title: RA_Polysome4

description:
polysome-associated RNA
RA_FPP4_translated_ORFs_filtered_sorted.bed

data_processing:
Adaptor sequences were trimmed using Cutadapt (v.2.8) with minimum read length of 25bp, and untrimmed outputs retained for RNA-seq reads.
Low-quality reads (score <20 for 10% or more of read) were discarded using FASTQ Quality Filter, FASTX-Toolkit (v.0.0.14).
Reads aligning to rRNA and tRNA sequences were discarded using Bowtie 2 (v2.3.5) and one base was removed from the 3' end of reads.
Unaligned Ribo-seq reads and RNA-seq reads were aligned to the Human reference genome (Gencode v30) using the split-aware aligner STAR (v2.6.1b). The STAR genome index was built with an sjdbOverhang of 73.
Alignments flagged as secondary alignment were filtered out with samtools (v1.9), ensuring 1 genomic position per aligned read. "samtools view -b -F 0X100"
RiboTaper was applied to these data  to find ORFs and quantify the p-site positions per ORF (reported in score column of processed data bed file).
Genome_build: GRCh38
Supplementary_files_format_and_content: bed file of open reading frames determined by RiboTaper pipeline.

extract_protocol:
RNA purification from RNaseI footprinted samples was performed by Trizol RNA extraction. RNA purification from polysome fractions  was  performed  by  isopropanol  precipitation,  followed  by  TURBO  DNase  treatment, acidic phenol/chloroform RNA purification and ethanol precipitation at -80oC overnight. RNA concentration was determined by Nano-drop 2000 software. Two rounds of polyA selection from polysome fractions were performed using oligo (dT) Dynabeads PolyA RNA  was  fragmented  by  alkaline  hydrolysis. 28–34  nt  ribosome  footprints  and  50–80  nt  mRNA fragments were gel purified in 10% (w/v) polyacrylamide-TBE-Urea gel. Ribosome footprints were subjected to rRNA depletion (Illumina RiboZero rRNA removal kit).
5’ stranded libraries were constructed using NEB Next Multiplex Small RNA Library Prep. Resulting cDNA was PCR amplified and gel purified prior to sequencing. Libraries were subjected to 75bp single end RNA Sequsing NextSeq 500 Illumina sequencer,High OutputKit v2.5 (75 Cycles)(Next Generation Sequencing Facility, Faculty of Medicine, University of Leeds).
RNA-seq, Ribo-seq

value: Retinoic acid (final conc. 30μM)


title: CTRL_ADAR_D4_3

status: Public on Jul 16 2021

type: SRA

city: Biberach a.d. Riß

first: Anna-Maria

last: Herzner

address: Birkendorfer Str 65

country: Germany

institute: Boehringer Ingelheim

description:
LIB1114328_SAM24343713
part_1_genes_counts.csv
part_1_intron_counts.csv
part_1_ECR_counts.csv
part_1_editingsites_total_counts.csv
part_1_editingsites_G_counts.csv

library_source: transcriptomic

data_processing:
Reads were aligned to GrCH37 v13 using STAR (V2.5.4a) with the basic two-pass mode allowing for a maximum number of multiple alignments of 1000 and 999 mismatches per read (--outFilterMultimapNmax 1000 --outFilterMismatchNmax 999), however 10% mismatches per read pair using --outFilterMismatchNoverReadLmax 0.1 to increase the detection of A-to-I editing sites. In addition, we allowed introns to be 20-1000000 nt and a 1000000 nt distance between read pair mates.
Aligned reads were summarized to gene level using the R Rsubread package featureCounts function in paired end mode (isPairedEnd=TRUE) based on the GrCH37 gencode V19 GTF annotation, using the default exons as features for counting and genes as meta-features (GTF.featureType="exon" and GTF.attrType="gene_id"). We only allowed uniquely mapping reads by setting the read-quality filter to 255 (minMQS=255).
To quantify introns, we first extracted intron ranges from appris annotation based on https://davetang.org/muse/2013/01/18/defining-genomic-regions/ from the GrCH37 gencode V19 GTF file using awk to filter for appris annotated transcripts (awk ’BEGIN’{OFS=”\t”;} /appris/ {print}’). Exons were extracted from the appris annotated transcripts into bed format using awk ('BEGIN{OFS="\t";} $3=="exon" {print $1,$4-1,$5,$10,$3}'), sorted using bedtools2 sortBed and overlapping exons merged with bedtools2 mergeBed. Next, unique genes of appris-annotated transcripts were extracted using awk as described above, their annotations extracted from the original GTF file, sorted and the merged appris-annotated exons subtracted from genes using bedtools2 subtractBed to yield introns delineated from appris annotated transcripts, saved in bed format for later quantification.
Reads mapping to intron- and editing-cluster-rich-region- features were counted using the R Rsubread package featureCounts function after converting bed files to SAF format, as described for gene quantification, not using the meta-feature flag.
Editing sites were discovered using the SAILOR pipeline (https://github.com/YeoLab/sailor). Total or G counts (indicating adenosine-to-inosine editing) were extracted from *.sorted.rmdup.readfiltered.bam intermediate files generated by the SAILOR pipeline using flags -B -d10000000 -t DPR,INFO/DPR,DP4 -uf, using the -l flag with a bed annotation of the primary selection of editing sites. INFO/DPR counts were used to determine nucleotide counts. T and C counts for sense or A and G counts for antisense reads, respectively, were considered sequencing errors and added to reference counts.
Genome_build: GrCH37 v13
Supplementary_files_format_and_content: Raw gene counts, comma separated values
Supplementary_files_format_and_content: Raw intron counts, comma separated values
Supplementary_files_format_and_content: Raw counts of regions rich in RNA editing clusters (ECR), comma separated values
Supplementary_files_format_and_content: Raw G counts at unfiltered, putative editing sites, comma separated values
Supplementary_files_format_and_content: Raw total (G+H) counts at unfiltered, putative editing sites, comma separated values

molecule: total RNA

organism: Homo sapiens

growth_protocol: THP-1 were grown in RPMI, 10% FBS, 1x glutamax and 1x Pen/Strep at 37°C and 5% CO2

extract_protocol:
Cells were precipitated by centrifugation and either directly subjected to RNA extraction or separated into cytosolic vs nuclear/mitochondrial fractions as described in Baghirova et al, 2015 (PMID 26740924), using an increased digitonin concentration of 300 µg/mL. RNA extraction was performed using the Qiagen RNeasy Mini Kit including on-column DNase digest.
Libraries were prepared using the TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero Gold kit (Illumina).

treatment_protocol: THP-1 were nucleofected with 2 ul of each gRNA (annealed crRNA:tracrRNA, idt) as described in Cuellar et al, 2017 (PMID 28887438).

tag: cell type

value: monocytic cell line

tag: cell line

tag: background genotype

value: STING deficient, cas9 transgenic

tag: grna #1

tag: grna #2

value: ADAR

tag: treatment

value: medium

tag: time point

value: day 4

tag: compartment

value: whole cell

tag: replicate


title: RA_Polysome3

city: Leeds

first: Julie

last: Aspden

address: Woodhouse

department: FBS

country: United Kingdom

institute: University of Leeds

description:
polysome-associated RNA
RA_FPP3_translated_ORFs_filtered_sorted.bed

source_name: human neuroblastoma

growth_protocol: Human neuroblastoma SH-SY5Y cells, were cultured in Dulbecco’s Modified Eagle Medium (DMEM 4.5g/L Glucose with L-Glutamine) supplemented with 1% (v/v) Penicillin/Streptomycin and 10% Fetal Bovine Serum (FBS) at 37oC, 5% CO2.

treatment_protocol: Neuronal differentiation was performed using retinoic acid (RA) at passage 4. All trans Retinoic Acid (RA, Sigma) was added to cells 24h after plating, at final concentration of 30μM.


title: rad53-1 tof1-aid +IAA BrdU IP rep1

city: New York

first: Xu

last: Hua

state: New York

address: 1130 St Nicholas Ave

department: Institute for Cancer Genetics

country: USA

institute: Columbia University

library_source: genomic

data_processing:
Library strategy: BrdU-Seq
Reads were mapped using bowtie2.
Read coverage in each bin was calculated using Deeptools. Histone bias was computed from trimmed, mapped, unique reads in each bin as Bias=(W-C)/(W+C), where W and C are the number of reads mapped on Crick and Watson strand in each bin, respectively.
Genome_build: For yeast, reads were mapped to saccer3.
Supplementary_files_format_and_content: bw files, the score represents reads coverage at each genomic position. Read coverage on plus strand, minus strand and total were calculated seperately.

molecule: genomic DNA

organism: Saccharomyces cerevisiae

source_name: rad53-1 tof1-aid +IAA BrdU IP

growth_protocol: Yeast cells grown to OD600=0.4-0.5 in yeast extract peptone + 2% dextrose (YPD) were synchronized with a-factor (5 mg/ml, synthesized by EZBiolab) for 1.5 hr at 25°C, adding additional 5 mg/ml a-factor after 1.5 hr. G1-arrested cells were released into YPD medium at 30°C containing 400 mg/ml bromodeoxyuridine (BrdU, Sigma B5002) and 0.2M hydroxyurea (HU, Chem-Impex 24533). 45 minutes after release into S phase at 30°C, cell fixation was performed with 1% paraformaldehyde for 20 minutes at room temperature followed by the quenching with 0.125M glycine for 5 minutes at room temperature.

extract_protocol:
Input DNA obtained from the Chelex-100 extraction was used for BrdU immunoprecipitation. Briefly, DNA was denatured at 95°C for 5 minutes followed by incubation in an ice-water bath for 5 minutes. Samples were then diluted 10 fold with BrdU IP buffer solution (1XPBS, 0.0625% Triton X-100(v/v), 6.7 mg/mL Escherichia coli tRNA, 0.40mL/mL BrdU antibody (BD Bioscience)). After a 2 hr incubation at 4°C, 20 mL of protein G Sepharose beads (GE Healthcare) were added followed by an additional 1 hr incubation at 4°C. Protein G beads were extensively washed and DNA was eluted with 100 mL Tris-EDTA buffer containing 1% SDS at 65°C for 15 minutes.
The eluted DNA was purified with Minelute PCR kit (QIAGEN) and sequenced after  ssDNA library preparation using the Accel-NGS 1S Plus DNA library kit (Swift BioSciences). Samples were pooled and sequenced using paired-end sequencing on Illumina platforms at Columbia University Genome Center.

treatment_protocol: ChIP-ssSeq and BrdU-IP-ssSeq experiments were performed as described previously (Gan et al., 2017)

tag: experiment

value: BrdU

tag: condition

value: with IAA

tag: genotype

value: rad53-1 tof1-aid

tag: chip antibody

value: BrdU antibody (BD Bioscience)


title: CTRL_ADAR_D4_2

description:
LIB1114327_SAM24343712
part_1_genes_counts.csv
part_1_intron_counts.csv
part_1_ECR_counts.csv
part_1_editingsites_total_counts.csv
part_1_editingsites_G_counts.csv


title: human fetal skin-10w

city: Guangzhou

first: Yingping

last: Xu

state: Guangdong

address: LuJing Road

country: China

institute: Sourthern Medical University

data_processing:
10x cellrange pipeline
Supplementary_files_format_and_content: features
Supplementary_files_format_and_content: matrix
Supplementary_files_format_and_content: barcodes

source_name: Embryo

extract_protocol:
Human fetal skin was dissected and washed with phosphate-buffered saline (PBS; HyClone, Logan, UT, USA: SH30256.01) on ice after removing fat tissue. The skin was cut into small pieces in digestion medium composed of 1 mg/ml collagenase IV (Shanghai Yeasen Biotechnology Co, Shanghai, China; 40510ES60) in RPMI1640 medium (HyClone; C11875500BT), and incubated at 37°C for 40-60 min. The suspension was filtered through a 70-μm cell strainer (BD Biosciences; Franklin Lakes, NJ, USA; 352350) with gently grinding to release cells. After neutralizing the enzymes with FACS buffer (1 PBS with 2% fetal bovine serum), cells were pelleted at 2000 rpm for 7 min at 4°C and resuspended in FACS buffer, and labeled with specific antibodies in FACS buffer for 30 min on ice. After washing, the cells were resuspended in 1 PBS and were confirmed to be living cells by 4’, 6-diamidino-2-phenylindole (DAPI) staining for 5 min. CD45+ cells were sorted on a FACSAria III flow cytometer (BD Biosciences), and data analysis was performed using FlowJo v10 software (TreeStar, Ashland, OR, USA). Fetal skin was processed as described above and cell suspensions were labeled with appropriate antibodies against cell surface markers on ice for 30 min, followed by staining for 5 min with DAPI. Cells were obtained on a Celesta cytometer (BD Biosciences) and analyzed using FlowJo v10 (TreeStar).
Single cells were obtained as gel bead-in-emulsions (GEMs) using the 10× Genomics (Pleasanton, CA, USA) Chromium platform according to the manufacturer’s protocol. Briefly, skin cell suspensions were combined with reverse transcription master mix and loaded onto the 10× Genomics Single Cell 3’ chip, and partitioned into GEMs with gel beads precoated with oligonucleotides containing a poly-dT primer sequence to capture released mRNAs, a 16-bp 10× barcode for cell indexing, and a 10-bp unique molecular identifier (UMI) to distinguish between transcripts. After reverse transcription, barcoded cDNAs for each sample were amplified to generate a sufficient volume for library construction using the Single Cell 3’ Reagent Kit (v2 or v3 chemistry).
Libraries were subjected to 150-bp paired-end sequencing, which was performed by Novogene (Beijing, China) on a NovaSeq 6000 system (Illumina, San Diego, CA, USA).

tag: developmental stage

value: human fetal skin-10w


title: rad53-1 tof1-aid -IAA BrdU IP rep1

source_name: rad53-1 tof1-aid -IAA BrdU IP

value: no IAA


title: RA_FP4

description:
ribosome footprints
RA_FPP4_translated_ORFs_filtered_sorted.bed


title: RA_FP5

description:
ribosome footprints
RA_FPP5_translated_ORFs_filtered_sorted.bed


title: CTRL_ADAR_D4_1

description:
LIB1114326_SAM24343711
part_1_genes_counts.csv
part_1_intron_counts.csv
part_1_ECR_counts.csv
part_1_editingsites_total_counts.csv
part_1_editingsites_G_counts.csv


title: mrc1D_rad9_IAA input rep2

source_name: mrc1D_rad9_IAA input

value: Input

value: mrc1D rad9


title: rad53-1 mrc1-aid +IAA BrdU IP rep1

source_name: rad53-1 mrc1-aid +IAA BrdU IP

value: rad53-1 mrc1-aid


title: CTRL_ADAR_D3_3

description:
LIB1114325_SAM24343710
part_1_genes_counts.csv
part_1_intron_counts.csv
part_1_ECR_counts.csv
part_1_editingsites_total_counts.csv
part_1_editingsites_G_counts.csv

value: day 3


title: IgG_sequence

city: San Francisco

first: Wei

last: Qin

state: CA

address: 550 Gene Friend Way Apt509

institute: Stanford University

data_processing:
Briefly, paired-end reads were harvested from Illumina NovaSeq 6000 sequencer, and were quality controlled by Q30. After 3’ adaptor-trimming and low quality reads removing by cutadapt software (v1.9.3), the high quality trimmed reads were aligned to the human reference genome (UCSC hg19) with hisat2 software (v2.0.4). Then, guided by the Ensembl gtf gene annotation file , cuffdiff software (v2.2.1, part of cufflinks) was used to get the gene level FPKM as the expression profiles of  mRNA, and fold change and p-value were calculated based on FPKM, differentially expressed mRNAs were identified.
Genome_build: UCSC hg19
Supplementary_files_format_and_content: FPKM

source_name: HEK IgG

growth_protocol: HEK293T cells from the ATCC (passages <25) were cultured in a 1:1 DMEM/MEM mixture (Cellgro) supplemented with 10% fetal bovine serum, 100 units/mL penicillin, and 100 mg/mL streptomycin at 37 °C under 5% CO2.

extract_protocol:
Cells were lysed in an ice-cold lysis buffer. Then, RNA immunoprecipitation (RIP) was performed as described (Zhao et al., 2008). RNA extracted using Trizol by following manufacturer’s instruction (Invitrogen).
rRNAs were removed from the immunoprecipitated RNA and input RNA samples by using Ribo-Zero™ rRNA Removal Kit (Illumina, San Diego, CA,  USA). RNA libraries were constructed by using rRNA-depleted RNAs with TruSeq Stranded Total RNA Library Prep Kit (Illumina, San Diego, CA,  USA) according to the manufacturer’s instructions. Libraries were controlled for quality and quantified using  the BioAnalyzer 2100 system (Agilent Technologies, Inc., USA).
10 pM libraries were denatured as single-stranded DNA molecules, captured on Illumina flow cells, amplified in situ as clusters and finally sequenced for 150 cycles on Illumina NovaSeq Sequencer according to the manufacturer’s instructions.

treatment_protocol: No treatment

tag: antibody

value: IgG negative control


title: IP_sequence

value: SYNJ2BP antibody (HPA000866-100UL, Sigma-Aldrich)


title: RA_FP3

description:
ribosome footprints
RA_FPP3_translated_ORFs_filtered_sorted.bed

value: Retinoic acid (final conc. 30μM)


title: RA_Polysome5

description:
polysome-associated RNA
RA_FPP5_translated_ORFs_filtered_sorted.bed


title: CTRL_ADAR_D3_2

description:
LIB1114324_SAM24343709
part_1_genes_counts.csv
part_1_intron_counts.csv
part_1_ECR_counts.csv
part_1_editingsites_total_counts.csv
part_1_editingsites_G_counts.csv

value: monocytic cell line

value: STING deficient, cas9 transgenic

value: ADAR


title: mtrA3pJR965-H37Rv-16

city: Seattle

first: Eliza

last: Peterson

state: WA

address: 401 Terry Ave N

institute: Institute for Systems Biology

data_processing:
Illumina RiboZero bacteria kit was used for rRNA depletion. Samples were sequenced on the NextSeq sequencing instrumetn in mid output 150 v2 flow cell. Paired-end 75 bp reads were checked for technical artifacts using FastQC following Illumina default quality filtering steps. Raw FASTQ read data were processed using the R package DuffyNGS.
Genome_build: Mycobacterium tuberculosis H37Rv ASM19595v2 or Mycobacterium smegmatis mc2155 (ASM1500v1)
Supplementary_files_format_and_content: tab-delimited text file includes RPKM and read counts for each sample

organism: Mycobacterium tuberculosis

source_name: bacterial culture

growth_protocol: Samples grown in 7H9-rich media at 37 degrees C with shaking

extract_protocol:
Cells pellets were spun down and immediately frozen in liquid nitrogen and stored at -80 degrees C until RNA isolation. Cell pellets were transferred to a tube containing Lysing Matrix B, and vigorously shaken at max speed for 30 s in a FastPrep 120 homogenizer three times. This mixture was centPOAuged at max speed for 1 min and the supernatant was transferred to a fresh tube. RNA was isolated using phenol-chloroform extraction method, followed by DNase treatment.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Anhydrotetracycline induced knockdown of mtrA

tag: strain

tag: induction

value: uninduced

tag: induction time

value: 4 days


title: Control_Polysome5

description:
polysome-associated RNA
Control_FPP5_translated_ORFs_filtered_sorted.bed

tag: cell type

value: Control (DMSO)


title: human fetal skin-11w

value: human fetal skin-11w


title: mtrA3pJR965-H37Rv-15


title: CTRL_ADAR_D3_1

description:
LIB1114323_SAM24343708
part_1_genes_counts.csv
part_1_intron_counts.csv
part_1_ECR_counts.csv
part_1_editingsites_total_counts.csv
part_1_editingsites_G_counts.csv

tag: cell line

tag: background genotype

value: medium

value: whole cell


title: rad53-1 tof1-aid +IAA input rep1

source_name: rad53-1 tof1-aid +IAA input

value: with IAA

value: rad53-1 tof1-aid


title: rad53-1 mrc1-aid -IAA BrdU IP rep1

source_name: rad53-1 mrc1-aid -IAA BrdU IP

value: BrdU

value: no IAA

value: BrdU antibody (BD Bioscience)


title: rad53-1 tof1-aid -IAA input rep1

source_name: rad53-1 tof1-aid -IAA input

value: Input


title: Control_Polysome4

description:
polysome-associated RNA
Control_FPP4_translated_ORFs_filtered_sorted.bed


title: mtrA3pJR965-H37Rv-14


title: hnRNPC_CTRL_D5_3

description:
LIB1114313_SAM24343698
part_1_genes_counts.csv
part_1_intron_counts.csv
part_1_ECR_counts.csv
part_1_editingsites_total_counts.csv
part_1_editingsites_G_counts.csv

tag: grna #1

value: hnRNPC

tag: grna #2

value: day 5


title: rad53-1 mrc1-aid +IAA input rep1

source_name: rad53-1 mrc1-aid +IAA input

value: rad53-1 mrc1-aid


title: Control_Polysome3

description:
polysome-associated RNA
Control_FPP3_translated_ORFs_filtered_sorted.bed

tag: treatment


title: mtrA3pJR965-H37Rv-13


title: rad53-1 mrc1-aid -IAA input rep1

source_name: rad53-1 mrc1-aid -IAA input


title: hnRNPC_CTRL_D5_1

description:
LIB1114311_SAM24343696
part_1_genes_counts.csv
part_1_intron_counts.csv
part_1_ECR_counts.csv
part_1_editingsites_total_counts.csv
part_1_editingsites_G_counts.csv

value: monocytic cell line

value: STING deficient, cas9 transgenic

tag: time point

tag: compartment


title: Control_FP5

description:
ribosome footprints
Control_FPP5_translated_ORFs_filtered_sorted.bed


title: hnRNPC_CTRL_D4_3

description:
LIB1114310_SAM24343695
part_1_genes_counts.csv
part_1_intron_counts.csv
part_1_ECR_counts.csv
part_1_editingsites_total_counts.csv
part_1_editingsites_G_counts.csv

value: day 4

tag: replicate


title: Control_FP4

description:
ribosome footprints
Control_FPP4_translated_ORFs_filtered_sorted.bed


title: hnRNPC_CTRL_D5_2

description:
LIB1114312_SAM24343697
part_1_genes_counts.csv
part_1_intron_counts.csv
part_1_ECR_counts.csv
part_1_editingsites_total_counts.csv
part_1_editingsites_G_counts.csv


title: mec1-100sml1DBrdU rep1

tag: experiment

value: mec1-100 sml1D


title: mtrA3pJR965-H37Rv-ATc-12

value: ATc induced

value: 4 days


title: Control_FP3

description:
ribosome footprints
Control_FPP3_translated_ORFs_filtered_sorted.bed

value: Control (DMSO)


title: mtrA3pJR965-H37Rv-ATc-11


title: mtrA3pJR965-H37Rv-ATc-10


title: hnRNPC_CTRL_D4_2

description:
LIB1114309_SAM24343694
part_1_genes_counts.csv
part_1_intron_counts.csv
part_1_ECR_counts.csv
part_1_editingsites_total_counts.csv
part_1_editingsites_G_counts.csv

value: medium

value: whole cell


title: PAPERCLIP for LN229 cells, siPCF11, replicate 2

city: Pittsburgh

first: Hun-Way

last: Hwang

state: PA

address: 3550 Terrace Street

department: Department of Pathology

institute: University of Pittsburgh

data_processing:
Library strategy: PAPERCLIP (Poly(A) binding Protein-mediated mRNA 3′ End Retrieval by CrossLinking ImmunoPrecipitation)
The processing of raw reads was performed using the CIMS software package previously described (Moore et al. 2014). In brief, the raw reads were filtered based on quality score.
Filtered reads with the exact sequence were collapsed into one.
The 5′ degenerate linker was removed.
Poly(A) sequence at the 3′ end was then trimmed using CutAdapt (Martin 2011). Trimmed reads that are at least 25-nt in length are retained for mapping to reference genome (hg19).
Mapping was performed using Novoalign without trimming. A minimum of 25-nt match to the genome sequence was required and only those reads mapped unambiguously to the genome (single hits) were kept for downstream analysis.
Reads mapping to the same genomic positions without distinct barcodes were further collapsed into a single tag as previously described (Moore et al. 2014). All reads went through the entire process are referred to as “unique reads” and were used for poly(A) site annotation and other downstream analysis.
Unique reads from both replicates were merged. CIMS software package was used to cluster overlapping reads and to determine the read counts (PH) for each cluster. The clusters were filtered by PH before downstream analysis. For each filtered cluster, the most abundant 3′ end from all reads in the cluster was assigned as the poly(A) site. The 3′ most position was selected if there was a tie in abundance for multiple 3′ ends. Please refer to the accompanying publication for further information.
Note: The submitted raw files are de-multiplexed and quality-filtered without further processing.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: txt files for unique read counts at gene level (RefSeq).

source_name: LN229 cells

extract_protocol:
Sample preparation, immunoprecipitation, SDS-PAGE and RNA extraction were performed using the PAPERCLIP protocol (Hwang et al. Cell Rep. 2016).
The sequencing library was constructed using the PAPERCLIP method (Hwang et al. Cell Rep. 2016). The library contains a 11-nt degenerate linker sequence at the 5′ end (3-nt degenerate sequence, 4-nt sample multiplexing index and 7-nt random barcode) as described in (Hwang et al. Neuron 2017).

tag: sirna

tag: index

value: Index 6:GACT


title: mec1-100sml1Dinput rep2

tag: genotype

tag: chip antibody


title: hnRNPC_CTRL_D4_1

description:
LIB1114308_SAM24343693
part_1_genes_counts.csv
part_1_intron_counts.csv
part_1_ECR_counts.csv
part_1_editingsites_total_counts.csv
part_1_editingsites_G_counts.csv


title: hnRNPC_CTRL_D3_3

description:
LIB1114307_SAM24343692
part_1_genes_counts.csv
part_1_intron_counts.csv
part_1_ECR_counts.csv
part_1_editingsites_total_counts.csv
part_1_editingsites_G_counts.csv

value: day 3


title: mtrA2pJR965-H37Rv-8

tag: strain

value: uninduced


title: mec1-100sml1Dinput rep1


title: mtrA2pJR965-H37Rv-7

tag: induction


title: PAPERCLIP for LN229 cells, siPCF11, replicate 1

value: Index 4:TAGC


title: hnRNPC_CTRL_D3_2

description:
LIB1114306_SAM24343691
part_1_genes_counts.csv
part_1_intron_counts.csv
part_1_ECR_counts.csv
part_1_editingsites_total_counts.csv
part_1_editingsites_G_counts.csv


title: mtrA2pJR965-H37Rv-6

tag: induction time


title: mec1-100BrdU rep1

value: BrdU

value: BrdU antibody (BD Bioscience)


title: PAPERCLIP for LN229 cells, siCtrl, replicate 2

value: siCtrl

value: Index 5:AGTC


title: mec1-100input rep2

value: Input


title: mec1-100BrdU rep2


title: hnRNPC_CTRL_D3_1

description:
LIB1114305_SAM24343690
part_1_genes_counts.csv
part_1_intron_counts.csv
part_1_ECR_counts.csv
part_1_editingsites_total_counts.csv
part_1_editingsites_G_counts.csv

tag: cell type

value: monocytic cell line

value: STING deficient, cas9 transgenic

value: hnRNPC


title: A549-mgt1 cells-chip_RNAPII + GSK126

city: Berlin

first: Gaetano

last: Gargiulo

address: Robert-Rössle-Straße 10

institute: Max-Delbrück-Centrum für Molekulare Medizin

data_processing:
Basecalls were performed using bcl2fastq v2.17 for NextSeq output.
ChIP-seq reads were trimmed from 3' end until the final base had a quality score > 30, using Trimmomatic v0.33, discarding reads left with < 20 bp.
Reads were aligned to genome hg38 using Bowtie version 0.12.9. Only uniquely mapping reads with at most two mismatches were retained.
Peak calling performed using MAC2 version 1.4, peaks  were calculated using MACS with cut-off P > 1.0e-5 and assuming fragment size of 300bp.
Genome_build: hg38
Supplementary_files_format_and_content: bigWig files were generated using the genomicRanges R package. Score represents the normalized coverage of fragments at a given genomic coordinate.

growth_protocol: A549 cells were cultured in RPMI medium with 10% FBS and antibiotics

extract_protocol:
Chip assay was conducte following the SimpleCHIP Enzymatic Chromatin IP kit (magnetic bead #9003)
Libraries were prepared according to Illumina's instructions .

treatment_protocol: All ChIP-seq experiments were performed under standard conditions, with the exception of the GSK126-RNAPII. For this experiment, A549 were propagated under 5 uM GSK126 for eleven days and split at low confluence.

value: human lung adenocarcinoma cell line

value: lung carcinoma

tag: tissue

tag: antibody


title: mec1-100sml1DBrdU rep2

value: mec1-100 sml1D


title: mtrA2pJR965-H37Rv-5

value: 4 days


title: CTRL_CTRL_D5_3

description:
LIB1114304_SAM24343689
part_1_genes_counts.csv
part_1_intron_counts.csv
part_1_ECR_counts.csv
part_1_editingsites_total_counts.csv
part_1_editingsites_G_counts.csv

tag: cell line

tag: background genotype

tag: grna #1

value: medium

value: day 5

value: whole cell


title: PAPERCLIP for LN229 cells, siCtrl, replicate 1

value: Index 3:CGAT


title: mtrA2pJR965-H37Rv-ATc-4

value: ATc induced


title: A549-mgt1 cells-chip_RNAPII

tag: treatment

value: untreated


title: mec1-100input rep1


title: mrc1D input rep2

source_name: mrc1D input


title: mtrA3pJR965-H37Rv-ATc-9


title: mtrA2pJR965-H37Rv-ATc-3


title: CTRL_CTRL_D5_1

description:
LIB1114302_SAM24343687
part_1_genes_counts.csv
part_1_intron_counts.csv
part_1_ECR_counts.csv
part_1_editingsites_total_counts.csv
part_1_editingsites_G_counts.csv

tag: grna #2

tag: time point

tag: compartment


title: mtrA2pJR965-H37Rv-ATc-2


title: mrc1D input rep1

tag: experiment


title: A549-mgt1 cells- chip IgG

value: chip IgG


title: mrc1D brdu rep2

source_name: mrc1D brdu

value: BrdU

value: BrdU antibody (BD Bioscience)


title: CTRL_CTRL_D4_3

description:
LIB1114301_SAM24343686
part_1_genes_counts.csv
part_1_intron_counts.csv
part_1_ECR_counts.csv
part_1_editingsites_total_counts.csv
part_1_editingsites_G_counts.csv

value: day 4

tag: replicate


title: mtrA2pJR965-H37Rv-ATc-1


title: CTRL_CTRL_D4_2

description:
LIB1114300_SAM24343685
part_1_genes_counts.csv
part_1_intron_counts.csv
part_1_ECR_counts.csv
part_1_editingsites_total_counts.csv
part_1_editingsites_G_counts.csv

value: monocytic cell line


title: A549-mgt1 cells- chip DOT1L

value: chip DOT1L


title: A549-mgt1 cells- chip BRD2

value: chip BRD2


title: mrc1D brdu rep1

tag: genotype


title: CTRL_CTRL_D4_1

description:
LIB1114299_SAM24343684
part_1_genes_counts.csv
part_1_intron_counts.csv
part_1_ECR_counts.csv
part_1_editingsites_total_counts.csv
part_1_editingsites_G_counts.csv

value: STING deficient, cas9 transgenic


title: mrc1-AQ input rep2

source_name: mrc1-AQ input

value: Input

tag: chip antibody


title: MtrA-pH5-induced-2_S12

data_processing:
Illumina RiboZero bacteria kit was used for rRNA depletion. Samples were sequenced on the NextSeq sequencing instrumetn in mid output 150 v2 flow cell. Paired-end 75 bp reads were checked for technical artifacts using FastQC following Illumina default quality filtering steps. Raw FASTQ read data were processed using the R package DuffyNGS.
Genome_build: Mycobacterium tuberculosis H37Rv ASM19595v2
Supplementary_files_format_and_content: tab-delimited text file includes RPKM and read counts for each sample

extract_protocol:
Cell pellets were spun down and immediately frozen in liquid nitrogen and stored at -80 degrees C until RNA isolation. Cell pellets were transferred to a tube containing Lysing Matrix B, and vigorously shaken at max speed for 30 s in a FastPrep 120 homogenizer three times. This mixture was centrifuged at max speed for 1 min and the supernatant was transferred to a fresh tube. RNA was isolated using phenol-chloroform extraction method, followed by DNase treatment.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Induction of mtrA overexpression in either pH 7.0 or pH 5.6 for 18 h

tag: strain

tag: time

value: 18 hour

tag: ph


title: MtrA-pH5-induced-2_S11

tag: induction


title: A549-mgt1 cells- chip ARID1A

tag: cell type

value: human lung adenocarcinoma cell line

value: lung carcinoma

tag: tissue

value: chip ARID1A


title: CTRL_CTRL_D3_3

description:
LIB1114298_SAM24343683
part_1_genes_counts.csv
part_1_intron_counts.csv
part_1_ECR_counts.csv
part_1_editingsites_total_counts.csv
part_1_editingsites_G_counts.csv

tag: cell line

value: medium

value: day 3

value: whole cell


title: CTRL_CTRL_D5_2

description:
LIB1114303_SAM24343688
part_1_genes_counts.csv
part_1_intron_counts.csv
part_1_ECR_counts.csv
part_1_editingsites_total_counts.csv
part_1_editingsites_G_counts.csv

tag: background genotype

value: day 5


title: mrc1-AQ input rep1


title: A549-mgt1 cells- chip H3K273ac

value: untreated

tag: antibody

value: chip H3K273ac


title: mrc1-AQ brdu rep2

source_name: mrc1-AQ brdu

value: BrdU

value: BrdU antibody (BD Bioscience)


title: MtrA-pH5-uninduced-2_S9

value: uninduced


title: MtrA-pH5-induced-2_S10

value: ATc induced


title: CTRL_CTRL_D3_2

description:
LIB1114297_SAM24343682
part_1_genes_counts.csv
part_1_intron_counts.csv
part_1_ECR_counts.csv
part_1_editingsites_total_counts.csv
part_1_editingsites_G_counts.csv

value: monocytic cell line

tag: grna #1

tag: treatment


title: A549-mgt1 cells- input

value: input


title: mrc1-AQ brdu rep1


title: CTRL_CTRL_D3_1

description:
LIB1114296_SAM24343681
part_1_genes_counts.csv
part_1_intron_counts.csv
part_1_ECR_counts.csv
part_1_editingsites_total_counts.csv
part_1_editingsites_G_counts.csv

value: STING deficient, cas9 transgenic

tag: grna #2

tag: time point


title: MtrA-pH5-uninduced-2_S8

value: 18 hour

tag: experiment


title: A549-mgt1 cells- chip H3K273me

value: human lung adenocarcinoma cell line

value: chip H3K273me


title: MtrA-pH5-uninduced-2_S7


title: mec1-100 sml1D Rfa1 ChIP rep1

data_processing:
Reads were mapped using bowtie2.
Read coverage in each bin was calculated using Deeptools. Histone bias was computed from trimmed, mapped, unique reads in each bin as Bias=(W-C)/(W+C), where W and C are the number of reads mapped on Crick and Watson strand in each bin, respectively.
Genome_build: For yeast, reads were mapped to saccer3.
Supplementary_files_format_and_content: bw files, the score represents reads coverage at each genomic position. Read coverage on plus strand, minus strand and total were calculated seperately.

source_name: mec1-100 sml1D Rfa1 ChIP

value: mec1-100 sml1D

value: anti-Rfa1 antibody (gift from Dr. Steven Brill)


title: mec1-100 sml1D Rfa1 ChIP rep2


title: MtrA-pH7-induced-2_S6


title: EV_TGFb_3

city: Sydney

first: Mayada

last: Metwally

state: NSW

address: 176 Hawkesbury Rd , Westmead

country: Australia

institute: WIMR

description:
Control Empty vector
EV_TGFb_3
X167

data_processing:
Image analysis and base calling were done with Illumina CASAVA-1.8.2. This yielded a median of 29.9M usable reads per sample. . Read alignment and junction mapping to genome build GRCh38 was accomplished using STAR version 2.7.2b (Dobin, 2013 #573). Known splice junctions from mm10 were supplied to the aligner and de novo junction discovery was also permitted. Differential gene expression analysis and statistical testing were performed using Cuffdiff2 version 2.2.1, employing the Ensembl genome annotation. Transcript expression was calculated as gene-level relative abundance in fragments per kilobase of exon model per million mapped fragments and employed correction for transcript abundance bias.
Genome_build: mm10
Supplementary_files_format_and_content: FPKM

organism: Mus musculus

source_name: JS1 cell line

extract_protocol: Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers. Then the second strand cDNA was synthesized using dUTP, instead of dTTP. The directional library was ready after end repair, A-tailing, adapter ligation, size selection, USER enzyme digestion, amplification, and purification

value: TLR4-/- Mouse Hepatic Stellate Cells Expressing WT TLR4

value: Hepatic Stellate Cells

tag: transduced with

value: Control Empty vector

value: TGFBeta


title: A549-mgt1 cells- chip ZMYND8

value: lung carcinoma

value: untreated

value: chip ZMYND8


title: mec1-100 Rfa1 chip rep2

source_name: mec1-100 Rfa1 chip

tag: genotype


title: EV_3

description:
Control Empty vector
EV_3
X165

value: No treatment (Baseline)


title: EV_2

description:
Control Empty vector
EV_2
X164


title: MtrA-pH7-induced-2_S5

value: ATc induced


title: MtrA-pH7-induced-2_S4


title: MtrA-pH7-uninduced-2_S3

value: uninduced


title: 3367_construct_isotype_24h_rep3

city: Bonn

first: Joachim

last: Schultze

state: NRW

address: Carl-Troll-Strasse 31

department: Genomics and Immunoregulation

institute: LIMES (Life and Medical Sciences Center Genomics and Immunoregulation)

description:
3367
mRNA
processed data file: raw_expression.csv
processed data file: normalized_expression.csv

data_processing:
Base calling and de-multiplexing using CASAVA version 1.8.2.
Pseudo-alignment was performed with Kallisto version 0.44.0 with default settings against the gencode reference transcriptome vM16.
Transcript abundance estimations were imported to R and summarized on gene level using tximport (Soneson et al., 2015).
Downstream analyses were performed using DESeq2 (Love et al., 2014).
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: Comma-separated files containing raw (raw_expression.csv) and DESeq2 normalized (normalized_expression.csv) expression values.

source_name: Bone-marrow derived macrophages

growth_protocol: Bone marrow was flushed from the femurs and tibias of mice and cultured for 7 days in medium containing 2.5 % supernatant of a GM-CSF-producing cell line.

extract_protocol:
RNA was isolated with Trizol and miRNeasy micro kit (Qiagen) according to the manufacturer’s protocol.
Library construction was performed according to the manufacturer´s instructions using the Tru-Seq RNA library preparation kit v2. 100 ng of RNA was converted into cDNA libraries.
75 bp single-end run was performed on a HiSeq1500.

treatment_protocol: Bone-marrow-derived macrophages were treated with FcMR or isotype control for 4 h, 12 h and 24 h.

tag: genetic background

value: Bone-marrow derived macrophages


title: mec1-100 Rfa1 chip rep1

tag: chip antibody


title: Plasmid_TGFb_2

description:
Over expression of XPO4
Plasmid_TGFb_2
X162

value: Over expression of XPO4


title: 3366_construct_isotype_24h_rep2

description:
3366
mRNA
processed data file: raw_expression.csv
processed data file: normalized_expression.csv


title: MtrA-pH7-uninduced-2_S2

tag: strain

tag: time

value: 18 hour


title: Plasmid_TGFb_3

description:
Over expression of XPO4
Plasmid_TGFb_3
X163


title: Plasmid_2

description:
Over expression of XPO4
Plasmid_2
X160


title: EV_TGFb_2

description:
Control Empty vector
EV_TGFb_2
X166


title: MtrA-pH7-uninduced-2_S1

tag: induction

tag: ph


title: 3364_construct_FcMR_24h_rep3

description:
3364
mRNA
processed data file: raw_expression.csv
processed data file: normalized_expression.csv

tag: cell type


title: EV_TGFb_1

description:
Control Empty vector
EV_TGFb_1
X159

tag: cell line


title: EV_TGFb_0

description:
Control Empty vector
EV_TGFb_0
X158


title: EV_1

description:
Control Empty vector
EV_1
X157


title: MtrA-pH5-induced-1_S11


title: 3362_construct_FcMR_24h_rep1

description:
3362
mRNA
processed data file: raw_expression.csv
processed data file: normalized_expression.csv


title: MtrA-pH5-induced-1_S12


title: 3365_construct_isotype_24h_rep1

description:
3365
mRNA
processed data file: raw_expression.csv
processed data file: normalized_expression.csv


title: MtrA-pH5-induced-1_S10


title: EV_0

description:
Control Empty vector
EV_0
X156


title: 3361_construct_isotype_12h_rep3

description:
3361
mRNA
processed data file: raw_expression.csv
processed data file: normalized_expression.csv


title: MtrA-pH5-uninduced-1_S9


title: Plasmid_TGFb_1

description:
Over expression of XPO4
Plasmid_TGFb_1
X155


title: MtrA-pH5-uninduced-1_S8


title: Plasmid_TGFb_0

description:
Over expression of XPO4
Plasmid_TGFb_0
X154


title: 3363_construct_FcMR_24h_rep2

description:
3363
mRNA
processed data file: raw_expression.csv
processed data file: normalized_expression.csv


title: 3359_construct_isotype_12h_rep1

description:
3359
mRNA
processed data file: raw_expression.csv
processed data file: normalized_expression.csv


title: 3360_construct_isotype_12h_rep2

description:
3360
mRNA
processed data file: raw_expression.csv
processed data file: normalized_expression.csv


title: Plasmid_1

description:
Over expression of XPO4
Plasmid_1
X153


title: MtrA-pH5-uninduced-1_S7


title: MtrA-pH7-induced-1_S6


title: 3358_construct_FcMR_12h_rep3

description:
3358
mRNA
processed data file: raw_expression.csv
processed data file: normalized_expression.csv


title: Plasmid_0

description:
Over expression of XPO4
Plasmid_0
X152


title: 3357_construct_FcMR_12h_rep2

description:
3357
mRNA
processed data file: raw_expression.csv
processed data file: normalized_expression.csv


title: 3356_construct_isotype_4h_rep3

description:
3356
mRNA
processed data file: raw_expression.csv
processed data file: normalized_expression.csv


title: MtrA-pH7-induced-1_S4


title: Clock delta 19/delta 19 -ZT19, biological rep 3

type: RNA

city: Guelph

first: Dr. Tami

middle: A.

last: Martino

state: Ontario

address: 50 Stone Road E

department: Centre for Cardiovascular Investigations, Department of Biomedical Science

country: Canada

institute: University of Guelph

hyb_protocol: Following fragmentation, cRNA were hydridized on Affymetrix GeneChip Mouse Gene 2.0 ST arrays, according to manufacturer's instructions. GeneChips were washed and stained on the Gene Atlas platform.

scan_protocol: GeneChips were scanned on the GeneAtlas platform.

data_processing: The data were analyzed with GeneSpring GX software v. 14.9 using default Affymetrix settings.

label: biotin

source_name: Clock delta 19/delta 19 -ZT19

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 500ng total RNA.

growth_protocol: The heart were collected from the mice with 8 weeks old.

extract_protocol: Total RNA was extracted using the TRIzol method according to manufacturer's instructions.

treatment_protocol: The hearts were collected and snap frozen in liquid nitrogen and stored at -80C.

tag: strain/genotype

value: Clock delta 19/delta 19

tag: Sex

value: male

tag: tissue

value: myocardium


title: Clock delta 19/delta 19 -ZT23, biological rep 4

source_name: Clock delta 19/delta 19 -ZT23


title: Clock delta 19/delta 19 -ZT19, biological rep 4


title: 3355_construct_FcMR_12h_rep1

description:
3355
mRNA
processed data file: raw_expression.csv
processed data file: normalized_expression.csv

tag: treatment


title: Clock delta 19/delta 19 -ZT23, biological rep 3


title: 3354_construct_isotype_4h_rep2

description:
3354
mRNA
processed data file: raw_expression.csv
processed data file: normalized_expression.csv


title: Clock delta 19/delta 19 -ZT15, biological rep 4

source_name: Clock delta 19/delta 19 -ZT15


title: P10 Alk5 rep E7

city: Montreal

first: Alexandre

last: Dubrac

state: Quebec

address: 3175 Côte-Sainte-Catherine Road

institute: University of Montreal

data_processing:
Generated libraries were sequenced on an Illumina HiSeq4000
Sequenced reads were  de-multiplexed and mapped to the mouse genome (mm10) using CellRanger (pipeline version 3.1.0) (10x Genomics)
Genome_build: mm10
Supplementary_files_format_and_content: tsv files contain cell barcodes or gene names for the corresponding mtx file
Supplementary_files_format_and_content: mtx files are gene by cell count matrices

molecule: polyA RNA

source_name: Retina

extract_protocol:
Four retinas from P6 or P10 and WT or Alk5iEKO pups were dissected and dissociated with a modified version of the Neural Tissue Dissociation kit (P) (Miltenyi Biotec, Cat#130- 092-628). The retinas were digested in buffer P supplemented with DNase I (2000 U/mL, Qiagen #79254) for 5 min. The digestion was stopped by adding FBS (10% final) and the cells were immediately filtered through a 70 μm cell strainer. After centrifugation (300g for 3 min), the cells were resuspended in PBS supplemented with 2mM EDTA and 0.5% BSA. The single cell suspension was enriched for ECs using CD31 MicroBeads (Miltenyi Biotec, Cat#130-097-418) according to the manufacturer’s instructions. Single cell suspensions of retinal cells were resuspended in PBS containing 0.04% ultra556 pure BSA.
Libraries were prepared using the Chromium Single Cell 30 Reagent Kits v3.1 (10x Genomics; Pleasanton, CA, USA) according to the manufacturer’s instructions.
scRNA-seq

treatment_protocol: To induce postnatal gene deletion, mice were injected intragastrically with 100μg of tamoxifen (Sigma, T5648; 25 mg/ml in corn oil) for three consecutive days. Tamoxifen-treated, Cre-negative littermates were used as controls.

value: Retina

tag: age


title: P10 WT rep C7


title: P10 Alk5 rep B7


title: MtrA-pH7-induced-1_S5

source_name: bacterial culture


title: MtrA-pH7-uninduced-1_S2


title: Clock delta 19/delta 19 -ZT23, biological rep 2

tag: time point


title: P10 WT rep D7


title: Clock delta 19/delta 19 -ZT15, biological rep 3


title: 3353_construct_isotype_4h_rep1

description:
3353
mRNA
processed data file: raw_expression.csv
processed data file: normalized_expression.csv


title: Clock delta 19/delta 19 -ZT23, biological rep 1


title: Clock delta 19/delta 19 -ZT11, biological rep 4

source_name: Clock delta 19/delta 19 -ZT11


title: Clock delta 19/delta 19 -ZT19, biological rep 2


title: Clock delta 19/delta 19 -ZT15, biological rep 1


title: MtrA-pH7-uninduced-1_S1

tag: experiment


title: Clock delta 19/delta 19 -ZT11, biological rep 2


title: MtrA-pH7-uninduced-1_S3


title: Clock delta 19/delta 19 -ZT15, biological rep 2


title: 3352_construct_FcMR_4h_rep3

description:
3352
mRNA
processed data file: raw_expression.csv
processed data file: normalized_expression.csv


title: P6 Alk5


title: P6 WT


title: 3351_construct_FcMR_4h_rep2

description:
3351
mRNA
processed data file: raw_expression.csv
processed data file: normalized_expression.csv


title: Clock delta 19/delta 19 -ZT19, biological rep 1


title: Lung_FOXC2lecKO_rep3 [AG60i_lung_KO]

city: Lausanne

first: Tania

last: Wyss

address: Rue du Bugnon 25A

country: Switzerland

institute: SIB Swiss Institute of Bioinformatics

description: processed data file: Loyola_Foxc2_RNAseq_lung_counts.csv

data_processing:
Illumina bcl2fastq v. 2.17
Each library was sequenced on three lanes. The 3 fastq files of each sample were concatenated, and read alignment and count summarization were performed using the bcbio-nextgen pipeline (v.19.03)
Reads were aligned using HISAT v. 2.1.0, and counts per gene were summarized using featureCounts of the Subread package v.1.6.3
Genome_build: mm10
Supplementary_files_format_and_content: comma-separated values file of counts per gene generated by featureCounts. Gene symbols are contained in the first column. The counts of the lung and the mesentery samples are contained in two separate files. Sample names contain indication of the genotype of each sample (WT=wildtype, KO=Foxc2 LEC KO)

extract_protocol:
Tissue samples were collected and washed twice in ice-cold PBS and were maintained for 30min in RNA laterTM solution (Invitrogen). Next, tissues were transferred to RNAeasy plus lysis buffer (Qiagen)+ Bmercaptoethanol (AppliChem) and and snap-frozen on dry ice.  Tissues were homogenized using Fast Prep-24 disruptor (MP) and the RNA isolated according to Qiagen RNeasy Plus Mini Kit (Qiagen) instruction manual. RNA concentration and quality were verified using 2100 Bioanalyzer (Agilent).
RNA-seq libraries were prepared from 500 ng of total RNA. RNA sequencing library preparation used Truseq Stranded RNA Library Prep Kit for Illumina by following the manufacturer’s recommendations (NEB, Ipswich, MA, USA).
Briefly, enriched RNAs were fragmented for 15 minutes at 94 °C. First strand and second strand cDNA were subsequently synthesized. cDNA fragments were end-repaired and adenylated at 3’ends, and universal adapter was ligated to cDNA fragments, followed by index addition and library enrichment with limited cycle PCR. Sequencing libraries were validated on the Agilent TapeStation (Agilent Technologies, Palo Alto, CA, USA), and quantified by using Qubit 2.0 Fluorometer (Invitrogen, Carlsbad, CA) as well as by quantitative PCR (Applied Biosystems, Carlsbad, CA, USA). After clustering, the flowcell was loaded on the Illumina HiSeq instrument according to manufacturer’s instructions. The samples were 2x150 single-end sequencing using HiSeq 4000 SR, each sample being sequenced on three separate lanes to increase coverage per sample.

treatment_protocol: 5 week old mice received 3 i.p. injections of  50 μg/g tamoxifen during first week, RNA from tisues was isolated from 15 week old mice

value: 15 weeks old

value: tamoxifen injected mice

value: Lung


title: Lung_WT_rep4 [AG59i_lung_WT]

value: wildtype


title: 3350_construct_FcMR_4h_rep1

description:
3350
mRNA
processed data file: raw_expression.csv
processed data file: normalized_expression.csv


title: 03_Mtb_pH5_24h

growth_protocol: Samples grown in 7H9-rich media supplemented with 0.05% Tyloxapol at 37 degrees C with shaking

extract_protocol:
In three biological replicates, Mtuberculosis cultured in 7H9 rich media with 0.05% tyloxapol were washed 3x in sterile 1x PBS and diluted in 7H9 rich media with 0.05% tyloxapol buffered to either pH7 or pH 5.6 to an OD of 0.05 and grown in roller bottles in a 37 degrees C incubator for either 0 or 24 h.  After harvesting at 0 or 24 h, cells pellets were spun down and immediately frozen in liquid nitrogen and stored at -80 degrees C until RNA isolation . Cell pellets were transferred to a tube containing Lysing Matrix B, and vigorously shaken at max speed for 30 s in a FastPrep 120 homogenizer three times. This mixture was centrifuged at max speed for 1 min and the supernatant was transferred to a fresh tube. RNA was isolated using phenol-chloroform extraction method, followed by DNase treatment.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Samples grown in 7H9-rich media supplemented with 0.05% Tyloxapol and buffered to pH 5.6 at 37 degrees C with shaking

tag: culture ph

value: 24 hour


title: 02_Mtb_pH5_24h


title: 01_Mtb_pH5_24h


title: 03_Mtb_pH5_0h

value: 0 hour


title: 3349_construct_untreated_0h_rep3

description:
3349
mRNA
processed data file: raw_expression.csv
processed data file: normalized_expression.csv


title: Lung_FOXC2lecKO_rep2 [AG58i_lung_KO]

tag: genotype


title: 02_Mtb_pH5_0h


title: 3348_construct_untreated_0h_rep2

description:
3348
mRNA
processed data file: raw_expression.csv
processed data file: normalized_expression.csv

tag: genetic background


title: Clock delta 19/delta 19 -ZT11, biological rep 3


title: 3347_construct_untreated_0h_rep1

description:
3347
mRNA
processed data file: raw_expression.csv
processed data file: normalized_expression.csv


title: Lung_WT_rep3 [AG57i_lung_WT]


title: Lung_WT_rep2 [AG56i_lung_WT]


title: Lung_FOXC2lecKO_rep1 [AG55i_lung_KO]


title: 6963_Control

city: Oxford

first: Robin

last: Choudhury

address: L6 West Wing, John Radcliffe Hospital, Headley Way

department: Cardiovascular Medicine, Radcliffe Department of Medicine

institute: University of Oxford

data_processing:
Illumina HiSeq Control Software (HCS) HD 3.4.0.38 was used for the data acquisition on the sequencing instrument
On-instrument base-calling performed by the Illumina Real-Time Analysis (RTA) software 2.7.7.
BCL to BAM file conversion and demultiplexing with custom programmes (https://github.com/epigen/picard/) based on Picard tools 2.19.2 (https://broadinstitute.github.io/picard/)
BAM to fastq file conversion using samtools v1.7 bam2fq
Transcripts were quantified from reads using Salmon v1.2.1 with parameters --validateMappings --gcBias --seqBias -l A
Counts were analysed using DESeq2 v1.28.1 / Bioconductor v3.11 / R v4.0.0. Transcripts with fewer than 20 counts across all samples were removed.
Variance stabilizing transformation was performed and normalised abundance values exported.
Genome_build: Ensembl 98 based on GRCh38
Supplementary_files_format_and_content: Comma-delimited matrix table with normalised abundance values for each sample and gene

source_name: Peripheral blood mononuclear cells

growth_protocol: Cells were maintained in low glucose DMEM (5.5mM), 2mM L-glutamine, 10% foetal bovine serum and 1% penicillin and streptomycin

extract_protocol:
Total RNA was extracted from sorted cell pools with the RNeasy mini kit (Qiagen).
RNA-seq libraries were prepared with the TruSeq Stranded mRNA LT sample preparation kit (Illumina) using Sciclone and Zephyr liquid handling robotics (PerkinElmer). Library amounts were quantified using the Qubit 2.0 Fluorometric Quantitation system (Life Technologies) and the size distribution was assessed using the Experion Automated Electrophoresis System (Bio-Rad). For sequencing, libraries were pooled, diluted and sequenced on an Illumina HiSeq 3000 instrument using 50 bp single-read chemistry.

treatment_protocol: Cells were treated with vehicle (PBS) or 100 ng / mL lipopolysaccharide and 10 ng / mL recombinant human-IFN-gamma for 6 hours

value: Peripheral blood mononuclear cells

value: Unstimulated

tag: disease state

value: Diabetic


title: 6961_M1

value: LPS + IFN-gamma


title: 02_Mtb_pH7_24h

tag: strain


title: 01_Mtb_pH5_0h


title: Lung_WT_rep1 [AG54i_lung_WT]


title: 03_Mtb_pH7_24h


title: 01_Mtb_pH7_24h


title: Clock delta 19/delta 19 -ZT07, biological rep 3

source_name: Clock delta 19/delta 19 -ZT07


title: 6961_Control


title: 03_Mtb_pH7_0h


title: Clock delta 19/delta 19 -ZT07, biological rep 4


title: Clock delta 19/delta 19 -ZT07, biological rep 2


title: Clock delta 19/delta 19 -ZT03, biological rep 2

source_name: Clock delta 19/delta 19 -ZT03


title: Mesentery_FOXC2lecKO_rep4 [AG50j_mese_KO]

description: processed data file: Loyola_Foxc2_RNAseq_mesentery_counts.csv

value: Mesentery


title: Clock delta 19/delta 19 -ZT03, biological rep 4


title: Mesentery_WT_rep3 [AG49j_mese_WT]


title: Clock delta 19/delta 19 -ZT07, biological rep 1


title: Clock delta 19/delta 19 -ZT03, biological rep 1


title: 6963_M1


title: Clock delta 19/delta 19 -ZT11, biological rep 1


title: Clock delta 19/delta 19 -ZT03, biological rep 3


title: Wildtype-ZT23, biological rep 4


title: Wildtype-ZT23, biological rep 3


title: Wildtype-ZT23, biological rep 2


title: 6958_M1

value: Control


title: Mesentery_FOXC2lecKO_rep3 [AG48j_mese_KO]


title: 6958_Control


title: 6957_M1


title: 01_Mtb_pH7_0h


title: Mesentery_WT_rep2 [AG47j_mese_WT]


title: Mesentery_FOXC2lecKO_rep2 [AG46j_mese_KO]


title: Genomic DNA from lung adenocarcinoma_584

type: genomic

first: Varshini

last: Vasudevaraja

state: NY

address: 550 1st Avenue

department: Pathology

institute: NYU Langone Health

hyb_protocol: The DNA is bisulfite-converted using the Zymo Bisulfite Conversion protocol

scan_protocol: Arrays were imaged using iScan using standard recommended Illumina scanner setting

data_processing:
minfi- R package was used to analyze the data. Data was preprocessed, quantile normalized and poor samples and probes were removed based on mean detection Pvalues.
The processed_data.txt contain Average Beta and detection Pvalues
The signal_intensities.txt contains unmethylated and methylated signal intensities

label: Cy5 and Cy3

source_name: Lung

label_protocol: Standard Illumina Protocol

extract_protocol: Using a Promega Maxwell 16 instrument, DNA was extracted from fresh tissue specimens with the Maxwell® 16 Tissue DNA Purification Kit

tag: gender

value: Female

tag: Stage

value: I

tag: tissue type

value: tumor sample


title: Genomic DNA from lung adenocarcinoma_543


title: Genomic DNA from lung adenocarcinoma_537

value: Male


title: Mesentery_FOXC2lecKO_rep1 [AG45j_mese_KO]


title: 6950_M1

tag: cell type


title: 6950_Control


title: Genomic DNA from lung adenocarcinoma_522

value: IV


title: 02_Mtb_pH7_0h


title: LECs_FOXC2lecKO_ rep3_scRNA-seq

data_processing:
Post processing done using Illumina bcl2fastq2 Conversion Software 2.20
Reads in fastq files aligned to the mouse genome and reads per gene were counted using the 10x Genomics Cell Ranger Pipeline (version 3.1.0)
Genome_build: Mus musculus mm10
Supplementary_files_format_and_content: comma-separated values file of 10x Cell Ranger output, filtered feature x barcode count matrix. Gene symbols are included in the first column. Sample origin of each cell is contained within each cell name, directly following the barcode of each cell. Cells with suffix "-1" belong to sample 1 (wildtype), cells with suffix "-2" belong to sample 2 (wildtype), cells with suffix "-3" belong to sample 3 (Foxc2 knockout), cells with suffix "-4" belong to sample 4 (wildtype), cells with suffix "-5" belong to sample 5 (Foxc2 knockout) and cells with suffix "-6" belong to sample 6 (Foxc2 knockout).

source_name: sorted lymphatic endothelial cells (LECs)

extract_protocol:
Mesenteries were collected and digested in Liberase TL solution, washed, blocked and stained with FACs antibodies before sorting. Sorted cells were were loaded on a Chromium Next GEM Chip B (10X genomics). Sequencing was performed on 2 runs in the Illumina HiSeq 4000 using HiSeq 3000/4000 SBS Kit reagents (Illumina) according to Illumina 10X Genomics recommendations.
The sequencing libraries were prepared following the manufacturer’s recommendations (Chromium Single Cell 3ʹ GEM Kit v3).
Chromium Next GEM Chip B (10X genomics); Chromium Single Cell 3ʹ GEM Kit v3.

treatment_protocol: 3 week old mice received 3 i.p. injections of  50 μg/g tamoxifen during first week, cells are sorted from 6 week old mice

value: lymphatic endothelial cells

value: mesentery

value: 6 weeks old


title: Genomic DNA from lung adenocarcinoma_514

value: Lung


title: 6957_Control


title: 6943_M1


title: LECs_FOXC2lecKO_ rep2_scRNA-seq

value: tamoxifen injected mice


title: 6943_Control


title: Wildtype-ZT19, biological rep 3

value: male

value: myocardium


title: Wildtype-ZT19, biological rep 4


title: Wildtype-ZT23, biological rep 1


title: Wildtype-ZT15, biological rep 4


title: Wildtype-ZT19, biological rep 2


title: Wildtype-ZT15, biological rep 2


title: Wildtype-ZT15, biological rep 1


title: LECs_WT_rep3_scRNA-seq

value: wildtype


title: Wildtype-ZT11, biological rep 4


title: Wildtype-ZT19, biological rep 1


title: Mesentery_WT_rep1 [AG44j_mese_WT]

value: 15 weeks old


title: LECs_FOXC2lecKO_ rep1_scRNA-seq


title: Genomic DNA from lung adenocarcinoma_434


title: 6942_Control

value: Peripheral blood mononuclear cells

value: Unstimulated

value: Diabetic


title: Genomic DNA from lung adenocarcinoma_422

value: Female


title: LECs_WT_ rep1_scRNA-seq


title: Genomic DNA from lung adenocarcinoma_410

value: I


title: 6926_Control

value: Control


title: 6942_M1

value: LPS + IFN-gamma


title: Genomic DNA from lung adenocarcinoma_427

value: tumor sample


title: Wildtype-ZT15, biological rep 3


title: Genomic DNA from lung adenocarcinoma_445

value: Male


title: Wildtype-ZT11, biological rep 3


title: Wildtype-ZT11, biological rep 1


title: 6916_M1


title: Wildtype-ZT07, biological rep 4


title: Wildtype-ZT11, biological rep 2


title: Genomic DNA from lung adenocarcinoma_389

value: III


title: Genomic DNA from lung adenocarcinoma_407


title: 6916_Control


title: 6926_M1


title: LECs_WT_ rep2_scRNA-seq

value: lymphatic endothelial cells

value: mesentery

value: 6 weeks old


title: 6860_M1


title: Genomic DNA from lung adenocarcinoma_384

value: II

value: Lung


title: 6860_Control


title: Genomic DNA from lung adenocarcinoma_380


title: Genomic DNA from lung adenocarcinoma_377


title: mtrA1pJR962-MC2-155-ATc-8

organism: Mycolicibacterium smegmatis

tag: induction

value: ATc induced

tag: induction time

value: 14 hour


title: mtrA1pJR962-MC2-155-ATc-7


title: Genomic DNA from lung adenocarcinoma_374


title: Wildtype-ZT07, biological rep 3

tag: Sex

value: male

value: myocardium


title: Genomic DNA from lung adenocarcinoma_355

tag: tissue


title: mtrA1pJR962-MC2-155-ATc-6


title: Wildtype-ZT07, biological rep 2


title: 24h-2.gProcessedSignal

city: Meguro-ku

first: Rina

last: Kunishige

state: Tokyo

address: 202A, Building 3, 3-8-1 Komaba

department: Department of Life Sciences  Graduate School of Arts and Sciences

country: Japan

institute: The University of Tokyo

hyb_protocol: Following fragmentation, 1.65 ug of cRNA were hybridized to the Agilent expression microarray according to the protocols provided by the manufacturer

scan_protocol: Arrays were scanned using the Agilent Technologies G4900DA SG12494263

data_processing: Array data export processing and analysis was performed using Agilent Feature Extraction v11.0.1.1

source_name: CPP stimulation, 24hr, replicate 2

label_protocol: labeled cRNA were prepared from 1~5 ug total RNA using the Agilent’s Quick Amp Labeling Kit

extract_protocol: RNA was prepared using the Rneasy Mini Kit (Qiagen) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies).

tag: cells

value: HK2 culture cells


title: Wildtype-ZT07, biological rep 1


title: Wildtype-ZT03, biological rep 2


title: mtrA1pJR962-MC2-155-ATc-5


title: 24h-1.gProcessedSignal

source_name: CPP stimulation, 24hr, replicate 1


title: Genomic DNA from lung adenocarcinoma_352

tag: age


title: ATAC-seq_MGT#1-low_FAC-sorted-A549-MGT#1_TGFB1_rep2

data_processing:
FASTQ files from sequencing experiments were mapped to the genome build hg38 using Bowtie2 with default parameters.
BigWIG were generated by using bamcoverage tool and peaks were called using MACS2.
Genome_build: hg38
Supplementary_files_format_and_content: The BigWIG file corresponds to the output from the bamcoverage tool.

extract_protocol:
Cells were incubated 60 min at 37 C  and lysed in Proteinase K and AL buffer (quiagen)
Libraries were prepared according to Nextera library prep (Illumina).

treatment_protocol: Cells treated were treated with GSK126 5 uM. Cells were treated with 5ng/ml of TGFB

value: human lung adenocarcinoma cell line

tag: cell line

tag: fac-sorting

value: FAC-sorting low MGT1 levels

tag: treatment


title: ATAC-seq_MGT#1-low_FAC-sorted-A549-MGT#1_TGFB1_rep1


title: 6h-3.gProcessedSignal

source_name: CPP stimulation, 6hr, replicate 3


title: 6h-4.gProcessedSignal

source_name: CPP stimulation, 6hr, replicate 4


title: mtrA1pJR962-MC2-155-4

value: uninduced


title: Genomic DNA from lung adenocarcinoma_323

value: I


title: Wildtype-ZT03, biological rep 3

tag: time point


title: 24h-4.gProcessedSignal

source_name: CPP stimulation, 24hr, replicate 4


title: mtrA1pJR962-MC2-155-3


title: Genomic DNA from lung adenocarcinoma_318

value: tumor sample


title: 24h-3.gProcessedSignal

source_name: CPP stimulation, 24hr, replicate 3


title: ATAC-seq_MGT#1-high_FAC-sorted-A549-MGT#1_TGFB1_rep2

value: FAC-sorting high MGT1 levels


title: mtrA1pJR962-MC2-155-2


title: Wildtype-ZT03, biological rep 4


title: Genomic DNA from lung adenocarcinoma_315

value: Female


title: ATAC-seq_MGT#1-high_FAC-sorted-A549-MGT#1_TGFB1_rep1


title: Wildtype-ZT03, biological rep 1


title: 6h-2.gProcessedSignal

source_name: CPP stimulation, 6hr, replicate 2


title: 6h-1.gProcessedSignal

source_name: CPP stimulation, 6hr, replicate 1


title: 3h-4.gProcessedSignal

source_name: CPP stimulation, 3hr, replicate 4


title: mtrA1pJR962-MC2-155-1


title: 3h-3.gProcessedSignal

source_name: CPP stimulation, 3hr, replicate 3


title: ATAC-seq_MGT#1-low_FAC-sorted-A549-MGT#1_GSK126_rep2


title: Genomic DNA from lung adenocarcinoma_299


title: 3h-2.gProcessedSignal

source_name: CPP stimulation, 3hr, replicate 2


title: 3h-1.gProcessedSignal

source_name: CPP stimulation, 3hr, replicate 1


title: ATAC-seq_MGT#1-high_FAC-sorted-A549-MGT#1_GSK126_rep2


title: Genomic DNA from lung adenocarcinoma_234


title: ATAC-seq_MGT#1-low_FAC-sorted-A549-MGT#1_GSK126_rep1


title: Genomic DNA from lung adenocarcinoma_216

value: Male


title: ATAC-seq_MGT#1-high_FAC-sorted-A549-MGT#1_GSK126_rep1


title: Induced D6  gonad

city: Yokohama

first: Takahiro

last: Suzuki

state: Kanagawa

address: 1-7-22 Suehiro-cho, Tsurumi-ku

department: Center for Integrative Medical Sciences

institute: RIKEN

data_processing:
Raw paired-end sequence data were converted to FASTQ files and mapped to mouse mm10 genome using Cell Ranger software version 3.0.2(10X Genomics).
Genome_build: mm10
Supplementary_files_format_and_content: MTX

source_name: gonad somatic cells

growth_protocol: ES cell-derived gonad somatic cells were differentiated from ES cells, culturing as aggregates with CHIR, BMP4 , and EGF for 2 days; with BMP4, Retinoic acid, PD0325901, SHH, and EGF for next 2 days; and with BMP4, and FGF9 for next 2 days.

extract_protocol:
cells were dissociated enzymatically by papain for 30 mins and then harvested by centrifugation.
Single-cell RNA sequencing libraries were prepared from the freshly isolated female mouse gonad tissues and ES-derived gonad cells by using Chromium Single Cell 3ʹ v2 Reagent Kits (10X Genomics) as previously described (Hashimoto et. al. PNAS, 2019). Briefly, the dissociated cells were mixed with the Single cell Master Mix and generated gel bead-in-emulsions (GEMs). The RNAs in each GEM were revers-transcribed and the resulting cDNAs were amplified by PCR. Illumina sequencer adapted sequencing libraries were constricted from the amplified cDNAs. Single-cell RNA sequencing libraries were sequenced with paired-end reads on the Illumina HiSeq X Ten platform.

value: 129svj x C57BL/6J

value: ES-derived gonad somatic cells


title: ATAC-seq_A549-MGT#1_rep2

value: lung

value: untreated


title: Genomic DNA from lung adenocarcinoma_122

value: Lung


title: E12.5XX gonad

source_name: gonad

value: ICR

value: in vivo gonad


title: E13.5XX gonad

data_processing:
Raw paired-end sequence data were converted to FASTQ files and mapped to mouse mm10 genome using Cell Ranger software version 3.0.2(10X Genomics).
Genome_build: mm10


title: E14.5XX gonad


title: Genomic DNA from lung adenocarcinoma_82


title: ydhB_2

city: La Jolla

first: Ye

last: Gao

address: 9500 Gilman Dr.

institute: UCSD

data_processing:
The base calling was done using Illumina’s Real-Time Analysis (RTA) v2.7.7; data was converted to fastq and demultiplexed using Illumina’s bcl2fastq2 Conversion Software v2.20;
Sequence reads generated from ChIP-exo were mapped onto the each reference genome using bowtie with default options to generate SAM output files
MACE program was used to define peak candidates from biological duplicates for each experimental condition with sequence depth normalization.
To reduce false-positive peaks, manual curation was performed based on the signal-to-noise(S/N) ratio value.
The calculation of S/N ratio resembles the way to calculate ChIP-chip peak intensity where IP signal was divided by Mock signal. Then, each peak was assigned to the nearest gene.
Genome_build: The reference genome  MG1655 =  NC_000913.2
Supplementary_files_format_and_content: Tab-delimited text files in gff format which has 8 columns: sequence id, source(empty), feature (+/- strand), start position, end position, intensity score, strand(+/-), frame(.), attribute(.).

organism: Escherichia coli K-12

source_name: bacteria cells

growth_protocol: Glycerol stocks of E. coli strains were inoculated into M9 minimal media with 0.2% (w/v) glucose. The culture was incubated at 37 oC overnight with agitation, and then was used to inoculate the fresh media (1/200 dilution). The volume of the fresh media was 150 mL for each biological replicate. The fresh culture was incubated at 37 oC with agitation to the mid-log phase (OD600 ≈ 0.5).

extract_protocol:
Lysates were clarified from sonicated uncharacterized transcripton factors-DNA complexes were isolated with myc antibody.
ChIP-exo experiment was performed following the procedures:  to identify each TF candidate binding maps in vivo, we isolated the DNA bound to each TF candidate from formaldehyde cross-linked E. coli cells by chromatin immunoprecipitation (ChIP) with the specific antibodies that specifically recognizes myc tag (9E10, Santa Cruz Biotechnology), and Dynabeads Pan Mouse IgG magnetic beads (Invitrogen) followed by stringent washings as described previously [42]. ChIP materials (chromatin-beads) were used to perform on-bead enzymatic reactions of the ChIP-exo method [11]. Briefly, the sheared DNA of chromatin-beads was repaired by the NEBNext End Repair Module (New England Biolabs) followed by the addition of a single dA overhang and ligation of the first adaptor (5’-phosphorylated) using dA-Tailing Module (New England Biolabs) and NEBNext Quick Ligation Module (New England Biolabs), respectively. Nick repair was performed by using PreCR Repair Mix (New England Biolabs). Lambda exonuclease- and RecJf exonuclease-treated chromatin was eluted from the beads and the protein-DNA cross-link was reversed by overnight incubation at 65oC. RNAs- and Proteins-removed DNA samples were used to perform primer extension and second adaptor ligation with following modifications. The DNA samples incubated for primer extension as described previously [12] were treated with dA-Tailing Module (New England Biolabs) and NEBNext Quick Ligation Module (New England Biolabs) for second adaptor ligation. The DNA sample purified by GeneRead Size Selection Kit (Qiagen) was enriched by polymerase chain reaction (PCR) using Phusion High-Fidelity DNA Polymerase (New England Biolabs). The amplified DNA samples were purified again by GeneRead Size Selection Kit (Qiagen) and quantified using Qubit dsDNA HS Assay Kit (Life Technologies). Quality of the DNA sample was checked by running Agilent High Sensitivity DNA Kit using Agilent 2100 Bioanalyzer (Agilent) before sequenced using HiSeq (Illumina) in accordance with the manufacturer’s instructions. Each modified step was also performed in accordance with the manufacturer’s instructions. ChIP-exo experiments were performed in biological duplicate.

treatment_protocol: For regulatory condition, M9 minimal media was supplemented with 1 mL trace element solution (100X) containing 1 g EDTA, 29 mg ZnSO4.7H2O, 198 mg MnCl2.4H2O, 254 mg CoCl2.6H2O, 13.4 mg CuCl2, and 147 mg CaCl2.

tag: myc-tagging

value: YdhB myc-tagging cells

tag: chip-exo antibody

value: c-myc(9E10) mouse monoclonal IgG1,sc-40, lot#J2413, Santa Cruz Biotechnology


title: ATAC-seq_A549-MGT#1_rep1

value: human lung adenocarcinoma cell line


title: E11.5XX gonad

tag: strain


title: E10.5XX gonad


title: Genomic DNA from lung adenocarcinoma_254

source_name: Lung

tag: gender


title: 48h-1

status: Public on Jul 15 2021

city: La Tronche

last: Bougdour

state: Isère

address: Domaine de la Merci, Campus santé

department: Prevention and Therapy of Chronic diseases

country: France

institute: Centre de Recherche Inserm U1209 / CNRS UMR5309 / UGA

data_processing:
The RNA-Seq reads (FASTQ) were processed and analyzed using the Lasergene Genomics Suite version 15 (DNASTAR, Madison, WI, USA) using default parameters.
The paired-end reads were uploaded onto the SeqMan NGen (version 15, DNASTAR. Madison, WI, USA) platform for reference-based assembly using the Toxoplasma type II ME49 strain (ToxoDB-46, ME49 genome) as reference template. Wiggle files were generated.
The ArrayStar module (version 15, DNASTAR. Madison, WI, USA) was used for normalization, variant detection and statistical analysis of uniquely mapped paired-end reads using the default parameters.
The expression data quantification and normalization were calculated using the RPKM (Reads Per Kilobase of transcript per Million mapped reads) normalization method.
In parallel, the FASTQ reads were aligned to the ToxoDB-48 build of the Toxoplasma gondii ME49 genome (ToxoDB-48) using Subread version 2.0.1 with the following options “ subread-align -d 50 -D 600 --sortReadsByCoordinates”. Read counts for each gene were calculated using featureCounts from the Subread package. Differential expression analysis was conducted using DESeq2 and default settings within the iDEP.92 web interface. Transcripts were quantified and normalized using TPMCalculator.
Genome_build: Toxoplasma type II ME49 strain (build ToxoDB-46 or ToxoDB-48, ME49 genome)
Supplementary_files_format_and_content: xlsx format. The matrix table includes RNA-Seq report, RPKM values, raw counts, and TPM valules of T. gondii transcripts for each sample. Differential expression analysis was performed usind iDEP.92.

organism:
Toxoplasma gondii
Homo sapiens

source_name: HFF and parasites

growth_protocol: Cells were maintained in Dulbecco’s modified Eagle’s medium (DMEM, Invitrogen) supplemented with 10% heat-inactivated FBS (Invitrogen), 10 mM HEPES buffer, pH 7.2, 2 mM L-glutamine, and 50 μg/ml penicillin and streptomycin (Thermo Fisher Scientific). Cells were incubated at 37°C in 5% CO2.

extract_protocol:
18-24 hours post-infection, cells were harvested and total RNAs were extracted and purified using TRIzol (Invitrogen, Carlsbad, CA, USA) and RNeasy Plus Mini Kit (Qiagen). RNA quantity and quality were measured by NanoDrop 2000 (Thermo Scientific). RNA integrity was assessed by standard non-denaturing 1.2% TBE agarose gel electrophoresis. Then, RNA quantity and integrity were further determined using the Qubit® Fluorometer and the Fragment Analyzer system with the PROSize 3.0 software (Agilent Technologies, Palo Alto, California, USA). The RQN were ranging from 8.8 to 10 for all samples.
RNA libraries were prepared using polyA selected RNAs for sequencing using standard Illumina protocols (Illumina TruSEQ RNA library prep).

treatment_protocol: To induce CPSF4-mAID-HA knockdown, 500 µM IAA was added to the cell culture medium.

tag: t. gondii strain

value: Rhdeltaku80 CPSF4-mAID-HA

tag: strain background

value: HFF

value: 48h CPSF4 KD


title: 0h-4.gProcessedSignal

source_name: CPP stimulation, 0hr, replicate 4

value: HK2 culture cells


title: 24h-2

value: 24h CPSF4 KD


title: 0h-1.gProcessedSignal

source_name: CPP stimulation, 0hr, replicate 1


title: 0h-3.gProcessedSignal

source_name: CPP stimulation, 0hr, replicate 3


title: 24h-1


title: 7h-1

value: 7h CPSF4 KD


title: 48h-2


title: 0h-2.gProcessedSignal

source_name: CPP stimulation, 0hr, replicate 2


title: ydhB_1


title: UT-2


title: 7h-2


title: A8_F92_I1 Replicate 1

city: San Diego

first: Bernhard

middle: O.

last: Palsson

state: California

address: 9500 Gilman Dr

department: Bioengineering

institute: University of California, San Diego

description:
Ribosomal RNA depleted total RNA
deseq2-tpm-galactose.csv

data_processing:
Raw RNA-Seq reads were mapped to the original reference genome using Bowtie2 and transcript abundance was analyzed using summarizeOverlaps (Lawrence et al., 2013). Calculation of transcripts per million (TPM) and prediction of differentially expressed genes were conducted using DESeq2 (Love et al., 2014).
Genome_build: NC_002947.4
Supplementary_files_format_and_content: Calculated TPM values for each gene.

organism: Pseudomonas putida KT2440

source_name: Lab cultures of a genetically engineered KT2454

growth_protocol: All microbial cultures were conducted at 30 ˚C using the modified minimal M9 medium (4 g/L xylose or galactose, 2 g/L (NH4)2SO4, 6.8 g/L Na2HPO4, 3 g/L KH2PO4, 0.5 g/L NaCl, 2 mM MgSO4, 0.1 mM CaCl2, 500 μL/L 2000X trace element solution). The composition of the trace element solution is 4.5 g/L ZnSO4⋅7H2O, 0.7 g/L MnCl2⋅4H2O, 0.3 g/L CoCl2⋅6H2O, 0.2 g/L CuSO4⋅2H2O, 0.4 g/L Na2MoO4⋅2H2O, 4.5 g/L CaCl2⋅2H2O, 3.0 g/L FeSO4⋅7H2O, 1.0 g/L H3BO3, 0.1 g/L KI, 15 g/L disodium ethylenediaminetetraacetate.

extract_protocol:
For transcriptomic analysis, cell cultures at the exponential phase (OD600 0.4-0.6) were mixed with two volumes of RNA protect Bacteria Reagent (Qiagen, Hilden, Germany) for stabilization and their total RNA was extracted by using Quick-RNA Fungal/Bacterial Miniprep Kit (Zymo Research). Residual genomic DNA was removed by incubating the samples with DNase I (RNase-free, NEB). Ribosomal RNA was removed by hybridizing with 30-bp oligonucleotides designed to bind the ribosomal RNA of KT2440 specifically and treating with Thermostable RNase H purchased from Lucigen (Middleton, WI, USA). The remaining oligonucleotides were removed by incubating the resulting samples with DNase I (NEB). The samples were purified by using an RNA Clean & Concentrator Kit (Zymo Research).
Paired-end RNA-Seq libraries were constructed using a KAPA RNA HyperPrep kit from Kapa Biosystems (Wilmington, MA, USA).

tag: genotype

value: KT2440 galETKM


title: A8_F92_I1 Replicate 2

source_name: Lab cultures of a genetically engineered KT2455


title: UT-1


title: A3_F14_I1 Replicate 2

description:
Ribosomal RNA depleted total RNA
Xylose_isolate_3_Rep_2
deseq2-tpm-xylose.csv

source_name: Lab cultures of a genetically engineered KT2445

value: KT2440 xylD


title: A2_F10_I1 Replicate 2

description:
Ribosomal RNA depleted total RNA
Xylose_isolate_2_Rep_2
deseq2-tpm-xylose.csv

source_name: Lab cultures of a genetically engineered KT2443


title: A4_F11_I1 Replicate 1

description:
Ribosomal RNA depleted total RNA
Xylose_isolate_4_Rep_1
deseq2-tpm-xylose.csv

source_name: Lab cultures of a genetically engineered KT2446


title: A5_F85_I1 Replicate 2

source_name: Lab cultures of a genetically engineered KT2451


title: A4_F11_I1 Replicate 2

description:
Ribosomal RNA depleted total RNA
Xylose_isolate_4_Rep_2
deseq2-tpm-xylose.csv

source_name: Lab cultures of a genetically engineered KT2447


title: A6_F90_I1 Replicate 2

source_name: Lab cultures of a genetically engineered KT2453


title: A1_F11_I1 Replicate 2

description:
Ribosomal RNA depleted total RNA
Xylose_isolate_1_Rep_2
deseq2-tpm-xylose.csv

source_name: Lab cultures of a genetically engineered KT2441


title: A1_F11_I1 Replicate 1

description:
Ribosomal RNA depleted total RNA
Xylose_isolate_1_Rep_1
deseq2-tpm-xylose.csv

source_name: Lab cultures of a genetically engineered KT2440


title: A3_F14_I1 Replicate 1

description:
Ribosomal RNA depleted total RNA
Xylose_isolate_3_Rep_1
deseq2-tpm-xylose.csv

source_name: Lab cultures of a genetically engineered KT2444


title: A6_F90_I1 Replicate 1

source_name: Lab cultures of a genetically engineered KT2452


title: JQ control rep3

city: Ste anne de bellevue

first: Jessica

last: Head

state: QC

address: 21111 Lakeshore Road

institute: McGill University

description: JQ_KO_abundance_table_all_birds_Seq2Fun2.txt

data_processing:
Seq2Fun used for quantification of protein-coding genes
Seq2Fun starts the raw reads quality check and employs the translated search and does not require transcriptome de novo assembly. In brief, each pair of reads was first trimmed by both ends with an average base quality 20 in a sliding window size 4, followed by poly(G) trimming. The sequencing errors were corrected on the overlapped region of the read pair before ploy(A) removal. The overlapped read pair was joined to form a single end clean read. For the translated search, the clean read was translated to amino acid fragments using all possible reading frames from both directions. Length filtering was performed on the fragments and only the longest were kept for searching. The fragment homology searching was  performed using FMI based on Burrows-Wheeler transform data structure in Seq2Fun GREEDY mode. The gene abundance tables were generated by summarizing all the read-gene pairs. The protein sequences used by Seq2Fun for JQ and DCCO were retrieved from the KEGGREST database, consisting of 370644 protein sequences representing 36448 ortholog genes from 24 birds species (Tenenbaum and Maintainer 2020). The Gene Entrez IDs were used to retrieve Kyoto Encyclopedia of Genes and Genomes (KEGG) ortholog (KO) IDs.
Differential gene expression analysis was performed using EdgeR.
Genes were first filtered for low counts using minimum counts per million threshold of 0.5, then differentially expressed genes were identified between each treatment group (medium or high dose) and the control based on the combination of fold-change expression (log2FC ≥ 1) and adjusted p-value based on a false discovery rate (FDR < 0.05).
Genome_build: KEGGREST database with 24 bird species
Supplementary_files_format_and_content: tab delimited txt file with gene abundance counts for every gene and every sample

organism: Coturnix japonica

source_name: embryonic liver

growth_protocol: Eggs were incubated at 37oC and 60% humidity

extract_protocol:
Individual liver samples were homogenized in buffer RLT using a TissueLyser II (Qiagen, Toronto, ON, CA), and RNA extracted using the RNeasy® Mini QIAcube Kit (Qiagen, Toronto, ON, CA) following the manufacturer’s protocol. An extra DNAse I digestion step was included in order to eliminate genomic DNA contamination. Total RNA concentration and purity was spectrophotometrically measured using the QIAxpert.
Library preparation and mRNA sequencing was performed by the Genome Quebec Innovation Centre (Montreal. QC). Libraries were sequenced to produce paired-end 101 bp reads using Illumina HiSeq 4000.

treatment_protocol: Dosing solutions were injected into the air cell of fertilized, un-incubated eggs, and included DMSO control, medium dose, and high dose. The high dose was selected to result in <20% embryonic mortality based on preliminary species-specific data. Nominal doses of chlorpyrifos were 0.4, 4.0, and 40 µg/g egg for both species and injected doses were also analytically determined from egg samples.

value: liver

value: embryo development day 9


title: A2_F10_I1 Replicate 1

description:
Ribosomal RNA depleted total RNA
Xylose_isolate_2_Rep_1
deseq2-tpm-xylose.csv

source_name: Lab cultures of a genetically engineered KT2442


title: JQ control rep4


title: JQ control rep2


title: JQ medium dose rep5


title: JQ control rep1


title: JQ medium dose rep1


title: JQ medium dose rep4


title: JQ high dose rep5


title: JQ medium dose rep3


title: A5_F85_I1 Replicate 1

source_name: Lab cultures of a genetically engineered KT2450


title: JQ medium dose rep2


title: JQ high dose rep4


title: JQ control rep5

value: embryo development day 16


title: JQ high dose rep2


title: JQ high dose rep1


title: hESC differentiated towards interneurons using lenti Ascl1 and Dlx2, replicate 2

city: Los Angeles

first: Kathrin

last: Plath

address: 615 Charles E. Young Drive South

institute: University of California, Los Angeles

description:
AD2_TA23_N704_AD
Drop-Seq Single Cell RNA Sequencing

data_processing:
Raw sequencing data were demultiplexed using custom Python scripts. Read 1 contains both a cell barcode and a molecular barcode (also known as a UMI), read 2 contains the cDNA sequence that is aligned to the reference genome.
Demultiplexed sequencing data were filtered by read quality, adapter- and polyA-trimmed, and reads satisfying a length threshold of 30 nucleotides were aligned to the human (hg38) genome using Bowtie2 (v2.2.9 with the ‘--very-sensitive’ mode).
Aligned reads were tagged to gene exons using Bedtools Intersect (v2.26.0).
DGE matrices were then generated by counting gene transcripts for all cells within each time point from all Drop-seq experiments using Python.
To correct for any bead synthesis errors/read errors leading to false barcodes, reads with the same corresponding cell barcode were aggregated together, and unique molecular identifiers (UMIs) and cell barcodes were merged within 1 Hamming and 2 Levenshtein distances, respectively.
A digital expression matrix was built by counting the number of unique UMIs per gene within each cell.
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: Digital Gene Expression (DGE) matrix in compressed, flat text file format with tab delimiters. Columns represent cells and rows represent genes. Column names are delimited by an underscore indicating experiment, time point, and cell barcode, where applicable.

source_name: embryonic stem cells

growth_protocol: Undifferentiated hESCs were plated in a Matrigel coated plate in mTESR and 10μm Y27632.

extract_protocol:
Cultures were dissociated in Trypsin and passed through 100uM cell strainers in preparation for single cell sequencing.
Single cell suspensions were co-flowed with poly-dT beads, and then cDNA was formed following the standard DropSeq protocol using RT, Kapa polymerase, and Nextera XT transposase. Libraries were size selected against adapters by gel extraction above 200bp.
Libraries were sequenced at 25bp through the Read1 barcode and 75bp through the Read2 genomic sequence.

treatment_protocol: hESCs were dissociated into a single cell suspension and plated into matrigel coated flasks with mTESR and 10μm Y27632. For infection, after 24h media was replaced with mTESR minus Y27632 and cells were maintained until confluency. Expression of lentiviral vectors was accomplished with the addition of 1μg/mL of Doxycycline to induce Ascl1/Dlx2 expression. After 24h of induction, puromycin (1μg/mL) and hygromycin (100μg/mL) were added to the mTESR/DOX media for a further 2 days. On day 7 of induction, media was changed to NBND and 10μm pluriSIn-1 (SCT) was added for 24h to kill proliferating cells. For 3i induction, hESC were treated with NIMX media for approximately one week and then neural progenitors were ventralized using N2/B27 containing 2μM purmorphamine and 100ng/μL Shh for 8 days, with daily media changes. Induced interneurons were maintained in NBND for the remainder of the experiments.

tag: cell type

value: embryonic stem cells

value: directed differentiation into interneurons using lenti Ascl1 and Dlx2


title: 3 inhibitor directed differentiation towards interneurons

description:
3m-non-trans-NKX2-1_
Drop-Seq Single Cell RNA Sequencing

value: directed differentiation into interneurons using 3i


title: hESC differentiated towards interneurons using lenti Ascl1 and Dlx2, replicate 1

description:
AD1_TA20_N701_AD
Drop-Seq Single Cell RNA Sequencing


title: Intestinal biopsy, PK-13

city: London

first: Kelly

last: Pauk

address: Turner Street

department: Blizard Institute

institute: Queen Mary University of London

description:
Adult_FPKM_deidentified.xlsx
PK-13

data_processing:
Reads were filtered by removing reads with adaptor sequence, reads with >10% unknown bases, and reads with >50% quality <=5.
Bowtie read alignment
RSEM (Li B and Dewey C N.,2011) computes maximum likelihood abundance estimates using the Expectation-Maximization (EM) algorithm for its statistical model,including the modeling of paired-end (PE) and variable-length reads, fragment length distributions, and quality scores, to determine which transcripts are isoforms of the same gene.
FPKM values were generated  in RSEM (FPKM = 10^6C / NL/ 10^3), where C to be number of fragments that are uniquely aligned to gene A , N to be total number of fragments that  are uniquely aligned to all genes, and L to be number of bases on gene
Genome_build: not stated in BGI report
Supplementary_files_format_and_content: Excel spreadsheet with FPKM values for each gene and sample

source_name: Intestinal biopsy

extract_protocol:
Intestinal biopsies were flash-frozen in liquid N2, then extracted using Trizol and RNA-easy minikits. RNA was transported to BGI, then quality checked using an Agilent 2100 bioanalyser. RNA was treated with Dnase, then mRNA enriched using oligo-dT beads
Mixed with the fragmentation buffer, the mRNA was fragmented into short fragments. Then the first strand of cDNA was synthesized using random hexamer-primer. Buffer, dNTPs, RNase H and DNA polymerase I were added to synthesize the second strand. Double strand cDNA was purified with magnetic beads. End reparation and 3’-end single nucleotide A (adenine) addition was then performed. Finally, sequencing adaptors were ligated to the fragments. The fragments were enriched by PCR amplification. During the QC step, Agilent 2100 Bioanaylzer and ABI StepOnePlus Real-Time PCR System were used to qualify and quantify of the sample library.

value: Intestinal biopsy

tag: condition

value: Environmental enteropathy

value: F


title: Intestinal biopsy, PK-44

description:
Adult_FPKM_deidentified.xlsx
PK-44

tag: Sex


title: Intestinal biopsy, PK-30

description:
Adult_FPKM_deidentified.xlsx
PK-30

tag: tissue


title: Intestinal biopsy, PK-19

description:
same individual as PK-18
Adult_FPKM_deidentified.xlsx
PK-19


title: Intestinal biopsy, PK-22

description:
Adult_FPKM_deidentified.xlsx
PK-22


title: Intestinal biopsy, PK-36

description:
same individual as PK-37
Adult_FPKM_deidentified.xlsx
PK-36

value: M


title: Intestinal biopsy, PK-15

description:
Adult_FPKM_deidentified.xlsx
PK-15


title: Intestinal biopsy, PK-74

description:
Adult_FPKM_deidentified.xlsx
PK-74


title: Intestinal biopsy, PK-17

description:
same individual as PK-16
Adult_FPKM_deidentified.xlsx
PK-17


title: Intestinal biopsy, PK-39

description:
same individual as PK-38
Adult_FPKM_deidentified.xlsx
PK-39


title: Intestinal biopsy, PK-46

description:
Adult_FPKM_deidentified.xlsx
PK-46


title: shCFAT1-3

first: Cunyu

last: Wang

address: 10833 Le Conte Ave

department: School of Dentistry

institute: university of California, Los Angeles

description:
extracting RNA after transfected with shCFAT1
B3

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence.
Transcripts per million(TPM) were calculated using RSEM(1.1.21) with parameters(-p 8 --estimated-rspd --no-bam-output).
Genome_build: mm9
Supplementary_files_format_and_content: xls files including RPKM values for each RNA-seq samples.

extract_protocol:
Total RNA was extracted using the RNeasy® Mini Kit
The libraries were prepared according to Illumina TruSeq® RNA sample preparation Kit.

value: Laryngeal squamous cell carcinoma

tag: passage

tag: transfected with


title: JQ high dose rep3

tag: age


title: Intestinal biopsy, PK-9

description:
same individual as PK-8
Adult_FPKM_deidentified.xlsx
PK-9


title: Intestinal biopsy, PK-8

description:
same individual as PK-9
Adult_FPKM_deidentified.xlsx
PK-8


title: shCFAT1-1

description:
extracting RNA after transfected with shCFAT1
B1

tag: cell line


title: shCtrl-3

description:
extracting RNA after transfected with shCtrl
NC3

value: shCtrl


title: shCFAT1-2

description:
extracting RNA after transfected with shCFAT1
B2


title: shCtrl-1

description:
extracting RNA after transfected with shCtrl
NC1


title: lrx345_NaCl_72h_rep3

city: West Lafayette

first: Jian-Kang

last: Zhu

state: IN

address: 625 Agriculture Mall Dr.

department: Department of Horticulture and Landscape Architecture

institute: Purdue University

description: Treated with 150mM NaCl for 72 hours

data_processing:
Quality control was checked using FastQC (www.bioinformatics.babraham.ac.uk/projects/fastqc). RNA-Seq reads were trimmed using the fastx_trimmer command FASTX-Toolkit (hannonlab.cshl.edu/fastx_toolkit/index.html) with parameter “-f 13 -l 95” before alignment. The trimmed reads were aligned to the Arabidopsis genome (TAIR10) using TopHat2.
Genome_build: TAIR10
Supplementary_files_format_and_content: The processed file was generated using featureCounts with parameter "-p -t exon -g gene_id -a tair10_ensembl.gtf".

organism: Arabidopsis thaliana

source_name: JKZ320 lrx345 NaCl 72h rep3

extract_protocol: The 10-day-old seedlings before and after NaCl treatment were collect for RNA isolation by using Trizol reagent (Invitrogen) according to the manufacturer’s instructions. The isolated RNAs were sent to Shanghai Center for Plant Stress Biology (PSC), SIBS CAS for RNA sequencing.


title: Intestinal biopsy, PK-56

description:
Adult_FPKM_deidentified.xlsx
PK-56


title: lrx345_NaCl_72h_rep1

description: Treated with 150mM NaCl for 72 hours

source_name: JKZ320 lrx345 NaCl 72h rep1


title: lrx345_NaCl_24h_rep3

description: Treated with 150mM NaCl for 24 hours

source_name: JKZ320 lrx345 NaCl 24h rep3


title: Intestinal biopsy, PK-18

description:
same individual as PK-19
Adult_FPKM_deidentified.xlsx
PK-18


title: lrx345_NaCl_72h_rep2

description: Treated with 150mM NaCl for 72 hours

source_name: JKZ320 lrx345 NaCl 72h rep2


title: lrx345_NaCl_24h_rep2

description: Treated with 150mM NaCl for 24 hours

source_name: JKZ320 lrx345 NaCl 24h rep2


title: Intestinal biopsy, PK-16

description:
same individual as PK-17
Adult_FPKM_deidentified.xlsx
PK-16


title: Intestinal biopsy, PK-11

description:
Adult_FPKM_deidentified.xlsx
PK-11


title: lrx345_NaCl_6h_rep2

description: Treated with 150mM NaCl for 6 hours

source_name: JKZ320 lrx345 NaCl 6h rep2


title: lrx345_NaCl_6h_rep1

description: Treated with 150mM NaCl for 6 hours

source_name: JKZ320 lrx345 NaCl 6h rep1


title: shCtrl-2

description:
extracting RNA after transfected with shCtrl
NC2


title: lrx345_NaCl_6h_rep3

description: Treated with 150mM NaCl for 6 hours

source_name: JKZ320 lrx345 NaCl 6h rep3


title: WT_NaCl_6h_rep3

description: Treated with 150mM NaCl for 6 hours

source_name: JKZ320 WT NaCl 6h rep3

value: WT


title: WT_NaCl_72h_rep2

description: Treated with 150mM NaCl for 72 hours

source_name: JKZ320 WT NaCl 72h rep2


title: WT_NaCl_24h_rep1

description: Treated with 150mM NaCl for 24 hours

source_name: JKZ320 WT NaCl 24h rep1


title: WT_NaCl_24h_rep2

description: Treated with 150mM NaCl for 24 hours

source_name: JKZ320 WT NaCl 24h rep2


title: WT_NaCl_6h_rep2

description: Treated with 150mM NaCl for 6 hours

source_name: JKZ320 WT NaCl 6h rep2


title: WT_NaCl_24h_rep3

description: Treated with 150mM NaCl for 24 hours

source_name: JKZ320 WT NaCl 24h rep3


title: WT_NaCl_72h_rep1

description: Treated with 150mM NaCl for 72 hours

source_name: JKZ320 WT NaCl 72h rep1


title: lrx345_NaCl_0h_rep1

source_name: JKZ320 lrx345 NaCl 0h rep1


title: WT_NaCl_0h_rep1

source_name: JKZ320 WT NaCl 0h rep1


title: lrx345_NaCl_rep3

description: treated with 150mM NaCl for 6 hours

data_processing:
The reads were aligned to the Arabidopsis genome (TAIR10) using TopHat2 with default parameter and "-G tair10_ensembl.gtf".
Genome_build: TAIR10
Supplementary_files_format_and_content: The bedGraph files were generated using genomeCoverageBed from bedtools with parameter  -bga -split

source_name: seedlings

extract_protocol: The 10-day-old seedlings before and after NaCl treatment (150mM for 6 hours) were collect for RNA isolation by using Trizol reagent (Invitrogen) according to the manufacturer’s instructions. The isolated RNAs were sent to Shanghai Center for Plant Stress Biology (PSC), SIBS CAS for RNA sequencing.

tag: genotype/variation

tag: treatment

value: NaCl


title: WT_NaCl_6h_rep1

description: Treated with 150mM NaCl for 6 hours

source_name: JKZ320 WT NaCl 6h rep1


title: WT_NaCl_72h_rep3

description: Treated with 150mM NaCl for 72 hours

source_name: JKZ320 WT NaCl 72h rep3


title: WT_NaCl_0h_rep2

source_name: JKZ320 WT NaCl 0h rep2


title: lrx345_NaCl_rep2

description: treated with 150mM NaCl for 6 hours


title: lrx345_MS_rep3

value: MS


title: lrx345_NaCl_24h_rep1

description: Treated with 150mM NaCl for 24 hours

source_name: JKZ320 lrx345 NaCl 24h rep1


title: lrx345_MS_rep1


title: lrx345_NaCl_rep1

description: treated with 150mM NaCl for 6 hours


title: Col0_NaCl_rep2

description: treated with 150mM NaCl for 6 hours


title: Col0_NaCl_rep3

description: treated with 150mM NaCl for 6 hours


title: Col0_NaCl_rep1

description: treated with 150mM NaCl for 6 hours


title: Col0_MS_rep3


title: lrx345_MS_rep2


title: Col0_MS_rep2


title: lrx345_NaCl_0h_rep2

source_name: JKZ320 lrx345 NaCl 0h rep2


title: Barcoded, pooled single B cells [J_7]

city: Groningen

first: Marco

last: de Bruyn

address: Hanzeplein 1

department: Obstetrics&Gynecology

country: Netherlands

institute: University Medical Center Groningen

data_processing:
mRNA sequencing data was demultiplexed into individual FASTQ files followed by alignment to the human reference genome hg38 using STAR (version 2.5.2).
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Endometrial Cancer

extract_protocol:
Tumours were cut into ca. 1cm3, enzymatically digested in RPMI medium (Gibco, Paisley, UK) with 1 mg/µL collagenase type IV (Gibco Life Technologies, Grand Island, USA) and 12,6 µg/mL recombinant human DNase (Pulmozyme, Roche, Woerden, the Netherlands) for 30 minutes at 37 °C or overnight at room temperature. Digests were filtered using 70 µm cell strainers (Falcon) and enriched for peripheral blood mononuclear cells (PBMCs) using Ficoll-Paque PLUS (GE Healthcare Life Sciences, Marlborough, MA, USA). Cells were stored in liquid nitrogen until cell sorting. For cell sorting, tumour digests were thawed and washed with PBS and incubated with Zombie Aqua (1:100, Biolegend, San Diego, USA) for 15 minutes at room temperature. Samples were washed and stained with anti-CD27 APC-efluor 780 (clone O323; 47-0279-42; eBioscience) and either CD19-PE (clone HIB19; 12-0199-41; eBioscience), CD19-BV421 (clone HIB19; 562440; BD Biosciences), CD19-APC (clone HIB19; 17-0199-41; eBioscience) or CD19-PE-cy7 (clone HIB19; 25-0199-41; eBioscience) for 45 minutes at 4°C. Cells were washed and filtered using a 35 µm strainer (Falcon). Patient samples were pooled to minimize differences due to plate effects and sorted on a Beckman Coulter MoFlo Astrios. Each well contained 2 µl lysis buffer (0,2% Triton X-100 (Sigma-Aldrich) and 2U RNase inhibitor (Takara)) with 1 µl 10 µM oligo-dT primer and 1 µl 10 mM dNTP mix (Thermo Scientific). After sorting, the plate was spun down and incubated at 72°C for 3 minutes.
SmartScribe reverse transcriptase (Westburg-Clontech) and a template switching oligo (BC-TSO) were used to generate cDNA. Next, an exonuclease step was performed using 1:400 dilution of Exonuclease I.  A PCR preamplification step was done with KAPA HiFi HotStart Ready Mix (Roche Diagnostics, 23 cycles in experiment 1 and 25 cycles in experiment 2) and a custom-made PCR primer. The cDNA samples were purified using Ampure XP beads (Beckman Coulter) in a ratio of 0,8:1 (Ampure bead : cDNA). Samples were analysed on a 2100 Bioanalyzer using a PerkinElmer LabChip GX high-sensitivity DNA chip (Agilent) and on a Qubit™ 4 Fluorometer (ThermoFisher Scientific) according to manufacturer's instructions. 500 pg of each sample was tagmented and N7xx and S5xx index adapters were used for barcoding according to the Illumina Nextera XT DNA sample preparation kit (Illumina). Thereafter, samples were purified with Ampure XP beads (ratio 0,6 Ampure : 1 cDNA) and analysed on a 2100 Bioanalyzer. Samples were equimolar pooled (4 nM) and samples were sequenced on an Illumina Nextseq500 2500 using 75 bp paired end reads.
Modified SMARTseq2

tag: patient

value: B cells

tag: disease

value: Endometrial Cancer


title: Barcoded, pooled single B cells [J_8]


title: Barcoded, pooled single B cells [F_7]


title: Barcoded, pooled single B cells [J_1]


title: Barcoded, pooled single B cells [J_2]


title: Barcoded, pooled single B cells [F_5]


title: Barcoded, pooled single B cells [F_8]


title: Barcoded, pooled single B cells [F_6]


title: Barcoded, pooled single B cells [J_4]


title: Barcoded, pooled single B cells [F_4]


title: Barcoded, pooled single B cells [J_12]


title: Barcoded, pooled single B cells [F_3]


title: Barcoded, pooled single B cells [J_3]


title: Barcoded, pooled single B cells [J_16]


title: Barcoded, pooled single B cells [J_13]


title: Barcoded, pooled single B cells [J_11]


title: Barcoded, pooled single B cells [J_6]


title: Barcoded, pooled single B cells [F_2]


title: Barcoded, pooled single B cells [F_1]


title: Col0_MS_rep1


title: Barcoded, pooled single B cells [J_15]