title: C11 nar+ BC 7d

city: Baton Rouge

first: Jaroslaw

last: Staszkiewicz

state: LA

address: 6400 Perkins Rd

department: Genomics Core Facility

institute: Pennington Biomedical Research Center

description: total RNA 11μl, 35ng/μl

data_processing:
Lexogen Quantseq pipeline V1.8.8 on the Bluebee platform, quality control, mapping, and read count tables
Annotation and preparation for analysis, 3.5.2(2018-12-2), Rstudio V1.2.1511 and biomaRt V2.38.0
DESeq2  V1.22.2 differential gene expression
JMP Genomics V9 quality control, principal components, ANOVA, hierarchical clustering
Assembly: Human – GRCh38.77
Supplementary files format and content: tab-delimited text containing raw counts and DESeq2 normalized counts

source_name: donor C1901 BMI 36

growth_protocol: Human adipose-derived stem cells from overweight and obese female donors were  seeded in DMEM/F12 1:1 supplemented with 10% FBS and 1% antibiotic (penicillin/streptomycin/amphotericin). One day after reaching confluence, cells were differentiated (hADSC) in media containing 70% DMEM and 30% DMEM/F12 1:1 supplemented with 3% FBS, 1% antibiotic, 1µM dexamethasone, 33uM biotin, 0.1µM insulin, 20µM pantothenate, 5µM rosiglitazone and 500µM 3-isobutylmethylxanthine for 5 days

extract_protocol: Tri-reagent and RNeasy Mini Kit were used to isolate cellular RNA.

treatment_protocol: Treatments (naringenin 8µM and beta-carotene 2µM) started from day 5 post differentiation, were administered every two days over a period of 6 days, and cells were harvested the following day on the 7th day

tag: cell origin

value: abdominal subcut stem cells

tag: cell phenotype

value: differentiated mature adipocytes

tag: original sample_names

value: Sample 23

tag: days

tag: bmi


title: C8 nar+ BC 7d

status: Public on May 10 2023

type: SRA

country: USA

description: total RNA 11μl, 35ng/μl

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

value: Sample 20


title: C9 nar+ BC 7d

description: total RNA 11μl, 35ng/μl

value: Sample 21


title: C12 nar+ BC 7d

description: total RNA 11μl, 35ng/μl

value: Sample 24


title: C7 nar+ BC 7d

description: total RNA 11μl, 35ng/μl

value: Sample 19


title: C6 control 7d

description: total RNA 11μl, 35ng/μl

value: Sample 18


title: C5 control 7d

description: total RNA 11μl, 35ng/μl

value: Sample 17


title: noUV_hnRNPc_Rep1

city: Lausanne

first: Christina

last: Ernst

state: Vaud

address: EPFL SV GHI LVG, AI 3147 (Bâtiment AI), Station 19

department: School of Life Science

country: Switzerland

institute: EPFL

data_processing:
Sequencing data was demultiplexed by i7 index reads using bcl2fastq without any read trimming. Further demultiplexing by in-read 5’ barcodes and trimming of adapter sequences was performed using Flexbar v.3.5.0 (https://github.com/seqan/flexbar)20 in a two-step approach. In the first step, reads are demultiplexed by in-read barcodes allowing no mismatches, and UMIs are moved into the read header. Barcode sequences (see Supplementary Table 2) including the UMI designated by the wildcard character ’N’ are provided in fasta format, with the arguments “-b barcodes.fasta --barcode-trim-end LTAIL --barcode-error-rate 0 --umi-tags”. In the second step, any adapter contamination at the 3’ end of the reads is removed allowing an error rate of 0.1 with the following arguments “--adapter-seq 'AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG' --adapter-trim-end RIGHT --adapter-error-rate 0.1 --adapter-min-overlap 1”. In addition, potential T-stretches at the 5’ end that are the result of ribotailing during ligation are removed by trimming ‘T’ homopolymers of 1-2 nucleotide length (Supplementary Fig. 3) using “--htrim-left T --htrim-max-length 2 --htrim-min-length 1” and reads shorter than 18 nucleotides post trimming are discarded by “--min-read-length 18”.
Flexbar-trimmed reads were aligned against hg19 using STAR v.2.7.3a (https://github.com/alexdobin/STAR)21 with the following parameters, to keep only uniquely mapping reads, removing the penalty for opening deletions and insertions and fully extending the 5-prime end of reads to preserve the end of cDNA molecules: “--outFilterMultimapNmax 1 --scoreDelOpen 0 --scoreInsOpen 0 --alignEndsType Extend5pOfRead1”. To retain UMI in read header during STAR alignment, any space in header needs to be removed prior to mapping.
Aligned reads were deduplicated based on unique molecular identifiers using UMI-tools v.1.0.1 (https://github.com/CGATOxford/UMI-tools)22. The dedup command was used with the parameters “--extract-umi-method read_id --method unique --spliced-is-unique” to group reads with the same mapping position and identical UMI, while treating reads starting at the same position as unique if one is spliced and the other is not.
Enriched regions were identified using the peak calling algorithm CLIPper v. 2.0.0 (https://github.com/YeoLab/clipper)8,17 with default settings and a p-value cutoff of 0.01 “--poisson-cutoff 0.01”.
Assembly: hg19
Supplementary files format and content: bed format - Peaks obtained from CLIPper

growth_protocol: Adherent 293T cells (ATCC® CRL-1573™) were grown to ~80% confluency in Dulbecco’s Modified Eagle Medium (Gibco, #41966-029) supplemented with 10% FCS (Sigma-Aldrich, #F9665-500ML, Lot #19A124) and 1% Penicillin-Streptomycin-L-Glutamine (MED30-009-CI).

extract_protocol:
Protein-G beads (Thermo Fisher, 10004D) were washed twice in 1ml iCLIP Lysis buffer and resuspended in 100 µl per condition (100 µl of protein-G beads bind 20-30 µg of antibody - scale accordingly). Per IP, 1 µg of antibody against hnRNPc (Santa Cruz Biotechnology, sc-32308), RBM9 (Bethyl Laboratories, A300-864A), hnRNPA1 (4B10) (Santa Cruz Biotechnology, sc-32301), or hnRNPI (Santa Cruz Biotechnology, sc-56701) were added, and antibody-bead mixture was incubated at room temperature (RT) for 30-60 minutes on a rotating wheel. Antibody-bead mixture was washed twice in iCLIP lysis buffer to remove unbound antibody and RNase-treated cell lysates were added alongside cOmplete EDTA-free Protease Inhibitor Cocktail (Merck, #11836170001) and incubated for 2 hours at 4ºC on a rotating wheel. After IP, beads were washed twice in 200 µl High Salt Buffer (50 mM Tris-HCl pH 7.4, 1 M NaCl, 1 mM EDTA, 1% Igepal CA-630, 0.1% SDS, 0.5% sodium-deoxycholate), with the second wash at 4ºC for 3 minutes on a rotating wheel, followed by two washes in 200 µl PNK Wash Buffer (20 mM Tris-HCl, pH 7.4, 10 mM MgCl2, 0.2% Tween-20). Dephosphorylation of 3’ ends was performed in 20 µl of PNK reaction for 30 minutes at 37ºC (70 mM Tris-HCl, pH 6.5, 10 mM MgCl2, 1 mM DTT, 10U SUPERaseIN RNase Inhibitor (ThermoFisher, #AM2696), 5U T4 Polynucleotide Kinase (NEB, #M0201L). Beads were washed twice in PNK Wash Buffer and resuspended in 20 µl of ligation mix for overnight incubation at 16ºC and 1200 rpm (50 mM Tris-HCl, pH 7.8, 10 mM MgCl2, 1mM DTT, 10U SUPERaseIN RNase Inhibitor, 10U T4 RNA Ligase (NEB, #M0204), 1 µl of 1 µM L3 adapter and 20% PEG400 (Sigma-Aldrich, #91893)).
Following the first adapter ligation, beads were washed twice in 200 µl High Salt Buffer, twice in 200 µl PNK Wash buffer and then resuspended in 20 µl 1X LDS sample buffer (Thermo Fisher, #NP0008) containing 5% beta-mercaptoethanol (Sigma-Aldrich, #M6250). Samples were denatured for 1 minute at 70ºC and RNA-protein complexes were resolved on NuPAGE 4-12% Bis-Tris Gels (Thermo Fisher, #WG1402A) at 180V for 1 hour. Transfer was performed onto nitrocellulose (BioRad, #1620115) in 1X NuPAGE transfer buffer (Thermo Fisher, #NP00061) with 10% methanol at 30V for 2 hours at RT.   Nitrocellulose membranes were scanned on Odyssey® CLx Infrared Imager (LI-COR, 9141) with 169 µm resolution to visualise RNA localisation and then placed on filter paper soaked in PBS. Regions of interest were cut out from nitrocellulose membrane corresponding to ~20-100 kDa above the molecular weight of the RBP of interest due to the ligation of L3 adapter (~15.9 kDa) and associated RNA (with 70nt of RNA averaging ~20kDa). Nitrocellulose pieces were placed in LoBind Eppendorf tubes and 200 µl Proteinase K buffer (100mM Tris-HCl, pH 7.4, 50 mM LiCl, 1 mM EDTA, 0.2% LiDS) containing 200 µg Proteinase K (Thermo Fisher, #AM2546) were added and incubated at 50ºC for 45 minutes at 800rpm.  Meanwhile, 10 µl of Oligo(dT)25 Dynabeads™ (Thermo Fisher, #61005) per sample were washed in 1 ml of oligo(dT) Binding Buffer (20 mM Tris-HCl, pH 7.4, 1 M LiCl, 2 mM EDTA) and resuspended in 50 µl of oligo(dT) Binding Buffer per sample. Following Proteinase K treatment, supernatant was transferred to fresh tubes containing 50 µl of oligo(dT) beads and incubated for 10 minutes at RT on a rotating wheel. Following RNA capture, beads were washed twice in 125 µl oligo(dT) Wash Buffer (10 mM Tris-HCl, pH 7.4, 150 mM LiCl, 0.1 mM EDTA) and once in 20 µl 1X First-Strand Buffer (50 mM Tris-HCl, pH 8.3, 75 mM KCl, 3 mM MgCl2). Beads were resuspended in 10 µl of Reverse Transcription Mix (1X First-Strand Buffer, 0.5 mM dNTPs, 1 mM DTT, 6U SUPERase IN RNase Inhibitor, 20U SuperScript™ IV Reverse Transcriptase (Thermo Fisher, #18090050) and incubated for 15 minutes at 50ºC followed by 10 minutes at 80ºC heating up to 96ºC. Samples were vortexed for 30 seconds at 96ºC and then immediately placed on a magnet on ice. Supernatant containing adapter-ligated RNA was removed and efficiency of elution can be confirmed by dot-blotting on nitrocellulose membrane.   Solid-phase cDNA was washed once in 60 µl oligo(dT) Wash Buffer and once in 20 µl 1X T4 RNA Ligase Buffer (50 mM Tris-HCl, 10 mM MgCl2, 1mM DTT, pH 7.5). Beads were resuspended in 5 µl of 5’ Adapter mix (2 µl 10X T4 RNA Ligase Buffer, 2 µl of 10 µM L## oligo (see Supplementary Table 2), 1 µl 100% DMSO), incubated at 75ºC for 2 minutes then immediately placed on ice. 4 µl of Ligation Mix (5 mM ATP, 7U Terminal Deoxynucleotidyl Transferase (TdT) (2230B, Takara), 15 U T4 RNA Ligase High Concentration (M0437, NEB)) were added as well as 10 µl 50% PEG8000 and reaction was mixed by pipetting up- and down until beads are resuspended. Reaction was incubated at 37ºC for 30 minutes, then cooled down to room temperature. 30 U of T4 RNA Ligase were added, the reaction mixed by pipetting and incubated at RT overnight with occasional vortexing for 15 seconds at 2000 rpm every two minutes.  Following overnight incubation, ligation reaction was removed and beads washed in 100 µl oligo(dT) Wash Buffer and 20 µl 1X Phusion HF Buffer (Thermo Fisher, #F518L). Beads were resuspended in 25 µl cDNA amplification mix (1X Phusion HF PCR Master Mix (NEB, #M0531L) and 0.5uM P5 and P7 short primer mix (see Supplementary Table 2)) and amplification was performed with the following programme: 30 seconds at 98ºC, 7 cycles of 10 seconds at 98ºC, 30 seconds at 65ºC and 30 seconds at 72ºC followed by final extension at 72ºC for 3 minutes. Meanwhile, 2µl of oligo(dT) beads per sample were washed once in 1 ml oligo(dT) Binding buffer and resuspended in 5 µl per sample. After cDNA amplification, 5 µl of oligo(dT) beads were added and incubated at RT for 5 minutes on a rotating wheel to capture unwanted amplification by-products (see Fig. S3). Samples were placed on magnet and supernatant containing amplified cDNA was transferred to a fresh tube.   Size-selection of cDNA was performed using ProNEX® Size-Selective Purification System (Promega, #NG2002) with a ratio of 2.8X to enrich for cDNA inserts of at least 20 nucleotides in length (>80bp). Library yield was then estimated by amplifying 1 µl of purified cDNA via qPCR using the full length P5 and P7 index primers and 2-3 cycles were subtracted from the obtained Ct value for final library amplification. Following PCR amplification, libraries were size-selected again using the ProNEX® Size-Selective Purification System, with a ratio of 1.8X to select fragments larger than 165bp.
CLIP-seq

treatment_protocol: Cells were rinsed in ice-cold PBS and crosslinked on ice with 254 nm UV-C light at 0.3 J/cm2 in a CL-3000 Ultraviolet Crosslinker (UVPA849-95-0615-02). Cells were collected into PBS by scraping, counted and desired cell number was aliquoted and spun down. Cell pellets were resuspended in iCLIP Lysis buffer (50 mM Tris-HCl pH 7.4, 100 mM NaCl, 1% Igepal CA-630, 0.1% SDS, 0.5% sodium deoxycholate) using 50 µl per 50.000 cells. Lysates were incubated on ice for 5 minutes followed by sonication for 5-10 seconds at 0.5 seconds ON and 0.5 seconds OFF at 10% amplitude using a tip sonicator (Branson LPe 40:0.50:4T).

tag: cell line

tag: cell type

value: Human embryonic kidney

tag: clip antibody

value: hnRNP C1/2 (4F4) (SantaCruz, sc-32308)

tag: cell number

tag: rnase [u]


title: C2 control 7d

description: total RNA 11μl, 35ng/μl

value: Sample 14


title: hnRNPc_10k_Rep1


title: C4 control 7d

description: total RNA 11μl, 35ng/μl

value: Sample 16


title: L11 nar+ BC 7d

description: total RNA 11μl, 35ng/μl

source_name: donor L101130W BMI 27

value: Sample 11


title: L12 nar+ BC 7d

description: total RNA 11μl, 35ng/μl

value: Sample 12


title: L9 nar+ BC 7d

description: total RNA 11μl, 35ng/μl

value: Sample 9


title: L8 nar+ BC 7d

description: total RNA 11μl, 35ng/μl

value: Sample 8


title: C1 control 7d

description: total RNA 11μl, 35ng/μl

value: abdominal subcut stem cells

value: Sample 13


title: L7 nar+ BC 7d

description: total RNA 11μl, 35ng/μl

value: differentiated mature adipocytes

value: Sample 7


title: L6 control 7d

description: total RNA 11μl, 35ng/μl

value: Sample 6


title: L10 nar+ BC 7d

description: total RNA 11μl, 35ng/μl

value: Sample 10


title: hnRNPc_1k_Rep2


title: L3 control 7d

description: total RNA 11μl, 35ng/μl

value: Sample 3


title: L4 control 7d

description: total RNA 11μl, 35ng/μl

value: Sample 4


title: L1 control 7d

description: total RNA 11μl, 35ng/μl

value: Sample 1


title: C10 nar+ BC 7d

description: total RNA 11μl, 35ng/μl

value: Sample 22


title: VAL

city: Bellinzona

first: Luciano

last: Cascione

state: Ticino

address: Via Chiesa 5

department: Lymphoma & Genomics Research Program

institute: IOR

data_processing:
Illumina Casava1.7 software used for basecalling and demultiplexing.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using STAR with default paramenters. Genes' Expression have been quantified using HT-Seq count using gencode v22 as gtf.
Read counts have been normalized with TMM algorithm, and converted to log2 counts per million of mapped reads (lcpm)
Assembly: hg38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample (Raw_Counts sheet)
Supplementary files format and content: Matrix table with lcpm for every gene in every sample (Normalized lcpm)

source_name: cell line

extract_protocol:
Total RNA was extracted using the TRIzol Reagent (Invitrogen) according to the manufacturer’s instructions
RNA libraries for RNA-seq were prepared using the NEBNext Ultra II Directional RNA Library Prep Kit following manufacturer's protocols.

tag: condition

value: B-cell

value: VAL


title: VL51


title: Z138


title: UPN1


title: C3 control 7d

description: total RNA 11μl, 35ng/μl

value: Sample 15


title: SUDHL8


title: TMD8


title: SUDHL4


title: SUDHL16


title: SSK41


title: SUDHL10


title: SP49


title: SUDHL2


title: REC1


title: PFEIFFER

value: PFEIFFER


title: L2 control 7d

description: total RNA 11μl, 35ng/μl

value: Sample 2


title: L5 control 7d

description: total RNA 11μl, 35ng/μl

value: Sample 5


title: RCK8


title: OCILY8


title: RAMOS

value: RAMOS


title: PCL12


title: WSUDLCL2


title: OCILY3


title: OCILY7


title: OCILY2


title: U2932


title: TOLEDO

value: TOLEDO


title: OCILY19


title: OCILY18


title: SUDHL5


title: OCILY10


title: MINO

value: MINO


title: MEC1


title: SP53


title: KARPAS422


title: RIVA

value: RIVA


title: KARPAS1718


title: JEKO1


title: JVM2


title: HC1


title: HBL1


title: GRANTA519


title: HAIRM

value: HAIRM


title: FARAGE

value: FARAGE


title: DB

value: DB


title: DOHH2


title: ESKOL

value: ESKOL


title: TXN_IP_2

city: Wuhan

first: Dong

last: Chen

state: Hubei

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

department: Center for Genome Analysis

country: China

institute: ABLife, Inc.

data_processing:
Illumina bcl2fastq software used for basecalling.
Raw reads containing more than 2-N bases were first discarded. Then adaptors and low-quality bases were trimmed from raw sequencing reads using FASTX-Toolkit (Version 0.0.13). The short reads less than 16nt were also dropped.
3' adapter (end1:AGATCGGAAGAGC;end2:AGATCGGAAGAGC) and low quality bases trimmed using FASTX-Toolkit (Version 0.0.13). the short reads less than 16nt were also dropped.
Reads were mapped using tophat2 --read-edit-dist 4 -N 4 --b2-N 1 -a 8 -m 0 -g 2 -p 12 --microexon-search --no-coverage-search --report-secondary-alignments. Uniquely mapped reads were remained. One more reads with the same start and end position, only one is considered.
After reads were aligned onto the genome, we analysed the unique reads binding regions of Txn1 on genome using “ABLIRC” strategy.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include peak information for each group.

source_name: HeLa

extract_protocol:
The Txn1-bound RNA was isolated from the immunoprecipitation of anti-Txn1 using Trizol (Invitrogen).
The cDNA libraries used the Illumina ScriptSeq™ v2 RNA-Seq Library Preparation Kit(Epicentre).The cDNAs were purified and amplified and PCR products corresponding to 200-500 bps were purified, quantified and stored at -80 °C until used for sequencing.

value: HeLa

value: Cervical cancer cells

tag: rip antibody


title: TXN_IP_1


title: TXN_input_1

value: none (input)


title: TXN_input_2


title: OCILY1

value: B-cell


title: Psoriatic arthritis skin uninvolved 11 [PSA_U_11]

city: Glasgow

first: John

middle: Joseph

last: Cole

address: University Avenue

country: United Kingdom

institute: University of Glasgow

description: Skin biopsy from psoriatic arthritis uninvolved

data_processing:
Firstly, the fastQ files were QC’d using FastQC (FastQC v0.11.7).
Sequences were aligned to the reference genome using STAR (Dobin et al 2013, v2.6) with –quantMode GeneCounts –outFilterMultimapNmax 1 and –outFilterMatchNmin 35. We used a Star index with a –sjdbOverhang of the maximum read length − 1.
Read count files were merged and genes with mean of < 1 read per sample were excluded.
Finally, the expression and differential expression values were generated using DESeq2 (Love, Huber Anders 2014, v1.24). For differential comparisons we used an A versus B model with no additional covariates. All other parameters were left to default.
The data was explored and visualised using Searchlight2 (Cole et al 2021). Specifying 3 differential expression workflows (PsA L vs HC, PsA U vs HC and PsA L vs PsA U) and one multiple differential expression workflow (PsA L vs HC + PsA U vs HC). The significance threshold for genes was set to p.adj = 0.05 and log2fold = 1. Over representation analysis was included using the default human GO biological processes database (Ashburner et al 2000), and a threshold for significant enrichment of p.adj = 0.05. All other parameters were left to default.
Assembly: Sequences were aligned to the genome and transcriptome GRCh38 (release 91).
Supplementary files format and content: Raw read counts are provided in read_counts.csv

source_name: skin biopsy

extract_protocol:
Control and PsA uninvolved skin biopsies (>8 cm from any lesion) were taken from the buttock area, and lesional biopsies were taken from within a skin lesion, 1 cm from the edge. Each full-thickness, 6 mm punch biopsy was cut in half and the halves placed in either RNAlater (Ambion) for RNA extraction or 10% neutral buffered formalin (SIGMA) for tissue fixation, processing and embedding. Biopsies in RNAlater were cut into smaller pieces before they were disrupted and homogenised in RLT buffer (Qiagen) with added β-mercaptoethanol in a TissueLyser (Qiagen) at 50 Hz with steel beads. RNA was extracted from the lysate as per the RNeasy Mini RNA extraction kit (Qiagen) protocol. The extracted RNA was treated with DNase MAX (Qiagen) to remove genomic contamination.
Polyadenylated RNA was selected using the NEBNext Poly(A) mRNA Magnetic Isolation Module kit (NEB #E7490) to preferentially sequence mRNA. The NEBNext Ultra II Directional RNA Library Prep Kit with sample purification beads (NEB # E7765S) was used for the subsequent library preparation and each sample was labelled using i5 and i7 primers from the NEBNext Multiplex Oligos for Illumina (Dual Index Primers Set 1) (NEB #E7600S).
The samples were pooled, and quality controlled by Qubit and Bioanalyzer. Sequencing was performed at Edinburgh Genomics (https://genomics.ed.ac.uk/) on the NovaSeq S1 (Illumina) using paired end sequencing of 50 base pairs with a total of 750M + 750M reads.

tag: tissue

value: skin biopsy

tag: tissue type

value: Psoriatic arthritis skin uninvolved


title: Psoriatic arthritis skin uninvolved 10 [PSA_U_10]


title: Psoriatic arthritis skin uninvolved 8 [PSA_U_8]


title: Psoriatic arthritis skin uninvolved 7 [PSA_U_7]


title: MAVER1


title: Psoriatic arthritis skin uninvolved 2 [PSA_U_2]


title: Psoriatic arthritis skin uninvolved 4 [PSA_U_4]


title: Psoriatic arthritis skin uninvolved 3 [PSA_U_3]


title: Psoriatic arthritis skin uninvolved 5 [PSA_U_5]


title: KARPAS1106P


title: Psoriatic arthritis skin lesion 11 [PSA_L_11]

description: Skin biopsy from psoriatic arthritis lesions

value: Psoriatic arthritis skin lesion


title: Psoriatic arthritis skin lesion 10 [PSA_L_10]


title: Psoriatic arthritis skin lesion 8 [PSA_L_8]


title: Psoriatic arthritis skin lesion 7 [PSA_L_7]


title: UT-BMDM-KDM5B

city: Shanghai

first: Xingguang

last: Liu

address: Xiangyin road 800

department: National Key Laboratory of Immunity & Inflammation

institute: Naval medical university

library_source: genomic

data_processing:
Basecalls were performed using bcl2fastq v2.17 for Novaseq output.
CUT&Tag reads were trimmed from 3' end until the final base had a quality score > 20, using Fastx v0.0.13, discarding reads left with < 20 bp.
CUT&Tag reads were aligned to the UCSC mm10 genome using Bowtie2 version v2.2.6. Only uniquely mapping reads with at most two mismatches were retained.
To create CUT&Tag coverage plots, the locations of the mapped ChIP-seq reads were extended to 150 bp to represent sequenced fragments, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
Peaks were called using MACS v2.2.7.1 with the significance cut-off p-value <=0.01.
bigWig files were generated using the bamCoverage. Score represents the normalized coverage of DNA fragments at a given genomic coordinate. narrowPeak files were generated using MACS v2 with default settings.
Assembly: mm10
Supplementary files format and content: bigWig files
Library strategy: CUT&Tag

molecule: genomic DNA

organism: Mus musculus

source_name: Primary bone marrow-derived macrophages (BMDM)

growth_protocol: BMDMs are harvested from bone marrow cells, and cultured in M-CSF (20ng/ml) RPMI 1640 medium for 6 days (day 3 replaced with fresh medium).

extract_protocol:
CUT&Tag was performed with Hyperactive Universal CUT&Tag Assay Kit for Illumina (Vazyme) according to the manufacturer’s protocol, using antibody against KDM5B (A301-813) from Bethyl.
Library construction was performed using TruePrep® DNA Library Prep Kit V2 for Illumina (Vazyme) and TruePrep® Index Kit V2 for Illumina (Vazyme).

treatment_protocol: LPS (100ng/ml) stimulation for 1h.

tag: strain

tag: treatment

value: Untreated

tag: antibody

value: KDM5B (A301-813, Bethyl)


title: LPS-BMDM-KDM5B

value: Primary bone marrow-derived macrophages (BMDM)

value: LPS (100ng/ml) for 2h


title: Psoriatic arthritis skin lesion 4 [PSA_L_4]


title: Psoriatic arthritis skin lesion 5 [PSA_L_5]


title: E18

city: Hong Kong

first: Tin-Lap

last: Lee

address: LKSIBSB, CUHK, Shatin, Hong Kong

department: School of Biomedical Sciences

country: Hong Kong

institute: The Chinese University of Hong Kong

description:
E18_FKDL202576001-1a_H7WFNCCX2_L3
E18_FKDL202576001-1a_HCGMGCCX2_L2

data_processing:
Sequencing data were processed using the Bio-Rad ATAC-Seq Analysis Toolkit, which performed FASTQ debarcoding, read trimming, alignment, bead filtration, bead deconvolution, cell filtration and peak calling.
For generation of the fragments file, which contain the start and end genomic coordinates of all aligned sequenced fragments, sorted bam files were further process with “bap-frag” module of BAP
Genome_build: mm10
Supplementary_files_format_and_content: Fragments file

source_name: scATAC on whole testis

extract_protocol:
The testes were collected and with tunica albuginea removed. The testes were then digested into single cell suspension with type 4 collagenase and hyaluronidase. Cell tagmentation was performed according to SureCell ATAC-Seq Library Prep Kit (17004620, Bio-Rad) User Guide (10000106678, Bio-Rad) and the protocol based on Omni-ATAC was followed (Corces et al. 2017). In brief, washed and pelleted cells were lysed with the Omni-ATAC lysis buffer containing 0.1% NP-40, 0.1% Tween-20, 0.01% digitonin, 10 mM NaCl, 3 mM MgCl2 and 10 mM Tris-HCl pH 7.4 for 3 min on ice. The lysis buffer was diluted with ATAC-Tween buffer that contains 0.1% Tween-20 as a detergent. Nuclei were counted and examined under microscope to ensure successful isolation. Same number of nuclei were subjected to tagmentation with equal ratio of cells/Tn5 transposase to minimize potential batch effect. Nuclei were resuspended in tagmentation mix, buffered with 1×PBS supplemented with 0.1% BSA and agitated on a ThermoMixer for 30 min at 37 °C. Tagmented nuclei were kept on ice before encapsulation.
Tagmented nuclei were loaded onto a ddSEQ Single-Cell Isolator (Bio-Rad). scATAC-Seq libraries were prepared using the SureCell ATAC-Seq Library Prep Kit (17004620, Bio-Rad) and SureCell ATAC-Seq Index Kit (12009360, Bio-Rad). Bead barcoding and sample indexing were performed with PCR amplification as follows: 37 °C for 30 min, 85 °C for 10 min, 72 °C for 5 min, 98 °C for 30 s, eight cycles of 98 °C for 10 s, 55 °C for 30 s and 72 °C for 60 s, and a single 72 °C extension for 5 min to finish. Emulsions were broken and products were cleaned up using Ampure XP beads. Barcoded amplicons were further amplified for 8 cycles. PCR products were purified using Ampure XP beads and quantified on an Agilent Bioanalyzer (G2939BA, Agilent) using the High-Sensitivity DNA kit (5067-4626, Agilent). Libraries were sequenced on HiSeq 2000 with 150 bp paired-end reads.

tag: age

value: Embryonic day 18.5

value: Testis

tag: molecule subtype

value: genomic DNA, open chromatin region


title: P0

description:
P0_FKDL202576002-1a_H7WFNCCX2_L3
P0_FKDL202576002-1a_HCGMGCCX2_L2

value: Postnatal day 0.5


title: Psoriatic arthritis skin lesion 3 [PSA_L_3]


title: Psoriatic arthritis skin lesion 2 [PSA_L_2]


title: Healthy control skin 15 [HC_15]

description: Skin biopsy from non-arthritic healthy controls

value: Healthy control skin


title: Psoriatic arthritis skin lesion 1 [PSA_L_1]


title: P6

description:
P6_FKDL202576004-1a_H7WFNCCX2_L3
P6_FKDL202576004-1a_HCGMGCCX2_L2

value: Postnatal day 6


title: P3

description:
P3_FKDL202576003-1a_H7WFNCCX2_L3
P3_FKDL202576003-1a_HCGMGCCX2_L2

value: Postnatal day 3


title: SPM_2: Adult-3 (P60) 9pm supernatant

city: Boston

first: Maria

last: Lehtinen

state: MA

address: 300 Longwood Ave

department: Pathology

institute: Boston Children's Hospital

data_processing:
The raw fastq data of 50-bp single-end sequencing reads were aligned to the mouse mm10 reference genome using STAR 2.4.0 RNA-Seq aligner
The mapped reads were processed with cufflinks software to calculate gene FPKM values.
Gene differential expression test between two different animal groups was performed using cuffdiff module of cufflinks software with geometric data normalization.
Genes with adjusted p-value <0.05 were chosen as differentially expressed genes
Genome_build: mm10
Supplementary_files_format_and_content: txt

source_name: ChP-tagged mRNAs

extract_protocol:
Translating Ribosome Affinity Purification
Clonetech SMARTer Pico with ribodepletion
The quality of prepared bar-coded libraries was assessed using an Advanced Analytical-fragment Analyzer before mixing for sequencing on the Illumina HiSeq platform at the MIT BioMicro Center.

tag: age at harvest

value: 60 days

tag: mouse genotype

value: FoxJ1:cre x bacTRAP (EGFP:L10a)

value: choroid plexus (ChP)


title: SPM_0: Adult-1 (P60) 9pm supernatant


title: PM_2: Adult-3 (P60) 9pm TRAP


title: Healthy control skin 14 [HC_14]

value: skin biopsy


title: PM_1: Adult-2 (P60) 9pm TRAP


title: Psoriatic arthritis skin uninvolved 1 [PSA_U_1]

value: Psoriatic arthritis skin uninvolved


title: Healthy control skin 13 [HC_13]


title: Healthy control skin 12 [HC_12]


title: PM_0: Adult-1 (P60) 9pm TRAP


title: Healthy control skin 9 [HC_9]


title: SAM_2: Adult-3 (P60) 9am supernatant


title: SAM_1: Adult-2 (P60) 9am supernatant


title: Healthy control skin 11 [HC_11]


title: Healthy control skin 8 [HC_8]


title: AM_2: Adult-3 (P60) 9am TRAP


title: SAM_0: Adult-1 (P60) 9am supernatant


title: Healthy control skin 6 [HC_6]


title: Healthy control skin 7 [HC_7]


title: AM_1: Adult-2 (P60) 9am TRAP


title: AM_0: Adult-1 (P60) 9am TRAP


title: SPM_1: Adult-2 (P60) 9pm supernatant


title: Thy171_H3K4me3

city: Paris

first: Vahid

last: Asnafi

address: 149 rue de Sèvres

country: France

institute: APHP

data_processing:
Base calling was performed using RTA version 2.
Reads were trimmed with Sickle v1.33 and aligned to the hg19 genome assembly using Bowtie v2.3.4.3 and defaults parameters.
Coverage tracks were generated with deepTools v3.2.1.
Peaks were called using Macs2 v2.1.1 and –broad argument.
hg19
Assembly: bw: RPKM-normalized coverage track
Supplementary files format and content: bed: peaks

source_name: thymus

extract_protocol:
ChIP were performed following the BLUEPRINT protocol (http://dcc.blueprint-epigenome.eu/#/md/methods).
Paired-end sequencing 50+30bp was performed using Illumina NextSeq 500.

treatment_protocol: no treatment

value: thymus

value: thymocytes

tag: chip antibody


title: Thy171_H3K27ac


title: 802_BT11_H3K4me3

data_processing:
Base calling was performed using RTA version 2.
Reads were trimmed with Sickle v1.33 and aligned to the hg19 genome assembly using Bowtie v2.3.4.3 and defaults parameters.
Coverage tracks were generated with deepTools v3.2.1.
Peaks were called using Macs2 v2.1.1 and –broad argument.
hg38
Assembly: bw: RPKM-normalized coverage track
Supplementary files format and content: bed: peaks

source_name: T-acute lymphoblastic leukemia

extract_protocol:
ChIP were performed following the BLUEPRINT protocol (http://dcc.blueprint-epigenome.eu/#/md/methods).
Single-end sequencing 75bp was performed using Illumina NextSeq 500.

value: T-acute lymphoblastic leukemia

tag: blueprint donor_id


title: 753_BT8_H3K4me3

tag: cell type


title: 427_BT3_H3K27ac


title: CD34_RNA

data_processing:
Base calling was performed using RTA version 2.
Reads were trimmed with Sickle v1.33 (-q 20) and aligned to the hg19 genome assembly using STAR v2.7.9 with default parameters
Coverage tracks were generated with deepTools v3.2.1. (--binsize 20 --minMappingQuality 0 --normalizeUsing RPKM) and by strand (--filterRNAstrand reverse or forward)
Gene-level counting was done using subread featureCounts (-O) against Ensembl release 67 gtf file
Assembly: hg19
Supplementary files format and content: tab-delimited text files include raw and RPKM values for each Sample

source_name: CD34 thymocytes

extract_protocol:
RNA were extracted following the BLUEPRINT protocol (http://dcc.blueprint-epigenome.eu/#/md/methods).
Single-end sequencing 75bp was performed using Illumina NextSeq 500.

value: CD34 thymocytes


title: genomic DNA from whole blood normal 87

type: genomic

city: Seoul

first: Sue K.

last: Park

address: 103, Daehak-ro, Jongno-gu

department: Preventive Medicine

country: South Korea

institute: Seoul National University

description:
Sample was bisulfite-converted and hybridized to the array following the manufacturer's protocol
SAMPLE 180

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human MethylationEPIC Beadchip using standard Illumina protocol

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

data_processing:
We performed quality control of DNA methylation data extracted from raw intensity data (IDAT), including the signal intensities for each of the probes on the chip. To minimize the unintended variation within and between samples, we implemented quantile normalization, which considers the methylated and unmethylated signal intensities separately. The methylation levels at each CpG probe are represented as M-values. Quality control and genome-wide analyses were conducted using the Minfi package from the Bioconductor platform in R.
Average beta

label: Cy5 and Cy3

source_name: whole blood

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from samples using Qiagen DNeasy Kit according to standard instructions

tag: ckd

value: non-progression

value: whole blood


title: genomic DNA from whole blood normal 83

description:
Sample was bisulfite-converted and hybridized to the array following the manufacturer's protocol
SAMPLE 176


title: genomic DNA from whole blood normal 82

description:
Sample was bisulfite-converted and hybridized to the array following the manufacturer's protocol
SAMPLE 175


title: genomic DNA from whole blood normal 86

description:
Sample was bisulfite-converted and hybridized to the array following the manufacturer's protocol
SAMPLE 179


title: genomic DNA from whole blood normal 85

description:
Sample was bisulfite-converted and hybridized to the array following the manufacturer's protocol
SAMPLE 178


title: 885_BT6_RNA


title: 864_BT5_RNA


title: genomic DNA from whole blood normal 84

description:
Sample was bisulfite-converted and hybridized to the array following the manufacturer's protocol
SAMPLE 177


title: genomic DNA from whole blood normal 81

description:
Sample was bisulfite-converted and hybridized to the array following the manufacturer's protocol
SAMPLE 174


title: genomic DNA from whole blood normal 79

description:
Sample was bisulfite-converted and hybridized to the array following the manufacturer's protocol
SAMPLE 172


title: 845_BT9_RNA


title: 802_BT11_RNA


title: genomic DNA from whole blood normal 77

description:
Sample was bisulfite-converted and hybridized to the array following the manufacturer's protocol
SAMPLE 170


title: genomic DNA from whole blood normal 80

description:
Sample was bisulfite-converted and hybridized to the array following the manufacturer's protocol
SAMPLE 173


title: genomic DNA from whole blood normal 78

description:
Sample was bisulfite-converted and hybridized to the array following the manufacturer's protocol
SAMPLE 171


title: 820_BT10_RNA


title: 753_BT8_RNA


title: 398_BT4_RNA


title: genomic DNA from whole blood normal 75

description:
Sample was bisulfite-converted and hybridized to the array following the manufacturer's protocol
SAMPLE 168


title: 760_BT12_RNA


title: genomic DNA from whole blood normal 74

description:
Sample was bisulfite-converted and hybridized to the array following the manufacturer's protocol
SAMPLE 167


title: hnRNPc_500_noPAGE_RecJ_Rep2

extract_protocol:
Protein-G beads (Thermo Fisher, 10004D) were washed twice in 1ml iCLIP Lysis buffer and resuspended in 100 µl per condition (100 µl of protein-G beads bind 20-30 µg of antibody - scale accordingly). Per IP, 1 µg of antibody against hnRNPc (Santa Cruz Biotechnology, sc-32308), RBM9 (Bethyl Laboratories, A300-864A), hnRNPA1 (4B10) (Santa Cruz Biotechnology, sc-32301), or hnRNPI (Santa Cruz Biotechnology, sc-56701) were added, and antibody-bead mixture was incubated at room temperature (RT) for 30-60 minutes on a rotating wheel. Antibody-bead mixture was washed twice in iCLIP lysis buffer to remove unbound antibody and RNase-treated cell lysates were added alongside cOmplete EDTA-free Protease Inhibitor Cocktail (Merck, #11836170001) and incubated for 2 hours at 4ºC on a rotating wheel. After IP, beads were washed twice in 200 µl High Salt Buffer (50 mM Tris-HCl pH 7.4, 1 M NaCl, 1 mM EDTA, 1% Igepal CA-630, 0.1% SDS, 0.5% sodium-deoxycholate), with the second wash at 4ºC for 3 minutes on a rotating wheel, followed by two washes in 200 µl PNK Wash Buffer (20 mM Tris-HCl, pH 7.4, 10 mM MgCl2, 0.2% Tween-20). Dephosphorylation of 3’ ends was performed in 20 µl of PNK reaction for 30 minutes at 37ºC (70 mM Tris-HCl, pH 6.5, 10 mM MgCl2, 1 mM DTT, 10U SUPERaseIN RNase Inhibitor (ThermoFisher, #AM2696), 5U T4 Polynucleotide Kinase (NEB, #M0201L). Beads were washed twice in PNK Wash Buffer and resuspended in 20 µl of ligation mix for overnight incubation at 16ºC and 1200 rpm (50 mM Tris-HCl, pH 7.8, 10 mM MgCl2, 1mM DTT, 10U SUPERaseIN RNase Inhibitor, 10U T4 RNA Ligase (NEB, #M0204), 1 µl of 1 µM L3 adapter and 20% PEG400 (Sigma-Aldrich, #91893)).
Following the first adapter ligation, beads were washed twice in 200 µl High Salt Buffer, twice in 200 µl PNK Wash buffer and then resuspended in 20 µl 1X LDS sample buffer (Thermo Fisher, #NP0008) containing 5% beta-mercaptoethanol (Sigma-Aldrich, #M6250). Samples were denatured for 1 minute at 70ºC and RNA-protein complexes were resolved on NuPAGE 4-12% Bis-Tris Gels (Thermo Fisher, #WG1402A) at 180V for 1 hour. Transfer was performed onto nitrocellulose (BioRad, #1620115) in 1X NuPAGE transfer buffer (Thermo Fisher, #NP00061) with 10% methanol at 30V for 2 hours at RT.   Nitrocellulose membranes were scanned on Odyssey® CLx Infrared Imager (LI-COR, 9141) with 169 µm resolution to visualise RNA localisation and then placed on filter paper soaked in PBS. Regions of interest were cut out from nitrocellulose membrane corresponding to ~20-100 kDa above the molecular weight of the RBP of interest due to the ligation of L3 adapter (~15.9 kDa) and associated RNA (with 70nt of RNA averaging ~20kDa). Nitrocellulose pieces were placed in LoBind Eppendorf tubes and 200 µl Proteinase K buffer (100mM Tris-HCl, pH 7.4, 50 mM LiCl, 1 mM EDTA, 0.2% LiDS) containing 200 µg Proteinase K (Thermo Fisher, #AM2546) were added and incubated at 50ºC for 45 minutes at 800rpm.  Meanwhile, 10 µl of Oligo(dT)25 Dynabeads™ (Thermo Fisher, #61005) per sample were washed in 1 ml of oligo(dT) Binding Buffer (20 mM Tris-HCl, pH 7.4, 1 M LiCl, 2 mM EDTA) and resuspended in 50 µl of oligo(dT) Binding Buffer per sample. Following Proteinase K treatment, supernatant was transferred to fresh tubes containing 50 µl of oligo(dT) beads and incubated for 10 minutes at RT on a rotating wheel. Following RNA capture, beads were washed twice in 125 µl oligo(dT) Wash Buffer (10 mM Tris-HCl, pH 7.4, 150 mM LiCl, 0.1 mM EDTA) and once in 20 µl 1X First-Strand Buffer (50 mM Tris-HCl, pH 8.3, 75 mM KCl, 3 mM MgCl2). Beads were resuspended in 10 µl of Reverse Transcription Mix (1X First-Strand Buffer, 0.5 mM dNTPs, 1 mM DTT, 6U SUPERase IN RNase Inhibitor, 20U SuperScript™ IV Reverse Transcriptase (Thermo Fisher, #18090050) and incubated for 15 minutes at 50ºC followed by 10 minutes at 80ºC heating up to 96ºC. Samples were vortexed for 30 seconds at 96ºC and then immediately placed on a magnet on ice. Supernatant containing adapter-ligated RNA was removed and efficiency of elution can be confirmed by dot-blotting on nitrocellulose membrane.   Solid-phase cDNA was washed once in 60 µl oligo(dT) Wash Buffer and once in 20 µl 1X T4 RNA Ligase Buffer (50 mM Tris-HCl, 10 mM MgCl2, 1mM DTT, pH 7.5). Beads were resuspended in 5 µl of 5’ Adapter mix (2 µl 10X T4 RNA Ligase Buffer, 2 µl of 10 µM L## oligo (see Supplementary Table 2), 1 µl 100% DMSO), incubated at 75ºC for 2 minutes then immediately placed on ice. 4 µl of Ligation Mix (5 mM ATP, 7U Terminal Deoxynucleotidyl Transferase (TdT) (2230B, Takara), 15 U T4 RNA Ligase High Concentration (M0437, NEB)) were added as well as 10 µl 50% PEG8000 and reaction was mixed by pipetting up- and down until beads are resuspended. Reaction was incubated at 37ºC for 30 minutes, then cooled down to room temperature. 30 U of T4 RNA Ligase were added, the reaction mixed by pipetting and incubated at RT overnight with occasional vortexing for 15 seconds at 2000 rpm every two minutes.  Following overnight incubation, ligation reaction was removed and beads washed in 100 µl oligo(dT) Wash Buffer and 20 µl 1X Phusion HF Buffer (Thermo Fisher, #F518L). Beads were resuspended in 25 µl cDNA amplification mix (1X Phusion HF PCR Master Mix (NEB, #M0531L) and 0.5uM P5 and P7 short primer mix (see Supplementary Table 2)) and amplification was performed with the following programme: 30 seconds at 98ºC, 7 cycles of 10 seconds at 98ºC, 30 seconds at 65ºC and 30 seconds at 72ºC followed by final extension at 72ºC for 3 minutes. Meanwhile, 2µl of oligo(dT) beads per sample were washed once in 1 ml oligo(dT) Binding buffer and resuspended in 5 µl per sample. After cDNA amplification, 5 µl of oligo(dT) beads were added and incubated at RT for 5 minutes on a rotating wheel to capture unwanted amplification by-products (see Fig. S3). Samples were placed on magnet and supernatant containing amplified cDNA was transferred to a fresh tube.   Size-selection of cDNA was performed using ProNEX® Size-Selective Purification System (Promega, #NG2002) with a ratio of 2.8X to enrich for cDNA inserts of at least 20 nucleotides in length (>80bp). Library yield was then estimated by amplifying 1 µl of purified cDNA via qPCR using the full length P5 and P7 index primers and 2-3 cycles were subtracted from the obtained Ct value for final library amplification. Following PCR amplification, libraries were size-selected again using the ProNEX® Size-Selective Purification System, with a ratio of 1.8X to select fragments larger than 165bp.

tag: cell line

value: Human embryonic kidney

tag: clip antibody

value: hnRNP C1/2 (4F4) (SantaCruz, sc-32308)

tag: cell number


title: genomic DNA from whole blood normal 76

description:
Sample was bisulfite-converted and hybridized to the array following the manufacturer's protocol
SAMPLE 169


title: genomic DNA from whole blood normal 73

description:
Sample was bisulfite-converted and hybridized to the array following the manufacturer's protocol
SAMPLE 166


title: hnRNPc_500_noPAGE_RecJ_Rep1

tag: rnase [u]


title: hnRNPc_5k_noPAGE_RecJ_Rep2


title: genomic DNA from whole blood normal 71

description:
Sample was bisulfite-converted and hybridized to the array following the manufacturer's protocol
SAMPLE 164

tag: tissue


title: genomic DNA from whole blood normal 72

description:
Sample was bisulfite-converted and hybridized to the array following the manufacturer's protocol
SAMPLE 165


title: hnRNPc_5k_noPAGE_RecJ_Rep1


title: genomic DNA from whole blood normal 70

description:
Sample was bisulfite-converted and hybridized to the array following the manufacturer's protocol
SAMPLE 163


title: hnRNPc_500_noPAGE_Rep1


title: genomic DNA from whole blood normal 67

description:
Sample was bisulfite-converted and hybridized to the array following the manufacturer's protocol
SAMPLE 160


title: genomic DNA from whole blood normal 68

description:
Sample was bisulfite-converted and hybridized to the array following the manufacturer's protocol
SAMPLE 161


title: genomic DNA from whole blood normal 69

description:
Sample was bisulfite-converted and hybridized to the array following the manufacturer's protocol
SAMPLE 162


title: genomic DNA from whole blood normal 66

description:
Sample was bisulfite-converted and hybridized to the array following the manufacturer's protocol
SAMPLE 159


title: genomic DNA from whole blood normal 65

description:
Sample was bisulfite-converted and hybridized to the array following the manufacturer's protocol
SAMPLE 158


title: hnRNPc_5k_noPAGE_Rep1


title: hnRNPc_5k_noPAGE_Rep2


title: hnRNPc_500_noPAGE_Rep2


title: genomic DNA from whole blood normal 64

description:
Sample was bisulfite-converted and hybridized to the array following the manufacturer's protocol
SAMPLE 157


title: genomic DNA from whole blood normal 63

description:
Sample was bisulfite-converted and hybridized to the array following the manufacturer's protocol
SAMPLE 156


title: RBFOX2_50k_noPAGE_RecJ_Rep1

value: RBM9 (Bethyl Laboratories, #A300-864A)


title: genomic DNA from whole blood normal 61

description:
Sample was bisulfite-converted and hybridized to the array following the manufacturer's protocol
SAMPLE 154


title: hnRNPI_50k_noPAGE_RecJ_Rep2

value: hnRNPI (SH54) (SantaCruz, sc-56701)


title: genomic DNA from whole blood normal 60

description:
Sample was bisulfite-converted and hybridized to the array following the manufacturer's protocol
SAMPLE 153


title: RBFOX2_50k_noPAGE_RecJ_Rep2


title: hnRNPc_50k_noPAGE_RecJ_Rep1


title: hnRNPc_50k_noPAGE_RecJ_Rep2


title: hnRNPA1_50k_noPAGE_RecJ_Rep2

value: hnRNPA1 (4B10) (SantaCruz, sc-32301)


title: genomic DNA from whole blood normal 59

description:
Sample was bisulfite-converted and hybridized to the array following the manufacturer's protocol
SAMPLE 152


title: hnRNPI_50k_noPAGE_RecJ_Rep1


title: genomic DNA from whole blood normal 58

description:
Sample was bisulfite-converted and hybridized to the array following the manufacturer's protocol
SAMPLE 151


title: hnRNPA1_50k_noPAGE_RecJ_Rep1


title: genomic DNA from whole blood normal 57

description:
Sample was bisulfite-converted and hybridized to the array following the manufacturer's protocol
SAMPLE 150


title: RBFOX2_50k_noPAGE_Rep2


title: genomic DNA from whole blood normal 56

description:
Sample was bisulfite-converted and hybridized to the array following the manufacturer's protocol
SAMPLE 149


title: RBFOX2_50k_noPAGE_Rep1


title: hnRNPI_50k_noPAGE_Rep2


title: genomic DNA from whole blood normal 55

description:
Sample was bisulfite-converted and hybridized to the array following the manufacturer's protocol
SAMPLE 148


title: genomic DNA from whole blood normal 54

description:
Sample was bisulfite-converted and hybridized to the array following the manufacturer's protocol
SAMPLE 147


title: hnRNPc_50k_noPAGE_Rep2


title: hnRNPI_50k_noPAGE_Rep1


title: genomic DNA from whole blood normal 62

description:
Sample was bisulfite-converted and hybridized to the array following the manufacturer's protocol
SAMPLE 155


title: genomic DNA from whole blood normal 51

description:
Sample was bisulfite-converted and hybridized to the array following the manufacturer's protocol
SAMPLE 144


title: genomic DNA from whole blood normal 52

description:
Sample was bisulfite-converted and hybridized to the array following the manufacturer's protocol
SAMPLE 145


title: genomic DNA from whole blood normal 50

description:
Sample was bisulfite-converted and hybridized to the array following the manufacturer's protocol
SAMPLE 143


title: hnRNPI_50k_lowRNase_Rep2


title: genomic DNA from whole blood normal 53

description:
Sample was bisulfite-converted and hybridized to the array following the manufacturer's protocol
SAMPLE 146


title: hnRNPc_50k_noPAGE_Rep1


title: hnRNPA1_50k_noPAGE_Rep1


title: hnRNPI_50k_lowRNase_Rep1


title: hnRNPA1_50k_noPAGE_Rep2


title: genomic DNA from whole blood normal 47

description:
Sample was bisulfite-converted and hybridized to the array following the manufacturer's protocol
SAMPLE 140


title: genomic DNA from whole blood normal 49

description:
Sample was bisulfite-converted and hybridized to the array following the manufacturer's protocol
SAMPLE 142


title: genomic DNA from whole blood normal 46

description:
Sample was bisulfite-converted and hybridized to the array following the manufacturer's protocol
SAMPLE 139


title: genomic DNA from whole blood normal 45

description:
Sample was bisulfite-converted and hybridized to the array following the manufacturer's protocol
SAMPLE 138


title: genomic DNA from whole blood normal 48

description:
Sample was bisulfite-converted and hybridized to the array following the manufacturer's protocol
SAMPLE 141


title: RBFOX2_50k_lowRNase_Rep1


title: hnRNPc_50k_mediumRNase_Rep2


title: genomic DNA from whole blood normal 44

description:
Sample was bisulfite-converted and hybridized to the array following the manufacturer's protocol
SAMPLE 137


title: hnRNPc_50k_mediumRNase_Rep1


title: hnRNPA1_50k_mediumRNase_Rep2


title: genomic DNA from whole blood normal 42

description:
Sample was bisulfite-converted and hybridized to the array following the manufacturer's protocol
SAMPLE 135


title: hnRNPA1_50k_mediumRNase_Rep1


title: hnRNPc_50k_lowRNase_Rep2


title: genomic DNA from whole blood normal 41

description:
Sample was bisulfite-converted and hybridized to the array following the manufacturer's protocol
SAMPLE 134


title: hnRNPc_50k_lowRNase_Rep1


title: hnRNPA1_50k_lowRNase_Rep2


title: genomic DNA from whole blood normal 39

description:
Sample was bisulfite-converted and hybridized to the array following the manufacturer's protocol
SAMPLE 132


title: genomic DNA from whole blood normal 40

description:
Sample was bisulfite-converted and hybridized to the array following the manufacturer's protocol
SAMPLE 133


title: Transplant_ret_org_rep3

city: Pittsburgh

first: Clayton

middle: Pio

last: Santiago

state: Pennsylvania

address: 1622 Locust Street

department: Ophthalmology

institute: University of Pittsburgh

description: Raw data file scR026

data_processing:
scRNA-Seq: Sequencing results were processed through the Cell Ranger pipeline (10x Genomics) with default parameters. Seurat V3 was used to perform downstream analysis following the standard pipeline.
Genome_build: GRCh38
Supplementary_files_format_and_content: Bam file
Supplementary_files_format_and_content: Cell-by-gene count matrix for all the samples as csv
Supplementary_files_format_and_content: Metadata for the cell-by-gene count matrix as csv

source_name: H9 CRX:TdTomato organoid

extract_protocol:
Papain dissociation to prepare single cell suspension
scRNA-Seq following 10x ver3.1 guideline

value: retinal organoid

tag: condition

value: Transplant

value: ~270 days


title: Transplant_ret_org_rep2

description: Raw data file scR025


title: hnRNPA1_50k_lowRNase_Rep1


title: genomic DNA from whole blood normal 37

description:
Sample was bisulfite-converted and hybridized to the array following the manufacturer's protocol
SAMPLE 130


title: RBFOX2_50k_lowRNase_Rep2


title: genomic DNA from whole blood normal 38

description:
Sample was bisulfite-converted and hybridized to the array following the manufacturer's protocol
SAMPLE 131


title: genomic DNA from whole blood normal 35

description:
Sample was bisulfite-converted and hybridized to the array following the manufacturer's protocol
SAMPLE 128


title: genomic DNA from whole blood normal 34

description:
Sample was bisulfite-converted and hybridized to the array following the manufacturer's protocol
SAMPLE 127


title: genomic DNA from whole blood normal 36

description:
Sample was bisulfite-converted and hybridized to the array following the manufacturer's protocol
SAMPLE 129


title: Cultured_ret_org_rep1

description: Raw data file scR029

value: Cultured


title: Cultured_ret_org_rep2

description: Raw data file scR030


title: genomic DNA from whole blood normal 32

description:
Sample was bisulfite-converted and hybridized to the array following the manufacturer's protocol
SAMPLE 125


title: Transplant_ret_org_rep1

description: Raw data file scR024


title: genomic DNA from whole blood normal 31

description:
Sample was bisulfite-converted and hybridized to the array following the manufacturer's protocol
SAMPLE 124


title: LNCaP + R1881 rep2

city: Nottingham

first: Nigel

middle: P

last: Mongan

address: University Park

department: Biodiscovery Institute

institute: University of Nottingham

data_processing:
Contaminating adapters and low quality reads with phred scores <30 were removed using the Trimgalore wrapper for Cutadapt and Fastqc
The resultant quality controlled fastq files were aligned to the Ensembl annoted Human genome (GRCh38.83) using STAR
Gene expression was quantified using FeatureCounts
Genome_build: GRCh38.83
Supplementary_files_format_and_content: Tab delimited text file contain gene expression in counts

source_name: Androgen treated LNCaP

growth_protocol: LNCaP cells were grown in phenol red-free RPMI-1640 medium supplemented with 1% penicillin-streptomycin, 2mM L-Glutamine and 1 mM sodium pyruvate and either 10% hormone depleted dialyzed or charcoal-stripped FBS.

extract_protocol:
RNA was extracted using Qiagen RNeasy Mini kit
Illumina

treatment_protocol: For androgen treatments, cells were treated for 72 hours with R1881 (1nM) dissolved in ethanol, and 0.1% ethanol treatments were used as vehicle control. CPI-455 was dissolved in DMSO and used at a final concentration of 50µM with DMSO <0.01%.

value: Prostate cancer cells

value: LNCaP

value: Androgen treated


title: genomic DNA from whole blood normal 33

description:
Sample was bisulfite-converted and hybridized to the array following the manufacturer's protocol
SAMPLE 126


title: genomic DNA from whole blood normal 30

description:
Sample was bisulfite-converted and hybridized to the array following the manufacturer's protocol
SAMPLE 123


title: LNCaP + R1881 rep1


title: genomic DNA from whole blood normal 43

description:
Sample was bisulfite-converted and hybridized to the array following the manufacturer's protocol
SAMPLE 136


title: genomic DNA from whole blood normal 28

description:
Sample was bisulfite-converted and hybridized to the array following the manufacturer's protocol
SAMPLE 121


title: genomic DNA from whole blood normal 27

description:
Sample was bisulfite-converted and hybridized to the array following the manufacturer's protocol
SAMPLE 120


title: NaCl+MT seeds, biol rep 3 (RNA-seq)

city: Yangzhou

first: Rujia

address: Wenhui

institute: Yangzhou unversity

data_processing:
The generated reads were firstly filtered and then mapped onto the reference genome of Zea mays using HISAT2
The featureCounts software was used to count the read numbers mapped to each gene.
DESeq2 was used to detect differentially expressed genes among three different comparisons.
Assembly: Maize B73 RefGen_v3
Supplementary files format and content: tab-delimited text file includes FPKM values for each Sample

organism: Zea mays

source_name: seed

extract_protocol:
RNA was harvested using the RNA extraction kit (Tiangen Biotech). 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NEB mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: seed

value: NaCl+MT

tag: Stage

value: seed germination


title: NaCl+MT seeds, biol rep 1 (RNA-seq)

tag: treatment


title: NaCl seeds, biol rep 3 (RNA-seq)

value: NaCl


title: genomic DNA from whole blood normal 26

description:
Sample was bisulfite-converted and hybridized to the array following the manufacturer's protocol
SAMPLE 119

value: non-progression

value: whole blood


title: LNCaP + R1881 +CPI455 rep2

source_name: Androgen and CPI455 treated LNCaP

value: Androgen and CPI455 treated


title: LNCaP + R1881 +CPI455 rep1


title: genomic DNA from whole blood normal 25

description:
Sample was bisulfite-converted and hybridized to the array following the manufacturer's protocol
SAMPLE 118


title: NaCl seeds, biol rep 1 (RNA-seq)


title: genomic DNA from whole blood normal 23

description:
Sample was bisulfite-converted and hybridized to the array following the manufacturer's protocol
SAMPLE 116


title: NaCl seeds, biol rep 2 (RNA-seq)


title: genomic DNA from whole blood normal 24

description:
Sample was bisulfite-converted and hybridized to the array following the manufacturer's protocol
SAMPLE 117


title: CK seeds, biol rep 2 (RNA-seq)

value: CK


title: CK seeds, biol rep 3 (RNA-seq)


title: genomic DNA from whole blood normal 19

description:
Sample was bisulfite-converted and hybridized to the array following the manufacturer's protocol
SAMPLE 112


title: genomic DNA from whole blood normal 21

description:
Sample was bisulfite-converted and hybridized to the array following the manufacturer's protocol
SAMPLE 114


title: CK seeds, biol rep 1 (RNA-seq)


title: Small RNA-Seq Parent Mo17, wild type, rep2

city: Oxford

first: Beibei

state: OH

address: Heather Ln. Apt.5

department: Biology Department

institute: Miami university (Ohio)

description: Parent Mo17, wild type, rep2

data_processing:
The raw reads were quality controlled by FastQC.
The clean reads were aligned against the Rfam database (v14.6) to remove rRNAs, tRNAs, snRNAs, and snoRNAs.
The maintained reads from B73, WTF1, and mop1F1 were mapped to the B73 reference genome (v4), and the reads from Mo17 were mapped to the Mo17 genome that was generated by replacing the single nucleotide polymorphisms between Mo17 and B73 using bowtie.
For the parents, only perfectly and uniquely mapped reads were kept, and one mismatch was allowed for the F1 hybrids.
The intersect module in BEDTools was used to compare the mapping results (sam files) of small RNAs to the positions of differentially methylated regions to obtain the 24 nt small RNA reads that are in the differentially methylated regions.
Assembly: B73 V4
Supplementary files format and content: Tab-delimited txt file includes the number of 24nt siRNAs at CHH differentially methylated regions in parents, WTF1 and mop1F1.

source_name: immature ear

extract_protocol:
Total RNA was extracted using QIAGEN RNeasy Plant Mini Kit, Cat. No. / ID: 74904.
Library construction was perfomred at Novogene.

value: immature ear

tag: genotype


title: genomic DNA from whole blood normal 18

description:
Sample was bisulfite-converted and hybridized to the array following the manufacturer's protocol
SAMPLE 111


title: Small RNA-Seq Parent B73, wild type, rep2

description: Parent B73, wild type, rep2


title: genomic DNA from whole blood normal 17

description:
Sample was bisulfite-converted and hybridized to the array following the manufacturer's protocol
SAMPLE 110


title: NaCl+MT seeds, biol rep 2 (RNA-seq)


title: Small RNA-Seq Parent B73, wild type, rep1

description: Parent B73, wild type, rep1


title: genomic DNA from whole blood normal 29

description:
Sample was bisulfite-converted and hybridized to the array following the manufacturer's protocol
SAMPLE 122


title: genomic DNA from whole blood normal 16

description:
Sample was bisulfite-converted and hybridized to the array following the manufacturer's protocol
SAMPLE 109


title: genomic DNA from whole blood normal 13

description:
Sample was bisulfite-converted and hybridized to the array following the manufacturer's protocol
SAMPLE 106


title: genomic DNA from whole blood normal 12

description:
Sample was bisulfite-converted and hybridized to the array following the manufacturer's protocol
SAMPLE 105


title: genomic DNA from whole blood normal 14

description:
Sample was bisulfite-converted and hybridized to the array following the manufacturer's protocol
SAMPLE 107


title: genomic DNA from whole blood normal 22

description:
Sample was bisulfite-converted and hybridized to the array following the manufacturer's protocol
SAMPLE 115


title: WGBS mop1-derived-BC1, individual 7

description: mop1-derived-BC1, individual 7

data_processing:
The raw reads were quality controled by FastQC.
Clean reads were mapped to the B73 reference genome (V4) or the Mo17 genome that was generated by replacing the single nucleotide polymorphisms between Mo17 and B73 using bismark bowtie2 with the following parameters (-n 2, -I 50, -N 1).
We kept the perfectly matched reads for two parents, and allowed one mismatch for the hybrids.
PCR duplicates were removed by Picardtools.
Bismark methylation extractor was used to extract the methylated cytosines.
Coverage2cytosine in bismark was used to obtain the final report which includes the ctyosine position, methylated and unmethylated reads at each cytosine.
Assembly: B73 V4
Supplementary files format and content: tab-delimited txt files includes the number of methylated reads and unmethylated reads for each cytosine.

extract_protocol:
Genomic DNA was extracted using the modified CTAB method, and the quality of DNA was examined by Nanodrop
Library construction was performed at Novogene


title: WGBS mop1-derived-BC1, individual 6

description: mop1-derived-BC1, individual 6


title: RNA-Seq Parent Mo17, wild type, rep1

description: Parent Mo17, wild type, rep1

data_processing:
The raw reads were quality controled by FastQC, and the low-quality reads and the adapter sequences were removed by Trimmomatic.
The cleaned reads of B73, WTF1, and mop1F1 were mapped to the B73 reference genome (v4), and the reads from Mo17 were mapped to the Mo17 genome that was generated by replacing the single nucleotide polymorphisms between Mo17 and B73 using Hisat2 allowing one mismatch.
HTSeq-count was used to calculate the total number of reads for each gene.
These values were loaded to DESeq2 to identify genes that were differentially expressed between WTF1 and parents, and between WTF1 and mop1F1.
Assembly: B73 V4
Supplementary files format and content: Tab-delimited txt file includes the ht-seq count of all genes for each sample.


title: WGBS mop1-derived-BC1, individual 5

description: mop1-derived-BC1, individual 5


title: genomic DNA from whole blood normal 9

description:
Sample was bisulfite-converted and hybridized to the array following the manufacturer's protocol
SAMPLE 102


title: RNA-Seq Parent Mo17, wild type, rep2

description: Parent Mo17, wild type, rep2


title: RNA-Seq Parent B73, wild type, rep2

description: Parent B73, wild type, rep2


title: Small RNA-Seq Parent Mo17, wild type, rep1

description: Parent Mo17, wild type, rep1


title: genomic DNA from whole blood normal 20

description:
Sample was bisulfite-converted and hybridized to the array following the manufacturer's protocol
SAMPLE 113


title: RNA-Seq Parent B73, wild type, rep1

description: Parent B73, wild type, rep1


title: genomic DNA from whole blood normal 11

description:
Sample was bisulfite-converted and hybridized to the array following the manufacturer's protocol
SAMPLE 104


title: genomic DNA from whole blood normal 8

description:
Sample was bisulfite-converted and hybridized to the array following the manufacturer's protocol
SAMPLE 101


title: WGBS mop1-derived-BC1, individual 4

description: mop1-derived-BC1, individual 4


title: WGBS mop1-derived-BC1, individual 1

description: mop1-derived-BC1, individual 1


title: WGBS mop1-derived-BC1, individual 2

description: mop1-derived-BC1, individual 2


title: genomic DNA from whole blood normal 3

description:
Sample was bisulfite-converted and hybridized to the array following the manufacturer's protocol
SAMPLE 96


title: genomic DNA from whole blood normal 5

description:
Sample was bisulfite-converted and hybridized to the array following the manufacturer's protocol
SAMPLE 98


title: genomic DNA from whole blood normal 4

description:
Sample was bisulfite-converted and hybridized to the array following the manufacturer's protocol
SAMPLE 97


title: WGBS Wild type BC1, individual 7

description: Wild type BC1, individual 7

value: Wild type BC1 (WTBC1)


title: WGBS mop1-derived-BC1, individual 3

description: mop1-derived-BC1, individual 3


title: WGBS Wild type BC1, individual 8

description: Wild type BC1, individual 8


title: genomic DNA from whole blood normal 6

description:
Sample was bisulfite-converted and hybridized to the array following the manufacturer's protocol
SAMPLE 99


title: genomic DNA from whole blood normal 15

description:
Sample was bisulfite-converted and hybridized to the array following the manufacturer's protocol
SAMPLE 108


title: WGBS mop1-derived-BC1, individual 8

description: mop1-derived-BC1, individual 8


title: genomic DNA from whole blood normal 10

description:
Sample was bisulfite-converted and hybridized to the array following the manufacturer's protocol
SAMPLE 103


title: genomic DNA from whole blood normal 2

description:
Sample was bisulfite-converted and hybridized to the array following the manufacturer's protocol
SAMPLE 95


title: WGBS Wild type BC1, individual 6

description: Wild type BC1, individual 6


title: genomic DNA from whole blood normal 1

description:
Sample was bisulfite-converted and hybridized to the array following the manufacturer's protocol
SAMPLE 94


title: WGBS Wild type BC1, individual 5

description: Wild type BC1, individual 5


title: genomic DNA from whole blood CKD 93

description:
Sample was bisulfite-converted and hybridized to the array following the manufacturer's protocol
SAMPLE 93

value: progression


title: WGBS Parent Mo17, wild type, rep2

description: Parent Mo17, wild type, rep2


title: genomic DNA from whole blood CKD 91

description:
Sample was bisulfite-converted and hybridized to the array following the manufacturer's protocol
SAMPLE 91


title: genomic DNA from whole blood CKD 92

description:
Sample was bisulfite-converted and hybridized to the array following the manufacturer's protocol
SAMPLE 92


title: WGBS Wild type BC1, individual 1

description: Wild type BC1, individual 1


title: genomic DNA from whole blood CKD 89

description:
Sample was bisulfite-converted and hybridized to the array following the manufacturer's protocol
SAMPLE 89


title: WGBS Wild type BC1, individual 4

description: Wild type BC1, individual 4


title: WGBS Parent B73, wild type, rep2

description: Parent B73, wild type, rep2


title: genomic DNA from whole blood normal 7

description:
Sample was bisulfite-converted and hybridized to the array following the manufacturer's protocol
SAMPLE 100


title: genomic DNA from whole blood CKD 90

description:
Sample was bisulfite-converted and hybridized to the array following the manufacturer's protocol
SAMPLE 90


title: WGBS Parent Mo17, wild type, rep1

description: Parent Mo17, wild type, rep1


title: WGBS Wild type BC1, individual 2

description: Wild type BC1, individual 2


title: genomic DNA from whole blood CKD 88

description:
Sample was bisulfite-converted and hybridized to the array following the manufacturer's protocol
SAMPLE 88


title: genomic DNA from whole blood CKD 87

description:
Sample was bisulfite-converted and hybridized to the array following the manufacturer's protocol
SAMPLE 87


title: genomic DNA from whole blood CKD 86

description:
Sample was bisulfite-converted and hybridized to the array following the manufacturer's protocol
SAMPLE 86


title: WGBS Parent B73, wild type, rep1

description: Parent B73, wild type, rep1


title: genomic DNA from whole blood CKD 84

description:
Sample was bisulfite-converted and hybridized to the array following the manufacturer's protocol
SAMPLE 84


title: genomic DNA from whole blood CKD 83

description:
Sample was bisulfite-converted and hybridized to the array following the manufacturer's protocol
SAMPLE 83


title: genomic DNA from whole blood CKD 85

description:
Sample was bisulfite-converted and hybridized to the array following the manufacturer's protocol
SAMPLE 85


title: S72-M, Control

city: Madison

last: Ortega

state: Wisconsin

address: 1675 Observatory Drive

department: Department of Animal and DairySciences

institute: University of Wisconsin

description: Individual embryo

data_processing:
The quality of fastq files of sequences data was checked with a FastQC tool
Illumina adapters were trimmed
Reads were mapped to the bovine reference genome using the Star
Read counts were determined using FeatureCounts program
Differentially expressed genes (DEGs) between sample groups were determined by edgeR-robust
Assembly: Bos_taurus.ARS-UCD1.2
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

organism: Bos taurus

source_name: preimplantation embryo

growth_protocol: in vitro embryo development

extract_protocol:
Qiagen  (RNAeasy micro kit)
TruSeq® mRNA Stranded Sample preparation kit

treatment_protocol: addition of recombinant Wnt5A

value: preimplantation embryo

value: Male

value: Control

tag: developmental stage

value: Blastocyst


title: S73-F, Control

description: Individual embryo

value: Female

value: Morula


title: S71-M, Control

description: Individual embryo


title: genomic DNA from whole blood CKD 82

description:
Sample was bisulfite-converted and hybridized to the array following the manufacturer's protocol
SAMPLE 82


title: S70-M, Control

description: Individual embryo


title: genomic DNA from whole blood CKD 81

description:
Sample was bisulfite-converted and hybridized to the array following the manufacturer's protocol
SAMPLE 81


title: WGBS Wild type BC1, individual 3

description: Wild type BC1, individual 3


title: S69-M, Control

description: Individual embryo


title: genomic DNA from whole blood CKD 80

description:
Sample was bisulfite-converted and hybridized to the array following the manufacturer's protocol
SAMPLE 80


title: genomic DNA from whole blood CKD 79

description:
Sample was bisulfite-converted and hybridized to the array following the manufacturer's protocol
SAMPLE 79


title: genomic DNA from whole blood CKD 78

description:
Sample was bisulfite-converted and hybridized to the array following the manufacturer's protocol
SAMPLE 78


title: genomic DNA from whole blood CKD 77

description:
Sample was bisulfite-converted and hybridized to the array following the manufacturer's protocol
SAMPLE 77


title: S67-M, Control

description: Individual embryo


title: S66-F, Control

description: Individual embryo


title: S62-F, Control

description: Individual embryo


title: S61-F, Control

description: Individual embryo


title: genomic DNA from whole blood CKD 74

description:
Sample was bisulfite-converted and hybridized to the array following the manufacturer's protocol
SAMPLE 74


title: S59-F, CSF2KO

description: Individual embryo


title: S58-F, CSF2KO

description: Individual embryo


title: genomic DNA from whole blood CKD 73

description:
Sample was bisulfite-converted and hybridized to the array following the manufacturer's protocol
SAMPLE 73


title: genomic DNA from whole blood CKD 75

description:
Sample was bisulfite-converted and hybridized to the array following the manufacturer's protocol
SAMPLE 75


title: S57-F, CSF2KO

description: Individual embryo


title: genomic DNA from whole blood CKD 72

description:
Sample was bisulfite-converted and hybridized to the array following the manufacturer's protocol
SAMPLE 72


title: S75-M, CSF2KO

description: Individual embryo


title: S52-F, Control

description: Individual embryo


title: genomic DNA from whole blood CKD 70

description:
Sample was bisulfite-converted and hybridized to the array following the manufacturer's protocol
SAMPLE 70


title: S50-M, CSF2KO

description: Individual embryo

value: male


title: genomic DNA from whole blood CKD 69

description:
Sample was bisulfite-converted and hybridized to the array following the manufacturer's protocol
SAMPLE 69


title: S51-M, Control

description: Individual embryo


title: S5-F, CSF2KO

description: Individual embryo


title: genomic DNA from whole blood CKD 68

description:
Sample was bisulfite-converted and hybridized to the array following the manufacturer's protocol
SAMPLE 68


title: S49-F, CSF2KO

description: Individual embryo


title: genomic DNA from whole blood CKD 67

description:
Sample was bisulfite-converted and hybridized to the array following the manufacturer's protocol
SAMPLE 67


title: genomic DNA from whole blood CKD 66

description:
Sample was bisulfite-converted and hybridized to the array following the manufacturer's protocol
SAMPLE 66


title: S46-F, Control

description: Individual embryo


title: S41-M, Control

description: Individual embryo


title: genomic DNA from whole blood CKD 76

description:
Sample was bisulfite-converted and hybridized to the array following the manufacturer's protocol
SAMPLE 76


title: genomic DNA from whole blood CKD 65

description:
Sample was bisulfite-converted and hybridized to the array following the manufacturer's protocol
SAMPLE 65


title: genomic DNA from whole blood CKD 63

description:
Sample was bisulfite-converted and hybridized to the array following the manufacturer's protocol
SAMPLE 63


title: genomic DNA from whole blood CKD 64

description:
Sample was bisulfite-converted and hybridized to the array following the manufacturer's protocol
SAMPLE 64


title: S4-F, CSF2KO

description: Individual embryo


title: S39-M, Control

description: Individual embryo


title: S54-M, Control

description: Individual embryo


title: S35-M, Control

description: Individual embryo


title: S36-M, Control

description: Individual embryo


title: genomic DNA from whole blood CKD 71

description:
Sample was bisulfite-converted and hybridized to the array following the manufacturer's protocol
SAMPLE 71


title: genomic DNA from whole blood CKD 60

description:
Sample was bisulfite-converted and hybridized to the array following the manufacturer's protocol
SAMPLE 60


title: S31-F, CSF2KO

description: Individual embryo


title: genomic DNA from whole blood CKD 56

description:
Sample was bisulfite-converted and hybridized to the array following the manufacturer's protocol
SAMPLE 56


title: S18-F, Control

description: Individual embryo


title: genomic DNA from whole blood CKD 58

description:
Sample was bisulfite-converted and hybridized to the array following the manufacturer's protocol
SAMPLE 58


title: S3-F, CSF2KO

description: Individual embryo


title: genomic DNA from whole blood CKD 55

description:
Sample was bisulfite-converted and hybridized to the array following the manufacturer's protocol
SAMPLE 55


title: genomic DNA from whole blood CKD 54

description:
Sample was bisulfite-converted and hybridized to the array following the manufacturer's protocol
SAMPLE 54


title: S11-F, Control

description: Individual embryo


title: genomic DNA from whole blood CKD 52

description:
Sample was bisulfite-converted and hybridized to the array following the manufacturer's protocol
SAMPLE 52


title: genomic DNA from whole blood CKD 53

description:
Sample was bisulfite-converted and hybridized to the array following the manufacturer's protocol
SAMPLE 53


title: chmods_w1118_16_18hrs_R3

city: Freiburg

first: Valérie

last: Hilgers

address: Stübeweg 51

country: Germany

institute: MPI of Immunobiology and Epigenetics

data_processing:
RNA-seq data were analyzed using the RNA-seq module from snakePipes (Bhardwaj et al., 2019) with default parameters for --trim , -m “alignment-free,alignment”.
Normalized abundance measures were obtained with DESeq2 for each relevant pairwise comparison (default settings)
Assembly: D. melanogaster Assembly: dm6_ensembl ; D. melanogaster Annotation: ensembl release 96
Supplementary files format and content: rawcounts.tsv files containing raw counts as created by featureCounts within the snakePipes pipeline
Supplementary files format and content: DESeq2 standard results output for all relevant comparisons

organism: Drosophila melanogaster

source_name: embryos

growth_protocol: Flies were grown in 25C on standard apple juice based food

extract_protocol: Eggs from mutant flies grown in heterozygosis with GFP-marked balancer chromosomes were collected for two hours on agar plates and aged for the appropriate amount of time at 25°C. Embryos were dechorionated following standard procedures and placed on a plate containing halocarbon oil. 20 to 30 mutant embryos were selected according to morphology and against GFP signal and homogenized prior to Trizol extraction.

treatment_protocol: untreated

value: embryo


title: S12-F, Control

description: Individual embryo


title: genomic DNA from whole blood CKD 62

description:
Sample was bisulfite-converted and hybridized to the array following the manufacturer's protocol
SAMPLE 62


title: S1-M, CSF2KO

description: Individual embryo


title: S37-M, Control

description: Individual embryo


title: genomic DNA from whole blood CKD 51

description:
Sample was bisulfite-converted and hybridized to the array following the manufacturer's protocol
SAMPLE 51


title: genomic DNA from whole blood CKD 59

description:
Sample was bisulfite-converted and hybridized to the array following the manufacturer's protocol
SAMPLE 59


title: genomic DNA from whole blood CKD 50

description:
Sample was bisulfite-converted and hybridized to the array following the manufacturer's protocol
SAMPLE 50


title: genomic DNA from whole blood CKD 61

description:
Sample was bisulfite-converted and hybridized to the array following the manufacturer's protocol
SAMPLE 61


title: genomic DNA from whole blood CKD 48

description:
Sample was bisulfite-converted and hybridized to the array following the manufacturer's protocol
SAMPLE 48


title: chmods_SppsG8810_16_18hrs_R3


title: S21-F, CSF2KO

description: Individual embryo


title: genomic DNA from whole blood CKD 57

description:
Sample was bisulfite-converted and hybridized to the array following the manufacturer's protocol
SAMPLE 57


title: chmods_w1118_16_18hrs_R2


title: S17-F, CSF2KO

description: Individual embryo


title: genomic DNA from whole blood CKD 46

description:
Sample was bisulfite-converted and hybridized to the array following the manufacturer's protocol
SAMPLE 46


title: genomic DNA from whole blood CKD 47

description:
Sample was bisulfite-converted and hybridized to the array following the manufacturer's protocol
SAMPLE 47


title: genomic DNA from whole blood CKD 45

description:
Sample was bisulfite-converted and hybridized to the array following the manufacturer's protocol
SAMPLE 45


title: chmods_psh27_16_18hrs_R3


title: chmods_SppsG8810_16_18hrs_R1


title: genomic DNA from whole blood CKD 44

description:
Sample was bisulfite-converted and hybridized to the array following the manufacturer's protocol
SAMPLE 44


title: chmods_psch27_16_18hrs_R2


title: chmods_psch27_16_18hrs_R1


title: genomic DNA from whole blood CKD 42

description:
Sample was bisulfite-converted and hybridized to the array following the manufacturer's protocol
SAMPLE 42


title: genomic DNA from whole blood CKD 43

description:
Sample was bisulfite-converted and hybridized to the array following the manufacturer's protocol
SAMPLE 43


title: genomic DNA from whole blood CKD 41

description:
Sample was bisulfite-converted and hybridized to the array following the manufacturer's protocol
SAMPLE 41


title: chmods_psce22_16_18hrs_R1


title: chmods_w1118_16_18hrs_R1


title: genomic DNA from whole blood CKD 39

description:
Sample was bisulfite-converted and hybridized to the array following the manufacturer's protocol
SAMPLE 39


title: chmods_ez731_16_18hrs_R3


title: genomic DNA from whole blood CKD 38

description:
Sample was bisulfite-converted and hybridized to the array following the manufacturer's protocol
SAMPLE 38


title: chmods_ez731_16_18hrs_R2


title: chmods_SppsG8810_16_18hrs_R2


title: genomic DNA from whole blood CKD 37

description:
Sample was bisulfite-converted and hybridized to the array following the manufacturer's protocol
SAMPLE 37


title: genomic DNA from whole blood CKD 40

description:
Sample was bisulfite-converted and hybridized to the array following the manufacturer's protocol
SAMPLE 40


title: chmods_ez731_16_18hrs_R1


title: genomic DNA from whole blood CKD 49

description:
Sample was bisulfite-converted and hybridized to the array following the manufacturer's protocol
SAMPLE 49


title: genomic DNA from whole blood CKD 35

description:
Sample was bisulfite-converted and hybridized to the array following the manufacturer's protocol
SAMPLE 35


title: chmods_Dfd1_16_18hrs_R2


title: chmods_Dfd1_16_18hrs_R1


title: genomic DNA from whole blood CKD 36

description:
Sample was bisulfite-converted and hybridized to the array following the manufacturer's protocol
SAMPLE 36


title: w1118_embryos_14_16hours_Rep3


title: genomic DNA from whole blood CKD 34

description:
Sample was bisulfite-converted and hybridized to the array following the manufacturer's protocol
SAMPLE 34


title: w1118_embryos_14_16hours_Rep4


title: genomic DNA from whole blood CKD 33

description:
Sample was bisulfite-converted and hybridized to the array following the manufacturer's protocol
SAMPLE 33


title: w1118_embryos_14_16hours_Rep1


title: genomic DNA from whole blood CKD 32

description:
Sample was bisulfite-converted and hybridized to the array following the manufacturer's protocol
SAMPLE 32


title: w1118_embryos_14_16hours_Rep2


title: genomic DNA from whole blood CKD 31

description:
Sample was bisulfite-converted and hybridized to the array following the manufacturer's protocol
SAMPLE 31


title: nejEP1179_embryos_14_16hours_Rep3


title: genomic DNA from whole blood CKD 30

description:
Sample was bisulfite-converted and hybridized to the array following the manufacturer's protocol
SAMPLE 30


title: chmods_psce22_16_18hrs_R2


title: genomic DNA from whole blood CKD 29

description:
Sample was bisulfite-converted and hybridized to the array following the manufacturer's protocol
SAMPLE 29


title: nejEP1179_embryos_14_16hours_Rep2


title: genomic DNA from whole blood CKD 28

description:
Sample was bisulfite-converted and hybridized to the array following the manufacturer's protocol
SAMPLE 28


title: nej3_embryos_14_16hours_Rep4


title: nej3_embryos_14_16hours_Rep3


title: nejEP1179_embryos_14_16hours_Rep1


title: nej3_embryos_14_16hours_Rep2


title: genomic DNA from whole blood CKD 25

description:
Sample was bisulfite-converted and hybridized to the array following the manufacturer's protocol
SAMPLE 25


title: ovaries_rep1

description: normalized gene counts table from Salmon

data_processing:
RNA-seq data were analyzed using the RNA-seq module from snakePipes (Bhardwaj et al., 2019) with default parameters for --trim , -m “alignment-free,alignment”.
Assembly: D. melanogaster Assembly: dm6_ensembl ; D. melanogaster Annotation: ensembl release 96
Supplementary files format and content: tsv file contains gene counts per sample obtained using Salmon output from snakePipes, scores represent transcript per million normalization

source_name: ovaries

extract_protocol:
For head transcriptomes, 3-day-old w1118 flies were collected and flash-frozen in liquid nitrogen and heads were used for RNA extraction. For ovary transcriptomes, 3 day old w1118 virgin females were collected and dissected using 20 ovaries per replicate.
RNA-seq illumina

value: ovaries

value: adults

value: wild type (w1118)


title: genomic DNA from whole blood CKD 26

description:
Sample was bisulfite-converted and hybridized to the array following the manufacturer's protocol
SAMPLE 26

value: whole blood


title: ovaries_rep2


title: nejEP1179_embryos_14_16hours_Rep4


title: genomic DNA from whole blood CKD 23

description:
Sample was bisulfite-converted and hybridized to the array following the manufacturer's protocol
SAMPLE 23


title: genomic DNA from whole blood CKD 24

description:
Sample was bisulfite-converted and hybridized to the array following the manufacturer's protocol
SAMPLE 24


title: nej3_embryos_14_16hours_Rep1


title: genomic DNA from whole blood CKD 27

description:
Sample was bisulfite-converted and hybridized to the array following the manufacturer's protocol
SAMPLE 27


title: genomic DNA from whole blood CKD 20

description:
Sample was bisulfite-converted and hybridized to the array following the manufacturer's protocol
SAMPLE 20


title: Small RNA-Seq mop1 mutant F1, rep2

description: mop1 mutant F1, rep2

value: B73/Mo17;mop1/mop1 (mop1F1)


title: heads_rep2

source_name: heads

value: heads


title: heads_rep1


title: Small RNA-Seq mop1 mutant F1, rep1

description: mop1 mutant F1, rep1

value: immature ear


title: genomic DNA from whole blood CKD 21

description:
Sample was bisulfite-converted and hybridized to the array following the manufacturer's protocol
SAMPLE 21


title: Small RNA-Seq Wild type F1, rep2

description: Wild type F1, rep2


title: genomic DNA from whole blood CKD 19

description:
Sample was bisulfite-converted and hybridized to the array following the manufacturer's protocol
SAMPLE 19


title: Wild-type mouse ES cells on tissue-culture plastic (serum/LIF), single-cell sequencing

city: Cambridge

first: Florian

last: Hollfelder

address: 80 tennis court road

institute: University of Cambridge

description:
Mouse ES cells were culture on tissue-culture plastic under serum/LIF conditions.
mES_wt_SLIF_TCP.csv

data_processing:
FastQC quality control
For single-cell, de-multiplexing using Pheniqs
For bulk RNA-seq experiments, alignment to the genome using the STAR aligner. For single-cell data, processing into gene expression matrices using zUMIs
For bulk RNA-seq experiments, quantification of events using featureCounts.
For bulk RNA-seq experiments, downstream processing using DESeq2. For single-cell experiments, downstream processing using Scanpy and scVelo.
Genome_build: For bulk RNA-seq experiments, mm10. For single-cell experiments GRCm38
Supplementary_files_format_and_content: For bulk RNA-seq experiments, the processed data files are normalized gene expression counts. For single-cell data, the processed data files are UMI counts for both introns and exons after pre-processing fwith the zUMIs pipeline

molecule: polyA RNA

source_name: tissue culture

growth_protocol: Tissue-culture plastic, cultured in serum/LIF

extract_protocol:
inDrop
inDrop

treatment_protocol: Washed twice with PBS

value: mouse embryonic stem cells

tag: agent

value: cultured in serum/LIF

tag: library strategy

value: inDrop


title: DKTKRO_128_HNSCC_tumor_HPV-negative

type: RNA

city: Munich

first: Kristian

last: Unger

address: Marchioninistr. 15

department: Department of radiation oncology

institute: LMU University Hospital

hyb_protocol: According to the manufacturer's protocol.

data_processing: Text files were imported into R using the AgiMicroRna Bioconductor package. After quality filtering using Agilent quality filters and removing non-human miRNAs from the data set scanned intensities were background corrected, quantile normalized. The resulting expressions were log2-transformed after averaging signals determining expression of the same miRNA.

source_name: head and neck tumor

growth_protocol: Formalin-fixed paraffin-embedded tumour specimens were derived from treatment-naive surgically resected tumour tissues. Haematoxylin-eosin-stained tissue sections were histopathologically reviewed by a pathologist (DKTK-ROG: KS; LMU-KKG: CW/AW), the tumour area was defined and micro-dissected whereby only samples with at least 60% tumour cells were included.

extract_protocol: Total RNA including the small RNA fraction was extracted using the Qiagen miRNeasy FFPE (DKTK-ROG) or the AllPrep DNA/RNA FFPE Kit (LMU-KKG) according to the manufacturer's protocols (Qiagen, Hilden, Germany).

treatment_protocol: not applicable

tag: hpv-status

value: negative


title: DKTKRO_126_HNSCC_tumor_HPV-positive

scan_protocol: According to the manufacturer's protocol.

value: positive


title: DKTKRO_125_HNSCC_tumor_HPV-positive

label_protocol: According to the manufacturer's protocol.


title: Small RNA-Seq Wild type F1, rep1

description: Wild type F1, rep1


title: DKTKRO_127_HNSCC_tumor_HPV-positive


title: DKTKRO_124_HNSCC_tumor_HPV-positive


title: genomic DNA from whole blood CKD 17

description:
Sample was bisulfite-converted and hybridized to the array following the manufacturer's protocol
SAMPLE 17

value: progression


title: genomic DNA from whole blood CKD 22

description:
Sample was bisulfite-converted and hybridized to the array following the manufacturer's protocol
SAMPLE 22


title: genomic DNA from whole blood CKD 18

description:
Sample was bisulfite-converted and hybridized to the array following the manufacturer's protocol
SAMPLE 18


title: RNA-Seq mop1 mutant F1, rep2

description: mop1 mutant F1, rep2


title: Wild-type mouse ES cells on tissue-culture plastic (2iLIF), single-cell sequencing

description:
Mouse ES cells were cultured on tissue-culture plastic in 2iLIF conditions.
mES_wt_2ILIF_TCP.csv

growth_protocol: Cultured in 2iLIF

value: cultured in 2iLIF


title: genomic DNA from whole blood CKD 16

description:
Sample was bisulfite-converted and hybridized to the array following the manufacturer's protocol
SAMPLE 16


description:
Mouse ES cells with low Jup overexpression were cultured on tissue-culture plastic in serum/LIF conditions.
mES_JUP_OELOW_SLIF_TCP.csv
mouse ES cells with low plakoglobin overexpression under constitutive expression via the CAG promoter. Culture on tissue-culture plastic under serum/LIF conditions, single-cell sequencing.

value: PGLOW


title: RNA-Seq Wild type F1, rep2

description: Wild type F1, rep2


title: RNA-Seq mop1 mutant F1, rep1

description: mop1 mutant F1, rep1


description:
Mouse ES cells with high Jup overexpression were cultured on tissue-culture plastic in serum/LIF conditions.
mES_JUP_OEHIGH_SLIF_TCP.csv
mouse ES cells with high plakoglobin overexpression under constitutive expression via the CAG promoter. Culture on tissue-culture plastic under serum/LIF conditions, single-cell sequencing.

value: PGHIGH


title: RNA-Seq Wild type F1, rep1

description: Wild type F1, rep1


title: Wild-type mouse ES cells in gels (serum/LIF), single-cell sequencing

description:
Mouse ES cells were encapsualted in agarose microgels and cultured in serum/LIF conditions.
mES_wt_SLIF_Gel.csv

growth_protocol: Agarose microgels embedding, cultured in serum/LIF


title: genomic DNA from whole blood CKD 15

description:
Sample was bisulfite-converted and hybridized to the array following the manufacturer's protocol
SAMPLE 15


title: DKTKRO_123_HNSCC_tumor_HPV-positive


title: genomic DNA from whole blood CKD 14

description:
Sample was bisulfite-converted and hybridized to the array following the manufacturer's protocol
SAMPLE 14


title: WGBS lbl1 mutant F1, rep2

description: lbl1 mutant F1, rep2

value: B73/Mo17;lbl1/lbl1 (lbl1F1)


title: genomic DNA from whole blood CKD 13

description:
Sample was bisulfite-converted and hybridized to the array following the manufacturer's protocol
SAMPLE 13


title: DKTKRO_121_HNSCC_tumor_HPV-positive


title: DKTKRO_122_HNSCC_tumor_HPV-positive


title: WGBS lbl1 mutant F1, rep1

description: lbl1 mutant F1, rep1


title: DKTKRO_120_HNSCC_tumor_HPV-positive


title: genomic DNA from whole blood CKD 12

description:
Sample was bisulfite-converted and hybridized to the array following the manufacturer's protocol
SAMPLE 12


title: WGBS B73/Mo17;+/+ (WTF1) Wild type F1, rep2

description: Wild type F1, rep2


title: WGBS B73/Mo17;+/+ (WTF1) Wild type F1, rep1

description: Wild type F1, rep1


title: genomic DNA from whole blood CKD 11

description:
Sample was bisulfite-converted and hybridized to the array following the manufacturer's protocol
SAMPLE 11


title: DKTKRO_119_HNSCC_tumor_HPV-negative


title: PFFs, pTK-642-1

city: nanning

first: Ren

last: xuan

address: xixiangtang street

institute: guangxi university

data_processing:
FastQC initially processed raw sequence reads for quality control, and then adapter sequences and poor quality reads were removed.
Quality filtered reads were then mapped to reference genome using BWA or Bowtie, and only uniquely mapped reads were kept, Sam files were converted to Bam format using Samtools and used for peak calling.
MACS2 was used to call peaks with the sonicated input as a control and an initial threshold q-value of 0.01 as cutoff.
Visualization of read count data was performed by converting raw bam files to bigwig files using IGV tools. BETA or ChIP seeker was used to analysis Expression data and Binding data.
pvalue<0.05
Assembly: Sscrofa11.1
Supplementary files format and content: bigWig, narrowPeak (except for Input sample)

organism: Sus scrofa

source_name: skin

extract_protocol:
Cells were collected and lysed to obtain purified nucleus; The Tn5 enzyme transposable reaction was carried out and the open regions of chromatin were fragmented;
the fragmented DNA was purified; the purified DNA was amplified. The amplified DNA was sized to remove non-target fragments.

value: skin

value: PFFs

value: Fibroblasts

value: WT

value: Serum starvation


title: PFFs, pTK-642-BRG1-4


title: PFFs, pTK-642-4


title: PFFs, pTK-642-BRG1-1


title: DKTKRO_118_HNSCC_tumor_HPV-positive


title: genomic DNA from whole blood CKD 10

description:
Sample was bisulfite-converted and hybridized to the array following the manufacturer's protocol
SAMPLE 10

value: whole blood


title: DKTKRO_117_HNSCC_tumor_HPV-positive


title: WGBS mop1 mutant F1, rep2

description: mop1 mutant F1, rep2

value: immature ear

value: B73/Mo17;mop1/mop1 (mop1F1)


title: genomic DNA from whole blood CKD 9

description:
Sample was bisulfite-converted and hybridized to the array following the manufacturer's protocol
SAMPLE 9


title: genomic DNA from whole blood CKD 8

description:
Sample was bisulfite-converted and hybridized to the array following the manufacturer's protocol
SAMPLE 8


title: Porcine fetal fibroblasts, pTK-642-BRG1-1

data_processing:
FastQC initially processed raw sequence reads for quality control, and then adapter sequences and poor quality reads were removed.
Quality filtered reads were then mapped to reference genome using STAR, and only uniquely mapped reads were kept.
Sam files were converted to Bam format using Samtools. Cufflinks softerware was used to computing gene expression level and difference.
R packages such as DEseq2, edgeR were futher used to perform data.
cutoff: pvalue<0.05 ，|log2FoldChange| > 1；
Assembly: Sscrofa11.1
Supplementary files format and content: files include FPKM values for each Sample

extract_protocol:
RNA was harvested using using trizol method.  1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using QIAGEN RNeasy Mini kit following manufacturer's protocols.


title: WGBS Mo17/B73/;+/+ (WTF1) Wild type F1, rep2

description: Wild type F1, rep2


title: DKTKRO_115_HNSCC_tumor_HPV-negative


title: WGBS mop1 mutant F1, rep1

description: mop1 mutant F1, rep1


title: genomic DNA from whole blood CKD 7

description:
Sample was bisulfite-converted and hybridized to the array following the manufacturer's protocol
SAMPLE 7


title: Porcine fetal fibroblasts, pTK-642-BRG1-2


title: Porcine fetal fibroblasts, pTK-642-1


title: Porcine fetal fibroblasts, pTK-642-2


title: genomic DNA from whole blood CKD 6

description:
Sample was bisulfite-converted and hybridized to the array following the manufacturer's protocol
SAMPLE 6


title: DKTKRO_114_HNSCC_tumor_HPV-positive


title: WGBS Mo17/B73/;+/+ (WTF1) Wild type F1, rep1

description: Wild type F1, rep1


title: A_CC_H3K27_IP_rep2

city: 天津市

first: Xinyue

last: Lei

state: 天津市

address: 天津市和平区气象台路22号天津医科大学

institute: 天津医科大学

data_processing:
Basecalls performed using CASAVA version 1.4
Data were filtered using Trimmomatic
ChIP-seq reads were aligned to the hg38 genome assembly using bowtie2-2.3.5
Determination of the normalized factor using deeptools
peaks were called using MACS2
Assembly: hg38
Supplementary files format and content: bigWig

source_name: A549 cells

growth_protocol: A549 cells  were maintained in 1640 supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37°

extract_protocol:
1 × 10^7 cells were washed with PBS and fixed with 37 °C pre-heated 10% FBS MEDIA/1% formaldehyde at room temperature for 10 min, and quenched with 0.125 M glycine (V900144, Sigma) for 5 min, and sonicated to generate chromatin fragments of 200-600bp. The sheared chromatin was immunoprecipated with a specific antibody.
Libraries were prepared according to Illumina's instructions accompanying the Paired-End DNA Samples Prep Kit. Briefly, DNA fragment end repair, add A base to 3'end, and connect sequencing adapter. PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq 2500 following the manufacturer's protocols.

value: A549 cells

value: lung cancer

value: CC

value: homozygous mutation

tag: chip antibody

value: H3K27ac (ab4729, Abcam)


title: DKTKRO_112_HNSCC_tumor_HPV-positive

value: positive


title: DKTKRO_113_HNSCC_tumor_HPV-positive


title: DKTKRO_116_HNSCC_tumor_HPV-negative

value: negative


title: genomic DNA from whole blood CKD 5

description:
Sample was bisulfite-converted and hybridized to the array following the manufacturer's protocol
SAMPLE 5

value: progression


title: genomic DNA from whole blood CKD 4

description:
Sample was bisulfite-converted and hybridized to the array following the manufacturer's protocol
SAMPLE 4


title: Zy2_S5

city: State College

first: Aswathy

last: Sebastian

institute: PennState

data_processing:
Data was trimmed using fastp
Trimmed data was mapped  to the reference genome using hisat2
Gene-level raw read counts were obtained using featureCounts
Differential expression was performed with DESeq2
Assembly: PlasmoDB-55_Pyoeliiyoelii17X_Genome
Supplementary files format and content: Tab delimited file with gene-level raw read counts for each sample

organism: Plasmodium yoelii

source_name: Zygote

growth_protocol: Plasmodium yoelii 17XNL parasites were grown in swiss webster mice, with ex vivo culture of zygotes.

extract_protocol:
RNA was purified by a Qiagen Rneasy kit with in-solution DNaseI digestion
Library preparation was via the Illumina stranded mRNA kit for 150nt single end reads.

treatment_protocol: Female gametocytes and zygotes were purified by flow cytometry

tag: strain

value: Zygote


title: Zy3_S6

tag: cell type


title: A_CC_H3K27_IP_rep1

address: 天津市和平区气象台路22号天津医科大学


title: Zy1_S4


title: genomic DNA from whole blood CKD 3

description:
Sample was bisulfite-converted and hybridized to the array following the manufacturer's protocol
SAMPLE 3

tag: ckd


title: A_CC_H3K27_input_rep1

address: 天津市和平区气象台路22号天津医科大学

tag: cell line


title: A_CC_H3K27_input_rep2

address: 天津市和平区气象台路22号天津医科大学


title: DKTKRO_111_HNSCC_tumor_HPV-positive


title: DKTKRO_109_HNSCC_tumor_HPV-positive


title: Fe1_S1

source_name: Female Gametocyte

value: Female Gametocyte

value: WT with pylap4 promoter driving GFP expression


title: A_TT_H3K27_IP_rep2

address: 天津市和平区气象台路22号天津医科大学

value: TT


title: genomic DNA from whole blood CKD 1

description:
Sample was bisulfite-converted and hybridized to the array following the manufacturer's protocol
SAMPLE 1


title: DKTKRO_110_HNSCC_tumor_HPV-positive


title: A_TT_H3K27_IP_rep1

address: 天津市和平区气象台路22号天津医科大学