouse
Patient-derived breast cancer xenograft (PDX).
Processed data file: xeno.exp.txt


title: 0047

description:
LZ37312
LZML_37312_NoIndex
Human/Mouse
Patient-derived breast cancer xenograft (PDX).
Processed data file: xeno.exp.txt


title: CTRL_635-260-2-LV

description:
CTRL_260-2-LV
Processed data file: counts.txt
Processed data file: deResults.xlsx

source_name: left ventricle, control, E13.5


title: sRNA_Salinas 12hpi mock


title: sRNA_Salinas 5dpi with Bremia


title: sRNA_Salinas 5dpi mock


title: 0002

description:
LZ37246
LZML_37246_NoIndex
Human/Mouse
Patient-derived breast cancer xenograft (PDX).
Processed data file: xeno.exp.txt


title: spinal_KI_ZT20

status: Public on Apr 12 2017

city: ShangHai

first: Haifang

last: Wang

address: NO 320, Yueyang Road

department: functional genomics group

country: China

institute: PICB

data_processing:
The FASTQ files containing raw sequence reads were aligned to rat genome (rn5) by Tophat program (default parameters). Then bed tools program (v2.16.2) was applied to calculate the number of reads mapped on each transcript based on the gene annotations from UCSC genome browser (www.genome.ucsc.edu). The reads numbers were normalized to Reads Per Kilobases per Million reads (RPKM). The genes with summed RPKM<2 over all samples in each tissue were removed. Paired t-test was applied first to identify the differential expressed genes between WT and FUS knock in rat in each tissue. The differentially expressed genes were defined as paired t-test p-value<0.05 and |log2-transformed fold change|>0.2. Then the circadian peak and trough of each transcript were calculated by fitting them to cosine functions with 24 hours’ period and shifting phases as described previously.
Genome_build: rn5
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

organism: Rattus norvegicus

growth_protocol: The rat were housed under a 12-h light/12-h dark regimen with food and water available ad libitum for one week before being switched to complete darkness. The rat were switched to complete darkness two days before execution. ZT0 is defined as the time when the lights are turned on. All animal works were performed in accordance with the regulations by the Animal Care and Use Committee of the Institute of Neuroscience, Shanghai Institutes for Biological Sciences.

extract_protocol:
Tissues were quickly dissected and snap-frozen in liquid nitrogen and stored at −80 °C. Total RNA was extracted from each sample using Trizol.
The RNA samples were converted into Illumina sequencing libraries by using Illumina TruSeq RNA Sample Prep Kit v2 as per manufacturer’s protocol.

treatment_protocol: The detailed procedures to establish the FUS R521C knock-in rats and the characterization of the animals were described elsewhere (manuscript in preparation, T.Z. et al). Briefly, we designed and validated a guide RNA(GTGAGCACAGACAGGATCGC ) to target the rat Fus gene for the point mutation (CGC to TGC) at the residue FUS 513, which is a conserved residue corresponding to the human 521 residue. The repair oligo DNA containing homologous sequences approximately 50 bps to the 5’ and 3’ arm of the mutation site. Guide RNA, cas9 mRNA and oligo DNA were co-injected into pronuclear-stage embryos of SD rats, and transferred to surrogates. Those offspring with successful knock-in point mutations were detected by PCR and sequencing using the skin tissue. The germ-line transmission of R521C was achieved by natural mating and confirmed. After obtaining the F1 offspring, the R521C mutant rat was named Fusem1Ionsz, with Rat Genome Database ID 10047084. The details of this rat model can be found in the following website http://rgd.mcw.edu/rgdweb/report/gene/main.html?id=10047084 .

tag: strain background

value: Sprague Dawley

tag: age

value: 3.3 month old

value: R521C knock-in

value: Spinal cord

tag: time point


title: spinal_KI_ZT16

tag: genotype/variation


title: spinal_WT_ZT8

value: wild type


title: spinal_KI_ZT12


title: spinal_WT_ZT20


title: spinal_KI_ZT8


title: spinal_WT_ZT12


title: spinal_WT_ZT16


title: spinal_KI_ZT4


title: liver_WT_ZT8

value: Liver


title: liver_WT_ZT20


title: spinal_KI_ZT0


title: liver_WT_ZT12


title: liver_WT_ZT16


title: liver_WT_ZT4


title: liver_KI_ZT8


title: liver_KI_ZT4


title: liver_KI_ZT0


title: cortex_WT_ZT20

value: Cortex


title: liver_KI_ZT20


title: cortex_WT_ZT12


title: liver_KI_ZT12


title: cortex_WT_ZT0


title: cortex_WT_ZT4


title: cortex_WT_ZT16


title: sRNA_Salinas 12hpi with Bremia

description: Text containing distinct small RNAs with their raw abundance after removing the adapter sequences

value: 12hpi with Bremia


title: spinal_WT_ZT0


title: liver_WT_ZT0


title: liver_KI_ZT16


title: Control ChIP [SL34968]

city: Baltimore

first: Anand

last: Venkataraman

state: MD

address: 733 N Broadway, MRB 322

department: Neuroscience

institute: Johns Hopkins University

description: Control ChIP-seq used for ZNF639(SL39345),ZNF639(SL39347)

data_processing:
CHIP-seq reads were aligned to hg19-female using Bowtie2 with default parameters
Peaks were called using MACS2 with default parameters
Genome_build: hg19-female
Supplementary_files_format_and_content: bed (narrowPeak) files were generated using macs2

extract_protocol:
Exponentially growing cells from ENCODE Tier 1 and Tier 2 cell lines were crosslinked in 1% formaldehyde and harvested in batches of 20 million cells per replicate.  Prepared nuclei were resuspended in RIPA buffer and chromatin shearing was performed on a Bioruptor Twin instrument (Diagenode).   Antibody (5 µg/rxn) was coupled to M-280 Dynabeads (ThermoFisher Scientific; 11201) overnight prior to addition of sheared chromatin.  A small aliquot of the sheared chromatin was reserved as an input control.  Following incubation and wash steps, captured chromatin and input control were reverse crosslinked overnight at 65°C and recovered using the QIAquick PCR Purification System (Qiagen; 28104).
ChIP-seq libraries (illumina) were prepared and run on an Illumina HiSeq 2500 instrument.

tag: antibody  (clone id#) used


title: cortex_KI_ZT20


title: cortex_KI_ZT8


title: Control ChIP [SL41842]

description: Control ChIP-seq used for ZNF410(SL43822),MED1(SL140314)


title: Control ChIP [SL36398]

description: Control ChIP-seq used for ZMYM3(SL39968)


title: Control ChIP [SL31888]

description: Control ChIP-seq used for SMAD4(SL42192),SMAD4(SL42193)


title: cortex_KI_ZT0


title: Control ChIP [SL34967]

description: Control ChIP-seq used for RUVBL1(SL42191),ZMYM3(SL35275)


title: Control ChIP [SL68156]

description: Control ChIP-seq used for ZNF75A(SL116167),ZMYM3(SL75587),DPF1(SL101262),NFIA(SL122675)


title: cortex_WT_ZT8


title: cortex_KI_ZT4


title: Control ChIP [SL113691]

description: Control ChIP-seq used for NFIL3 (SL116118)


title: Control ChIP [SL23149]

description: Control ChIP-seq used for L3MBTL4(SL29056),ZMYM3(SL39970),ZMYM3(SL39971)


title: Control ChIP [SL57455]

description: Control ChIP-seq used for ZMYM3(SL81108),BATF3(SL141813),HMG20A(SL141801)


title: cortex_KI_ZT12


title: Control ChIP [SL12049]

description: Control ChIP-seq used for ZBTB2(SL81092)


title: Control ChIP [SL68153]

description: Control ChIP-seq used for ZBTB2(SL81092),NFIA(SL122673),NRF1(SL77444)


title: Control ChIP [SL83449]

description: Control ChIP-seq used for KLF10(SL115579),WDHD1(SL116135,SL116137),ZNF701(SL116165),ZNF75A(SL116166),ZXDC(SL83760),DPF1(SL101263),NRF1(SL83732),ZMYM3(SL83747),ZSCAN2(SL127154),NRF1(SL83733)


title: Control ChIP [SL12050]

description: Control ChIP-seq used for FOXO3(SL16038),SMAD4(SL13764)


title: Control ChIP [SL23147]

description: Control ChIP-seq used for TSC22D4(SL30778),STAT2(SL23812)


title: cortex_KI_ZT16


title: Control ChIP [SL77414]

description: Control ChIP-seq used for ZNF18(SL42197),ZMYM3(SL75589),BATF3(SL140322),HMG20A(SL140310),DRAP1(SL140307),TP73(SL140318)


title: Control ChIP [SL41843]

description: Control ChIP-seq used for NRF1(SL44336,SL44337,SL44338),ZNF18(SL42197),ZNF410(SL45964)


title: Control ChIP [SL41841]

description: Control ChIP-seq used for BATF(SL42189)


title: Control ChIP [SL83448]

description: Control ChIP-seq used for HES1(SL83725),NFATC3(SL93437),TSC22D4(SL83741),SMAD4(SL83734),ATF2(SL140306)


title: Control ChIP [SL12793]

description: Control ChIP-seq used for FOXO3(SL16038)


title: Control ChIP [SL113693]

description: Control ChIP-seq used for EZH2(SL115572),MED1(SL141805)


title: Control ChIP [SL77415]

description: Control ChIP-seq used for ETV6(SL115570,SL115580),ZNF597(SL116161),TSC22D4(SL82570),USF2(SL101266)


title: Control ChIP [SL31887]

description: Control ChIP-seq used for ATF2(SL141797)


title: Control ChIP [SL68154]

description: Control ChIP-seq used for ARID3A(SL71122),ZSCAN2(SL82574),ZMYM3(SL70086),USF2(SL101267)


title: ChIP-seq for DPF1 [SL101263]


title: ChIP-seq for ZSCAN2 [SL127154]


title: ChIP-seq for NRF1 [SL83732]


title: ChIP-seq for NRF1 [SL83733]


title: ChIP-seq for ZXDC [SL83760]


title: ChIP-seq for ZNF75A [SL116166]


title: Input_pool

city: Indianapolis

first: Keith

last: Goldstein

state: IN

address: Lilly Corporate Center

department: Investigative Toxicology

institute: Eli Lilly & Co.

data_processing:
Reads were aligned to the rat genome (rn5) using the BWA algorithm (default settings). Duplicate reads were removed and only uniquely mapped reads (mapping quality ≥ 25) were used for further analysis. Alignments were extended in silico at their 3’-ends to a length of 200 bp, which is the average genomic fragment length in the size-selected library, and assigned to 32-nt bins along the genome.
Peak locations were determined using the MACS algorithm (v1.4.2; parameters used were --gsize=2e9 --bw=200 --mfold=12,32 --pvalue=1e-07).
Genome_build: rn5.1
Supplementary_files_format_and_content: Bigwig files were generated using the BWA algorithm.The resulting files show the fragment density for 32-nt bins along the genome (“signal map”). The files can be uploaded to the UCSC browser.
Supplementary_files_format_and_content: Peak files were generated using the MACS algorithm.

source_name: Input pool of liver RNA

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody
Illumina sequencing libraries were prepared from the ChIP and Input DNAs by the standard consecutive enzymatic steps of end-polishing, dA-addition, and adaptor ligation.

tag: surgery

tag: time following surgery(d)

tag: chip antibody


title: BDL_1d_FXR

source_name: liver from animals with ligated bile duct, 1 day after surgery

value: bile duct ligation

value: FXR (Santa Cruz Biotechnology sc-13063)


title: BDL_14d_FXR

source_name: liver from animals with ligated bile duct, 14 days after surgery


title: sham_1d_HNF

source_name: liver from animals with sham surgery, 1 day after surgery

value: sham

value: HNF (Santa Cruz Biotechnology sc-8986)


title: sham_1d_FXR


title: BDL_5d_HNF

source_name: liver from animals with ligated bile duct, 5 days after surgery


title: sham_14d_FXR

source_name: liver from animals with sham surgery, 14 days after surgery


title: BDL_1d_HNF


title: BDL_14d_HNF


title: sham_5d_HNF

source_name: liver from animals with sham surgery, 5 days after surgery


title: ChIP-seq for KLF10 [SL115578]


title: sham_14d_HNF


title: BDL_1d_Sp1

value: Sp1 (EMD Millipore # 07-645)


title: sham_5d_Sp1


title: ChIP-seq for SMAD4 [SL83734]


title: ChIP-seq for ATF2 [SL140306]


title: sham_1d_Sp1


title: BDL_14d_Sp1


title: ChIP-seq for ZMYM3 [SL83747]


title: sham_5d_FXR


title: BDL_5d_FXR


title: ChIP-seq for WDHD1 [SL116137]


title: ChIP-seq for TSC22D4 [SL83741]


title: sham_14d_Sp1


title: ChIP-seq for NFATC3 [SL93437]


title: sham_1d_cJun

value: cJun (Santa Cruz Biotechnology #sc-1694)


title: NHEKM-GRHL3-rep1

city: Irvine

first: Bogi

last: Andersen

state: CA

address: 839 Health Sciences Dr.

department: Medicine

institute: University of California, Irvine

data_processing:
Base-calls were made using RTA version 1.12.4.2
Reads were aligned to human genome hg19 using Bowtie version 0.12.7
Bam file were converted to BED using Bedtools (bamToBed v2.11.2)
Peaks were called using MACS (v1.4), with FDR <.05
Galaxy was used for further data analysis (performing intersection/subtraction analysis, extracting features)
Genome_build: hg19
Supplementary_files_format_and_content: bed files- columns are: chromosome, start, stop, name, score, strand

source_name: primary human neonatal keratinocytes (NHEK)

growth_protocol: Normal Human Epidermal Keratinocytes (NHEK) were purchased from Invitrogen and grown according to the manufacturer’s instructions in EpiLife medium (Invitrogen) supplemented with EDGS (Invitrogen).

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with the Grhl3 antibody.
Sequencing libraries were generated for the samples using the NEB Next reagents and Illumina adaptors and oligos, according to the Illumina protocol for ChIP-Seq library preparation, with some modification. After adaptor ligation, PCR amplification was performed prior to size selection of the library (Schmidt, 2009). Clustering and 50-cycle single end sequencing were performed on the Illumina Hi-Seq 2000 Genome Analyzer.

treatment_protocol: To induce migration, cells were grown to a confluent monolayer and scratched with a p200 pipette tip. Scratches were made approximately every 1 cm horizontally and vertically, resulting in a grid of scratches. Migration was induced 60 hours after transfection, and cells were collected 12 hours later (72 hours after transfection).

tag: Stage

value: migrating

tag: antibody


title: BDL_1d_cJun


title: ChIP-seq for HES1 [SL83725]


title: sham_5d_cJun


title: ChIP-seq for USF2 [SL101266]


title: sham_14d_cJun


title: Jurkat A Dam control

city: Edinburgh

first: Jose

middle: Ignacio

last: de las Heras

address: Max Born Crescent

department: Wellcome Trust Centre

country: United Kingdom

institute: University of Edinburgh

description:
processed data file:
sq77.dpn_smooth_60_A.bw
LADs_A_15cut_sm60.bed
DR1_A_30.bed
DR3_A_30.bed

data_processing:
library strategy: DamID-seq
Basecalls and quality filtering performed by BGI according to their standard procedures
Clean reads were aligned to the human hg19 genome using the Burrows-Wheeler aligner bwa mem. Mitochondrial sequences and unaligned reads were filtered out.
Reads were counted per DpnI fragment (genomic sequence flanked by GATC motifs), and log2(ratio LaminB1/dam) measurements were obtained for resting and activated samples. The log2 ratios were then normalised using quantile normalisation (Bioconductor Limma package) and converted to bigwig format for visualisation purposes.
To identify LADs, we used a circular binary segmentation algorithm (CBS) from the R/Bioconductor package 'DNAcopy' (Venkatraman E. Seshan and Adam Olshen (). DNAcopy: DNA copy number data analysis. R package version 1.44.0) using default parameters. Positive signal segments identified by the CBS algorithm were merged if closer than 5Kb, and then any regions smaller than 15Kb were removed.
Regions that change peripheral association between conditions (PI regions represent loss of peripheral association after activation, and IP regions represent a gain) were then identified by comparing the LAD regions between the two conditions. Regions smaller than 15Kb were discarded.
Genome_build: hg19

Supplementary_files_format_and_content:
sq77.dpn_smooth_60_R.bw contains the DamID LaminB1/Dam profile for resting Jurkat cells, per DpnI fragment, quantile normalised, smoothened in 60-fragment windows (~15Kb) with a 1-fragment shift
sq77.dpn_smooth_60_A.bw contains the DamID LaminB1/Dam profile for activated Jurkat cells, per DpnI fragment, quantile normalised, smoothened in 60-fragment windows (~15Kb) with a 1-fragment shift
LADs_R_15cut_sm60.bed contains LAD regions for resting Jurkat cells
LADs_A_15cut_sm60.bed contains LAD regions for activated Jurkat cells
DR1_R_30.bed contains differential regions representing a loss of peripheral association upon activation (PI regions) - these regions were obtained by subtracting activated Jurkat LADs from resting Jurkat LADs with post-filtering to eliminate very small regions or those with very small signal difference between conditions * These regions were used for the associated publication
DR1_A_30.bed contains differential regions representing a gain of peripheral association upon activation (IP regions) - these regions were obtained by subtracting resting Jurkat LADs from activated Jurkat LADs with post-filtering to eliminate very small regions or those with very small signal difference between conditions * These regions were used for the associated publication
DR3_R_30.bed contains differential regions representing a loss of peripheral association upon activation (PI regions) - these regions were called using an approach where subtraction of LADs and a method using comparison of signals between conditions along a running window were combined.
DR3_A_30.bed contains differential regions representing a gain of peripheral association upon activation (IP regions) - these regions were called using an approach where subtraction of LADs and a method using comparison of signals between conditions along a running window were combined.

source_name: lymphocyte

growth_protocol: Jurkat clone E6-1 T-cells and Raji B-cells were cultured inn RPMI 1640 with 10% FBS, 100u/ml penicillin and 100ug/ml streptomycin. Jurkat and raji cells were diluted 1:6 and 1:10 respectively in fresh media every 2-3 days. Cellular debris was removed by centrifugation.

extract_protocol:
Genomic DNA was extracted using Qiagen DNA-Easy kit, following manufacturer's instructions.
DamID enrichment protocol: Dam-methylated genomic DNA was enriched using the standard protocol as described by Vogel et al. (2007) Nature Protocols 2:1467-1478. It involves digesting gDNA with DpnI enzyme, which cuts at non-Adenine-methylated GATC motifs.
Libraries were prepared by Beijing Genomics Institute (BGI) to Illumina's specifications

treatment_protocol:
Raji B-cells were incubated for 30min at a concentration of 1E06 cells/ml in medium containing 0.5ug/ml SEE (Toxin Technologies, EP404). SEE loaded Raji cells were pelleted, washed in PBS and resuspended in medium, then mixed at a 1:10 ratio with Jurkat cells to a total density of 1E06 cells/ml. Naive CD4+ cells were isolated by FACS. Activation was performed by incubation with 20ng/ml PMA for 24h. Activation was determined and selected for by FACS staining for CD69-APC. Activated cell samples were used if they were CD69+ for at least 78% of the population.
DamID protocol: Lentivirus encoding the control Dam, or LaminB1-Dam fusion, was used to transduce HT1080 cells. Transduction was allowed for 24h, and then the medium refreshed. At 72h post-transduction genomic DNA was extracted.

tag: cell type

value: Jurkat T-cells

tag: treated with

value: PMA-activated

tag: damid

value: Dam


title: ChIP-seq for WDHD1 [SL116135]


title: ChIP-seq for ZNF597 [SL116161]


title: SFM1923P5

city: Los Angeles

middle: E

last: Decato

address: 1050 Childs Way

department: Molecular and Computational Biology

institute: University of Southern California

description: Mice were housed under a 14:10 hour light cycle with food and water ad libidum. For all crosses, a single stud and dam were housed together for four and a half days, and then split. 10 days later, females were euthanized, uteri were collected and the number of viable conceptuses counted. The embryos and placenta were dissected and weighed. Two placentae were sampled from a single litter in each cross direction and snap frozen in liquid nitrogen. For M. domesticus, reciprocal crosses between strains BIK (originally isolated from Kefar Galim, Israel) and DOT (Tahiti) were generated; for M. musculus, MPB (Bialowieza, Poland) and MBS (Sokolovo, Bulgaria) were crossed; and for M. spretus, STF (Fondouk Djedid, Tunisia) and SFM (Montpellier, France) were mated. Placenta are named according to their maternal strain.

data_processing:
Reads aligned to mm10 reference genome using WALT (https://github.com/smithlabcode/walt)
Methylation levels computed from reads using methpipe v3.4.2
Genome_build: mm10
Supplementary_files_format_and_content: All processed data files are bigWig format with the value equal to the methylation level for .meth.bw files and coverage depth for .read.bw files.

organism: Mus spretus

source_name: Whole placenta

growth_protocol: See individual samples: the two datasets (interspecific and intraspecific) were grown using separate growth protocols.

extract_protocol:
Using a Qiagen DNA extraction kit, DNA was extracted and purified for all whole placental, labyrinthine, and junctional zone samples. Samples were sent to the Beijing Genomics Institute for bisulfite conversion and sequencing.
BGI library construction protocols for WGBS samples

value: whole placenta

tag: strain

value: SFMxSTF

tag: Sex

value: female


title: Jurkat R LaminB1-Dam

description:
processed data file:
sq77.dpn_smooth_60_R.bw
LADs_R_15cut_sm60.bed
DR1_R_30.bed
DR3_R_30.bed

value: none (resting, untreated control)


title: ChIP-seq for TSC22D4 [SL82570]


title: STF1955P3

tag: tissue

value: STFxSFM


title: BDL_5d_Sp1


title: SFM1923P4

value: male


title: Jurkat R Dam control


title: Jurkat A LaminB1-Dam


title: BDL_5d_cJun


title: ChIP-seq for ETV6 [SL115580]

tag: cell line


title: STF1955P2


title: siGRHL3 H3K4me1 rep2

description: ChIP-Seq library

data_processing:
Base-calls were made using RTA
Reads were aligned to human genome hg19 using Bowtie version 0.12.7, only uniquely aligning reads were retained (-m 1)
Bam file were converted to BED using Bedtools (bamToBed v2.11.2)
Peaks were called using SICER (v1.1), with input aligned sequences as the control file, and FDR <.05
MEME-ChIP was used for motif analysis, DiffBind (Bioconductor) for differential peak analysis, and Galaxy was used for further data analysis (performing intersection/subtraction analysis, extracting features)
Genome_build: hg19
Supplementary_files_format_and_content: bed

source_name: epidermal keratinocyte

growth_protocol: Normal Human Epidermal Keratinocytes (NHEK) were purchased from LifeLine Technologies and grown according to the manufacturer’s instructions in DermaLife medium (LifeLine Tech) supplemented with DermaLife growth factors (LifeLine Tech).

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes, then lysed and sonicated prior to pull down with antibodies
Libraries were created using the Illumina Tru-Seq adapters with NEBNext reagents

treatment_protocol: Lipofectamine RNAi Max (Life Technologies) in OptiMEM medium was used for siRNA transfections: 30nM pooled siRNA was used for knockdown of GRHL3 (Dharmacon L-014017-02). 48 hours after transfection, cells were induced to differentiate by addition of high calcium medium (1.8mM Ca2+) for 24 hours.

tag: treatment


title: ChIP-seq for TP73 [SL140318]


title: siGRHL3 H3K4me1 rep1

description: ChIP-Seq library

value: Normal Human Epidermal Keratinocytes (NHEK)


title: ChIP-seq for ETV6 [SL115570]


title: NHEKM-GRHL3-rep2


title: BDL_14d_cJun

value: bile duct ligation


title: ChIP-seq for HMG20A [SL140310]


title: scramble H3K4me3 rep1

description: ChIP-Seq library

value: scramble


title: ChIP-seq for BATF3 [SL140322]


title: scramble Input

description: Input library


title: scramble H3K27ac rep1

description: ChIP-Seq library


title: scramble H3K27ac rep2

description: ChIP-Seq library


title: scramble H3K4me1 rep2

description: ChIP-Seq library


title: ChIP-seq for ZNF18 [SL77427]


title: ChIP-seq for NFIA [SL122675]


title: scramble H3K4me1 rep1

description: ChIP-Seq library


title: siGRHL3 H3K4me3 rep2

description: ChIP-Seq library


title: siGRHL3 H3K4me3 rep1

description: ChIP-Seq library


title: ChIP-seq for ZMYM3 [SL75587]


title: ChIP-seq for ZNF75A [SL116167]


title: siGRHL3 H3K27ac rep2

description: ChIP-Seq library


title: siGRHL3 H3K27ac rep1

description: ChIP-Seq library


title: ChIP-seq for ZMYM3 [SL70086]


title: ChIP-seq for USF2 [SL101267]


title: siGRHL3 input

description: Input library


title: ChIP-seq for ZSCAN2 [SL82574]


title: ChIP-seq for ARID3A [SL71122]


title: ChIP-seq for DRAP1 [SL140307]


title: scramble H3K4me3 rep2

description: ChIP-Seq library


title: ChIP-seq for NRF1 [SL77444]


title: NHEK-M H3K27ac-2

data_processing:
Base-calls were made using RTA  version 1.12.4.2
Reads were aligned to human genome hg19 using Bowtie version 0.12.7, only uniquely aligning reads were retained (-m 1)
Samtools was used to combine files from the two libraries for each sample
Bam file were converted to BED using Bedtools (bamToBed v2.11.2)
Peaks were called using SICER (v1.1),  with  FDR <.05, Input library was used as the control
Galaxy was used for further data analysis (performing intersection/subtraction analysis, extracting features)
Genome_build: Human hg19
Supplementary_files_format_and_content: interval files from SICER, containing chromosome and coordinates of peak locations
column headers: chromosome, start, end, ChIP island read count, Control island read count, p value, fold change, fdr threshold

source_name: Primary human epidermal keratinocytes (NHEK)

growth_protocol: NHEK cells were grown in EpiLife medium supplemented with EDGS (Invitrogen) at 37C, 5%CO2

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with the respective histone antibodies.
Sequencing libraries were generated for the H3K27ac, H3K4me1, and H3K4me3 samples (samples were divided in half, and two libraries made for each using different multiplexed adaptors) Clustering and 50-cycle single end sequencing were performed on the Illumina Illumina HiSeq 2000 Genome Analyzer.
Libraries were sequenced on the Illumina Illumina HiSeq 2000, with 50bp single end sequencing

treatment_protocol: To induce migration, cells at 95% confluency were scratched with a pipet tip, and cells were collected 12 hours later.

tag: antibody vendor/catalog

value: antibody:millipore 07-360


title: ChIP-seq for NFIA [SL122673]


title: NHEK-M Input-2

value: Input


title: NHEK-M H3K27ac


title: ChIP-seq for ZMYM3 [SL75589]


title: NHEK-M Input


title: ChIP-seq for ZBTB2 [SL81092]


title: NHEK-M H3K4me3

value: millipore 07-473


title: ChIP-seq for DPF1 [SL101262]


title: NHEK-M H3K4me1

value: abcam ab8895


title: NHEK-M H3K4me1-2


title: IGG-L10

city: East Lansing

first: Rance

last: Nault

state: United States

address: 1355 Bogue St. B403

department: Department of Pharmacology and Toxicology

institute: Michigan State University

description: Mice gavaged once and livers collected 2 hours following exposure

data_processing:
Quality control: FASTQC v0.11.2
Adaptor sequence removal: Cutadapt v1.4.1
Cleaning of low complexity reads: FASTX v0.0.14
Mapping: Bowtie 2.0.0
Normalization and peak calling: CisGenome
Genome_build: GRCm38 release 76; mm10
Supplementary_files_format_and_content: bigWig file showing relative enrichment to IgG control (log2fold-change)

source_name: Liver

extract_protocol:
ChIP was performed as previously described (Dere et al., 2001. BMC Genomics 12, 365; Lo and Matthews, 2012. Toxicol Sci 130(2), 349-61). Briefly, mouse livers (~100 mg) were homogenized in 1% formaldehyde and incubated at room temperature for 10 minutes. Homogenates were centrifuged at 10,000 RPM for 3 minutes at 4°C and pellets washed with cold PBS followed by resuspension in TSEI with Protease Inhibitor Cocktail. Samples were sonicated 12 times for 10 seconds and supernatants transferred to new tubes and incubated with rabbit IgG and anti-AhR or just rabbit IgG overnight at 4°C.  Protein A/G-Sepharose was added and samples incubated for 1.5h.  Pellets were washed for 10 minutes in buffer 1, buffer 2, LiCl buffer, and TE. Protein-DNA complexes were then eluted using TE and cross-links reversed by overnight incubation at 65°C followed by DNA purification.
Libraries were prepared using the MicroPlex kit (Diagenode) according to manufacturer's instructions

treatment_protocol: Female C57BL/6 mice were gavaged once with sesame oil vehicle or 30 ug/kg TCDD and livers collected 2 hours following treatment.

value: Liver

value: Female

tag: age

tag: age unit

value: days

value: TCDD

tag: dose

tag: dose unit

value: ug/kg

tag: duration

tag: duration unit

value: hours

tag: replicate

tag: antibody vendor


title: IGG-L09

tag: chip antibody


title: IGG-L11


title: IGG-L07


title: IGG-L08


title: ChIP-seq for NRF1 [SL44336]

tag: antibody  (clone id#) used


title: ChIP-seq for ZNF410 [SL45964]


title: ChIP-seq for NRF1 [SL44337]


title: ChIP-seq for ZMYM3 [SL81108]


title: ChIP-seq for NRF1 [SL44338]


title: ChIP-seq for ZNF18 [SL42197]


title: AHR-L11

value: Enzo Life Sciences


title: ChIP-seq for MED1 [SL140314]


title: ChIP-seq for ZNF410 [SL43822]


title: AHR-L10


title: AHR-L08


title: ChIP-seq for ZMYM3 [SL39968]


title: AHR-L09


title: NHEK-M H3K4me3-2

tag: antibody


title: ChIP-seq for BATF [SL42189]


title: IGG-L10

treatment_protocol: Male C57BL/6 mice were gavaged once with sesame oil vehicle or 30 ug/kg TCDD and livers collected 2 hours following treatment.

tag: strain

value: Male


title: ChIP-seq for ZMYM3 [SL68997]


title: AHR-L07

tag: Sex


title: ChIP-seq for ZMYM3 [SL65248]


title: ChIP-seq for ZNF639 [SL39347]


title: IGG-L09

tag: tissue


title: ChIP-seq for HMG20A [SL141801]

tag: cell line


title: ChIP-seq for ZMYM3 [SL35275]


title: ChIP-seq for SMAD4 [SL42193]


title: ChIP-seq for SMAD4 [SL42192]


title: IGG-L06

tag: treatment


title: IGG-L07


title: AHR-L10


title: ChIP-seq for ZMYM3 [SL39971]


title: AHR-L08


title: ChIP-seq for ZMYM3 [SL39970]


title: ChIP-seq for L3MBTL4 [SL29056]


title: ChIP-seq for ZNF639 [SL39345]


title: ChIP-seq for STAT2 [SL23812]


title: AHR-L07


title: ChIP-seq for TSC22D4 [SL30778]


title: ChIP-seq for FOXO3 [SL16034]


title: ICM_XX

city: Cambridge

first: Kendell

last: Clement

state: MA

address: 7 Divinity Ave.

institute: Harvard University

description: Pooled female ICM in vitro cultured for 4.5 days.

data_processing:
Sequencing reads were trimmed using timgalore, as well as NuGEN-provided script for diversity trimming and filtering.
Alignment: bisulfite-converted reads were aligned to a the mm9 genome using Bsmap version 2.89 with the following flags: -v 0.05 -s 16 -w 100 -S 1 -p 8 -u
Methylation calling: CpGs in the reference sequence were compared to the sequence in the aligned read. If bisulfite conversion (signifying an unmethylated cytosine) was detected, the read added to the unmethylated count for that CpG, otherwise, it added to the methylated count.
Genome_build: mm9
Supplementary_files_format_and_content: Bed files contain the number of methylated and total reads for CpGs covered by RRBS with the columns: chromosome, start, end, number of reads methylated divided by number of reads seen, methylation percent/1000

source_name: ICM

growth_protocol: generation protocol: Isolated zygotes were cultured in KSOM for 4 days. The trophectoderm was removed from the E4.5 blastocysts to isolate ICMs using rabbit anti- mouse serum and subsequently guinea-pig complement serum.

extract_protocol:
Genomic DNA was collected using phenol/chloroform extraction
RRBS libraries were prepared using a commercial kit (Ovation RRBS Methyl-Seq System, NuGen, San Carlos, CA) following the manufacturer's protocol except that we pooled 12 individually barcoded reactions after the final repair step and performed the bisulfite conversion and library amplification as a pool. Libraries were sequenced on an Illumina HiSeq2500 high-output flowcell without a PhiX spike-in using Nugen's custom sequencing primer for read 1 (36 bases) and standard Illumina sequencing primers to read the 8-base sample barcodes.

tag: sex chromosomes

value: XX


title: AHR-L06

tag: age


title: ICM_XY

description: Pooled male ICM in vitro cultured for 4.5 days.

value: XY


title: ChIP-seq for SMAD4 [SL13764]


title: ChIP-seq for EZH2 [SL115572]


title: CTNNB1_PIK3CA_186

city: Berlin

first: Markus

last: Morkel

address: Charitéplatz 1

department: Dept. of Pathology

country: Germany

institute: Charité - Universitätsmedizin Berlin

data_processing:
The following Illumina HiSeq software suite versions were employed: HCS 2.2.58; RTA: 1.18.64; BCL Converter: 2.17.1.14
RNAseq reads were aligned to the mouse genome GRCm38 using STAR aligner and Gencode exon annotations
Read counts were calculated for each gene_id using HTSeq
After removal of ribosomal reads, raw counts were normalized using the DESeq function estimateSizeFactors, and dispersion in replicates were calculated using the DESeq function estimateDispersions with default parameters
Genome_build: GRCm38
Supplementary_files_format_and_content: Tab-delimied text file containing processed read counts per gene_id and sample

source_name: small intestinal organoids

growth_protocol: Organoid cultures of transgenic mouse small intestine were propagated as described in Sato et al., Gastroenterology (2011), using 48-well plates with 15µl droplets of medium and Matrigel (BD) per well overlaid with 300µl CCM-REN.

extract_protocol:
Total RNA from sorted cells was extracted using the RNeasy micro Kit (Qiagen)
100ng total RNA were used for library preparation with the ScriptSeq Kit (Illumina) according to the manufacturer’s instructions

treatment_protocol: Transgenes (luc-tdTomato, PIK3CAH1047R-tdTomato, CTNNB1stab-tdTomato, PIK3CAH1047R-CTNNB1stab-tdTomato) were induced by adding 2µg/ml doxycycline to the cultures for 24h. Fluorescence activated cell sorting was done after dissociation in TrypLE (Gibco) and 100U/µl DNAseI (Sigma) for 15min. at 37°C, followed by filtering through a 30µM strainer (Costar), using an ARIA II SORP (BD). Cells positive for the tdTomato transgene and negative for a green live/dead stain were collected.

value: intestine, duodenum

tag: dev. stage

value: adult

tag: transgene


title: IGG-L08

tag: age unit

tag: dose

tag: dose unit


title: ChIP-seq for FOXO3 [SL16038]


title: EL16.7 Dusp9+/-

description: EL16.7 ESC line with Dusp9 heterozygous deletion.

source_name: ESC

growth_protocol: generation protocol: EL16.7 ESCs were cotransfected with a construct containing an sgRNA targeting the first exon of Dusp9 and a Cas9 expression vector.


title: Haploid ESC

description: Haploid ESC (X).

growth_protocol: generation protocol: Elling et al., 2011

value: X


title: ChIP-seq for ZBTB2 [SL22158]


title: ChIP-seq for NFIL3 [SL116118]


title: CTNNB1_PIK3CA_3


title: PIK3CA_97


title: ChIP-seq for RUVBL1 [SL42191]


title: AHR-L09

tag: duration

tag: duration unit

tag: replicate


title: ChIP-seq for KLF10 [SL115579]

tag: antibody  (clone id#) used


title: PIK3CA_100


title: CTNNB1_2250


title: CTNNB1_2249


title: LUC_989


title: 4 month, rep3

city: Bethesda

first: Cynthia

last: Jawoski

address: bldg 6, room 136

department: NEI

institute: NIH

description:
mRNA
6_4M_L6
Processed data file: rsem_gfpkm_matrix.txt

data_processing:
FASTQ sequencing read output files were produced by CASAVA v. 1.ll8.2 and Expression Analysis tools.
Sequence reads were processed using EA-Quintiles' mRNAv8 pipeline: adaptor sequences and low quality bases are removed from ends of reads.
Reads were aligned to the human transcriptome using Bowtie version 0.12.9.
RSEM v1.2.0 was used to quantify transcripts using the UCSC known gene transcriptome.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: *rsem.genes.results: Tab-delimited text files include RNA fragment counts per gene, coverage estimates, detection calls, and other metrics.
Supplementary_files_format_and_content: rsem_gfpkm_matrix.txt: Tab-delimited text file; table of gfpkm for each sample, 27939 genes represented.

source_name: ARPE-19 cells, 4 months

growth_protocol: Cells were grown on Primaria® tissue culture plates in Dulbecco's modified Eagle's medium (DMEM) with 4.5 g/L glucose, L-glutamine and 1 mM sodium pyruvate supplemented with fetal bovine serum, penicillin and streptomycin.

extract_protocol:
Total RNA was extracted using miRNeasy Mini Kit (Qiagen).
cDNA libraries were prepared from total RNA samples using the TruSeq Stranded mRNA Sample Prep Kit (Illumina).
The libraries were sequenced using a 2x50 bp paired end protocol with the median number of 87.3 million reads across all samples on the Illumina HiSeq 2500 (Illumina).

tag: cell type

value: retinal pigment epithelial (RPE) cell line

tag: duration of culture

value: 4 months


title: 4 month, rep1

description:
mRNA
4_4M_L5
Processed data file: rsem_gfpkm_matrix.txt


title: 4 day, rep2

description:
mRNA
2_4D_L2
Processed data file: rsem_gfpkm_matrix.txt

source_name: ARPE-19 cells, 4 days

value: 4 days


title: 4 day, rep1

description:
mRNA
1_4D_L4
Processed data file: rsem_gfpkm_matrix.txt


title: 521D_BK

city: Stanford

first: Thomas

last: Quertermous

address: 300 Pasteur Drive

department: Medicine Cardiology

institute: Stanford University

data_processing:
Reads contained in raw fastq files were mapped to hg19 using the RNA-seq aligner STAR (v2.4.0i), that processes data with short run times and yields high numbers of uniquely mapped reads (https://github.com/alexdobin/STAR). Second pass mapping with STAR was then performed using a new index that is created with splice junction information contained in the file SJ.out.tab from the first pass STAR mapping. Read that have been mapped with STAR second pass mapping algorithm were subsequently counted using the htseq-count script distributed with the HTSeq Python package (https://pypi.python.org/pypi/HTSeq). Differential expression of exons, genes, and transcripts were assayed using the DESeq2 R package from Bioconductor (http://bioconductor.org/packages/release/bioc/html/DESeq2.html), which uses negative binomial distribution to estimate dispersion and model differential expression such as to permit biological variability to be different among tested genes (transcripts).
Genome_build: hg19
Supplementary_files_format_and_content: [.txt] FeatureCounts - with Gencode annotation - gencode.v19.annotation.gtf
Supplementary_files_format_and_content: [.csv] DESeq output table

source_name: TCF21 overexpression - biological replicate 4

growth_protocol: Primary human coronary artery smooth muscle cells (HCASMC) were purchased from three different manufacturers, Lonza, PromoCell and Cell Applications and were cultured in complete smooth muscle basal media (Lonza, #CC-3182) according to the manufacturer's instructions. All experiments were performed with HCASMC between passages 4–7.

extract_protocol:
HCASMC were cultured as described in Nurnberg at al, Plos Genetics 2015 ,and total RNA was purified from 5.0x10e5 cells using the Qiagen miRNeasy kit. RNA was isolated using RNeasy mini kit (Qiagen) and total cDNA was prepared using iScript cDNA synthesis kit (Biorad).
RNA libraries were prepared using the Illumina TruSeq library kit as described by the manufacturer. RNA molecules were sequenced using Illumina HiSeq 2500.

treatment_protocol: For the TCF21 overexpression study, HCASMC were transduced with 2nd generation lentivirus with TCF21 cDNA cloned into pWPI (Addgene #12254). The cells were collected 48 hours after transduction and processed using RNeasy kit (Qiazol) for RNA isolation.

tag: genotype/variation

value: TCF21 overexpression


title: 521C_BK

source_name: TCF21 overexpression - biological replicate 3

value: human coronary artery smooth muscle cells (HCASMC)


title: 520D_BK

source_name: Control - biological replicate 4

value: control


title: 521B_BK

source_name: TCF21 overexpression - biological replicate 2


title: 520C_BK

source_name: Control - biological replicate 3


title: LUC_987

tag: strain

tag: tissue

value: tdTomato-LUC


title: Control5_3

first: David

middle: A

last: Bulger

address: Box 289, Addenbrooke's Hospital

department: Institute of Metabolic Science

institute: University of Cambridge

data_processing:
RNA-seq reads were aligned to GRCh37 genome assembly using Tophat V2.0.8
Fragment counts were determined using Cufflinks V2.2.1
Genome_build: GRCh37
Supplementary_files_format_and_content: tab-delimited files include ENSEMBL_ID, gene_short_name, tss_id, locus, and raw count values

source_name: Interscapular subcutaneous adipose tissue

extract_protocol:
Adipose tissue was removed surgically, dissected from surrounding connective and vascular tissue on dry ice and frozen in liquid nitrogen, 2-3 frozen aliquots per subject were transferred into 1 mL QIAzol (Qiagen) and homogenized on thawing with a hand-held TissueRuptor (Qiagen) before centrifugation at 13,000g for 3 minutes, and infranatant beneath the fatty layer was mixed with 1 ML 100% ethanol before binding to RNeasy columns and purifying using the RNAeasy kit according to manufacturer's instructions.
RNA was concentrated with the Rneasy MinElute Cleanup Kit (Qiagen) and the RNA samples were whole transcriptome-amplified with NuGEN RNA-Seq System V2 and converted to indexed libraries with NuGEN Ovation Rapid DR Multiplex Library System following manufacturer's instructions.

tag: gender

value: female

tag: genotype

value: WT


title: Control5_1

value: Interscapular subcutaneous adipose tissue


title: 521A_BK

source_name: TCF21 overexpression - biological replicate 1


title: siRNA_mlo3Δ

city: Munich

first: Mario

last: Halic

department: Biochemistry - Gene Center

institute: Ludwig-Maximilians-Universität

data_processing:
base calling with RTA1.18.64
Sequenced reads were trimmed for the adaptor sequence, then mapped to the S.pombe genome with Novoalign (http://www.novocraft.com) randomly assigned.
Reads mapping with two or fewer mismatches were retained.
Enrichments were calculated with our house Perl scripts
Normalisation to reads per million for siRNA and ChIP experiments, normalisation to reads mapping to protein coding genes for RNAseq /RIPseq
Genome_build: Schizosaccharomyces_pombe.ASM294v1.18
Supplementary_files_format_and_content: can be viewed with IGV browser: http://www.broad.mit.edu/igv

organism: Schizosaccharomyces pombe

growth_protocol: cells were grown in liquid, rich YES medium

extract_protocol:
RNA libraries were prepared with NEBnext Ultra Directional RNA Library Prep Kit for Illumina (NEB); DNA library construction with NEBNext Ultra II DNA Library Prep Kit for Illumina kit (NEB). siRNA library: ligation of 3’ adapter (5'-App CTG TAG GCA CCA TCA AT/ddC/-3') and 5’ adapter (5'-GUU CAG AGU UCU ACA GUC CGA CGA UC-3'), reverse transcription, PCR of cDNA with Illumina P5 5' primer and barcoded llumina P7 3' primer.
Endogenous 3xFLAG-tagged Ago1-bound siRNA were purified by protein affinity purification and subsequent size selection on an 18% acrylamide gel. 2 pmol of a preadenylated 3' adaptor oligonucleotide (miRNA Cloning Linker-1 from IDT, 5'-App CTG TAG GCA CCA TCA AT/ddC/-3') were ligated in a 10 µl reaction with 5 U T4 RNA ligase (TaKaRa), ligation buffer without ATP and 5 U RNasin (Promega) at 20°C for 2 hours. The 3' ligated products were purified on an 18% acrylamide urea gel with subsequent phenol-chloroform purification and ethanol purification. The 5' adaptor ligation was performed in a 10 µl reaction with 2 pmol 5' adaptor oligonucleotide (5'-GUU CAG AGU UCU ACA GUC CGA CGA UC-3'), 5 U RNasin (Promega), 0.06 µg BSA, 5 U T4 RNA ligase (Thermo Scientific) and 1x ligation buffer with ATP (Thermo Scientific) for 2 h at 20°C. The ligated products were gel purified and reverse transcribed with 10 pmol primer (RT primer: 5'- GTG ACT GGA GTT CAG ACG TGT GCT CTT CCG ATC GAT TGA TGG TGC CTA CAG-3') and the SuperScript III First Strand Synthesis System (Thermo Scientific). The cDNA was PCR-amplified with Q5 High-Fidelity 2x Master Mix (NEB) for 14-20 cycles using the Illumina P5 5' primer (5' -AAT GAT ACG GCG ACC ACC GAG ATC TAC ACT CTT TCC CTA CAC GAC G -3') and the Illumina P7 3' primer with inserted barcode (5'-CAA GCA GAA GAC GGC ATA CGA GAT XXXXXX GTG ACT GGA GTT CAG ACG TG -3').

tag: antibody for ip

value: anti-FLAG

tag: strain number

tag: target molecule

value: siRNA


title: 4 day, rep3

description:
mRNA
3_4D_L3
Processed data file: rsem_gfpkm_matrix.txt

tag: cell line


title: 4 month, rep2

description:
mRNA
5_4M_L1
Processed data file: rsem_gfpkm_matrix.txt


title: siRNA_caf1Δdcr1Δ


title: siRNA_wild_type

source_name: wild type


title: Control4_2


title: siRNA_exo2Δ


title: Control4_1


title: Control4_3


title: siRNA_caf1Δ


title: Control3_3