title: splenic-derived macrophage, no extra-cytokine, 72h, rep4


title: CleftProband_251

status: Public on Dec 01 2022

type: genomic

city: Iowa City

first: J.

middle: Robert

last: Manak

state: Iowa

address: 455 Biology Building, 129 East Jefferson Street

department: Biology and Pediatrics

country: USA

institute: The University of Iowa

hyb_protocol: 34 ug of each labeled DNA was co-hybridized to a Roche NimbleGen human whole genome tiling microarray (Human CGH 2.1M Whole-Genome Tiling v2.0D Array)

scan_protocol: Arrays were scanned on a Roche NimbleGen microarray scanner.

data_processing:
532.tif and 635.tif files were analyzed using DEVA software to generate a data_summary.txt file and segMNT.txt file. Data_summary.txt files were analyzed using Nexus 7 Software to generate NexusData.bed files and then compared to the segMNT.txt file using BEDTOOLS 50% reciprocal overlap function. Only calls which shared a reciprocal overlap of 50% or greater were retained for further analysis.
BioDiscovery’s FASST2 Segmentation Algorithm, a Hidden Markov Model (HMM) based approach, was the algorithm used to make copy number calls using Nexus 7 Software. The significance threshold for segmentation was set at 1.0E-6 also requiring a minimum of 3 probes per segment and a maximum probe spacing of 1000 between adjacent probes before breaking a segment. The log ratio thresholds for single copy gain and single copy loss were set at 0.3 and -0.3, respectively. A 3:1 sex chromosome gain threshold was set to 1.2 and a 4:1 sex chromosome gain threshold was set to 1.7. NimbleGen's DEVA segMNT algorithm, which minimizes squared error relative to the segment means, was used as a second algorithm for all copy number calls after data extraction, LOESS spatial correction and background correction. Default parameters were used with the exception of setting the minimum segment difference to 0.3 and requiring a minimum of 3 probes per segment.

molecule: genomic DNA

organism: Homo sapiens

source_name: genomic DNA from whole blood

label_protocol: 1 ug of case DNA was labeled with Cy3-coupled nonamers and 1 ug of control DNA (from an unaffected male from the Philippines) was labeled with Cy5-coupled nonamers.

extract_protocol: DNA was extracted from whole blood samples using the Quickgene610L.

tag: Sex

value: male

tag: syndromic versus non-syndromic

value: non-syndromic

tag: cleft type

value: cleft palate only

tag: cleft laterality

value: not applicable

source_name: DNA from an unaffected male from the Philippines

value: unaffected


title: splenic-derived macrophage, no extra-cytokine, 72h, rep3

type: RNA

city: London

first: JONATHAN

last: CARON

state: Greater London

address: New Hunt's House, Newcomen St

department: Cancer Studies

country: United Kingdom

institute: KING'S COLLEGE LONDON

hyb_protocol: As recommended by the array manufacturer with the following exception: NuGEN recommended hybridization temperature of 48°C. Staining with Cy3-Streptavidin.

scan_protocol: Image BeadChip on the iScan System

data_processing: Raw fluorescence signals were collected using GenomeStudio (Illumina), and imported into Partek Genomics Suite (PGS) for further analysis. Background was subtracted from the raw data and fluorescence signals were normalized using the quantiles method.

label: biotin

molecule: total RNA

organism: Mus musculus

label_protocol: mRNA was converted to cDNA, amplified using the Ovation® PicoSL WTA system V2 (NuGEN), biotinylated using the Encore® BiotinIL Module (NuGEN)

growth_protocol: RPMI 10% FCS, penicillin/streptomycin, 50ng/ml M-CSF

extract_protocol: According to the manufacturers’ protocol, PureLink RNA Mini Kit

treatment_protocol: Miltenyi magnetic beads

tag: strain

value: Balb/c

tag: gender

value: Female

tag: disease state

value: 4T1 mouse model of breast cancer

tag: tissue

value: spleen from 4T1-bearing mouse

tag: cell type

value: in-vitro-polarized macrophage, M0

tag: treatment

value: no extra-cytokine


title: CleftProband_246

value: female

value: cleft lip and cleft palate

value: right


title: CleftProband_245

value: bilateral


title: CleftProband_244

value: left


title: splenic-derived macrophage, no extra-cytokine, 72h, rep1


title: CleftProband_243


title: F4/80+ TAMs isolated from enzyme-digested 4T1 tumors, rep2

description: 4T1 TAM 2

source_name: TAM

value: tumor from 4T1-bearing mouse

value: tumor-associated macrophage (TAM)


title: splenic-derived macrophage, IL6, 72h, rep1

source_name: splenic-derived macrophage, IL6, 72h

value: in-vitro-polarized macrophage, M6


title: CleftProband_250

value: male

value: non-syndromic


title: splenic-derived macrophage, IL6, 72h, rep3


title: splenic-derived macrophage, IL4, 72h, rep1

source_name: splenic-derived macrophage, IL4, 72h

value: in-vitro-polarized macrophage, M2


title: splenic-derived macrophage, IL6, 72h, rep2

value: Balb/c


title: splenic-derived macrophage, IL4, 72h, rep2

value: Female


title: splenic-derived macrophage, IL4, 72h, rep3

value: 4T1 mouse model of breast cancer


title: splenic-derived macrophage, LPS/IFNg, 72h, rep2

value: spleen from 4T1-bearing mouse

value: in-vitro-polarized macrophage, M1

value: LPS/IFNg


title: splenic-derived macrophage, IL6, 72h, rep4


title: splenic-derived macrophage, LPS/IFNg, 72h, rep4


title: CleftProband_241

value: unaffected


title: splenic-derived macrophage, LPS/IFNg, 72h, rep3


title: splenic-derived macrophage, IL4, 72h, rep4


title: CleftProband_238

value: cleft lip and cleft palate


title: CQ2A

type: SRA

city: Shenzhen

first: Yan

last: WANG

address: 1068 Xueyuan Ave

country: China

institute: Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences

library_source: transcriptomic

data_processing:
Raw sequencing reads (fastq) were quality checked using SOAPnuke (v1.5.2).
Bowtie2 (v2.2.5) was applied to align the clean reads to the genomes.
The expression level of gene was calculated by RSEM (v1.2.12).
Differential expression analysis was performed using DESeq2 (v1.4.5)
Genome_build: GCF_000409795.2_Chlorocebus_sabeus_1.1
Supplementary_files_format_and_content: excel

organism: Chlorocebus sabaeus

source_name: Vero E6 cell line

growth_protocol: Vero E6 cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% fetal bovine serum (FBS) and 1% penicillin–streptomycin.

extract_protocol:
RNAs were extracted from culture tissues. The samples were homogenized in Trizol (Invitrogen) and processed for RNA extraction according to the manufacturer’s instructions.
BGI in-house kit (BGI-Shenzhen, China)

treatment_protocol: Vero E6 cells were treated with or without antivirals at their EC50 values for 48 h and then collected for bulk RNA sequencing.

tag: cell line

value: Vero E6

value: kidney epithelial cells

value: Chloroquine 5 uM, 48 h


title: CQ3A


title: CQ1A


title: CleftProband_239

value: bilateral


title: splenic-derived macrophage, LPS/IFNg, 72h, rep1


title: HCQ2A

value: Hydroxychloroquine 5 uM, 48 h


title: CleftProband_236


title: HCQ1A


title: CleftProband_235


title: FAV3A

value: Favipiravir 65 uM, 48 h


title: CleftProband_242

value: female

value: left

value: male


title: HCQ3A


title: FAV2A


title: CleftProband_234

value: non-syndromic


title: CleftProband_233

value: syndromic

value: unknown


title: FAV1A


title: CleftProband_232


title: CleftProband_230

value: cleft lip only


title: CleftProband_231


title: GS1A


title: RDV3A

value: Remdesivir 1 uM, 48 h


title: CleftProband_228

value: right


title: RDV2A


title: RDV1A


title: CleftProband_226

value: unaffected


title: CleftProband_229

value: cleft lip and cleft palate


title: CleftProband_227


title: CleftProband_225

value: cleft palate only

value: not applicable


title: NC3A

value: Vero E6

value: kidney epithelial cells


title: NC1A


title: CleftProband_222


title: CleftProband_240

value: bilateral


title: CleftProband_221


title: CleftProband_223


title: Ribo-Seq H1299-R213X5FUR-4

city: Utrecht

first: Sebastiaan

last: van Heesch

address: Heidelberglaan 25

country: Netherlands

institute: Princess Maxima Center

description: cytoplasmic RNA

data_processing:
use cutadapt v3.4 to trim low-quality read segments and remove low-quality reads
map reads with bowtie2 v2.4.2 with a custom fasta containing mitochondrial, ribosomal, small nuclear, small nucleolar, and transfer RNA sequences to rermove them from the reads
STAR v2.7.8a with reference assembly ensembl 102 and the following parameters: --outFilterMismatchNmax 2; --outFilterMultimapNmax 20; --alignSJoverhangMin 1000
run riboseqc v1.1 to extract P sites and coverage tracks for downstream analyses with the following parameters: readlength_choice_method = "max_coverage" ; rescue_all_rls = FALSE ; fast_mode = FALSE
run featurecount with the following parameters: -t "CDS"  -g "gene_id" -O  -s 1
Genome_build: hg38
Supplementary_files_format_and_content: count files with raw gene counts for all data generated by FeatureCount

source_name: epithelial

growth_protocol: H1299 human lung adenocarcinoma parental cells (ATCC, USA), which are p53 null, were stably transfected with R213X nonsense mutant TP53, Empty Vector (EV) as a control, or other plasmid constructs as described (Zhang et al., Front Oncol 2018). Stably transfected cells were cultured in RPMI-1640 medium (Hyclone, USA) supplemented with 25 mM HEPES Buffer solution (Gibco, USA) and 10% fetal bovine serum (Gibco, USA).

extract_protocol:
RPFs were then extracted using 3V (660 µl) Trizol LS, followed by RNA purification using the Zymo Direct-zol RNA micro prep kit with modifications to the manufacturer's instructions: Columns were spun dry for 2 min at 12,000 g and isolated RPFs were eluted in 20 µl nuclease-free water.
Ribosome profiling was performed as described in (McGlincy and Ingolia, 2017; van Heesch et al., 2019), with several modifications. Snap-frozen cells were scraped off in 1 ml of ice-cold lysis buffer (20 mM Tris-Cl pH 7.4, 150 mM NaCl, 5 mM MgCl2, 1% Triton X-100, 0.1% IGEPAL CA-630, 1 mM DTT, 10 U/mL RNase-free DNase 1, 100 µg/mL cycloheximide) and transferred to Eppendorf tubes for lysis on ice for 10 min. Lysates were clarified through centrifugation at 20,000 g at 4°C for 10 min. Total RNA content of sample lysates was estimated using the Qubit™ RNA broad range (BR) Assay Kit on a Invitrogen™ Qubit™ 4 fluorometer. Lysates were then digested per 200 µl aliquots with RNAse I for generation of ribosome-protected fragments (RPFs), using 20 units of RNAse I per 20 µg of RNA measured in lysate. After 45 min of digestion at 23°C while shaking at 400 RPM on a thermomixer, the digestion reaction was stopped by adding 10 µl (10U) of SUPERase*In RNAse inhibitor and placing the samples on ice. Digested lysates were then transferred to Microspin S-400 HR sephacryl columns equilibrated with 3 ml of cold polysome buffer (20 mM Tris-Cl pH 7.4, 150 mM NaCl, 5 mM MgCl2) each and centrifuged at 600 g at room temperature for 2 min using an Eppendorf 5425 R microcentrifuge. 20 µl 10% SDS were then added to digested lysates and RPFs were then extracted using 3V (660 µl) Trizol LS, followed by RNA purification using the Zymo Direct-zol RNA micro prep kit with modifications to the manufacturer's instructions: Columns were spun dry for 2 min at 12,000 g and isolated RPFs were eluted in 20 µl nuclease-free water. rRNA was depleted using RiboPOOL technology with modifications to the manufacturer's instructions: 200 pmol of RiboPOOL and 100 µl of beads were used per sample. RNA was purified using the Zymo RNA Clean and Concentrator-5 kit with modifications to the manufacturer's instructions as mentioned above. Purified RNA was then size-selected through denaturing PAGE using 15% TBE-Urea gels. RNA fragments corresponding to 26-34 nucleotides were excised and recovered from gel slices by rocking at 37°C at 700 RPM on a thermomixer. RNA solutions were transferred to Costar Spin-X filter tubes and filtered through centrifugation at 5000 RPM for 6 min using an Eppendorf 5425 R microcentrifuge. 2 µl of GlycoBlue and 700 µl of isopropanol were then added per aliquot and RNA was left to precipitate overnight at -80°C. Following precipitation, RNA fragments were pelleted by centrifugation at 21,000 g at 4°C for 45 min. Pellets were washed once with 800 µl of ice-cold ethanol and centrifuged at 21,000 g at 4°C for 15 min. RNA pellets were then air-dried for 3-4 min and dissolved in 60.75 µl nuclease-free water on ice. RNA fragments were dephosphorylated using 30 U of T4 PNK for 1 h at 37°C and purified using Zymo RNA Clean and Concentrator-5 kit, where isolated RNA fragments were eluted in 9.5 µl nuclease-free water. Purified fragments were then ligated to a pre-adenylated 3’oligonucleotide linker using 100 U of T4 RNA ligase 2 Deletion Mutant and 5 U T4 RNA ligase 1 at 23°C for 3 h. Leftover linker was removed using 5’Deadenylase and Rec J Exonuclease. Linker-ligated RNA fragments were reverse-transcribed into cDNA using EpiScript reverse transcriptase. cDNA was treated with Exonuclease I for 30 min at 37°C, followed by 15 min at 80°C with a reduction to 4°C: and further treated with 5 U of RNAse I and 2.5 U of Hybridase Thermostable RNase H at 55°C for 5 min followed by an incubation step at 4°C to stop the reaction. Treated cDNA was purified using the Zymo Oligo Clean and Concentrator Kit with modifications to the manufacturer's instructions: Columns were spun dry for 2 min at 12,000 g and isolated RPFs were eluted in 9.5 µl nuclease-free water. cDNA containing ligated linkers was size-selected through denaturing PAGE using 10% TBE-Urea gels. cDNA fragments corresponding to 70-80 nucleotides were excised and precipitated with ammonium acetate and SDS followed by overnight precipitation with isopropanol as described above. Size-selected cDNA was circularised for 3 h at 60°C using 100 U of circLigase I followed by heat inactivation for 10 min at 80°C and amplified using Phusion high-fidelity polymerase (New England Biolabs) with reverse primers containing unique barcode sequences for 10 cycles of: 30 sec at 98°C, 15 sec at 94°C, 5 sec at 55°C, 10 sec at 65°C. Following amplification, 5 µl of 3 M NaCl, 1 ml of ethanol and 2 µl of GlycoBlue were added per aliquot cDNA left to precipitate overnight at -80°C. Amplified cDNA libraries were size-selected using 7% non-denaturing TBE-Urea gels. cDNA libraries corresponding to 150 nucleotides were excised and recovered from gel slices by rocking at 37°C at 700 RPM on a thermomixer. cDNA solutions were then transferred to Costar Spin-X filter tubes and filtered through centrifugation at 5000RPM for 6 min using an Eppendorf 5425 R microcentrifuge. cDNA libraries were purified using the Zymo DNA Clean and Concentrator-5 kit with modifications to the manufacturer's instructions: Columns were spun dry for 2 min at 12,000 g and isolated RPFs were eluted in 13 µl nuclease-free water. cDNA libraries were quantified using Qubit™ DNA high sensitivity (HS) Assay Kit according to the manufacturer's instructions on an Invitrogen™ Qubit™ 4 fluorometer and Bioanalyzer 2100 using the High Sensitivity DNA kit and pooled in equimolar ratios. Sequencing was performed on a NextSeq2000 following standard Illumina protocols.

treatment_protocol: Cells were seeded at a density of 0.3 x 106 cells/15 cm dish for non-treated and G418-treated conditions or at a density of 2.3 x 106 cells/15 cm dish for FUr-treated condition in a final volume of 32 ml. One day after seeding the cells, they were treated with 100 µM of G418 or 3 µM of 5-Fluorouridine for 72h, respectively, using four replicate treatments per condition. Next, medium was aspirated, cells were washed once with 5 ml of ice-cold Dulbecco’s Phosphate Buffered Saline (DPBS), and plates were snap frozen with liquid nitrogen.

tag: vector

value: FUr


title: Ribo-Seq H1299-R213X5FUR-5

description: cytoplasmic RNA


title: NC2A


title: CleftProband_220


title: CleftProband_219


title: GS3A


title: Ribo-Seq H1299-R213X5FUR-2

description: cytoplasmic RNA


title: Ribo-Seq H1299-R213XG418-5

description: cytoplasmic RNA


title: GS2A


title: CleftProband_218


title: Ribo-Seq H1299-R213X5FUR-1

description: cytoplasmic RNA


title: Ribo-Seq H1299-R213XG418-3

description: cytoplasmic RNA


title: CleftProband_217


title: CleftProband_237


title: Ribo-Seq H1299-R213XG418-2

description: cytoplasmic RNA


title: Ribo-Seq H1299-R213XG418-1

description: cytoplasmic RNA


title: CleftProband_215


title: CleftProband_214

value: female


title: Ribo-Seq H1299-R213X-3

description: cytoplasmic RNA

value: untreated


title: Ribo-Seq H1299-R213X-5

description: cytoplasmic RNA


title: Ribo-Seq H1299-R213X-2

description: cytoplasmic RNA


title: CleftProband_213

value: male


title: CleftProband_216

value: non-syndromic


title: Ribo-Seq H1299-R213X-1

description: cytoplasmic RNA


title: CleftProband_211


title: CleftProband_210


title: CleftProband_224

value: left


title: Ribo-Seq H1299-EV5FUR-3

description: cytoplasmic RNA

value: EV


title: Ribo-Seq H1299-EV5FUR-4

description: cytoplasmic RNA


title: CleftProband_212

value: cleft lip only


title: Ribo-Seq H1299-EV5FUR-1

description: cytoplasmic RNA


title: Ribo-Seq H1299-EV5FUR-2

description: cytoplasmic RNA


title: CleftProband_208


title: CleftProband_206


title: Ribo-Seq H1299-EVG418-5

description: cytoplasmic RNA


title: CleftProband_205


title: Ribo-Seq H1299-EVG418-4

description: cytoplasmic RNA


title: CleftProband_204


title: Ribo-Seq H1299-EVG418-1

description: cytoplasmic RNA


title: CleftProband_203


title: Ribo-Seq H1299-EV-5

description: cytoplasmic RNA


title: Ribo-Seq H1299-EVG418-2

description: cytoplasmic RNA


title: Ribo-Seq H1299-EV-4

description: cytoplasmic RNA


title: CleftProband_201


title: CleftProband_199


title: CleftProband_200


title: CleftProband_202


title: CleftProband_198


title: Ribo-Seq H1299-EV-1

description: cytoplasmic RNA


title: iNeuron_TDGKD_day30_RNAseq_rep3

city: Shanghai

first: Wei

last: Wu

state: Shanghai

address: 320 yueyang road

department: Center for Excellence in Molecular Cell Science

description: iNeuron-TDGKD-timeCouse-RNA-seq.count.txt

data_processing:
SAR-seq, END-seq and SEAL reads were aligned to the reference genome (hg19 for human i3Neuron and mm10 for mouse macrophage cells using bowtie (v1.1.2) with parameters -n 3 -l 50 -k 1 for END-seq and -n 2 -l 50 -m 1 for the rest. RNA-seq reads were aligned by STAR (v2.7.6a). PB-seq was mapped by BSMAP (v2.90) with parameters -p 10 -w 2 -v 0 -q 30. Functions “view” and “sort” of samtools (v1.11) were used to convert and sort the aligned sam files to sorted bam files. Bam files were further converted to bed files by the bedtools (v2.29.2) bamToBed command. Mitochondrial reads were removed in SAR-seq for intensity comparisons.
For RNA-seq, fragments per kilobase of Read per million mapped reads (RPKM) was calculated by cufflinks based on the annotation from GENCODE v33 for iNeuron. And count was used for iMacrophage using GENCODEvM24.
Assembly: hg19 for human, mm10 for mouse.

molecule: polyA RNA

source_name: iNeuron

growth_protocol: For neuronal differentiation, 20–25 million iPSCs were plated on day 0 onto a 15-cm plate in N2 medium (knockout Dulbecco’s modified Eagle’s medium (DMEM)/F12 medium; Life Technologies Corporation, cat. no. 12660012) with N2 supplement (Life Technologies, cat. no. 17502048), 1× GlutaMAX (Thermofisher Scientific, cat. no. 35050061), 1× MEM nonessential amino acids (NEAA) (Thermofisher Scientific, cat. no. 11140050), 10 μM ROCK inhibitor (Y-27632; Selleckchem, cat. no. S1049), and 2 μg/ml doxycycline (Clontech, cat. no. 631311). N2 medium was changed once a day for two more days. On day 3, cells were replated onto freshly prepared dishes coated with freshly prepared poly-L-ornithine (PLO; 0.1 mg/ml; Sigma, cat. no. P3655-10MG). Pre-neuron cells were cultured in i3Neuron Culture Media: BrainPhys media (Stemcell Technologies, cat. no. 05790) supplemented with 1× B27 Plus Supplement (ThermoFisher Scientific, cat. no. A3582801), 10 ng ml−1 BDNF (PeproTech, cat. no. 450-02), 10 ng ml−1 NT-3 (PeproTech, cat. no. 450-03), 1 μg ml−1 mouse laminin (Sigma, cat. no. L2020-1MG), and 2 μg ml−1 doxycycline (Clontech, cat. no. 631311). i3Neurons were then fed by half media change on day 6 and then, collected on day 7. For iMacrophage transdifferentiation, 10 million C10 cells were induced to reprogram by the addition of 100 nM of β-estradiol (Sigma-Aldrich; Cat. #E8875) and grown with 10 ng/ml of IL-3 (Peprotech; Cat. #213-13), CSF-1 (Peprotech; Cat. #315-02) and 350 nM Ascorbic acid (Sigma-Aldrich; Cat. # A8960) and then collected on day 1, day 2 and day3.

extract_protocol: To extract RNA, cells were plated on 6-well dishes, washed with PBS, and then 500 L of tri-reagent (Zymo research corporation, Cat. No. R2050-1-200) was added directly to the cells. The lysed cells were collected using a cell scraper. To isolate RNA, we used a Direct-zol RNA miniprep kit (Zymo Research Corporation, Cat. No. R2052), following manufacturer’s instructions including the optional DNAse step.For RNA sequencing, two biological replicates were sequenced. Total RNA was enriched for polyA and sequenced 2x75 bp on a NextSeq550 machine.

tag: harvested day

tag: genotype

value: TDG KD


title: Ribo-Seq H1299-EV-3

description: cytoplasmic RNA


title: CleftProband_197


title: CleftProband_209


title: iNeuron_TDGKD_day30_RNAseq_rep1

institute: Center for Excellence in Molecular Cell Science


title: CleftProband_196


title: CleftProband_207

value: syndromic


title: iNeuron_WT_day30_RNAseq_rep2

value: WT


title: CleftProband_195

value: cleft lip and cleft palate

value: unaffected


title: CleftProband_194


title: CleftProband_192


title: iNeuron_TDGKD_day17_RNAseq_rep5


title: iNeuron_TDGKD_day17_RNAseq_rep6


title: CleftProband_189

value: right


title: iNeuron_TDGKD_day17_RNAseq_rep4


title: CleftProband_191


title: iNeuron_TDGKD_day17_RNAseq_rep3


title: CleftProband_188


title: CleftProband_190


title: iNeuron_TDGKD_day17_RNAseq_rep1


title: iNeuron_TDGKD_day30_RNAseq_rep2


title: iNeuron_WT_day17_RNAseq_rep6


title: iNeuron_TDGKD_day17_RNAseq_rep2


title: iNeuron_WT_day17_RNAseq_rep5


title: CleftProband_185


title: iNeuron_WT_day17_RNAseq_rep4


title: iNeuron_WT_day30_RNAseq_rep3


title: CleftProband_193


title: CleftProband_187


title: CleftProband_184

value: unknown


title: iNeuron_WT_day17_RNAseq_rep3


title: iNeuron_WT_day30_RNAseq_rep1


title: CleftProband_186


title: iNeuron_WT_day17_RNAseq_rep2


title: CleftProband_182


title: CleftProband_183


title: CleftProband_181


title: iNeuron_WT_day17_RNAseq_rep1


title: iNeuron_TDGKD_day7_RNAseq_rep3


title: CleftProband_180


title: iNeuron_TDGKD_day7_RNAseq_rep2


title: CleftProband_178


title: CleftProband_179


title: iNeuron_WT_day7_RNAseq_rep3


title: iNeuron_WT_day7_RNAseq_rep2


title: iNeuron_TDGKD_day7_RNAseq_rep1


title: CleftProband_177


title: CleftProband_175


title: iPSC_TDGKD_day7_RNAseq_rep3

source_name: iPSC


title: iNeuron_WT_day7_RNAseq_rep1


title: CleftProband_176


title: iPSC_TDGKD_day7_RNAseq_rep2


title: CleftProband_174


title: CleftProband_173


title: CleftProband_171


title: CleftProband_172


title: iPSC_WT_day7_RNAseq_rep3


title: CleftProband_170


title: CleftProband_169


title: iPSC_TDGKD_day7_RNAseq_rep1


title: iPSC_WT_day7_RNAseq_rep1


title: Human_Tonsil_naive_IgK_1

city: Boston

first: Frederick

middle: W

last: Alt

state: MA

address: 1 Blackfan Circle

department: Program in Cellular and Molecular Medicine

institute: Boston Children's Hospital

description: HTGTS-Rep-Seq

library_source: genomic

data_processing:
HTGTS-rep-seq and LAM-HTGTS-Rep-SHM-Seq data analysis was done by the LAM-HTGTS-Rep-SHM-Seq bioinformatics pipeline (Github address: https://github.com/Yyx2626/HTGTSrep), using IgBLAST with default parameters for qualified reads mapping. Only reads with more than 98% of the sequences having a sequencing Quality Score ≥20 were kept; only joined reads (R1 and R2 had an overlap region ≥10 bp and mismatch rate ≤8%) were kept.
Assembly: mm9
Supplementary files format and content: .db.txt files were generated using LAM-HTGTS-Rep-SHM-Seq pipeline (IgBLAST).

source_name: Tonsil

extract_protocol:
Splenic B cells used for HTGTS-rep-seq were purified from unimmunized 5-8 weeks old mice by MACS® Microbeads according to the manufacturer’s protocol. In brief, spleens were dissected out from unimmunized mice, prepared into single cell suspensions and stained with anti-B220 Microbeads for 20 minutes at 4°C. The splenic B cells were collected using the LS column and MACSTM Separater. GC B cells used for LAM-HTGTS-Rep-SHM-Seq were purified from 8-12 weeks old mice after eOD-GT8 60mer immunization. GC B cells were sorted for the phenotype B220+ (BV711: BioLegend 103255), CD95+ (PE-Cy7: eBioscience 557653) and GL7+ (PE: BioLegend 144607). Genomic DNA from sorted cells was prepared using a DNeasy Blood and Tissue Kit (Qiagen) according to the manufacturer’s protocol.
The libraries of LAM-HTGTS-Rep-SHM-Seq was constructed as previous described (Chen et al., 2020) and the libraries of HTGTS-Rep-seq was constructed as previous described (Lin et al., PNAS 2016)

value: Tonsil IgD+CD38- B cells

value: Human

value: Tonsil

tag: locus (ig heavy-chain or light-chain)

value: IgK

tag: conditions

value: naïve

tag: primers


title: Human_Tonsil_naive_IgK_2

description: HTGTS-Rep-Seq


title: CleftProband_167

tag: Sex

value: male


title: Human_Tonsil_naive_IgK_3

description: HTGTS-Rep-Seq


title: CleftProband_168

tag: syndromic versus non-syndromic

value: non-syndromic

value: bilateral


title: CleftProband_166

tag: cleft type


title: iNeuron_AraA_RNA-seq

data_processing:
SAR-seq, END-seq and SEAL reads were aligned to the reference genome (hg19 for human i3Neuron and mm10 for mouse macrophage cells using bowtie (v1.1.2) with parameters -n 3 -l 50 -k 1 for END-seq and -n 2 -l 50 -m 1 for the rest. RNA-seq reads were aligned by STAR (v2.7.6a). PB-seq was mapped by BSMAP (v2.90) with parameters -p 10 -w 2 -v 0 -q 30. Functions “view” and “sort” of samtools (v1.11) were used to convert and sort the aligned sam files to sorted bam files. Bam files were further converted to bed files by the bedtools (v2.29.2) bamToBed command. Mitochondrial reads were removed in SAR-seq for intensity comparisons.
For RNA-seq, fragments per kilobase of Read per million mapped reads (RPKM) was calculated by cufflinks based on the annotation from GENCODE v33 for iNeuron. And count was used for iMacrophage using GENCODEvM24.
Assembly: hg19 for human, mm10 for mourse.

value: AraA, 18 hours prior to cell harvesting

tag: dose

value: 40 µM


title: iNeuron_AraC_RNA-seq

value: AraC, 18 hours prior to cell harvesting

value: 20 µM


title: CleftProband_165

value: cleft lip only

tag: cleft laterality


title: CleftProband_164

value: syndromic

value: cleft lip and cleft palate


title: iNeuron_ddC_RNA-seq

value: WT

value: ddC, 18 hours prior to cell harvesting


title: iNeuron_NT_RNA-seq

value: NT


title: CleftProband_162

value: unaffected


title: CleftProband_161


title: iNeuron_POLBKD_ddC_S1ENDseq

data_processing:
SAR-seq, END-seq and SEAL reads were aligned to the reference genome (hg19 for human i3Neuron and mm10 for mouse macrophage cells using bowtie (v1.1.2) with parameters -n 3 -l 50 -k 1 for END-seq and -n 2 -l 50 -m 1 for the rest. RNA-seq reads were aligned by STAR (v2.7.6a). PB-seq was mapped by BSMAP (v2.90) with parameters -p 10 -w 2 -v 0 -q 30. Functions “view” and “sort” of samtools (v1.11) were used to convert and sort the aligned sam files to sorted bam files. Bam files were further converted to bed files by the bedtools (v2.29.2) bamToBed command. Mitochondrial reads were removed in SAR-seq for intensity comparisons.
bigwig files were made for positive (*.pos.bw) and negativ (*.neg.bw) strand separately using Bedtools genomecov function followed by UCSC toolkit function bedGraphToBigWig
Assembly: hg19 for human, mm10 for mourse.
Library strategy: END-seq

growth_protocol: For neuronal differentiation, 20–25 million iPSCs were plated on day 0 onto a 15-cm plate in N2 medium (knockout Dulbecco’s modified Eagle’s medium (DMEM)/F12 medium; Life Technologies Corporation, cat. no. 12660012) with N2 supplement (Life Technologies, cat. no. 17502048), 1× GlutaMAX (Thermofisher Scientific, cat. no. 35050061), 1× MEM nonessential amino acids (NEAA) (Thermofisher Scientific, cat. no. 11140050), 10 μM ROCK inhibitor (Y-27632; Selleckchem, cat. no. S1049), and 2 μg/ml doxycycline (Clontech, cat. no. 631311). N2 medium was changed once a day for two more days. On day 3, cells were replated onto freshly prepared dishes coated with freshly prepared poly-L-ornithine (PLO; 0.1 mg/ml; Sigma, cat. no. P3655-10MG). Pre-neuron cells were cultured in i3Neuron Culture Media: BrainPhys media (Stemcell Technologies, cat. no. 05790) supplemented with 1× B27 Plus Supplement (ThermoFisher Scientific, cat. no. A3582801), 10 ng ml−1 BDNF (PeproTech, cat. no. 450-02), 10 ng ml−1 NT-3 (PeproTech, cat. no. 450-03), 1 μg ml−1 mouse laminin (Sigma, cat. no. L2020-1MG), and 2 μg ml−1 doxycycline (Clontech, cat. no. 631311). i3Neurons were then fed by half media change on day 6 and then, collected on day 7. For the pre-B-to-macrophage transdifferentiation, C10 cells were induced to reprogram by the addition of 100 nM of β-estradiol (Sigma-Aldrich; Cat. #E8875) and grown with 10 ng/ml of IL-3 (Peprotech; Cat. #213-13), CSF-1 (Peprotech; Cat. #315-02) and 350 nM Ascorbic acid (Sigma-Aldrich; Cat. # A8960) and then collected on day 2.

extract_protocol:
For END-seq, live cells were harvested and embedded into agarose plugs (Bio-Rad cat#1703591). Cells were lysed in agarose using proteinase K, follwed by Rnase treatment. DNA was later precipitated after plug melting and shearing. For S1-END-seq, cells were collected and embedded in 1% agarose plugs, lysed and digested with Proteinase K (1 hour at 50°C, followed by 7 hours at 37°C), washed with TE buffer, and then treated with RNAse A for 1 hour at 37°C. Plugs were then washed in EB and equilibrated in S1 nuclease buffer (40 mM sodium acetate pH 5.2, 300 mM NaCl, 2 mM ZnSO4) for 30 minutes. 1.8 U of S1 nuclease was added to 100 µL of S1 nuclease buffer per plug and incubated on ice for 15 minutes to allow for the enzyme to diffuse into the plug. The reaction mix was then placed at 37°C for 20 minutes before addition of EDTA (10 mM final concentration) to terminate the reaction. Finally, plugs were processed through the standard END-seq protocol
Libraries were quantified using with the KAPA Library Quantification Kit (Kapa Biosciences) and sequenced in a NextSeq 550 system (Illumina, 75 bp single end reads).

treatment_protocol: In the indicated experiments cells were treated with the following compounds: For iMacrophages, Aphidicolin (APH; 4 μM) 4 hours before EdU incubation; PARPi (Olaparib; 5 μM) and ddC (20 µM) were added 20 hours prior to harvest. For chain-terminating nucleosides, 20 µM of each of ddA, ddT, ddG and ddC was added to cells for 18 hours prior to cell harvesting for END-seq and S1-END-seq.

value: POLB knockdown

tag: in-situ treatment

value: 1.8 U of S1 nuclease @15 mins on ice, followed by 37°C for 20 mins.


title: CleftProband_160

value: left


title: CleftProband_159

value: male

value: right


title: iPSC_WT_day7_RNAseq_rep2


title: iNeuron_ddC_paired_withddATG_S1ENDseq


title: CleftProband_157

value: non-syndromic

value: bilateral


title: CleftProband_156

value: cleft palate only

value: not applicable


title: iNeuron_ddT_S1ENDseq

value: ddT, 18 hours prior to cell harvesting

value: 40 µM


title: CleftProband_155

value: cleft lip only


title: CleftProband_153

value: cleft lip and cleft palate


title: iNeuron_ddA_S1ENDseq

value: WT

value: ddA, 18 hours prior to cell harvesting


title: CleftProband_152


title: CleftProband_163


title: CleftProband_150


title: iNeuron_NT_pairedwithAraA_S1ENDseq

value: NT


title: iNeuron_ddC_pairedwithAraA_S1ENDseq

value: ddC, 18 hours prior to cell harvesting


title: CleftProband_149

value: unaffected


title: CleftProband_148


title: CleftProband_147


title: iNeuron_AraA_S1ENDseq

value: AraA, 18 hours prior to cell harvesting

value: 1.8 U of S1 nuclease @15 mins on ice, followed by 37°C for 20 mins.


title: iNeuron_ddG_S1ENDseq

value: ddG, 18 hours prior to cell harvesting


title: CleftProband_158

value: male

value: syndromic

value: right


title: PTZ+ Oxaprozin rep04

city: New Delhi

first: Manoj

middle: Ramesh

last: Teltumbade

state: Delhi

address: Mathura Road, Near Sukhdev Vihar, bus depo

country: India

institute: Institute of Genomics and Integrative Biology

description: Gene expression data using Affymetrix Drosophila Genome 2.0 array

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G.

data_processing: The data was analysed using R/Bioconductor affy and limma packages. Quantile Normalization and RMA background correction was used.

organism: Drosophila melanogaster

source_name: adult head, 7 days of treatment

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 250 ng total RNA (GeneChip 3’ IVT Express Kit).

growth_protocol: 30 adult unmated males Oregon R flies per vial fed respective diet for 7 days at 25C temperature.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions (RNeasy Microarray Tissue Handbook) .

treatment_protocol: At the end of treatment, flies were anesthetized using CO2 and collected in Trizol.

value: head

tag: diet fed

value: PTZ+ Oxaprozin

value: Oregon R

tag: gender

tag: age

value: 10 days

tag: Stage

value: adult


title: PTZ+ Oxaprozin rep03

tag: tissue


title: CleftProband_146

value: non-syndromic

value: cleft lip and cleft palate

value: bilateral


title: PTZ+ Quinapril Hydrochloride rep04

value: PTZ+ Quinapril Hydrochloride


title: PTZ+ Oxaprozin rep02


title: iNeuron_AraC_S1ENDseq

value: WT

tag: treatment

value: AraC, 18 hours prior to cell harvesting

value: 20 µM


title: CleftProband_145

value: left

value: unaffected


title: CleftProband_154

value: male


title: PTZ+ Quinapril Hydrochloride rep02


title: CleftProband_143

value: syndromic

value: cleft palate only

value: not applicable


title: CleftProband_151

value: cleft lip only

value: right


title: iNeuron_ddC_S1ENDseq

value: ddC, 18 hours prior to cell harvesting

value: 40 µM

value: 1.8 U of S1 nuclease @15 mins on ice, followed by 37°C for 20 mins.

tag: harvested day


title: PTZ+ Oxaprozin rep01

value: head

value: PTZ+ Oxaprozin

tag: genotype

value: Oregon R

value: 10 days

value: adult


title: PTZ+ Quinapril Hydrochloride rep03

value: PTZ+ Quinapril Hydrochloride


title: CleftProband_142

value: non-syndromic

value: cleft lip and cleft palate

value: bilateral


title: iNeuron_ddC_ENDseq

value: WT


title: PTZ+ Olmesartan Medoxonil rep04

value: PTZ+ Olmesartan Medoxonil

value: male


title: CleftProband_141

value: unaffected


title: CleftProband_140

value: right


title: CleftProband_139


title: CleftProband_138

value: left


title: CleftProband_137


title: iNeuron_ENDseq

value: NT


title: CleftProband_136


title: CleftProband_144

value: cleft lip only


title: CleftProband_134


title: iNeuron_sgTDG_ddC_S1ENDseq_rep2

value: TDG CRISPRi

value: ddC, 18 hours prior to cell harvesting

value: 40 µM

value: 1.8 U of S1 nuclease @15 mins on ice, followed by 37°C for 20 mins.


title: PTZ+ Olmesartan Medoxonil rep03

value: head

value: Oregon R

value: 10 days

value: adult


title: iNeuron_WT_controlfor_sgTDG_ddC_S1ENDseq_rep2


title: PTZ+ Olmesartan Medoxonil rep02


title: PTZ+ Quinapril Hydrochloride rep01

value: PTZ+ Quinapril Hydrochloride


title: CleftProband_133

value: non-syndromic

value: cleft lip and cleft palate

value: bilateral


title: CleftProband_131

value: male

value: unaffected


title: CleftProband_130

value: left


title: iNeuron_TDGdegron_dTAG_ddC_S1ENDseq_rep2

value: TDGdegron

value: dTAG and ddC, 18 hours prior to cell harvesting

value: dTAG 0.5 µM; ddC 40 µM


title: iNeuron_S1ENDseq

value: WT

value: NT


title: PTZ+ Mannitol rep04

value: PTZ+ Mannitol


title: CleftProband_128


title: iNeuron_sgTDG_ddC_S1ENDseq

value: TDG CRISPRi

value: ddC, 18 hours prior to cell harvesting

value: 40 µM

value: 1.8 U of S1 nuclease @15 mins on ice, followed by 37°C for 20 mins.


title: CleftProband_127

value: cleft lip only

value: right


title: CleftProband_135

value: non-syndromic

value: cleft lip and cleft palate


title: CleftProband_126

value: male

value: syndromic

value: bilateral


title: PTZ+ Glucosamine Hydrochloride rep04

value: head

value: PTZ+ Glucosamine Hydrochloride

value: Oregon R

value: 10 days

value: adult


title: PTZ+ Mannitol rep01

value: PTZ+ Mannitol


title: PTZ+ Mannitol rep02


title: iNeuron_WT_controlfor_sgTDG_ddC_S1ENDseq

value: WT


title: PTZ+ Olmesartan Medoxonil rep01

value: PTZ+ Olmesartan Medoxonil


title: CleftProband_123

value: unaffected


title: CleftProband_124


title: iNeuron_TDGdegron_NT_ddC_S1ENDseq

value: TDGdegron

value: ddC, 18 hours prior to cell harvesting

value: 40 µM

value: 1.8 U of S1 nuclease @15 mins on ice, followed by 37°C for 20 mins.


title: PTZ+ Glucosamine Hydrochloride rep03


title: CleftProband_132

value: non-syndromic

value: cleft lip only

value: left


title: iNeuron_TDGdegron_dTAG_ddC_S1ENDseq

value: dTAG and ddC, 18 hours prior to cell harvesting

value: dTAG 0.5 µM; ddC 40 µM


title: CleftProband_121

value: male

value: bilateral


title: CleftProband_129

value: cleft lip and cleft palate


title: PTZ+ Mannitol rep03

value: head

value: Oregon R

value: 10 days

value: adult


title: CleftProband_122

value: syndromic

value: Microform

value: unaffected


title: iNeuron_TDGdegron_NT_ddC_S1ENDseq_rep2

value: TDGdegron

value: ddC, 18 hours prior to cell harvesting

value: 40 µM


title: PTZ+ Glucosamine Hydrochloride rep02

value: PTZ+ Glucosamine Hydrochloride


title: CleftProband_120

value: non-syndromic

value: cleft lip only

value: left


title: iNeuron_ddC_SAR-seq

description: EdU incorporated DNA

data_processing:
SAR-seq, END-seq and SEAL reads were aligned to the reference genome (hg19 for human i3Neuron and mm10 for mouse macrophage cells using bowtie (v1.1.2) with parameters -n 3 -l 50 -k 1 for END-seq and -n 2 -l 50 -m 1 for the rest. RNA-seq reads were aligned by STAR (v2.7.6a). PB-seq was mapped by BSMAP (v2.90) with parameters -p 10 -w 2 -v 0 -q 30. Functions “view” and “sort” of samtools (v1.11) were used to convert and sort the aligned sam files to sorted bam files. Bam files were further converted to bed files by the bedtools (v2.29.2) bamToBed command. Mitochondrial reads were removed in SAR-seq for intensity comparisons.
BedGraph files were generated by bedtools genomecov, normalized by reads per million (RPM) and then converted to bigWig files using bedGraphToBigWig from UCSC pre-compiled utilities for visualization at UCSC genome browser
Assembly: hg19 for human, mm10 for mourse.
Library strategy: SAR-seq

growth_protocol: For neuronal differentiation, 20–25 million iPSCs were plated on day 0 onto a 15-cm plate in N2 medium (knockout Dulbecco’s modified Eagle’s medium (DMEM)/F12 medium; Life Technologies Corporation, cat. no. 12660012) with N2 supplement (Life Technologies, cat. no. 17502048), 1× GlutaMAX (Thermofisher Scientific, cat. no. 35050061), 1× MEM nonessential amino acids (NEAA) (Thermofisher Scientific, cat. no. 11140050), 10 μM ROCK inhibitor (Y-27632; Selleckchem, cat. no. S1049), and 2 μg/ml doxycycline (Clontech, cat. no. 631311). N2 medium was changed once a day for two more days. On day 3, cells were replated onto freshly prepared dishes coated with freshly prepared poly-L-ornithine (PLO; 0.1 mg/ml; Sigma, cat. no. P3655-10MG). Pre-neuron cells were cultured in i3Neuron Culture Media: BrainPhys media (Stemcell Technologies, cat. no. 05790) supplemented with 1× B27 Plus Supplement (ThermoFisher Scientific, cat. no. A3582801), 10 ng ml−1 BDNF (PeproTech, cat. no. 450-02), 10 ng ml−1 NT-3 (PeproTech, cat. no. 450-03), 1 μg ml−1 mouse laminin (Sigma, cat. no. L2020-1MG), and 2 μg ml−1 doxycycline (Clontech, cat. no. 631311). i3Neurons were then fed by half media change on day 6 and then, collected on day 7. For the iMacrophage transdifferentiation, 10 million C10 cells were induced to reprogram by the addition of 100 nM of β-estradiol (Sigma-Aldrich; Cat. #E8875) and grown with 10 ng/ml of IL-3 (Peprotech; Cat. #213-13), CSF-1 (Peprotech; Cat. #315-02) and 350 nM Ascorbic acid (Sigma-Aldrich; Cat. # A8960) and then collected on day 2.

extract_protocol:
15 million i3Neuron or iMacrophages were incubated with 20 μM EdU for 18 hr. For i3Neurons, cells were harvested and washed with PBS and incubated with accutase for 5-10 minutes. Cells were then collected using a cell scrapper (Corning), pelleted at 200xg for 5 minutes and resuspended in cold 0.1% BSA in PBS. For iMacrophages, cells were washed, trypsinized and resuspended in cold 0.1% BSA in PBS. Cold methanol was then added dropwise into all samples during slow vortexing to 80% final concentration. Samples were stored at -20C until processed.
Cells were permeabilized on ice for 10 min and resuspended in 1 mL of Click-iT reaction solution for 2 hrs shaking at room temperature. Cells were then lysed with Proteinase K overnight at 37C. DNA was extracted with UltraPure Phenol:Chloroform:Isoamyl Alcohol (25:24:1, v/v) (Invitrogen) according to manufacturer’s instructions. DNA was sonicated to 150-200 bp fragments using a Covaris S220 sonicator. Biotin-EdU labeled DNA fragments were pulled down using MyOne Streptavidin C1 Beads (ThermoFisher #650-01) and incubated at 24C shaking in a ThermoMixer C at 800 rpm for 30 min. Dynabeads were washed 3x in W&B (10 mM Tris-HCl pH 7.5, 1 mM EDTA, 1 M NaCl, 0.1% Tween (freshly added)), 2x in EB (10 mM Tris-HCl pH 8.0), and 1x T4 DNA Ligase Buffer (NEB). Dynabeads were resuspended in end-repair reaction and incubated at 24C shaking at 800 rpm for 30 min. Dynabeads were washed 1x in 1X W&B, 2x EB, and 1x NEBuffer 2 (NEB) and resuspended in A-tailing reaction mix (NEB), followed by incubation at 37C shaking at 800 rpm for 30 min. Dynabeads were washed 1x in NEBuffer 2 and resuspended in ligation reaction mix (NEB), 5 nM annealed TruSeq truncated adapter and incubated at 25C shaking at 600 rpm for 20 min. Ligation reaction was stopped by adding 50 mM EDTA, and Dynabeads were washed 3x in 1X W&B, 3x EB. PCR amplified for 16 cycles with Kapa HiFI HotStart Ready Mix using TruSeq index adapters. PCR products were separated from DynaBeads and cleaned using AMPure Beads XP. library concentrations were calculated by KAPA Library Quantification Kit for Illumina Platforms (Kapa Biosystems) and sequenced on Illumina NextSeq 550 (75 bp single read).   In the indicated experiments C/EBPα-induced macrophages were treated with the following compounds: Aphidicolin (APH; 4 μM) 4 hours before EdU incubation. PARPi (Olaparib; 5 μM) and ddC, ddA, ddG or ddT (40 µM) were added 20 hours prior to harvest. For i3Neurons, 40 µM of ddA, ddT, ddG or ddC chain-terminating nucleosides, 40 µM Ara-A and 20 µM Ara-C were added to cells for 18 hours prior to cell harvesting for SAR-seq experiments. 40 µM Gemcitabine was added to cells 2 hours prior to cell harvesting for SAR-seq experiments.

treatment_protocol: Neurons and iMacrophage cells were incubated with 20 uM EdU for 18 hours, unless otherwise noted.

value: WT


title: CleftProband_119

value: male

value: right


title: CleftProband_118


title: CleftProband_117

value: cleft lip and cleft palate


title: CleftProband_125


title: PTZ+ Glucosamine Hydrochloride rep01

value: head

value: Oregon R


title: Quinapril Hydrochloride rep04

value: Quinapril Hydrochloride

value: 10 days

value: adult


title: iNeuron_ddA_SAR-seq

description: EdU incorporated DNA

value: ddA, 18 hours prior to cell harvesting


title: CleftProband_116

value: bilateral

value: unaffected


title: CleftProband_114


title: CleftProband_115


title: iNeuron_NTfor_ddA_ddC_SAR-seq

description: EdU incorporated DNA

value: NT


title: Quinapril Hydrochloride rep03


title: CleftProband_113

value: syndromic


title: CleftProband_112

value: non-syndromic


title: iNeuron_NTforAraC_AraA_SAR-seq

description: EdU incorporated DNA


title: CleftProband_111


title: CleftProband_110

value: cleft lip only


title: CleftProband_108

value: left


title: CleftProband_109


title: CleftProband_107


title: iNeuron_AraA_SAR-seq

description: EdU incorporated DNA

value: WT

value: AraA, 18 hours prior to cell harvesting

value: 40 µM


title: iNeuron_AraC_SAR-seq

description: EdU incorporated DNA

value: AraC, 18 hours prior to cell harvesting

value: 20 µM


title: Quinapril Hydrochloride rep02

value: head

value: Oregon R

value: male


title: iNeuron_d7_NTforAraC_gemcitabine_SAR-seq_rep2

description: EdU incorporated DNA


title: CleftProband_105

value: cleft lip and cleft palate

value: right


title: Quinapril Hydrochloride rep01

value: Quinapril Hydrochloride

value: 10 days

value: adult


title: iNeuron_d7_NTforAraC_gemcitabine_SAR-seq_rep1

description: EdU incorporated DNA

value: NT


title: CleftProband_103

value: non-syndromic

value: unaffected


title: Gemfibrozil rep03

value: Gemfibrozil


title: Gemfibrozil rep04


title: CleftProband_104

value: left


title: Gemfibrozil rep01


title: CleftProband_102

value: syndromic

value: cleft lip only


title: Gemfibrozil rep02


title: iNeuron_d7_AraC_SAR-seq_rep1

description: EdU incorporated DNA

value: WT

value: AraC,  18 hours prior to cell harvesting


title: CleftProband_101


title: CleftProband_100


title: Moxifloxacin Hydrochloride rep02

value: head

value: Moxifloxacin Hydrochloride


title: iNeuron_d7_Gemcitabine_SAR-seq_rep2

description: EdU incorporated DNA

value: Gemcitabine, 2 hours prior to cell harvesting

value: 40 µM


title: Moxifloxacin Hydrochloride rep01

value: Oregon R

value: male


title: CleftProband_99

value: cleft lip and cleft palate


title: CleftProband_98


title: CleftProband_96


title: iNeuron_d7_AraC_SAR-seq_rep2

description: EdU incorporated DNA

value: 20 µM


title: CleftProband_106

value: right


title: CleftProband_97

value: non-syndromic


title: AT2 SARS-CoV2 infection replicate r4 Input control

city: Philadelphia

first: Karl

middle: Michael

last: Glastad

state: PA

address: 3400 Civic Center Blvd, Bldg 421

department: CDB

institute: University of Pennsylvania

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then aligned to hg38 whole genome using bowtie2, followed by peak calling using MACS2
MACS2 was used for calling peaks for each replicate and hPTM indivdually
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited bed files of per-replicate individual peak calls for hPTMs

extract_protocol:
Following infection, cells were fixed in 4% PFA for 30 minutes, followed by freezing, lysis, sonication, and ChIP agains the hPTMs H3K27ac, H3K27me3, H3K9ac, H3K9me3
ChIP-seq libraries were prepared for sequencing using standard Illumina protocols

tag: cell line

value: lung avleolar type 2 cells

value: SARS-CoV2 infection


title: CleftProband_95

value: left

value: unaffected


title: CleftProband_94

value: cleft lip only


title: CleftProband_93


title: Olmesartan Medoxonil rep03

value: Olmesartan Medoxonil

value: 10 days

value: adult


title: AT2 Mock infection replicate r4 Input control

value: Mock infection


title: CM SARS-CoV2 infection replicate r3 Input control

value: induced cardiomyocytes


title: CleftProband_92


title: CM Mock infection replicate r3 Input control


title: CleftProband_91

value: bilateral


title: Olmesartan Medoxonil rep02

value: head

value: Oregon R


title: CleftProband_90

value: female

value: syndromic

value: cleft lip and cleft palate

value: male


title: CleftProband_89

value: non-syndromic


title: Olmesartan Medoxonil rep01


title: CleftProband_87


title: iNeuron_d7_Gemcitabine_SAR-seq_rep1

description: EdU incorporated DNA

value: WT

value: Gemcitabine, 2 hours prior to cell harvesting

value: 40 µM


title: CleftProband_85

value: left

value: unaffected


title: Olmesartan Medoxonil rep04

value: Olmesartan Medoxonil

value: 10 days


title: AT2 Mock infection replicate r3 Input control

value: lung avleolar type 2 cells

value: Mock infection


title: AT2 SARS-CoV2 infection replicate r3 Input control

value: SARS-CoV2 infection


title: Mannitol rep03

value: head

value: Mannitol

value: adult


title: Mannitol rep02

value: Oregon R


title: Mannitol rep04


title: CleftProband_84

value: cleft lip and cleft palate


title: CleftProband_82

value: male

value: bilateral


title: CM SARS-CoV2 infection replicate r2 Input control

value: induced cardiomyocytes


title: CleftProband_83

value: non-syndromic


title: CM Mock infection replicate r2 Input control


title: CleftProband_81


title: CleftProband_79

value: cleft lip only


title: CleftProband_88

value: right


title: Mannitol rep01


title: AT2 SARS-CoV2 infection replicate r2 Input control


title: CleftProband_80

value: unaffected


title: AT2 Mock infection replicate r2 Input control


title: CleftProband_77


title: CleftProband_86


title: CleftProband_76


title: CleftProband_75


title: AT2 SARS-CoV2 infection replicate r1 Input control


title: Glucosamine Hydrochloride rep01

value: Glucosamine Hydrochloride


title: Glucosamine Hydrochloride rep03

value: 10 days


title: Glucosamine Hydrochloride rep02


title: Glucosamine Hydrochloride rep04


title: CleftProband_74


title: CleftProband_73


title: AT2 Mock infection replicate r1 Input control

value: lung avleolar type 2 cells


title: CleftProband_72


title: CleftProband_71

value: left


title: CM SARS-CoV2 infection replicate r3 ChIP of K9m3

value: SARS-CoV2 infection


title: CleftProband_70


title: CleftProband_69


title: CM Mock infection replicate r3 ChIP of K9m3

value: Mock infection


title: CleftProband_78


title: AT2 SARS-CoV2 infection replicate r4 ChIP of K9m3


title: CleftProband_67

value: syndromic


title: PTZ+Levetiracetam rep04

value: head

value: PTZ+Levetiracetam

value: adult


title: CleftProband_68

value: male

value: cleft lip and cleft palate


title: PTZ+Levetiracetam rep01

value: Oregon R


title: PTZ+Levetiracetam rep02


title: AT2 SARS-CoV2 infection replicate r3 ChIP of K9m3


title: CleftProband_65

value: non-syndromic


title: CleftProband_66

value: bilateral


title: Levetiracetam rep04

value: Levetiracetam


title: CleftProband_63

value: cleft lip only

value: unaffected


title: AT2 SARS-CoV2 infection replicate r2 ChIP of K9m3


title: CleftProband_64


title: CleftProband_62


title: CleftProband_60


title: CleftProband_61

value: right


title: AT2 Mock infection replicate r4 ChIP of K9m3

value: lung avleolar type 2 cells


title: AT2 Mock infection replicate r3 ChIP of K9m3


title: PTZ+Levetiracetam rep03

value: 10 days


title: CleftProband_59


title: Levetiracetam rep03


title: Levetiracetam rep01


title: AT2 Mock infection replicate r2 ChIP of K9m3


title: Levetiracetam rep02


title: CleftProband_56

value: left


title: CleftProband_57


title: CleftProband_55


title: CleftProband_53


title: CM SARS-CoV2 infection replicate r3 ChIP of K9ac

value: induced cardiomyocytes

value: SARS-CoV2 infection


title: CleftProband_54


title: CleftProband_52


title: Pentylenetetrazole rep03

value: head

value: Pentylenetetrazole


title: CM SARS-CoV2 infection replicate r2 ChIP of K9ac


title: CM Mock infection replicate r3 ChIP of K9ac

value: Mock infection


title: Pentylenetetrazole rep02

value: male

value: adult


title: Pentylenetetrazole rep04

value: Oregon R


title: CleftProband_51

value: syndromic

value: cleft lip and cleft palate


title: CleftProband_50

value: non-syndromic

value: bilateral


title: CM Mock infection replicate r2 ChIP of K9ac


title: CleftProband_48

value: unaffected


title: CleftProband_46


title: CleftProband_47


title: CleftProband_49


title: Pentylenetetrazole rep01


title: CleftProband_58


title: CleftProband_45


title: Biological replicate 2 of vibrio with mucin glycans

city: Palo Alto

first: Benjamin

last: Wang

state: CA

address: 299 Campus Drive

institute: Stanford

data_processing:
BWA was applied to map the reads to the V. cholerae type strain, using unique mapping reads. Any read that overlapped with any region of a gene was counted as a read. We then employed DEseq analysis to identify significant changes in gene expression between cells grown in the presence and absence of mucin glycans.
Assembly: Vibrio_cholerae_o1_biovar_el_tor_str_l_3226 (type strain)
Supplementary files format and content: The processed data is after DEseq2 analysis of the raw reads, to identify changes in gene expression +/- mucin glycans through relative transcript abundance
Supplementary files format and content: This processed data is a table of raw counts under each condition/replicate

organism: Vibrio cholerae

source_name: bacterial cell

extract_protocol:
We pelleted 50 μL of cells grown with or without mucin glycans at 12,000g in a tabletop centrifuge for 2 min. Cells were generally grown in AKI media under anaerobic conditions unless otherwise indicated. We resuspended cell pellets in 300 μL of 2x Tissue and Cell Lysis Buffer (Lucigen) with 2 μL of proteinase K. Samples were incubated at 65 °C to aid in cell lysis. Next, 175 μL of MPC Protein Precipitation Reagent (Lucigen) was added to the samples, which were spun for 10 min at the maximum speed in a tabletop centrifuge to precipitate out proteins. The supernatant was then mixed with 500 μL of isopropanol and spun down for 15 min at the maximum speed. The resulting pellet of RNA was washed twice with 70% ethanol and centrifuged for 15 min at the maximum speed following each wash. The RNA was then air-dried for 5 min and dissolved in 50 μL of nuclease-free water. To remove contaminating DNA from the RNA preparation, we incubated each sample with 5 μL of Ambion RNA Turbo Buffer and 2 μL of Turbo DNAse (Thermo Fisher) for 30 min at 37 °C. Next, we added 5 μL of Ambion reaction inactivator to each sample to remove DNAse. Samples were spun at the maximum speed for 2 min, and then supernatant containing purified RNA was collected and stored at -20 °C until use.
We depleted the purified RNA of ribosomal RNA using the Illumina RiboZero depletion kit. Depleted RNA was submitted to the MIT BioMicro Center for strand-specific library preparation.

tag: strain

tag: cell type

value: bacterial cell

value: 0.1% w/v mucin glycans


title: CleftProband_44

tag: Sex


title: AT2 SARS-CoV2 infection replicate r4 ChIP of K9ac

value: lung avleolar type 2 cells


title: AT2 SARS-CoV2 infection replicate r3 ChIP of K9ac


title: CleftProband_43

tag: syndromic versus non-syndromic

value: cleft lip only

value: right


title: AT2 SARS-CoV2 infection replicate r2 ChIP of K9ac

value: SARS-CoV2 infection


title: normal food rep04

value: head

value: Normal food

value: 10 days


title: normal food rep03

value: male


title: normal food rep01

value: adult


title: normal food rep02

value: Oregon R


title: Biological replicate 1 of vibrio with mucin glycans


title: CleftProband_42

tag: cleft type


title: CleftProband_39


title: Biological replicate 2 of vibrio with no glycans

value: no glycans


title: CleftProband_38

value: cleft lip and cleft palate

value: unknown


title: CleftProband_40

value: non-syndromic

value: left


title: Biological replicate 1 of vibrio with no glycans

value: bacterial cell


title: AT2 Mock infection replicate r4 ChIP of K9ac

value: Mock infection


title: AT2 SARS-CoV2 infection replicate r1 ChIP of K9ac

value: lung avleolar type 2 cells


title: AT2 Mock infection replicate r3 ChIP of K9ac


title: CleftProband_37

value: unaffected


title: CleftProband_36

value: cleft lip only


title: AT2 Mock infection replicate r2 ChIP of K9ac


title: CleftProband_35


title: CleftProband_34

value: right


title: WT-3mm-LT replicate 2

first: Jin

last: Shi

address: 800 Dongchuan Rd

department: Life Science and technology Department

institute: Shanghai Jiaotong University

description: WT-3mm-LT replicate 2

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using trimmomatic software
Trimmed sequence reads were mapped to reference genome IRGSP-1.0 using HISAT2
Read count extraction and normalization were performed using HTSeq
Assembly: IRGSP-1.0
Supplementary files format and content: tab-delimited text files include count values for each Sample

organism: Oryza sativa

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen).
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: inflorescence

value: wild type

value: Low temperature

tag: time

value: 3mm inflorescence 2


title: AT2 Mock infection replicate r1 ChIP of K9ac


title: CleftProband_33

value: male

tag: cleft laterality


title: CleftProband_32

value: bilateral


title: CM SARS-CoV2 infection replicate r3 ChIP of K27m3

value: induced cardiomyocytes

value: SARS-CoV2 infection


title: WT-2mm-LT replicate 3

description: WT-2mm-LT replicate 3

value: 2mm inflorescence 3


title: CleftProband_29

value: non-syndromic


title: CM SARS-CoV2 infection replicate r2 ChIP of K27m3


title: CleftProband_31

value: cleft lip and cleft palate

value: left


title: WT-2mm-LT replicate 2

description: WT-2mm-LT replicate 2

value: 2mm inflorescence 2


title: CleftProband_41

value: syndromic


title: WT-3mm-LT replicate 1

description: WT-3mm-LT replicate 1

value: 3mm inflorescence 1


title: CleftProband_28

value: cleft lip only

value: unaffected


title: CleftProband_30


title: CM Mock infection replicate r3 ChIP of K27m3

value: Mock infection


title: CleftProband_27


title: CM Mock infection replicate r2 ChIP of K27m3


title: WT-2mm-LT replicate 1

description: WT-2mm-LT replicate 1

value: inflorescence

value: wild type

value: 2mm inflorescence 1


title: ild-3mm-LT replicate 3

description: ild-3mm-LT replicate 3

value: tap mutant

value: Low temperature

value: 3mm inflorescence 3


title: AT2 SARS-CoV2 infection replicate r4 ChIP of K27m3

value: lung avleolar type 2 cells

value: SARS-CoV2 infection


title: WT-3mm-LT replicate 3

description: WT-3mm-LT replicate 3


title: ild-3mm-LT replicate 2

description: ild-3mm-LT replicate 2

value: 3mm inflorescence 2


title: AT2 SARS-CoV2 infection replicate r3 ChIP of K27m3


title: CleftProband_21

value: male

value: non-syndromic

value: cleft palate only

value: not applicable


title: ild-3mm-LT replicate 1

description: ild-3mm-LT replicate 1

value: 3mm inflorescence 1


title: CleftProband_26

value: cleft lip only

value: left


title: CleftProband_20

value: syndromic

value: cleft lip and cleft palate

value: unaffected


title: AT2 SARS-CoV2 infection replicate r2 ChIP of K27m3


title: CleftProband_18

value: right


title: CleftProband_17


title: AT2 SARS-CoV2 infection replicate r1 ChIP of K27m3


title: ild-2mm-LT replicate 3

description: ild-2mm-LT replicate 3

value: inflorescence

value: tap mutant

value: 2mm inflorescence 3


title: CleftProband_16


title: CleftProband_19


title: CleftProband_15


title: CleftProband_25

value: bilateral


title: ild-2mm-LT replicate 2

description: ild-2mm-LT replicate 2

value: Low temperature

value: 2mm inflorescence 2


title: AT2 Mock infection replicate r3 ChIP of K27m3

value: lung avleolar type 2 cells

value: Mock infection


title: ild-2mm-LT replicate 1

description: ild-2mm-LT replicate 1

value: 2mm inflorescence 1


title: CleftProband_13

value: male

value: non-syndromic


title: CleftProband_14

value: cleft lip only


title: AT2 Mock infection replicate r2 ChIP of K27m3


title: AT2 Mock infection replicate r4 ChIP of K27m3


title: CleftProband_24


title: WT-3mm-HT replicate 3

description: WT-3mm-HT replicate 3

value: wild type

value: High temperature

value: 3mm inflorescence 3


title: CleftProband_12

value: cleft lip and cleft palate

value: unaffected


title: CleftProband_23

value: right


title: CleftProband_22

value: left


title: WT-3mm-HT replicate 2

description: WT-3mm-HT replicate 2

value: inflorescence

value: 3mm inflorescence 2


title: CleftProband_10

value: bilateral


title: AT2 Mock infection replicate r1 ChIP of K27m3


title: CleftProband_8


title: WT-3mm-HT replicate 1

description: WT-3mm-HT replicate 1

value: 3mm inflorescence 1


title: CleftProband_9


title: CM SARS-CoV2 infection replicate r3 ChIP of K27ac

value: induced cardiomyocytes

value: SARS-CoV2 infection


title: CleftProband_7


title: WT-2mm-HT replicate 3

description: WT-2mm-HT replicate 3

value: 2mm inflorescence 3


title: CleftProband_6

value: male


title: CleftProband_4

value: non-syndromic


title: CM Mock infection replicate r3 ChIP of K27ac

value: Mock infection


title: WT-2mm-HT replicate 2

description: WT-2mm-HT replicate 2

value: wild type

value: 2mm inflorescence 2


title: CleftProband_5


title: CleftProband_3


title: WT-2mm-HT replicate 1

description: WT-2mm-HT replicate 1

value: High temperature

value: 2mm inflorescence 1


title: CleftProband_2

value: cleft lip and cleft palate

value: unaffected


title: CleftProband_11

value: syndromic

value: right


title: CleftProband_1


title: CM Mock infection replicate r2 ChIP of K27ac


title: AT2 SARS-CoV2 infection replicate r3 ChIP of K27ac

value: lung avleolar type 2 cells


title: KHUD_S3.VAN.R1

city: Seoul

first: Jae-Hyung

last: Lee

address: 26 Kyungheedae-ro, Dongdaemun-gu

country: South Korea

institute: Kyung Hee University

data_processing:
Illumina Casava software used for basecalling.
The sequencing raw reads were mapped onto the S. aginosus J4211 strain using Bowtie2. Uniquely and properly mapped read pairs were used for further analysis.
Expression levels of genes, the FPKM (fragments per kilobase of exon per million mapped reads) measure was calculated by cufflinks
Genome_build: S. aginosus J4211
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample

organism: Streptococcus anginosus

source_name: RNA-Seq of S. anginosus KHUD_S3 treated with vancomycin rep1

growth_protocol: S. anginosus was grown in Brain Heart Infusion Broth (Difco Laboratories) at 37°C under anaerobic conditions (80% N2, 10% H2, 10% CO2).

extract_protocol:
RNA was extracted using TRIzol (Invitrogen) and cleaned with RNeasy® Plus Mini Kit (QIAGEN).
To perform transcriptome sequencing (RNA-Seq) analysis, quality and integrity of the extracted total RNA was assessed by BioAnalyzer and the ribosomal RNA was removed by Ribo-Zero rRNA Removal Kit for Bacteria (Illumina). Standard illumina sequencing system protocol (TruSeq Stranded Total RNA prep) have been used to make libraries for RNA-Seq. Around 300 bp fragments were isolated using gel electrophoresis, amplified by PCR and sequenced on the Illumina HiSeq 3000 in the paired-end sequencing mode.

treatment_protocol: S. anginosus grown to an early exponential phase (OD600 = 0.3) was divided in half. One aliquot was left untreated, while the other one was treated with 8 μg/ml vancomycin for 1 h.

value: Vancomycin treatment


title: KHUD_S3.CON.R2

source_name: RNA-Seq of S. anginosus KHUD_S3 control rep2

value: No treatment


title: ild-3mm-HT replicate 1

description: ild-3mm-HT replicate 1

value: inflorescence

value: tap mutant

value: 3mm inflorescence 1


title: KHUD_S3.VAN.R2

source_name: RNA-Seq of S. anginosus KHUD_S3 treated with vancomycin rep2


title: ild-3mm-HT replicate 2

description: ild-3mm-HT replicate 2

value: 3mm inflorescence 2


title: AT2 SARS-CoV2 infection replicate r2 ChIP of K27ac

value: SARS-CoV2 infection


title: KHUD_S3.CON.R1

source_name: RNA-Seq of S. anginosus KHUD_S3 control rep1


title: KHUD_S1.VAN.R1

source_name: RNA-Seq of S. anginosus KHUD_S1 treated with vancomycin rep1


title: ild-2mm-HT replicate 3

description: ild-2mm-HT replicate 3

value: 2mm inflorescence 3


title: ild-3mm-HT replicate 3

description: ild-3mm-HT replicate 3

value: 3mm inflorescence 3


title: ild-2mm-HT replicate 2

description: ild-2mm-HT replicate 2

value: 2mm inflorescence 2


title: KHUD_S1.VAN.R2

source_name: RNA-Seq of S. anginosus KHUD_S1 treated with vancomycin rep2


title: CleftProband_868

source_name: genomic DNA from whole blood

value: female

value: non-syndromic

value: cleft lip only

value: left

source_name: DNA from an unaffected male from the Philippines

value: male


title: CleftProband_869

value: right

value: unaffected


title: CleftProband_867

value: cleft lip and cleft palate


title: CM SARS-CoV2 infection replicate r2 ChIP of K27ac

value: induced cardiomyocytes


title: ild-2mm-HT replicate 1

description: ild-2mm-HT replicate 1

value: inflorescence

value: High temperature

value: 2mm inflorescence 1


title: AT2 SARS-CoV2 infection replicate r4 ChIP of K27ac

value: lung avleolar type 2 cells


title: AT2 Mock infection replicate r3 ChIP of K27ac

value: Mock infection


title: rrp6D_RNAPIIser2p_2

city: Daejeon

first: Yoonjung

last: Choi

address: 291 Daehak-ro, Yuseong-gu

institute: KAIST

data_processing:
ChIP-seq samples were sequenced on either Hiseq2500 with single-end method (50-bp reads) or Novaseq6000 with pair-end method (150-bp reads). S.pombe Hi-C samples were sequenced on Hiseq4000 with pair-end method (100-bp reads).
ChIP-seq reads were aligned to the S.pombe genome (ASM294v2) using NovoAlign (V3.04.04, Novocraft technologies) with default parameters. Aligned reads were converted into BAM and replicates were merged using samtools (v1.10). Significantly enriched peaks were identified using MACS2 (v.2.1.4) and mapped reads were quantified using Deeptools (v3.1.3) and bwtool (v1.0).
For mRNA-seq analysis, raw reads were aligned to S. pombe genome (ASM294v2) using STAR aligner. Strand-specific signal tracks of RNA-seq were generated by using bam2wig.py from RseQC (v3.0.1).
Hi-C data were aligned to the S.pombe genome (ASM294v2) using bowtie2 and normalized using HiC-Pro (v2.11.0-beta). The raw and ICE-normalized matrix was generated at 1-kb and 2.5-kb bin resolution using valid interaction pairs.
Genome_build: S. pombe EF2 genome assembly; ASM294v2
Supplementary_files_format_and_content: ChIP-seq: Yeast ChIP-seq bigwig files were created using deeptools bamCoverage (RPM normalization). In case of calibrated bigWigs for set4 experiments, samtools flagstat was used to count reads that were mapped to s.pombe and s.cerevisiae respectively. The occupancy ratio (OR) was calculated according to the previous publication (Hu, B. et al 2015). Then the calibrated s.pombe ChP (Rad21-5FLAGand notag) bigwigs were created using bamCoverage –scaleFactor option; Hi-C: ICE normalized HiC matrix text files and abs files (in HiC-Pro format); RNA-seq: bigwig files and normalized forward/reverser RPKM test files. The number of mapped reads was further analyzed using HOMER and DESeq.

organism: Schizosaccharomyces pombe

source_name: S.pombe cells

growth_protocol: S. pombe: 1) For Hi-C experiments, yeast cells were grown to mid-log phases at 32 degrees, unless indicated otherwise. 2) For ChIP-seq in tetracycline-regulated system, cells were grown to mid-log phase at 30 degress in YES medium supplied with 2.5 ug/ml of anhydrotetracycline (ahTet). Depletion of rrp6+ was achieved by culturing cells in YES medium that lacks ahTet at indicated times (8, 12hr). Recovery of rrp6+ was achieved by culturing cells at fresh YES medium containing 2.5ug/ml of ahTet. 3) for ChIP-seq experiments, yeast cells were grown to mid-log phases at 30 degrees, unless indicated otherwise.

extract_protocol:
S. pombe (ChIP) :  Fixed cells were sonicated twelve times (15 sec on, 180 sec off) using a Fisher Scientific sonic Dismembrator Model 500 sonicator at 30% output. The immunoprecipitated DNA was eluted using SigmaPrep™ spin column and then subjected to protease treatment and cross-linking reversal. Subsequently, the DNA was purified using Qiaquick PCR purification kit (Qiagen).
S. pombe (RNA isolation): DNase-treated mRNA was purified using NEBNext® Poly(A) mRNA Magnetic Isolation Module (NEB), and subjected to library preparation using NEXTflex™ Rapid Directional mRNA-Seq Kit (BIOO) following the manufacturer’s instructions.
S.pombe (in situ Hi-C): formaldehyde-fixed cells (1.6 x 10^7 cells) were digested with zymolyase. Restriction enzyme digestion (MboI – 4 cutter), filling-in, ligation, crosslink reversal, DNA shearing and library construction were done according to previous publications (Rao, SSP et al 2014) with minor modifications.
ChIP-seq libraries for genome-wide sequencing were prepared using either a NEXTflex™ Illumina ChIP-Seq Library Prep kit (5143-02, BIOO) or Accel-NGS 2S Plus DNA Library Kit (21024, SWIFT). mRNA-seq libraries were made using NEXTflex™ Rapid Directional mRNA-Seq kit (5138-10, BIOO) from purified mRNA.

tag: chip antibody

value: anti-CTD-Ser2P (ab5095, Abcam).


title: CleftProband_865


title: AT2 Mock infection replicate r2 ChIP of K27ac


title: rrp6D_RNAPIIser2p_1


title: CleftProband_864

value: bilateral


title: CleftProband_866


title: AT2 Mock infection replicate r1 ChIP of K27ac


title: input_rrp6D_RNAPIIser2p_2


title: CleftProband_863


title: KHUD_S1.CON.R2

source_name: RNA-Seq of S. anginosus KHUD_S1 control rep2

value: No treatment


title: AT2 SARS-CoV2 infection replicate r1 ChIP of K27ac

value: SARS-CoV2 infection


title: NHDF KD2 (3)

city: Brno

first: Fabiana

last: Martino

address: Studentska

department: CTM

country: Czech Republic

institute: ICRC

description:
A3SS.MATS.JCEC.tsv
A5SS.MATS.JCEC.tsv
MXE.MATS.JCEC.tsv
RI.MATS.JCEC.tsv
SE.MATS.JCEC.tsv

data_processing:
Basecalls performed using bcl2fastq version 2.20.0.422
Quality trimming of raw reads performed using Trimmomatic version 0.36 with parameters CROP:250 LEADING:3  TRAILING:3 SLIDINGWINDOW:4:5 MINLEN:35
Sequenced reads were mapped to hg38 genome (with Ensembl GRCh38 version 94 annotation) using STAR version 2.5.3a as splice-aware short read aligner and the default parameters, with the exception of --outFilterMismatchNoverLmax 0.1 and --twopassMode basic
Alternative splicing analysis performed by rMATS version 3.1.0 with parameters -t paired --readLength 75 --libType fr-secondstrand
Genome_build: Ensembl GRCh38 version 94
Supplementary_files_format_and_content: differential alternative splicing tables were generated using rMATS version 3.1.0

source_name: Normal human dermal fibroblasts

extract_protocol:
RNA was extracted by High Pure RNA Isolation Kit (Roche) according to the manufacturer's instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: NHDF cells were transfected using two different human hnRNPC1/C2 stealth select small interfering RNAs (siRNAs) (Invitrogen) and a stealth siRNA negative control low GC (Invitrogen) at a final concentration of 10 nM. Transfection efficiency was tested after 96 hours

value: Normal human dermal fibroblasts

tag: sirna


title: KHUD_S1.CON.R1

source_name: RNA-Seq of S. anginosus KHUD_S1 control rep1


title: CleftProband_860

value: non-syndromic


title: CleftProband_858

value: female

value: cleft palate only

value: not applicable


title: input_rrp6D_RNAPIIser2p_1


title: CleftProband_859

value: male

value: unaffected


title: CleftProband_861

value: cleft lip and cleft palate

value: left


title: NHDF KD2 (2)


title: CleftProband_857

value: cleft lip only


title: AT2 Mock infection replicate r4 ChIP of K27ac


title: NHDF KD2 (1)


title: CleftProband_856


title: input_wild-type_RNAPIIser2p_1

extract_protocol:
S. pombe (ChIP) : Fixed cells were sonicated twelve times (15 sec on, 180 sec off) using a Fisher Scientific sonic Dismembrator Model 500 sonicator at 30% output. The immunoprecipitated DNA was eluted using SigmaPrep™ spin column and then subjected to protease treatment and cross-linking reversal. Subsequently, the DNA was purified using Qiaquick PCR purification kit (Qiagen).
S. pombe (RNA isolation): DNase-treated mRNA was purified using NEBNext® Poly(A) mRNA Magnetic Isolation Module (NEB), and subjected to library preparation using NEXTflex™ Rapid Directional mRNA-Seq Kit (BIOO) following the manufacturer’s instructions.
S.pombe (in situ Hi-C): formaldehyde-fixed cells (1.6 x 10^7 cells) were digested with zymolyase. Restriction enzyme digestion (MboI – 4 cutter), filling-in, ligation, crosslink reversal, DNA shearing and library construction were done according to previous publications (Rao, SSP et al 2014) with minor modifications.
ChIP-seq libraries for genome-wide sequencing were prepared using either a NEXTflex™ Illumina ChIP-Seq Library Prep kit (5143-02, BIOO) or Accel-NGS 2S Plus DNA Library Kit (21024, SWIFT). mRNA-seq libraries were made using NEXTflex™ Rapid Directional mRNA-Seq kit (5138-10, BIOO) from purified mRNA.

value: wt


title: CleftProband_854


title: CleftProband_862


title: CleftProband_853


title: NHDF KD1 (2)


title: CleftProband_852


title: wt_a-FLAG_notag_1

value: ANTI-FLAG M2 antibody (F1804, Sigma)


title: CleftProband_855

value: right


title: CleftProband_851


title: NHDF KD1 (1)


title: CleftProband_850


title: CleftProband_849


title: NHDF CTR3

value: siRNA negative control


title: pfs2-11_2_32c_Rad215F


title: pfs2-11_1_32c_Rad215F


title: CleftProband_848


title: CleftProband_847


title: NHDF CTR2


title: input_wild-type_RNAPIIser2p_2


title: pfs2-11_32c_a-FLAG_notag_2


title: CleftProband_845

value: bilateral


title: NHDF KD1 (3)


title: CleftProband_844


title: wt_a-FLAG_notag_2


title: pfs2-11_32c_a-FLAG_notag_1


title: CleftProband_843


title: wt_32c_Rad215F


title: CleftProband_842

value: syndromic


title: CleftProband_841

value: unknown


title: Input (total lysate, patient 2)

description:
IG1_input_length_norm.tsv
IG2_input_length_norm.tsv
IG3_input_length_norm.tsv
IP1_input_length_norm.tsv
IP2_input_length_norm.tsv
IP3_input_length_norm.tsv

data_processing:
Basecalls performed using bcl2fastq version 2.20.0.422
Quality trimming of raw reads performed using Trimmomatic version 0.36 with parameters CROP:250 LEADING:3  TRAILING:3 SLIDINGWINDOW:4:5 MINLEN:35
Sequenced reads were mapped to hg38 genome (with Ensembl GRCh38 version 94 annotation) using STAR version 2.5.3a as splice-aware short read aligner and the default parameters, with the exception of --outFilterMismatchNoverLmax 0.1 and –twopassMode basic
Ensembl GRCh38 version 94 annotation was modified to contain only regions for exons , CDS, intorns, 3’UTRs and 5’UTRs and this was used to get raw counts using featureCounts version 1.5.2.
Input (total lysate) samples were normalised on sequencing depth and further used as normalisation factor for normalisation of IgG-IP and hnRNPC-IP samples. IgG-IP and hnRNPC-IP were in the second round normalised on the length of each feature in logarithmic scale with base 2.
Genome_build: Ensembl GRCh38 version 94
Supplementary_files_format_and_content: genomic regions enrichment tables obtained following the processing steps; Contains genes with read counts over genomic regions (intron, CDS, 5’UTR, 3’UTR, exon) with ratio of intron/exon read counts, total expression over whole gene and log2 of ratio value.

source_name: Apex heart tissue

extract_protocol:
For immunoprecipitation of hnRNPC RNA complexes, 100 mg tissue from the human heart apex was used for each IP and control sample.After thawing, heart samples were washed, dissected, cross-linked and mechanically homogenized in lysis buffer. After sonication the sample was centrifuged and the supernatant was incubated O.N with antibody-conjugated-magnetic beads. After 3 washes reverse cross-linking was performed and proteins were digested by Proteinase K. RNA was extracted following TRIzol extraction protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: heart


title: CleftProband_840

data_processing:
532.tif and 635.tif files were analyzed using DEVA software to generate a data_summary.txt file and segMNT.txt file. Data_summary.txt files were analyzed using Nexus 7 Software to generate NexusData.bed files and then compared to the segMNT.txt file using BEDTOOLS 50% reciprocal overlap function. Only calls which shared a reciprocal overlap of 50% or greater were retained for further analysis.
BioDiscovery’s FASST2 Segmentation Algorithm, a Hidden Markov Model (HMM) based approach, was the algorithm used to make copy number calls using Nexus 7 Software. The significance threshold for segmentation was set at 1.0E-6 also requiring a minimum of 3 probes per segment and a maximum probe spacing of 1000 between adjacent probes before breaking a segment. The log ratio thresholds for single copy gain and single copy loss were set at 0.3 and -0.3, respectively. A 3:1 sex chromosome gain threshold was set to 1.2 and a 4:1 sex chromosome gain threshold was set to 1.7. NimbleGen's DEVA segMNT algorithm, which minimizes squared error relative to the segment means, was used as a second algorithm for all copy number calls after data extraction, LOESS spatial correction and background correction. Default parameters were used with the exception of setting the minimum segment difference to 0.3 and requiring a minimum of 3 probes per segment.

extract_protocol: DNA was extracted from whole blood samples using the Quickgene610L.

value: non-syndromic


title: CleftProband_839

value: female


title: CleftProband_838


title: CleftProband_837


title: swi6d_a-FLAG_notag_1


title: Input (total lysate, patient 1)


title: IgG-IP (control) in failing heart (patient3)

tag: antibody

value: IgG


title: CleftProband_846


title: rrp6d_a-FLAG_notag_2


title: CleftProband_834


title: NHDF CTR1

value: Normal human dermal fibroblasts


title: CleftProband_835

value: male


title: rrp6d_a-FLAG_notag_1


title: CleftProband_836

value: unaffected


title: CleftProband_833

value: cleft lip and cleft palate


title: CleftProband_832

value: left


title: dis3-54_a-FLAG_notag_1


title: CleftProband_830


title: dis3-54_a-FLAG_notag_2


title: swi6d_a-FLAG_notag_2


title: IgG-IP (control) in failing heart (patient2)


title: rrp6dtfs1d_Rad215F_set5_1


title: hnRNPC-IP in failing heart (patient2)

value: hnRNPC


title: CleftProband_828


title: CleftProband_831

value: cleft lip only


title: hnRNPC-IP in failing heart (patient1)


title: IgG-IP (control) in failing heart (patient1)


title: CleftProband_826


title: CleftProband_825


title: rrp6dtfs1d_Rad215F_set5_2

value: ANTI-FLAG M2 antibody (F1804, Sigma)


title: CleftProband_824


title: Input (total lysate, patient 3)


title: tfs1d_Rad215F_set5_2


title: CleftProband_823


title: tfs1d_Rad215F_set5_1


title: CleftProband_821


title: CleftProband_822


title: hnRNPC-IP in failing heart (patient3)


title: CleftProband_820


title: rrp6d_Rad215F_set5_2


title: CleftProband_818

value: cleft palate only

value: not applicable


title: CleftProband_819


title: CleftProband_827


title: BulkChIPseq_ONECUT2_RANKL_rep_3

city: Nijmegen

first: Maria

middle: Victoria

last: Luna Velez

state: Gelderland

address: Geert Grooteplein Zuid, 30, Route 274

department: Molecular Biology

institute: Radboud University

description: ChIPmentation with ONECUT2 antibody treatment with RANKL for 6 days; experiment 3

data_processing:
The ChIPmentation reads were processed with the chip-seq workflow from seq2science v.0.3.1 (Van der Sande, Frölich, Smits, & van Heeringen, 2021), taking the 1% input samples of either control or RANLK-treated organoids as background for peak calling. The workflow of preprocessing, alignment, deduplication and quality filtering was similar to the workflow described for the ATAC-seq analysis, but without shifting sequencing reads in alignment or during peak calling. ChIPmentation alignments, corresponding to the H3k27ac signal, were quantified using the coverage_table function from GimmeMotifs v0.16.0 (Bruse & Heeringen, 2018) with a window of 2 kb. For the ONECUT2 ChIPmentation, we used Diffbind (78) (v.3.4.11) to identify differentially bound genomic loci between RANKL- and control-treated organoids, with an FDR-cutoff of 0.05. For visualization of the results, we used the coverage_table function from GimmeMotifs to generate a table of log-transformed counts for these differential regions for RANKL and control samples.
Assembly: mm10
Supplementary files format and content: Processed ChIP-seq data is in three files: One file is a tab delimited file with all identified peak locations for H3K27ac mark per replicate (sample), one with the GimmeMotifs normalized and log-transformed readcounts per sample, per peak and one is a tab delimited file with all identified peak locations per replicate (sample), output of DiffBind.

source_name: mouse small intestinal organoid

growth_protocol: Small intestinal organoids derived from a female Lgr5GFPDTR/+ mouse (Tian et al., 2011) were cultured as described previously (Sato et al., 2009). Briefly, organoids were grown embedded in a mix of 90% ice-cold RGF BME Type 2 PathClear (Cultrex, R&D Systems) and 10% Dulbecco’s modified Eagle’s Medium/Ham’s F12 (Gibco), in a humidified atmosphere at 37°C and 5% CO2. For maintenance and control conditions organoids grew in ENR medium which contained advanced Dulbecco’s modified Eagles Medium/F12 (Gibco) supplemented with 1x Penicillin‐Streptomycin (Gibco), 10 mM HEPES (Gibco), and 1x GlutaMAX Supplement (Gibco), 1x B27 (Gibco), 1,25 mM N‐acetylcysteine (Sigma Aldrich), 50 ng/mL mEGF (Gibco), 10% final volume NOGGIN conditioned medium, 5% final volume R‐SPONDIN1 conditioned medium. For maintenance, organoids were split by mechanical dissociation using a Pasteur pipette every 5 days and the culture medium was refreshed every other day (Sato et al., 2009).

extract_protocol:
Following harvesting, organoids were crosslinked with 1 % formaldehyde, and glycine was added to quench the reaction. After a washing step with 1x ice-cold PBS, cell pellets were snap frozen and stored at -80°C until being processed for ChIPmentation.
A total of 250.000 cells per replicate were lysed in a buffer containing 20 mM HEPES pH 7,6, 1% SDS, 1x Protease Inhibitor Cocktails (Roche). Chromatin was sheared using the medium setting of the Biorupter Pico (Diagenode) with 6 cycles (20 seconds on/30 seconds off) to achieve fragments between 200 and 600 bp. Samples were then spun at 13.000 rpm for 5 minutes at room temperature and supernatant containing fragmented chromatin was used for ChIPmentation as described by (Schmidl et al., 2015) with the modifications published in Lindeboom et al., 2018. Briefly, before starting the immunoprecipitation, we saved 1% of the input material of either control or RANKL-treated organoids and stored it at 4° C until further processing (tagmentation). Then, chromatin of each replicate was incubated with 1 µg of antibody against H3K27ac (C15410196, Diagenode) or 1 µg of antibody against ONECUT2 (Proteintech, 21916-1-AP, AB_2848180) in dilution buffer (1% Triton X-100, 1,2 mM EDTA, 16,7 mM Tris pH 8, 167 mM NaCl, 1x Protease Inhibitor Cocktail (Roche)), rotating overnight at 4°C. Antibody-bound chromatin was purified using protein A and protein G Dynabeads (Invitrogen) followed by two washing steps with increasing concentration of NaCl and one washing step with TE buffer as described before (Lindeboom et al., 2018). Tagmentation of immunoprecipitated and input chromatin was performed with in-house generated Tn5 enzyme for 10 minutes at 37°C while shaking at 550 rpm, followed by washing steps with decreasing amounts of NaCl and soap (Lindeboom et al., 2018). Lastly, samples were de-crosslinked with 20 µg of proteinase K (Sigma) in elution buffer (0,5% SDS, 300 mM NaCl, 5 mM EDTA, 10 mM Tris pH 8) for 1 hour at 55°C and 1.000 rpm shaking followed by an overnight incubation at 65°C and 1.000 rpm shaking. The eluted, tagmented chromatin was treated with 10 µg proteinase K (Sigma) for 1 additional hour at 55°C and purified using 2x AMPure XP beads (Beckman Coulter). The generated libraries were amplified using the KAPA HiFi Hotstart Ready Mix and Nextera Index Kit 1 (i7) and 2 (i5) primers (Illumina). Amplified libraries were purified using a 0,65x AMPure XP beads (Beckman Coulter) followed by a 1,8x AMPure XP beads (Beckman Coulter) purification. Library concentration was measured using the dsDNA Fluorescence Quantification Assays (DeNovix), and library size was determined using the BioAnalyzer High Sensitivity DNA Kit (Agilent Technologies). DNA libraries were sequenced with an Illumina NextSeq 500, and 38-bp paired-end reads were generated.

treatment_protocol: For microfold (M) cell enrichment, organoids were cultured in ENR supplemented with 3 µM CHIR99021 (Axon) and 1,5 mM valproic acid (Sigma) for three days, followed by one day in ENR medium. Afterwards, treatment with 100 ng/mL of recombinant mouse TRANCE (RANKL) (BioLegend) was done for 6. Organoids grown in ENR medium was used as a control. Medium was refreshed every three days.

tag: line

value: line26 wild type, Lgr5GFPDTR/+

value: small intestinal organoid

value: RANKL

tag: time point

value: Day 6

tag: assay

value: ChIP-seq


title: Control_input

description: ChIPmentation 1% input sample from ENR medium (control) for 6 days

tag: tissue

tag: treatment

value: ENR medium


title: CleftProband_817

value: female

value: non-syndromic


title: BulkChIPseq_ONECUT2_RANKL_rep_2

description: ChIPmentation with ONECUT2 antibody treatment with RANKL for 6 days; experiment 2


title: CleftProband_816

value: male


title: BulkChIPseq_ONECUT2_RANKL_rep_1

description: ChIPmentation with ONECUT2 antibody; treatment with RANKL for 6 days; experiment 1


title: BulkChIPseq_ONECUT2_Control_rep_3

description: ChIPmentation with ONECUT2 antibody ENR medium for 6 days; experiment 3


title: wt_Rad215F_set5_1

tag: genotype

value: wt


title: CleftProband_815

value: cleft lip and cleft palate

value: right

value: unaffected


title: CleftProband_814

value: bilateral


title: RANKL_input

description: ChIPmentation 1% input sample from RANKL treatment for 6 days


title: CleftProband_813


title: rad21K1_mRNA- seq_2

description:
pombe_RNAseq_antisense_RPKM.txt
pombe_RNAseq_sense_RPKM.txt


title: CleftProband_812

value: left


title: BulkChIPseq_ONECUT2_Control_rep_2

description: ChIPmentation with ONECUT2 antibody ENR medium for 6 days; experiment 2


title: CleftProband_810


title: CleftProband_811


title: BulkChIPseq_ONECUT2_Control_rep_1

description: ChIPmentation with ONECUT2 antibody; ENR medium for 6 days; experiment 1


title: CleftProband_829

value: cleft palate only


title: rad21K1_mRNA- seq_1


title: CleftProband_809

value: cleft lip only


title: rrp6d_Rad215F_set5_1

value: ANTI-FLAG M2 antibody (F1804, Sigma)


title: CleftProband_807


title: CleftProband_808


title: rrp6d_mRNA- seq_2


title: CleftProband_806


title: CleftProband_805


title: EC-OSB, replicate 2

city: Houston

first: Guocan

state: TX

address: 1515 Holcombe Blvd, T7.3900

institute: MD Anderson Cancer Center

data_processing:
RNA fastqs were aligned to the mus musculus (version mm10 from Genome Reference Consortium GRCm38) using STAR (2.6.0b)  (Dobin et al., 2013),      raw counts are obtained using  HTSeq  (Anders et. al. 2014)  (python/3.6/anaconda3/bin/htseq-count, with options -m union -a 10 -s  no)    (  rsem-calculate-expression  (1.2.3) with options --bowtie2 (2.2.3) against reference mm10.refgenes were run separated for to obtain TPM ((transcripts per million reads)) ).
Assembly: mm10
Supplementary files format and content: tab-delimited text files include raw count values for each Sample

source_name: EC-OSB (GFP+/RFP+ cells)

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
Libraries were prepared according to Roche KAPA Stranded RNA-Seq Library Prep Kit (Illumina). Briefly, polyA+ mRNAs were enriched by oligo (dT) magnetic beads from the total RNA samples; RNA-seq library preparation using KAPA Stranded RNA-Seq Library Prep Kit (Illumina), which incorporates dUTP into the second cDNA strand and renders the RNA-seq library strand-specific; The completed libraries were qualified with Agilent 2100 Bioanalyzer and quantified by absolute quantification qPCR method; The barcoded libraries were mixed, denatured to single strands in NaOH, captured on Illumina flow cell, amplified in situ, and sequenced for 150 cycles for paired-ends on an Illumina llumina NextSeq500 system.

value: EC-OSB (GFP+/RFP+ cells)

value: Sample 2 (ECOSB_2)


title: RFP+ cells, replicate 2

source_name: Non EC-OSB (RFP+ cells)

value: Non EC-OSB (RFP+ cells)

value: Sample 4 (RFP_2)


title: RFP+ cells, replicate 1

value: Sample 3 (RFP_1)


title: CleftProband_804

value: female


title: CleftProband_803

value: non-syndromic


title: EC-OSB, replicate 1

value: Sample 1 (ECOSB_1)


title: CleftProband_802

value: male


title: CleftProband_800


title: CleftProband_801

value: syndromic

value: cleft lip and cleft palate


title: WT_mRNA- seq_2

value: wt


title: RNA-Seq Tet2-/- #4

city: New York

first: Cem

last: Meydan

state: New York

address: 1305 York

department: Physiology & Biophysics

institute: Weill Cornell Medical College

description: Tet2-/- #4

data_processing:
Trimming by TrimGalore
Alignment by STAR
Counts by FeatureCounts
Assembly: mm10

source_name: Lin-cKit+Sca1+  cells

extract_protocol: To isolate LSK cells, the femur, tibia and humerus bones were dissected from mice with genotypes of interest. The bone marrow cells were isolated by flushing in 5 mL MACS buffer (phosphate-buffered saline without MgCl2 and CaCl2, supplemented with 0.5% bovine serum albumin and 2mM EDTA pH8.0) using syringes with 26 gauge needles. The isolated cells were filtered through a 70 µm nylon mesh. The cells were centrifuged at 300 x g for 5 minutes at 4°C, and resuspended in 1 mL red blood cell lysis buffer (Sigma) followed by incubation for 5 minutes at ambient temperature. 10 mL cold buffer was added, the cells were centrifuged at 300 x g for 5 minutes a 4°C, and resuspended in 1 mL cold buffer prior to counting on a ViCell Counter. The cells were then washed with 5 mL buffer, centrifuged at 300 x g for 5 minutes a 4°C, and process for lineage depletion using the Mouse Lineage Cell Depletion Kit (Miltenyi Biotec # 130-090-858), following the manufacturer’s instructions: cells were resuspended at 2.5 x 108 cells/mL in MACS buffer, and 10 µl of biotinylated mouse lineage antibody cocktail was added per 10 million cells, followed by incubation on ice for 15 minutes. 30 µl of MACS buffer and 20 µl of streptavidin-conjugated magnetic microbeads were added per 10 million cells, followed by incubation ice for 15 minutes, and filtering through a 30 µm nylon mesh in 10 mL cold MACS buffer. The cells were centrifuged at 300 x g for 5 minutes at 4°C, resuspended in 1 mL cold MACS buffer, and processed for lineage separation using an AutoMACS Pro instrument (Miltenyi Biotec) using the “Deplete” settings. Lineage-negative cells were collected.  Cells were incubated for 15 minutes on ice with MACS buffer containing 1:100 Fc blocking antibody (Tonbo Biosciences # 70-0161-M001). Cells were stained with the following antibodies in FACS or MACS buffer for 30 minutes on ice: cKIT-PE/Cy7 (BioLegend # 105814; 1:100), SCA1-FITC (BioLegend # 122505, 1:100), STREPTAVIDIN- APC/Cy7 (BioLegend # 405208; 1:50), alongside DAPI (2ug/mL). After staining, cells were washed twice with cold buffer, resuspended, and sorted using a FACSAria II fluorescence-activated cell sorter (BD Biosciences) into MACS buffer at 4°C. 1 x 105 cells were processed for RNA and DNA extraction using the AllPrep DNA/RNA Micro Kit (Qiagen #80284), following the manufacturer’s instructions.

value: Bone marrow


title: wild-type_RNAPIIser2p_1

description:
wt_Ser2P_IP_rpm.bw
wt_Ser2P_IP_normalizedby_FLAGnotag.bw

value: anti-CTD-Ser2P (ab5095, Abcam).


title: CleftProband_799

value: cleft palate only

value: not applicable

value: unaffected


title: RNA-Seq Tet2-/- #3

description: Tet2-/- #3


title: CleftProband_798

value: left


title: CleftProband_797


title: rrp6d_mRNA- seq_1


title: notag_5Flag_ChIP-seq_set#1_2

value: ANTI-FLAG M2 antibody (F1804, Sigma)


title: CleftProband_796


title: CleftProband_795

value: bilateral


title: RNA-Seq Tet2-/- #2

description: Tet2-/- #2


title: RNA-Seq Tet2-/- #1

description: Tet2-/- #1


title: rrp6∆_Psc3_5Flag ChIP-seq_set#1_2


title: CleftProband_794


title: RNA-Seq Idh2R172K/+ #4

description: Idh2R172K/+ #4


title: WT_mRNA- seq_1


title: CleftProband_792


title: CleftProband_793

value: cleft lip only

value: right


title: wild-type_RNAPIIser2p_2


title: RNA-Seq Idh2R172K/+ #3

description: Idh2R172K/+ #3


title: CleftProband_790

value: female


title: CleftProband_791

value: non-syndromic


title: rrp6∆_Psc3_5Flag ChIP-seq_set#1_1


title: CleftProband_787


title: CleftProband_788


title: CleftProband_789


title: Psc3_5Flag ChIP-seq_set#1_2


title: RNA-Seq Idh2R172K/+ #2

description: Idh2R172K/+ #2


title: Psc3_5Flag ChIP-seq_set#1_1


title: RNA-Seq Idh2R172K/+ #1

description: Idh2R172K/+ #1


title: rrp6∆_Rad21_5Flag ChIP-seq_set#3_2


title: CleftProband_786


title: RNA-Seq Idh2R140Q/+ #3

description: Idh2R140Q/+ #3


title: CleftProband_780


title: CleftProband_784


title: RNA-Seq Idh2R140Q/+ #2

description: Idh2R140Q/+ #2


title: RNA-Seq Idh2R140Q/+ #4

description: Idh2R140Q/+ #4


title: notag_5Flag_ChIP-seq_set#1_1


title: CleftProband_785


title: CleftProband_782


title: rrp6∆_Rad21_5Flag ChIP-seq_set#3_1


title: CleftProband_783


title: RNA-Seq Idh2R140Q/+ #1

description: Idh2R140Q/+ #1


title: CleftProband_779


title: CleftProband_781


title: CleftProband_777


title: exo2∆_Rad21_5Flag ChIP-seq_set#3_1


title: CleftProband_778


title: cid14∆_Rad21_5Flag ChIP-seq_set#2_2


title: Rad21_5Flag ChIP-seq_set#3_1


title: RNA-Seq Idh1R132H/+ #4

description: Idh1R132H/+ #4


title: CleftProband_776


title: CleftProband_774


title: CleftProband_773


title: CleftProband_775


title: RNA-Seq Idh1R132H/+ #3

description: Idh1R132H/+ #3


title: CleftProband_772


title: cid14∆_Rad21_5Flag ChIP-seq_set#2_1


title: CleftProband_771


title: swi6∆_Rad21_5Flag ChIP-seq_set#2_1


title: exo2∆_Rad21_5Flag ChIP-seq_set#3_2


title: RNA-Seq Idh1R132H/+ #1

description: Idh1R132H/+ #1


title: Rad21_5Flag ChIP-seq_set#2_1


title: RNA-Seq WT #4

description: WT #4

value: +/+;Vav-Cre


title: CleftProband_769

value: male


title: CleftProband_770


title: CleftProband_768


title: RNA-Seq Idh1R132H/+ #2

description: Idh1R132H/+ #2


title: rrp6∆_Rad21_5Flag ChIP-seq_set#1_2


title: CleftProband_766


title: BS-Seq Tet2-/- #4

description: Tet2-/- #4

data_processing:
Alignment by bwa-meth
Processing by MethylDackel
Assembly: mm10


title: CleftProband_767


title: RNA-Seq WT #2

description: WT #2


title: CleftProband_762


title: dis3-54_Rad21_5Flag ChIP-seq_set#1_2


title: dis3-54_Rad21_5Flag ChIP-seq_set#1_1


title: swi6∆_Rad21_5Flag ChIP-seq_set#1_1


title: CleftProband_760


title: RNA-Seq WT #3

description: WT #3


title: RNA-Seq WT #1

description: WT #1


title: BS-Seq Tet2-/- #3

description: Tet2-/- #3


title: CleftProband_765


title: CleftProband_761


title: CleftProband_763

value: syndromic


title: CleftProband_757

value: cleft lip and cleft palate


title: CleftProband_758


title: CleftProband_764


title: CleftProband_759


title: rrp6∆_Rad21_5Flag ChIP-seq_set#1_1


title: Rad21_5Flag ChIP-seq_set#1_2

value: wt


title: BS-Seq Tet2-/- #2

description: Tet2-/- #2

value: Bone marrow


title: CleftProband_756


title: Rad21_5Flag ChIP-seq_set#1_1


title: BS-Seq Tet2-/- #1

description: Tet2-/- #1


title: BS-Seq Idh2R172K/+ #3

description: Idh2R172K/+ #3


title: BS-Seq Idh2R172K/+ #4

description: Idh2R172K/+ #4


title: CleftProband_751


title: BS-Seq Idh2R172K/+ #2

description: Idh2R172K/+ #2


title: CleftProband_747


title: CleftProband_749


title: CleftProband_753


title: BS-Seq Idh2R140Q/+ #4

description: Idh2R140Q/+ #4


title: CleftProband_745


title: CleftProband_750


title: CleftProband_748


title: CleftProband_742


title: NGS02472b_S8

city: Bethesda

first: Julie

middle: E

last: Niemela

state: MD

address: 10 Center Dr.

department: Dept. of Lab. Medicine

institute: NIH Clinical center

data_processing:
Demultiplexed reads were mapped to the hg19 genome using the splice-aware aligner Tophat (Trapnell et al., 2009)
Read counts were variance stabilized (normalized) using DeSeq2
Assembly: Homo sapiens (human) genome assembly GRCh37 (hg19)
Supplementary files format and content: File with raw counts for every gene and every sample

source_name: Blood

extract_protocol:
AmpliSeq for Illumina Transcriptome Human Gene Expression panel
Targeted Sequencing Library (>20,000 human RefSeq genes)

value: CD4+ T-cell blasts

value: TCF3 wild-type / TCF3 E555K (DN)

tag: disease state

value: affected


title: NGS02471b_S6

value: TCF3 wild-type / TCF3 Y200Cfs*54 (HI)


title: NGS02472b_S7


title: CleftProband_744

first: J.

address: 455 Biology Building, 129 East Jefferson Street

institute: The University of Iowa

value: left

value: unaffected


title: CleftProband_743


title: CleftProband_741

value: bilateral


title: CleftProband_746


title: BS-Seq Idh2R140Q/+ #3

description: Idh2R140Q/+ #3

tag: strain


title: NGS02471b_S5

tag: cell type


title: BS-Seq Idh2R140Q/+ #2

description: Idh2R140Q/+ #2


title: CleftProband_740

tag: Sex

value: cleft lip only


title: CleftProband_755

tag: syndromic versus non-syndromic


title: CleftProband_739

tag: cleft type


title: BS-Seq Idh2R140Q/+ #1

description: Idh2R140Q/+ #1


title: CleftProband_754


title: BS-Seq Idh2R172K/+ #1

description: Idh2R172K/+ #1


title: CleftProband_738

value: Midline


title: NGS02465

value: TCF3 wild-type / TCF3 G486Lfs*4 (HI)


title: CleftProband_736

value: female

value: non-syndromic


title: CleftProband_733

value: male


title: CleftProband_737


title: BS-Seq Idh1R132H/+ #3

description: Idh1R132H/+ #3


title: CleftProband_732


title: CleftProband_731


title: NGS02463

description: healthy control 4

value: TCF3 wild-type / TCF3 wild-type

value: apparently healthy


title: NGS02464


title: NGS02464b


title: NGS02463b

description: healthy control 4


title: CleftProband_752

value: cleft lip and cleft palate


title: BS-Seq WT #4

description: WT #4

value: Bone marrow

value: +/+;Vav-Cre