title: PBMC_HC4

city: Newcastle upon Tyne

first: Anastasia

last: Resteu

address: M3.127, 3rd Floor Leech Building, Framlington Place

institute: Newcastle University

data_processing:
Reads were trimmed with Cutadapt v 1.14  to remove TruSeq adapters (Read 1: AGATCGGAAGAGCACACGTCTGAACTCCAGTCA and Read 2: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT) and bases with quality scores below Q20. Reads shorter than 50bp were dropped.
Remaining reads were aligned with STAR v 2.7.7a using the following parameters: --outFilterMultimapNmax 50, --peOverlapNbasesMin 10, alignSplicedMateMapLminOverLmate 0.5, --alignSJstitchMismatchNmax 5 -1 5 5, --chimSegmentMin 10, --chimOutType WithinBAM HardClip, --chimJunctionOverhangMin 10, --chimScoreDropMax 30, --chimScoreJunctionNonGTAG 0, --chimScoreSeparation 1, --chimSegmentReadGapMax 3, and --chimMultimapNmax 50
Read counts for gene expression analysis were obtained with HTSEQ v 0.9.1 using the BAM files produced by STAR as input. The following parameters were specified: minimum alignment quality of 4 and stranded “reverse”.
Fusion detection analysis was undertaken with Arriba v 2.0.0. The following files were used as input: BAM files produced by the STAR software, reference GRCh37 fasta file, GENCODE19 reference genome GTF, as well as the lists of known fusions, protein domains, and the blacklist provided within Arriba software installation. The recurrent alignment artefacts and transcripts present in healthy tissue listed within the Arriba blacklist were filtered out.
Genome_build: GRCh37
Supplementary_files_format_and_content: txt files containg HTSEQ counts and tsv files containing detected RNA fusions

source_name: PBMC

growth_protocol: Fibroblasts were cultured in RPMI 1640 medium with the addition of 20% FCS, 1% penicillin-streptomycin and 1% glutamine

extract_protocol:
QIAGEN AllPrep DNA/RNA Mini Kit
Illumina TruSeq Stranded Total RNA

tag: donor

value: Control

tag: source

value: primary

tag: culture medium


title: ATAC-seq-regulatory T cells-deficiency of Foxp3 enhancer CNS0 and CNS3 (CNS03DKO)

status: Public on May 10 2021

type: SRA

city: Memphis

first: Beisi

last: Xu

state: Tennessee

address: 262 Danny Thomas Pl

department: Center for Applied Bioinformatics

country: USA

institute: St Jude Children's Research Hosipital

library_source: genomic

data_processing:
100 bp paired-end reads obtained from all samples were trimming for Nextera adapter by cutadapt(version 1.9, paired-end mode, default parameter with “ -m 25 -O 6 ”) and aligned to mouse genome mm9 (MGSCv37 from Sanger) by BWA (version 0.7.12-r1039, default parameter), duplicated reads were then marked with biobambam2 (version v2.0.87) and only non-duplicated proper paired reads were chosen by samtools (parameter “-q 1 -F 1804” version 1.2).
Both regulatory T cell and naive CD4 T cell samples have more than 20 million nucleosome free fragments. Therefore, we considered all important nucleosome free regions were called.
We adjust Tn5 shift (reads were offset by +4 bp for the sense strand and -5 bp for the antisense strand) and separated reads into nucleosome free, mononucleosome, dinucleosome, and trinucleosome by fragment size. We generated bigwig files by using the center 80bp of fragments and scale to 20 million nucleosome free reads. We confirmed nucleosome tracks surrounded nucleosome free tracks, and provided nucleosome free tracks here.
Genome_build: mm9(MGSCv37 )
Supplementary_files_format_and_content: bigwig

molecule: genomic DNA

organism: Mus musculus

source_name: Regulatory T cells were sorted by GFP expression from mixed bone marrow chimeric mice generated with bone marrows from male donors of CD45.1 wild-type mice and CD45.2 mice of indicated genotypes

growth_protocol: Regulatory T cells or naive CD4 T cells were FACS sorted from mixed bone marrow chimeric mice.

extract_protocol:
Sorted cells were harvested by centrifugation before being permeabilized for Tn5 transposition according to published protocols (PMID: 25559105).
Library was constructed according to published protocols (PMID: 25559105).

tag: strain

tag: cell type

value: FACS sorted regulatory T cells (CD4+GFP+)

tag: genotype


title: ATAC-seq-regulatory T cells-deficiency of Foxp3 enhancer CNS0 (CNS4KO)

value: deficiency of Foxp3 enhancer CNS0 (CNS0KO)


title: Cachexia2

city: Shanghai

first: Diya

last: Sun

address: Dongan Street

country: China

institute: Zhongshan Hospital Fudan University

library_source: transcriptomic

data_processing:
Illumina CASAVA 1.7software was used for basecalling
Raw reads generated during high-throughput sequencing were fastq format sequences. In order to get high-quality reads that could be used for later analysis, raw reads needed to be further quality filtered. Trimmomatic version 0.36 software was first used for adpter removing, And then low-quality bases and N-bases or low-quality reads were filtered out. Finally, we got high-quality clean reads.
Using hisat2 version 2.2.1.0 to align clean reads to the reference genome of the experimental specie, the sample should be assessed by genomic and gene alignment.
Genome_build: Genome Database GRCh38.p12
Supplementary_files_format_and_content: Table with raw gene counts or normalized abundance measurements for every gene and every sample

molecule: total RNA

organism: Homo sapiens

source_name: Adipose tissue_Cachexia

extract_protocol:
Total RNA was extracted using the mirVana miRNA Isolation Kit (Ambion) following the manufacturer’s protocol. RNA integrity was evaluated using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA)
The libraries were constructed using TruSeq Stranded Total RNA with Ribo-Zero Gold according to the manufacturer’s instructions. Then these libraries were sequenced on the Illumina sequencing platform and 150 bp/125bp paired-end reads were generated.

tag: subject status

value: Cancer-associated cachexia (CAC) patient

tag: gender

value: Male

tag: tumor stage

value: III stage

tag: tissue

value: Adipose tissue


title: PBMC_HC3

country: United Kingdom


title: 15717X14 SJL PLX CD4 rep 2

city: Salt Lake City

first: Ana Beatriz

last: DePaula-Silva

state: UT

address: 15N Medical Drive East room 2800

department: Pathology

institute: University of Utah

data_processing:
The mouse GRCm38 FASTA and GTF files were downloaded from Ensembl release 94.
The reference database was created using STAR version 2.6.1b with splice junctions optimized for 50 base pair reads.
Reads were trimmed of adapters and aligned to the reference database using STAR in two pass mode to output a BAM file sorted by coordinates.
Mapped reads were assigned to annotated genes in the GTF file using featureCounts version 1.5.1.
Differentially expressed genes were identified using a 5% false discovery rate with DESeq2 version 1.20.0
Supplementary_files_format_and_content: FeatureCount output files combined into tab-delimited file

source_name: Brain

extract_protocol:
RNA was extracted using RNeasy
Illumina TruSeq stranded RNA Kit with Ribo-Zero Gold

treatment_protocol: PLX5622 or control diet

tag: mouse strain

value: SJL/J

tag: diet

value: PLX

value: CD4 T cells


title: PBMC_GATA2_mut

value: GATA2 patient


title: Cachexia1


title: 15717X13 SJL PLX CD4 rep 1


title: ATAC-seq-regulatory T cells-deficiency of Foxp3 enhancer CNS3 (CNS3KO)


title: 24 hours post-infection pCHi-C replicate 3

city: London

first: Mikhail

last: Spivakov

address: Du Cane Road

institute: MRC London Institute of Medical Sciences

description:
Promoter Capture Hi-C
pCHi-C reads from one independent biological sample.

data_processing:
Sequence alignment and removal of invalid di-tags performed using HiCUP Version 0.7.4 (Wingett et al., F1000Res 2015).
Filtered bam files converted to CHiCAGO input (chinput) files using bam2chicago.sh provided with ChicagoTools. DpnII fragment-level reads were pooled over consecutive fragments over the total length of at least 5k, except for the baited promoter fragments that were left unbinned. For the following samples, the chinput files were then downsampled to 36% in order to balance the data across conditions: 8hpi_rep2 and 24hpi_rep2
Significant interactions were called for each full sized replicate and also for each timepoint jointly across the three replicates (with downsampled rep2 in 8h and 24hpi) by CHiCAGO (Cairns et al., Genome Biol 2016). For the joint analyses, minNPerBait was set to 90. All other parameters were left at defaults.
Genome_build: GRCh38
Supplementary_files_format_and_content: CHiCAGO objects (.Rds files) provide interaction data for individual replicates and for each condition (three replicate analyses).
Supplementary_files_format_and_content: The baitmap file (.baitmap) shows the targeted DpnII fragments.
Supplementary_files_format_and_content: The rmap file (.rmap) shows all DpnII fragments in the genome.

source_name: Human alveolar basal epithelial carcinoma cell line expressing the human SARS-CoV-2 entry receptor Ace2

growth_protocol: A549-ACE2 cells were maintained at 37°C and 5% CO2 and cultured in Dulbecco’s Modified Eagle’s Medium supplemented with 10% fetal bovine serum.

extract_protocol:
Crosslinking was performed with 2% formaldehyde followed by cell membrane lysis. Lysates were snap frozen and stored at -80C.
PCHi-C (Schoenfelder et al., 2015) was combined with Hi-C library generation as described previously (Nagano et al., 2017), with some modifications. Cell lysates were digested with DpnII (NEB) overnight at 37C rotating (950rpm). Restriction overhangs were filled-in with Klenow (NEB) using biotin-14-dATP (Jena Bioscience), and ligation was performed in ligation buffer for 4 hours at 16C (T4 DNA ligase; Life Technologies). After overnight decrosslinking at 65C, the ligated DNA was tagmented to produce fragments of 300-700 bp range. Ligation products were isolated using MyOne C1 streptavidin beads (Life Technologies), followed by washing with Wash&Binding buffer and nuclease-free water. Isolated Hi-C ligation products on the beads were then used directly for PCR amplification, and the final Hi-C library was purified with AMPure XP beads (Beckman Coulter). Promoter Capture Hi-C was performed using a custom-design Agilent SureSelect system following the manufacturer’s protocol.

treatment_protocol: Cells were either mock-infected (PBS only) or infected with SARS-CoV-2 virus at MOI 0.5. Infected cells were cultured for 8 or 24 hours.

tag: cell line

tag: treatment

value: SARS-CoV2 virus infection

tag: time point

value: 24 hours post-infection


title: fib_HC2

source_name: fibroblast

value: culture-derived

value: RPMI 1640 medium with the addition of 20% FCS, 1% penicillin-streptomycin and 1% glutamine


title: ATAC-seq-regulatory T cells-wild type Foxp3-GFP

value: wild type Foxp3-GFP


title: THP1 ATF4 noArg

city: Oxford

first: Thomas

middle: A

last: Milne

address: John Radcliffe Hospital, Headington

department: MRC Weatherall Institute of Molecular Medicine

institute: University of Oxford

description: ATF4 ChIP-seq in THP1 cells cutured in the absence of arginine

data_processing:
Alignment to the genome (Bowtie) maintaining strict read order
Trim_galore (to remove sequencing adaptors)
FLASH (to reconstruct paired end reads into single reads where possible)
Removal of PCR duplicates, parsing of informative reads using samtools rmdup
Genome_build: hg19
Peak calling using Homer v4.7

source_name: Leukemia cell line (THP1)

growth_protocol: Cells were grown in RPMI medium supplemented with 10% FCS and glutamax (Life Technologies)

extract_protocol:
Cells were washed with PBS and fixed in either 1% FA for 10 minutes (histones) or 2mM DSG for 30 minutes and 1% FA for 30 minutes (transcription factors). Cells were sonicated to give fragments of 100-300bp followed by IP.
DNA libraries were made using the NEBnext ultra DNA library preparation kit for Illumina (Cat no. E7370).

treatment_protocol: THP1 cells were cultured in full or arginine-free medium for 72h prior to harvest. Human CD4+ T-cells were purified from PBMCs isolated from commercially available leukocyte cones (NHS Blood and Transplant, Bristol, UK) by magnetic-activated cell sorting (MACS) purification using CD4 Microbead kits (Miltenyi Biotec) then stimulated using anti-CD3/CD28 antibodies (Life Technologies). Cells were cultured in low (20uM) arginine or arginine-free medium for 72h prior to harvest.

value: Leukemia cell line (THP1)

value: Cells cultured in arginine-free RPMI for 72h

value: Paediatric monocytic cell line derived from AML M5 with t(9;11)(q21;q23) translocation

tag: chip antibody

value: Cell Signaling Technology 11815


title: ATAC-seq-naive CD4 T cells-deficiency of Foxp3 enhancer CNS0 and CNS3 (CNS03DKO)

source_name: Naïve CD4 T cells were sorted by CD45.2+CD4+TCRbeta+GFP-CD25-CD44highCD62low from mixed bone marrow chimeric mice generated with bone marrows from male donors of CD45.1 wild-type mice and CD45.2 mice of indicated genotypes

value: FACS sorted naive CD4 T cells (CD45.2+CD4+TCRbeta+GFP-CD25-CD44highCD62low)


title: fib_HC1

value: Control


title: 15717X10 SJL CTL CD4 rep 2

value: CTL


title: fib_GATA2_mut


title: 15717X15 SJL PLX CD8 rep 1

value: CD8 T cells


title: 8 hours post-infection pCHi-C replicate 3

value: 8 hours post-infection


title: 15717X9 SJL CTL CD4 rep 1

value: SJL/J


title: Mock infected pCHi-C replicate 3

value: 0 hours


title: ATAC-seq-naive CD4 T cells-deficiency of Foxp3 enhancer CNS0 (CNS0KO)


title: 15717X7 BL/6 PLX CD8 rep 2

value: PLX


title: HDMEC cells treated with TNF replicate 3

city: West Haven

first: Francesc

last: Lopez

state: CT

department: Department of Genetics

institute: Yale University

description:
TNF treated HDMEC
HDMEC_TNF3C

data_processing:
Basecalls performed using CASAVA version 1.8.2
For each read, the first 6 and the last nucleotides were trimmed to the point where the Phred score of an examined base fell below 20 using in-house scripts. If, after trimming, the read was shorter than 45 bp, the whole read was discarded.
Trimmed reads were mapped to the human reference genome (hg38) with HISAT2 v2.1.0
Gene counts were produced with StringTie v1.3.3b and the Python script “prepDE.py” provided in the package. StringTie was limited to reads matching the reference annotation GENCODE v27
DESeq2 was used for differential expression analysis
Genome_build: hg38
Supplementary_files_format_and_content: tsv with Deseq2

source_name: Human dermal microvascular endothelial cells, primary isolates

growth_protocol: Primary isolated from human skin surgical pathology sampled, cultured in EGM2MV (Lonza), CD31 bead selected, passage 5 grown to 2 days post confluence and stimulated with 0.6 ng/mL TNF for 6 hours

extract_protocol:
Cell monolayers were washed with sterile phosphate buffered saline (PBS, Invitrogen) and total RNA was purified using the RNeasy Mini Kit (Qiagen) with an on-column DNase treatment.
Poly-A, strand-specific RNA library construction was performed by the Yale Center for Genomic Analysis utilizing the TruSeq Library Prep Kit 2.0 per the manufacturers specifications. . Following first-strand synthesis with random primers, second strand synthesis was performed with dUTP for generating strand-specific sequencing libraries.

treatment_protocol: Replicate cultures of HDMECs were maintained for 2 days post-confluence in a 12 well plate (Falcon) and stimulated with 0.5 ng/mL TNF (Invitrogen) for 6 hours or left untreated.

value: Capillary

value: Endothelial cell

value: Tumor Necrosis factor


title: 24 hours post-infection pCHi-C replicate 2

value: SARS-CoV2 virus infection

value: 24 hours post-infection


title: 15717X6 BL/6 PLX CD4 rep 2

value: CD4 T cells


title: ATAC-seq-naive CD4 T cells-deficiency of Foxp3 enhancer CNS3 (CNS3KO)


title: 24 hours post-infection pCHi-C replicate 1


title: HDMEC cells treated with TNF replicate 2

description:
TNF treated HDMEC
HDMEC_TNF3B


title: ATAC-seq-naive CD4 T cells-wild type Foxp3-GFP

value: wild type Foxp3-GFP


title: HDMEC cells treated with TNF replicate 1

description:
TNF treated HDMEC
HDMEC_TNF3A


title: 15717X5 BL/6 PLX CD4 rep 1


title: 8 hours post-infection pCHi-C replicate 2


title: HDMEC cells treated with PBS replicate 3

description:
PBS treated HDMEC
HDMEC_PBS1C

value: PBS


title: 8 hours post-infection pCHi-C replicate 1


title: 15717X3 BL/6 CTL CD8 rep 1


title: ATAC-seq-regulatory T cells-deficiency of Foxp3 enhancer CNS0 and CNS2 (CNS02DKO)

value: FACS sorted regulatory T cells (CD4+GFP+)


title: HDMEC cells treated with PBS replicate 2

description:
PBS treated HDMEC
HDMEC_PBS1B


title: 15717X11 SJL CTL CD8 rep 1


title: Mock infected pCHi-C replicate 2


title: 15717X2 BL/6 CTL CD4 rep 2


title: Mock infected pCHi-C replicate 1


title: 15717X1 BL/6 CTL CD4 rep 1


title: HDMEC cells treated with PBS replicate 1

description:
PBS treated HDMEC
HDMEC_PBS1A


title: ATAC-seq-regulatory T cells-deficiency of Foxp3 enhancer CNS2 (CNS2KO)


title: TIA1 input

status: Public on May 09 2021

city: La Jolla

first: Gene

last: Yeo

state: CA

address: 2880 Torrey Pines Scenic Dr. Room 3805/Yeo Lab

institute: UCSD

data_processing:
Sequenced reads were removed of inline barcodes and reformatted to include randomers in read headers with eclipdemux (v0.0.1). Args: --length 10
Reads were then trimmed with cutadapt (1.14). Args: --match-read-wildcards -O 1 --times 1 -e 0.1 --quality-cutoff 6 -m 18 -g g_adapters.fasta -A A_adapters.fasta -a a_adapters.fasta (fasta sequences generated from parsebarcodes.sh within the eclip 0.1.5+ pipeline)
Reads were then trimmed once more with cutadapt (1.9.1) to remove double-ligation events. Args: --match-read-wildcards -O 5 --times 1 -e 0.1 --quality-cutoff 6 -m 18 -A A_adapters.fasta (fasta sequences generated from parsebarcodes.sh within the eclip 0.1.5+ pipeline)
Trimmed reads were then mapped with STAR (2.4.0i) against a human-specific repeat element database (RepBase 18.05). Args: --runThreadN 16 '--genomeDir human_repbase '--readFilesIn path/to/read1 path/to/read2 '--outFileNamePrefix out_prefix '--outReadsUnmapped Fastx '--outSAMtype BAM Unsorted '--outSAMattributes All '--outSAMunmapped Within '--outSAMattrRGline ID:foo '--outFilterType BySJout '--outFilterMultimapNmax 30 '--outFilterMultimapScoreRange 1 '--outFilterScoreMin 10 '--alignEndsType EndToEnd
Unmapped reads filtered of repeat elements were then mapped with STAR (2.4.0i) against a human genome (hg19). Args: --runThreadN 16 '--genomeDir genomedir '--readFilesIn /path/to/read1 /path/to/read2 '--outFileNamePrefix out_prefix '--outReadsUnmapped Fastx '--outSAMtype BAM   Unsorted '--outSAMattributes All '--outSAMunmapped Within '--outSAMattrRGline ID:foo '--outFilterType BySJout '--outFilterMultimapNmax 1 '--outFilterMultimapScoreRange 1 '--outFilterScoreMin 10 '--alignEndsType EndToEnd
Aligned reads were sorted with samtools (1.4.1)
Sorted reads were collapsed with barcodecollapsepe.py included in eclip 0.1.5+ pipelines. Args: -o preRmDup.bam -m metrics_file -b rmDup.bam
PCR de-duped reads from each inline barcode were then merged with samtools (1.4.1) merge (merged.bam)
Merged alignments were split to keep just read2 using samtools (1.4.1) view. Args: -h -b -f 128
Read2 BAM files were used to identify peak clusters with Clipper (1.2.2). Args: --species hg19 --bam path/to/input.bam --timeout 3600000 --maxgenes 1000000 --save-pickle --outfile path/to/output.bam
Peak clusters were normalized using read2 BAM files for IP against read2 BAM files for INPUT with peaksnormalize.pl (overlap_peakfi_with_bam_PE.pl), included in eclip 0.1.5+.
Overlapping normalized peak regions were merged with compress_l2foldenrpeakfi_for_replicate_overlapping_bedformat.pl, included within eclip-0.1.5+
Normalized peak (compressed.bed) files were ranked by entropy score (make_informationcontent_from_peaks.pl included within the merge_peaks pipeline) and used as inputs to IDR (2.0.2) to determine reproducible peaks.
Genome_build: hg19
Supplementary_files_format_and_content: BigWig, BED

growth_protocol: HEK293 cells were maintained in DMEM (4.5 g/L D-glucose) supplemented with 10% FBS (Gibco) at 37o C with 5% CO2. Cells were periodically passaged once at 70-90% confluency by dissociating with TrypLE Express Enzyme (Gibco) at a ratio of 1:10

extract_protocol:
Biological replicates (according to ENCODE requirements) of 20 million cells were treated with 600mJ of UV using the Stratalinker 2400, harvested in ice cold PBS and pellets flash frozen in liquid nitrogen and stored in -80 degrees until ready to IP with TIA1 bound Dynabeads Subsequent protocol exactly as detailed in Van Nostrand et al 2016. Sequencing was performed on Illumina Hi Seq paired end reads and data processed through Dr. Yeo's eCLIP pipeline.
Libraries were constructed as per the eCLIP protocol using Illumina 50x forward and 70x reverse primers.
eCLIP

treatment_protocol: HEK293 cells were UV cross-linked with 600mJ and processed through the eCLIP protocol as previously described (van Nostrand et al, 2016). Msi1 antibody employed for immunoprecipitation was RN014P (MBL)

tag: rip antibody

tag: inline barcode1

value: None (NIL)

tag: inline barcode2


title: TIA1 rep2 clip

tag: antibody manufacturer

value: MBL

tag: antibody catalog #

value: C01 (ACAAGTT)

value: D8f (TGGTCCT)


title: TIA1 rep1 clip

value: A01 (AAGCAAT)

value: B06 (GGCTTGT)


title: 13817X18: PC3 ZBTB4 si2 RNA-seq

first: Aneesa

middle: T

last: Al-Soodani

department: Chemistry

data_processing:
The human GRCh38 FASTA and GTF files were downloaded from Ensembl release 87 and the reference database was created using STAR version 2.5.2b with splice junctions optimized for 50 base pair reads.
Reads were trimmed of adapters and aligned to the reference database using STAR in two pass mode to output a BAM file sorted by coordinates.
Mapped reads were assigned to annotated genes in the GTF file using featureCounts version 1.5.1.  The output files from FastQC, STAR, and featureCounts were summarized using MultiQC to check for any sample outliers.
Differentially expressed genes between PC3 and ZBTB KD cells, or between PrEC and PC3 cells, were identified using a 5% false discovery rate, respectively, with DESeq2 version 1.16.0.
Genome_build: GRCh38
Supplementary_files_format_and_content: Raw counts (featureCounts output files combined into a single matrix)

source_name: PC3; Prostate Adenocarcinoma Cell Line

growth_protocol: PC3 cells were cultured in F-12K medium supplemented with 10% FBS in a humidified incubator at 37 deg. C with 5% CO2. PrEC cells were cultured using the Lonza PrEGM BulletKit  in a humidified incubator at 37 deg. C with 5% CO2.

extract_protocol:
Transfected PC3 cells or PrEC cells were washed with PBS and resuspended in TRIzol prior to RNA extraction with the Direct-zol RNA Kit (Zymo Research). RNA quality was measured on a Bioanalyzer RNA 6000 Nano Chip.
RNA libraries were prepared for sequencing by Illumina TruSeq Stranded mRNA Sample Prep with poly(A) selection

treatment_protocol: PC3 cells were transfected with either a scrambled (Scr) siRNA or one of two ZBTB33, ZBTB4 or ZBTB38 targeting siRNAs (Thermo Fisher Scientific) using Lipofectamine RNAiMAX (Thermo Fisher Scientific) and incubated for 24 hr.

value: cell line PC3

tag: cell type

value: Prostate Adenocarcinoma

tag: passage

value: 5 to 8

tag: ID


title: ATAC-seq-regulatory T cells-deficiency of Foxp3 enhancer CNS0 (CNS0KO)

tag: strain

tag: genotype


title: 13817X10: PrEC RNA-seq

source_name: Normal Prostate Epithelial Cell Line

tag: tissue

value: cell line PrEC

value: Normal Prostate

value: 2 to 5


title: 13817X19: PC3 ZBTB4 si2 RNA-seq


title: 13817X29: PC3 ZBTB38 si2 RNA-seq


title: 13817X30: PrEC RNA-seq


title: 13817X17: PC3 ZBTB4 si2 RNA-seq


title: 13817X15: PC3 ZBTB4 si1 RNA-seq


title: 13817X28: PC3 ZBTB38 si2 RNA-seq


title: 13817X26: PC3 ZBTB38 si1 RNA-seq


title: 13817X27: PC3 ZBTB38 si2 RNA-seq


title: 13817X16: PC3 ZBTB4 si1 RNA-seq


title: 13817X24: PC3 ZBTB38 si1 RNA-seq


title: 13817X9: PC3 ZBTB33 si2 RNA-seq


title: ATAC-seq-regulatory T cells-wild type Foxp3-GFP


title: HEK293T, APOBEC

data_processing:
The double stranded cDNA for each sample was converted to sequencing libraries as recommended (PacBio SMRTbell Express Template Prep Kit 2.0) but with separate barcoded adapters for each sample (PacBio Barcoded Overhang Adapter Kit).
All of the samples were pooled in an equimolar fashion and sequenced on a SMRTcell 8M with the PacBio Sequel II instrument (2.0 chemistry/2.1 polymerase with 2 hour pre-extension and 30 hour movie times). After barcodes were demultiplexed, the initial data was used to re-balance the pooling by barcode counts before further sequencing. In total, the samples were sequenced over 5 SMRTcell 8M. The PacBio Sequel II system was used for all sample sequencing.
Following sequencing, the circular consensus sequence (CCS) reads for each set of technical replicates were processed using the Isoseq v3 pipeline (https://github.com/PacificBiosciences/IsoSeq) to generate full-length non-concatamer reads in fasta format. For this step, software package lima v2.0.0 was used with parameters: --isoseq and --dump-clips. In addition, isoseq3 v3.4.0 refine was used with parameters: --require-polya. Fasta files for each set of technical replicates were the pooled together and the full-length non-concatemer reads for each sample were aligned to the hg19 reference genome using minimap2 v2.17-r941 using parameters: --ax-splice, -uf, --secondary=no, -t 30.
Genome_build: hg19
Supplementary_files_format_and_content: BED, txt

molecule: polyA RNA

source_name: Human embryonic kidney

growth_protocol: All stable STAMP HEK293T cell lines were generated using human lenti-X HEK293T cells (HEK293XT, Takara Bio) which are derived from transformed female human embryonic kidney tissue. Cells were maintained in DMEM (4.5 g/L D-glucose) supplemented with 10% FBS (Gibco) at 37o C with 5% CO2. Cells were periodically passaged once at 70-90% confluency by dissociating with TrypLE Express Enzyme (Gibco) at a ratio of 1:10.

extract_protocol:
Trizol extraction (Fisher) and Direct-zol miniprep (Zymo Research) column purification in accordance with manufacturer protocol
PacBio Iso-seq express protocol with 300ng of total RNA amplified for 13-15 cycles

treatment_protocol: For STAMP fusion protein expression STAMP stable HEK293T cells were induced with 50ng/ml (low) or 1ug/ml (high) doxycycline in DMEM for 24-72 hours, followed by Trizol extraction and Direct-zol miniprep (Zymo Research) column purification in accordance with manufacturer protocol.  Uninduced cells of the same genetic background were used as negative controls. For mTOR perturbation experiments, cells were treated with 100nM Torin-1 or 100nM insulin alongside 1ug/ml doxycycline induction and harvested for RNA after 72 hours 37C incubation.


title: HEK293T, RBFOX


title: 13817X25: PC3 ZBTB38 si1 RNA-seq


title: control-STAMP Direct RNA

description:
RNA isolated from HEK293T cells expressing only APOBEC was directly sequenced on a MinION
instrument model: MinION-Mk1B

data_processing:
Raw reads were aligned to hg19 (genomic) or ENSEMBL (cDNA) reference using Minimap2 with the following parameters: "-ax splice -uf -k14". Aligned reads were then passed through Bcftools mpileup command with a "-Q 5" parameter. The pileup files were then filtered for G & C reference positions. For direct-RNA data the strand was inferred based on mapping directionality. For cDNA alignments the strand as assumed to be positive. For direct-cDNA reads aligned to hg19 sites were intersected with an annotation file and strand was assigned based on gene directionality with ambiguous strands being removed. Sites were then further filtered for C positions based on strand. Confidence scores were calculated using manual implementation of SAILOR with a modification rate of 5%. Bed files were generated by filtering SAILOR confidence scores >=0.5. Sites found in the APOBEC-only control were removed from the RBFOX2 files. SNPs were removed by bedtools intersect with dbSNP (v147).
Genome_build: hg19 or ENSEMBL cDNA
Supplementary_files_format_and_content: bed

source_name: control-STAMP

extract_protocol:
Trizol extraction (Fisher) and Direct-zol miniprep (Zymo Research) column purification in accordance with manufacturer protocol
Nanopore direct-RNA or direct-cDNA

tag: expressing

value: only APOBEC

tag: sequencing protocol

value: directly sequenced on a MinION


title: RBFOX2-STAMP Direct RNA

description:
RNA isolated from HEK293T cells expressing a RBFOX2-APOBEC fusion was directly sequenced on a MinION
instrument model: MinION-Mk1B

tag: cell line

value: RBFOX2-APOBEC fusion


title: 13817X8: PC3 ZBTB33 si2 RNA-seq


title: 13817X6: PC3 ZBTB33 si1 RNA-seq


title: 13817X4: PC3 ZBTB33 si1 RNA-seq


title: SynCom35_Flg22_3

city: Köln

first: Yulong

last: Niu

state: Nordrhein-Westfalen

address: Carl-von-Linne-Weg 10

department: Plant Microbe Interactions

country: Germany

institute: Max Planck Institute for Plant Breeding Research

description:
2x150bp paired-end sequence reads
Col-0_RNA-Seq_raw_counts.txt

data_processing:
Illumina Casava software used for basecalling.
Raw Illumina RNA-Seq reads were pre-processed using fastp (v0.19.10) with default settings for paired-end (Col-0 experiment) or single-end reads (pWER::FLS2-GFP experiment). For single-end reads, low quality sequences from the head (8 bases) and tail (2 bases) were trimmed.
High quality reads were pseudo-aligned to TAIR 10 Arabidopsis thaliana transcriptome reference (Ensembl) using kallisto (v0.46.1).
After removal of low abundant transcripts that were absent in at least two replicates under each condition, count data were imported using the tximport package.
Raw counts were normalized with respect to the library size (rlog function) in DESeq2.
Genome_build: TAIR 10 Arabidopsis thaliana transcriptome reference (Ensembl).
Supplementary_files_format_and_content: Matrix table with raw transcript counts for every gene and every sample generated by Kallisto and sample-size normalized by DESeq2.

organism: Arabidopsis thaliana

source_name: Col-0 with suppressive SynCom and flg22, root

growth_protocol: Plants were germinated with the indicated SynCom in the presence or absence of 1 µM flg22 and incubated for 14 days before harvesting. Col-0 and pWER::FLS2-GFP plants were inoculated with non-suppressive and suppressive SynComs.

extract_protocol:
Roots were washed briefly with sterile water and blotted dry before being transferred into Lysing Matrix E tubes (MP Biomedicals) at -80˚C until processing. Roots were homogenized with Lysing Matrix E using prechilled adapter and TissueLyser II (Qiagen, 20/sec, 1 minute). RNA was extracted with the Plant RNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions. RNA quality was determined using a 2100 Bioanalyzer (Agilent Technologies, USA).
Preparation of Illumina sequencing libraries was conducted by the Max Planck Genome Center) using an input of 1μg total RNA.

treatment_protocol: Plants were not transferred to minimize induced damage. Roots from three plates (minimal 15 plants) were combined as one replicate and a total of three replicates were sampled for each condition

value: root

tag: flg22 treatment

value: 1 microM flg22

tag: syncom treatment

value: living suppressive

tag: treatment duration

value: incubation for 14 days


title: SynCom35_Flg22_2


title: SynCom35_Flg22_4


title: SynCom35_Flg22_1


title: SynCom35_4

source_name: Col-0 with suppressive SynCom, root

value: no


title: SynCom35_3


title: SynCom35_2


title: 13817X1: PC3 Scr RNA-seq


title: SynCom35_1


title: 13817X3: PC3 Scr RNA-seq


title: WT_D5_2hr_r1-2

first: Erinke

last: van Grinsven

address: Roosevelt Drive

department: Kennedy Institute of Rheumatology

description:
PolyA RNA
hoxb8_rna_2_featureCounts.txt

data_processing:
Reads were mapped to the mm10 genome using STAR with the options: “—runMode alignReads –outFilterMismatchNmax 2.” Uniquely mapped read pairs were counted over annotated genes using feature Counts with the options: “-T 18 -s 2 -Q 255.” Differential expression was then analysed with DESeq2
Genome_build: mm10 (GRCm38)

source_name: ER-Hoxb8 neutrophils

growth_protocol: ER-Hoxb8 progenitor cells were routinely cultured in RMPI-1640 medium supplemented with 10% FCS, 30 mM β-mercaptoethanol, 1% supernatant from stem cell factor (SCF)-producing CHO cells and 1 μM β-estradiol. Differentiation was induced by estrogen removal and culture in medium containing 1% SCF supernatant. The progenitor cells were differentiated into neutrophils by culturing with complete RPMI 1640 medium supplemented with 30 mM b-mercaptoethanol, 4% SCF containing supernatant and 20 ng/mL G-CSF in 5% CO2 tissue culture incubator at 37°C.

extract_protocol:
HoxB8 neutrophils differentiated for five days were incubated with Zymosan(50ug/ml) or DMSO vehicle for two hours. After RNA isolation, oly-A selected mRNA libraries were sequenced on Illumina HiSeq4000 yielding 20-30x106 150 b.p. paired end reads per sample.
Total RNA of Hoxb8 neutrophils  were extracted using RNeasy mini kit (Qiagen) according to the manufacturer’s instruction.
cDNA

value: ER-Hoxb8 neutrophils

tag: number of days of in vitro differentiation

tag: phenotype

value: WT

tag: treatment

value: Zymosan 2h

tag: replicate


title: 13817X20: PrEC RNA-seq


title: 13817X14: PC3 ZBTB4 si1 RNA-seq

value: cell line PC3


title: WT_D5_2hr_r2-2

description:
PolyA RNA
hoxb8_rna_2_featureCounts.txt

treatment_protocol: HoxB8 neutrophils differentiated for five days were incubated with Zymosan(50ug/ml) or DMSO vehicle for two hours.


title: HKSynCom35_Flg22_3

source_name: Col-0 with heat-killed suppressive SynCom and flg22, root

value: heat-killed suppressive


title: WT_D5_0hr_r1-2

description:
PolyA RNA
hoxb8_rna_2_featureCounts.txt

value: DMSO 2h


title: HKSynCom35_Flg22_2


title: 13817X7: PC3 ZBTB33 si2 RNA-seq

value: Prostate Adenocarcinoma

value: 5 to 8


title: HKSynCom35_Flg22_1


title: WT_D5_0hr_r2-2

description:
PolyA RNA
hoxb8_rna_2_featureCounts.txt


title: RELB_D5_2hr_r2

description:
PolyA RNA
hoxb8_rna_2_featureCounts.txt

value: RELB-/-


title: RELB_D5_2hr_r1

description:
PolyA RNA
hoxb8_rna_2_featureCounts.txt


title: HKSynCom35_3

source_name: Col-0 with heat-killed suppressive SynCom, root


title: HKSynCom35_4


title: 13817X5: PC3 ZBTB33 si1 RNA-seq


title: 13817X2: PC3 Scr RNA-seq


title: IRF5_D5_2hr_r2

description:
PolyA RNA
hoxb8_rna_2_featureCounts.txt


title: IRF5_D5_2hr_r1

description:
PolyA RNA
hoxb8_rna_2_featureCounts.txt


title: SynCom33_Flg22_3

source_name: Col-0 with non-suppressive SynCom and flg22, root

value: living non-suppressive


title: HKSynCom35_Flg22_4


title: IRF5_D5_0hr_r2

description:
PolyA RNA
hoxb8_rna_2_featureCounts.txt


title: RELB_D5_0hr_r1

description:
PolyA RNA
hoxb8_rna_2_featureCounts.txt


title: SynCom33_Flg22_4


title: SynCom33_4

source_name: Col-0 with non-suppressive SynCom, root


title: WT_D5_2hr_r2-1

description:
PolyA RNA
hoxb8_rna_1_featureCounts.txt


title: HKSynCom35_2


title: SynCom33_Flg22_1


title: SynCom33_2


title: SynCom33_1


title: WT_D5_0hr_r1-1

description:
PolyA RNA
hoxb8_rna_1_featureCounts.txt


title: WT_D5_0hr_r2-1

description:
PolyA RNA
hoxb8_rna_1_featureCounts.txt


title: SynCom33_3


title: IRF5_D5_0hr_r1

description:
PolyA RNA
hoxb8_rna_2_featureCounts.txt


title: RELB_D5_0hr_r2

description:
PolyA RNA
hoxb8_rna_2_featureCounts.txt


title: JUNB_D5_2hr_r2

description:
PolyA RNA
hoxb8_rna_1_featureCounts.txt

value: JUNB-/-


title: HKSynCom33_Flg22_2

source_name: Col-0 with heat-killed non-suppressive SynCom and flg22, root

value: heat-killed non-suppressive


title: HKSynCom33_Flg22_3

value: root


title: JUNB_D5_0hr_r1

description:
PolyA RNA
hoxb8_rna_1_featureCounts.txt


title: HKSynCom35_1


title: SynCom33_Flg22_2

value: 1 microM flg22


title: HKSynCom33_Flg22_1


title: WT_D5_2hr_r1-1

description:
PolyA RNA
hoxb8_rna_1_featureCounts.txt


title: HKSynCom33_3

source_name: Col-0 with heat-killed non-suppressive SynCom, root


title: HKSynCom33_4


title: CEBPB_D5_0hr_r2

description:
PolyA RNA
hoxb8_rna_1_featureCounts.txt

value: CEBPB-/-


title: CEBPB_D5_2hr_r1

description:
PolyA RNA
hoxb8_rna_1_featureCounts.txt


title: HKSynCom33_2

value: incubation for 14 days


title: RNA Pol II-CutRun-regulatory T cells-Foxp3 CNS0 knockout

data_processing:
Library strategy: Cut&Run
Paired-end reads of 50bp were mapped mouse genome mm9 (MGSCv37 from Sanger) by BWA (version 0.7.12-r1039, default parameter) after trimming for adapters by cutadapt(version 1.9, paired-end mode, default parameter with “ -m 25 -O 6 ”), duplicated reads were then marked with biobambam2(version v2.0.87).
Only non-duplicated reads have been kept by samtools (parameter “-q 1 -F 1804” version 1.2).
All samples have more than 5M fragments as suggested by Cut&Run protocols paper after merging replicates. We then generated bigwig files by using the center 80bp of fragments smaller than 2000bp and normalized to 10M fragments. We confirmed clear peak patterns.
Genome_build: mm9(MGSCv37 )
Supplementary_files_format_and_content: bigwig

source_name: Regulatory T cells were sorted by GFP expression from mixed bone marrow chimeric mice generated with bone marrows from male donors of CD45.1 wild-type mice and CD45.2 mice of indicated genotypes

growth_protocol: Regulatory T cells were sorted by GFP expression from mixed bone marrow chimeric mice.

extract_protocol:
Cut&Run was performed according to a method recently described (PMID: 28079019).
Libraries were constructed according to standard protocols for Cut&Run sequencing.

value: FACS sorted regulatory T cells (CD4+GFP+)

value: deficiency of Foxp3 enhancer CNS0 (CNS4KO)

tag: chip antibody


title: HKSynCom33_1

value: no


title: CEBPB_D5_0hr_r1

description:
PolyA RNA
hoxb8_rna_1_featureCounts.txt

tag: cell type

value: ER-Hoxb8 neutrophils


title: HKSynCom33_Flg22_4


title: RNAseq_Neu_MEM_2

description:
PolyA RNA
airpouch_rna_featureCounts.txt

source_name: Air pouch membrane

extract_protocol: Neutrophils from bone marrow, blood, membrane and exudate were sorted from CX3CR1GFP Ly6GCre-tdTomato mice subjected to air pouch of inflammation. Amplified cDNA was prepared for “small bulk” RNA-sequencing using the Smart-seq2 protocol. Libraries were prepared using Nextera XT kits (Illumina) and sequenced to a mean depth of 17M read pairs (Illumina HiSeq 4000).

value: Neutrophils

value: air pouch membrane


title: Mock_Flg22_4

source_name: Col-0 with flg22, root


title: RNAseq_Neu_MEM_1


title: JUNB_D5_0hr_r2

description:
PolyA RNA
hoxb8_rna_1_featureCounts.txt

value: DMSO 2h


title: RNAseq_Neu_BM_3

source_name: Bone marrow

value: bone marrow


title: JUNB_D5_2hr_r1

description:
PolyA RNA
hoxb8_rna_1_featureCounts.txt

value: Zymosan 2h


title: Mock_4

source_name: Col-0, root


title: RNAseq_Neu_BL_5

source_name: Blood

value: blood


title: Mock_Flg22_2


title: Mock_Flg22_1


title: RNAseq_Neu_BM_2


title: RNAseq_Neu_BL_4


title: Mock_2


title: Mock_3


title: RNAseq_Neu_BL_3


title: RNAseq_Neu_BL_2


title: CEBPB_D5_2hr_r2

description:
PolyA RNA
hoxb8_rna_1_featureCounts.txt


title: Mock_1


title: pWER_Flg22_SynCom35_3

description:
150bp single-end sequence reads
pWER_RNA-Seq_raw_counts.txt

source_name: pWER::FLS2-GFP with suppressive SynCom and flg22, root

value: living suppressive


title: RNAseq_Neu_BL_1


title: Mock_Flg22_3


title: pWER_Flg22_SynCom35_2


title: RNAseq_Neu_AP_5

source_name: Air pouch exudate

value: air pouch exudate


title: RNAseq_Neu_BM_1


title: pWER_Flg22_SynCom33_3

source_name: pWER::FLS2-GFP with non-suppressive SynCom and flg22, root

value: living non-suppressive


title: RNAseq_Neu_AP_4


title: pWER_Flg22_SynCom35_1

value: root


title: NCGR1363 leaf 42D replicate 2

city: Oslo

first: Relindis

middle: Ghai

last: Njah

address: Blindernveien 31

department: Department of Biosciences

country: Norway

institute: University of Oslo

description:
processed data header: 63-NL42DR2
Count table_AN_gene_level_RSEM_Bowtie2.txt
Count table_AN_isofrom_level_RSEM_Bowtie2.txt

data_processing:
Illumina HiSeq4000 sequencing platform was used for basecalling
Sequenced reads were trimmed of adapter and low quality sequences followed my merging of technical replicates and mappeing to  mRNA sequences from the F. vesca v.4.a2 reference genome using RSEM and Bowtie2.
Differentially expressed genes were identified using the edgeR Bioconductor package. A false discovery rate (FDR) cut off of 0.05; generalized linear model (GLM) quasi-likelihood F-test; counts per million reads (CPM) cutoff of 0.5 in a minimum of 2 of 3 biological replicates; and sample normalization based on TMM (weighted trimmed mean of M-values) as recommended by the package user guide.
Genome_build: FvH4 (https://www.rosaceae.org/rosaceae_downloads/Fragaria_vesca/Fvesca-genome.v4.0.a1/assembly/Fragaria_vesca_v4.0.a1.fasta.gz), a2-annotation (https://www.rosaceae.org/rosaceae_downloads/Fragaria_vesca/Fvesca-genome.v4.0.a2/genes/Fragaria_vesca_v4.0.a2.genes.gff3.gz)
Supplementary_files_format_and_content: Matrix table (tab .txt format) with read counts for every gene, transcript isoforms in all samples

organism: Fragaria vesca

source_name: leaf tissue

growth_protocol: Runners from respective genotypes were rooted and grown in pots containing peat based compost (90% peat, 10% clay) and 1:5 granulated perlite for 5 weeks at 20 ± 2 °C and an 18-hour photoperiod. Plants were watered twice a week with a balanced nutrient solution containing 7.8 mmol N, 1 mmol P, and 4.6 mmol K per litre

extract_protocol:
Tissues were harvested and pulverized under liquid nitrogen. Total RNA was extracted from powder tissue using the Spectrum Plant Total RNA Kit (Sigma) according to manufacturer’s instructions.
RNA libraries were prepared from 1 ug of total RNA, using strand-specific TruSeq™ RNA-seq (Illumina) library protocol.

treatment_protocol: Plants were cold treated at 2 °C for 42 days

value: Cold treated at 2 C for 42 days

value: leaf


title: RNAseq_Neu_AP_2


title: RNAseq_Neu_AP_3


title: NCGR1363 leaf 42D replicate 3

description:
processed data header: 64-NL42DR3
Count table_AN_gene_level_RSEM_Bowtie2.txt
Count table_AN_isofrom_level_RSEM_Bowtie2.txt


title: NCGR1363 leaf 42D replicate 1

description:
processed data header: 62-NL42DR1
Count table_AN_gene_level_RSEM_Bowtie2.txt
Count table_AN_isofrom_level_RSEM_Bowtie2.txt


title: pWER_Flg22_SynCom33_2

value: 1 microM flg22

value: incubation for 14 days


title: NCGR1363 leaf 0H replicate 3

description:
processed data header: 61-NL0HR3
Count table_AN_gene_level_RSEM_Bowtie2.txt
Count table_AN_isofrom_level_RSEM_Bowtie2.txt

value: Untreated


title: NCGR1363 leaf 0H replicate 2

description:
processed data header: 60-NL0HR2
Count table_AN_gene_level_RSEM_Bowtie2.txt
Count table_AN_isofrom_level_RSEM_Bowtie2.txt


title: NCGR1363 crown 42D replicate3

description:
processed data header: 58-NK42DR3
Count table_AN_gene_level_RSEM_Bowtie2.txt
Count table_AN_isofrom_level_RSEM_Bowtie2.txt

source_name: crown tissue

value: crown


title: RNAseq_Neu_AP_1


title: NCGR1363 leaf 0H replicate 1

description:
processed data header: 59-NL0HR1
Count table_AN_gene_level_RSEM_Bowtie2.txt
Count table_AN_isofrom_level_RSEM_Bowtie2.txt


title: pWER_Flg22_SynCom33_1


title: pWER_Flg22_3

source_name: pWER::FLS2-GFP with flg22, root

value: no


title: ATACseq_Neu_BL_2

description:
DNA fragments
DA_peaks_BL_VS_BM_decrease.bed
DA_peaks_BL_VS_BM_increase.bed

data_processing:
Reads were trimmed with Cutadapt prior to mapping with Bowtie2 with the options: "--local --X 2000" Duplicates were removed with PicardTools markDuplicates, as were reads with MAPQ scores < 10 or insert sizes > 150 bp Peak calling was conducted using MACS2 with the following settings: "--format BAMPE --nomodel --keep-dup-all --mfold 5,50". DeepTools was used to generate normalised (FPKM) bigWigs of ATAC signal Differentially accessible sites were determined by counting reads over a union interval set of all detected peaks and analysis with DESeq2 Genome_build: mm10 Supplementary_files_format_and_content: bigWig - ATAC signal (FPKM)
Genome_build: mm10 (GRCm38)

extract_protocol:
75,000 Ly6G +ve Neutrophils were sorted from bone marrow, blood, membrane, and air pouch and used to generate ATAC libraries. Nuclei isolated and accessible DNA tagmented and purified following ATAC-seq protocol. DNA fragments 100 bp - 1 kb were selected with AMPure XP beads and amplified by PCR prior to pooling and sequencing
Nuclei isolated and accessible DNA tagmented and purified following ATAC-seq protocol. DNA fragments 100 bp - 1 kb were selected with AMPure XP beads and amplified by PCR prior to pooling and sequencing
Other

value: Neutrophils

value: Blood


title: ATACseq_Neu_BM_2

description:
DNA fragments
DA_peaks_AP_VS_BM_decrease.bed
DA_peaks_AP_VS_BM_increase.bed

value: Bone marrow


title: NCGR1363 crown 0H replicate 3

description:
processed data header: 55-NK0HR3
Count table_AN_gene_level_RSEM_Bowtie2.txt
Count table_AN_isofrom_level_RSEM_Bowtie2.txt


title: pWER_Flg22_2


title: NCGR1363 crown 42D replicate1

description:
processed data header: 56-NK42DR1
Count table_AN_gene_level_RSEM_Bowtie2.txt
Count table_AN_isofrom_level_RSEM_Bowtie2.txt


title: NCGR1363 crown 42D replicate2

description:
processed data header: 57-NK42DR2
Count table_AN_gene_level_RSEM_Bowtie2.txt
Count table_AN_isofrom_level_RSEM_Bowtie2.txt


title: pWER_Flg22_1


title: ATACseq_Neu_MEM_2

description:
DNA fragments
DA_peaks_MEM_VS_BM_decrease.bed
DA_peaks_MEM_VS_BM_increase.bed

value: Air pouch membrane


title: Alta leaf 42D replicate 2

description:
processed data header: 51-AL42DR2
Count table_AN_gene_level_RSEM_Bowtie2.txt
Count table_AN_isofrom_level_RSEM_Bowtie2.txt

value: Alta


title: NCGR1363 crown 0H replicate 2

description:
processed data header: 54-NK0HR2
Count table_AN_gene_level_RSEM_Bowtie2.txt
Count table_AN_isofrom_level_RSEM_Bowtie2.txt


title: Alta leaf 42D replicate 3

description:
processed data header: 52-AL42DR3
Count table_AN_gene_level_RSEM_Bowtie2.txt
Count table_AN_isofrom_level_RSEM_Bowtie2.txt


title: NCGR1363 crown 0H replicate 1

description:
processed data header: 53-NK0HR1
Count table_AN_gene_level_RSEM_Bowtie2.txt
Count table_AN_isofrom_level_RSEM_Bowtie2.txt


title: pWER_Mock_3

description:
150bp single-end sequence reads
pWER_RNA-Seq_raw_counts.txt

source_name: pWER::FLS2-GFP, root


title: ATACseq_Neu_AP_2

description:
DNA fragments
DA_peaks_AP_VS_BL_decrease.bed
DA_peaks_AP_VS_BL_increase.bed

value: Air pouch exudate


title: Alta leaf 0H replicate 3

description:
processed data header: 49-AL0HR3
Count table_AN_gene_level_RSEM_Bowtie2.txt
Count table_AN_isofrom_level_RSEM_Bowtie2.txt


title: pWER_Mock_2


title: Alta leaf 42D replicate 1

description:
processed data header: 50-AL42DR1
Count table_AN_gene_level_RSEM_Bowtie2.txt
Count table_AN_isofrom_level_RSEM_Bowtie2.txt


title: pWER_Mock_1


title: ATACseq_Neu_MEM_1


title: ATACseq_Neu_BL_1


title: Alta leaf 0H replicate 2

description:
processed data header: 48-AL0HR2
Count table_AN_gene_level_RSEM_Bowtie2.txt
Count table_AN_isofrom_level_RSEM_Bowtie2.txt


title: ATACseq_Neu_BM_1


title: Alta leaf 0H replicate 1

description:
processed data header: 47-AL0HR1
Count table_AN_gene_level_RSEM_Bowtie2.txt
Count table_AN_isofrom_level_RSEM_Bowtie2.txt


title: Alta crown 42D replicate 1

description:
processed data header: 44-AK42DR1
Count table_AN_gene_level_RSEM_Bowtie2.txt
Count table_AN_isofrom_level_RSEM_Bowtie2.txt


title: Alta crown 0H replicate 3

description:
processed data header: 43-AK0HR3
Count table_AN_gene_level_RSEM_Bowtie2.txt
Count table_AN_isofrom_level_RSEM_Bowtie2.txt


title: ATACseq_Neu_AP_1


title: Alta crown 42D replicate 3

description:
processed data header: 46-AK42DR3
Count table_AN_gene_level_RSEM_Bowtie2.txt
Count table_AN_isofrom_level_RSEM_Bowtie2.txt


title: Muscle_HTN+uncDM_Postop_rep4

type: genomic

city: Providence

first: Alexey

middle: V

last: Fedulov

state: Rhode Island

address: 593 Eddy St.

department: RIH / Surgical Research

institute: Alpert Medical School of Brown University

description:
205138650044_R08C01
Hypertension and uncontrolled diabetes, after surgery

hyb_protocol: Standard Illumina procedure.

scan_protocol: Standard Illumina procedure.

data_processing: IDAT files were a source of average beta values normalized via functional normalization with NOOB background adjustment and dye correction followed by m-value transformation.

label: biotin, DNP

source_name: skeletal muscle

label_protocol: Standard Illumina procedure.

extract_protocol: Probe grinding homogenization followed by lysis and DNA isolation via Qiagen DNeasy protocol.

value: skeletal muscle

tag: diagnosis

value: Hypertension + uncontrolled diabetes

tag: time point

value: Post-op


title: Alta crown 0H replicate 1

description:
processed data header: 41-AK0HR1
Count table_AN_gene_level_RSEM_Bowtie2.txt
Count table_AN_isofrom_level_RSEM_Bowtie2.txt


title: Muscle_HTN+uncDM_Postop_rep3

description:
205138650044_R07C01
Hypertension and uncontrolled diabetes, after surgery


title: Muscle_HTN+uncDM_Postop_rep1

description:
205138650044_R05C01
Hypertension and uncontrolled diabetes, after surgery


title: Muscle_HTN+uncDM_Postop_rep2

description:
205138650044_R06C01
Hypertension and uncontrolled diabetes, after surgery


title: Muscle_HTN+cDM_Postop_rep4

description:
205138650044_R04C01
Hypertension and controlled diabetes patient, after surgery

value: Hypertension + controlled diabetes


title: Muscle_HTN+cDM_Postop_rep3

description:
205138650044_R03C01
Hypertension and controlled diabetes patient, after surgery


title: Alta crown 42D replicate 2

description:
processed data header: 45-AK42DR2
Count table_AN_gene_level_RSEM_Bowtie2.txt
Count table_AN_isofrom_level_RSEM_Bowtie2.txt

value: Cold treated at 2 C for 42 days


title: Muscle_HTN+cDM_Postop_rep2

description:
205138650044_R02C01
Hypertension and controlled diabetes patient, after surgery


title: Muscle_HTN+cDM_Postop_rep1

description:
205138650044_R01C01
Hypertension and controlled diabetes patient, after surgery


title: ATAC_E12.5_LRF_KO_Hom

city: Headington

first: Damien

last: Downes

state: Oxfordshire

address: John Radcliffe Hospital

department: MRC Weatherall Institute of Medicine

institute: The University of Oxford

description:
Genome-wide library of tagmented fragments.
LRF∆/LRF∆

data_processing:
Mapping : bowtie -m 2 --maxIns 350,mm9
For un-mapping reads : trimming adaptors trim_galore -- length 10, combining overlapping R1-R2 reads : flash -m 9 -x 0.125
Combining trimmed+flashed and originally mapped reads, mapping again with bowtie -m 2 --maxIns 350
Removing read pairs overlapping Blacklisted regions.
Removing duplicates : samtools rmdup
Reconstructing sequenced fragments from R1+R2 read pairs (bedtools bedpe | cut -f 1,2,6) - for visualisation.
Pileup of fragments (bedtools genomecov -counts).
Generating bigWig tracks.
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: bigWig : (DEEPtools) bamCoverage conversion of filtered fragments (reconstructed, duplicate-filtered fragments : see above) from bam to bigwig, (--binSize 10 --normalizeUsingRPKM --minMappingQuality 30).

source_name: Definitive erythroid

growth_protocol: Fetal livers were dissected from E12.5 mouse embryos, and the dissociated cell suspension was expanded for 5–7 d in Stempro (Invitrogen) supplemented with Epo (1 U/ml), SCF (50 ng/ml) and dexamethasone (1 μM). After expansion of the cultures, mature red blood cells were removed by negative selection for Ter119 using anti-Ter119 magnetic beads (Miltenyi Biotec), to obtain a population of erythroid precursors, which was then purified by CD44 positive cell sorting before being placed into expansion media to recover for 6 hours.

extract_protocol:
ATAC-seq was performed as published (Buenrostro et al., 2013). 10,000-50,000 cells were used per biological replicate where possible; if cells numbered less than 10,000 an optimised low cell number protocol was used. Cells were spun at 500g for 10 min, then lysed using cold lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl 3 mM MgCl2, 0.1% IGEPAL CA-630). Transposition was then performed with Tn5 transposase (Nextera, Illumina) for 30 min at 37oC following the reaction volumes as published. DNA was purified using the Qiagen MinElute kit following the manufacturer’s instructions, then eluted in 20μl of elution buffer; samples could be stored at this point at -20oC. Libraries were amplified and barcoded using the NEBNext 2xMastermix kit with custom primers as published (Buenrostro et al., 2013). ATAC-seq library profiles were visualized using the D1000 tape on the Agilent Tapestation to ensure correct tagmentation. Libraries were quantified using the universal library quantification kit (KAPA Biosystems) prior to massively parallel sequencing using a standard Illumina protocol (NextSeq High Output v2 75 cycle sequencing kit). The low cell number protocol uses proportionally less lysis buffer and Tn5 transposase (Corces et al., 2017). After spinning at 500g for 10 min and removing the supernatant, cells were permeabilised and tagmented with Dig-transposition buffer (25 μL 2x TD buffer [Illumina], 2.5 μL Tn5 Transposase, 0.5 μL 1% digitonin and 22 μL H2O) for 30 min. After the transposition step, samples were processed as per larger cell numbers.
Libraries were amplified and barcoded using the NEBNext 2xMastermix (NEB) and the custom primers as published in Buenrostro et al., 2013. ATAC-Seq libraries profiles were visualized using D1000 tape on the Tapestation (Agilent). The libraries were quantified using the universal library quantification kit (KAPA Biosystems).

value: Cultured fetal liver cells

value: LRF<delta>/LRF<delta>

tag: strain


title: ATAC_E12.5_BCL11A_EnhKO_Hom_rep1

description:
Genome-wide library of tagmented fragments.
BCL11A_Enh∆/BCL11A_Enh∆

tag: genotype


title: ATAC_E12.5_BCL11A_EnhKO_Hom_rep2


title: ATAC_E12.5_LRF_KO_Het

description:
Genome-wide library of tagmented fragments.
LRF-FLOX/LRF∆

value: LRF-FLOX/LRF<delta>


title: ATAC_E12.5_BCL11A_EnhKO_Hom_rep3


title: Alta crown 0H replicate 2

description:
processed data header: 42-AK0HR2
Count table_AN_gene_level_RSEM_Bowtie2.txt
Count table_AN_isofrom_level_RSEM_Bowtie2.txt

value: Untreated

tag: tissue


title: ATAC_E12.5_LRF_KO_FLOX

description:
Genome-wide library of tagmented fragments.
LRF-FLOX/LRF-FLOX

value: LRF-FLOX/LRF-FLOX


title: HEK293T, TIA1 rep2 clip

data_processing:
Sequenced reads were reformatted to include randomers in read headers with umi_tools (1.0.0). Args: --random-seed 1 --bc-pattern NNNNNNNNNN
Reads were then trimmed with cutadapt (1.14). Args: --match-read-wildcards -O 1 --times 1 -e 0.1 --quality-cutoff 6 -m 18 -a InvRNA*.fasta (fasta sequences can be found at: https://github.com/YeoLab/eclip/tree/master/example/inputs/)
Reads were then trimmed once more with cutadapt (1.14) to remove double-ligation events. Args: --match-read-wildcards -O 5 --times 1 -e 0.1 --quality-cutoff 6 -m 18  -a InvRNA*.fasta (fasta sequences can be found at: https://github.com/YeoLab/eclip/tree/master/example/inputs/)
Trimmed reads were then mapped with STAR (2.4.0i) against a human-specific repeat element database (RepBase 18.05). Args: --runThreadN 16 \  --genomeDir human_repbase \  --readFilesIn path/to/read1 \  --outFileNamePrefix out_prefix \  --outReadsUnmapped Fastx \  --outSAMtype BAM Unsorted \  --outSAMattributes All \  --outSAMunmapped Within \  --outSAMattrRGline ID:foo \  --outFilterType BySJout \  --outFilterMultimapNmax 30 \  --outFilterMultimapScoreRange 1 \  --outFilterScoreMin 10 \  --alignEndsType EndToEnd
Unmapped reads filtered of repeat elements were then mapped with STAR (2.4.0i) against a human genome (hg19). Args: --runThreadN 16 \  --genomeDir genomedir \  --readFilesIn /path/to/read1 \  --outFileNamePrefix out_prefix \  --outReadsUnmapped Fastx \  --outSAMtype BAM   Unsorted \  --outSAMattributes All \  --outSAMunmapped Within \  --outSAMattrRGline ID:foo \  --outFilterType BySJout \  --outFilterMultimapNmax 1 \  --outFilterMultimapScoreRange 1 \  --outFilterScoreMin 10 \  --alignEndsType EndToEnd
Aligned reads were sorted with samtools (1.6)
Sorted reads were collapsed with umi_tools (1.0.0). Args: --random-seed 1 --method unique
BAM files were used to identify peak clusters with Clipper (1.2.2). Args: --species hg19 --bam path/to/input.bam --timeout 3600000 --maxgenes 1000000 --save-pickle --outfile path/to/output.bam
Peak clusters were normalized using BAM files for IP against BAM files for INPUT with peaksnormalize.pl (overlap_peakfi_with_bam_PE.pl), included in eclip 0.1.5+.
Overlapping normalized peak regions were merged with compress_l2foldenrpeakfi_for_replicate_overlapping_bedformat.pl, included within eclip-0.1.5+
Normalized peak (compressed.bed) files were ranked by entropy score (make_informationcontent_from_peaks.pl included within the merge_peaks pipeline) and used as inputs to IDR (2.0.2) to determine reproducible peaks.
Genome_build: hg19
Supplementary_files_format_and_content: BigWig, BED

extract_protocol:
Biological replicates (according to ENCODE requirements) of 20 million cells were treated with 600mJ of UV using the Stratalinker 2400, harvested in ice cold PBS and pellets flash frozen in liquid nitrogen and stored in -80 degrees until ready to IP with TIA1 bound Dynabeads Subsequent protocol exactly as detailed in Van Nostrand et al 2016. Sequencing was performed on Illumina Hi Seq single end reads and data processed through Dr. Yeo's eCLIP pipeline.
Libraries were constructed as per the eCLIP protocol using Illumina 50x forward and 70x reverse primers.
eCLIP

treatment_protocol: HEK293 cells were UV cross-linked with 600mJ and processed through the eCLIP protocol as previously described (van Nostrand et al, 2016). Anti-HA tag antibody was employed for immunoprecipitation.

tag: rip antibody

value: anti-HA tag antibody

tag: antibody manufacturer

value: Abcam

tag: antibody catalog #

tag: adapter


title: HEK293T, RBFOX2 rep2 input

tag: cell line


title: HEK293T, RBFOX2 rep1 input


title: HEK293T, RBFOX2 rep2 clip


title: HEK293T, RBFOX2 rep1 clip


title: ATAC_E12.5_BCL11A_EnhKO_Het_rep2

description:
Genome-wide library of tagmented fragments.
BCL11A_Enh∆/WT


title: Muscle_HTN_Postop_rep2

description:
205138650123_R06C01
Hypertension only patient, after surgery

value: Hypertension


title: HEK293T, TIA1 rep2 input


title: Muscle_HTN_Postop_rep1

description:
205138650123_R05C01
Hypertension only patient, after surgery


title: Muscle_Control_Postop_rep4

description:
205138650123_R04C01
Control patient, after surgery

value: Control


title: ATAC_E12.5_BCL11A_EnhKO_Het_rep1


title: Muscle_Control_Postop_rep3

description:
205138650123_R03C01
Control patient, after surgery


title: Muscle_Control_Postop_rep2

description:
205138650123_R02C01
Control patient, after surgery


title: HEK293T, TIA1 rep1 input


title: WT mouse 4, sample B

city: Cambridge

first: Abbe

middle: R

last: Clark

state: Massachusetts

address: 415 M St

institute: Broad Institute

data_processing:
Cellranger toolkit (v2.1.1) used to perform de-multiplexing using the “cellranger mkfastq” command, and the “cellranger count” command for alignment to the mouse pre-mRNA transcriptome, cell barcode partitioning, collapsing unique molecular identifier (UMI) to transcripts, and gene-level quantification.
Genome_build: mm10
Supplementary_files_format_and_content: genes.tsv: This file contains all annotated genes; barcodes.tsv: This file contains the filtered barcodes (barcodes that were filtered as cells) represented in the mtx file; matrix.mtx: UMI counts per gene and barcode combination

source_name: Kidney glomerulus

growth_protocol: iCrepod-Ctcfwt/fl mice were generated as previously described and inbred to generate iCrepod-Ctcffl/fl (iCTCFfl/fl) and iCrepod-Ctcfwt/wt (WT) mice. Both male and female mice were used in this study.

extract_protocol:
iCTCFpod-/- and WT mice were sacrificed after 1 week of doxycycline treatment and kidneys were quickly dissected and washed with ice-cold Hanks’ Balanced Salt Solution. Glomeruli were enriched using a sieving technique. Single cell suspensions were generated via enzymatic and mechanical dissociation.
Single cells were processed through the 10X Chromium 3' Single Cell Platform following the manufacturer's protocol.

treatment_protocol: Doxycycline (4 g/L) (Sigma D9891) was continuously administered in drinking water containing sucrose (50 g/L) (VWR BDH0308) to both iCTCFfl/fl (generates iCTCFpod-/- mice) and WT littermate control mice (age 6-8 weeks at start of doxycycline) to drive Cre expression specifically in podocytes.

value: CTCF wt/wt

tag: age

value: 2 months

tag: Sex

value: female


title: APOBEC-STAMP 48h high Torin-1

data_processing:
Raw reads were trimmed using cutadapt (v1.14) using the following parameters -O 5 -f  fastq --match-read-wildcards --times 2 -e 0.0 --quality-cutoff 6 -m 18 -o data.fastqTr.fq -b TCGTATGCCGTCTTCTGCTTG -b ATCTCGTATGCCGTCTTCTGCTTG -b CGACAGGTTCAGAGTTCTACAGTCCGACGATC -b GATCGGAAGAGCACACGTCTGAACTCCAGTCAC -b AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA -b TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT data.fastq.gz
Trimmed reads were mapped to and filtered of repeat elements (RepBase 18.05) with STAR (2.4.0i) using the following parameters: --alignEndsType  EndToEnd  --genomeDir  repbase  --genomeLoad  NoSharedMemory  --outBAMcompression  10  --outFileNamePrefix  data  --outFilterMultimapNmax  10  --outFilterMultimapScoreRange  1  --outFilterScoreMin  10  --outFilterType  BySJout  --outReadsUnmapped  Fastx  --outSAMattrRGline  ID:foo  --outSAMattributes  All  --outSAMmode  Full  --outSAMtype  BAM  Unsorted  --outSAMunmapped  Within  --outStd  Log  --readFilesIn data.fastqTr.fq  --runMode  alignReads  --runThreadN  8
Reads unmapped to repeat elements were mapped to the human genome with STAR using the same parameters as the previous step, using an hg19 index in place of the repeat element index
Subread featureCounts (-a gencode.v19.annotation.gtf -s 2 -p -o counts.txt data.bam) was used to count features using human annotations (Gencode v19)
Edits were called using SAILOR (http://github.com/yeolab/sailor) using default parameters and dbSNP (v147) to remove known SNPs.
bigwig files were generated from filtered BAM files (intermediates from SAILOR), using the following commands from BedTools (v2.27.1). :     bedtools genomecov -split -strand - -g hg19.chrom.sizes -bg -ibam fwd.bam > fwd.bg  bedtools sort -I fwd.bg > fwd.sorted.bg   bedGraphToBigWig fwd.sorted.bg hg19.chrom.sizes fwd.sorted.bw    bedtools genomecov -split -strand + -g hg19.chrom.sizes -bg -ibam rev.bam > rev.bg  bedtools sort -I rev.bg > rev.sorted.bg   bedGraphToBigWig rev.sorted.bg hg19.chrom.sizes rev.sorted.bw
Genome_build: hg19

source_name: APOBEC-STAMP

extract_protocol:
Trizol extraction (Fisher) and Direct-zol miniprep (Zymo Research) column purification in accordance with manufacturer protocol
Illumina TruSeq stranded mRNA or total RNA


title: Muscle_Control_Postop_rep1

description:
205138650123_R01C01
Control patient, after surgery

value: skeletal muscle


title: WT mouse 4, sample A


title: Muscle_HTN_Postop_rep3

description:
205138650123_R07C01
Hypertension only patient, after surgery


title: Muscle_HTN_Postop_rep4

description:
205138650123_R08C01
Hypertension only patient, after surgery


title: Muscle_HTN+uncDM_Preop_rep3

description:
203952880012_R07C01
Hypertension and uncontrolled diabetes, before surgery

value: Hypertension + uncontrolled diabetes

value: Pre-op


title: WT mouse 2, sample A


title: HEK293T, TIA1 rep1 clip


title: WT mouse 1, sample B

value: male


title: WT mouse 1, sample A


title: CTCF KO mouse 4, sample B

value: CTCF fl/fl


title: Muscle_HTN+uncDM_Preop_rep4

description:
203952880012_R08C01
Hypertension and uncontrolled diabetes, before surgery


title: WT mouse 2, sample B


title: HEK293T-RPS2-STAMP 48h high Torin-1 rep2


title: HEK293T-RPS2-STAMP 48h high insulin rep1


title: WT mouse 3, sample A


title: HEK293T-RPS2-STAMP 48h high Torin-1 rep1


title: HEK293T-RPS2-STAMP 48h high insulin rep2


title: HEK293T-RPS3-STAMP high


title: CTCF KO mouse 4, sample A


title: Muscle_HTN+uncDM_Preop_rep1

description:
203952880012_R05C01
Hypertension and uncontrolled diabetes, before surgery


title: HEK293T-RPS3-STAMP none


title: Muscle_HTN+uncDM_Preop_rep2

description:
203952880012_R06C01
Hypertension and uncontrolled diabetes, before surgery


title: Muscle_HTN_Preop_rep3

description:
203952880069_R07C01
Hypertension only patient, before surgery


title: Muscle_HTN_Preop_rep1

description:
203952880069_R05C01
Hypertension only patient, before surgery


title: Muscle_HTN+cDM_Preop_rep2

description:
203952880012_R02C01
Hypertension and controlled diabetes patient, before surgery

value: Hypertension + controlled diabetes


title: Muscle_HTN+cDM_Preop_rep4

description:
203952880012_R04C01
Hypertension and controlled diabetes patient, before surgery


title: Muscle_HTN+cDM_Preop_rep3

description:
203952880012_R03C01
Hypertension and controlled diabetes patient, before surgery


title: Muscle_HTN_Preop_rep4

description:
203952880069_R08C01
Hypertension only patient, before surgery


title: Muscle_Control_Preop_rep2

description:
203952880069_R02C01
Control patient, before surgery


title: CTCF KO mouse 3, sample B


title: Muscle_Control_Preop_rep3

description:
203952880069_R03C01
Control patient, before surgery


title: CTCF KO mouse 3, sample A


title: HEK293T-RPS2-STAMP 72h low rep1


title: Muscle_Control_Preop_rep1

description:
203952880069_R01C01
Control patient, before surgery


title: HEK293T-RPS2-STAMP 72h low rep2


title: Muscle_Control_Preop_rep4

description:
203952880069_R04C01
Control patient, before surgery


title: CTCF KO mouse 2


title: Muscle_HTN_Preop_rep2

description:
203952880069_R06C01
Hypertension only patient, before surgery


title: CTCF KO mouse 1, sample B


title: HEK293T-RPS2-STAMP 48h high rep1


title: HEK293T-RPS2-STAMP 48h high rep2


title: CTCF KO mouse 1, sample A


title: KO2

city: Cold Spring Harbor

first: Allen

middle: Tingjun

last: Yu

state: NY

address: 1 Bungtown Road

institute: CSHL

data_processing:
Illumina Casava software used for basecalling
The quality of the raw data was evaluated using FastQC.
The reads were mapped to mm10 using STAR.
The GENCODE M20 annotation set was used as a reference and the reads per gene record were counted using the HTSeq package.
Differential gene expression was performed with DESeq2
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include raw counts of sequencing reads (generated with HTSeq-count) for each Sample

source_name: HepA1-6 cells

growth_protocol: HepA1-6 cell lines were cultured in standard DMEM + 10%FBS + 1% P/S

extract_protocol:
Trizol RNA extraction
Libraries were prepared according to Illumina's instructions in TruSeq RNA Library Prep Kit v2

value: PHAROH -/-


title: HEK293T-RPS2-STAMP 48h low rep1


title: HEK293T-RPS2-STAMP 24h high rep2


title: Control 1

value: wild type


title: KO1


title: HEK293T-RPS2-STAMP 24h high rep1


title: Control 2


title: HEK293T-RPS2-STAMP high


title: Rep3_RNA_S6_P53

city: Stanford

first: Gerald

last: Tiu

state: California

address: 279 Campus Dr., Beckman Center B309

institute: Stanford University

description: rRNA depleted total RNA

data_processing:
For analysis pre-processing, UMI-tools63 was used to extract sample barcodes and UMIs. Reads were demultiplexed, sample barcodes were removed, and reads were quality filtered (fastq_quality_filter -Q33 -q 20 -p 70) using FASTX-Toolkit (http://hannonlab.cshl.edu/fastx_toolkit/).
The 3’ adapter sequence CTGTAGGCACCATCAAT was removed using cutadapt64, and the 5’ end of each read was then removed using fastx_trimmer from FASTX-Toolkit. Raw files included have been preprocessed up to this point.
To remove reads that aligned to rRNA, tRNA, and snRNAs, reads were first aligned to these sequences using bowtie265 (bowtie2 parameters: -L 18) and subsequently discarded. Filtered reads that did not align to rRNA/tRNA/snRNAs were then aligned using bowtie2 (bowtie2 parameters: --norc -L 18) to an GRCm38/mm10 transcriptome reference derived from UCSC/GENCODE VM20 knownCanonical annotations filtered for high confidence transcripts that contain at least one of the following: a Uniprot ID, a RefSeq ID, or an Entrez ID.
PCR duplicates were then removed using UMI-tools. (Note 9 base UMI is in description of each read in FASTQ files)
Ribosome protected fragments (RPFs) were then parsed for uniquely aligned reads, separated into read length groups, and ribosome A site positions were determined by offsetting the distance of the 5’ end of each read to canonical start sites in each length group and adding 4 nucleotides62. RNA-Seq reads were also parsed for uniquely aligned reads and were assigned to the center of each read. RPFs and RNA-Seq reads were then counted using the transcriptome annotations detailed above.
Reads aligning to the CDS (with the first 15 codons and last 5 codons removed) were used for RPF libraries, and reads aligning to the entire transcript were used for RNA-Seq libraries.
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: Counts aligning to CDS (with the first 15 codons and last 5 codons removed) for ribosome protected fragments; counts aligning to entire transcript for RNA-Seq

source_name: E10.5 mouse forelimbs

growth_protocol: Embryos were harvested at E10.5 from Prx1Cre x Rps6lox/lox;Trp53+/- mice

extract_protocol:
Limb pairs from each embryo were lysed via vigorous pipetting and 30 minute incubation at 4oC in 215 μL buffer A (25 mM Tris-HCl pH 7.5, 150 mM NaCl, 15 mM MgCl2, 1 mM DTT, 8% glycerol, 1% Triton X-100, 100 μg/ml CHX (Sigma-Aldrich, C7698-1G), 20 U/ml Turbo DNAse (Thermo Fisher, AM2238), and Complete Protease Inhibitor EDTA-free (Sigma-Aldrich, 11836170001). Lysates were cleared via sequential centrifugation at 1,300g, 5 min and 10,000g, 10 min at 4oC. For RNA input for RNA-Seq, 70 μL of lysate was diluted in 55 μL of water and stored at -80oC in 375 μL of TRIzol LS (Thermo Fisher, 10296010). For ribosome profiling, 120 μL of cleared lysate was treated with 0.5 μg RNase A (Thermo Fisher, AM2271) and 300 U RNase T1 (Thermo Fisher, EN0541) for 30 min, RT with gentle rocking. The reaction was stopped by the addition of 100 U SUPERase RNase Inhibitor (Thermo Fisher, AM2694). Ribosomes were enriched by adding 110 μL lysate onto 900 μL sucrose cushion buffer (1 M sucrose in buffer A containing 20 U/mL SUPERase RNase Inhibitor), and centrifuging in a TLA 120.2 rotor (Beckman) 70,000 rpm, 4 h, 4 °C. The ribosome pellet containing the ribosome footprinted Ribo-Seq library was resuspended in 500 μL TRIzol.
Library preparation was adapted from previous protocols59,61 and the ARTseq Ribosome Profiling Kit manual (Epicentre, Illumina). In summary, total RNA and ribosome footprints were extracted using the Direct-zol Micro Kit (Zymo, R2060) with in-column DNase I treatment. To have an adequate amount of RNA for subsequent steps, pairs of samples of the same genotype were pooled to generate a single replicate sample, brought up to 90 μL with water, and precipitated with 150 μL isopropanol overnight -80oC after addition of 10 μL 3 M NaOAc pH 5.5 and 1.5 μL 15 mg/mL GlycoBlue Coprecipitant (Thermo Fisher, AM9515). The samples were then centrifuged at 21,000g, 30 min, 4oC, supernatant was removed, and the RNA pellet was washed 500 μL cold 75% ethanol. Pellets were dried for 10 min, RT and resuspended in 15 μL nuclease free water. After extraction and precipitation, both ribosome footprinting and total RNA samples were depleted of rRNA using the Ribo-Zero Gold rRNA Removal Kit (H/M/R) (Illumina, catalog no. MRZG126) with the modification that the 50oC incubation was not performed for the ribosome footprinting samples. The samples were then column purified (RNA Clean & Concentrator 5, Zymo Research, catalog no. R1016) with the modifications that 2 volumes of RNA Binding Buffer and 4.5 volumes of ethanol were added to ribosome footprinting samples to purify small RNAs and 1 volume of RNA Binding Buffer and 1 volume of ethanol was added to total RNA samples to isolate RNA > 200 nt. Total RNA samples were then fragmented by partial alkaline hydrolysis. The samples were diluted to 100 μL with 5 mM Tris-HCl, pH 7.5 and incubated with 100 μL 2x alkaline fragmentation buffer (100 mM Na2CO3 pH 9.2, 2 mM EDTA) for 20 minutes at 95oC. The reaction was neutralized with 440 μL STOP Buffer (70 μL 3 M NaOAc pH 5.5, 2 μL Glycoblue, and 370 μL nuclease free water) and isopropanol precipitated overnight at -80oC.   Ribosome protected fragments and total RNA samples were then size selected by running the samples out on a 15% TBE-Urea polyacrylamide gel. Ribosome protected fragments were size selected between 28-nt and 34-nt as marked by RNA oligonucleotides oNTI199 and oNTI265, respectively62. Total RNA samples were size selected between 34-70 nt as marked by a 10 bp DNA ladder (Invitrogen, catalog no. 10821015). Gel slices were crushed and extracted at room temperature overnight in 400 μL RNA extraction buffer (300 mM NaOAc pH 5.5, 1 mM EDTA, 0.25% SDS) and isopropanol precipitated. Samples were then 3’dephosphorylated by denaturing at 65oC for 5 min and incubating with T4 PNK (NEB, catalog no. M0201S) in a 10 μL reaction (7 μL precipitated RNA, 1 μL 10x T4 PNK Buffer, 1 μL SUPERase Inhibitor, 1 μL 10 U/μL T4 PNK) at 37oC for 1 hour. The reaction was stopped through heat inactivation at 65oC for 20 min. To ligate adaptor, samples were then incubated with 0.5 μL of 50 μM Universal miRNA Cloning Linker (NEB, catalog no. S1315S) and denatured at 65oC for 5 min. The denatured sample was then incubated with 1 μL T4 RNA Ligase 2, truncated KQ (NEB, M0373S), 1 μL 10x buffer, 6 μL 50% PEG 8000, and 1.5 μL water for 4.5 h at 25oC. Free adaptor was then removed by addition of 1 μL 10 U/μL 5’-Deadenylase (NEB, M0331S). 1 μL 10 U/μL RecJ Exonuclease (Lucigen/Epicentre, RJ411250). and 1 μL 20 U/μL SUPERase Inhibitor. Samples were then purified using Zymo RNA Clean & Concentrator-5 columns using the protocol above to preserve small RNAs (100 μL sample, 200 μL RNA binding buffer, 450 μL 100% ethanol).    To perform reverse transcription, 10 μL sample was incubated with 2 μL of 1.25 μM RT primer (see table) and denatured at 65oC for 5 min. Reverse transcription (RT) was performed with primers containing sample barcodes and unique molecular identifiers. RT was performed with SuperScript III (Thermo Fisher, 18080-044) in a 20 μL reaction (48oC, 40 min). RNA was then hydrolyzed by adding 2.2 μL of 1N NaOH and incubating for 20 min at 98oC. Samples were then purified using Zymo RNA Clean & Concentrator-5 columns (100 μL sample, 200 μL RNA binding buffer, 450 μL 100% ethanol). RT products were size selected and gel extracted from 10% TBE Urea polyacrylamide gels as described above instead that DNA extraction buffer was used for overnight extraction (300 mM NaCl, 10 mM Tris-HCl pH 8, 1 mM EDTA, 0.1% SDS). Eluate was then isopropanol precipitated overnight at -80oC overnight. Samples were then circularized with CircLigase (Illumina, CL4115K) in a 20 μL reaction (15 μL cDNA, 2 μL 10x CircLigase Buffer, 1 μL 1 mM ATP, 1 μL MnCl2, 1 μL CircLigase) for 12 hours at 60oC and subsequently purified by Zymo RNA Clean & Concentrator 5 columns (100 μL sample, 200 μL RNA binding buffer, 450 μL 100% ethanol) and eluted with 12 μL 10 mM Tris-HCl pH 8. 1 μL of library was used for PCR amplification with Phusion High-Fidelity DNA Polymerase (Thermo Fisher, catalog no. F530S) (98oC 30s, 98oC 10s, 65oC 10s, 72oC 5s) for 9-10 cycles (see table for primers). PCR product was PAGE purified from native 8% TBE polyacrylamide gels, extracted overnight using DNA extraction buffer, and isopropanol precipitated for > 2 h at -80oC. DNA was measured and quality controlled on the Agilent 2100 Bioanalyzer (High-Sensitivity DNA) by the Stanford Protein and Nucleic Acid (PAN) Facility. Libraries were sequenced by the Stanford Functional Genomics Facility (SFGF) on the Illumina NextSeq 500 (1x75nt).
Ribosome profiling, RNA-Seq

tag: genotype simplified

value: Rps6 WT; Trp53 null

value: Replicate 3


title: HEK293T-RPS2-STAMP 48h low rep2


title: HEK293T-RPS2-STAMP low


title: Rep3_RNA_S6

description: rRNA depleted total RNA

value: Rps6 WT; Trp53 WT


title: HEK293T-RPS2-STAMP none


title: Leaf_Control_10 DAS_rep 3

city: Antwerp

first: SHWETA

last: KALVE

state: ANTWERP

address: 171 Groenenborgerlaan

department: Department of Biology

country: Belgium

institute: University of Antwerp

description: 3rd biological replicate of leaves grown on control medium. Leaf 1 and 2 were harvested at 10 DAS.

data_processing:
Trim sequences  CLC Genomics Server 6.5.2
RNA-seq analyis References = Arabidopsis thaliana (Col-0 TAIR10) sequence-1 Default settings   CLC Genomics Server 6.5.2
Set Up experiment,  CLC Genomics Server 6.5.2
Normalized experiment Normalization method = ScalingScaling method = Mean, Trimming = 5%  Normalized data = Original expression values
Count based statistics Test = Baggerley's test  All pairs = yes Data used = Normalized expression values Calculate Bonferroni corrected p-values = Yes   Calculate FDR corrected p-values = Yes
Genome_build: Arabidopsis thaliana (Col-0 TAIR10) sequence
Supplementary_files_format_and_content: CLC data files

source_name: Leaf_Control_10 DAS

growth_protocol: Seedlings of Arabidopsis thaliana were grown in vitro in 150x25 mm round petri dishes in a growth chamber with an air temperature of 22°C and shelves cooled to 19°C to avoid condensation against the lid and a 16h day [80-90 µmols-1m-2 s-1 photosynthetically active radiation (PAR), supplied by fluorescent tubes (cool white, LUMILUX, Germany)] and 8 h night regime.

extract_protocol:
The total RNA was extracted using the TRIZOL reagent (Invitrogen) and purified using the RNeasy Plant Mini Kit (Qiagen, Netherlands), following manufacturer's instructions.
TruSeq ®  stranded mRNA HT kit

treatment_protocol: Arabidopsis seeds were sown on half-strength MS (Murashige and Skoog) medium and medium supplemented with 25mM mannitol, 0.1μM NAA and 0.1μM NAA + 25mM mannitol and plants were grown in vitro for 10 DAS.

tag: developmental stage

value: proliferation

tag: treated with

value: 10 DAS

value: leaf


title: Leaf_NAA_10 DAS_rep 1

description: 1st biological replicate of leaves grown on medium supplemented with 0.1µM NAA. Leaf 1 and 2 were harvested at 10 DAS.

source_name: Leaf_NAA_10 DAS

value: 0.1μM NAA


title: Leaf_Control_10 DAS_rep 2

description: 2nd biological replicate of leaves grown on control medium. Leaf 1 and 2 were harvested at 10 DAS.

value: Control


title: Leaf_NAA+Mannitol_10 DAS_rep 1

description: 1st biological replicate of leaves grown on medium supplemented with 0.1µM NAA+25mM mannitol. Leaf 1 and 2 were harvested at 10 DAS.

source_name: Leaf_NAA+Mannitol_10 DAS

value: 0.1μM NAA + 25mM mannitol


title: Leaf_NAA+Mannitol_10 DAS_rep 3

description: 3rd biological replicate of leaves grown on medium supplemented with 0.1µM NAA+25mM mannitol. Leaf 1 and 2 were harvested at 10 DAS.


title: Leaf_NAA+Mannitol_10 DAS_rep 2

description: 2nd biological replicate of leaves grown on medium supplemented with 0.1µM NAA+25mM mannitol. Leaf 1 and 2 were harvested at 10 DAS.


title: Leaf_Mannitol_10 DAS_rep 1

description: 1st biological replicate of leaves grown on medium supplemented with 25mM mannitol. Leaf 1 and 2 were harvested at 10 DAS.

source_name: Leaf_Mannitol_10 DAS

value: 25mM mannitol


title: Leaf_Mannitol_10 DAS_rep 3

description: 3rd biological replicate of leaves grown on medium supplemented with 25mM mannitol. Leaf 1 and 2 were harvested at 10 DAS.


title: Leaf_Mannitol_10 DAS_rep 2

description: 2nd biological replicate of leaves grown on medium supplemented with 25mM mannitol. Leaf 1 and 2 were harvested at 10 DAS.


title: Leaf_NAA_10 DAS_rep 2

description: 2nd biological replicate of leaves grown on medium supplemented with 0.1µM NAA. Leaf 1 and 2 were harvested at 10 DAS.


title: Leaf_NAA_10 DAS_rep 3

description: 3rd biological replicate of leaves grown on medium supplemented with 0.1µM NAA. Leaf 1 and 2 were harvested at 10 DAS.


title: Leaf_Control_10 DAS_rep 1

description: 1st biological replicate of leaves grown on control medium. Leaf 1 and 2 were harvested at 10 DAS.


title: Rat 1 C-2

type: RNA

city: Tangshan

first: zhang

last: ronghua

address: 21 Bohai Road, Caofeidian

institute: North China University of Science and Technology

hyb_protocol: Add the nuclease free water to fluorescent labeled DNA sample  to make up the volume to 40 µ L. Then add 41.6 µL Hybrid solution prepared by mixing and centrifuged slightly and mixed well with the sampler. The hybrid device was assembled and 45 µ L hybridizing solution is added to the hybridizing cover piece, the chip is placed, and the hybridizing device is tightened. The hybridization device was put in Agilent company's crossbred furnace for the night (about 16hr, 20rpm).

scan_protocol: Chip was  washed for 5 min in 2×SSC lotion I which contain 2% SDS at 42 ℃, and then at room temperature was washed for 5 min in 0.2 × SSC lotion II, the slides can be used for scanning after drying. Agilent chip scanner (g2565ca) was used to scan the cleaned chips to get the hybridization images.

data_processing: Agilent feature extraction (v10.7) software was used to analyze the hybrid images and extract the data. Then we use Boao expression profile Analyzer software (CBC analyzer, which is an expression profile analysis process based on R Bioconductor and Perl) to analyze.

organism: Rattus norvegicus

source_name: normal liver tissues

label_protocol: The cDNA product was purified after reverse transcription and Labeled with fluorescence. Samples purified using Nucleospin® Extract II (MN company，Cat. No. 740609.250)purification kit before hybridization.

extract_protocol: Trizol method (Invitrogen, Gaithersburg, MD, USA) was used to extract total RNA from tissue blocks. And then the total RNA was purified by NucleoSpin® RNA clean-up kit (MACHEREY- NAGEL,Germany).

value: normal liver tissues


title: Rat 6 M-8

source_name: liver fibrosis tissues

value: liver fibrosis tissues


title: Rat 4 M-4


title: Rat 5 M-5


title: RPS2-STAMP

data_processing:
Alignment, cell barcode processing, umis processing, abundance measurements: cellranger count (version 3.0.2)
MD tags were added to alignments with samtools calmd --threads 15 -rb possorted_genome_bam.bam refdata-cellranger-hg19-3.0.0/fasta/genome.fa > possorted_genome_bam_MD.bam
Reads were split based on the CB:Z tag, resulting in one BAM file per barcode.
Edits were called on each "split-BAM" file using SAILOR (http://github.com/yeolab/sailor) using default parameters and dbSNP (v147) to remove known SNPs.
Coverage was generated from filtered BAM files (intermediates from SAILOR) for each cell barcode, using the following commands from BedTools (v2.27.1). :
bedtools genomecov -split -strand - -g refdata-cellranger-hg19-3.0.0/star/chrNameLength.txt -bg -ibam fwd.bam > fwd.bg
bedtools sort -I fwd.bg > fwd.sorted.bg
bedGraphToBigWig fwd.sorted.bg refdata-cellranger-hg19-3.0.0/star/chrNameLength.txt fwd.sorted.bw
bedtools genomecov -split -strand + -g refdata-cellranger-hg19-3.0.0/star/chrNameLength.txt -bg -ibam rev.bam > rev.bg
bedtools sort -I rev.bg > rev.sorted.bg
bedGraphToBigWig rev.sorted.bg refdata-cellranger-hg19-3.0.0/star/chrNameLength.txt rev.sorted.bw
For each barcode, edit sites were annotated across exons (Gencode v19) and the cumulative C>T depth across each gene was divided by the cumulative depth across C's as obtained from the previous step.
Genome_build: hg19
Supplementary_files_format_and_content: Edit fractions across barcodes with detectable edits were merged to obtain processed STAMP_edits.txt files for each sample.

growth_protocol: All stable STAMP HEK293T cell lines were generated using human lenti-X HEK293T cells (HEK293XT, Takara Bio) which are derived from transformed female human embryonic kidney tissue. Cells were maintained in DMEM (4.5 g/L D-glucose) supplemented with 10% FBS (Gibco) at 37o C with 5% CO2. Cells were periodically passaged once at 70-90% confluency by dissociating with TrypLE Express Enzyme (Gibco) at a ratio of 1:10.  Untransduced HEK293T cells were used for transient transfection comparison to neural progenitor cells.  Small molecule neural progenitor cells (smNPCs) were grown in medium consisting of DMEM/F12+Glutamax, 1:200 N2 supplement, 1:100 B27 supplement, penicillin/streptomycin (Life technologies), 100mM ascorbic acid (Sigma, A4544), 3mM CHIR99021 (CHIR, Tocris 4423) and 0.5mM Purmorphamine (PMA) (Tocris 4551) and passaged using Accutase. Generation of smNPCs from iPSCs was adapted from (Reinhardt et al., 2013).

extract_protocol:
10X Chromium Single Cell 3' polyA v3 Chemistry
10X Chromium Single Cell 3' polyA and feature capture v3 Chemistry

treatment_protocol: For STAMP fusion protein expression STAMP stable HEK293T cells were induced with 1ug/ml (high) doxycycline in DMEM for 72 hours, followed by Trizol extraction and Direct-zol miniprep (Zymo Research) column purification in accordance with manufacturer protocol.  For transient HEK293T and NPC transfections, ~4 million cells were transfected with 2000ng of control- or RBFOX2-STAMP expression plasmids using Fugene HD (Promega) as per manufacturer's recommendations.

tag: expressing


title: HEK293T-TIA1-STAMP high rep2


title: Rep3_RNA_Cre_S6_P53

description: rRNA depleted total RNA

value: Rps6 het; Trp53 null

tag: replicate


title: Rep3_RNA_Cre_S6

description: rRNA depleted total RNA

value: Rps6 het; Trp53 WT


title: Rat 2 C-3


title: control-STAMP


title: Rat 3 C-4


title: RBP-STAMP

description: polyA RNA and feature capture


title: HEK293T-TIA1-STAMP high rep1


title: NPC_HEK_RBFOX2-STAMP

source_name: HEK293T/NPC mix

value: HEK293T/NPC mix


title: NPC_HEK_control-STAMP


title: Rep3_Ribo_S6_P53

description: Ribosome-Protected Fragments (RPFs)


title: HEK293T-RPS2-STAMP 72h high rep2


title: HEK293T-RPS2-STAMP none rep1


title: Rep3_Ribo_Cre_S6_P53

description: Ribosome-Protected Fragments (RPFs)


title: Rep2_RNA_S6_P53

description: rRNA depleted total RNA

value: Replicate 2


title: Rep3_Ribo_S6

description: Ribosome-Protected Fragments (RPFs)


title: HEK293T-RPS2-STAMP none rep2


title: HEK293T-RPS2-STAMP 24h low rep1


title: HEK293T-SLBP-STAMP high 48h rep1


title: Rep3_Ribo_Cre_S6

description: Ribosome-Protected Fragments (RPFs)


title: HEK293T-SLBP-STAMP high 48h rep3


title: HEK293T-TIA1-STAMP low rep2


title: HEK293T-SLBP-STAMP high 72h rep3


title: HEK293T-TIA1-STAMP none rep2


title: HEK293T-SLBP-STAMP high 48h rep2


title: Rep2_RNA_Cre_S6_P53

description: rRNA depleted total RNA


title: HEK293T-RBFOX2-STAMP none


title: HEK293T-SLBP-STAMP high 72h rep1


title: HEK293T-SLBP-STAMP none rep3


title: HEK293T-SLBP-STAMP none rep2


title: HEK293T-RPS2-STAMP 24h low rep2


title: HEK293T-RBFOX2-STAMP high


title: HEK293T-control-STAMP 72h high vehicle rep2


title: HEK293T-TIA1-STAMP low rep1


title: Rep2_RNA_S6

description: rRNA depleted total RNA


title: HEK293T-RPS2-STAMP 72h high rep1


title: HEK293T-RBFOX2-STAMP low


title: Rep2_Ribo_S6_P53

description: Ribosome-Protected Fragments (RPFs)


title: HEK293T-SLBP-STAMP high 72h rep2


title: HEK293T-SLBP-STAMP none rep1


title: HEK293T-TIA1-STAMP none rep1


title: HEK293T-RBFOX2- STAMP 72h high rep1


title: HEK293T-RBFOX2- STAMP 72h low rep2


title: HEK293T-RBFOX2- STAMP 72h high rep2


title: Rep2_Ribo_Cre_S6_P53

description: Ribosome-Protected Fragments (RPFs)


title: HEK293T-RBFOX2- STAMP 72h low rep1


title: HEK293T-RBFOX2- STAMP 48h high rep1


title: Rep2_Ribo_Cre_S6

description: Ribosome-Protected Fragments (RPFs)


title: HEK293T-RBFOX2- STAMP 48h low rep2


title: HEK293T-control-STAMP 72h high Torin-1 rep1


title: HEK293T-RBFOX2- STAMP 48h low rep1


title: HEK293T-control-STAMP 48h high rep2


title: Rep1_RNA_S6_P53

description: rRNA depleted total RNA

value: Replicate 1


title: HEK293T-RBFOX2- STAMP 24h high rep2


title: Rep1_RNA_S6

description: rRNA depleted total RNA


title: HEK293T-control-STAMP 48h high rep1


title: HEK293T-RBFOX2- STAMP 24h high rep1


title: HEK293T-RBFOX2- STAMP 24h low rep2


title: HEK293T-control-STAMP 24h high rep2


title: HEK293T-control-STAMP 72h high vehicle rep1


title: HEK293T-control-STAMP 72h high Torin-1 rep2


title: Rep1_RNA_Cre_S6_P53

description: rRNA depleted total RNA


title: HEK293T-RBFOX2-STAMP none rep2


title: HEK293T-RBFOX2- STAMP 48h high rep2


title: HEK293T-control-STAMP high


title: Rep1_RNA_Cre_S6

description: rRNA depleted total RNA


title: HEK293T-control-STAMP 72h low rep1


title: HEK293T-control-STAMP 72h low rep2


title: HEK293T-control-STAMP low


title: Rep1_Ribo_S6_P53

description: Ribosome-Protected Fragments (RPFs)

value: Rps6 WT; Trp53 null


title: HEK293T-control-STAMP 72h high rep1


title: HEK293T-control-STAMP none


title: Rep1_Ribo_Cre_S6_P53

description: Ribosome-Protected Fragments (RPFs)


title: HEK293T-control-STAMP 48h low rep1


title: HEK293T-control-STAMP 24h high rep1


title: Rep1_Ribo_S6

description: Ribosome-Protected Fragments (RPFs)


title: HEK293T-control-STAMP 24h low rep2


title: RBFOX2-STAMP Direct cDNA

description: RNA isolated from HEK293T cells expressing a RBFOX2-APOBEC fusion was converted to cDNA sequenced on a ProthemION

extract_protocol:
Trizol extraction (Fisher) and Direct-zol miniprep (Zymo Research) column purification in accordance with manufacturer protocol
Nanopore direct-RNA or direct-cDNA

value: RBFOX2-APOBEC fusion

tag: sequencing protocol


title: HEK293T-control-STAMP none rep2


title: Rep2_Ribo_S6

description: Ribosome-Protected Fragments (RPFs)

value: Rps6 WT; Trp53 WT


title: HEK293T-control-STAMP none rep1


title: control-STAMP Direct cDNA

description: RNA isolated from HEK293T cells expressing only APOBEC was converted to cDNA sequenced on a ProthemION

source_name: control-STAMP

value: only APOBEC


title: Muscle_HTN+cDM_Preop_rep1

description:
203952880012_R01C01
Hypertension and controlled diabetes patient, before surgery

value: skeletal muscle

tag: diagnosis

value: Hypertension + controlled diabetes

tag: time point

value: Pre-op


title: HEK293T-control-STAMP 72h high rep2


title: wildtype-control_rep3

status: Public on May 08 2021

city: Ithaca

first: Tobias

last: Doerr

address: 525 N Campus Rd

department: Microbiology

institute: Cornell University

description: V. cholerae N16961 carrying empty vector control; isolated at mid-log phase in LB medium

data_processing:
Libraries were sequenced on an Illumina HiSeq instrument with at least 10M reads were generated per library.
Reads were be trimmed for low quality and adaptor sequences with TrimGalore v0.6.0 (Babraham Institute), a wrapper for cutadapt (Martin et al., EMBnet Journal) and fastQC (Babraham Institute) using the following parameters: -j 1 -e 0.1 --nextseq-trim=20 -O 1 -a AGATCGGAAGAGC --length 50 --fastqc
Reads were mapped to the reference genome/transcriptome (Vibrio cholerae O1 El Tor N16961 taxonomy ID: 243277) using STAR v2.7.0e (Dobin et al, Bioinformatics, 2013) with the following parameters: --outSAMstrandField intronMotif , --outFilterIntronMotifs RemoveNoncanonical , --outSAMtype BAM SortedByCoordinate, --quantMode GeneCounts
SARTools and DESeq2 v1.26.0 were used to generate normalized counts and statistical analysis of differential gene expression (Varet et al., PLOS ONE, 2016; Love et al., Genome Biology, 2014) using the following parameters: fitType parametric, cooksCutoff TRUE, independentFiltering TRUE, alpha 0.05, pAdjustMethod BH, typeTrans VST, locfunc median
Genome_build: Vibrio cholerae O1 biovar El Tor str. N16961 (taxonomy ID: 243277)
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample
Supplementary_files_format_and_content: Combined matrix table with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: Matrix table with differential expression values and p-values for each gene

source_name: bacteria harvested from broth culture

growth_protocol: Overnight cultures were diluted 1:100 and grown shaking in LB broth containing kanamycin (50 ug/mL) and inducer (IPTG, 500 uM) at 37ºC until cultures reached mid-log phase (optical density at 600 nm = 0.5)

extract_protocol:
Cells were harvested via centrifguation, resuspended in 1X phosphate buffered solution, and treated with RNA protect (Qiagen). mirVana™ miRNA Isolation Kit (Ambion) was used according to manufacturer instructions. Total RNA was treated with DNAfree (Ambion) and precipitated with ethanol and ammonium acetate.
Ribosomal RNA was subtracted by hybridization from total RNA samples using the NEBNext rRNA Depletion Kit (New England Biolabs). TruSeq-barcoded RNAseq libraries were generated with the NEBNext Ultra II [Directional] RNA Library Prep Kit (New England Biolabs).

tag: genotype

value: N16961 pHLmob(Piptg-empty)


title: Rep1_Ribo_Cre_S6

description: Ribosome-Protected Fragments (RPFs)


title: wildtype-vc0513_rep2

description: V. cholerae N16961 with vc0513 containing vector; isolated at mid-log phase in LB medium

organism: Vibrio cholerae O1 biovar El Tor str. N16961

value: N16961 pHLmob(Piptg-vc0513)


title: wildtype-vc0513_rep1


title: wildtype-vc0515_rep3

description: V. cholerae N16961 with vc0515 containing vector; isolated at mid-log phase in LB medium

value: N16961 pHLmob(Piptg-vc0515)


title: wildtype-vc0513_rep3


title: wildtype-vc0515_rep1


title: wildtype-control_rep2


title: wildtype-vc0515_rep2


title: HEK293T-control-STAMP 48h low rep2


title: wildtype-control_rep1


title: RRBS WT rep1

city: Melbourne

first: Andres

last: Tapia del Fierro

state: Victoria

address: 1G Royal Parade

department: EDD

country: Australia

institute: WEHI

description: RRBS_methylation_difference_Smchd1_MD43_NSCs.bedgraph

data_processing:
Base calling using Real-Time Analysis v2.4.6
Demultiplexing and fastq.gz file generation using bcl2fastq conversion software v2.15.0.4
Alignment to GRCm38.p6 reference genome using Bismark v0.19.0 with default parameters  after trimming adapters with Trim Galore! v0.4.4
The bismark coverage files produced were then loaded into R v3.6.1 and processed using the methylKit v1.10 package
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: bedGraph file with difference in methylation calculated with methylKit

source_name: NSCs

growth_protocol: NSCs derived and cultured for less than 10 passages as described in Jansz et al., Nature Structural Molecular Biology 2018 DOI:10.1038/s41594-018-0111-z

extract_protocol:
Genomic DNA wasextracted using a Qiagen Dneasy kit.
RRBS was performed with 100ng of genomic DNA from each sample of female primary Smchd1MommeD43/MommeD43 and Smchd1+/+ NSCs (3 independent cell lines of each genotype) with the Ovation RRBS Methyl-seq kit (NuGen) following the manufacturer’s instructions. The bisulphite conversion was performed with the EpiTect Fast Bisulfite Conversion kit (Qiagen) following the instructions.

tag: cell type

value: Neural stem cells

tag: strain

value: FVB/NJ

tag: cell line name

value: female


title: RRBS MommeD43 rep1


title: RRBS MommeD43 rep2


title: RRBS WT rep2


title: RRBS MommeD43 rep3


title: RRBS WT rep3


title: Smchd1-GFP HiC WT rep3

description: HiC_Smchd1MD43_differential_interactions_FDR_0.1.txt

data_processing:
Base calling using Real-Time Analysis v2.4.6
Demultiplexing and fastq.gz file generation using bcl2fastq conversion software v2.15.0.4
fastq files for the same library were concatenated using bash cat command (sequencing was performed across two flowcells)
Trimming of adapters using Trim Galore! V0.4.4
Primary-data processing was performed with HiCUP v0.7.277,  mapping reads to the mm10 mouse genome assembly, or using TADbit 0.4.39
Genome_build: mm10
Supplementary_files_format_and_content: Tab-separated txt file containing log2-transformed normalized interaction counts within statistically significant differentially interacting regions at 1Mb resolution. Biological replicates were merged.

extract_protocol:
NSCs crosslinked in 1% formaldehyde. Followed protocol from Rao et al. Cell 2014
MboI restriction enzyme.

tag: restriction enzyme

value: MboI


title: Smchd1-GFP HiC WT rep1


title: Smchd1-GFP HiC MommeD43 rep2


title: Smchd1-GFP HiC MommeD43 rep3


title: Smchd1-GFP HiC MommeD43 rep1


title: FNP RNAseq Smchd1 MD43 male rep2

description: Dissected from embryo 1664.1

data_processing:
Base calling using Real-Time Analysis v2.4.6
Demultiplexing and fastq.gz file generation using bcl2fastq conversion software v2.15.0.4
Alignment to GRCm38.p6 reference genome using hisat2 v2.0.5 with default parameters  after trimming adapters with Trim Galore! v0.4.4
Data were normalized for read depth and log2-transformed RPKM counts were calculated for each gene using Seqmonk's RNAseq pipeline.
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: Tab-separated txt file containing mean values across biological replicates of log2-transformed RPKM counts normalized by sequencing depth for all genes. Transcript isoforms were merged, and libraries are opposing strand-specific.

source_name: FNP

extract_protocol:
100ng total RNA from snap-frozen dissected tissue used for library prep
stranded mRNA TruSeq library prep kit

tag: tissue

value: Frontonasal prominence

value: male


title: FNP RNAseq Smchd1 WT female rep1

description: Dissected from embryo 1639.1 (#mother.#embryo)


title: FNP RNAseq Smchd1 MD43 male rep1

description: Dissected from embryo 1656.8


title: FNP RNAseq Smchd1 WT male rep2

description: Dissected from embryo 1664.6


title: Smchd1-GFP HiC WT rep2


title: RNAseq NSCs Smchd1GFP WT rep4 batch3

data_processing:
Base calling using Real-Time Analysis v2.4.6
Demultiplexing and fastq.gz file generation using bcl2fastq conversion software v2.15.0.4
Alignment to GRCm38.p6 reference genome using hisat2 v2.0.5 with default parameters  after trimming adapters with Trim Galore! v0.4.4
Data were analysed using limma v3.40.6
Data were normalized for read depth and log2-transformed RPKM counts were corrected for batch effects using limma's removeBatchEffect function
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: Tab-separated txt file containing log2-transformed RPKM counts normalized by sequencing depth for all genes and corrected for batch effects by using technical replicates. Transcript isoforms were merged.

source_name: Neural stem cells

extract_protocol:
100ng total RNA from lysed NSCs used for library prep
mRNA TruSeq library prep kit

tag: cell line number


title: RNAseq NSCs Smchd1GFP MD43 rep2 batch3


title: RNAseq NSCs Smchd1GFP WT rep3 batch3


title: RNAseq NSCs Smchd1GFP MD43 rep4 batch3


title: RNAseq NSCs Smchd1GFP MD43 rep3 batch3