title: Cin-S replicate 1

description:
Cin-S_1
counts_RAW.tsv
counts_TPM_normalized.tsv
countsProteinCoding_TPM_normalized.tsv
counts_medianOfRatiosNormalized.tsv
countsProteinCoding_medianOfRatiosNormalized.tsv
DifferentialExpression_Cin-S_vs_Con-B.tsv
DifferentialExpression_RiboMinus_vs_Cin-S.tsv


title: TILAC_293t_500nMFP_s6GFP_s4UCntl_Rep1

status: Public on Aug 04 2022

type: SRA

city: West Haven

first: Matthew

last: Simon

state: Connecticut

address: PO Box 27392

department: Molecular Biophysics and Biochemistry

country: USA

institute: Yale University

description: Reads filtered for number of T-to-C mutations (0-5+), G-to-A mutations (0-5+) and strandedness (min/pos)

library_source: transcriptomic

data_processing:
Reads were filtered for unique sequences using FastUniq
Reads were trimmed using cutadapt (--minimum-length=20)
Reads were aligned to the GRCh38 genome or dm6 genome using HISAT2 aligned with default parameters and --mp 4,2 .
Reads were processed using Picard tools, including FixMateInformation, SortSam and BuildBamIndex
Reads were filtered for those that aligned uniquely (flag: 83/163, 99/147), with MAPQ ≥ 2, and without insertions.
HTSeq-count was used to identify mapped reads in UCSC transcripts (union mode)
T-to-C and G-to-A mutations were identified using Rsamtools and a custom R script (available upon request). Only mutations at positions with a base quality score of greater than 45 that were at least three nt from the end of the read were counted.
SNP sites were filtered from our data in two ways: 1, bcftools was used to identify T-to-C and G-to-A SNP sites in control samples, and these sites were excluded from analysis; 2, sites exhibiting high T-to-C or G-to-A mutation rates in non-s4U treated controls were excluded from analysis.
To examine the distribution of reads with each minimum number of T-to-C or G-to-A mutations, bam files were filtered using Picard tools.
STAR aligner was used to make genome-coverage tracks (inputAlignmentsFromBam mode, outWigType bedGraph).
Tracks were converted to binary format using IGVtools (toTDF).
Genome_build: GRCh38 or dm6
Supplementary_files_format_and_content: TDF

molecule: total RNA

organism: Homo sapiens

source_name: Human embryonic kidney 293T cells

growth_protocol: 293T were grown in Dulbecco’s Modified Essential Media supplemented with 10% fetal bovine serum (Gibco) and Pen/Strep (50 U/ml). S2 cells were grown in Dulbecco’s Modified Essential Media supplemented with 10% fetal bovine serum (Gibco) and Pen/Strep (50 U/ml). 293T cell cultures were maintained at 37℃. S2 cell cultures were maintained at 27℃.

extract_protocol:
RNA was harvested by two different protocols. For normal RNA sequencing, cells were resuspended in Trizol reagent, followed by chloroform extraction and isopropanol precipitation of the RNA. Genomic DNA was depleted using Turbo DNAse, followed by cleanup with RNAclean beads. Total RNA was treated with oxidative-nucleophilic-aromatic-substitution chemistry as described in Schofield et al. Nature Methods 2018 and Kiefer et al. Journal of the American Chemical Society 2018. To isolate RNA from untreated polysome fractions, each fraction went through 1 phenol:chlorofom isoamyl alcohol extraction and 2 chloroform extractions. RNA was isopropanol precipitated, fractions were combined, and genomic DNA was depleted using Turbo DNase, followed by cleanup with RNAclean beads. Polysome-associated RNA was treated with oxidative-nucleophilic-aromatic-substitution chemistry as described in Schofield et al. Nature Methods 2018 and Kiefer et al. Journal of the American Chemical Society 2018. To isolate RNA from stressed polysome fractions, each fraction was ethanol precipitated, resuspended and fractions were combined, and then samples were TRIzol extracted.  Genomic DNA was depleted using Turbo DNase, followed by cleanup with RNAclean beads. Total RNA was treated with oxidative-nucleophilic-aromatic-substitution chemistry as described in Schofield et al. Nature Methods 2018 and Kiefer et al. Journal of the American Chemical Society 2018.
RNA sequencing libraries were generated following standard protocols using the SMARTer Stranded Total RNA-Seq Kit-Pico Input Mammalian, V2 (Takara Bio USA, cat. 634413).

treatment_protocol: S2 cells were heat shocked at 37℃ for 1 hour minutes and 100uM s4U, 100uM s6G, or control water and DMSO for 45 minutes. 293T cells were treated with 500nM flavopiridol or DMSO control for 2 hour and 100uM s4U or 100uM s6G or water and DMSO control 2 hours. Or 293T cells were treated with 100uM s4U, 100uM s6G or water and DMSO control for 4 hours. Cell lysates were treated +/- 2mM puromycin on ice for 20 minutes, and then at 37℃ for 20 minutes.

tag: cell line

tag: genotype

value: WT

tag: s4u feed

value: Yes

tag: s6g feed

tag: molecule subtype

value: total RNA


title: Methylation_450k_sample7

type: genomic

city: Ann Arbor

first: Lulu

last: Shang

state: Michigan

address: 1415 Washington Heights

department: Biostatistics

institute: University of Michigan

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to IIllumina Infinium HumanMethylation450 BeadChip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: For each chip, the Minfi R package was used to perform background correction and normalization. The regression on correlated probes (RCP) method was then used to adjust probe-type bias.

label: Cy5 and Cy3

molecule: genomic DNA

source_name: peripheral blood leukocytes

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted from stored peripheral blood leukocytes using AutoGen FlexStar (AutoGen, Holliston, MA) and DNA was bisulfite converted using the EZ DNA Methylation Kit (Zymo Research, Irvine, CA)

tag: race

value: African American (AA)

tag: gender

value: M

tag: age(yrs)

tag: plate

tag: column

tag: row

value: D

tag: pedigreeid

tag: subjectid

tag: phase


title: TILAC_293t_500nMFP_s4UFP

value: No


title: Methylation_450k_sample6

value: F

value: A


title: PD1mid TIL RNAseq 3

city: Pittsburgh

first: B. Rhodes

last: Ford

state: PA

address: 4401 Penn Ave.

department: Department of Pediatrics

institute: University of Pittsburgh

description:
TPM_TIL_LN_VVova.csv
TIL_PD1mid_rep3

data_processing:
trimmed high quality reads were aligned to genome using HISAT2
Transcripts per Million (TPMs) calculated using Subread
Differentially expressed genes (DEG) determined using DEseq2 with cutoffs of 2 fold and padj<0.05
Genome_build: mm10 ensembl
Supplementary_files_format_and_content: Transcripts per Million (TPM) file, normalized counts

organism: Mus musculus

source_name: B16 melanoma tumor

growth_protocol: Mice were injected intradermally with 2.5 × 105 B16 melanoma cells. Mice were sacrificed and dLN and TIL harvested on day 14, when tumors were typically 8-10 mm in diameter.

extract_protocol:
CD8 T cells were isolated from tumors by surgical excision followed by flow sorting. cDNA was prepared from ~1,000 cells using the SMART-seq v4 Ultra Low Input RNA Kit for Sequencing
Libraries were prepared using the Nextera XT DNA Library Preparation kit. Libraries were denatured and diluted using the NextSeq 500 protocol Revision D.Cluster generation and 75-bp paired-end, dual-indexed sequencing were performed on the Illumina NextSeq 500.

treatment_protocol: In immunotherapy experiments, when tumors were palpable (typically day 5), mice began anti-PD-1, anti-4-1BB, or isotype control therapy. Mice were treated with 200 μg of anti-PD-1, 200 μg of anti-4-1BB, or equivalent isotype control intraperitoneally three times per week for the duration of the experiment.

tag: cell type

value: CD8+ T cell

tag: disease state

value: B16 melanoma

tag: treatment

tag: timepoint

value: Day 14 post-tumor

tag: sorting scheme


title: PD1mid TIL RNAseq 2

description:
TPM_TIL_LN_VVova.csv
TIL_PD1mid_rep2


title: Methylation_450k_sample4

value: H


title: Thymus

city: Gainesville

first: John

middle: P.

last: Driver

state: FL

address: 2250 Shealy Dr

institute: University of Florida

data_processing:
The 10X Genomics Cell Ranger (v3.1) program was used to process the raw sequence data, demultiplex raw base call files into FASTQ files, align the reads to the Sscrofa 11.1 reference genome, and generate count matrices. The filtered gene-barcode matrix was read using Seurat (v3.1). Quality control was processed by removing genes expressed in fewer than 3 cells, excluding cells with very few genes or aberrantly high genes and high mitochondrial gene expression.
Genome_build: Sscrofa 11.1
Supplementary_files_format_and_content: barcodes.tsv, features.tsv, matrix.mtx files.

organism: Sus scrofa

source_name: Thymus

extract_protocol:
Total thymocytes were isolated from two 22-week-old mix-breed pigs. iNKT cells were purified from same thymi through positive selection using magnetic beads. FACS sorted live total thymocytes and iNKT thymocytes from both pigs were respectively combined and used for sequencing.
Single-cell sequencing libraries were generated using the 10X Genomics Chromium Single Cell 3’ Reagent Kit (v3.1 Chemistry) following manufacturer’s protocol. Libraries were sequenced using a NovaSeq 6000 sequencer (Illumina).

tag: breed

value: mixed

tag: age

value: 22 weeks

value: total thymocytes

value: untreated


title: Methylation_450k_sample11


title: TILAC_293t_500nMFP_s4UFP_s6GCntl_Rep1

tag: cell line

tag: genotype

value: WT

tag: s4u feed

tag: s6g feed

tag: molecule subtype


title: PD1mid TIL RNAseq 1

description:
TPM_TIL_LN_VVova.csv
TIL_PD1mid_rep1


title: iNKT

value: iNKT thymocytes


title: foxh1MO_AC_RNAseq_rep2

city: Irvine

first: Ken

last: Cho

address: University of California, Irvine

institute: University of California, Irvine

data_processing:
The multiplexed libraries were sequenced on the Novaseq 6000. The version of Novaseq control software was NVCS ver 1.7.0 with real time analysis software, RTA 3.4.4.
reads were aligned to Xenopus tropicalis v10.0 genome (Xenbase) using STAR v2.7.3a
RSEM v1.3.3 was used to calculate raw counts and expression values in transcripts per million (TPM)
differential expression analysis was performed using edgeR v3.36.0 in R v4.1.2
Assembly: Xenopus tropicalis v10.0 genome
Supplementary files format and content: raw count values and TPM values for each sample is included
Supplementary files format and content: output file for differential gene expression analysis using edgeR is included

organism: Xenopus tropicalis

source_name: Xenopus tropicalis animal cap explant, Foxh1 MO, st10.5

growth_protocol: All embryos were cultured in 1/9X Marc’s modified Ringers (MMR) at 25C.

extract_protocol:
For RNA-seq, total RNA from dissected animal cap explants was extracted using Trizol as described (Amin et al., 2014). mRNA was then isolated using NEBNext PolyA mRNA Magnetic Isolation Module (NEB E7490S).
Sequencing libraries were prepared using NEBNext Ultra II RNA library prep kit (NEB E7770S)

treatment_protocol: For Foxh1 morpholino (MO) experiments, injections were performed at the 1-cell stage. A total of 22.5 ng of foxh1 MO (Chiu et al., 2014) or standard control MO (Genetools) was used.

tag: tissue

value: animal cap explant

tag: Stage

value: wildtype

value: Foxh1 morpholino injection


title: ctlMO_AC_RNAseq_rep2

source_name: Xenopus tropicalis animal cap explant, control MO, st10.5

value: control morpholino injection


title: PD1lo TIL RNAseq 3

description:
TPM_TIL_LN_VVova.csv
TIL_PD1lo_rep3


title: foxh1MO_AC_RNAseq_rep1


title: Methylation_450k_sample3

tag: race

value: African American (AA)

tag: gender

tag: age(yrs)

tag: plate

tag: column

tag: row

value: B

tag: pedigreeid


title: PD1lo TIL RNAseq 2

description:
TPM_TIL_LN_VVova.csv
TIL_PD1lo_rep2

tag: cell type

tag: disease state

tag: treatment

tag: timepoint

tag: sorting scheme


title: ctlMO_AC_RNAseq_rep1

tag: genotype


title: Deaths 3

status: Public on Aug 03 2022

type: RNA

city: São Paulo

first: Talita

middle: Souza

last: Siqueira

state: São Paulo

address: Galvão Bueno, 868 - Liberdade

department: Interdisciplinary Post-Graduate Program in Health Sciences

country: Brazil

institute: Cruzeiro do Sul University

description: Death

data_processing: Matrix non-normalized: Data were recorded with a QuantStudio 3 device and analyzed using the QuantStudio 3 Design and Analysis Software v1.5.1 (Thermo).                                                                 Matrix normalized: The global mean normalization method was used to normalize the miRNA PCR array data. Initially, data were calibrated by spiking samples with the exogenous control cel-miR-39. Then the global mean of the CT was calculated for the miRNA targets commonly expressed in all samples and presented a CT<30, Due to the dilution in the pre-amplification step, samples with CT above 30 were excluded. The 2-∆∆CT (where -ΔCt = -(Ct_Target − Ct_global mean) calculation determined the relationship between the miRNA target CT and global CT.  Fold change data = mean survivor/mean death

label: SYBR Green

source_name: Plasma from a septic patient who death

label_protocol: The miRNA's quantity and purity were assessed spectrophotometrically at 260/280 nm using a NanoDrop 2000 spectrophotometer (Thermo). Complementary DNA (cDNA) was synthesized using the miScript II RT kit (Qiagen) with 1.5 μL of miRNA (final reaction volume=10 μL) in a LongGene MG96G thermal cycler (LongGene, Zhejiang, Hangzhou, China).   Pre-amplified miScript miRNA Quality Control PCR Array (Qiagen) plates were included to verify the quality and integrity of the samples. Pre-amplification was performed using the miScript PreAMP PCR kit (Qiagen) with 5 µL of cDNA. The pre-amplified cDNA was diluted 20-fold and stored at -80°C.  For the PCR array analysis, 12.5 µL SYBR Green PCR Master Mix, 2.5 µL Universal Prime (10×), 9 µL RNase water-free and 1 µL pre-amplified cDNA (total volume=25 µL) was added to each well of the miRNA PCR Array plate. The plate was centrifuged at 1,000×g for one minute at room temperature. Data were recorded with a QuantStudio 3 device and analyzed using the QuantStudio 3 Design and Analysis Software v1.5.1 (Thermo).

extract_protocol: The miRNA from three randomly selected samples from the survivor and death groups was extracted using the miRNeasy Serum/Plasma kit (Qiagen,Hilden, Düsseldorf, Germany )

value: M

tag: age


title: Deaths 1

description: Death


title: Methylation_450k_sample1

value: A

tag: subjectid

tag: phase


title: Combined water deficit and heat stress replicate 2

city: Columbia

first: Sidharth

last: Sen

state: Missouri

address: Agriculture Bldg, University of Missouri

department: The Division of Plant Sciences and Technology

institute: University of Missouri

data_processing:
Sequencing, and bioinformatic analyses were performed by Novogene, Inc.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to G_max V2.1 whole genome using Hisat2 V2.2.1
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Trapnell et al., Nature Biotechnology, 20110.
Genome_build: Glycine_max_v2.1.51
Supplementary_files_format_and_content: Matrix tables for raw counts & FPKM values for all samples

organism: Glycine max

source_name: Buds

growth_protocol: Soybean (Glycine max, cv Magellan) seeds were inoculated with Bradyrhizobium japonicum inoculum  and germinated in Promix under short day growth condition (12-h light/12-h dark), 500 μmol photons m-2 s-1, at 28/24 ℃ day/night temperature for a week in growth chambers BDR16, Conviron. After a week, seedlings from trays were transplanted into pots containing 1 kg of Promix HP soaked in 1 l of water-fertilizer, Zack’s classic blossom booster 10-30-20. Plants were then grown for the next 16-18 days (until start of first open flower, R1 developmental stage) under 28/24 ℃ day/night temperatures as above, but the light intensity (12-h light/12-h dark photoperiod) was increased to 1000 μmol photons m-2 s-1. Plants were fertilized twice a week.

extract_protocol:
Soybean flowers (Stage II and III, from R2 plants) were collected from plants and immediately frozen in liquid nitrogen. About 30-40 flowers were pooled together from 8-10 different plants for each biological repeat and total RNA was isolated using Qigen Plant RNeasy mini kit.
RNA libraries for sequencing were prepared using standard Illumina protocols.

treatment_protocol: At R1 developmental stage, plants in the WD and WD+HS treatments were supplied with 30% of the water available for transpiration, while plants in the CT and HS treatments were well watered. Plants in the HS and WD+HS treatments were further subjected to HS 38 °C.

tag: tissue

value: Buds

tag: cultivar

value: Magellan


title: Methylation_450k_sample5

tag: race

tag: gender

value: F

value: C


title: Deaths 2

description: Death


title: Survivor 3

description: Survivor

source_name: Plasma from a septic patient who survived


title: Combined water deficit and heat stress replicate 3


title: Survivor 2

description: Survivor


title: Heat stress soybean bud replicate 3

value: Heat stress


title: Methylation_450k_sample2

tag: age(yrs)

tag: plate

value: G


title: Combined water deficit and heat stress replicate 1


title: Heat stress soybean bud replicate 1


title: PD1lo TIL RNAseq 1

description:
TPM_TIL_LN_VVova.csv
TIL_PD1lo_rep1

value: CD8+ T cell

value: B16 melanoma

value: Day 14 post-tumor


title: Water deficit soybean bud replicate 3

value: Water deficit


title: Control soybean bud replicate 3

value: Control


title: Survivor 1

description: Survivor


title: Control soybean bud replicate 1


title: Water deficit soybean bud replicate 2


title: Control soybean bud replicate 2


title: sgScd2/sgIrf9 (n=4)

city: Kisarazu

first: Toshio

last: Kanno

state: Chiba

address: 2-6-7 Kazusa-kamatari

country: Japan

institute: KAZUSA DNA Research Institute

data_processing:
For RNA-sequence, read sequences (75 bp) were aligned to the mm10 mouse reference genome (University of California, Santa Cruz (UCSC) December 2011) using STAR (version 2.7.9a).
Fragments per kilobase of transcripts for each gene were calculated using Subread (version 2.0.1, 13 ).
Assembly: mm10 mouse reference genome (University of California, Santa Cruz (UCSC) December 2011)
Supplementary files format and content: Text files include TPM values for each Sample

source_name: Spleen

growth_protocol: See "description".

extract_protocol:
Total cellular RNA was extracted with TRIzol reagent (Invitrogen).
QuantSeq 3' mRNA-Seq Library Prep Kit FWD (LEXOGEN) was used for library constraction according to the manufacturer's protocol.

treatment_protocol: Pharmacolgical drug was not treated in this assay

tag: strain

value: Spleen

value: Naive CD4 T Cells

value: SCD2/IRF9 DKO

value: Naïve CD4 T cells were stimulated under Th1 culture conditions (10 ng/ml IL-12) for 5 days in vitro.


title: sgScd2/sgIrf9 (n=5)


title: sgScd2/sgIrf9 (n=3)


title: sgScd2/sgIrf7 (n=5)

value: SCD2/IRF7 DKO


title: sgScd2/sgIrf7 (n=4)


title: Heat stress soybean bud replicate 2


title: sgScd2/sgIrf7 (n=3)


title: sgScd2/sgIrf3 (n=5)

value: SCD2/IRF3 DKO


title: sgScd2/sgIrf3 (n=4)


title: sgScd2/sgIrf3 (n=3)


title: sgScd2 (n=5)

value: SCD2 KO


title: Water deficit soybean bud replicate 1

value: Buds

value: Magellan


title: sgScd2 (n=4)


title: control (n=3)

value: WT


title: control (n=4)


title: 15WT

city: Victoria

first: Harley

last: Gordon

state: BC

address: 3800 Finnerty Rd

department: Biology

country: Canada

institute: University of Victoria

data_processing:
Alignment to reference using HiSAT2, samtools was used for file conversion from .SAM to .BAM
Cufflinks and cuffmerge was used to identify differentially expressed genes
HTSeq was used to construct count matrices
DeSeq2 in Rstudio was used to construct gene tables
Genome_build: P.tremula transcriptome V.2
Supplementary_files_format_and_content: csv files with raw transcript counts for every sample

organism: Populus tremula x Populus alba

source_name: fully expanded Populus tremula x alba leaves

growth_protocol: Clonal poplars from in vitro cultures were grown under greenhouse conditions with supplemental 16 hr lighting. Plants were watered as required. Samples were collected from the mid-stem of the plant following 3 months of greenhouse growth.

extract_protocol:
RNA was extracted from flash frozen, homogenized samples using a phenol chloroform extraction. mRNA isolation and enrichement was conducted using a MagJET enrichment kit (Thermofisher Scientific)
Library construction was conducted using Illumina RNA-Seq Next Gen library kit

treatment_protocol: All genotypes were grown under identical conditions

tag: clone

value: INRA 717 hybrid

value: 3 Months

value: Wild-type


title: control (n=5)

tag: cell type


title: 11INT

value: Intermediate Phenotype


title: 13EV

value: Empty-Vector


title: 16INT


title: 8EV


title: 5WT


title: 7WT


title: 12EV


title: 1M

value: Knockout


title: 3M


title: Mono_So34_3

city: Columbus

first: Justin

middle: Ray

last: Kaspar

state: OH

address: 305 W 12th Ave

department: Biosciences

institute: The Ohio State University

description: repeat 3 of 3

data_processing:
Step 1: FASTQ Groomer
Step 2: FASTQ Quality Trimmer
Step 3: FastQC
Step 4: Map with Bowtie2
Step 5: sort
Step 6: featurecounts (see our publication for details)
Assembly: Streptococcus mutans: NC_004350.2
Assembly: Streptococcus gordonii: NC_009785.1
Assembly: Streptococcus sanguinis: NC_009009.1
Assembly: Streptococcus oralis: CP079724.1
Supplementary files format and content: Counts obtained from step 6: featurecounts, listed along side each open reading frame

organism: Streptococcus oralis

source_name: Whole cell lysate

growth_protocol: Bacterial cells used for extraction of RNA were grown in TYG medium, in the presence of 5% CO2 at 37°C without agitation, until they reached mid-exponential phase (OD600 ≈ 0.5)

extract_protocol:
Total RNA was extracted from bacterial cells using the RNeasy Mini kit (Qiagen), with chromosomal DNA removed using a DNase I kit (Qiagen).
cDNA libraries were constructed by MiGS
RNA-Seq: single-ended short reads were obtained from a set of bar-coded cDNA libraries

treatment_protocol: Cells were harvested by centrifugation at 4°C for 5 min, treated with bacterial RNAprotect Bacteria Reagent (Qiagen), and immediately stored at -80°C.

value: grown in monoculture (TYG) to OD600 nm = 0.5

value: 36 wild-type (lab stock)


title: Mono_SK36_2

description: repeat 2 of 3

organism: Streptococcus sanguinis

value: SK36 wild-type (reference strain)


title: Mono_So34_1

description: repeat 1 of 3

value: 34 wild-type (lab stock)


title: Mono_SK36_3

description: repeat 3 of 3


title: Mono_So34_2

description: repeat 2 of 3

value: 35 wild-type (lab stock)


title: Nl5d_3

city: Hangzhou

first: Ni

last: Wang

address: Sundun Street

country: China

institute: Institute of Insect Sciences, Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province

data_processing:
Raw reads were subjected to an in-house program, ACGT101-miR(LC Sciences,Houston,Texas,USA)to remove adapter dimers,junk,low complexity,common RNA families（rRNA、tRNA、snRNA、snoRNA）and repeats.
Subsequently, unique sequences with length in 18-26 nucleotide were mapped to specific species precursors in miRase 22.0 by BLAST search to identify known miRNAs and novel  3p- and 5p- derived miRNAs.
Length variation at both 3’ and 5’ ends and one mismatch inside of the sequence were allowed in the alignment.
The unique sequences mapping to specific species mature miRNAs in hairpin arms were identified as known miRNAs.
The unique sequences mapping to the other arm of known specific species precursor hairpin opposite to the annotated mature miRNA-containing arm were considered to be novel 5p- or 3p derived miRNA candidates.
The remaining sequences were mapped to other selected species precursors (with the exclusion of specific species) in miRBase 22.0 by BLAST search, and the mapped pre-miRNAs were further BLASTed against the specific species genomes to determine their genomic locations.
The unmapped sequences were BLASTed against the specific genomes, and the hairpin RNA structures containing sequences were predicated from the flank 80 nt sequences using RNA fold software.
Genome_build: Nilaparative lugens
Supplementary_files_format_and_content: tab-delimited text files include norm values for each Sample

organism: Nilaparvata lugens

source_name: Whole body

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0.
Approximately 10 ug of total RNA representing a specific adipose type was subjected to isolate Poly (A) mRNA with poly-T oligoattached magnetic beads (Invitrogen). Following purification, the poly(A)- or poly(A)+ RNA fractions is fragmented into small pieces using divalent cations under elevated temperature. Then the cleaved RNA fragments were reverse-transcribed to create the final cDNA library in accordance with the protocol for the mRNA-Seq sample preparation kit (Illumina, San Diego, USA), the average insert size for the paired-end libraries was 300 bp (±50 bp). And then we performed the paired-end sequencing on an Illumina Novaseq™ 6000 at the (lc-bio, China) following the vendor's recommended protocol.

tag: developmental stage

value: 5th day after eclosion

value: untreated

tag: morph

value: short-wing


title: Mono_SK36_1

description: repeat 1 of 3

tag: treatment


title: Nl5d_2


title: Nl5d_1


title: Nl3d_3

value: 3rd day after eclosion


title: Nl3d_2


title: sgScd2 (n=3)

value: Spleen

value: Naive CD4 T Cells

value: SCD2 KO

value: Naïve CD4 T cells were stimulated under Th1 culture conditions (10 ng/ml IL-12) for 5 days in vitro.


title: 10INT

value: INRA 717 hybrid

value: 3 Months


title: Nl1d_3

value: 1st day after eclosion


title: 4M

value: Knockout


title: Nl3d_1


title: D6 GLI3R OE input rep1

city: Chicago

first: Ivan

last: Moskowitz

state: IL

address: 900 East 57th Street, KCBD Room 5102

institute: Univeristy of Chicago

description: 10% input

library_source: genomic

data_processing:
Reads were aligned to mouse genome version mm10 with bowtie2 (v2.3.2) with default settings
Aligned reads were sorted with  samtools (v1.5) and duplicates were marked and remove with picardTool marDuplicates 2.8.1
Reads with q > 30 and uniquely mapped reads were kept for peak calling
Peaks were called with MACS2 (v 2.1.1) with parameters --SPMR -B -q 0.05 combing replicates to make one output
Fold Enrichment Bedgraphs were made with MACS2 with parameter -FE and then converted to bigWigs with UCSC tool bedgraphTobigWig
Assembly: mm10
Supplementary files format and content: narrowPeak file
Supplementary files format and content: bigWig with scores from MACS2 fold enrichment

source_name: cardiac progenitor cells

growth_protocol: mESCs were maintained and differentiated into CMs as previously described (Kattman et al., 2011).

extract_protocol:
0.5x106 cells were cross-linked in 1% PFA for 5 minutes at room temperature, with rocking. The reaction was then quenched with 125 mM glycine. The cross-linked tissues were incubated in LB1 (50 mM HEPES-KOH, pH 7.5, 140 mM NaCl, 1 mM EDTA, 10% Glycerol, 0.5% NP-40, 0.25% Triton X-100) with protease and phosphatase inhibitors on ice for 10 minutes. The tissues were then sonicated in LB3 (10 mMTris-HCl, pH 8.0, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% sodium deoxycholate, 0.5% N-lauroyl sarcosine, 1% Triton X-100) with protease and phosphatase inhibitors for 5 minutes at 4°C. Chromatin extract was then cleared by centrifugation at 14,000g, 4°C for 10 minutes. To pull-down GLI1-FTA, the chromatin extract was incubated with 50ul M-280 Streptavidin-conjugated magnetic beads (Life Technologies, 11205D) for 30 minutes at room temperature with rotation, washed in sequence by LB3, LB3 with 1 M NaCl, LB3 with 0.5 M NaCl, LB3, and TE. For H3K27ac ChIP, chromatin extract was incubated overnight with 1ul anti-H3K27ac antibody (Wako 306-34849). The next day, immunocomplexes were incubated with 50ul protein G-conjugated dynabeads (ThermoFisher, 10004D) for 4 hours with rotation, before washing as above. The captured chromatin, and input samples, were eluted in ChIP Elution Buffer (10 mM Tris-HCl, pH 8.0, 1 mM EDTA, 1% SDS, 250 mM NaCl) at 65°C. After RNase and proteinase K treatment and reverse cross-linking, DNA was purified.
High-throughput sequencing libraries from ChIP and input DNA were prepared using the NEBNext Ultra II DNA Library Prep Kit (New England Biolabs, E7645L). During library preparation, adaptor-ligated DNA fragments of 200-650 bp in size were selected before PCR amplification using Ampure XP magnetic beads (Beckman Coulter, A63880).

treatment_protocol: GLI1 OE samples were treated with 500ng/ml doxycycline for 24 hours from D5 to D6.

value: mESC-derived cardiac progenitor cells

tag: cell line

value: 500ng/ml doxycycline from D5-6

tag: day of harvest

tag: ip strategy


title: D6 GLI3R OE GLI3R IP rep2

description: GLI3R-FTA IP using Avi-tag

value: Streptavidin-conjugated dynabeads


title: D6 GLI3R OE GLI3R IP rep1

description: GLI3R-FTA IP using Avi-tag


title: D6 control GLI3R IP rep2

description: GLI3R-FTA IP using Avi-tag


title: Nl1d_1


title: D6 control GLI3R IP rep1

description: GLI3R-FTA IP using Avi-tag


title: SOX9_WCE2

city: Rehovot

first: Jakub

last: Abramson

address: 234 Herzl st.

department: Department of Immunology

country: Israel

institute: Weizmann Institute of Science

data_processing:
Paired-end ChIP-seq libraries were sequenced on Illumina NextSeq500. Reads were preprocessed with cutadapt to remove adapters and low-quality bases (parameters: --times 2 -q 20 -m 25), and mapped to mm10 genome (Gencode) using bowtie2  (parameters: --local, -X 2000). Uniquely mapped reads were extracted using samtools (-F 4, -f 0x2, -q 39). Narrow peaks were called using MACS2 compared to background input samples (WCE, whole cell extract) (parameters: --bw 300 -B -f --SPMR -keep-dup auto -q 0.05 BAMPE --nomodel).
Assembly: mm10
Supplementary files format and content: Peaks detected by MACS2

extract_protocol:
Thymi were removed and enzymatically dissociated with Liberase TH and DNase. TEC were sorted and Six1 or Sox9 binding sites in the genome were determined by ChIPseq.
ChIPseq libraries were prepared for sequencing using a modified ChIPseq protocol (Blecher-Gonen et al., 2013, Bansal et al, 2017)

value: Mteci (EpCAM+CD45-MHCIIloItgb4+L1cam-)

tag: age

value: 5-6 weeks

tag: genotype

value: wildtype

tag: chip antibody

value: none (input)


title: SOX9_ChIP3

tag: tissue

value: anti-Sox9 (AB5535, Millipore)


title: SOX9_WCE3


title: Nl1d_2

value: untreated

value: short-wing


title: Six1_WCE1

value: ICR

value: total TEC


title: SOX9_WCE1


title: Six1_ChIP1

value: anti-Six1 (HPA0011893, Sigma)


title: WT sham blood 2

first: Xiaoming

last: Hu

address: 200 lothrop street

department: Neurology

description: Sham model

data_processing:
Fastq files were quality controlled using FastQC
Reads were mapped to the GRCm38 (mm10) mouse genome using Tophat
We applied Cufflinks9 (2.2.1) to estimate gene and isoform abundance.
The abundance of mapped reads is expressed as Fragment Per Kilobase of transcript per Million mapped reads (FPKM) format.
We used R software (version: 3.6.0) with several packages for the bioinformatics analysis.
Assembly: GRCm38.95

extract_protocol:
The SMART-Seq HT Kit was used to generate cDNA from total RNA. For FACS-sorted CD8+CD122+CD49dlow TRLs, 500-1000 cells were sorted to a plate with lysis buffer. cDNA was generated from cell lysis using the SMART-Seq Ultralow Input RNA Kit (Qiagen).
The sequencing library was constructed by following the Illumina Nextera XT Sample Preparation Guide. One nanogram of input cDNA was tagmented (tagged and fragmented) and amplified using the Illumina Nextrera XT kit. Sequence libraries of each sample were finally equimolarly pooled and sequenced on an Illumina Nextseq 500 system, using a paired-end 75-bp strategy.

tag: allelic composition

value: WT

value: 9-week old

tag: genetic background

value: sham


title: WT tMCAO blood 2

description: tMCAO model

value: middle cerebral artery occlusion


title: WT tMCAO blood 1

description: tMCAO model


title: WT sham blood 1

description: Sham model


title: SOX9_ChIP1


title: WT tMCAO brain 1

description: tMCAO model


title: sgScd2/sgIrf9 (n=2)

value: Spleen

value: Naive CD4 T Cells

value: SCD2/IRF9 DKO

value: stimulated under Th1 culture conditions (10 ng/ml IL-12) for 5 days in vitro.


title: sgScd2/sgIrf7 (n=2)

value: SCD2/IRF7 DKO


title: sgScd2/sgIrf9 (n=1)


title: WT tMCAO brain 2

description: tMCAO model


title: sgScd2/sgIrf7 (n=1)


title: sgScd2/sgIrf3 (n=2)

value: SCD2/IRF3 DKO


title: D6 control input rep1 (GLI3R control)

description: 10% input

value: mESC-derived cardiac progenitor cells


title: sgScd2/sgIrf3 (n=1)


title: SOX9_ChIP2

value: Mteci (EpCAM+CD45-MHCIIloItgb4+L1cam-)

value: 5-6 weeks

value: wildtype

value: anti-Sox9 (AB5535, Millipore)


title: sgScd2 (n=1)

value: SCD2 KO


title: sgScd2 (n=2)


title: sgScd2_Input (n=2)

data_processing:
ChIP-seq reads were aligned to the mm10 mouse reference genome (University of California, Santa Cruz (UCSC) December 2011)  using Bowtie2.
Normalization was performed using RPGC method with Bamcoverage of Deeptools.
mm10 mouse reference genome (University of California, Santa Cruz (UCSC) December 2011)
Assembly: mm10 mouse reference genome (University of California, Santa Cruz (UCSC) December 2011)
Supplementary files format and content: wig files were generated using "Deep tools".

extract_protocol: NEBNext Ultra II DNA Library Prep with Sample Purification Beads (NEW ENGLAND BioLabs) was used for library constraction according to the manufacturer's protocol.

treatment_protocol: IFNβ (100U/ml) were treated for last 3 days.

tag: antibody


title: sgScd2/sgIrf9_Input (n=2)


title: Mock_Input (n=1)


title: control (n=2)


title: sgScd2_Input (n=1)


title: Mock_Input (n=2)


title: sgScd2/sgIrf9_IP (n=2)


title: sgScd2/sgIrf9_IP (n=1)


title: Mock_IP (n=1)


title: sgScd2_IP (n=1)


title: non-treat_Input (n=2)


title: sgScd2_IP (n=2)


title: IFNβ/sgIrf9_Input (n=1)

value: IFNb/IRF9 DKO

value: stimulated under Th1 culture conditions (10 ng/ml IL-12) for 5 days in vitro.  IFNb (100U/ml) were treated for last 3 days.


title: IFNβ/sgIrf9_Input (n=2)


title: IFNβ_Input (n=2)

value: IFNb


title: IFNβ/sgIrf9_IP (n=2)


title: IFNβ_Input (n=1)


title: IFNβ_IP (n=2)


title: non-treat_IP (n=2)

value: WT


title: control (n=1)


title: 6w_WT_196_mTEC4

data_processing:
Data was processed using UTAP pipeline (Kohen et al., 2019). Bcl files were converted into fastq by bcl2fastq. Demultiplexing is done using the sample barcode found on R2, the UMI found on R2 is inserted in the read name (in R1 fastq). R1 Fastq data submitted.
Reads were trimmed using Cutadapt (parameters: -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -a “A{10}” –times 2 -u 3 -u -3 -q 20 -m 25) and mapped to the Mus_musculus genome using STAR v2.4.2a (parameters: –alignEndsType EndToEnd, –outFilterMismatchNoverLmax 0.05, –twopassMode Basic, –alignSoftClipAtReferenceEnds No).
The pipeline quantifies the 3’ of Gencode annotated genes (The 3’ region contains 1,000 bases upstream of the 3’ end and 100 bases downstream). Counting proceeded over genes annotated in RefSeq release using htseq-count (union mode). Genes having minimum 5 UMI-corrected reads in at least one sample, were considered. Normalization of the counts and differential expression analysis was performed using DESeq2 package.
Differential expression analysis was performed using DESeq2 with the betaPrior set to False. Raw P values were adjusted for multiple testing using the procedure of Benjamini and Hochberg. Differentially expressed genes were defined as genes that had a significant adjusted p value of less than 0.05 and at least 2-fold change.
Assembly: mm10
Supplementary files format and content: Tab delimited file includes normalized abundance measurements

source_name: 6w, WT, 196, mTEC

extract_protocol:
Thymi were removed and enzymatically dissociated with Liberase TH and DNase. HFC were trypsinized from shaved dorsal skin. HFC and TEC populations were sorted and RNA was extracted using Dynabeads. MARSseq protocol was used construction of sequencing libraries.
RNA libraries were prepared for sequencing using the MARSseq protocol (Jaitin et. Al. 2014)
Bulk Mars-Seq (3' end-RNA-seq)

value: TEC

value: wild type


title: non-treat_IP (n=1)

value: Spleen

value: Naive CD4 T Cells


title: non-treat_Input (n=1)

value: stimulated under Th1 culture conditions (10 ng/ml IL-12) for 5 days in vitro.


title: IFNβ/sgIrf9_IP (n=1)


title: 6w_WT_196_mTEC3


title: IFNβ_IP (n=1)


title: 6w_WT_196_cTEC

source_name: 6w, WT, 196, cTEC


title: Mock_IP (n=2)


title: 6w_WT_196_mTEC1


title: sgScd2/sgIrf9_Input (n=1)

value: SCD2/IRF9 DKO


title: 6w_WT_195_mTEC4

source_name: 6w, WT, 195, mTEC


title: 6w_WT_195_mTEC3


title: 6w_WT_195_mTEC1


title: 6w_WT_191_mTEC4

source_name: 6w, WT, 191, mTEC


title: 6w_WT_195_mTEC2


title: 6w_WT_191_mTEC3


title: 6w_WT_195_cTEC

source_name: 6w, WT, 195, cTEC


title: D6 GLI1 OE H3K27ac ChIP rep2

description: H3K27ac ChIP using antibody

data_processing:
Reads were aligned to mouse genome version mm10 with bowtie2 (v2.3.2) with default settings
Aligned reads were sorted with  samtools (v1.5) and duplicates were marked and remove with picardTool marDuplicates 2.8.1
Reads with q > 30 and uniquely mapped reads were kept for peak calling
Peaks were called with MACS2 (v 2.1.1) with parameters --SPMR -B -q 0.05 combing replicates to make one output
Fold Enrichment Bedgraphs were made with MACS2 with parameter -FE and then converted to bigWigs with UCSC tool bedgraphTobigWig
Genome_build: mm10
Supplementary_files_format_and_content: narrowPeak file
Supplementary_files_format_and_content: Bed file
Supplementary_files_format_and_content: bigWig with scores from MACS2 fold enrichment

extract_protocol:
2x106 cells were cross-linked in 1% PFA for 5 minutes at room temperature, with rocking. The reaction was then quenched with 125 mM glycine. The cross-linked tissues were incubated in LB1 (50 mM HEPES-KOH, pH 7.5, 140 mM NaCl, 1 mM EDTA, 10% Glycerol, 0.5% NP-40, 0.25% Triton X-100) with protease and phosphatase inhibitors on ice for 10 minutes. The tissues were then sonicated in LB3 (10 mMTris-HCl, pH 8.0, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% sodium deoxycholate, 0.5% N-lauroyl sarcosine, 1% Triton X-100) with protease and phosphatase inhibitors for 5 minutes at 4°C. Chromatin extract was then cleared by centrifugation at 14,000g, 4°C for 10 minutes. To pull-down GLI1-FTA, the chromatin extract was incubated with 50ul M-280 Streptavidin-conjugated magnetic beads (Life Technologies, 11205D) for 30 minutes at room temperature with rotation, washed in sequence by LB3, LB3 with 1 M NaCl, LB3 with 0.5 M NaCl, LB3, and TE. For H3K27ac ChIP, chromatin extract was incubated overnight with 1ul anti-H3K27ac antibody (Wako 306-34849). The next day, immunocomplexes were incubated with 50ul protein G-conjugated dynabeads (ThermoFisher, 10004D) for 4 hours with rotation, before washing as above. The captured chromatin, and input samples, were eluted in ChIP Elution Buffer (10 mM Tris-HCl, pH 8.0, 1 mM EDTA, 1% SDS, 250 mM NaCl) at 65°C. After RNase and proteinase K treatment and reverse cross-linking, DNA was purified.
High-throughput sequencing libraries from ChIP and input DNA were prepared using the NEBNext Ultra II DNA Library Prep Kit (New England Biolabs, E7645L). During library preparation, adaptor-ligated DNA fragments of 200-650 bp in size were selected before PCR amplification using Ampure XP magnetic beads (Beckman Coulter, A63880).

value: 500ng/ml doxycycline from D5-6

value: H3K27ac antibody (Wako 306-34849)


title: 6w_WT_191_mTEC1


title: 6w_WT_189_mTEC3

source_name: 6w, WT, 189, mTEC


title: 6w_WT_189_mTEC2


title: 6w_WT_191_cTEC

source_name: 6w, WT, 191, cTEC


title: 6w_WT_189_cTEC

source_name: 6w, WT, 189, cTEC


title: D6 GLI1 OE GLI1 IP rep2

description: GLI1-FTA IP using Avi-tag

value: mESC-derived cardiac progenitor cells

value: Streptavidin-conjugated dynabeads


title: D6 GLI1 OE GLI1 IP rep1

description: GLI1-FTA IP using Avi-tag


title: D6 GLI1 OE input rep1

description: 10% input


title: D6 GLI1 OE H3K27ac ChIP rep1

description: H3K27ac ChIP using antibody


title: 6w_WT_191_mTEC2


title: D6 GLI1 OE input rep2

description: 10% input


title: 6w_WT_196_mTEC2


title: D7 GLI1 OE rep1

description: ATAC-seq on D7 GLI1 OE cells

data_processing:
Single end reads were aligned to mouse genome version mm10 with bowtie2 version 2.3.2
Aligned reads were sorted with samtools version 1.5 before removing duplicates with Picard tool MarkDuplicates version 2.8.1.
Reads with q < 30 were removed with samtools version 1.5
peaks were called with MACS2 version 2.1.1 on all replicates to make one peak file
Fold enrichment bigwig  were generated with MACS2, then converted to bigWig files with UCSC tool bedgraphTobigWig
Genome_build: mm10
Supplementary_files_format_and_content: narrowPeak
Supplementary_files_format_and_content: bigWig

extract_protocol:
ATAC-seq was performed as previously described (Buenrostro et al. Nat Methods 2013). 150,000 cells were collected from GLI1 OE and control samples. Cell samples were then lysed, as described (Buenrostro et al. Nat Methods 2013), and transposition was carried out at 37C for 30 minutes with Tn5 enzyme.
Libraries were generated from transposed DNA using Illumina’s Nextera DNA Library Prep kit (Illumina 15028212).

treatment_protocol: GLI1 OE samples were treated with 500ng/ml doxycycline for 48 hours from D5 to D7.

value: 500ng/ml doxycycline from D5-7


title: D6 control input rep2

description: 10% input

value: untreated


title: D6 control H3K27ac ChIP rep2

description: H3K27ac ChIP using antibody


title: D6 control GLI1 IP rep2

description: GLI1-FTA IP using Avi-tag


title: D6 control input rep1

description: 10% input


title: D6 control GLI1 IP rep1

description: GLI1-FTA IP using Avi-tag


title: D5 control rep2

description: ATAC-seq on D5 control cells


title: D7 GLI1 OE rep2

description: ATAC-seq on D7 GLI1 OE cells


title: D7 GLI1 OE rep3

description: ATAC-seq on D7 GLI1 OE cells


title: d6_mTEC2_1 [ATAC-Seq]

description: nucleosome-free chromatin

data_processing:
Paired-end raw reads were trimmed using cutadapt (with the parameters -q 25 -m 30), and mapped to genome mm10 (Gencode) using bowtie2 (with the parameter --local).
Following alignment, mitochondrial genes are removed from the analysis, and duplicated reads were removed using picard-tools.
Nucleosome-free fragments at the length <120bp were selected from the remaining unique reads, and broad peaks were called using MACS2 (with the parameters --bw 120 -B -f BAMPE --SPMR –B --shift -50 --extsize 100 -keep-dup all -q 0.05).
Genome_build: mm10
Supplementary_files_format_and_content: Peaks detected by MACS2

source_name: TEC

extract_protocol:
Thymi were removed and enzymatically dissociated with Liberase TH and DNase. TEC populations were sorted and chromaton accessible regions purified.
ATAcseq libraries were prepared for sequencing using using a modified ATACseq protocol (Buenrostro et al., 2016, Lara-Astiaso et al., 2014)

value: day 6


title: 6w_WT_189_mTEC4


title: D7 control rep3

description: ATAC-seq on D7 control cells


title: CD1 HT rep1

description: ATAC-seq on E10.0 HT

data_processing:
Single end reads were aligned to mouse genome version mm10 with bowtie2 version 2.3.2
Aligned reads were sorted with samtools version 1.5 before removing duplicates with Picard tool MarkDuplicates version 2.8.1.
Reads with q < 30 were removed with samtools version 1.5
peaks were called with MACS2 version 2.1.1 combing all replicates to make one output
Fold enrichment bigwig  were generated with MACS2, then converted to bigWig files with UCSC tool bedgraphTobigWig
Genome_build: mm10
Supplementary_files_format_and_content: narrowPeak file
Supplementary_files_format_and_content: bigWig

source_name: embryonic atria (HT)

extract_protocol:
ATAC-seq was performed as previously described (Buenrostro et al. Nat Methods 2013). The pSHF and atria (HT) were microdissected from CD1 embryos, pooled, and dissociated with TrypLE (ThermoFisher Scientific 12605-010). Cell samples were then lysed, as described (Buenrostro et al. Nat Methods 2013), and transposition was carried out at 37C for 30 minutes with Tn5 enzyme.
Libraries were generated from transposed DNA using Illumina’s Nextera DNA Library Prep kit (Illumina 15028212).

value: atria (HT)


title: CD1 pSHF rep2

description: ATAC-seq on E10.0 pSHF

source_name: embryonic posterior second heart field (pSHF)

value: posterior second heart field (pSHF)


title: CD1 HT rep2

description: ATAC-seq on E10.0 HT


title: CD1 pSHF rep3

description: ATAC-seq on E10.0 pSHF


title: 6w_WT_189_mTEC1


title: D7 control rep2

description: ATAC-seq on D7 control cells


title: CD1 HT rep3

description: ATAC-seq on E10.0 HT


title: E15_1 [ATAC-Seq]

description: nucleosome-free chromatin

value: embryonic 15


title: E17_2 [ATAC-Seq]

description: nucleosome-free chromatin

value: embryonic 17


title: E17_1 [ATAC-Seq]

description: nucleosome-free chromatin

value: TEC


title: D6 control H3K27ac ChIP rep1

description: H3K27ac ChIP using antibody


title: D7 control rep1

description: ATAC-seq on D7 control cells


title: d6_mTEC1_1 [ATAC-Seq]

description: nucleosome-free chromatin

value: wild type


title: d6_mTEC2_2 [ATAC-Seq]

description: nucleosome-free chromatin


title: E15_2 [ATAC-Seq]

description: nucleosome-free chromatin


title: nude_3

data_processing:
Data was processed using UTAP pipeline (Kohen et al., 2019). Bcl files were converted into fastq by bcl2fastq. Demultiplexing is done using the sample barcode found on R2, the UMI found on R2 is inserted in the read name (in R1 fastq).  R1 Fastq data submitted.
Reads were trimmed using Cutadapt (parameters: -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -a “A{10}” –times 2 -u 3 -u -3 -q 20 -m 25) and mapped to the Mus_musculus genome using STAR v2.4.2a (parameters: –alignEndsType EndToEnd, –outFilterMismatchNoverLmax 0.05, –twopassMode Basic, –alignSoftClipAtReferenceEnds No).
The pipeline quantifies the 3’ of Gencode annotated genes (The 3’ region contains 1,000 bases upstream of the 3’ end and 100 bases downstream). Counting proceeded over genes annotated in RefSeq release using htseq-count (union mode). Genes having minimum 5 UMI-corrected reads in at least one sample, were considered. Normalization of the counts and differential expression analysis was performed using DESeq2 package.
Differential expression analysis was performed using DESeq2 with the betaPrior set to False. Raw P values were adjusted for multiple testing using the procedure of Benjamini and Hochberg. Differentially expressed genes were defined as genes that had a significant adjusted p value of less than 0.05 and at least 2-fold change.
Genome_build: mm10
Supplementary_files_format_and_content: normalized abundance measurements and DESeq2 analysis

value: ICR

value: nu/nu


title: nude_1


title: d6_mTEC4_2 [ATAC-Seq]

description: nucleosome-free chromatin


title: CD1 pSHF rep1

description: ATAC-seq on E10.0 pSHF

value: WT


title: D5 control rep1

description: ATAC-seq on D5 control cells


title: d6_mTEC1_2 [ATAC-Seq]

description: nucleosome-free chromatin


title: AR3_Het_1

value: Foxn1 del AR3 het


title: d6_mTEC4_1 [ATAC-Seq]

description: nucleosome-free chromatin


title: AR3_mut_3

value: Foxn1 del AR3 mut


title: AR3_mut_1


title: nude_2


title: Foxn1_HFC_GFP_pos_3

data_processing:
Data was processed using UTAP pipeline (Kohen et al., 2019). Bcl files were converted into fastq by bcl2fastq. Demultiplexing is done using the sample barcode found on R2, the UMI found on R2 is inserted in the read name (in R1 fastq).  R1 Fastq data submitted.
Reads were trimmed using Cutadapt (parameters: -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -a “A{10}” –times 2 -u 3 -u -3 -q 20 -m 25) and mapped to the Mus_musculus genome using STAR v2.4.2a (parameters: –alignEndsType EndToEnd, –outFilterMismatchNoverLmax 0.05, –twopassMode Basic, –alignSoftClipAtReferenceEnds No).
The pipeline quantifies the 3’ of Gencode annotated genes (The 3’ region contains 1,000 bases upstream of the 3’ end and 100 bases downstream). Counting proceeded over genes annotated in RefSeq release using htseq-count (union mode). Genes having minimum 5 UMI-corrected reads in at least one sample, were considered. Normalization of the counts and differential expression analysis was performed using DESeq2 package.
Differential expression analysis was performed using DESeq2 with the betaPrior set to False. Raw P values were adjusted for multiple testing using the procedure of Benjamini and Hochberg. Differentially expressed genes were defined as genes that had a significant adjusted p value of less than 0.05 and at least 2-fold change.
Genome_build: mm10
Supplementary_files_format_and_content: Tab delimited files include raw counts values for each sample

value: HFC

value: Foxn1.EGFP positive


title: Foxn1_HFC_GFP_pos_1


title: nude_4


title: Foxn1_HFC_GFP_pos_2


title: AR3_mut_2


title: AR3_Het_3


title: d6_mTEC2_2

source_name: day 6


title: d6_mTEC2_1


title: d6_mTEC1_2


title: AR3_Het_2


title: d6_mTEC1_1


title: E17_2

source_name: E17 TEC


title: d6_mTEC4_2


title: E15_1

source_name: E15 TEC


title: d6_mTEC4_1


title: E17_1


title: HCT116 cells, Ctrl_NC_3

city: Wuhan

first: Dong

last: Chen

state: Hubei

address: 388 GaoXin 2nd Road, East Lake Hi-Tech Development Zone

department: Center for Genome Analysis

institute: ABLife, Inc.

description:
expressed_gene_FPKM.txt
expressed_gene_reads.txt

data_processing:
Illumina bcl2fastq software used for basecalling.
3' adapter (end1:AGATCGGAAGAGC;end2:AGATCGGAAGAGC) and low quality bases trimmed using FASTX-Toolkit (Version 0.0.13). the short reads less than 16nt were also dropped.
Reads were mapped using tophat2 --read-edit-dist 4 -N 4 --b2-N 1 -a 8 -m 0 -g 2 -p 12 --microexon-search --no-coverage-search --report-secondary-alignments. Uniq mapped reads were remained. while several mapped reads have the same start position and end position, only one is considered.
edgeR was used to the DEG analysis with FC>2  Qvalue <= 0.05
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include gene FPKM values for each Sample

source_name: Negative control under empty control, replicate 3

growth_protocol: The human CRC cell lines HCT116 was obtained from Procell (Wuhan, Hubei, China). The cell line has been authenticated with short tandem repeat (STR) analysis by Cell Bank, Type Culture Collection, Chinese Academy of Sciences (CBTCCCAS), and tested for the free of mycoplasma contamination. STR analysis was performed as previously described (Masters, Thomson et al. 2001).  HCT116 cell lines were cultured in McCoy’5A medium (Procell, China) with 10% fetal bovine serum (BI) and 1% penicillin-streptomycin (Hyclone) at 37 °C in a humidified atmosphere of 5% CO2.

extract_protocol:
Total RNA of CRC was extracted by using TRIZOL (Invitrogen).
The sequencing library of each RNA sample was prepared using the KAPA RNA HyperPrep Kit according to the protocol provided by the manufacture (Roche).
For high-throughput sequencing, the libraries were prepared following the manufacturer's instructions using the illumina platform for 151 nt pair-end sequencing by ABLife Inc. (Wuhan, China).

treatment_protocol: The humanHNRNPK gene was cloned by reverse transcription from total RNAs extracted from multiple cancer and non-cancer cell lines, followed by PCR amplification. The DNA fragment corresponding to a complete cDNA length was purified from a gel (MinElute PCR Purification Kit, Qiagen, 28004), and then cloned into the pTSB vector (TranSheepBio, China) using the hot fusion method were designed with CE Design V1.04 (Vazyme Biotech Co., Ltd). Each of the primer comprises a fragment of gene specific sequence and a 17–30 bp sequence of the pTSB vector.   pTSB vector was digested by EcoRI (NEB, 3101S) and XhoI (NEB R0146V) at 37℃ for 2h~3h. Then enzyme-digested vector was run on 1.0% agarose gel and purified by Qiagen column kit (MinElute PCR Purification Kit, Qiagen, 28004). Then the insert fragment was synthesized by PCR amplification and PCR insert were added to a PCR microtube for ligation (T4 DNA ligase, NEB, M0202V) with ClonExpress® II One Step Cloning Kit (Vazyme, C112). Plasmids were introduced into Escherichia coli strain by chemical transformation. Cells were plated onto LB agar plates containing 1µL/ml ampicillin (sigma, 7177-48-2), and incubated overnight at 37℃. Colonies were screened by colony PCR (28 cycles) with universal primers (located on the backbone vector). The insert sequence was verified by Sanger sequencing.

tag: treatment 1

value: Negative control

tag: treatment 2

value: Empty control


title: E15_2

tag: strain


title: Mono_SMU_2

description: repeat 2 of 3

organism: Streptococcus mutans

source_name: Whole cell lysate

value: grown in monoculture (TYG) to OD600 nm = 0.5

value: UA159 wild-type (reference strain)


title: Mono_SMU_1

description: repeat 1 of 3


title: E7_5_E8_5_E9_5_doublets

city: Dongjak-Gu

first: Junil

last: Kim

state: Seoul

address: 369 Sangdo-Ro

department: Department of Bioinformatics

country: South Korea

institute: SOONGSIL UNIVERSITY

description:
Embryonic days E7.5, E8.5, and E9.5.
E7_5_doublets_20190402
E7_5_doublets_20190412
E8_5_doublets_20190403
E9_5_doublets_20190412
Fastq: read2 concatenated to R1 header separated to plate barcode - cell barcode - UMI

data_processing:
Sequences were mapped to mouse mm9 genome, de-multiplexed and filtered.
We estimated the level of spurious unique molecular identifier (UMIs) in the data using statistics on empty MARS-seq wells.
Mapping of reads was done using HISAT (version 0.1.6); reads with multiple mapping positions were excluded.
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: combinedExpression_4R.txt: Tab-delimited text file includes UMI counts.
Supplementary_files_format_and_content: metadata_4R.txt: Tab-delimited text file includes metadata describing each cell.
Supplementary_files_format_and_content: design_file_doublet.xlsx: Excel file includes metadata describing each well.

source_name: Embryonic endoderm

extract_protocol:
Cells were sorted directly into lysis buffer containing first RT primer and RNase inhibitor, immediately frozen and later processed by MARS-seq1 protocol.
All scRNAseq libraries were sequenced using Illumina NextSeq 500.

value: Embryonic endoderm

tag: embryonic day

value: mixed sample (non-demultiplexed)


title: HCT116 cells, Ctrl_NC_2

source_name: Negative control under empty control, replicate 2


title: HCT116 cells, Ctrl_hnRNPK_3

source_name: HNRNPK overexpression under empty control, replicate 3

value: HNRNPK overexpression


title: HCT116 cells, Ctrl_hnRNPK_2

source_name: HNRNPK overexpression under empty control, replicate 2


title: HCT116 cells, Ctrl_hnRNPK_1

source_name: HNRNPK overexpression under empty control, replicate 1


title: HCT116 cells, CRLM1_NC_3

source_name: Negative control under CRLM1 overexpression, replicate 3

value: CRLM1 overexpression


title: HCT116 cells, CRLM1_NC_2

source_name: Negative control under CRLM1 overexpression, replicate 2


title: HCT116 cells, CRLM1_NC_1

source_name: Negative control under CRLM1 overexpression, replicate 1


title: HCT116 cells, CRLM1_hnRNPK_3

source_name: HNRNPK overexpression under CRLM1 overexpression, replicate 3


title: HCT116 cells, CRLM1_hnRNPK_2

source_name: HNRNPK overexpression under CRLM1 overexpression, replicate 2


title: HCT116 cells, CRLM1_hnRNPK_1

source_name: HNRNPK overexpression under CRLM1 overexpression, replicate 1


title: HCT116 cells, Antisense_NC_2

source_name: Negative control under antisense control, replicate 2

value: antisense control


title: HCT116 cells, DCtrl_input_2

data_processing:
Illumina Casava1.9 software used for basecalling.
3' adapter (end1:AGATCGGAAGAGC;end2:AGATCGGAAGAGC) trimmed with cutadapt
Reads were mapped using bowtie2 -N 1. Uniq mapped reads were remained.
macs14 was used to peakcalling with  default parameters
Genome_build: GRCh38
Supplementary_files_format_and_content: peak files (bed)

source_name: Input DNA with empty control, replicate 2

growth_protocol: The human CRC cell lines HCT116 was obtained from Procell (Wuhan, Hubei, China). The cell line has been authenticated with short tandem repeat (STR) analysis by Cell Bank, Type Culture Collection, Chinese Academy of Sciences (CBTCCCAS), and tested for the free of mycoplasma contamination. STR analysis was performed as previously described (Masters, Thomson et al. 2001).  HCT116 cell lines were cultured in McCoy’5A medium (Procell, China)  with 10% fetal bovine serum (BI) and 1% penicillin-streptomycin (Hyclone) at 37 °C in a humidified atmosphere of 5% CO2.

extract_protocol:
After sequential RNase A and proteinase K treatment, DNA fragments were purified by phenol extraction and ethanol precipitation.
The libraries were performed by using ThruPLEX® DNA-seq kit (Rubicon Genomics) according to manufacturer’s instructions and applied to illumina platform for 151 nt pair-end sequencing by ABlife. Inc (Wuhan, China).

treatment_protocol: Approximately 1 × 107 cells were crosslinked in 1% Formaldehyde for 10 min and we stopped the reaction by 0.125 M glycine for 5 min. The crosslinked cells were lyses in Lysis buffer (1× PBS, 0.1% SDS, 0.5% NP-40 and 0.5% sodium deoxycholate) and sonicated to generate DNA fragments for 200–1000 bp. For immunoprecipitation, Protein-DNA complex was immunoprecipitated by incubating with ChIP-grade Protein A/G Magnetic Beads conjugated with anti-hnRNPK antibody, or IgG at 4℃ for 2h. The beads were washed with LiCl Immune Complex wash buffer (0.5 M LiCl) for five times, TE buffer (10Mm Ttis (PH 8.0)，1mM EDTA (PH 8.0) ) for one time, respectively. The beads were then resuspend with 100ul Elution Buffer (100 mM NaHCO3 ,1% SDS) and reverse cross-linked by overnight incubation at 65 ℃.

value: empty control


title: HCT116 cells, DCtrl_input_1

source_name: Input DNA with empty control, replicate 1


title: HCT116 cells, DCRLM1_input_1

source_name: Input DNA with CRLM1 overexpression, replicate 1


title: Mono_SMU_3

description: repeat 3 of 3


title: HCT116 cells, Antisense_NC_1

source_name: Negative control under antisense control, replicate 1


title: HCT116 cells, Antisense_hnRNPK_2

source_name: HNRNPK overexpression under antisense control, replicate 2


title: HCT116 cells, DCtrl_IP_2

source_name: HNRNPK IP with empty control, replicate 2

value: HNRNPK  (Proteintech, Catalog:11426-1-AP, Lot:00022887)


title: HCT116 cells, Antisense_hnRNPK_3

source_name: HNRNPK overexpression under antisense control, replicate 3


title: HCT116 cells, DAnti_input_2

source_name: Input DNA with antisense control, replicate 2


title: HCT116 cells, DCRLM1_input_2

source_name: Input DNA with CRLM1 overexpression, replicate 2


title: HCT116 cells, Ctrl_NC_1

source_name: Negative control under empty control, replicate 1


title: HCT116 cells, DAnti_IP_1

source_name: HNRNPK IP with antisense control, replicate 1


title: HCT116 cells, DCRLM1_IP_1

source_name: HNRNPK IP with CRLM1 overexpression, replicate 1


title: HCT116 cells, DAnti_IP_2

source_name: HNRNPK IP with antisense control, replicate 2


title: HCT116 cells, DAnti_input_1

source_name: Input DNA with antisense control, replicate 1


title: HCT116 cells, LINC01767_anti_3

molecule: polyA RNA

source_name: Antisense control replicate 3

growth_protocol: The human CRC cell lines HCT116, and SW620 were obtained from Procell (Wuhan, Hubei, China). The cell line has been authenticated with short tandem repeat (STR) analysis by Cell Bank, Type Culture Collection, Chinese Academy of Sciences (CBTCCCAS), and tested for the free of mycoplasma contamination. STR analysis was performed as previously described (Masters, Thomson et al. 2001).  HCT116 cell lines were cultured in McCoy’5A medium (Procell, China) and SW620 cell lines were cultured in DMEM medium (Procell, China) both with 10% fetal bovine serum (BI) and 1% penicillin-streptomycin (Hyclone) at 37 °C in a humidified atmosphere of 5% CO2.

treatment_protocol: The human CRLM1 gene was cloned by reverse transcription from total RNAs extracted from multiple cancer and non-cancer cell lines, followed by PCR amplification. The DNA fragment corresponding to a complete cDNA length was purified from a gel (MinElute PCR Purification Kit, Qiagen, 28004), and then cloned into the pTSB vector (TranSheepBio, China) using the hot fusion method were designed with CE Design V1.04 (Vazyme Biotech Co., Ltd). Each of the primer comprises a fragment of gene specific sequence and a 17–30 bp sequence of the pTSB vector. The primers used for cDNA cloning were CRLM1 F Primer agcccgggcggatccgaattcACCAGGTACAAAATCCCCTGG  R-primer: gtcatccttgtagtcctcgagTGGCTTGAACAATAAAAAGAGTTTATT  pTSB vector was digested by EcoRI (NEB, 3101S) and XhoI (NEB R0146V) at 37℃ for 2h~3h. Then enzyme-digested vector was run on 1.0% agarose gel and purified by Qiagen column kit (MinElute PCR Purification Kit, Qiagen, 28004). Then the insert fragment was synthesized by PCR amplification and PCR insert were added to a PCR microtube for ligation (T4 DNA ligase, NEB, M0202V) with ClonExpress® II One Step Cloning Kit (Vazyme, C112). Plasmids were introduced into Escherichia coli strain by chemical transformation. Cells were plated onto LB agar plates containing 1µL/ml ampicillin (sigma, 7177-48-2), and incubated overnight at 37℃. Colonies were screened by colony PCR (28 cycles) with universal primers (located on the backbone vector). The insert sequence was verified by Sanger sequencing.

value: Antisense control


title: HCT116 cells, DCRLM1_IP_2

source_name: HNRNPK IP with CRLM1 overexpression, replicate 2


title: HCT116 cells, LINC01767_anti_2

source_name: Antisense control replicate 2


title: HCT116 cells, DCtrl_IP_1

source_name: HNRNPK IP with empty control, replicate 1


title: HCT116 cells, Antisense_NC_3

source_name: Negative control under antisense control, replicate 3


title: HCT116 cells, LINC01767_Ctrl_2

source_name: Empty control replicate 2


title: HCT116 cells, LINC01767_Ctrl_3

source_name: Empty control replicate 3


title: HCT116 cells, LINC01767_3

source_name: CRLM1 overexpression replicate 3


title: HCT116 cells, Antisense_hnRNPK_1

source_name: HNRNPK overexpression under antisense control, replicate 1


title: HCT116 cells, LacZ_1

data_processing:
Library strategy: ChIRP-seq
Illumina Casava1.9 software used for basecalling.
3' adapter (end1:AGATCGGAAGAGC;end2:AGATCGGAAGAGC) trimmed with cutadapt
Reads were mapped using bowtie2 -N 1. Uniq mapped reads were remained.
macs14 was used to peak calling with  default parameters
Genome_build: GRCh38
Supplementary_files_format_and_content: peak files (bed)

source_name: LacZ associated DNA in HCT116 cells, replicate 1

growth_protocol: The human CRC cell lines HCT116 was obtained from Procell (Wuhan, Hubei, China). The cell line has been authenticated with short tandem repeat (STR) analysis by Cell Bank, Type Culture Collection, Chinese Academy of Sciences (CBTCCCAS), and tested for the free of mycoplasma contamination. STR analysis was performed as previously described (Masters, Thomson et al. 2001).  HCT116 cell lines were cultured in McCoy’5A medium (Procell, China) and SW620 cell lines were cultured in DMEM medium (Procell, China) both with 10% fetal bovine serum (BI) and 1% penicillin-streptomycin (Hyclone) at 37 °C in a humidified atmosphere of 5% CO2.

extract_protocol:
For ChIRP-DNA beads resuspend in 150ul DNA elution buffer (50 mM NaHCO 3, 1 % SDS), add RNase A and RNase H incubate at 7℃ for 30min with shaking, eluted chromatin was pK treated at 50℃ for 45 min with mixing. DNA was then extracted with equal volume of phenol:chloroform:isoamyl and precipitated with ethanol at -80℃ overnight.
High-throughput sequencing libraries were constructed from ChIRPed DNA using ThruPLEX® DNA-seq kit (Rubicon Genomics) according to manufacturer’s instructions and applied to illumina platform for 151 nt pair-end sequencing by ABLife. Inc. (Wuhan, China).

treatment_protocol: Approximately 1×10e7 cells were crosslinked in 1% Formaldehyde for 10 min and stop the reaction by 0.125 M glycine for 5 min. The crosslinked cells were lyses in Lysis buffer (50 mM Tris–Cl pH 7.0, 10 mM EDTA, 1 %SDS) and sonicated to generate DNA fragments for 100 – 500 bp. Chromatin is diluted in two times volume of hybridization buffer (750mMNaCl, 1% SDS, 50 mM Tris 7.0, 1 mM EDTA, 15% Formamide). The DNA oligonucleotides were designed as probes to capture the lncRNA-CRLM1. LacZ from E. coli was used as a negative control.Probes of 100 pmol were added to 3 ml of diluted chromatin, which was mixed by end-to-end rotation at 37℃ for 4 hr. Streptavidinmagnetic C1 beads were washed three times in nuclear lysis buffer, use 1 ml of sample to transfer beads into the reaction, and the whole reaction was mixed for another 1hr at 37℃. Beads:biotin-probes:RNA:chromatin adducts were captured by magnets (Invitrogen) and washed five times with wash buffer (2x SSC, 0.5% SDS, v/v to original beads volume). At last wash, transfer 50% of sample to a fresh tube, this is for MS analysis. Use another material for DNA extraction and analysis.

value: LacZ antisense oligos


title: HCT116 cells, Input_2

source_name: Genomic DNA in  HCT116 cells, replicate 2

value: control


title: HCT116 cells, LINC01767_Ctrl_1

source_name: Empty control replicate 1


title: HCT116 cells, LacZ_2

source_name: LacZ associated DNA in HCT116 cells, replicate 2


title: P. aeruginosa_single biofilm [PA4-N0789]

city: Braga

first: Ângela

last: França

address: Campus de Gualtar

department: Biological Engineering

country: Portugal

institute: University of Minho

description: P. aeruginosa_single vs dual-species

data_processing:
Bcl2fastq version 2 (Illumina) was used for base calling and to convert data to FASTQ files.
CLC Genomics Workbench version 21 (QIAGEN) was used for quality, ambiguity and length trimming, using default settings. In addition, CLC was used for alignment, normalization of the reads (to Transcripts Per Million – TPM) and for the analysis of differential gene expression in single- vs dual-species biofilms. In the case of dual-species biofilms, reads were aligned with either S. aureus or P. aeruginosa genomes. Fold-change was calculated using single-species biofilms as control. Baggerley's test was applied to identify statistically significant alterations.
In the case of genes whose sequences were not detected (TPM = 0), TPM was replaced with 1 in order to be able to determined the minimum expression value for that particular gene.
Genome_build: CP009361 (S. aureus)
Genome_build: NZ_CP034244 (P. aeruginosa)
Supplementary_files_format_and_content: Processed data files are tab-delimited text files that contain (i) the gene locus tag, (ii) expression values (TPM) for each sample (in duplicates), (iii) mean of expression values (TPM) for each sample and, finaly, (iv) expression fold-change (using single species biofilms as a control). The list of genes presented was defined considering fold-change values greater than 2 and p-values less than 0.05.

organism: Pseudomonas aeruginosa

source_name: P. aeruginosa_single biofilm

growth_protocol: Single- and dual-species biofilms were grown as described in Magalhaes et al., 2021, Environmental Microbiology, 23(9), 5639-5649. In brief, overnight cultures of each species, grown in Tryptic Soy Broth (TSB) at 37ºC and 120 rpm in air conditions, were washed in sterile water and diluted in fresh TSB to obtain 1x10E7 CFU/mL. For dual-species cultures, a combination of 50% of the suspended inoculum of each species was used. Bacterial suspensions were further transferred to 24-well polystyrene plates (Orange Scientific, Braine- l’Alleud, Belgium) and incubated at 37ºC on a horizontal shaker (120 rpm) for 24h. This assay was performed six independent times.

extract_protocol:
Total RNA was extracted using RNeasy mini kit (QIAGEN) and as described in França et al., 2012, PLoS One 7 (5): e37480. In brief, cells were suspended in 600 µL of the lysis buffer provided by the kit, plus 500 µL of phenol and 12 µL of β-mercaptoethanol. This suspension was transferred to a safe lock tube (2 mL) with 0.4 g of acid-washed 150–212 mm glass beads (Sigma) and, using a BeadBugTM 6 (Benchmark Scientific) cells disruptor, the cells were lysed (4× 4500 rpm for 35 seconds, with 5 minutes intervals on ice between cycles). Finally, the tubes were centrifuged, and the suspension was transferred into a new tube. An equal volume of 70% of ethanol was added, the suspensions transferred into the RNeasy mini kit columns and the manufacturer's instructions were strictly followed. RNA quality was determined using Agilent TapeStation 4200 (Agilent) and RNA quality indicators were above 8 for all samples. Thereafter, total RNA obtained from three independent experiments were mixed and treated with TURBO DNase (Ambion) to degrade genomic DNA. Additionally, before the library construction, a NEBNext rRNA Depletion Kit (Bacteria) (NEB) was used to remove bacterial ribosomal RNA.
RNA libraries were prepared by strictly following the instructions of the kit KAPA HyperPrep (Roche). Libraries quality was determined using Agilent TapeStation 4200 and data were generated using Illumina NovaSeq 6000 (Illumina) from paired-end read (2 × 150 bp).

treatment_protocol: Biofilms cells (24h-old) were then collected and suspended in 1 mL of RNA protect bacteria reagent (Qiagen), diluted 2:1 in RNase-free water, as indicated by the manufacturer. After 5 minutes of incubation at room temperature, biofilm cells were harvested by centrifugation (3132 g, 20 minutes) and RNA isolation was performed.

tag: cell type

value: Biofilm cells (24h)


title: HCT116 cells, Input_1

source_name: Genomic DNA in  HCT116 cells, replicate 1


title: P. aeruginosa_single biofilm [PA3-N0788]

description: P. aeruginosa_single vs dual-species


title: HCT116 cells, CRLM1_IP_1

description:
CRLM1_IP_1_vs_Input_1_peaks.bed
CRLM1_IP_1_vs_LacZ_1_peaks.bed

source_name: CRLM1 associated DNA in HCT116 cells, replicate 1

value: CRLM1 antisense oligos


title: HPMVEC Opti Only 4

first: Helen

middle: N

last: Jones

state: Florida

address: 1345 Center Dr

department: Physiology and FUnctional Genomics

description: Sample 21

data_processing:
FastQ-QC: FASTQC,Trimmomatic
RNA seq mapping/count: Bowtie2, FeatureCounts,
Differential Expression analyses: EdgeR
Assembly: hg38
Supplementary files format and content: data matrix of raw count data, not filtered, not normalized

source_name: HPMVEC

extract_protocol:
Total RNA was isolated using the RNeasy Mini Kit, QIAshredder, and on-column DNA digest (Qiagen) following the protocol provided by the manufacturer
poly-A RNA libraries were generated using (NEBNext Ultra Directional RNA Library Prep kit, New England Biolabs, Ipswich, MA and the TruSeq SR Cluster kit v3 Illumina

value: HPMVEC

value: Human Placenta Microvascular Endothelial Cells

value: no treatment


title: HPMVEC Opti Only 2

description: Sample 19


title: HPMVEC Allstar 1

description: Sample 14

value: siRNA- negative control


title: HPMVEC Allstar 4

description: Sample 17


title: HPMVEC Hand 1 KO 1

description: Sample 10

value: siRNA - HAND1/2


title: HPMVEC Hand 1 KO 4

description: Sample 13


title: HPMVEC Opti Only 1

description: Sample 18


title: HPMVEC Hand 1 KO 3

description: Sample 12


title: HT29 xenograft tumor RNA-seq rep.1

city: New York

first: Royce

last: Zhou

address: 1470 Madison Avenue

institute: Icahn School of Medicine at Mount Sinai

data_processing:
FastQC - quality control of sequenced reads to assess duplication levels for ChIP-seq and detect adapter contamination during library prep.
cutadapt - removal of adapter contamination within raw sequenced reads
bowtie - Reads were mapped to the hg19 human genome using bowtie under the following parameters: bowtie -k 1 -m 1 --best -S -n 2 -l 60 -q --chunkmbs 200.
Samtools - Duplicate reads were removed using samtools.
MACS2 - Peak calling was performed using MACS2 with the following parameters: –f BAM –g 2.7e9 –s 75 --nomodel --extsize 200 –B –-SPMR –p 1e-10. For H3K27ac, a p-value cutoff of 10-10 was used for peak calling
deeptools - Bigwig tracks were generated using deepTools bamCoverage using the parameters: -of bigwig --effectiveGenomeSize 2736124973 --normalizeUsing RPKM
bedtools - Blacklisted regions (Duke_Hg19SignalRepeatArtifactRegions.bed, downloaded from the Broad Institute) were excluded from called peaks using bedtools
Salmon - Sequenced reads were mapped to the hg38 transcriptome using Salmon quasi-mapping under the default parameters and expression output in TPM was extracted.
Genome_build: ChIP-seq - hg19. RNA-seq hg38.
Supplementary_files_format_and_content: ChIP-seq processed data files are in the bigwig format ready for easy viewing on a genome broswer such as IGV or UCSC. RNA-seq processed data files are Salmon output excel files with raw and normalized read counts for each gene/transcript (ENSEMBL ID).

source_name: cancer cell line -> xenograft tumor

growth_protocol: Cells were grown as subcutaneous xenograft tumors in nude mice for ~6-8 weeks

extract_protocol:
Xenograft tumors and patient surgical specimens were digested with 1X collagenase/hyaluronidase (Stem Cell Technologies), minced, and passed through a 100μM filter. Cells were double crosslinked with 0.25M disuccinimidyl glutarate followed by 1% formaldehyde. ChIP-seq was performed as previously described3. Briefly, 2X crosslinked chromatin was sonicated on a Diagenode Bioruptor for 15 cycles 30s ON/30s OFF on the low power setting. Cells were precleared using 100μL of Magna-ChIP Protein A+G magnetic bead slurry (Millipore) before overnight incubation with 10μg ChIP antibody conjugated to100μL beads. Beads were washed once with IP Wash Buffer I, twice with High Salt Wash Buffer, once with IP Wash Buffer II, and twice with TE buffer. For buffer recipes refer to Fontanals-Cirera, Hasson et al3. Beads were eluted with 1% SDS at 65 degrees Celsius with agitation and reverse crosslinked overnight with high salt with RNase treatment (Roche). The next day, DNA underwent Proteinase K treatment at 42 degrees Celsius before elution using QIAquick PCR purification kit (QIAGEN).  DNA was run on an Agilent High Sensitivity DNA chip using an Agilent Technologies 2100 Bioanalyzer for quality control. H3K27ac ChIP-seq antibodies were purchased from abcam (#ab177178). Total RNA was extracted using the QIAGEN Rneasy Mini Kit. For ChIP-seq, antibody bound DNA was purified using the QIAGEN QIAquick PCR cleanup kit.
For ChIP-seq, DNA underwent end repair, poly-adenylation, and barcoding using enzymes from New England Biolabs. ChIP libraries were amplified 12-15 PCR cycles using the 2X KAPA HiFi DNA HotStart ReadyMix before quality assessment by running on a High Sensitivity chip using a Bioanalyzer 2100 (Agilent) followed by a Qubit fluorometer (Thermo Fisher). The Mount Sinai Oncological Sciences Sequencing Core Facility prepared poly-A-capture RNA-seq libraries using the TruSeq RNA Library Prep Kit v2 (Illumina) according to manufacturer’s instructions.

tag: cells/tissue

value: tissue


title: HT29 xenograft tumor RNA-seq rep.2


title: HPMVEC Hand 1 KO 2

description: Sample 11

tag: treatment


title: HCT116 cells, LINC01767_2

source_name: CRLM1 overexpression replicate 2

tag: cell line


title: HT29 xenograft tumor RNA-seq rep.3


title: HT29 cells RNA-seq rep.2

source_name: cancer cell line

growth_protocol: Cells were cultured in full RPMI-1640 media, incubator at 37 degrees celsius with 5% CO2.

value: cells


title: HCT116 cells, LINC01767_1

source_name: CRLM1 overexpression replicate 1


title: HT29 cells RNA-seq rep.1


title: HT29 cells RNA-seq rep.3


title: HCT116 cells, CRLM1_IP_2

description:
CRLM1_IP_2_vs_Input_2_peaks.bed
CRLM1_IP_2_vs_LacZ_2_peaks.bed

source_name: CRLM1 associated DNA in HCT116 cells, replicate 2


title: 19441T RNA-seq

source_name: Primary CRC


title: 19395N RNA-seq

source_name: Normal colon mucosa


title: 19441N RNA-seq


title: 19395T RNA-seq


title: 19342N RNA-seq


title: HPMVEC Opti Only 3

description: Sample 20


title: 19342T RNA-seq


title: 19282N RNA-seq


title: 19282T RNA-seq


title: 19107N RNA-seq


title: 19107T RNA-seq


title: 18607N RNA-seq


title: 18810T RNA-seq


title: HPMVEC Allstar 2

description: Sample 15


title: 19057T RNA-seq


title: 19057N RNA-seq


title: 18481T RNA-seq


title: 18481N RNA-seq


title: 18081T RNA-seq


title: 18607T RNA-seq


title: 17787T RNA-seq


title: Control_1_3

city: Kaifeng

first: ruizhen

last: wang

address: Jinming Avenue, Kaifeng City, Henan Province

institute: Henan University

data_processing:
Base calling and the quality score of each base are calculated based on the phred-33 quality score standard by the sub-Pixel Registration algorithm according to the optical signal intensity of each lane
This project uses the filtering software SOAPnuke (Versionv1.5.2) developed by BGI independently for filtering. SOAPnuke   Official Websitehttps://github.com/BGI-flexlab/SOAPnuke The specific steps are as follows: 1) Remove the reads containing the adaptor (adaptor pollution); 2) Remove reads whose N content is greater than 5%; 3) Remove low-quality reads (we define reads with bases with a quality score less than 10 as the proportion of total bases in the reads that are greater than 20% as low-quality reads).
Hierarchical Indexing for Spliced Alignment of Transcripts (HISTAT) is software for mapping RNA-seq reads. HISAT will use the global FM index to anchor the position of partial sequences in each read on the genome; then, use the partial genome indexes of these alignment positions to align the remaining sequences of each read to extend the alignment area. Software information:HISAT2 (Version：v2.0.4) ,Official Website：http://www.ccb.jhu.edu/software/hisat
Bowtie2 (v2.2.5) was used to compare clean reads to reference sequences for gene alignment with -q --phred64 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -p 16 -k 200. And then RSEM (v1.2.8) was used to calculate gene and transcript expression levels with -p 8 --forward-prob 0.5 --paired-end.
Genome_build: GCF_000001635.26_GRCm38.p6 for Mus musculus GCF_000001405.39_GRCh38.p13 for Homo sapiens
Supplementary_files_format_and_content: Excel files include FPKM values, Reads Count for each Sample

source_name: human primary keratinocytes

growth_protocol: phKCs were seeded into 24 well plates and cultured in KBM-Gold medium with KBM Gold SingleQuot KC supplement (Lonza, Basel, Switzerland). Cells were maintained in the above medium for 3 days before use.

extract_protocol:
Remove the upper medium and wash it twice with cold PBS, frozen on ice, and RNA was harvested using Trizol reagent.The mix was centrifuged for 5 minutes at 12,000×g at 4°C, then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol (24:1). The mix was shacked vigorously for 15s, and then centrifuged at 12,000×g for 10 minutes at 4°C. After centrifugation, the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol, then centrifuged at 13,600 rpm for 20 minutes at 4°C. After deserting the supernatant, the RNA pellet was washed twice with 1 mL 75% ethanol, then the mix was centrifuged at 13,600 rpm for 3 minutes at 4°C to collect residual ethanol, followed by the pellet air dry for 5-10 minutes in the biosafety cabinet. Finally, 25µL~100µL of DEPC-treated water was added to dissolve the RNA. Subsequently, total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer (Thermo Fisher Scientific, MA, USA).
Oligo(dT)-attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First-strand cDNA was generated using random hexamer-primed reverse transcription, followed by a second-strand cDNA synthesis. afterwards, A-Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR, and products were purified by Ampure XP Beads, then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA (ssCir DNA) was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball (DNB) which had more than 300 copies of one molecular, DNBs were loaded into the patterned nanoarray and single end 50 bases reads were generated on DNBSeq platform (BGI-Shenzhen, China)

treatment_protocol: phKCs were treated with IL-20(500 ng/ml) for 6h

tag: tag

value: keratinocytes

value: untreated


title: 17787N RNA-seq


title: 18081N RNA-seq


title: 17753N RNA-seq


title: IL20_20_1_2

value: IL20(500ng/ml) treated


title: Control_1_2


title: IL20_20_1_1


title: 17753T RNA-seq


title: HCT116 cells, LINC01767_anti_1

source_name: Antisense control replicate 1


title: Control_1_1


title: 17627N RNA-seq


title: 17627T RNA-seq


title: hkcR2KD_C_3

city: Dublin

first: Jianghui

last: Meng

address: Glasnevin Avenue

country: Ireland

institute: Dublin City University

description: NHEK

data_processing:
Illumina Casava1.7 software used for basecalling.
After getting clean reads, we used HISAT to align the clean reads to the reference genome. The alignment results are shown as follows.
Align clean reads to the reference genes by using Bowtie2 to get the alignment result.
Genome_build: Human NCBI genome
Supplementary_files_format_and_content: xls files include FPKM values for each Sample ...

source_name: hkcR2KD_C (human keratinocytes with IL-13 receptor alpha 1 knockdown treated by vehicle)

extract_protocol: RNA-extraction protocol not provided.

tag: developmental stage

value: adult

value: skin

value: IL-13 receptor alpha 2 knockdown and treated with vehicle

tag: culture method

value: primary culture


title: hkcR2KD_C_2

description: NHEK


title: 17561N RNA-seq


title: 17561T RNA-seq


title: hkcR2KD_13_3

description: NHEK

source_name: hkcR2KD_13 (human keratinocytes with IL-13 receptor alpha 2 knockdown treated by IL-13)

value: IL-13 receptor alpha 2 knockdown and treated with IL-13


title: 17547N RNA-seq


title: hkcR2KD_13_1

description: NHEK


title: hkcR2KD_13_2

description: NHEK


title: IL20_20_1_3


title: hkcR1KD_C_3

description: NHEK

source_name: hkcR1KD_C (human keratinocytes with IL-13 receptor alpha 1 knockdown treated by vehicle)

value: IL-13 receptor alpha 1 knockdown and treated with vehicle


title: 17243N RNA_seq


title: 17547T RNA-seq


title: hkcR1KD_13_3

description: NHEK

source_name: hkcR1KD_13 (human keratinocytes with IL-13 receptor alpha 1 knockdown treated by IL-13)

value: IL-13 receptor alpha 1 knockdown and treated with IL-13


title: 17243T RNA-seq


title: hkcR1KD_C_1

description: NHEK


title: HT29 H3K27ac xenograft tumor rep.3

tag: chip-seq antibody


title: HT29 H3K27ac xenograft tumor rep.2


title: HT29 input


title: HT29 H3K27ac cells


title: hkcR1KD_C_2

description: NHEK


title: hkcR1KD_13_2

description: NHEK


title: hkcC_C_3

description: NHEK

source_name: hkcC_C (human keratinocytes treated by vehicle)

value: treated with vehicle


title: 19442N input


title: HT29 H3K27ac xenograft tumor rep.1


title: 19442T input


title: hkcR1KD_13_1

description: NHEK


title: hkcC_C_2

description: NHEK


title: 19441T input


title: hkcR2KD_C_1

description: NHEK


title: 19395N input


title: hkcC_13_1

description: NHEK

source_name: hkcC_13 (human keratinocytes treated by IL-13)

value: treated with IL-13


title: 19395T input


title: 19441N input


title: hkcC_C_1

description: NHEK


title: 19282N input


title: 19342T input


title: RNAseq Phalange Rep 2

city: Rotterdam

first: Karol

last: Nowosad

address: Doctor Molewaterplein 40

country: Netherlands

institute: Erasmus MC

data_processing:
In the ChIPseq primary analysis, the quality of reads was checked by FASTQC followed by removal of adapters using Trimmomatic tool.
Reads were mapped to the Gallus Gallus 6 reference genome using Bowtie2 followed by removal of PCR duplicates with Picard tool.
Peaks were called with MACS2.
In the RNAseq primary analysis, the quality of reads was validated with FASTQC and adapters were removed using Trimmomatic tool.
Reads were aligned to the  Gallus Gallus 6 reference genome using using STAR
Reads were counted by gene using FeatureCounts
Identification of differentially expressed genes was performed using DESeq2
Assembly: gg6
Supplementary files format and content: (RNA-seq) DESeq2 normalized abundance measurements ouput
Supplementary files format and content: (ChIP-seq) MACS2 narrow peaks files

organism: Gallus gallus

source_name: RNAseq Phalange

growth_protocol: Chick White Leghorn embryonated eggs were incubated at 38.5ºC in fixed humidity for 7.5 days, followed by evaluation of developmental stage based on the Hamilton Hamburger classification (HH). The joint interzones and adjacent phalange samples were microdissected from hindlimb digit-3

extract_protocol:
For RNAseq library preparation, total RNA was isolated using Syngen Tissue RNA Kit
The RNAseq library was prepared according to the Smart-seq2 method.In brief, cells were lised and poly(A)-RNA was reverse transcribed using oligo(dT) primers. The cDNA was pre-amplified with 18 cycles, followed by clean-up. Tagmentation was performed on 500 pg of cDNA. Then library was extended with Illumina adaptor sequences (PCR - 14 cycles). The library was sequenced according to the Illumina TruSeq v3 protocol on the HiSeq2500 with a single- read 50 bp and dual 9 bp indices.

value: phalange


title: RNAseq Phalange Rep 1


title: RNAseq Phalange Rep 3


title: RNAseq Interzone Rep 3

source_name: RNAseq Interzone

value: interzone


title: RNAseq Interzone Rep 2


title: 19106N input


title: 19106T input


title: Tendon_Control_3

city: Daejeon

first: Minhyeok

last: Lee

address: 158, Gwanjeodong-ro, Seo-gu

department: Department of Internal Medicine

institute: Konyang university hospital

data_processing:
RNA sequence data quality was checked using FastQC v0.11.7 and trimmed using Trimmomatic 0.38 to remove low-quality bases and adaptor sequences.
The preprocessed reads were aligned to reference genome (Rnor_6.0) using HiSAT2 version 2.1.0 alignment program.
After mapping reads, String Tie version 2.1.3b was used for transcript assembly and the expression profiles were calculated as fragments per kilobase of transcript per million mapped reads (FPKM).
Assembly: Rnor_6.0
Supplementary files format and content: tab-delimited text files include FRKM values for each Sample

organism: Rattus norvegicus

source_name: tendon

growth_protocol: Sexually mature male Sprague–Dawley rats weighing 250 to 300 g (8-week-old) had tenotomy and repaired.

extract_protocol:
Total RNA was extracted using TRIzol Reagent (Invitrogen, Carlsbad, CA, USA) and evaluated for purity using Agilent 2100 Bioanalyzer RNA Nano Chip.
Generation of cDNA and RNA-Seq libraries was conducted by TruSeq Stranded mRNA LT Sample Prep kit (Illumina at San Diego, CA, USA) following TruSeq Stranded mRNA Sample Preparation Guide, Part # 15031047 Rev. E, and sequenced by paired-end-sequencing method using Illumina NovaSeq 6000 system sequencer (Macrogen, South Korea)

treatment_protocol: PM group was exposed to PM2.5 for 3 times a week for 6 weeks

value: tendon

tag: Sex

value: male

value: Sprague-Dawley

tag: genotype

value: Non-PM group

value: Not exposed PM 2.5 inhalation


title: RNAseq Interzone Rep 1

tag: tissue


title: hkcC_13_2

description: NHEK

value: keratinocytes


title: 18946N input

value: tissue


title: Tendon_Control_2


title: Tendon_Control_1


title: Tendon_PM_3

value: PM group

value: Exposed PM 2.5 inhalation


title: hkcC_13_3

description: NHEK

value: adult

value: skin

value: primary culture


title: 18946T input


title: 18739N input


title: 18810T input


title: Tendon_PM_2


title: Tendon_PM_1


title: 18739T input


title: RPE-1_H3K27me3_rep2

city: Amsterdam

first: Anoek

last: Friskes

address: Plesmanlaan 121

institute: Netherlands Cancer Institute

data_processing:
54bp single-end reads. Mapped reads were filtered based on mapping quality of 20 using samtools version 0.1.19.
Reads were aligned to Hg38 using BWA (v0.7.17-r1188). Mapped reads were filtered for mapping quality using samtools (> 20)
Duplicates were marked with Picard MarkDupes function (v2.18) (http://broadinstitute.github.io/picard/).

growth_protocol: RPE-1 cells were grown in DMEMF12 with 6% FCS and 1%Pen/Strep. Cells were cultured at 37C at 5% CO2.

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using a E220 focused-ultrasonicator (Covaris).
H3K27me3 (Millipore 07-449), H3K36me3 (Abcam 9050), H3K4me1 (Abcam 8895), H3K4me3 (Abcam 8580) ChIP-seq samples were used from (https://doi.org/10.1101/2021.02.02.429315). 65bp single-end reads were trimmed to 54bp reads and aligned to hg38 using BWA (v0.7.17-r1188). Mapped reads were filtered for mapping quality using samtools < MQ20.  samtools version 0.1.19.Only r1_were used.
H3K27ac, H3K9me3 and H2A.Z ChIP-seq samples were processed for library preparation (Part# 0801-03003, KAPA Biosystems kit) and sequenced with Illumina NovaSeq6000 54bp paired-end reads. Mapped reads were filtered based on mapping quality of 20 using samtools version 0.1.19. Only r1_were used.

treatment_protocol: Chromatin immunoprecipitations (ChIP) were performed as described (Stelloo et al. Oncogene 2018). For each ChIP 5 μg of specified antibody prebound to protein A beads were used.

value: retinal pigment epithelial cells

tag: chip antibody

value: H3K27me3, Millipore 07-449


title: 19342N input


title: 18081N input


title: 18607N input


title: RPE-1_H3K27me3_rep1


title: 17787N input


title: 19282T input


title: 18607T input


title: RPE_H3K36me3_Rep1

value: H3K36me3, Abcam 9050


title: RPE_H3K4me3_Rep2

value: H3K4me3, Abcam 8580


title: 17753N input


title: RPE_H3K4me1_Rep2

value: H3K4me1, Abcam 8895


title: 17753T input


title: RPE_Input


title: 17627T input


title: 19442N H3K27ac ChIP-seq


title: 18481T input


title: BMDCs, fixed L. infantum, rep3

city: Athens

first: Evdokia

last: Karagouni

state: Attica

address: 127 Vas. Sofias Avenue

department: Department of Microbiology

country: Greece

institute: Hellenic Pasteur Institute

data_processing:
Transcript level quantification of RNA-Seq samples was performed using Salmon version 1.2.1. Mouse transcriptome was compiled from GENCODE
Differential Expression Analysis (DEA) was conducted using EdgeR, employing quasi-likelihood F-tests
Gene set enrichment analysis of differentially expressed genes was performed using the R packages limma and clusterProfiler
All samples were quality-checked and pre-processed using FastQC and cutadapt prior to downstream analyses
Assembly: mm10

source_name: bone marrow

growth_protocol:
BMDCs were maintained in RPMI-1640 supplemented with 2 mM L-glutamine, 10 mM HEPES, 24 mM NaHCO3, 100 U/mL penicillin, 10 µg/mL streptomycin and 10% (v/v) heat-inactivated fetal bovine serum in humidified atmosphere with 5% CO2 at 37°C
L. infantum parasites were maintained in RPMI-1640 supplemented with 2 mM L-glutamine, 10 mM HEPES, 24 mM NaHCO3, 100 U/mL penicillin, 10 µg/mL streptomycin and 10% (v/v) heat-inactivated fetal bovine serum at 26°C

extract_protocol:
RNA puriﬁcation was conducted using the Qiagen RNeasy mini kit
RNA libraries for RNA-seq were prepared using Ion Total RNA-Seq Kit v2 following manufacturer's protocols.

treatment_protocol:
BMDCs were exposed  to live or glutarhaldeyde-fixed stationary phase L. infantum promastigotes  (wherever applicable parasites were previously stained with CFSE) at a ratio of infection 20:1 for a total of 24h
L. infantum parasites were fixed by exposing them to 0.1% glutarhaldeyde for 10 min

value: bone marrow

value: dendritic cells

value: fixed L. infantum


title: RPE_H3K4me1_Rep1


title: 18081T input


title: 19441N H3K27ac ChIP-seq


title: BMDCs, live L.infantum, rep1

value: live L. infantum


title: 18810N input


title: 17787T input


title: RPE_H3K36me3_Rep2


title: RPE_H3K4me3_Rep1


title: 19395N H3K27ac ChIP-seq


title: 17627N input


title: 19395T H3K27ac ChIP-seq


title: 19342N H3K27ac ChIP-seq


title: BMDCs, fixed L. infantum, rep1


title: LINC00211_KO_2

city: Marburg

first: Leon

middle: Nicolas

last: Schulte

state: Hessen

address: Hans-Meerwein-Str. 2

department: Institute for Lung Research

country: Germany

institute: Philipps-Universität Marburg

description: LINC00211 promoter deficient THP1 cell clone

data_processing:
RTA version 1.18.66.4 was used for basecalling
bcl2fastq version 1.8.4. was used for demultiplexing
Reads were mapped using the CLC genomics workbench version 10.01 and the GRCh38 human genome annotation with standard settings: mismatch cost = 2; insertion cost = 3; deletion cost = 3; length fraction = 0.8; similarity fraction = 0.8.
RPKMs were calculated based on uniqely mapped read numbers reported by the CLC genomics worbench version 10.01
Genome_build: hg38
Supplementary_files_format_and_content: Tab-delimited text-file including ENSEMBL gene ID, gene alias, chromosome, genomic position, unique gene reads, RPKM

source_name: monocytic leukemia

growth_protocol: THP1 monocytes were cultured in RPMI 1640 medium (Thermo Fisher), containing 10 % FCS and 1% penicillin / streptomycin solution (Thermo Fisher).

extract_protocol:
Cells were washed once with PBS and RNA was extracted using the MirVana microRNA isolation kit (Ambion), following the total RNA isolation procedure. Obtained RNA was DNaseI digested, PCI extracted, precipitated with 30:1 ethanol / sodium-acetate and redissolved in water.
Libraries were prepared using the Illumina TruSeq Stranded mRNA kit according to the manufacturer's protocol
poly(A) RNA-Seq

treatment_protocol: For differentiation, THP1 cells were treated with 20 nM PMA (Sigma Aldrich) for 24 h

value: THP1 (monocytic cell line)

tag: precursor

value: monocyte

tag: donor

value: 1 year old male with acute monocytic leukemia


title: BMDCs, fixed L. infantum, rep2


title: BMDCs, live L.infantum, rep3


title: 19442T H3K27ac ChIP-seq

value: tissue


title: LINC00211_KO_1


title: BMDCs, live L.infantum, rep2


title: BMDCs, control, rep2


title: Ctrl_OE_2

description: Control-transduced THP1 cells (containing empty SparQ backnone)


title: 19441T H3K27ac ChIP-seq


title: BMDCs, control, rep1


title: WT_2

description: Wild-type THP1 cell clone


title: 19342T H3K27ac ChIP-seq


title: 19282N H3K27ac ChIP-seq


title: WT_1

description: Wild-type THP1 cell clone


title: Ctrl_OE_1

treatment_protocol: Cells were transduced with an empty SPARQ lentivector


title: LINC00211_OE_2

description: LINC00211 overexpression THP1 cells (containing LINC00211 cDNA on SparQ backnone)


title: 19282T H3K27ac ChIP-seq


title: LINC00211_OE_1


title: 19106T H3K27ac ChIP-seq


title: 18739T H3K27ac ChIP-seq


title: 18607N H3K27ac ChIP-seq


title: 18739N H3K27ac ChIP-seq


title: WUSCHEL_input

city: shenyang

first: lina

last: cheng

address: dongling road NO.120

department: college of Horticulture

institute: shenyang agriculture university

data_processing:
DAP-seq reads were aligned to the Tomato Genome version SL4.0 (https://solgenomics.net/organism/Solanum_lycopersicum/genome) using Bowtie2 (version:2.2.5).
MACS2 (version:2.1.2) software was used to identify read-enriched regions from the DAP-seq data.
Peak-related genes were annotated using the CHIPseeker R package
The MEME suite (http://meme-suite.org/) was used to detect motifs
MEME (http://meme-suite.org/tools/meme) and DREME (http://meme-suite.org/tools/dreme) were used to detect long and short consensus sequences, respectively.
Supplementary files format and content: SL4.0
Supplementary files format and content: bigWig, narrowPeak (except for Input sample)
Library strategy: DAP-Seq

organism: Solanum lycopersicum

source_name: Ailsa Craig

growth_protocol: greenhouse (16 h of light at 25°C, 8 h of dark at 15°C)

extract_protocol: The DAP genomic DNA (gDNA) library was prepared using the kit from NEBNext® DNA Library Prep Master Mix Set for Illumina

value: Ailsa Craig

value: flower abscission zone

value: Halo


title: 18946N H3K27ac ChIP-seq


title: 18946T H3K27ac ChIP-seq


title: 18810N H3K27ac ChIP-seq


title: 18810T H3K27ac ChIP-seq


title: 18481N H3K27ac ChIP-seq


title: WUSCHEL


title: 760T, Postmortem, Tumor

city: Washington

first: Erin

middle: R

last: Bonner

state: DC

address: 7144 13th Place NW

department: Center for Genetic Medicine Research

institute: Children's National Hospital

hyb_protocol: Illumina EPIC DNA methylation array protocol

scan_protocol: Illumina iScan System

data_processing: IDAT files were uploaded to the molecularneuropathology.org portal (https://www.molecularneuropathology.org/mnp/) and Brain Classifier V11b4 workflow was applied to generate Copy Number Variation plots.

source_name: Pontine tumor, postmortem autopsy

extract_protocol: Gentra PureGene Tissue Kit (QIAGEN)

tag: age at diagnosis

value: 9 years

tag: gender

value: Male

value: Pontine tumor

tag: tumor location

value: Pons

tag: time

value: at postmortem autopsy

tag: diagnosis

value: Diffuse midline glioma


title: 19106N H3K27ac ChIP-seq

tag: cells/tissue


title: 18081N H3K27ac ChIP-seq