title: ALLSIL_control_siRNA_repl2

description: Gene expression 72h post-electroporation of ALLSIL T-ALL cells with control siRNA, replicate 2

source_name: ALLSIL, control siRNA, 96h, replicate 2


title: young-homo3_RNA-seq

status: Public on Dec 01 2020

type: SRA

city: Boston

first: Catherine

last: Wu

state: MA

address: 450 Brookline Avenue

country: USA

institute: Dana-Farber Cancer Institute

description:
total RNA
Ikzf3 MT vs. WT.txt

library_source: transcriptomic

data_processing:
Illumina Casava1.8 software used for basecalling.
RNA-seq reads were aligned to the mouse reference genome using STAR (v2.4.0.1). ChIP-seq reads were aligned to the mouse reference genome using using Bowtie2 (v2.3.4.1).
TPM (Transcripts Per Kilobase Million) value was used to measure gene expression. Peak detection was performed with MACS2 (v2.2.0).
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files include TPM values for all samples
Supplementary_files_format_and_content: bigwig

molecule: total RNA

organism: Mus musculus

source_name: B cell

growth_protocol: RNA-seq was performed on purified splenic B cells (1x106) from 2-3 months wild-type and homozygous mutant mice.

extract_protocol:
Harvested spleens were mechanically dissociated to form a single cell suspension. Erythrocyte lysis was carried out using ACK buffer and B cells were immunomagnetically selected from the resulting cell suspension using the MACS B cell Isolation Kit. Cells were washed in cold PBS and total RNA was extracted using Qiagen RNAeasy kit.
Libraries were prepared using the TruSeq RNA Sample Prep Kit v2 (Illumina).

tag: cell type

value: Splenic B cell

tag: strain

tag: genotype

value: Ikzf3 fl/fl

tag: age

value: 3 months


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_E10_ad004

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

library_source: genomic

data_processing:
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted mm10 INTACT reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Genome_build: mm10 INTACT
Supplementary_files_format_and_content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column

molecule: genomic DNA

source_name: C57BL/6J P56 Mouse Brain

growth_protocol: All experimental procedures using live animals were approved by the Salk Institute Animal Care and Use Committee. The knock-in mouse line, R26R-CAG-loxp-stop-loxp-Sun1-sfGFP-Myc (INTACT) was used for most experiments4 and they were maintained on a C57BL/6J background. 42-49 day old adult male and female INTACT mice were used for the retrograde labeling experiment.

extract_protocol:
Approximately two weeks after the AAVretro injection, brains were extracted from the 56-63 day old INTACT mice, immediately submerged in ice-cold slicing buffer (2.5mM KCl, 0.5mM CaCl2, 7mM MgCl2, 1.25mM NaH2PO4, 110mM sucrose, 10mM glucose and 25mM NaHCO3) that was bubbled with carbogen, and sliced into 0.6 mm coronal sections starting from the frontal pole. From each AAVretro-injected brain, the slices were kept in the ice-cold dissection buffer from which selected brain regions (Supplementary Table 1) were manually dissected under a fluorescent dissecting microscope (Olympus SZX16), following the Allen Mouse Common Coordinate Framework (CCF), Reference Atlas, Version 3 (2015) (Extended Data Fig. 1). The dissected brain tissues were transferred to prelabeled microcentrifuge tubes, immediately frozen in dry ice, and subsequently stored at -80oC.   For each dissected brain region, samples from 2 males and 2 females were pooled separately as biological replicates for nuclei preparation. The 2-mL glass tissue dounce homogenizer and pestles (Sigma-Aldrich D8938-1SET) were pre-chilled on ice. Nuclei were prepared using a modified protocol as reported by Lacar et al., 201622. In summary, the frozen brain tissues were transferred to the dounce homogenizer with 1 mL ice-cold NIM buffer (0.25M sucrose, 25mM KCl, 5mM MgCl2, 10mM Tris-HCl (pH7.4), 1mM DTT (Sigma 646563), 10μl of protease inhibitor (Sigma P8340)), with 0.1% Triton X-100 and 5μM Hoechst 33342 (Invitrogen H3570), and gently homogenized on ice with the pestle 10-15 times. The homogenate was transferred to pre-chilled microcentrifuge tubes and centrifuged at 1000 rcf for 8 min at 4oC to pellet the nuclei. The pellet was resuspended in 1 mL ice-cold NIM buffer, and again centrifuged at 1000 rcf for 8 min at 4oC. The pellet was then resuspended in 450 μL of ice-cold NSB buffer (0.25M sucrose, 5mM MgCl2, 10mM Tris-HCl (pH7.4), 1mM DTT, 9ul of Protease inhibitor), and filtered through 40μM cell strainer. The filtered nuclei suspension was incubated on ice for at least 30 minutes with 50μl of nuclease-free BSA for at least 10 minutes, then incubated with GFP antibody, Alexa Fluor 488 (Invitrogen, A-21311) and anti-NeuN antibody (EMD Millipore MAB377) conjugated with Alexa Fluor 647 (Invitrogen A20173). GFP+/NeuN+ single nuclei were isolated using fluorescence-activated nuclei sorting (FANS) on a BD Influx sorter with 100μm nozzle, and sorted into 384-well plates preloaded with 2μl of digestion buffer for snmC-seq215 (20 mL digestion buffer consists of 10 mL M-digestion buffer (2×, Zymo D5021-9), 1 ml Proteinase K (20 mg, Zymo D3001-2-20), 9 mL water, and 10 µL unmethylated lambda DNA (100 pg/µL, Promega, D1521)). The collected plates were incubated at 50oC for 20 minutes then stored at -20 oC.
The bisulfite conversion and library preparation were performed following the detailed snmC-seq2 protocol as previously described (Luo, C. et al., Nat. Commun. 2018, 9(1):3824.). The snmC-Seq2 libraries were sequenced on Illumina Novaseq 6000 using the S4 flow cell 2 x 150 bp mode.

treatment_protocol: To label neurons projecting to regions of interest, injections of rAAV2-retro-Cre (produced by Salk Vector Core or Vigene, 2x10^12 to 1x10^13 viral genomes/ml, produced with capsid from Addgene plasmid #81070 packaging pAAV-EF1a-Cre from Addgene plasmid #55636) were made into both hemispheres of the INTACT mice. Animals were anesthetized with either ketamine/xylazine or isoflurane, placed in a stereotaxic frame, and 0.1 to 0.5 microliters of AAV was injected by pressure into stereotaxic coordinates corresponding to the desired projection target.

tag: tissue

value: brain

tag: source

value: PTLp

tag: target

value: VISp

tag: gender

value: female


title: EcN at timepoint t2, biological repA

type: RNA

city: Tuebingen

first: Stefan

last: Czemmel

address: Auf der Morgenstelle 10

department: University of Tuebingen

country: Germany

institute: Quantitative Biology Center (QBiC)

description: Gene expression data from HEK293 cells treated with flagellin of E. coli Nissle for 120min

hyb_protocol: The samples were hybridized to the Affymetrix GeneTitan:HumanGene 2.1 ST Array Plate for 16 h at 48 ºC.

scan_protocol: HT Array Plates were scanned using the HT Scanner (Affymetrix GeneChip®HT)

data_processing: The data was analyzed using robust multi-array average (RMA) analysis using the rma() function from the R package oligo (version 1.30.0) with default setting (target=core).

label: biotin

organism: Homo sapiens

source_name: TLR5 overexpressing human embryonic kidney cells (HEK293) treated with flagellin of E. coli Nissle (FliCEcN, acronym=EcN) for 120min (t2)

label_protocol: 100 ng of quality controlled (using Bioanalyzer) total RNA were used for processing of the biotinylated cRNA.

growth_protocol: Murine TLR5 overexpressing HEK cells were cultured in custom- made SILAC-DMEM media (SILAC heavy label (Lys8Arg10), SILAC medium label (Lys4Arg6) and SILAC light label (Lys0Arg0) at 37°C and 5% CO2. At a passage number of seven the cells were highly incorporated and used for stimulation.

extract_protocol: 60 minutes or 120 minutes stimulated murine TLR5 overexpressing HEK cells were resuspended in RLT buffer containing 1% ß-mercaptoethanol for total RNA isolation with Qiagen RNeasy kit following the manufacturer’s instructions (Qiagen).

treatment_protocol: 6.6 x106 murine TLR5 overexpressing HEK cells per flask were stimulated with isolated flagellin of E. coli Nissle (EcN) or isolated flagellin of Salmonella Typhimurium SL1344 (ST) with a concentration according to MOI 10 for 60 minutes (t1) or 120 minutes (t2).

tag: cell line

value: TLR5 overexpressing HEK293

tag: treatment

value: EcN

tag: time

value: 120 minutes


title: young-homo1_RNA-seq

description:
total RNA
Ikzf3 MT vs. WT.txt


title: ALLSIL_PHF6_siRNA2_repl1

city: Ghent

first: Kaat

last: Durinck

address: Corneel Heymanslaan 10

department: Biomolecular Medicine

country: Belgium

institute: Center for Medical Genetics

description: Gene expression 72h post-electroporation of ALLSIL T-ALL cells with PHF6 siRNA2, replicate 1

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >6 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25µl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 µl of 2x GEx Hybridization buffer HI-RPM was added to the fragmentation mixture and hybridized to the array for 17 hours at 65°C in a rotating  hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner with SureScan High-Resolution Technology using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3µm, Dye channel is set to Green).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-105_Dec08 and Grid: 041648_D_F_20120615) to obtain background subtracted and spatially detrended Processed Signal intensities. Normalization was performed using the VSN-package (Bioconductor) and background correction was performed during the normalization process, selecting those probes detecting at least a two-fold higher expression than the negative control probes of the array design in at least 60% of either treatment groups.

source_name: ALLSIL, PHF6 siRNA2, 96h, replicate 1

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100 ng RNA using the One-Color Low Input Quick Amp Labling kit (Agilent) according to the manufacturer's instructions, followed by miRNeasy column purification (Qiagen).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Cells were grown in RPMI supplemented with 20% fetal bovine serum, 1% glutamin and 1% penicilin/streptomycin

extract_protocol: Total RNA was harvested with the miRNeasy micro kit (Qiagen) with Dnase treatment on-column.

treatment_protocol: ALLSIL cells were electroporated with  control or PHF6 targeting siRNA and cells were harvested 96h post-electroporation

value: ALLSIL

value: PHF6 siRNA2

value: 96h post-electroporation


title: ALLSIL_PHF6_siRNA1_repl3

description: Gene expression 72h post-electroporation of ALLSIL T-ALL cells with PHF6 siRNA1, replicate 3

source_name: ALLSIL, PHF6 siRNA1, 96h, replicate 3

value: PHF6 siRNA1


title: young-homo2_RNA-seq

description:
total RNA
Ikzf3 MT vs. WT.txt


title: EcN at timepoint t1, biological repB

description: Gene expression data from HEK293 cells treated with flagellin of E. coli Nissle for 60min

source_name: TLR5 overexpressing human embryonic kidney cells (HEK293) treated with flagellin of E. coli Nissle (FliCEcN, acronym=EcN) for 60min (t1)

value: 60 minutes


title: mock control at timepoint t2, biological repC

description: Gene expression data from HEK293 cells treated with mock control for 120min

source_name: TLR5 overexpressing human embryonic kidney cells (HEK293) treated with mock control for 120min (t2)

value: mock control


title: EcN at timepoint t1, biological repA


title: CB_CD34pos_PHF6_shRNA_DLL1_donor3

description: Gene expression 72h post-transduction of lentivirally infected CB CD34pos cells with PHF6 shRNA cultured on OP9-DLL1, donor 3

source_name: CB CD34pos, PHF6 shRNA, 72h, DLL1, donor 3

growth_protocol: Transduced cells were cocultured on OP9-DLL1 for 72h supplemented with IL7, SCF and Flt3L

treatment_protocol: Primary cells were transduced with lentivirus of control or PHF6 hairpin, 24h after pre-culture. Cells were harvested 24 h after treatment to initiate co-cultures.

value: cord blood

tag: cell markers

value: CD34 positive

value: PHF6 shRNA

value: 72h co-culture on OP9-DLL1


title: ALLSIL_control_siRNA_repl1

description: Gene expression 72h post-electroporation of ALLSIL T-ALL cells with control siRNA, replicate 1

source_name: ALLSIL, control siRNA, 96h, replicate 1

value: control siRNA


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_D9_ad012

value: brain

value: RSP


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_D9_ad010

value: VISp

value: male


title: mock control at timepoint t2, biological repA

value: TLR5 overexpressing HEK293


title: mock control at timepoint t1, biological repC

description: Gene expression data from HEK293 cells treated with mock control for 60min

source_name: TLR5 overexpressing human embryonic kidney cells (HEK293) treated with mock control for 60min (t1)


title: CB_CD34pos_control_shRNA_DLL1_donor3

description: Gene expression 72h post-transduction of lentivirally infected CB CD34pos cells with control shRNA cultured on OP9-DLL1, donor 3

source_name: CB CD34pos, control shRNA, 72h, DLL1, donor 3

value: control shRNA


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_E10_ad007


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_D9_ad008

value: female


title: young-WT3_RNA-seq

description:
total RNA
Ikzf3 MT vs. WT.txt

value: Splenic B cell

value: wild type

value: 3 months


title: mock control at timepoint t1, biological repB

value: 60 minutes


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_D9_ad007


title: young-WT2_RNA-seq

description:
total RNA
Ikzf3 MT vs. WT.txt


title: ALLSIL_PHF6_siRNA1_repl1

description: Gene expression 72h post-electroporation of ALLSIL T-ALL cells with PHF6 siRNA1, replicate 1

source_name: ALLSIL, PHF6 siRNA1, 96h, replicate 1

value: ALLSIL

value: PHF6 siRNA1

value: 96h post-electroporation


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_D9_ad006

value: PTLp


title: young-WT1_RNA-seq

description:
total RNA
Ikzf3 MT vs. WT.txt


title: mock control at timepoint t2, biological repB

value: mock control

value: 120 minutes


title: PI Cell D (discarded)

city: Chicago

first: Daniel

last: Cavanaugh

state: IL

address: 1050 W Sheridan Rd., Life Sciences Building Room 215

department: Biology

institute: Loyola University Chicago

data_processing:
PolyA, adapter and low quality sequences were trimmed with Trim Galore (https://github.com/FelixKrueger/TrimGalore) and PRINSEQ.
Reads were mapped to Dmel Reference Genome (dm6) with RNA Star (33) in Galaxy (using the public Galaxy server at usegalaxy.org). Drosophila_melanogaster.BDGP6.87.gtf was used for the annotation file.
The aligned BAM files were processed with RNA Star to quantify the number of reads that mapped to each gene, and with MMQuant to determine reads mapping ambiguously to multiple genes.
Genome_build: dm6
Supplementary_files_format_and_content: Tab-delimited text files contain number of mapped reads per gene as quantified by RNA Star and MMquant.

organism: Drosophila melanogaster

source_name: Drosophila pars intercerebralis cell

extract_protocol:
Single-cell RNA was processed through three rounds of antisense RNA (aRNA) amplification
Libraries were made from the amplified aRNA using Illumina Truseq v2 reagents

tag: animal id

value: D

value: pars intercerebralis (PI) cells


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_D9_ad004

value: brain

value: VISp


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_D9_ad002

value: male


title: ESCCs, shTrp-M-387

first: Mirazul

last: Islam

address: D857A, Dana Farber Cancer Institute, 44 Binney St. Boston MA

department: Medical Oncology

institute: DFCI

data_processing:
Sequencing was performed using Illumina NextSeq500 and the read lengths were 75 bp.
Paired-end reads were aligned to the mouse genome mm9 using STAR 2.5.
Transcript expression quantification was performed using Cufflinks (v2.2.1).
Differential gene expression analysis was performed using the R package ‘DESeq2’.
Genome_build: mm9
Supplementary_files_format_and_content: Raw counts, csv

source_name: Mouse esophageal squamous cell carcinoma cells

extract_protocol:
Prior to cell isolation, all tools and solutions were autoclaved or filter sterilized. Mouse lungs were harvested and placed in cold DPBS, and were physically dissociated with scissors. To digest, dissociated tissues were mixed with 50ml of 1 mg/ml solution of collagenase type V (Sigma Aldrich, 9263), dissolved in prewarmed KSFM, and the mixture was stirred with a magnet for 20 min. at 37 oC. After digestion, the mixture was centrifuged twice at 1000 rpm for 5 min., resuspended in KSFM and plated on 10 cm cell culture dish. Cultured cells were washed with DPBS and replaced with new media every other day. After expansion, cells were trypsinized and flow cytometry sorted for YFP, and followed by western blotting to confirm p53 expression.  Total RNA was extracted with the RNAqueous kit (Invitrogen, AM1912).
cDNA was synthesized using Takara SmartSeq v4 reagnets from 1ng of total RNA. cDNA was fragmented by Covaris AFA to ~150bp and adapters ligated using Rubicon Thrulplex DNAseq library prep kit from 2ng of cDNA according to manufacturer's protocol.

value: Mixed background

value: Esophageal squamous cell carcinoma lung metastasis

value: Trp53R172H/- +shTrp53


title: ESCCs, shTrp-M-386

value: esophageal squamous cell carcinoma cells


title: CB_CD34pos_control_shRNA_DLL1_donor1

description: Gene expression 72h post-transduction of lentivirally infected CB CD34pos cells with control shRNA cultured on OP9-DLL1, donor 1

source_name: CB CD34pos, control shRNA, 72h, DLL1, donor 1

value: cord blood

value: CD34 positive

value: control shRNA

value: 72h co-culture on OP9-DLL1


title: CB_CD34pos_control_shRNA_DLL1_donor2

description: Gene expression 72h post-transduction of lentivirally infected CB CD34pos cells with control shRNA cultured on OP9-DLL1, donor 2

source_name: CB CD34pos, control shRNA, 72h, DLL1, donor 2


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_D9_ad001


title: CB_CD34pos_PHF6_shRNA_DLL1_donor2

description: Gene expression 72h post-transduction of lentivirally infected CB CD34pos cells with PHF6 shRNA cultured on OP9-DLL1, donor 2

source_name: CB CD34pos, PHF6 shRNA, 72h, DLL1, donor 2

value: PHF6 shRNA


title: PI Cell 2


title: ESCCs, shTrp-M-384


title: PI Cell 1


title: ESCCs, shCtrl-M-382

value: Trp53R172H/- +shCtrl


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_D8_ad010

value: RSP


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_D8_ad007


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_D8_ad008

value: female


title: ESCCs, shCtrl-M-378


title: PI Cell 3


title: PI Cell 4


title: ESCCs, shCtrl-M-377


title: ESCCs, shCtrl-M-383


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_D8_ad006

value: PTLp


title: CB_CD34pos_PHF6_shRNA_DLL1_donor1

description: Gene expression 72h post-transduction of lentivirally infected CB CD34pos cells with PHF6 shRNA cultured on OP9-DLL1, donor 1

source_name: CB CD34pos, PHF6 shRNA, 72h, DLL1, donor 1


title: DAPPL_Group_8_symmetric_modification

city: Baltimore

first: Heng

last: Zhu

state: Maryland

address: MRB 340, 733 N. Broadway

department: Pharmacology and Molecular Sciences

institute: Johns Hopkins School of Medicine

description:
synthesized oligonucleotides
virtual

data_processing:
All of the TF-captured sequences were partitioned by the TFs (via the TF barcodes).Using  R scripts which can download from https://github.com/HitTracy/DAPPL.
Since each TF was fused with GST, we first excluded the DNA binding activity contributed by the GST tag.Using  R scripts which can download from https://github.com/HitTracy/DAPPL.
The collection of the enriched 6-mers was used to construct the binding consensus sequences (i.e., motifs) using HOMER. Using  R scripts which can download from https://github.com/HitTracy/DAPPL.
Supplementary_files_format_and_content: Table files include bound sequences for every  TF

organism: synthetic construct

source_name: synthetic DNA

extract_protocol:
First, human proteins were purified as GST fusions and kept on glutathione beads. Second, each protein was covalently tethered to a single-stranded DNA (ssDNA) oligo (i.e., anchor oligo) through a thiol–maleimide “click” chemistry linkage; the anchor oligos of each protein were then annealed to the a unique barcode oligo, and converted to double-stranded DNA (dsDNA) with a DNA polymerization on beads. After removal of the free DNA oligos, an aliquot of beads for each barcoded protein was mixed together to generate a protein mixture. Third, a random N-mer dsDNA library was synthesized and capped by a BsaI restriction site to allow for proximity ligation and a fixed sequence (i.e., Primer 2) for PCR priming. Fourth, to carry out the DAPPL reactions, the N-mer DNA library was incubated with the barcoded protein bead mixture, followed by stringent washing steps to remove unbound DNA. After a crosslinking step, Golden Gate Assembly reactions were performed to ligate the DNA barcodes of the proteins to their captured DNA fragments.
The ligated DNA products were PCR-amplified with specific primers compatible with the Illumina NGS Systems to constructed the sequencing library.
DAPPL

tag: sample type

value: synthesized oligonucleotides


title: ESCCs, shTrp53

value: Esophagus


title: DAPPL_Group_7_symmetric_modification

description:
synthesized oligonucleotides
virtual


title: CB_CD34pos_control_shRNA_GFP_donor3

description: Gene expression 72h post-transduction of lentivirally infected CB CD34pos cells with control shRNA cultured on OP9-GFP, donor 3

source_name: CB CD34pos, control shRNA, 72h, GFP, donor 3

growth_protocol: Transduced cells were cocultured on OP9-GFP for 72h supplemented with IL7, SCF and Flt3L

treatment_protocol: Primary cells were transduced with lentivirus of control or PHF6 hairpin, 24h after pre-culture. Cells were harvested 24 h after treatment to initiate cocultures.

value: 72h co-culture on OP9-GFP


title: SlDof-8_3

city: Beijing

first: Yuying

last: Wang

address: No.20 Nanxincun, Xiangshan

country: China

institute: Institute of botany, the chinese academy of sciences

data_processing:
Illumina GA Pipeline v1.5 software used for basecalling.
Raw sequence reads were filtered for adaptor sequence, unknown base more than 10% and low-quaility reads, and filtered clean reads were then mapped to tomato whole genome using SOAPaligner/SOAP2 software.
Genome_build: ITAG, the International Tomato Annotation Group release version 2.5
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample .

organism: Solanum lycopersicum

source_name: fruit pericarp

extract_protocol:
Total RNA were isolated using SDS-phenol extraction method, from fruits pericarp which were frozen in liquid nitrogen immediately after harvest.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: development stage

value: 38 dpa

value: fruit pericarp

tag: genotype/variation

value: SlDof1 RNAi


title: SlDof-8_2


title: mock control at timepoint t1, biological repA

value: TLR5 overexpressing HEK293

value: mock control

value: 60 minutes


title: ESCCs, shCtrl-M-376

value: Mixed background

value: Esophageal squamous cell carcinoma lung metastasis

value: esophageal squamous cell carcinoma cells


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_D8_ad001

source_name: C57BL/6J P56 Mouse Brain

value: brain

value: VISp

value: male


title: DAPPL_Group_6_symmetric_modification

description:
synthesized oligonucleotides
virtual


title: CB_CD34pos_control_shRNA_GFP_donor2

description: Gene expression 72h post-transduction of lentivirally infected CB CD34pos cells with control shRNA cultured on OP9-GFP, donor 2

source_name: CB CD34pos, control shRNA, 72h, GFP, donor 2

value: cord blood

value: CD34 positive

value: control shRNA


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_D7_ad012

value: RSP

value: female


title: CB_CD34pos_PHF6_shRNA_GFP_donor2

description: Gene expression 72h post-transduction of lentivirally infected CB CD34pos cells with PHF6 shRNA cultured on OP9-GFP, donor 2

source_name: CB CD34pos, PHF6 shRNA, 72h, GFP, donor 2

value: PHF6 shRNA

value: 72h co-culture on OP9-GFP


title: CB_CD34pos_control_shRNA_GFP_donor1

description: Gene expression 72h post-transduction of lentivirally infected CB CD34pos cells with control shRNA cultured on OP9-GFP, donor 1

source_name: CB CD34pos, control shRNA, 72h, GFP, donor 1


title: CB_CD34pos_PHF6_shRNA_GFP_donor1

description: Gene expression 72h post-transduction of lentivirally infected CB CD34pos cells with PHF6 shRNA cultured on OP9-GFP, donor 1

source_name: CB CD34pos, PHF6 shRNA, 72h, GFP, donor 1


title: eys+/-; lrp5+/- eyes at 3.5 mpf

city: Indianapolis

first: Yoshikazu

last: Imanishi

state: Indiana

address: 1160 W Michigan Street

department: Department of Ophthalmology

institute: Indiana University School of Medicine

description: Gene expression data from eys+/-; lrp5+/- eyes at 3.5 mpf

hyb_protocol: Samples were hybridized using GeneChip Hybridization Kit materials • Heat cocktails at 99°for 5 minutes, then 45°for 5 minutes centrifuge at max speed for 1 minute. • Transfer 130μl of hyb solution to Zebrafish Gene 1.0 ST Arrays (ThermoFisher Scientific). • Hybridize 16 hours at 45° at 60rpm• Fluidics washing is FS450_0002.

scan_protocol: Arrays were scanned using GeneChip Scanner 3000 7G.

data_processing: The data were analyzed with Transcriptome Analysis Console 4.0 (qunatile normalization and RMA).

organism: Danio rerio

source_name: eys+/-; lrp5+/- eyes at 3.5 mpf

label_protocol: Single-stranded cDNA was generated from the amplified cRNA, fragmented and labeled with the WT PLUS Reagent Kit (ThermoFisher Scientific).

growth_protocol: The zebrafish were kept under 14 hr light/10 hr dark cycle at 28.5°C (standard condition).

extract_protocol: Total RNA was extracted with TRI Reagent (Merck) according to the manufacture’s instructions.

tag: Stage

value: 3.5 mpf

value: eyes

value: mixed sex


title: lrp5-/- eyes at 3.5 mpf

description: Gene expression data from lrp5-/- eyes at 3.5 mpf

source_name: lrp5-/- eyes at 3.5 mpf


title: eys-/- eyes at 3.5 mpf

description: Gene expression data from eys-/- eyes at 3.5 mpf

source_name: eys-/- eyes at 3.5 mpf

value: eys-/-


title: WT_3

value: 38 dpa

value: fruit pericarp

value: wild type


title: ESCCs, shCtrl

value: Mixed background

value: Esophagus

tag: cell type

value: esophageal squamous cell carcinoma cells

value: Trp53R172H/- +shCtrl


title: Wildtype eyes at 3.5 mpf

description: Gene expression data from wildtype eyes at 3.5 mpf

source_name: Wildtype eyes at 3.5 mpf

value: Wildtype


title: DAPPL_Group_5_symmetric_modification

description:
synthesized oligonucleotides
virtual

value: synthesized oligonucleotides


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_D7_ad007

tag: strain

value: brain

value: RSP

value: VISp

value: male


title: SlDof-8_1

value: SlDof1 RNAi


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_D7_ad008

value: female


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_D7_ad010


title: DAPPL_Group_4_symmetric_modification

description:
synthesized oligonucleotides
virtual


title: shMyb rep2

city: Charlottesville

first: Timothy

last: Bender

state: Virginia

address: 345 Crispell Dr. MR-6, RM #3707

institute: University of Virginia

data_processing:
Demultiplexing of the barcoded sequences was performed on line in BaseSpace.
Quality assessment of the sequencing reads was performed by running the FASTQC.
Fastq files were first quality filtered and then aligned to the mouse transcriptome mm10 using STAR followed by gene counting with HTSeq.
The count data were then imported into R-Bioconductor for differential expression analysis using DESeq2
Genome_build: mm10

source_name: Cell line

growth_protocol: Mouse Irf4/8-/- large pre-B cells were grown on an OP9 stromal cell layer in Opti-MEM, 10% FBS, 1% penicillin-streptomycin, 0.1% β-mercaptoethanol, and 10ng/ml IL-7.

extract_protocol:
Total cellular RNA was isolated using the TRIZOL reagent (Invitrogen) and purified using the Qiagen RNeasy Kit (Qiagen) by the manufacturer’s protocol.
Libraries were prepared with 1µg total RNA per sample using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England BioLab) following the manufacturer’s protocols.

treatment_protocol: Irf4/8-/- large pre-B cells were transduced with retroviruses that co-produce a GFP reporter and a Myb mRNA targeting shRNA (shMyb) or a a control Luciferase mRNA targeting shRNA (shLuc). Transductions were performed in duplicate sets of 12 wells of 24-well tissue culture plates per condition with 1 million cells per well in 1ml of Opti-MEM medium containing 10% FBS, 1% penicillin-streptomycin, 0.1% β-mercaptoethanol, 10ng/ml IL-7, and 8µg/ml polybrene. Post-transduction, cells were cultured for 72 hours in Opti-MEM, 10% FBS, 1% penicillin-streptomycin, 0.1% β-mercaptoethanol, and 10ng/ml IL-7. Transduced, GFP+ cells were electronically sorted on a BD Influx Cell Sorter.

tag: cell line genotype

value: large pre-B cell line

tag: treatment/variation

value: shMyb transduction


title: shMyb rep1


title: DAPPL_Group_3_symmetric_modification

description:
synthesized oligonucleotides
virtual


title: WT_2

value: 38 dpa

tag: tissue


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_D6_ad012

tag: age

tag: source


title: DAPPL_Group_2_symmetric_modification

description:
synthesized oligonucleotides
virtual


title: shLuc rep2

value: shLuc transduction


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_D7_ad004

value: PTLp

tag: target

tag: gender


title: DAPPL_Group_8_hemi_modification

description:
synthesized oligonucleotides
virtual


title: WT_1

value: fruit pericarp

value: wild type


title: shLuc rep1


title: WT-ChIP-3

data_processing:
Illumina GA Pipeline v1.5 software used for basecalling.
Raw sequence reads were filtered for adaptor sequence, unknown base more than 10% and low-quaility reads.
Filtered clean reads were mapped to tomato whole genome using SOAPaligner/SOAP2 software with parameter SOAPnuke filter -l 20 -q 0.5 -n 0.1 -i -c 25
Uniquely mapped reads were submitted to MACS Version 1.4.2 to call the enriched peaks with default parameter.
Genome_build: ITAG, the International Tomato Annotation Group release version 2.5
Supplementary_files_format_and_content: Wg files includes peak location, peak length, etc.

extract_protocol:
The enriched nuclei were sonicated to fragment DNA to 250-500 bp and the sheared chromatin was incubated with the anti-DOF1 antibody.The immunoprecipitated DNA and input DNA were purified with phenol/chloroform extraction.
Libraries was prepared for sequencing using standard Illumina protocols

tag: genotype

tag: antibody


title: DAPPL_Group_1_symmetric_modification

description:
synthesized oligonucleotides
virtual


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_D6_ad006


title: DAPPL_Group_7_hemi_modification

description:
synthesized oligonucleotides
virtual


title: DAPPL_Group_6_hemi_modification

description:
synthesized oligonucleotides
virtual


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_D6_ad007


title: WT-ChIP-1


title: WT-ChIP-2


title: DAPPL_Group_5_hemi_modification

description:
synthesized oligonucleotides
virtual


title: Input

value: input


title: Hepatocytes, CD302_M2

city: Hannover

first: Birthe

middle: Maren

last: Tegtmeyer

address: Feodor-Lynen-Str. 7

institute: TWINCORE - Centre for Experimental and Clinical Infection Research

description: hOChep Cd302-/-

data_processing:
Transcriptomic analyses were performed using CLC Genomics Workbench (Qiagen, Aarhaus)
Generated paired-end Fastq files were mapped against the mm9 mouse reference genome with annotated gene and mRNA tracks.
Gene expression was calculated for individual transcripts as reads per kilobase per million bases mapped (RPKM).
Genome_build: mm9
Supplementary_files_format_and_content: xlsx documents include total counts & RPKM values for each gene and each condition

source_name: hepatocytes

extract_protocol:
Total RNA from cells was extracted using a NucleoSpin RNA kit (Macherey-Nagel) according to the manufacturer’s instructions.
RNA sequencing library generated with ScriptSeq v2 RNA-Seq Library Preparation Kit (Epicentre, Illumina)

value: Cd302 knock out

tag: mouse id

value: hepatocytes


title: Hepatocytes, CD302_M3

description: hOChep Cd302-/-


title: DAPPL_Group_4_hemi_modification

description:
synthesized oligonucleotides
virtual

value: synthesized oligonucleotides


title: Hepatocytes, CD302_M1

description: hOChep Cd302-/-


title: Jurkat_PHF6_shRNA_repl3

description: Gene expression 72h post-transduction of lentivirally infected Jurkat T-ALL cells with PHF6 shRNA, replicate 3

source_name: Jurkat, PHF6 shRNA, 96h, replicate 3

growth_protocol: Cells were grown in RPMI supplemented with 10% fetal bovine serum, 1% glutamin and 1% penicilin/streptomycin

treatment_protocol: Jurkat cells were transduced with lentivirus for control or PHF6 hairpin, and cells were harvested 96h post-transduction

tag: cell line

value: Jurkat

tag: treatment

value: PHF6 shRNA

tag: time

value: 96h post-transduction


title: Hepatocytes, EFT_M6

description: hOChep


title: DAPPL_Group_2_hemi_modification

description:
synthesized oligonucleotides
virtual

tag: sample type


title: Hepatocytes, EFT_M5

description: hOChep


title: DAPPL_Group_3_hemi_modification

description:
synthesized oligonucleotides
virtual


title: DAPPL_Group_1_hemi_modification

description:
synthesized oligonucleotides
virtual


title: Hepatocytes, EFT_M4

description: hOChep


title: DAPPL_ETS Cyc1

description:
synthesized oligonucleotides
virtual


title: DAPPL_ETS Cyc2

description:
synthesized oligonucleotides
virtual


title: p1035906-7 [ngs-xyyeca3587_S3]

city: Oklahoma City

first: Courtney

middle: G

last: Montgomery

state: OK

address: 825 NE 13th St

department: Genes and Human Disease Research Program

institute: Oklahoma Medical Research Foundation

data_processing:
Single-cell libraries were processed with 10x Genomics cellranger informatics pipeline (v 3.0.2) with the count and aggr commands
Resulting count matrices output by cellranger aggr were generated with the Read10x function in Seurat v3.0.
genome build: GRCh38
processed data files format and content: RDS file, containing an R data object of the class "Seurat" following integration of control and sarcoid data: see https://satijalab.org/seurat/. The meta.data slot of the object contains 6 columns: donor (order sample is processed by cellranger aggr), library.id (sample subject name) , Barcode (10x Cell barcode identifier), celltype (the assigned cell type), classification (disease status for either Sarcoidosis or Control) and coordinates for the UMAP projection (UMAP_1, UMAP_2).
processed data files format and content: matrix_counts.mtx (Matrix market coordinate text file) containing raw scRNA-seq counts for genes for all cells (columns).
processed data files format and content: matrix_colData.txt (tab-delimited text file, the rows of which report information about cells in the order they are presented along columns in matrix_counts.mtx). The columns of this file contain 1) the column of the sparse matrix in matrix_counts.txt identifying the cell; 2) donor (order sample is processed by cellranger aggr);   3) library.id (sample subject name); 4) classification (whether the cell is classified as control or sarcoidosis), 5) celltype (the assigned cell type); 6) Barcode (10x Cell barcode identifier); 7 & 8) coordinates for the UMAP projection (UMAP_1, UMAP_2).
processed data files format and content: matrix_rowData.txt (tab-delimited text file, the rows of which report the genes in the order they are presented along rows in matrix_counts.mtx)

source_name: PBMC mixture

extract_protocol:
Peripheral blood mononuclear cells (PBMCs) and neutrophils (PMNs) were collected using LSM (Gibco) and Polymorphprep™ (Alere Technologies, Oslo, Norway). Fresh PBMCs (target 4,000/patient) and PMNs (target 1,000/patient) were combined and loaded at a concentration of 1000 cells/µL into a 10x Genomics Single Cell A v2 chip into the Chromium controller.
Following single cell emulsion generation, uniquely identifiable first strand template cDNA was generated by emulsion PCR and after emulsion was broken, the second cDNA strand was generated and Illumina compatible adapters were ligated.

tag: study classification

value: Control

tag: subject age

tag: subject sex

value: Male

tag: subject race

value: White

tag: active disease as defined by omrf sru

value: Non-active

tag: currently on any immunosuppressant

tag: currently on >20mg prednisone

tag: currently on biologics


title: Jurkat_scrambled_shRNA_repl3

description: Gene expression 96h post-transduction of lentivirally infected Jurkat T-ALL cells with scrambled shRNA, replicate 3

source_name: Jurkat, scrambled shRNA, 96h, replicate 3

value: scrambled shRNA


title: KO2

city: Research Triangle Park

first: Anton

middle: M

last: Jetten

state: NC

address: 111 TW Alexander Drive

department: DIR

institute: NIEHS, NIH

data_processing:
Raw reads were filtered to retain only those with average base quality score at least 20.
Adapter was trimmed from reads via cutadapt v1.2.1 (parameters: -a AGATCGGAAGAG -O 5 -q 0); only reads at least 30nt in length after trimming were retained.
ChIP-seq reads were aigned to mm10 via Bowtie v1.2 (parameters: -m 1), then deduplicated via MarkDuplicates.jar from the Picard tool suite v1.110.
ChIP-seq peaks were called via HOMER v4.9.1 (parameters: -style factor -fdr 0.00001), the re-sized to 200mers centered on the called peak midpoints.
For visualization, each uniquely-mapped non-duplicate ChIP-seq read was extended to estimated fragment length 200nt, converted to bedGraph format via BEDtools genomeCoverageBed (v2.24.0), normalized to 10M reads, then converted to bigWig format via UCSC utility bedGraphToBigWig.
RNA-seq read pairs were aligned to mm10 via STAR v2.5 (parameters: --alignSJoverhangMin 8 --limitBAMsortRAM 55000000000 --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical).
Read counts per gene were determined by Subread featureCounts v1.5.0-p1 (parameters: -s0 -Sfr -p).
Coverage tracks for the RNA-seq data were generated by STAR v2.5 (parameters: --outWigStrand Unstranded --outWigNorm None), normalized by DESeq2 size factors, then converted to bigWig format via UCSC utility bedGraphToBigWig.
Genome_build: mm10
Supplementary_files_format_and_content: normalized depth tracks in bigWig format; ChIP-seq peaks in BED format; RNAseq counts per gene in tab-delimited text format

source_name: mouse pancreatic islets

extract_protocol:
RNA was extracted using Trizol, followed by Purelink RNA micro kit purification and DNAse treatment according to manufacturer's protocol. For Chromatin, islets were snap frozen, and 6ug chromatin used for ChIP
standard protocols were followed to prepare Illumina Tru-Seq RNA library and Illumina Chip-seq library

treatment_protocol: Hand-picked mouse islets were used the same day as isolation with no additional treatment

tag: age

tag: chip antibody


title: Jurkat_PHF6_shRNA_repl2

description: Gene expression 72h post-transduction of lentivirally infected Jurkat T-ALL cells with PHF6 shRNA, replicate 2

source_name: Jurkat, PHF6 shRNA, 96h, replicate 2


title: KO3

tag: genotype


title: CAS_TF.sgNGN3.Low.Rep3

city: Durham

first: Charles

last: Gersbach

address: 101 Science Drive

department: Biomedical Engineering

institute: Duke University

description: Amplicon-seq (gRNA sequencing)

data_processing:
Library strategy: Amplicon-seq
FASTQ files were aligned to custom indexes using Bowtie 2 (Langmead and Salzberg, 2012) and further processed to extract gRNA counts
Differential gRNA abundance was determined using DESeq2 (Love et al., 2014)
Genome_build: custom index of gRNA library
Supplementary_files_format_and_content: Comma separated value files with gRNA label, protospacer sequence, raw counts, and DESeq2 results

source_name: TUBB3-2A-mCherry dCas9-2xVP64 iPSC

extract_protocol:
After sorting, genomic DNA was harvested with the DNeasy Blood and Tissue Kit (Qiagen 69506)
The gRNA libraries were amplified from each genomic DNA sample across 100 μL PCR reactions using Q5 hot start polymerase (NEB, M0493) with 1 μg of genomic DNA per reaction. The PCR amplification was done according to the manufacturer’s instructions, using 25 cycles at an annealing temperature of 60 °C

tag: cell type

value: induced pluripotent stem cell

tag: sorted bin

value: Low


title: CAS_TF.sgNGN3.High.Rep3

description: Amplicon-seq (gRNA sequencing)

value: High


title: Jurkat_scrambled_shRNA_repl2

description: Gene expression 96h post-transduction of lentivirally infected Jurkat T-ALL cells with scrambled shRNA, replicate 2

source_name: Jurkat, scrambled shRNA, 96h, replicate 2

tag: cell line


title: Jurkat_scrambled_shRNA_repl1

description: Gene expression 96h post-transduction of lentivirally infected Jurkat T-ALL cells with scrambled shRNA, replicate 1

source_name: Jurkat, scrambled shRNA, 96h, replicate 1

tag: treatment


title: p1035905-1 [ngs-r3te7ax5r6_S2]

value: Sarcoidosis

value: Black

value: Active


title: CAS_TF.sgNGN3.Unsort.Rep3

description: Amplicon-seq (gRNA sequencing)

value: Unsorted


title: p1035904-6 [ngs-771df6k2xy_S18]

value: Female


title: WT4


title: p1035903-3 [ngs-1591cr60ke_S1]


title: CAS_TF.sgNGN3.High.Rep2

description: Amplicon-seq (gRNA sequencing)


title: WT3


title: 1963F16: smRNA_set25nrde3_1

city: Mainz

first: Jan

last: Padeken

address: Ackermannweg 4

institute: Institute of Molecular Biology

data_processing:
Basecalling was performed using RTA v. 1.13.48.
Reads were aligned to the ce10 (WS220) genome assembly using the qAlign function from the QuasR R package (v. 3.2).
Adapter sequences were removed using the fastx_clipper and collapsed using the fastx_collapser functions implemented in the FASTX-Toolkit (http://hannonlab.cshl.edu/fastx_toolkit/).
The qCount function in the QuasR package was used to count reads overlapping the ce6 genome assembly split into fragments of 500bp.
Genome_build: ce10 (WS220)
Supplementary_files_format_and_content: Tab-delimited file. First column contains seqnames, followed by start and end position and columns contain raw counts of reads overlapping each fragment for each sample.

organism: Caenorhabditis elegans

source_name: early embryo

growth_protocol: RNA was isolated from early embryos (before bean stage) grown after L1 synchronization (60–65 h depending on each strain) in two independent biological replicates.

extract_protocol:
Small RNA purification from early embryos was performed using the Norgen Single Cell RNA purification kit (51800). Total small RNA was treated with 1 mlTAP (Lucigen) for 1h at 37°C, to allow sequencing of all small RNA species.
Library preparation including size selection was performed using the QiaSeq miRNA library. Single-end 50-bp reads were generated using an Illumina HiSeq 2500.

tag: strain

tag: tissue

value: early embryo


title: 1963F18: smRNA_set25nrde3_3


title: 1963F17: smRNA_set25nrde3_2


title: 1963F15: smRNA_met2nrde3_3


title: p1035902-2 [ngs-df1f5eak78_S17]

tag: study classification

value: Reject


title: p1035910-8 [ngs-36k43d31r6_S20]

tag: subject age


title: Jurkat_PHF6_shRNA_repl1

description: Gene expression 72h post-transduction of lentivirally infected Jurkat T-ALL cells with PHF6 shRNA, replicate 1

source_name: Jurkat, PHF6 shRNA, 96h, replicate 1

value: Jurkat

value: PHF6 shRNA

tag: time


title: WT2


title: CAS_TF.sgNGN3.Low.Rep2

description: Amplicon-seq (gRNA sequencing)


title: p1035898-1 [ngs-78k68xt4d9_S7]

value: Control

tag: subject sex

tag: subject race


title: KO1


title: CAS_TF.sgNGN3.Unsort.Rep2

description: Amplicon-seq (gRNA sequencing)


title: 1963F13: smRNA_met2nrde3_1


title: 1963F12: smRNA_nrde3_3


title: CAS_TF.sgNGN3.High.Rep1

description: Amplicon-seq (gRNA sequencing)


title: p1035897-5 [ngs-k2e14x8ak0_S5]

tag: active disease as defined by omrf sru

tag: currently on any immunosuppressant


title: Glis3-GFP

value: GFP (abcam ab290)


title: p1035894-7 [ngs-68582dtrdd_S16]

value: Male

tag: currently on >20mg prednisone

tag: currently on biologics


title: p1035892-3 [ngs-r0y7a6kcy9_S3]

value: White

value: Not Confirmed


title: CAS_TF.sgNGN3.Low.Rep1

description: Amplicon-seq (gRNA sequencing)

value: induced pluripotent stem cell


title: p1035891-0 [ngs-2ea1dytx89_S15]


title: 1963F10: smRNA_nrde3_1


title: Input

tag: age

tag: chip antibody


title: PiZ/Chop-/-.4

city: Napoli

first: Annamaria

last: Carissimo

address: via Castellino

country: Italy

institute: Tigem

data_processing:
reads were aligned to mouse genome using STAR
raw counts were quantified using HTSeq Count
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include raw counts

source_name: liver

extract_protocol:
Extraction of total RNA (n=4 for group) was performed according to the manufacturer's instructions (RNeasy Mini Kit Cat No./ID: 74106 (250), Quiagen). RNA extract was precisely quantified and mixed at 50ng/5 µL
Total RNA (100 ng) from each sample was prepared using QuantSeq 3'mRNA-Seq Library prep kit  (Lexogen, Vienna, Austria) according to manufacturer's instructions
The amplified fragmented cDNA of 300 bp in size were sequenced in single-end mode using the NextSeq500 (Illumina) with a read length of 75 bp

value: liver

value: 6 weeks

tag: genotype

value: PiZ/Chop-/-

tag: gender

value: male


title: p1035889-6 [ngs-888110d95k_S13]

value: Sarcoidosis

value: Non-active


title: PiZ/Chop-/-.2


title: 1963F9: smRNA_set25_3


title: PiZ/Chop-/-.3


title: 1963F14: smRNA_met2nrde3_2


title: CAS_TF.sgASCL1.High.Rep3

description: CAS_TF_sgASCL1_Screen_Rawcounts_DESeq2.csv

data_processing:
Library strategy: Amplicon-sequencing
FASTQ files were aligned to custom indexes using Bowtie 2 (Langmead and Salzberg, 2012) and further processed to extract gRNA counts
Differential gRNA abundance was determined using DESeq2 (Love et al., 2014)
Genome_build: custom index of gRNA library
Supplementary_files_format_and_content: Comma separated value files with gRNA label, protospacer sequence, raw counts, and DESeq2 results

tag: cell type

tag: sorted bin

value: High


title: CAS_TF.sgASCL1.Low.Rep3

value: Low


title: CAS_TF.sgNGN3.Unsort.Rep1

description: Amplicon-seq (gRNA sequencing)

value: Unsorted


title: WT1


title: CAS_TF.sgASCL1.Unsort.Rep3


title: PiZ/Chop-/-.1

tag: strain


title: 1963F7: smRNA_set25_1

tag: tissue

value: early embryo


title: 1963F8: smRNA_set25_2


title: p1035888-3 [ngs-a4x4d5ff8t_S2]

tag: study classification

value: Female


title: PiZ-4

value: PiZ


title: 1963F11: smRNA_nrde3_2


title: 1963F6: smRNA_met2_3


title: CAS_TF.sgASCL1.High.Rep2


title: p1035887-7 [ngs-2cr6rd5964_S1]

value: Reject

tag: subject age

value: Black


title: 1963F5: smRNA_met2_2


title: p1035890-6 [ngs-c625y92c43_S14]

value: White


title: PiZ-2


title: CAS_TF.sgASCL1.Unsort.Rep2


title: 1963F4: smRNA_met2_1


title: PiZ-1


title: CAS_TF.sgASCL1.High.Rep1


title: CAS_TF.sgASCL1.Low.Rep1


title: p1035860-1 [ngs-6301ec1y1e_S4]


title: D597A_with_siRNA_2

city: Shanghai

first: Ligang

state: Shanghai

address: 320 Yueyang Road

department: Shanghai Institutes for biological Sciences

institute: Chinese Academy of Sciences

data_processing:
The unique molecular identifier (UMI, 10-nt random sequence) added to the 5’ end of each read during library construction was removed and used as the read identity (ID) in the following analysis.
The adapter sequence at the 3’ end of the sequenced reads was removed with the FASTX program (version 0.0.14) (-l 1 -c).
Insert cDNAs that were either too short (less than 30 nt) or too long (more than 65 nt) were discarded. The remaining reads were mapped to the human genome (version hg38) using the STAR program with --outFilterMultimapScoreRange 1 --outFilterScoreMin 10 --outFilterMultimapNmax 1 (version 2.5.2b).
Reads that mapped to the same genomic position and had identical UMIs were categorized as PCR duplicates and then collapsed into a single read. All remaining reads after processing were regarded as “usable reads” and used to identify clusters.
Because the 3’ end of the insert cDNA was the RBP crosslinking site, clusters were identified based on the 5’ start position of usable reads using the iCount program with a 3-nt clustering window
Genome_build: Hg38
Supplementary_files_format_and_content: bed

source_name: HEK293 cell lines

growth_protocol: Lenti-X 293T (Clontech, Mountain View, CA, USA) cells were grown in Dulbecco’s modified Eagle’s medium (Clontech, Mountain View, CA, USA) with 10% fetal bovine serum (Gibco, Chagrin Falls, OH, USA)

extract_protocol: library construction were conducted according to SpyCLIP protocol

treatment_protocol: For production of the lentiviruses, Lenti-X 293T cells were transfected with a virus vector encoding an AGO protein as well as the VSVG and ΔR8.91 plasmids by using Lipofectamine 2000 (Invitrogen, Carlsbad, CA, USA). Lentiviruses were harvested 48 hr post-transfection. AGO-expressing Lenti-X 293T stable cell lines were generated by transduction with lentiviruses in the presence of 8 μg/ml polybrene (Sigma-Aldrich, St. Louis, MO, USA) overnight, followed by selection with 1 μg/ml puromycin (BBI, Shanghai, China) for 1 week. For induction of AGO protein expression, 1 ng/ml Dox (BBI, Shanghai, China) was added to the cell culture medium.

tag: cell line

tag: treatment

value: with siLMNA

tag: genotype/variation

value: AGO2 D597A mutant

tag: molecule subtype

value: AGO2 binding RNA


title: Harvest_Test_B [ngs-rcdea8xf4r_S2]

value: Control

tag: subject sex

tag: subject race

tag: active disease as defined by omrf sru

tag: currently on any immunosuppressant


title: Harvest_Test_A [ngs-aya5d3607a_S1]

tag: currently on >20mg prednisone

tag: currently on biologics


title: CAS_TF.sgASCL1.Unsort.Rep1

value: induced pluripotent stem cell

tag: genotype


title: 1963F3: smRNA_n2_3

value: N2 (Bristol)


title: 1963F2: smRNA_n2_2


title: AGO2_with_siRNA_2


title: RNAseq_T47D_TamR+sapitinib_rep3

city: Milwaukee

first: Victor

last: Jin

state: WI

address: 8701 Watertown Plank Rd

department: IHE

institute: Medical college of Wisconsin

data_processing:
All raw reads were mapped to HG19 reference genome by using tophat2.
raw bam files were further processed by samtools and picard
Differentail genes were identified by DESeq2
Genome_build: hg19
Supplementary_files_format_and_content: xlsx;Differentiated expression genes

growth_protocol: Human breast carcinoma cell lines MCF7 and T47D and their tamoxifen resistant (TR) cell lines were originated from Osborne et al (Osborne et al. 1994). MCF7 or T47D was cultured in RPMI-1640 supplemented with 10 % fetal bovine serum, 1% penicillin and streptomycin (pen/strep) until 90% confluent.

extract_protocol:
Total RNA was extracted by ZYMO Research Quick-RNA MiniPrep kit from the lysed 10 million of breast cancer cells in RNA Lysis Buffer, then removed most of gDNA with Spin-Away Filter. After that, the mixture of RNA was transferred with ethanol to Zymo-Spin IIICG column to remove trace DNA by DNase I on the column, then washed twice with RNA wash buffer followed by eluted with 50 μl DNase/RNase-free water.
RNA-seq library was prepared with NEBNext® Poly(A) mRNA Magnetic Isolation Module (NEB #E7490). Washed the Oligo dT Beads with RNA binding buffer incubated with total 1ug RNA to purify followed with washing by beads washing buffer. Then eluted mRNA with elution buffer and reverse transcripted. After that, the first and the second strand cDNA was synthesized with the synthesis reaction. After the purification of Double-stranded cDNA, do adaptor ligation and purification. Adaptor Ligated DNA was enriched by PCR followed by purification, then the DNA library was sequenced with Illumina HiSeq3000.

treatment_protocol: MCF7TR or T47DTR cells were cultured in phenol red free RPMI-1640 containing 10% charcoal-stripped FBS, 1% pen/strep and 100nM Tamoxifen (Sigma-Aldrich). Tamoxifen was replaced every 48 hours. All the cells were kept at cell culture incubator with 37 °C and 5% CO2 until they reach 90% confluence. The cells were treated with Sapitinib (AZD8931) at the concentrations at 0uM to 30uM, the gradient concentration is 5uM. Cells absorbance was recorded at day 1 and day 7.

tag: cell line background

tag: cell type

value: breast cancer cell line

tag: phenotype

value: tamoxifen resistant

tag: passages


title: D669A_without_siRNA

last: Wu

value: without siRNA

value: AGO2 D669A mutant


title: 1963F1: smRNA_n2_1

tag: strain

tag: tissue


title: CAS_TF.SingleFactor.Sublibrary.High.Rep3

description:
Amplicon-seq (gRNA sequencing)
CAS_TF_SingleFactor_Sublibrary_Rawcounts_DESeq2.csv

tag: sorted bin

value: High


title: PiZ-3

value: liver

tag: age

value: 6 weeks

tag: gender

value: male


title: D597A_without_siRNA

tag: cell line

tag: treatment

tag: genotype/variation

tag: molecule subtype


title: RNAseq_T47D_TamR+sapitinib_rep2


title: CAS_TF.SingleFactor.Sublibrary.Low.Rep3

value: Low


title: 1121F24: lin61_set25_eemb_20°C_rep3

data_processing:
Basecalling was performed using RTA v. 1.13.48.
Reads were aligned to the ce10(WS220) genome assembly using the qAlign function from the QuasR R package (v. 3.2) with the parameter "splicedAlignment = TRUE", which calls the SpliceMap aligner with default parameters.
Gene expression was quantified using WS220 annotations downloaded from UCSC. The qCount function in the QuasR package was used to count reads overlapping all annotated exons for each gene.
Genome_build: ce10 (WS220)
Supplementary_files_format_and_content: Tab-delimited file. First columns contain seqnames, start, end, width, strand information  following columns contain raw counts of reads overlapping each intervall for each sample.

extract_protocol:
Extraction of RNA was performed according to the WormBook protocol (Stiernagle, 2006). Total RNA was purified using RNeasy kit (QIAGEN 74104) including DNase treatment. Depletion of ribosomal RNA was done for 5 ľg of total RNA with Ribo-Zero Margnetic Gold Kit (Epicentre MRGZG12324) and further concentrated with RNA Clean & Concentrator kit (Zymo Research R1015) according to corresponding manufacturers instructions.
Libraries were prepared using the TruSeq Standard mRNA Library Prep Kit (Illumina, San Diego, CA, USA).

value: early embryo


title: 1121F23: lin61_set25_eemb_20°C_rep2


title: RNAseq_T47D_TamR+sapitinib_rep1


title: CAS_TF.SingleFactor.Sublibrary.Unsort.Rep3

value: Unsorted


title: CAS_TF.sgASCL1.Low.Rep2


title: 1121F22: lin61_set25_eemb_20°C_rep1


title: p1035865-5 [ngs-43txyd66at_S12]

tag: study classification

value: Sarcoidosis

tag: subject age

tag: subject sex

value: Male

tag: subject race

value: White

tag: active disease as defined by omrf sru

value: Active

tag: currently on any immunosuppressant


title: RNAseq_T47D_TamR_rep3

tag: cell line background

tag: cell type

tag: phenotype


title: CB_CD34pos_PHF6_shRNA_GFP_donor3

description: Gene expression 72h post-transduction of lentivirally infected CB CD34pos cells with PHF6 shRNA cultured on OP9-control, donor 3

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-105_Dec08 and Grid: 041648_D_F_20120615) to obtain background subtracted and spatially detrended Processed Signal intensities. Normalization was performed using the VSN-package (Bioconductor) and background correction was performed during the normalization process, selecting those probes detecting at least a two-fold higher expression than the negative control probes of the array design in at least 60% of either treatment groups.

source_name: CB CD34pos, PHF6 shRNA, 72h, GFP, donor 3

extract_protocol: Total RNA was harvested with the miRNeasy micro kit (Qiagen) with Dnase treatment on-column.

tag: tissue

value: cord blood

tag: cell markers

value: CD34 positive

value: PHF6 shRNA

tag: time

value: 72h co-culture on OP9-GFP


title: D669A_without_siRNA_input

value: without siRNA

value: input


title: CAS_TF.SingleFactor.Sublibrary.High.Rep2

value: induced pluripotent stem cell

tag: genotype

tag: sorted bin

value: High


title: D597A_without_siRNA_input

tag: cell line

tag: treatment

value: AGO2 D597A mutant


title: RNAseq_T47D_TamR_rep2

value: breast cancer cell line

value: tamoxifen resistant

tag: passages


title: 1121F20: lin61_met2_eemb_20°C_rep2

tag: strain

value: early embryo


title: AGO2_without_siRNA_input

tag: genotype/variation

tag: molecule subtype


title: RNAseq_T47D_TamR_rep1


title: 1121F19: lin61_met2_eemb_20°C_rep1


title: D597A_with_siRNA

value: AGO2 binding RNA


title: CAS_TF.SingleFactor.Sublibrary.Unsort.Rep2

value: Unsorted


title: CAS_TF.SingleFactor.Sublibrary.High.Rep1


title: CAS_TF.SingleFactor.Sublibrary.Low.Rep2

value: Low


title: 875F9: lin61_eemb_20°C_rep3


title: RNAseq_T47D_parental_rep2


title: AGO2_with_siRNA


title: CAS_TF.SingleFactor.Sublibrary.Low.Rep1


title: AGO2_without_siRNA


title: RNAseq_T47D_parental_rep1


title: 875F8: lin61_eemb_20°C_rep2


title: D597A_with_siRNA_input


title: CAS_TF.SingleFactor.Sublibrary.Unsort.Rep1


title: 875F7: lin61_eemb_20°C_rep1


title: AGO2_with_siRNA_input


title: RNAseq_MCF7L_TamR+sapitinib_rep3


title: 1121F18: nrde3_set25_eemb_20°C_rep3


title: CAS_TF.SingleFactor.High.Rep3

description:
Amplicon-seq (gRNA sequencing)
CAS_TF_SingleFactor_Screen_RawCounts_DESeq2.csv


title: 1121F21: lin61_met2_eemb_20°C_rep3


title: RNAseq_MCF7L_TamR+sapitinib_rep2


title: RNAseq_T47D_parental_rep3


title: CAS_TF.SingleFactor.Low.Rep3


title: 1121F17: nrde3_set25_eemb_20°C_rep2


title: RNAseq_MCF7L_TamR+sapitinib_rep1


title: RNAseq_MCF7L_TamR_rep3


title: 1121F16: nrde3_set25_eemb_20°C_rep1


title: CAS_TF.SingleFactor.Unsort.Rep3


title: 1121F15: nrde3_met2_eemb_20°C_rep3


title: CAS_TF.SingleFactor.Input.Rep3

source_name: TUBB3-2A-mCherry iPSC

value: Input


title: MCF7-AP-PD_rep2

first: Howard

last: MENG

state: Beijing

address: No.5 Yiheyuan Road Haidian District

department: School of Life Sciences

institute: Peking University

description: AP-seq PD rep2 in MCF7 cell

data_processing:
Library strategy: AP-seq
Cut adapter step: The raw FASTQ files are firstly but the sequencing adapters with cutadapt software with the following command: "cutadapt --times 1  -e 0.1  -O 3  --quality-cutoff 25  -m 50 -a  AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC  -A  AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT -o {read1.out}  -p {read2.out}  {read1.in}  {read2.in}"
Alignment step: After the cut adapter step, all the FASTQ files are mapped to the reference genome, hg38 for HEK293T and MCF7, mm10 for mESC, with bowtie2 aligner. And only record the best hit of alignment for each read.
BAM convert step:The alignment SAM results are converted to sorted BAM files with samtools software
Remove duplication step: The sorted BAM files are removed the PCR amplification bias with the PICARD MarkDuplicates command.
Peak calling step: The final AP site peak are generated by the macs2 software
Genome_build: mm10, hg38
Supplementary_files_format_and_content: The bigwig files are generated by the deeptools bamCoverage software with parameters as follows: "bamCoverage --bam {input} -o {output} -of bigwig --scaleFactor 1 --binSize 10  --normalizeUsing RPKM"

source_name: MCF-7 cells

growth_protocol: The HEK293T and MCF7 is separately cultivated in DMEM and MEM  with 10% FBS and 1% PS at 37°C cultivator with 5% CO2., while ESCs were cultured in the absence of feeder cells in DMEM supplemented with 15% mouse ESC (mESC)-screened fetal bovine serum, 2 mM l-glutamine, 1 mM sodium pyruvate, 1 mM nonessential amino acids, 0.1 mM 2-mercaptoethanol, and 1,000 U/mL murine LIF on 0.1% gelatin-coated tissue culture plastics at 37°C in humidified air with 5% CO2.

extract_protocol:
The human and mouse genome is extracted by Universal Genomic DNA Kit (CWbiotech, CW2298)from cultivated cells and was then digested to 200–500 bp with NEBNext dsDNA Fragmentase.
The fragmented genomic DNA was end repaired with NEBNext End Repair Module (NEB, E6050) and E. coli ligase was added to repair nicks in fragmented genomic DNA following NEBNext dA-Tailing Module (NEB, E6053) kit to add dA to the 3′ end of double-stranded DNA. Next is the AP labeling steps the following pull-down and Y adaptor ligation. Then the template is PCR amplified and sequenced on the Illumina HiSeq X Ten.

value: MCF-7 cells

value: breast derived epithelial cells

value: Wild Type

value: PD


title: MCF7-AP-Input_rep2

description: AP-seq Input rep2 in MCF7 cell


title: MCF7-AP-PD_rep1

description: AP-seq PD rep1 in MCF7 cell


title: MCF7-AP-Input_rep1

description: AP-seq Input rep1 in MCF7 cell


title: 1121F14: nrde3_met2_eemb_20°C_rep2


title: CAS_TF.SingleFactor.Low.Rep2


title: RNAseq_MCF7L_parental_rep3


title: CAS_TF.SingleFactor.Unsort.Rep2


title: RNAseq_MCF7L_TamR_rep1


title: 293T-AP-PD_rep2

description: AP-seq PD rep2 in HEK293T cell

source_name: HEK293T cells

value: HEK293T cells

value: embryonic kidney derived epithelial cells


title: 293T-AP-PD_rep1

description: AP-seq PD rep1 in HEK293T cell


title: RNAseq_MCF7L_parental_rep1


title: 1121F11: nrde3_eemb_20°C_rep2


title: CAS_TF.SingleFactor.Input.Rep2


title: 293T-AP-Input_rep2

description: AP-seq Input rep2 in HEK293T cell


title: 293T-AP-Input_rep1

description: AP-seq Input rep1 in HEK293T cell


title: RNAseq_MCF7L_parental_rep2


title: CAS_TF.SingleFactor.High.Rep1


title: 1121F10: nrde3_eemb_20°C_rep1


title: 875F15: N2_eemb_20°C_rep3

value: N2 (Bristol)


title: CAS_TF.SingleFactor.Low.Rep1

value: induced pluripotent stem cell


title: CAS_TF.SingleFactor.High.Rep2

value: High


title: HiC_T47DTamR+sapitinib_rep2

data_processing:
All raw reads were mapped to HG19 reference genome by using HiCUP.
HOMER (Heinz et al. 2010) was used to obtain HI-C interaction matrices with default parameters and 40Kb tiling window size.
The significant interactions (SIFs) were further mapped to promoter and distal regionsbased on UCSC RefSeq HG19 where the mapping definition was used in our previous studies (Gerrard et al, 2019; Zhou et al, 2019).
SIFs and P1D1/2 looping genes were compared by using an in-house python code to obtain DLGs
TopDom (Shin et al 2016) was used to identify TAD, boundary, and gap for intra-chromosomal interactions
Genome_build: hg19
Supplementary_files_format_and_content: xlsx;changed TADs files, differential gene loops

extract_protocol:
In situ Hi-C experiments were performed as described previously (Rao et al, 2015; Zhou et al, 2020). The breast cancer cells were crosslinked with 1% formaldehyde and lysed with ice cold lysis buffer (10mM Tris-Hcl pH 8.0, 10mM NaCl, 0.2 % NP-40, 1mM DTT) to collect nuclei. The pelleted nuclei were digested with 200 units of HINDIII (NEB, R3104L) at 37°C overnight. The restriction fragment overhangs were filled with biotin-labelled dATP (Life Technologies,19524-016) in a Klenow end-filling reaction. Four hundred units of T4 DNA Ligase (NEB, M0202) was added for ligation and samples were incubated for 4 h at room temperature with slow rotation.
The ligation products were purified, and the chromatin was sheared to a size of 300-500bp using Covaris sonicator (Covaris Woburn, MA). Dynabeads MyOne Streptavidin T1 beads (Life technologies, 65601) were used to pull down the Biotin-labelled DNA. The end repair, dA tailing was performed and ligated with Illumina TruSeq adapters to form the final Hi-C ligation products. Each Hi-C library was amplified with 12 cycles of PCR using Illumina primers. The Hi-C library was purified and then sequenced with Illumina HiSeq3000.

tag: restriction enzyme

value: HindIII


title: OW33_0.5% EtOH_HFHC_5_8_weeks

city: Boston

first: Olivia

last: Weeks

address: 77 Ave Louis Pasteur, New Research Building #458

institute: Brigham and Women's Hospital

description:
whole liver of each individual sibling was dissected into an independent tube and homogenized. Fish were treated with EtOH from 12 hpf - 5 dpf and raised in the absense of EtOH through adulthood.
diff_exp_deseq2_0pt5HFHCvsCtHFHC.csv
ADULT OW33

data_processing:
For larval RNAseq (13 dpf), reads were aligned to the GRCz10 reference assembly with the STAR aligner (v2.4, default parameters) and differential gene expression was performed with DESeq2 software (default parameters). Heatmap visualization and hierarchical clustering was performed using the R package pheatmap with the default parameters.
For the adult liver RNAseq, FASTQ files were analyzed using FASTQC to ensure uniform read quality (phred>30). Single end reads were aligned using Star v2.3 (default parameters) to the zebrafish genome (GRCz10). The mapped reads were counted using htseq-count (v0.6.0, parameters –t exon) and gene models from Ensembl transcriptome v89. Analysis of differential gene expression was performed using DESeq2 (default parameters).
Genome_build: GRCz10
Supplementary_files_format_and_content: .csv files containing gene names, raw read counts, and normalized read counts. For adult RNAseq, the differential gene expression analysis for manuscript-relevant pairwise comparisons are included.

growth_protocol: Larval zebrafish were housed on the nursery in 0.8L tanks with mesh baffles at a density of 32 fish per tank beginning at 5 dpf. At 5 dpf, fish received a paramecia starter culture and were kept overnight without flow. At 6 dpf, flow was initiated, and larvae were administered a specified diet. For larval RNA-seq studies, 6 dpf larvae were started on a normal or HFHC diet. Normal larval diet included hatched artemia two times per day at a density of ~8.8mg dry weight/fish. HFHC larval diet included the artemia plus a dietary supplement of 0.5g/tank of Hoosier Hill Farm Whole Egg Powder re-suspended in system water. All larvae were maintained on their diet until the point of collection (13 dpf) or grown until 30 dpf, during which time they were transferred from the nursery to the adult system. For adult studies, larvae were maintained on a normal larval diet until graduation from the nursery. Upon graduation from the nursery at ~30 days, juvenile fish were maintained at equal tank densities in 2.8L tanks and fed a standard artemia diet two times per day at a density of ~14.7mg dry weight/fish. Beginning at 65 dpf, fish were housed at a density of 12 fish/tank and fed a normal or HFHC diet. Adult normal diet consisted of 0.013 g/fish of Skretting Gemma Micro 300 feed per day (59% protein, 14% lipids, 14% ash, 8% moisture, 0.2% crude fiber, and 1.9% starch by mass). HFHC diet tanks received 0.063 g/fish of Skretting Gemma Micro 300 per day plus 0.02g/fish of Hoosier Hill Farm Whole Egg Powder (~49% lipids, ~49% protein, ~1.7% cholesterol).

extract_protocol:
RNA was extracted in TRIzol (Life Technologies) from whole pooled (15 individuals/sample) 13 dpf larvae or single livers isolated from WT (AB) fish and purified using the Qiagen RNeasy Mini Kit. RNA quality was verified on the Aligent Bioanalyzer and DNA contamination was removed with the TURBO DNA-free (Invitrogen) kit.
Single-end NextSeq Series High-Output RNA sequencing was performed on poly-A selected coding mRNAs at the Dana Farber Center for Cancer Computational Biology.

treatment_protocol: Zebrafish larvae were exposed to 0%, 0.5%, and 1.0% EtOH dissolved in fish water from 12 hpf – 5 dpf and administered the relevant diet as described under "growth parameters."

value: 0.5% EtOH

tag: diet

value: HFHC diet

value: AB

tag: developmental stage

value: Adult

value: homogenized dissected liver


title: OW32_0.5% EtOH_HFHC_4_8_weeks

description:
whole liver of each individual sibling was dissected into an independent tube and homogenized. Fish were treated with EtOH from 12 hpf - 5 dpf and raised in the absense of EtOH through adulthood.
diff_exp_deseq2_0pt5HFHCvsCtHFHC.csv
ADULT OW32


title: 1121F13: nrde3_met2_eemb_20°C_rep1

value: early embryo


title: RNAseq_MCF7L_TamR_rep2

tag: cell line background

value: breast cancer cell line

value: tamoxifen resistant


title: CAS_TF.SingleFactor.Unsort.Rep1

tag: cell type

value: Unsorted


title: 875F14: N2_eemb_20°C_rep2


title: 875F13: N2_eemb_20°C_rep1


title: HiC_MCF7LTamR+sapitinib_rep2

tag: phenotype


title: HiC_MCF7LTamR+sapitinib_rep1


title: 2080F18-2: lin61met2_H3K9me3_3

data_processing:
Basecalling was performed using RTA v. 1.13.48.
Reads were aligned to the ce10 (WS220) genome assembly using the qAlign function from the QuasR R package (v. 3.2).
The qCount function in the QuasR package was used to count reads overlapping the ce6 genome assembly split into fragments of 500bp.
Genome_build: ce10 (WS220)
Supplementary_files_format_and_content: Tab-delimited file. First column contains seqnames, followed by start and end position and columns contain raw counts of reads overlapping each fragment for each sample.

growth_protocol: chromatin was isolated from early embryos (before bean stage) grown after L1 synchronization (60–65 h depending on each strain) in two independent biological replicates.

extract_protocol:
ChIP experiments were performed as previously described (Zeller et al., 2016). In brief: Embryos were harvested from synchronized animals in three replicates. 40 μg of chromatin was incubated overnight with 3 μg of anti-LEM-2 antibody (Novus Biologicals) coupled to Dynabeads Sheep Anti-Rabbit IgG (Invitrogen), in FA buffer (50 mM HEPES/KOH pH 7.5, 1 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate, 150 mM NaCl)) containing 1% SDS. Antibody bound chromatin was washed 3 × 5 min FA buffer; 5 min FA buffer with 1 M NaCl; 10 min FA buffer with 500 mM NaCl; 5 min with TEL buffer (0.25 M LiCl, 1% NP-40, 1% sodium deoxycholate, 1 mM EDTA, 10 mM Tris-HCl, pH 8.0) and 2 × 5 min with TE. Complexes were eluted in 1% SDS in TE with 250 mM NaCl at 65°C for 15 min. Samples and inputs were treated with 20 μg of RNAse A for 30 min at 37°C and 20 μg of proteinase K for 1 hr at 55°C. Crosslinks were reversed by overnight incubation at 65°C. DNA was subsequently purified using Zymo DNA purification columns (Zymo Research).
Libraries were prepared from chromatin IP and input samples using the NEBNext ultra DNA library prep kit for Illumina (NEB # 7370) and the NEBNext Multiplex Oligos for Illumina (NEB # E7335), according to the manufacturers recommendations. No size selection was performed during sample preparation and the libraries were indexed and amplified using 12 PCR cycles, using the recommended conditions. After a final cleanup with Agencourt AmPure XP beads (Beckman # A63881), the library size distribution and concentrations were determined using a BioAnalyzer 2100 (Agilent technologies) and Qubit (Invitrogen) instrument, respectively. The final pools were prepared by mixing equimolar amounts of all individual indexed libraries and then sequenced on a HiSeq 2500 (Illumina) in Rapid mode (Paired-End 50).

tag: tissue


title: OW30_0.5% EtOH_HFHC_2_8_weeks

description:
whole liver of each individual sibling was dissected into an independent tube and homogenized. Fish were treated with EtOH from 12 hpf - 5 dpf and raised in the absense of EtOH through adulthood.
diff_exp_deseq2_0pt5HFHCvsCtHFHC.csv
ADULT OW30


title: CAS_TF.SingleFactor.Input.Rep1

value: Input


title: OW31_0.5% EtOH_HFHC_3_8_weeks

description:
whole liver of each individual sibling was dissected into an independent tube and homogenized. Fish were treated with EtOH from 12 hpf - 5 dpf and raised in the absense of EtOH through adulthood.
diff_exp_deseq2_0pt5HFHCvsCtHFHC.csv
ADULT OW31


title: HiC_MCF7L_parental_rep2


title: 1121F12: nrde3_eemb_20°C_rep3


title: OW29_0.5% EtOH_HFHC_1_8_weeks

description:
whole liver of each individual sibling was dissected into an independent tube and homogenized. Fish were treated with EtOH from 12 hpf - 5 dpf and raised in the absense of EtOH through adulthood.
diff_exp_deseq2_0pt5HFHCvsCtHFHC.csv
ADULT OW29


title: 5μMGSK343treatment_K562_5μMGSK343_MRR2A1_rep2_4Cseq

city: Singapore

first: Melissa

last: Fullwood

address: 14 Medical Drive

country: Singapore

institute: Cancer Science Institute

description: 4C experiment using a bait designed at MRR2-A1 region. This region is inside a H3K27me3-rich region (MRR2) and interacts with IGF2 gene promoter through HiC interactions.

data_processing:
Library strategy: 4C-seq
ChIP-seq reads of H3K27me3, H3K27ac and H3K4me3 from HAP1 WT and EZH2  KO cells were mapped by BOWTIE2(v2.2.5) using default parameters in  pair-end mode. We filtered out alignments with mapq scores smaller than 30. The  two replicates were combined and peaks and bigWig files were generated  by MACS2(2.1.0.20150731) using option '-q 0.01' for H3K27ac and  H3K4me3 and '--broad --broad-cutoff 0.1 -q 0.05' for H3K27me3.
For the RNA-seq reads of HAP1 EZH2KO/WT and K562 GSK343/DMSO, we first trimmed off adaptors by trimmomatic (0.38) using option ILLUMINACLIP:TruSeq3-PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36. Only those paired-end reads that remained properly paired would be then mapped to the hg19 reference GTF file using kallisto(0.44.0) with option '-b 100'. Differentially expressed genes were called using sleuth(0.29.0) with gene-level aggregation and wald test.
For 4C reads, we trimmed off the HINDIII digestion site using tagdust(2.33). The remaining read 1s were mapped by BOWTIE2(v2.2.5) with option '--end-to-end' in single-end mode. r3Cseq(1.24.0) was used to call interactions against the HINDIII digested genome background in hg19.
Genome_build: hg19
Supplementary_files_format_and_content: *.narrowPeak: ENCODE narrowPeak format generated by MACS2.
*.broadPeak: ENCODE broadPeak format generated by MACS2.
*_abundance.tsv: *_abundances.tsv is a plaintext file of the abundance estimates generated by Kallisto. Fields contained: 1. target_id. Transcript ID; 2. length. Transcript length; 3. eff_length. Effective length of the transcript; 4. est_counts. Estimated read counts given by the bootstrapping process of Kallisto; 5. tpm. Esmated transcript per million (TPM).
*interaction.txt: *.interaction.txt is the output generated by R3Cseq package. Field contained: 1. chromosome. Chromosome name; 2. start. Start of the fragment; 3. end. End of the fragment; 4. nReads. Number of reads mapped to this fragment; 5. RPMs. Reads per million per restriction fragment (RPM) as normalized interaction frequency values; 6. p.value. P value of this fragment interact with the 4C bait; 7. q.value. Q value of this fragment interact with the 4C bait.

source_name: K562 cells treated with 5μM GSK343

growth_protocol: Cell cultures were maintained at 37 °C, 5% CO2 humidified incubator.

extract_protocol:
Briefly, 4 × 107 cells were cross-linked with 1% formaldehyde. The nuclei pellets were isolated by cell lysis with cold lysis buffer (10mM Tris-HCl, 10mM NaCl, 5mM EDTA, 0.5% NP 40) supplemented with protease inhibitors (Roche). First step digestion was performed overnight at 37°C with HindIII enzyme (NEB). Digestion efficiency was measured by RT-qPCR with HindIII site–specific primers. After confirmation of good digestion efficiency, DNA was ligated overnight at 16°C by T4 DNA ligase (Thermo Scientific) and de-crosslinked. Following de-crosslinking, DNA was extracted by phenol-chloroform. The DNA was then processed for second digestion with DpnII enzyme (NEB) overnight at 37°C. After final ligation, 4C template DNA was obtained and the concentration was determined using Qubit assays (Thermo Scientific).
The 4C template DNA was then amplified using specific primers with illumina Nextera adapters and sent for sequencing on the MiSeq system.

treatment_protocol: Small molecular inhibitor GSK343 (Sigma-Aldrich) targeting EZH2 were solubilized in DMSO (Sigma-Aldrich) according to manufacturer’s instructions and used at a final concentration of 5μM. K562 cells with GSK343 were incubated at 37 °C, 5% CO2 humidified incubator for 48 hours before harvesting for various experiments.

value: K562 cell line

value: 5μM GSK343


title: 5μMGSK343treatment_K562_5μMGSK343_MRR2A1_rep1_4Cseq


title: HiC_MCF7L_parental_rep1


title: HiC_T47DTamR+sapitinib_rep1


title: 5μMGSK343treatment_K562_5μMGSK343_MRR1A1_rep2_4Cseq

description: 4C experiment using a bait designed at MRR1-A1 region. This region is inside a H3K27me3-rich region (MRR1) and interacts with FGF18 gene promoter through HiC interactions.


title: 2080F17-2: lin61met2_H3K9me3_2


title: p1035907-9

tag: study classification

value: Control

tag: subject age

tag: subject sex

value: Female

tag: subject race

value: White

tag: active disease as defined by omrf sru

value: Non-active

tag: currently on any immunosuppressant

tag: currently on >20mg prednisone

tag: currently on biologics


title: 5μMGSK343treatment_K562_5μMGSK343_MRR1A1_rep1_4Cseq

tag: cell line

tag: treatment


title: p1035906-7

value: Male


title: OW27_0.5% EtOH_ND_5_8_weeks

description:
whole liver of each individual sibling was dissected into an independent tube and homogenized. Fish were treated with EtOH from 12 hpf - 5 dpf and raised in the absense of EtOH through adulthood.
diff_exp_deseq2_0pt5NDvsCtND.csv
ADULT OW27

value: 0.5% EtOH

value: normal

tag: strain


title: OW24_0.5% EtOH_ND_2_8_weeks

description:
whole liver of each individual sibling was dissected into an independent tube and homogenized. Fish were treated with EtOH from 12 hpf - 5 dpf and raised in the absense of EtOH through adulthood.
diff_exp_deseq2_0pt5NDvsCtND.csv
ADULT OW24

tag: diet

value: AB


title: OW23_0.5% EtOH_ND_1_8_weeks

description:
whole liver of each individual sibling was dissected into an independent tube and homogenized. Fish were treated with EtOH from 12 hpf - 5 dpf and raised in the absense of EtOH through adulthood.
diff_exp_deseq2_0pt5NDvsCtND.csv
ADULT OW23

tag: developmental stage

value: Adult


title: 5μMGSK343treatment_K562_5μMGSK343_FGF18_rep2_4Cseq


title: 5μMGSK343treatment_K562_5μMGSK343_IGF2_rep1_4Cseq


title: p1035898-1

value: Black


title: 2080F15-2: lin61met2_input_3

value: early embryo


title: 2080F16-1: lin61met2_H3K9me3_1


title: OW25_0.5% EtOH_ND_3_8_weeks

description:
whole liver of each individual sibling was dissected into an independent tube and homogenized. Fish were treated with EtOH from 12 hpf - 5 dpf and raised in the absense of EtOH through adulthood.
diff_exp_deseq2_0pt5NDvsCtND.csv
ADULT OW25

value: homogenized dissected liver


title: p1035903-3


title: 5μMGSK343treatment_K562_5μMGSK343_FGF18_rep1_4Cseq


title: 2080F18-1: lin61met2_H3K9me3_3


title: OW22_1% EtOH_HFHC_5_8_weeks

description:
whole liver of each individual sibling was dissected into an independent tube and homogenized. Fish were treated with EtOH from 12 hpf - 5 dpf and raised in the absense of EtOH through adulthood.
diff_exp_deseq2_1HFHCvsCtHFHC.csv
ADULT OW22

value: 1% EtOH

value: HFHC diet


title: p1035855-7


title: p1035869-3


title: OW21_1% EtOH_HFHC_4_8_weeks

description:
whole liver of each individual sibling was dissected into an independent tube and homogenized. Fish were treated with EtOH from 12 hpf - 5 dpf and raised in the absense of EtOH through adulthood.
diff_exp_deseq2_1HFHCvsCtHFHC.csv
ADULT OW21


title: 2080F15-1: lin61met2_input_3


title: 5μMGSK343treatment_K562_DMSO_MRR2A1_rep2_4Cseq

source_name: K562 cells treated with DMSO

treatment_protocol: K562 cells with DMSO vehicle control were incubated at 37 °C, 5% CO2 humidified incubator for 48 hours before harvesting for various experiments.

value: DMSO


title: p1035822-1

source_name: PBMC mixture


title: 2080F17-1: lin61met2_H3K9me3_2


title: 2080F14-2: lin61met2_input_2


title: OW20_1% EtOH_HFHC_3_8_weeks

description:
whole liver of each individual sibling was dissected into an independent tube and homogenized. Fish were treated with EtOH from 12 hpf - 5 dpf and raised in the absense of EtOH through adulthood.
diff_exp_deseq2_1HFHCvsCtHFHC.csv
ADULT OW20


title: OW26_0.5% EtOH_ND_4_8_weeks

description:
whole liver of each individual sibling was dissected into an independent tube and homogenized. Fish were treated with EtOH from 12 hpf - 5 dpf and raised in the absense of EtOH through adulthood.
diff_exp_deseq2_0pt5NDvsCtND.csv
ADULT OW26


title: 5μMGSK343treatment_K562_DMSO_MRR2A1_rep1_4Cseq

value: K562 cell line


title: 2080F14-1: lin61met2_input_2


title: OW19_1% EtOH_HFHC_2_8_weeks

description:
whole liver of each individual sibling was dissected into an independent tube and homogenized. Fish were treated with EtOH from 12 hpf - 5 dpf and raised in the absense of EtOH through adulthood.
diff_exp_deseq2_1HFHCvsCtHFHC.csv
ADULT OW19


title: 2080F16-2: lin61met2_H3K9me3_1


title: OW18_1% EtOH_HFHC_1_8_weeks

description:
whole liver of each individual sibling was dissected into an independent tube and homogenized. Fish were treated with EtOH from 12 hpf - 5 dpf and raised in the absense of EtOH through adulthood.
diff_exp_deseq2_1HFHCvsCtHFHC.csv
ADULT OW18


title: 5μMGSK343treatment_K562_5μMGSK343_IGF2_rep2_4Cseq

value: 5μM GSK343


title: p1035905-1

value: Sarcoidosis

value: Active


title: 5μMGSK343treatment_K562_DMSO_IGF2_rep2_4Cseq


title: p1035868-6

value: Reject

value: Female

value: White


title: 5μMGSK343treatment_K562_DMSO_MRR1A1_rep2_4Cseq


title: 5μMGSK343treatment_K562_DMSO_MRR1A1_rep1_4Cseq


title: OW16_1% EtOH_ND_5_8_weeks

description:
whole liver of each individual sibling was dissected into an independent tube and homogenized. Fish were treated with EtOH from 12 hpf - 5 dpf and raised in the absense of EtOH through adulthood.
diff_exp_deseq2_1NDvsCtND.csv
ADULT OW16


title: p1035872-2

value: Non-active


title: 2080F13-1: lin61met2_input_1


title: 2080F12-2: lin61_H3K9me3_3


title: 2080F13-2: lin61met2_input_1


title: 2080F11-2: lin61_H3K9me3_2


title: OW15_1% EtOH_ND_4_8_weeks

description:
whole liver of each individual sibling was dissected into an independent tube and homogenized. Fish were treated with EtOH from 12 hpf - 5 dpf and raised in the absense of EtOH through adulthood.
diff_exp_deseq2_1NDvsCtND.csv
ADULT OW15

value: normal


title: p1035861-7


title: p1035871-4


title: 5μMGSK343treatment_K562_DMSO_IGF2_rep1_4Cseq


title: 2080F10-2: lin61_H3K9me3_1


title: p1035858-8

value: Male


title: OW14_1% EtOH_ND_3_8_weeks

description:
whole liver of each individual sibling was dissected into an independent tube and homogenized. Fish were treated with EtOH from 12 hpf - 5 dpf and raised in the absense of EtOH through adulthood.
diff_exp_deseq2_1NDvsCtND.csv
ADULT OW14

value: AB

value: Adult


title: 5μMGSK343treatment_K562_DMSO_FGF18_rep2_4Cseq


title: OW11_CT_HFHC_6_8_weeks

description:
whole liver of each individual sibling was dissected into an independent tube and homogenized. Fish were treated with EtOH from 12 hpf - 5 dpf and raised in the absense of EtOH through adulthood.
diff_exp_deseq2_1HFHCvsCtHFHC.csv
ADULT OW11

value: 0% EtOH


title: OW13_1% EtOH_ND_2_8_weeks

description:
whole liver of each individual sibling was dissected into an independent tube and homogenized. Fish were treated with EtOH from 12 hpf - 5 dpf and raised in the absense of EtOH through adulthood.
diff_exp_deseq2_1NDvsCtND.csv
ADULT OW13

value: homogenized dissected liver


title: p1035859-0


title: 2080F11-1: lin61_H3K9me3_2

value: early embryo


title: OW12_1% EtOH_ND_1_8_weeks

description:
whole liver of each individual sibling was dissected into an independent tube and homogenized. Fish were treated with EtOH from 12 hpf - 5 dpf and raised in the absense of EtOH through adulthood.
diff_exp_deseq2_1NDvsCtND.csv
ADULT OW12

value: 1% EtOH


title: 5μMGSK343treatment_K562_DMSO_FGF18_rep1_4Cseq

value: DMSO


title: 2080F10-1: lin61_H3K9me3_1


title: p1035857-4


title: 2080F12-1: lin61_H3K9me3_3


title: CS_dissection

city: Koto-ku

first: Osamu

last: Gotoh

state: Tokyo

address: Ariake 3-8-31

country: Japan

institute: Japanese Foundation For Cancer Research

data_processing:
Library strategy: TCR-seq
Demultiplexing, alignment, filtering, and annotation was performed by iRepertoire (http://www.irepertoire.com) using a proprietary pipeline.
Raw files were submitted to SRA without demultiplexing.  This is required for use with the iRepertoire protocol.
Genome_build: IMGT database
Supplementary_files_format_and_content: TCR CDR3 nucleotide and amino acid sequences, and V-D-J gene segment usage lists generated by iRepertoire.

source_name: uterine carcinosarcoma

extract_protocol:
Total RNA was extracted using RNeasy Micro kit (Qiagen).
The CDR3 region of the T-cell receptor (TCR) chain was amplified using the iRepertoire multiplex primer set (HTBI-M; iRepertoire, Huntsville, AL, USA) following the manufacturer’s instructions. The Qiagen OneStep RT-PCR kit (Qiagen, Valencia, CA, USA) was used for reverse transcription. Amplification and library preparation were performed with the iR-Processor and iRock 2.0 (iRepertoire, Huntsville, AL, USA).  Paired-end sequencing was performed on the purified libraries using the Illumina MiSeq v2 500-cycle Reagent Kit (Illumina, San Diego, CA, USA).

tag: anatomical site

value: uterus

tag: Sex

value: female

tag: age


title: OW9_CT_HFHC_4_8_weeks

description:
whole liver of each individual sibling was dissected into an independent tube and homogenized. Fish were treated with EtOH from 12 hpf - 5 dpf and raised in the absense of EtOH through adulthood.
diff_exp_deseq2_1HFHCvsCtHFHC.csv
ADULT OW9

value: HFHC diet

tag: tissue


title: 2080F9-2: lin61_input_3


title: CS_bulk_f


title: OW6_CT_HFHC_1_8_weeks

description:
whole liver of each individual sibling was dissected into an independent tube and homogenized. Fish were treated with EtOH from 12 hpf - 5 dpf and raised in the absense of EtOH through adulthood.
diff_exp_deseq2_1HFHCvsCtHFHC.csv
ADULT OW6


title: p1035852-6

tag: study classification

value: Sarcoidosis


title: CS_bulk_b


title: OW8_CT_HFHC_3_8_weeks

description:
whole liver of each individual sibling was dissected into an independent tube and homogenized. Fish were treated with EtOH from 12 hpf - 5 dpf and raised in the absense of EtOH through adulthood.
diff_exp_deseq2_1HFHCvsCtHFHC.csv
ADULT OW8


title: CS_bulk_e


title: 2080F7-2: lin61_input_1


title: p1035864-0

tag: subject age

value: Native American


title: CS_bulk_d

source_name: uterine or ovarian carcinosarcoma

value: ovary or uterus


title: 2080F7-1: lin61_input_1


title: 2080F9-1: lin61_input_3


title: OW7_CT_HFHC_2_8_weeks

description:
whole liver of each individual sibling was dissected into an independent tube and homogenized. Fish were treated with EtOH from 12 hpf - 5 dpf and raised in the absense of EtOH through adulthood.
diff_exp_deseq2_1HFHCvsCtHFHC.csv
ADULT OW7


title: 2080F8-2: lin61_input_2


title: CS_bulk_c


title: 2080F8-1: lin61_input_2


title: OW3_CT_ND_3_8_weeks

description:
whole liver of each individual sibling was dissected into an independent tube and homogenized. Fish were treated with EtOH from 12 hpf - 5 dpf and raised in the absense of EtOH through adulthood.
diff_exp_deseq2_1NDvsCtND.csv
ADULT OW3


title: OW5_CT_ND_5_8_weeks

description:
whole liver of each individual sibling was dissected into an independent tube and homogenized. Fish were treated with EtOH from 12 hpf - 5 dpf and raised in the absense of EtOH through adulthood.
diff_exp_deseq2_1NDvsCtND.csv
ADULT OW5


title: p1035849-2

tag: subject sex

value: Female

value: Black

value: Active


title: CS_bulk_g


title: CS_bulk_a


title: p1035846-3

tag: subject race


title: OW4_CT_ND_4_8_weeks

description:
whole liver of each individual sibling was dissected into an independent tube and homogenized. Fish were treated with EtOH from 12 hpf - 5 dpf and raised in the absense of EtOH through adulthood.
diff_exp_deseq2_1NDvsCtND.csv
ADULT OW4

value: normal


title: p1035845-9

value: White

tag: active disease as defined by omrf sru

value: Non-active


title: OW2_CT_ND_2_8_weeks

description:
whole liver of each individual sibling was dissected into an independent tube and homogenized. Fish were treated with EtOH from 12 hpf - 5 dpf and raised in the absense of EtOH through adulthood.
diff_exp_deseq2_1NDvsCtND.csv
ADULT OW2

value: 0% EtOH

value: AB

value: Adult


title: p1035851-9

value: Male

tag: currently on any immunosuppressant


title: 2236F21-2: met2nrde3_H3k9me3_3

value: early embryo


title: p1035843-7

tag: currently on >20mg prednisone


title: p1035850-3

tag: currently on biologics


title: p1035836-9


title: 2236F19-2: met2nrde3_H3k9me3_1


title: OW1_CT_ND_1_8_weeks

description:
whole liver of each individual sibling was dissected into an independent tube and homogenized. Fish were treated with EtOH from 12 hpf - 5 dpf and raised in the absense of EtOH through adulthood.
diff_exp_deseq2_1NDvsCtND.csv
ADULT OW1

value: homogenized dissected liver


title: 2236F20-1: met2nrde3_H3k9me3_2


title: p1035837-6


title: 2236F20-2: met2nrde3_H3k9me3_2


title: OW17_1% EtOH_HFHC_13dpf_2

description:
whole larvae (siblings) of mixed sizes were combined into three independent tubes/group and homogenized. Embryos were treated with EtOH from 12 hpf - 5 dpf.
20180702_OGWFAE_raw.data.csv
20180702_OGWFAE_TPM.csv
OW17

source_name: whole zebrafish larvae

value: 1% EtOH

value: 13 dpf

value: homogenized whole animals


title: PETRI_rep2

city: Tokyo

first: Stéphane

last: Poulain

address: Fw-203, 4-6-1, Komaba, Meguro-ku

department: Institute of Industrial Science

institute: The University of Tokyo

data_processing:
Basecalls performed using CASAVA.
Demultiplexing, filtering, mapping and molecule assembly were performed with the MOIRAI pipeline OP-WORKFLOW-CAGEscan-short-reads-v2.1 (Hasegawa et al., BMC Bioinformatics, 2014. doi: 10.1186/1471-2105-15-144).
Conversion from single pairs in BAM format to single pairs in BED12 format was done with https://github.com/Population-Transcriptomics/pairedBamToBed12
Assembly of single pairs in BED12 format to single molecules in BED12 format was done with https://github.com/mmendez12/umicount
CAGE peaks were called and gene expression tables generated using the CAGEr package (Haberle et al., Nucleic Acids Research, 2015. doi: 10.1093/nar/gkv054).
Genome_build: hg38
Supplementary_files_format_and_content: BED12 files, one RNA molecule per line; the score indicates how many read pairs were used to assemble the molecule.

source_name: induced Pluripotent Stem Cells (iPSC)

growth_protocol: Human iPSCs were cultured in biochips according to the protocol described by Danoy et al., Biotechnol Bioeng., 2019 (doi: 10.1002/bit.26970) using a new biochip design and applying an extended oncostatin stimulation period. Petri dishes cultures were performed following the protocol described by Si-Tayeb et al., Hepatology, 2010 (doi: 10.1002/hep.23354).

extract_protocol:
Total RNA was harvested using Trizol reagent. 250ng of total RNA from each sample were used for the construction of the sequencing libraries.
NanoCAGE sequencing libraries were prepared according to the protocol described by Poulain et al., Methods in Molecular Biology, 2017 (doi: 10.1007/978-1-4939-6716-2_4).

tag: cell type

value: induced pluripotent stem cells (hiPSCs) differentiated into hepatocyte-like cells (HLCs)

tag: cell culture type

value: Petri

tag: cell differentation stage

value: Hepato-Like Cells (HLC)

tag: nanocage template-switching oligo barcode sequence

value: ATCATA

tag: nanocage template-switching oligo barcode number


title: OW18_1% EtOH_HFHC_13dpf_3

description:
whole larvae (siblings) of mixed sizes were combined into three independent tubes/group and homogenized. Embryos were treated with EtOH from 12 hpf - 5 dpf.
20180702_OGWFAE_raw.data.csv
20180702_OGWFAE_TPM.csv
OW18

tag: treatment

tag: diet

value: HFHC diet

tag: strain

tag: developmental stage


title: p1035835-3

data_processing:
Single-cell libraries were processed with 10x Genomics cellranger informatics pipeline (v 3.0.2) with the count and aggr commands
Resulting count matrices output by cellranger aggr were generated with the Read10x function in Seurat v3.0.
genome build: GRCh38
processed data files format and content: RDS file, containing an R data object of the class "Seurat" following integration of control and sarcoid data: see https://satijalab.org/seurat/. The meta.data slot of the object contains 6 columns: donor (order sample is processed by cellranger aggr), library.id (sample subject name) , Barcode (10x Cell barcode identifier), celltype (the assigned cell type), classification (disease status for either Sarcoidosis or Control) and coordinates for the UMAP projection (UMAP_1, UMAP_2).
processed data files format and content: matrix_counts.mtx (Matrix market coordinate text file) containing raw scRNA-seq counts for genes for all cells (columns).
processed data files format and content: matrix_colData.txt (tab-delimited text file, the rows of which report information about cells in the order they are presented along columns in matrix_counts.mtx). The columns of this file contain 1) the column of the sparse matrix in matrix_counts.txt identifying the cell; 2) donor (order sample is processed by cellranger aggr);   3) library.id (sample subject name); 4) classification (whether the cell is classified as control or sarcoidosis), 5) celltype (the assigned cell type); 6) Barcode (10x Cell barcode identifier); 7 & 8) coordinates for the UMAP projection (UMAP_1, UMAP_2).
processed data files format and content: matrix_rowData.txt (tab-delimited text file, the rows of which report the genes in the order they are presented along rows in matrix_counts.mtx)

tag: study classification

value: Sarcoidosis

value: Female

value: Active


title: p1035827-8

tag: subject age

value: White

value: Non-active


title: OW15_CT_HFHC_13dpf_3

description:
whole larvae (siblings) of mixed sizes were combined into three independent tubes/group and homogenized. Embryos were treated with EtOH from 12 hpf - 5 dpf.
20180702_OGWFAE_raw.data.csv
20180702_OGWFAE_TPM.csv
OW15

value: 0% EtOH

value: AB

tag: tissue


title: PETRI_rep1

value: ACATGA


title: p1035838-2

tag: subject sex

value: Male

tag: subject race


title: PETRI_rep3

value: CACGTG


title: 2236F19-1: met2nrde3_H3k9me3_1

value: early embryo


title: 2236F21-1: met2nrde3_H3k9me3_3


title: 2236F18-2: nrde3_H3K9me3_3


title: OW14_CT_HFHC_13dpf_2

description:
whole larvae (siblings) of mixed sizes were combined into three independent tubes/group and homogenized. Embryos were treated with EtOH from 12 hpf - 5 dpf.
20180702_OGWFAE_raw.data.csv
20180702_OGWFAE_TPM.csv
OW14

value: 13 dpf

value: homogenized whole animals


title: 2236F18-1: nrde3_H3K9me3_3


title: OW13_CT_HFHC_13dpf_1

description:
whole larvae (siblings) of mixed sizes were combined into three independent tubes/group and homogenized. Embryos were treated with EtOH from 12 hpf - 5 dpf.
20180702_OGWFAE_raw.data.csv
20180702_OGWFAE_TPM.csv
OW13


title: p1035816-2

tag: active disease as defined by omrf sru

tag: currently on any immunosuppressant


title: 4TGFB_6dwithdrawn_Rep1

city: Waco

first: Joe

last: Taube

state: Texas

address: One Bear Place #97388

institute: Baylor University

description: 4d +TGFB, 6d -TGFB MCF10A mRNA

data_processing:
Adapter sequences and bases with lower quality than three removed using Trimmomatic (Galaxy Version 0.38.0).
Bases of reads less than window size 4, mean quality 15 were trimmed using Trimmomatic (Galaxy Version 0.38.0).
Reads trimmed to 36 bp using Trimmomatic (Galaxy Version 0.38.0).
Aligned to reference genome UCSC hg19 with HISAT2 (Galaxy Version 2.1.0+galaxy5)
Known genes assembled via StringTie (Galaxy Version 1.3.6)
Genome_build: hg19

source_name: MCF10A cells

growth_protocol: Cells were plated at 10,000 cells/mm^2 and treated with TGFB.  Cell density was maintained every other day and media was removed and replenished with TGFB

extract_protocol:
Cells lysed in TriZol reagent and phenol/chloroform extracted
Illumina TruSeq Stranded mRNA LT Sample Prep Kit

treatment_protocol: 5 ng/mL TGFB in 4 mM HCL with 0.01% BSA

value: 4d +TGFB, 6d -TGFB MCF10A mRNA


title: 4TGFB_10dwithdrawn_Rep1

description: 4d +TGFB, 10d -TGFB MCF10A mRNA

value: 4d +TGFB, 10d -TGFB MCF10A mRNA


title: p1035819-1

extract_protocol:
Peripheral blood mononuclear cells (PBMCs) and neutrophils (PMNs) were collected using LSM (Gibco) and Polymorphprep™ (Alere Technologies, Oslo, Norway). Fresh PBMCs (target 4,000/patient) and PMNs (target 1,000/patient) were combined and loaded at a concentration of 1000 cells/µL into a 10x Genomics Single Cell A v2 chip into the Chromium controller.
Following single cell emulsion generation, uniquely identifiable first strand template cDNA was generated by emulsion PCR and after emulsion was broken, the second cDNA strand was generated and Illumina compatible adapters were ligated.

tag: currently on >20mg prednisone

tag: currently on biologics


title: OW12_1% EtOH_ND_13dpf_3

description:
whole larvae (siblings) of mixed sizes were combined into three independent tubes/group and homogenized. Embryos were treated with EtOH from 12 hpf - 5 dpf.
20180702_OGWFAE_raw.data.csv
20180702_OGWFAE_TPM.csv
OW12

value: 1% EtOH

value: normal


title: 4TGFB_4dwithdrawn_Rep1

description: 4d +TGFB, 4d -TGFB MCF10A mRNA

value: 4d +TGFB, 4d -TGFB MCF10A mRNA


title: 2236F17-2: nrde3_H3K9me3_2


title: p1035814-3

value: Reject

value: Native American


title: p1035813-6

value: Sarcoidosis

value: Female

value: White