title: DMS seq WT D7 rep2

status: Public on May 17 2024

first: yongwoo

last: lee

department: Mol bio

institute: MASSACHUSETTS GENERAL HOSPITAL

data_processing:
3’ end adaptor sequences (-a AGATCGGAAGAGC) are trimmed from raw data files using cutadapt followed by duplicate removal by prinseq. 6 nt molecular barcodes were further clipped away with -g ^NNNNN argument of cutadapt. RT-stop reads out of the range of 18- 45 nt length were excluded from the final fastq file using prinseq -max_len 45 -min_len 18 command.
For RT-stop profile, processed sequencing reads are aligned with STAR aligner against GRCm38.p6 genome assembly. 1 mismatch was allowed for the read mapping. The subsequent sam files are converted to sorted bam files using samtools, RT-stops at the rG4 regions were counted using the rG4seeker pipeline. In vitro rG4 identification was computed from RT-stop counting of two biological replicates. Unknown and G>=40% classes are excluded from the assay due to their absence of rG4 motifs. In vivo rG4 DMS sensitivity was addressed by analyzing K+ dependent RT-stop frequency changes of DMS treated samples.
Assembly: mm10
Supplementary files format and content: "rG4 RT-stop count" Comma-separated files (.csv) indicate rG4 location information (Chr, start, end, class, genome position, splicing site, motif sequence, gene name, and annotation) and RT sequencing read coverage and stops in the K+ and Li+ samples.
Library strategy: DMS-seq

source_name: 129S1/CastEiJ x 129S1

growth_protocol: Clonal TsixTST/+  mESC (TST) line was cultured as routine procedure. mESC were grown on inactivated feeders in high glucose D-MEM supplemented with 15% Hyclone FBS, 25 mM HEPES pH 7.2-7.5, 1x MEM non-essential amino acids, 1x Pen/Strep, 0.1 mM βME, and 500 U/mL ESGRO recombinant mouse Leukemia Inhibitory Factor (LIF) protein at 37°C with 5% CO2. EB differentiation was performed with growing feeder-depleted cells in the medium without LIF. Cells were kept in suspension until 3 days of differentiation and transferred to gelatinized plates on day 3 for further adherent growth.

extract_protocol:
Frozen cells pellets are placed on dry ice, resuspended in nuclei isolation buffer (15 mM Tris-HCl pH 7.5, 60 mM KCl, 15 mM NaCl, 5 mM MgCl2, 1 mM CaCl2, 250 mM Sucrose, 0.3 % Igepal CA-630, 0.1% βME and 10 mM ribonucleoside vanadyl complex). The solution was repeatedly pipetted until the frozen pellet is completely dissolved. Nuclei were collected at 600 g and 4 °C for 5 min and washed twice with the nuclei isolation buffer without Igepal CA-630. To remove soluble nuclear fraction, nuclei pellet was resuspended in 500 ul NUN1 buffer (20 mM Tri-HCl, pH 8.0, 75mM NaCl, 0.5 mM EDTA, 50% Glycerol and proteinase inhibitor 1xComplete followed by 4.8 ml NUN2 buffer (20 mM HEPES-KOH pH 7.6, 7.5 mM MgCl2, 0.2 mM EDTA, 300 mM NaCl, 1 M Urea, 1% Igepal CA-630). The solution was incubated on ice for 15 min with brief vortexing every 5 mins. An insoluble chromatin pellet was obtained by centrifugation at 10000 g at 4 °C for 15 min centrifugation. 300 ml Trizol was added to the chromatin pellets, and under freeze-thaw cycles three times.  Then the pellets were ground with eppendorf tube pestles until completely resuspended in trizol. Additional 700 ml Trizol was applied on the top of the ground mixture and the remaining RNA isolation procedure was performed as following standard Trizol protocol. Poly A+ RNA was collected from 100 - 250 ug chromatin-bound RNA using Oligotex Direct mRNA kit.
1 - 5 ug of poly A+ RNA was chemically fragmented at 95 °C for 8 min in RNA fragmentation buffer (100 mM Tris-HCl pH 8 and 2 mM MgCl2). The fragmented RNA was ethanol precipitated, resuspended in urea gel loading buffer (1x TBE, 3.5M Urea, 0.005% Bromophenol blue, and 0.025% Xylene), and subjected to denaturing urea 8% acrylamide gel fraction. 60- 80 nt RNA fragment was excised and recovered from the gel. RNA samples are dephosphorylated with polynucleotide kinase (PNK) (NEB M0201S) in 10 ml solution comprising 1 ml 10x T4 RNA ligase buffer (NEB, B0216), 1.5 ml T4 PNK and 0.5 ml SUPERase•In RNase Inhibitor (Invitrogen, AM2696) at 37 °C for 5 hours. The samples are ligated to the 3’ adaptor by directly adding 6 ml 50 % PEG8000, 1 ml 10x T4 RNA ligase buffer, 2 ml 20 mM adenylated 3 DNA adaptor, and 1 ml T4 RNA Ligase 2 truncated K227Q (NEB, M0373) to the dephosphorylated mixture above and incubating 16 °C for 16 hours. Samples are ethanol precipitated and gel fractionated again, adaptor-ligated products appearing at 85 -105 nt position were gel-purified and resuspended in 13 ul water. For reverse transcription, 13 ml adaptor-ligated RNA was mixed with 4 ml 5x RT buffer (100 mM Tris-HCl pH 7.5, 750 mM KCl (or LiCl), 15 mM MgCl2), 1 ml 10 mM dNTP mix, 2 ml 10 mM phosphorylated iSp18 PE Reverse oligo and 0.1 ul SUPERase•In RNase Inhibitor. The mixture was incubated in PCR machine at 80 °C for 2 min and then 42 °C for 5min, 1 ml 0.1M DTT and 1 ml SuperScript III reverse transcriptase (Invitrogen, 18080085) was added to the mixture while PCR tubes are in the thermocycling block. After incubation at 42 °C for 10 min for cDNA synthesis, samples are moved on ice and then 2 ml 1 M NaOH was added to the reaction mixture. To hydrolyze RNA, samples were treated at 98°C for 15 minutes, and 2 ml 1 M HCl was applied to neutralize the solution. Resulting cDNAs were ethanol precipitated and urea gel fractionated, smearing band appearing at the 78 -105 nt length was purified from the gel. cDNA samples are circularized using 50 U CircLigase (Epicentre, CL4111K) at 60°C for 12 hours. Circularized cDNA was amplified using RT stop amp primer (Supplementary Table 7) and KAPA HiFi PCR master mix (Roche, KK2601) for 8–11 cycles of PCR. Second size selection was performed with native TBE- 8% acrylamide gel fractionation, PCR bands at 78- 105 bp are purified from the gel. 4 - 5 cycles of additional PCR reactions were run with NEBnext multiplex oligos (NEB, E7335) to introduce Illumina library sequences to the RT-stop profile library. ZR small-RNA PAGE Recovery Kit (Zymo Research, R1070) and SYBR Gold (Invitrogen, S11494) staining was used for gel purification during the preparation process.

treatment_protocol: Trypsinized ~ 2 x 107 cells were resuspended in the 5 ml culture medium and quickly transferred to the chemical fume hood. 200 ul (4% v/v) of DMS is directly applied to the media using a 1 ml syringe. The mixture was incubated at 37°C for 7 min with mild agitation. DMS modification was quenched by adding 1.3 ml βME after putting the tubes on ice. Cells were recovered by centrifugation at 400 g and 4 °C for 3 min. For complete removal of remaining DMS, cell pellets were repeatedly washed twice with 5ml ice-cold 1x PBS and 25% βME buffer. DMS-treated cells are stored in a – 80 °C deep freezer until the RNA purification.

value: 129S1/CastEiJ x 129S1

value: Day 7 differentiated mouse embryonic stem cells


title: DMS seq WT D3 rep1

type: SRA

city: Boston

state: MA

address: 185 Cambridge St

country: USA

library_source: other

molecule: other

organism: Mus musculus

tag: cell line

tag: cell type

value: Day 3 differentiated mouse embryonic stem cells

tag: genotype

value: WT

tag: treatment


title: DMS seq WT D7 rep1


title: DMS seq WT D0 rep1

value: mouse embryonic stem cells


title: DMS seq WT D0 rep2


title: Kidney cortex, CF2

status: Public on Jun 07 2024

city: Iowa city

first: Wenjie

last: Yu

state: IA

address: 200 Hawkins Dr, 6330 PBDB

institute: The University of Iowa

library_source: transcriptomic

data_processing:
Kallisto based pseudoalignment and quantification
Reads for different transcripts of the same gene were aggregated
Assembly: Sscrofa11.1 from RefSeq database
Supplementary files format and content: tsv format files for individual samples containing counts (est_counts) and tpms for each transcript

molecule: total RNA

organism: Sus scrofa

source_name: Kidney cortex

extract_protocol:
Kidney cortex tissues from similar position of newborn pigs were collected, total RNA of the tissues was extracted using a RNeasy Lipid Tissue Kit (Qiagen) according to the manufacturer’s instructions.
Illumina TruSeq Stranded Total RNA with RiboZero

tag: tissue

value: Kidney cortex

tag: age

value: newborn

value: CFTR-/-


title: UTSW63 Rep 3

status: Public on Apr 24 2024

city: Dallas

first: Samuel

middle: Kent

last: McBrayer

state: Texas

address: 6000 Harry Hines Boulevard, NL11.110K

department: Children's Research Institute

institute: UT Southwestern Medical Center

data_processing:
The sequencing read were filtered to remove adapter contamination and low quality reads and processed reads were aligned by HiSat2 to the human (UCSC hg38) reference for quantification.
Assembly: UCSC hg38
Supplementary files format and content: xls file contains raw reads for each sample
Supplementary files format and content: xls file contains FPKM values for each sample

organism: Homo sapiens

growth_protocol: TS516, TS603, BT054, BT260, UTSW5, UTSW63, and UTSW71 cells were cultured in NeuroCult NS-A Basal Medium (Human) with human Proliferation Supplement (StemCell Technologies 05750) supplemented with EGF (20 ng/mL), bFGF (20 ng/mL), heparin (2 μg/mL), 1% penicillin/streptomycin, amphotericin B (250 ng/mL), and Plasmocin (2.5 μg/mL). HK213, HK211, HK308, and HK157 cells were cultured in DMEM26 F12 medium (Gibco 11320033) supplemented with 3 mM glutamine, 1× B27, EGF (20 ng/mL), bFGF (20 ng/mL), heparin (2 μg/mL), 0.5% penicillin/streptomycin, amphotericin B (125 ng/mL), and Plasmocin (2.5 μg/mL). MGG152 cells were cultured in Neurobasal Medium (Gibco 21103049) supplemented with 3 mM glutamine, 1× B27, 0.25× N2, EGF (20 ng/mL), bFGF (20 ng/mL), heparin (2 μg/mL), 0.5% penicillin/streptomycin, amphotericin B (125 ng/mL), and Plasmocin (2.5 μg/mL).

extract_protocol:
RNA was harvested using the RNEasy Plus Mini Kit (QIAGen). 2 µg of total RNA served as input for polyA RNA capture and rRNA removal.
Strand-specific libraries were prepared by Novogene.

value: IDH WT glioma stem-like cell

tag: biologic replicate


title: UTSW71 Rep 2


title: UTSW71 Rep 3


title: Unaltered (non-rejection) [N2]

status: Public on May 02 2024

city: Derio

first: Ana

middle: Maria

last: Aransay

state: BIZKAIA

address: Parque tecnologico de Bizkaia, Building 801-A

department: Genome Analysis Platform

country: Spain

institute: CIC bioGUNE

description: Spatial transcriptome sequencing of fresh frozen tissue, without OCT.

data_processing:
*library strategy: Spatial Transcriptomics
Sequences were aligned to the hg38 human reference genome, the counts separated by cell, the data filtered and processed using Space Ranger version 1.3.1 according to manufacturer specifications
Assembly: hg38
Supplementary files format and content: barcodes.tsv.gz:  list of spatial barcodes
Supplementary files format and content: features.tsv.gz:  list of gene Ids
Supplementary files format and content: matrix.mtx.gz:  gene expresion count data in Matrix Market Exchange Format

source_name: Human Kidney

extract_protocol:
Fresh frozen tissue, without OCT. 10 µm sections were cut with cryostat.
Spatial Transcriptome sequencing libraries were prepared with 10xGenomics Visium Spatial Gene Expression Slides and Reagents, according to “Visium Spatial Gene Expression Reagent Kits”(CG000239 Rev E) user guide

value: Human Kidney

tag: diagnostic category

value: Non-rejection


title: UTSW5 Rep 2


title: UTSW5 Rep 3


title: UTSW63 Rep 2


title: UTSW63 Rep 1


title: UTSW5 Rep 1


title: TS603 Rep 3

value: IDH1 mutant glioma stem-like cell


title: TS603 Rep 2


title: TS603 Rep 1


title: TS516 Rep 1


title: TS516 Rep 2


title: MGG152 Rep 3


title: TS516 Rep 3


title: MGG152 Rep 1


title: HK308 Rep 2


title: HK252 Rep 2


title: DMS seq WT D3 rep2


title: HK308 Rep 3


title: HK308 Rep 1


title: HK252 Rep 3


title: UTSW71 Rep 1


title: HK252 Rep 1


title: HK213 Rep 3


title: HK213 Rep 1


title: HK213 Rep 2


title: HK211 Rep 3


title: HK157 Rep 2


title: HK157 Rep 3


title: HK211 Rep 1


title: BT260 Rep 3


title: HK157 Rep 1


title: BT260 Rep 2


title: MGG152 Rep 2


title: BT054 Rep 1


title: BT054 Rep 2


title: BT260 Rep 1


title: CCD-18CO, Vehicle, Rep2

status: Public on Apr 23 2024

city: Dublin

first: Mario

last: Manresa

address: UCD Belfield

country: Ireland

institute: School of Biomolecular and Biomedical Sciences

data_processing:
nf-Core RNA-seq pipeline v3.9
Raw FASTQ files were trimmed using Trim Galore.
Trimmed reads were then aligned to the human transcriptome followed by mapping to the genome (GRCh38) and quantified at the transcript level using STAR and SALMON.
Salmon gene-level counts were then passed to DeSeq2 for normalization and downstream analysis.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes normalized gene-level counts for each sample

growth_protocol: Human primary colonic fibroblasts (CCD-18CO, American Type Culture Collection (ATCC), Manassas, VA) were cultured in Eagle’s Minimum Essential Medium (EMEM, ATCC) supplemented with 10% Foetal bovine serum (FBS, BioSciences, Ireland)

extract_protocol: RNA was sent to BGI for library construction and sequencing.

treatment_protocol: Human primary colonic fibroblasts were serum deprived (in serum free EMEM) for a minimum of 6 hours,followed by stimulation with 50 ng/mL of TWEAK (PeproTech, UK) in serum-free medium for 24 hours.

value: colonic fibroblasts

value: Vehicle


title: FXS_470_iPSC_Nanopore

status: Public on Dec 21 2023

city: St. Louis

first: Jennifer

middle: E.

last: Phillips-Cremins

state: MO

address: 4515 McKinley Ave

department: Bioengineering

institute: Washington University in St. Louis

description:
GM07730_iPSC_Nanopore
Long reads

library_source: genomic

data_processing:
We performed base-calling of raw nanopore fast5 using guppy (version 6.2.1)and aligned the output fasta files to hg38 using minimap2 (version 2.22-r1101). We performed several quality-control steps to ensure only high-quality reads were used in downstream analysis: (1) removing reads that did not align to the FMR1 gene, (2) using only reads that mapped to the reverse strand due to cast errors for the ultra-high-GC content CGG STR in the forward strand, (3) filtering out truncated reads that did not contain an upstream sequence to the CGG tract “ACCAAACCAA” and at least four consecutive CGGs, and (4) removing reads that contain more than nine consecutive “TA” nucleotides within the CGG repeats, as these reflect base calling errors. We created a custom script to count the number of CGGs in the remaining high-quality reads by finding the first and last instances of the string “CGGCGGCGG”, counting the number of CGGs between them and subtracting five CGGs from the total sum. These five CGGs were excluded because they reflect CGGs located within the FMR1 5’UTR but upstream and external to the continuous CGG tract. We called DNA methylation from the long-reads using two different methods. We used nanopolish (version 0.13.2) to call methylation in the 19 CpG dinucleotides in the 500 bp FMR1 promoter (hg38 chrX:147911419-147911919). Because nanopolish cannot call DNA methylation over a variable number of CGG triplets, we used STRique (version 0.4.2) to call methylation over the CGG tract itself in our normal-length, pre-mutation, and FXS iPSCs.    For the FMR1 promoter, we first indexed the fast5 files using the nanopolish command 'index'. We called CpG methylation using the command 'call-methylation' in the window 'chrX:147,902,117-147,960,927'. We considered Log2 likelihood >0.1 as methylated and <-0.1 as un-methylated. For every single-molecule read in every iPSC line, we computed the proportion of 19 CpGs that were methylated.   To determine CpG methylation specifically at the CGG STR in the 5’UTR of FMR1, we first indexed the fast5 files using the STRique command 'index'. We then computed methylation status and CGG counts using the STRique command 'count' with the respective models 'r9_4_450bps_mCpG.model' and 'r9_4_450bps.model'. We only used reads with prefix and suffix scores greater than 4 for further analyses as the reads with <4 were of low-quality mapping scores to the upstream and downstream regions of the CGG tract. We then calculated the percentage of methylated CpGs over CGG and plotted methylated (1) and unmethylated (0) nucleotides as red and black stripes along the repeats, respectively.
Assembly: hg38

molecule: genomic DNA

source_name: iPSC

growth_protocol: Human iPS cells were cultured in mTeSR plus (STEMCELL Technology, 05825) supplemented with 1% (v/v) penicillin-streptomycin (Thermo Fisher, 15140122) at 37 °C and 5 % CO2 on Matrigel coated plates. Cells were passaged by incubating in 5 ml of Versene Solution (Thermo Fisher, 15040066) at 37 °C for 3 min, after which Versene was inactivated by mixing with 10 ml of full growth media. Cells were passaged every 2 - 7 days. All iPS culture plates were coated with 1.2 % (v/v) Matrigel hESC-Qualified Matrix (Corning, 354277) in DMEM/F-12 (Thermo Fisher, 11320033) for at least 1 hr at 37°C. All cell lines were male.

extract_protocol:
This protocol was modified from Giesselmann at el (16). Briefly, 1X10e7 hiPSCs were resuspended in 100 μl of 1XPBS. Cells were lysed by adding 10 ml of TLB solution composed of 10 mM Tris-Cl (pH 8), 25 mM EDTA (pH 8), 0.5 % SDS (wt/vol) and 20 μg ml-1 RNase A (Sigma) for 1 h at 37 °C. Then, proteins were digested at 50 °C for 3 hours using 50 μl of proteinase K (BIO-37084). The viscous solution was transferred into a 50-ml Falcon tube containing 5 g of phase-lock gel and 10 ml of ultrapure Phenol/Chloroform/Isoamyl Alcohol (Fisher) was added. Samples were mixed on a rotator at 40 r.p.m. for 10 min and phase separation was performed by centrifugation at 2,800g for 10 min. The aqueous phase was then carefully poured into a fresh 50-ml Falcon tube containing 5 g of phase-lock gel followed by a second phase separation using 10 ml of ultrapure Phenol/Chloroform/Isoamyl Alcohol. Samples were mixed and centrifuged as described above. The aqueous phase was poured into a fresh 50-ml Falcon tube, and the genomic DNA was precipitated using 4 ml of 5 M ammonium acetate together with 30 ml of ice-cold ethanol (100%) and gently inverted ten to twenty times. Precipitated DNA was centrifuged at 12,000g for 5 min and washed with 70% ethanol twice. Supernatant was removed and the DNA pellet was dried at room temperature (RT) for 2–5 min. Rehydration of DNA in 250 μl of 1XTris-EDTA (pH 8) was performed at RT on a rotator for 20 r.p.m. overnight. Samples were stored at 4 °C for 2 days before use.
To perform targeted sequencing of FMR1, we designed and synthesized CRISPR–Cas9 crRNAs targeting the genomic regions adjacent to the FMR1 CGG repeats with the ChopChop online tool. The crRNAs used are listed in Supplementary Table 2. Preparation of the Cas9 nucleoprotein complex (Cas9 RNPs) was performed as follows: lyophilized Cas9 crRNA and tracrRNA (IDT) were suspended at 100 μM in TE (pH 7.5). The 4 crRNA probes were pooled for the cleavage reaction by combining equal volumes of each crRNA probe (0.25 μl /each) and 1 μl tracrRNA (100 μM stock) in 8 μl of water. The pooled crRNAs and tracrRNA were annealed with a thermal cycler at 95º C for 5 mins, allowed to cool to room temperature, then spun down to collect any liquid in the bottom of the tube. To form Cas9 RNPs (for 10 reactions), components were assembled in a 1.5 ml Eppendorf DNA LoBind tube in the following order: annealed 10 μl crRNA•tracrRNA pool (10 μM), 10 μl 10x NEB CutSmart buffer, 79.2 μl Nuclease-free water, 0.8 μl HiFi Cas9 (62 μM, IDT). The tube was mixed thoroughly by flicking. RNPs were formed by incubating the tube at room temperature for 30 mins, then returned to ice until required. Meanwhile, dephosphorylated genomic DNA was prepared by assembling the components in a 1.5 ml Eppendorf DNA LoBind tube in the following order: 5 μg of high molecular weight (HMW) DNA in 24 μl, 3 μl NEB CutSmart Buffer (10x) and 3 μl of QuickCIP enzyme (NEBM0525S). The sample was then incubated in a thermocycler at 37º C for 20 minutes, 80º C for 2 minutes, then held at 20º C (room temperature). The reaction was mixed gently by flicking the tube and spun down. 10 μl RNPs from the previous step was incubated with 5 μg of dephosphorylated HMW DNA, 1 μl of 10 mM dATP, and 1 μl of Taq polymerase (NEB) for 60 min at 37 °C on a thermocycler followed by 5 min at 72 °C. 1 μl Proteinase K (Sigma, 20 mg/ml stock concentration) was added to each reaction, and samples were incubated at 43°C for 30 mins to remove proteins for following size selection. The reaction was then purified to remove high concentration salt as follows: Cas9-cut genomic DNA(total volume is 42 ul) was precipitated using 16 ul of 5 M ammonium acetate together with 126 ul of ice-cold ethanol (absolute) and gently inverted ten times. Precipitated DNA was spun down at 16,000g for 5 min. DNA was washed with 500 ul of 70% ethanol and centrifuged at 16,000g for 5 min, and this step was repeated two times. The supernatant was removed and the DNA pellet was dried at RT for 2-5 min. Rehydration of DNA was performed at 50 °C for 1 hour using 200 μl of 10 mM Tris-HCl (pH 8). DNA was further homogenized on a rotator at 37 °C and 20 r.p.m overnight. Size selection was then performed with the Bluepippin BLF7510 (sagescience) using the “0.75DF 3-10kb Marker S1” cassette definition with size range at 5-12 kb.   To perform barcode ligation, the following was performed: 3 μl unique barcode (ONT EXP-NBD104) was added to 50 μl of Blunt/TA Ligase Master Mix (NEB) for each sample. The reactions were incubated at RT for 10 min, spun down, and then put on a magnet. The beads were washed with 200 μl of freshly-prepared 70% ethanol, without disturbing the pellet, twice, and allowed to dry for 30~60 seconds. The remaining pellet was then resuspended in 16 μl nuclease-free water and incubated for 10 minutes at room temperature. The reaction was then placed on a magnet and 16 μl of supernatant was removed into a clean 1.5 ml Eppendorf DNA LoBind tube. Samples were then quantified using a Qubit fluorometer, together with the Qubit dsDNA HS assay kit (Thermo Fisher Scientific).   Adapters were then ligated by first adding 20 μl NEBNext® Quick Ligation Buffer (NEB#E6056S), 10 μl NEBNext Quick T4 DNA ligase(NEB#E6056S), and 5 μl Adapter Mix (AMII) at room temperature in a separate 1.5 ml Eppendorf DNA LoBind Tube. The ligation reaction was mixed thoroughly. 20 μl of the adapter ligation reaction was mixed with the pooled native barcode-ligated samples. Immediately after mixing, the remaining 15 μl of the adapter ligation mix was added to the native barcode-ligated sample, to yield a 100 μl ligation mix. The reaction was incubated for 10 minutes at room temperature. Then 1 volume (100 μl) of TE (pH 8.0) was added to the ligation mix, followed by 0.4x volume (80 μl) of AMPure XP Beads. The sample was then incubated for 10 minutes at room temperature, placed back on the magnet, and the supernatant was removed. The beads were then washed with 250 μl Long Fragment Buffer (LFB) twice and then air-dried for ~30 seconds. The library was eluted off the beads in 14 μl Elution Buffer (EB). 13 uL of the libary was then mixed with 37.5 μl sequencing buffer (SQB) and 25.5 μl loading beads (LB) and loaded onto the MinION flowcell.

value: iPSC


title: BT054 Rep 3


title: CCD-18CO, Vehicle, Rep3


title: CCD-18CO, Vehicle, Rep1


title: FXS_426_iPSC_Nanopore

description:
FXSSW_iPSC_Nanopore
Long reads


title: PMcut_scClone7_iPSC_Nanopore

description:
135-313_iPSC_Nanopore
Long reads


title: PMcut_scClone5_iPSC_Nanopore

description:
135-278_iPSC_Nanopore
Long reads


title: PMcut_scClone4_iPSC_Nanopore

description:
135-275_iPSC_Nanopore
Long reads


title: PMcut_scClone1_iPSC_Nanopore

description:
4D3_iPSC_Nanopore
Long reads


title: NL_27_iPSC_Nanopore

description:
20b_iPSC_Nanopore
Long reads


title: FXS_425_iPSC_Nanopore

description:
1H2_iPSC_Nanopore
Long reads


title: PMcut_scClone3_iPSC_Nanopore

description:
135-187_iPSC_Nanopore
Long reads


title: HK211 Rep 2


title: NL_18_iPSC_Nanopore

description:
176_iPSC_Nanopore
Long reads


title: NL_25_iPSC_Nanopore

description:
158_iPSC_Nanopore
Long reads


title: ML_scClone2_iPSC_Nanopore

description:
4H2_iPSC_Nanopore
Long reads


title: ML_scClone3_iPSC_Nanopore

description:
6D12_iPSC_Nanopore
Long reads


title: PMcut_scClone6_iPSC_Nanopore

description:
135-030_iPSC_Nanopore
Long reads


title: ML_scClone7_iPSC_Nanopore

description:
135-131_iPSC_Nanopore
Long reads


title: ML_scClone1_iPSC_Nanopore

description:
135-034_iPSC_Nanopore
Long reads


title: ML_scClone6_iPSC_Nanopore

description:
135-128_iPSC_Nanopore
Long reads


title: PMcut_scClone2_iPSC_Nanopore

description:
135-117_iPSC_Nanopore
Long reads


title: NL_18_iPSC_RNAseq_Rep1

data_processing:
RNA-seq reads were mapped to the hg38 ensembl reference transcriptome for both cDNA and ncRNA using kallisto quant with 100 bootstraps of transcript quantification. Reads were mapped to the ensembl cDNA and ncRNA transcriptomes as described in the kallisto documentation. The resulting quantifications were converted into DESEQ2 format, with transcript level counts mapped to gene level counts in R using the library("tximportData") according to DESEQ2 documentation recommendations. Genes with total counts less than 60 across all samples were dropped from analysis. Differentially called transcripts across the 7 cell lines studied were determined in a pairwise manner using DESEQ2 LRT with adjusted p < 0.005.
Assembly: hg38
Supplementary files format and content: The processed data files include abundance calculations (standard kallisto output, ending in .tsv) which includes the number of counts for each transcript. Additionally, Deseq output processed files includes the number of normalized counts for each transcript

extract_protocol:
We isolated total RNA from using the mirVana miRNA Isolation Kit (Thermo Fisher, AM1560) according to the manufacturer’s protocol. We used 100 ng of isolated RNA for RNA-seq library preparation using TruSeq Stranded Total RNA Library Prep Gold (Illumina, 20020598) according to the manufacturer’s instruction. In brief, we removed rRNA from the input RNA, followed by double stranded cDNA preparation using 0.8 U of SuperScript II RT (Thermo Fisher, 4376600) and A-tailing end repair. We ligated cDNA to TruSeq RNA Single Indexes Set A (Illumina, 20020492) to enable multiplex sequencing, followed by one round of of size selection (selecting for 300 bp) and bead clean-up : 42.5 uL of sample was purified with 42 uL of Agencourt AMPure XP beads (Beckman Coulter, A63881), then, 50 uL sample was cleaned with 50 uL Agencourt AMPure XP beads (Beckman Coulter, A63881). We amplified the purified samples by 15 PCR cycles and further purified using Agencourt AMPure XP beads (Beckman Coulter, A63881). We assessed library quality and quantities using the Agilent DNA 1000 reagent kit (Agilent, 5067–1504) on the Agilent Bioanalyzer 2100 (Agilent, 5067–4626) and Qubit high sensitivity RNA assay kit (Thermo Fisher, Q32852), respectively before sequencing on NextSeq500 (Illumina).
We ligated cDNA to TruSeq RNA Single Indexes Set A (Illumina, 20020492) to enable multiplex sequencing, followed by one round of of size selection (selecting for 300 bp) and bead clean-up : 42.5 uL of sample was purified with 42 uL of Agencourt AMPure XP beads (Beckman Coulter, A63881), then, 50 uL sample was cleaned with 50 uL Agencourt AMPure XP beads (Beckman Coulter, A63881). We amplified the purified samples by 15 PCR cycles and further purified using Agencourt AMPure XP beads (Beckman Coulter, A63881). We assessed library quality and quantities using the Agilent DNA 1000 reagent kit (Agilent, 5067–1504) on the Agilent Bioanalyzer 2100 (Agilent, 5067–4626) and Qubit high sensitivity RNA assay kit (Thermo Fisher, Q32852), respectively before sequencing on NextSeq500 (Illumina).


title: FXS_CN_2_IgG_CnR

data_processing:
We analyzed CUT&RUN sequencing data using Bowtie2 (version 2.2.5) with parameters “--local --very-sensitive-local --no-mixed --no-discordant --phred33 -I 10 -X 700”. We removed duplicates and unmapped reads and then converted the file to bam format using Samtools (version 1.11) fixmate, sort, markdup “-r”, and view “-F 4” commands. We downsampled mapped reads for IgG and H3K9me3 samples to the lowest number of mapped reads for each comparison group using Samtools view with parameters “-hbs” and a seed of 42. Indices were created for each file using Samtools “index”. We then input normalized bam files using BamCompare from deeptools (version 3.3.0) using the “–extendReads –binSize 10 –smoothLength 30 –operation subtract” parameters. For CUT&RUN data from brain tissue, we performed data processing as earlier described with minor modifications. After mapping, we kept duplicates instead of removing them. Unlike with ChIP-seq, this is an acceptable method of data processing. In CUT&RUN, targeted DNA fragmentation is performed using a pA/G-MNase fusion protein tether to an antibody which is bound to the target. As a result, duplicates are expected based on MNase cutting DNA in a non-random pattern. This is unacceptable in ChIP-seq as DNA is randomly sheared and therefore, duplicates are expected to be primarily from PCR over-cycling. Lastly, we converted downsampled bam files to bigwigs with log2 input normalization using BamCoverage from Deeptools (v3.3.0) with parameters “--extendReads –binSize 10 –smoothLength 30 --operation log2”. All other steps were the same.
Assembly: hg38
Supplementary files format and content: The CUT&RUN processed data files are in the ENCODE bigwig and BED format.
Library strategy: CUT&RUN

source_name: Brain

growth_protocol: We sectioned tissue from the caudate nucleus into aliquots of ~100 mg. We performed sectioning on dry ice with sterile forceps and a sterile, single-use razor using a petri dish as a platform after all equipment had been pre-chilled on dry ice. Prior to douncing and homogenization, we pre-chilled all buffers, reagents, and equipment on wet ice. We performed the entire procedure on wet ice. We placed tissue in 10 mL of ice-cold Homogenization Buffer (0.32 M sucrose (Sigma-Aldrich, S0389-500G), 5 mM CaCl2 (Thermo Fisher, J63122-AD), 10 mM Tris-HCl pH 8.0 (Invitrogen, 15568025), 3 mM MgAc2 (Sigma-Aldrich, 63052-100ML, 0.1% Triton X-100 (Sigma-Aldrich, T8787-100ML), 0.1 mM EDTA (Invitrogen, 15575020), 1X Protease Inhibitor Cocktail (Roche, 11873580001)) and dounced the tissue with 20 strokes of the loose pestle and 7 strokes of the tight pestle using a 15 mL Dounce Tissue Grinder (Wheaton, 357544). We performed douncing very slowly and gently to avoid unnecessary mechanical stress. We laid 10 mL of homogenized tissue over 14 mL of ice-cold Sucrose Cushion (1.8 M sucrose, 10 mM Tris-HCl pH 8.0, 3 mM MgAc2, 1X Protease Inhibitor Cocktail). We laid an additional 12 mL of ice-cold Homogenization Buffer on top of the homogenized tissue and centrifuged for 2 hours at 4°C at 25,700 RPM (~81,150xg) in a SW Ti 32 swinging bucket rotor. We removed the supernatant and added FANS Buffer (1X PBS (Corning, 21-040-CV), 1% Bovine Serum Albumin (Sigma-Aldrich, A7906-50G), 1X Protease Inhibitor Cocktail), to the pellet. We incubated the pellet on ice for 20 mins before resuspending. We counted the nuclei and centrifuged the solution for 6 mins at 4°C at 600xg. We resuspended nuclei in FANS buffer at a concentration of 3 million nuclei per mL. We blocked nuclei in FANS buffer for 15 mins at 4°C while rotating. We stained nuclei with anti-NeuN (1:1000, Sigma-Aldrich, MAB377X) for 90 mins and added DAPI (1:2000, Sigma-Aldrich, MBD0015-1ML) with 5 mins left on the staining timer. Staining was performed with end-over-end rotation at 4°C. Next, we centrifuged the nuclei for 6 mins at 4°C at 600xg. We resuspended nuclei in FANS buffer at a concentration of 6 million nuclei per mL, filtered the solution using a 5 mL FACS sorting tube (Corning, 352235), and sorted using the MoFlo Astrios (Beckman Coulter). All tissue samples were from male patients.

extract_protocol:
CUT&RUN was completed as previously described (Epicypher). In brief, iPS cells were harvested and then washed in wash buffer (20 mM Hepes KOH pH 7.5, 150 mM NaCl, 0.5 mM Spermadine, 1 Roche Complete Protease Inhibitor EDTA-free mini tablet per 10 mL) and bound to Concanavalin A beads (BioMagPlus) that had been activated and washed with binding buffer (20 mM Hepes KOH pH 8.0, 10 mM KCl, 1 mM CaCl2, 1 mM MnCl2). The cells were then incubated with the Concanavalin A magnetic beads, primary antibody (either IgG (Sigma I8140) or H3K9me3 (Abcam ab8898), and antibody buffer (digi-wash buffer – 0.1% digitonin in wash buffer – with 2 mM EDTA) overnight at 4 C while rotating. Cells were washed with digi-wash buffer and then incubated in a solution containing protein A-MNase and digi-wash buffer for 10 minutes at room temperature. After incubation, the samples were washed in digi-wash buffer and 100 uL digi-wash buffer was added to the samples which were then placed on ice to chill for five minutes. After chilling, 2 uL of 100 mM CaC was added to activate protein A-MNase chromatin digestion. After 2 hours at 4 C with rotation, 100 uL of 2X stop buffer (340 mM NaCl, 20 mM EDTA, 4 mM EGTA, 0.05% Digitonin, 50 ug/mL RNase A, 50 ug/mL Glycogen) was added to halt the reaction which was then incubated at 37 C for 30 minutes to release chromatin fragments. Supernatant was collected and DNA was extracted using phenol-chloroform and ethanol precipitation. The resulting DNA was quantified on a Qubit Fluorometer. For nuclei isolated from brain tissue, slight modifications were made. We performed CUT&RUN on sorted nuclei as described below with minor modifications. We sorted nuclei into CUT&RUN Wash Buffer and immediately bound nuclei to Concanavalin A beads after returning from sorting. Additionally, we substituted 0.1%, 0.1%, and 0.05% digitonin in the Antibody Buffer, Digi-Wash Buffer, and 2X Stop Buffer with 0.1%, 0.1%, and 0.04% Triton X-100. All other steps were the same.
CUT&RUN libraries were prepared for sequencing using the NEBNext Ultra II DNA Library Prep Kit (NEB #7103) according to manufacturer's protocol. Size selection of adaptor-ligated libraries was performed using AgenCourt Ampure XP beads (Beckman Coulter, A63881) according to the manufacturer’s protocol. Size selection targeted <1 kb fragment size and libraries were amplified using 11 PCR cycles. Input amounts for library preparation using the NEBNext Ultra II DNA Library Prep Kit were 1 ng of purified libraries. Library quality and quantities were assessed using the Agilent DNA 1000 reagent kit (Agilent, 5067–1504) on the Agilent Bioanalyzer 2100 (Agilent, 5067–4626) and Qubit high sensitivity RNA assay kit (Thermo Fisher, Q32852), respectively before sequencing on NextSeq500 (Illumina)

value: Brain

value: Patient-derived post-mortem brain tissue from caudate nucleus

value: FXS clinical diagnosis

tag: antibody

value: Sigma I8144


title: PM_137_iPSC_Nanopore

description:
111_iPSC_Nanopore
Long reads


title: FXS_421_iPSC_Nanopore [135]

description:
135_iPSC_Nanopore
Long reads


title: FXS_CN_2_H3K9me3_CnR

value: Abcam ab8898


title: FXS_CN_1_IgG_CnR


title: NL_CN_2_IgG_CnR

value: Clinically healthy


title: FXS_CN_1_H3K9me3_CnR


title: WTC11_iPSC_IgG_CnR

data_processing:
library strategy: CUT&RUN
Sequencing data was analyzed using Bowtie2 (version 2.2.5) with parameters “--local --very-sensitive-local --no-unal --no-mixed --no-discordant --phred33 -I 10 -X 700”. Duplicates and unmapped reads were removed using Samtools (version 1.11) markdup command. After removing duplicates and unmapped reads, files were converted to bam files using Samtools, and then the resulting bam files were converted to bigwig format using BamCoverage from Deeptools (version 3.3.0). The “--normalizeUsing RPKM –extendReads” parameters for BamCoverage were used.
Assembly: hg38
Supplementary files format and content: The CUT&RUN processed data files are in the ENCODE bigwig and BED format.

extract_protocol:
CUT&RUN was completed as previously described (Epicypher). In brief, iPS cells were harvested and then washed in wash buffer (20 mM Hepes KOH pH 7.5, 150 mM NaCl, 0.5 mM Spermadine, 1 Roche Complete Protease Inhibitor EDTA-free mini tablet per 10 mL) and bound to Concanavalin A beads (BioMagPlus) that had been activated and washed with binding buffer (20 mM Hepes KOH pH 8.0, 10 mM KCl, 1 mM CaCl2, 1 mM MnCl2). The cells were then incubated with the Concanavalin A magnetic beads, primary antibody (either IgG (Sigma I8140) or H3K9me3 (Abcam ab8898), and antibody buffer (digi-wash buffer – 0.1% digitonin in wash buffer – with 2 mM EDTA) overnight at 4 C while rotating. Cells were washed with digi-wash buffer and then incubated in a solution containing protein A-MNase and digi-wash buffer for 10 minutes at room temperature. After incubation, the samples were washed in digi-wash buffer and 100 uL digi-wash buffer was added to the samples which were then placed on ice to chill for five minutes. After chilling, 2 uL of 100 mM CaC was added to activate protein A-MNase chromatin digestion. After 2 hours at 4 C with rotation, 100 uL of 2X stop buffer (340 mM NaCl, 20 mM EDTA, 4 mM EGTA, 0.05% Digitonin, 50 ug/mL RNase A, 50 ug/mL Glycogen) was added to halt the reaction which was then incubated at 37 C for 30 minutes to release chromatin fragments. Supernatant was collected and DNA was extracted using phenol-chloroform and ethanol precipitation. The resulting DNA was quantified on a Qubit Fluorometer.
CUT&RUN libraries were prepared for sequencing using the NEBNext Ultra II DNA Library Prep Kit (NEB #7103) according to manufacturer's protocol. Size selection of adaptor-ligated libraries was performed using AgenCourt Ampure XP beads (Beckman Coulter, A63881) according to the manufacturer’s protocol. Size selection targeted <1 kb fragment size and libraries were amplified using 11 PCR cycles. Input amounts for library preparation using the NEBNext Ultra II DNA Library Prep Kit were 1 ng of purified libraries. Library quality and quantities were assessed using the Agilent DNA 1000 reagent kit (Agilent, 5067–1504) on the Agilent Bioanalyzer 2100 (Agilent, 5067–4626) and Qubit high sensitivity RNA assay kit (Thermo Fisher, Q32852), respectively before sequencing on NextSeq500 (Illumina)


title: ML_scClone5_iPSC_Nanopore

description:
135-125_iPSC_Nanopore
Long reads


title: WTC11_iPSC_H3K9me3_CnR


title: NL_CN_1_IgG_CnR


title: Kolf2.1J_iPSC_IgG_CnR

value: Sigma I8143


title: Kolf2.1J_iPSC_H3K9me3_CnR


title: ML_scClone4_iPSC_Nanopore

description:
135-116_iPSC_Nanopore
Long reads


title: ML_scClone3_iPSC_H3K9me3_CnR


title: ML_scClone2_iPSC_IgG_CnR

value: Sigma I8140


title: ML_scClone2_iPSC_H3K9me3_CnR


title: PMcut_scClone1_iPSC_IgG_CnR


title: PMcut_scClone1_iPSC_H3K9me3_CnR


title: FXS_425_iPSC_IgG_CnR


title: FXS_425_iPSC_H3K9me3_CnR


title: NL_18_iPSC_RNAseq_Rep2


title: NL_18_iPSC_IgG_CnR


title: NL_18_iPSC_H3K9me3_CnR


title: NL_CN_2_H3K9me3_CnR


title: PMcut_scClone7_iPSC_H3K9me3_CnR


title: FXS_421_iPSC_H3K9me3_CnR


title: PMcut_scClone7_iPSC_IgG_CnR


title: PMcut_scClone5_iPSC_IgG_CnR


title: PMcut_scClone4_iPSC_IgG_CnR


title: PMcut_scClone3_iPSC_IgG_CnR


title: NL_CN_1_H3K9me3_CnR


title: ML_scClone3_iPSC_IgG_CnR


title: ML_scClone7_iPSC_IgG_CnR


title: ML_scClone6_iPSC_IgG_CnR


title: PMcut_scClone3_iPSC_H3K9me3_CnR


title: ML_scClone5_iPSC_IgG_CnR


title: ML_scClone6_iPSC_H3K9me3_CnR


title: ML_scClone5_iPSC_H3K9me3_CnR


title: PMcut_scClone2_iPSC_H3K9me3_CnR


title: PMcut_scClone2_iPSC_IgG_CnR


title: ML_scClone4_iPSC_IgG_CnR


title: ML_scClone1_iPSC_IgG_CnR


title: ML_scClone4_iPSC_H3K9me3_CnR


title: ML_scClone1_iPSC_H3K9me3_CnR


title: FXS_421_iPSC_IgG_CnR


title: PMcut_scClone6_iPSC_H3K9me3_CnR


title: PMcut_scClone6_iPSC_IgG_CnR


title: PMcut_scClone5_iPSC_H3K9me3_CnR


title: PMcut_scClone1_iPSC_RNAseq_Rep2


title: FXS_421_iPSC_RNAseq_Rep2


title: PMcut_scClone1_iPSC_RNAseq_Rep1


title: FXS_421_iPSC_RNAseq_Rep1


title: PMcut_scClone4_iPSC_H3K9me3_CnR


title: FXS_470_NPC_RNAseq_Rep2

source_name: iPSC derived NPC

growth_protocol: Human iPSC were differentiated into NPCs using a previously established protocol (Xie et al 2013). Briefly, undifferentiated cells were maintained in mTESR Plus (STEMCELL Technology, 05825) on Matrigel coated plates. They were seeded onto fresh Matrigel plates in NPC media at a density of 16,000 cells/cm2. NPC media was changed every day and cells were harvested at the end of day 8. The NPC differentiation medium consists of DMEM/F12 (Thermo Fisher, 11320033) with 5 μg/ml insulin, 64 μg/ml L-ascorbic acid, 14 ng/ml sodium selenite, 10.7 ug/ml Holo-transferrin, 543 μg/ml sodium bicarbonate, 10 μM SB431542 and 100 ng/ml Noggin.

value: iPSC derived NPC


title: NL_25_NPC_RNAseq_Rep2


title: ML_scClone7_iPSC_H3K9me3_CnR


title: FXS_470_NPC_RNAseq_Rep1


title: NL_25_NPC_RNAseq_Rep1


title: FXS_B_900_RNAseq_Rep2

source_name: B-lymphocytes

growth_protocol: Patient-derived B-lymphocytes were cultured as previously described1. In brief, cells were grown in suspension in RPMI 1640 media (Sigma, R8758) supplemented with 2 mM glutamine, 15 % (v/v) Fetal Bovine Serum, 1 % (v/v) penicillin-streptomycin (Thermo Fisher, 15140122) at 37 °C and 5 % CO2. Cells were passaged every 2-4 days, when they reached a density of approximately 5e5 cells/mL. All cell lines were male.

value: B-lymphocytes


title: NL_27_NPC_RNAseq_Rep1


title: FXS_B_900_RNAseq_Rep1


title: FXS_B_650_RNAseq_Rep1


title: NL_B_RNAseq_Rep1


title: NL_B_RNAseq_Rep2


title: FXS_426_NPC_RNAseq_Rep2


title: FXS_B_650_RNAseq_Rep2


title: FXS_426_NPC_RNAseq_Rep1


title: NL_18_NPC_RNAseq_Rep2


title: FXS_421_NPC_RNAseq_Rep1


title: NL_18_NPC_RNAseq_Rep1


title: PM_137_NPC_RNAseq_Rep1


title: PM_137_NPC_RNAseq_Rep2


title: FXS_426_NPC_HiC

data_processing:
Paired-end reads were aligned independently to the hg38 human genome using bowtie2 (global parameters: --verysensitive –L 30 –score-min L,-0.6,-0.2 –end-to-end --reorder; local parameters: --very-sensitive –L 20 –score-min L,-0.6,-0.2 –end-to-end --reorder) through the HiC-Pro software8. Unmapped reads, non-uniquely mapped reads, and PCR duplicates were filtered and uniquely aligned reads were paired. Raw contact matrices for all samples were assembled into 20kb, 40kb, and 100kb non-overlapping bins and balanced using the Knight-Ruiz algorithm. The balanced cis matrixes were then normalized across samples being directly compared using median-of-ratios size factors conditioned on genomic distance. For trans interactions, because trans interactions are too sparse to quantify at higher matrix resolutions, each trans m x n contact matrix was assembled using Juicer by binning hg38 aligned, in situ Hi-C paired-end reads into uniform 1-Mb bins and then balanced using the Knight Ruiz algorithm with default parameters. Data was then quantile normalized across samples.
Assembly: hg38
Supplementary files format and content: The processed data files are the standard validPairs file format from the output of the software HiC-Pro. The data includes all paired reads that are valid.

extract_protocol:
We prepared Hi-C libraries using the Arima Genomics Hi-C kit (Arima Genomics, A510008) according to the manufacturer’s protocol. Briefly, we enzymatically digested genomic DNA within nuclei of crosslinked cell pellets, and created biotinylated ligation junctions between the digested ends at proximity. Then we extracted DNAs and sheared to an average size of ~400 bp using a Covaris S220 sonicator at 140 W peak incident power, 10 % duty factor, and 200 cycles per burst for 55 seconds. We further size selected the sheared DNA to 200-600 bp using AgenCourt Ampure XP beads (Beckman Coulter, A63881) according to manufacturer’s protocols. Biotin-tagged ligation junctions via pulldown using streptavidin breads from the Arima Hi-C kit (Arima Genomics, A510008) according to manufacturer’s protocol. Streptavidin beads containing Hi-C libraries were stored at -20 °C for no more than 3 days before Illumina sequencing library preparation was performed.
Hi-C libraries were prepped for sequencing by first washing adaptor-ligated Hi-C libraries on streptavidin beads twice in 150 uL of wash buffer at 55 °C and once in 100 ml of elution buffer at room temperature using Hi-C kit (Arima Genomics, A510008). DNA was eluted from streptavidin beads by boiling at 98 °C for 10 min in 15 uL elution buffer. Subsequently the libraries were amplified using NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB, E7645S) with 8 PCR cycles according to the manufacturer’s protocol.


title: NL_18_NPC_HiC


title: NL_27_NPC_RNAseq_Rep2


title: FXS_421_NPC_RNAseq_Rep2


title: FXS_425_iPSC_HiC


title: NL_27_NPC_HiC


title: FXS_470_NPC_HiC


title: NL_25_NPC_HiC


title: PM_137_NPC_HiC


title: 6718_iPSC_Input_ChIP_V2

data_processing:
ChIP-seq data was processed as previously described1. In brief, 75 bp single end reads were mapped to the hg38 reference genome using Bowtie with parameters: --tryhard -m 2. Optical and PCR duplicates were removed using samtools. Reads were downsampled to achieve equal read numbers across samples being compared. CTCF peaks were called using MACS2 with a cutoff of p <1x10-8. H3K9me3 domains were called using RSEG.
Assembly: hg38
Supplementary files format and content: The ChIP-seq processed data files are in the ENCODE narrowPeak, bigwig, or BED format.

extract_protocol:
ChIP-seq was performed as previously described with minor modification1-6. Briefly, crosslinked cell pellets (consisting of 10 million cells for CTCF ChIP-seq or 3 million cells for H3K9me3 ChIP-seq), were lysed in cell lysis buffer (10 mM Tris pH 8.0, 10 mM NaCl, 0.2 % NP-40/Igepal, Protease Inhibitor, PMSF) on ice for 10 min. The suspension was then homogenized with pestle A 30 times. The nuclei were pelleted from the initial lysate at 2,500 g at 4C and the resulting nuclei were further lysed in 500 μl of nuclear lysis buffer (50 mM Tris pH 8.0, 10 mM EDTA, 1 % SDS, Protease Inhibitor, PMSF) and incubated on ice for 20 min. Lysed nuclei were then sonicated by adding 300 μP IP Dilution Buffer (20 mM Tris pH 8.0, 2 mM EDTA, 150 mM NaCl, 1 % Triton X-100, 0.01 % SDS, Protease Inhibitor, PMSF) and transferring to sonication tubes. Samples were sonicated using a QSonica Q800R2 sonicator for 1 hour set at 100% amplitude, with pulse set to 30 seconds on and 30 seconds off. The sonicated lysate was then pelleted at 14,000 RPM in 4 °C and the supernatant was transferred to a reaction consisting of 3.7 ml IP Dilution Buffer, 500 μl Nuclear Lysis Buffer, 175 μl of a 1:1 ratio of ProteinA:ProteinG bead slurry (Thermofisher, 15918014 and 15920010, respectively) and 50 μg of rabbit IgG for preclearing. The preclearing reactions were rotated at 4 °C for 2 hours. 200 ul of the pre-clearing reactions was saved as the “input” control. The remaining solution was added to an immunoprecipitation reaction consisting of 1 ml cold PBS, 20 μl Protein A, 20 μl Protein G, and 1 ul/million cells of either CTCF or H3K9me3 antibody and rotated overnight at 4 °C. The immunoprecipitation reactions were prepared one day before cell lysis and rotated overnight at 4 °C. The next day, IP reactions were pelleted and the supernatant was discarded. The remaining pellet was washed once with IP Wash Buffer 1 (20 mM Tris pH 8, 2 mM EDTA, 50 mM NaCl, 1 % Triton X-100, 0.1 % SDS), twice with High Salt Buffer (20 mM Tris pH 8, 2 mM EDTA, 500 mM NaCl, 1 % Triton X-100, 0.01% SDS), once with IP Wash Buffer 2 (10 mM Tris pH 8, 1 mM EDTA, 0.25 M LiCl, 1 % NP-40/Igepal, 1 % sodium deoxycholate) and twice with TE buffer (10 mM Tris pH 8, 1 mM EDTA pH 8). The IP DNA was eluted from the washed beads in Elution buffer (100 mM NaHCO3, 1 %SDS, prepared fresh) by resuspending and then spinning at 7,500 rpm. RNA was degraded with 2 ul RNAse A (Sigma, 10109142001)  and incubated at 65 °C for 1 hour. To degrade residual DNA, 3 ul proteinase K (NEB P8107S) was added and all samples were incubated overnight at 65 °C. DNA was extracted using phenol:chloroform and ethanol precipitation methods. Antibodies used in this study were: CTCF (Millipore 07-729), H3K9me3 (Abcam ab8898), IgG (Sigma I8140).
ChIP-seq libraries were prepared for sequencing using the NEBNext Ultra II DNA Library Prep Kit (NEB #7103) according to manufacturer's protocol. For ChIP-seq, size selection of adaptor-ligated libraries was performed using AgenCourt Ampure XP beads (Beckman Coulter, A63881) according to the manufacturer’s protocol. For ChIP-seq, size selection targeted <1 kb fragment size and libraries were amplified using 11 PCR cycles. Input amounts for library preparation using the NEBNext Ultra II DNA Library Prep Kit were 1 ng of purified ChIP-seq libraries.


title: CS0002_iPSC_Input_ChIP_V2


title: 6718_iPSC_H3K9me3_ChIP_V2


title: PMcut_scClone1_iPSC_HiC


title: SA3-5_iPSC_Input_ChIP_V2


title: CS0002_iPSC_H3K9me3_ChIP_V2


title: NL_27_NPC_Input_C_ChIP


title: SA3-5_iPSC_H3K9me3_ChIP_V2


title: FXS_421_iPSC_Input_C_ChIP


title: FXS_421_iPSC_CTCF_ChIP

value: MIllipore 07-729


title: FXS_426_iPSC_H3K9me3_ChIP

description:
FXS_specific_Rseg_domains_iPS_v2.bed
FXSVariable_iPS_Domains.bed
common_Rseg_domains_iPS_v2.bed


title: FXS_421_iPSC_H3K9me3_ChIP


title: NL_27_NPC_CTCF_ChIP


title: NL_18_iPSC_H3K9me3_ChIP


title: FXS_426_iPSC_Input_ChIP


title: FXS_421_NPC_HiC


title: PM_137_iPSC_H3K9me3_ChIP


title: PMcut_scClone1_iPSC_CTCF_ChIP


title: FXS_425_iPSC_CTCF_ChIP


title: NL_18_iPSC_CTCF_ChIP


title: FXS_426_iPSC_CTCF_ChIP


title: FXS_425_iPSC_Input_ChIP


title: PMcut_scClone1_iPSC_Input_ChIP


title: PM_137_iPSC_CTCF_ChIP


title: FXS_421_iPSC_HiC


title: NL_18_iPSC_Input_ChIP


title: PM_137_iPSC_Input_ChIP


title: FXS_421_iPSC_Input_H_ChIP


title: FXS_470_NPC_Input_H_ChIP


title: FXS_470_NPC_CTCF_ChIP


title: FXS_470_NPC_Input_C_ChIP


title: FXS_470_iPSC_Input_ChIP


title: FXS_470_NPC_H3K9me3_ChIP

description:
FXS_specific_Rseg_domains_NPC_v2.bed
FXSVariable_NPC_Domains.bed
common_Rseg_domains_NPC_v2.bed


title: FXS_470_iPSC_H3K9me3_ChIP


title: NL_B_H3K9me3_ChIP

description:
FXS_Bcell_Denovo_Domains.bed
FXS_Bcell_Spreading_Domains.bed


title: NL_B_Input_ChIP


title: FXS_B_900_Input_ChIP


title: FXS_B_650_H3K9me3_ChIP


title: FXS_426_NPC_H3K9me3_ChIP


title: FXS_426_NPC_Input_ChIP


title: FXS_B_650_Input_ChIP


title: FXS_426_NPC_CTCF_ChIP


title: NL_27_iPSC_Input_ChIP


title: NL_27_iPSC_H3K9me3_ChIP


title: NL_27_NPC_H3K9me3_ChIP


title: NL_27_NPC_Input_H_ChIP


title: NL_18_NPC_Input_ChIP


title: NL_18_NPC_H3K9me3_ChIP


title: NL_18_NPC_CTCF_ChIP


title: NL_25_NPC_Input_C_ChIP


title: NL_25_NPC_Input_H_ChIP


title: NL_25_NPC_H3K9me3_ChIP


title: NL_25_iPSC_H3K9me3_ChIP


title: FXS_421_NPC_H3K9me3_ChIP


title: FXS_421_NPC_Input_ChIP


title: PM_137_NPC_Input_ChIP


title: PM_137_NPC_CTCF_ChIP


title: NL_25_NPC_CTCF_ChIP


title: NL_25_iPSC_Input_ChIP


title: FXS_B_900_H3K9me3_ChIP


title: FXS_426_iPSC_PCRFree_WGS

data_processing:
PCR Free whole genome sequencing libraries were aligned to hg38 using bwa-mem (v0.7.10-r789) and default parameters for coverage analysis. Prior to mapping, reads were qualitychecked using FastQC (v0.11.9). After reads were aligned to hg38 using bwa-mem, the results were converted to .bam files and sorted using Samtools (v1.11).
For STR analysis, we performed STR genotyping on the PCR-free whole genome sequencing data from N=120 ancestry-, sex-, sequencing depth, and cell type-matched non-diseased iPSC-lines from the HipSci Consortium (Streeter et al., 2017). We obtained PCR-free whole genome sequencing data from public repositories (Table S4) as pre-processed CRAM files aligned to hg19. We first converted cram files into fastq files using 'samtools fastq' with default parameters and realigned to hg38 using bwa mem with the parameter -T 0. We then downsampled all reads to ~500 million reads tobe comparable to the sequencing depth of the NL and FXS iPSC lines used in this study. Next, we ran GangSTR (version 2.5.0) on all hiPSC bam libraries with the STR input file 'hg38_ver13.bed' from GangSTR GitHub page (https://github.com/gymreklab/GangSTR), which consists of >830,000 STRs. Default parameters with one additional parameter declaring sex as males (--samp-sex M) were used. We then filtered out low quality GangSTR predictions using DumpSTR (version 4.0.0) with the following parameters '--gangstr-min-call-DP 10 --gangstr-max-call-DP 1000'. Since DumpSTR was limited by the quality score from a haploid X chromosome, we focused only on autosomes. The resulting data consisted of an allele-specific STR tract length estimate for 832,380 STRs genome-wide in N=120 non-diseased iPSC lines. We also ran ExpansionHunter (version 5.0.0) using a custom json file created using the STRs from GangSTR's "hg38_ver13.bed"file. We created a resulting data consisting of 832,380 STRs in N=120 non-diseased iPSC lines. We ran GangSTR and EH with the same parameters for the NL and FXS iPSC lines used in this study, including NL_18, NL_27, NL_25, FXS_421, FXS_426 & FXS_470. The N=120 sex-, sequencing depth-, ancestry-, and cell type-matched PCR-free whole genome sequencing datasets from the HipSci Consortium iPSC lines afforded us the ability to assess the distribution of allele lengths for a given STR tract across a set of non-diseased, normal-length iPSC. We generated more than 830,000 STR length distributions, one per each STR tract, representing the expected null distribution of lengths for non-diseased, normal-length iPSCs (Figure 6A). For each STR on autosomes, we generated an expected null distribution of allele lengths using both alleles per all N=120 normal-length iPSCs (N=240 alleles). We filtered out any STRs that were the same length across the entire hiPSC population and across FXS iPSC ? such STRs were classified as "Stable". All STRs that were not classified as "Stable" were moved forward for statistical testing. The resulting tables consist of p-values for individual cell-lines used in this study.
Assembly: hg38
Supplementary files format and content: The processed data files contain outputs from GangSTR and ExpansionHunter.

extract_protocol: For PCR free whole genome sequencing, DNA for samples was extracted using the ThermoFisher GeneJET Genomic DNA Purification Kit (K0721), then sent to GeneWiz for Illumina PCR free, paired end sequencing.


title: FXS_421_NPC_CTCF_ChIP


title: NL_CS0002_iPSC_PCRFree_WGS


title: FXS_470_iPSC_PCRFree_WGS


title: NL_27_iPSC_PCRFree_WGS


title: FXS_421_iPSC_Nanopore [135.P19]

description:
135_iPSC_Nanopore
Long reads


title: NL_25_iPSC_PCRFree_WGS


title: PM_137_iPSC_PCRFree_WGS


title: PM_137_NPC_H3K9me3_ChIP


title: input in normal media in 2D culture replicate

status: Public on Nov 19 2023

city: Parma

first: Roberto

last: Ferrari

state: Parma

address: Parco Area delle Scienze 23/A

department: Department of Chemistry, Life Sciences and Environmental Sustainability

country: Italy

institute: University of Parma

description: 2D growth

data_processing: Analysis of sequence data was carried out as previously described (Ferrari et al., 2014) with minor modifications. Reads were aligned to the hg38 human genome reference sequence (GRCh38) using Bowtie (Langmead et al., 2009) and aligning parameters of uniqueness (-S –m1 –v2 –t –q). p values for the significance of ChIP-seq counts compared to input DNA were calculated as described (Pellegrini and Ferrari, 2012) using a threshold of 10−8 and a false discovery rate (FDR) < 1%.

source_name: breast

growth_protocol:
2D growth of cells.T47D breast cancer cells were routinely grown in 10 cm dishese with RPMI 1640 medium supplemented with 10% FBS, 2 mM L-glutamine, 100 U/ml penicillin and 100μg/ml streptomycin.
3D growth of cells. Prechilled p60 plates were coated with a thin layer of Matrigel (Corning Life Sciences) and then incubated for 20–30 min at 37ºC to allow polymerization without over drying. 200,00 cells trypsinized cells were resuspended and plated on-top of the Matrigel without disrupting the capsule. Culture was maintained for 10 days changing the medium every 2-3 days.  Spheroids extraction from 3D matrix: Dishes containing the spheroids grown for 10 days were rinsed twice with PBS followed by addition of 3 ml ice-cold PBS-EDTA. Matrigel including the 3D spheroids was carefully detached with a plastic scraper and left on ice for 30 min to allow complete depolymerization of the gel. The liquid solution was transferred to a conical tube, centrifuged for 5 min at 112 x g and rinsed twice with 0.5 volume of PBS-EDTA. The cell pellet was then ready for further processing.

extract_protocol:
ChIP assays were performed as described (Strutt and Paro, 1999)
Single-end (SE) ChIP-seq libraries were constructed from 0,1-1 ng of immunoprecipitated and input DNA using the Ovation Ultralow DR Multiplex System 1-8 and 9-16 kit (NuGen). To minimize false positives calling, several input libraries were sequenced to reach saturation with a coverage of 4 reads/bp of the human genome for each condition.

treatment_protocol:
For the experiments with hormones, cells were plated in RPMI medium without phenol red supplemented with 10% dextran-coated charcoal treated FBS (DCC/FBS) and 48 h later medium was replaced by fresh medium without serum. After 24h in serum-free conditions, cells were incubated with 10 nM R5020 for different times at 37ºC.
For hormonal induction on the 3D spheroids, T47D cells were plated on top of phenol red-free Matrigel and after 7 days of culture medium was replaced by RPMI medium without phenol red supplemented with 10% dextran-coated charcoal treated FBS (DCC/FBS) and 48 h later medium was replaced by fresh medium without serum. After 24h in serum-free conditions, cells were incubated with 10 nM R5020 for different times at 37ºC.

value: breast

value: Epithelial cancer metastatic

value: 2D culture normal media


title: CUT&RUN, IgG, effector, WT (4dpi)

status: Public on Oct 10 2023

city: Nutley

first: Hai-Hui

last: Xue

state: NJ

address: 111 Ideation Way

department: Center for Discovery and Innovation

institute: Hackensack University Medical Center

data_processing:
Cut&Run reads were trimmed remaining 100 bp from 5'end using trim_galore (v3.5).
Cut&Run reads were aligned to the mm10 genome using Bowtie2 version 2.3.4.1.
Sam files were then processed to bam files using samtools (v1.7) and duplication reads were removed using picard MarkDuplicates (v2.21.6).
Bam files were then processed by macs2 (v2.1.1) with qval<0.05, FC>2 to call narrowPeak.
BigWig files were transfered from macs2 output bdg files normalized by reads on peaks. WT-IgG bigwig file was normalized by library depth.
Assembly: mm10
Supplementary files format and content: narrowPeak
Library strategy: Cut&Run-sequencing

source_name: splenocytes

growth_protocol: CD45.2+ WT, TbetKO, or Tbet/Runx double KO P14 TCR transgenic CD8 T cells were adoptively transferred into CD45.1+ B6.SJL recipients, followed by i.p. infection with LCMV-Armstrong. After 4-6 days,  CD45.2+CD8+ effector cells were sort-purified for downstream analysis.

extract_protocol:
CD8+ T cell subsets were crossed-linked with formaldehyde, and then incubated with Tle3 antibody overnight, followed by incubation with Protein A/G-MNase, calcium-mediated MNase activation. The reaction was stopped and then genomic DNA fragments were extracted.
The DNA segments from Tle3 Cut&Run were end-repaired and ligated to indexed Illumina adaptors, followed by amplification by PCR with a low number of cells (18-21 cycles). The resulting libraries were seqeunced with Illumina Hiseq-X platform.

treatment_protocol: Ex vivo sorted effector CD8 T cell subsets were used directly for downstream analyses.

value: splenocytes

value: WT

tag: chip antibody

value: IgG

tag: time point

value: 4 dpi


title: input in normal media in 2D culture replicate 2

description: 2D growth


title: CUT&RUN, Tle3, effector, Tbet KO (6dpi), 4

value: Tbet KO

value: 6 dpi


title: CUT&RUN, Tle3, effector, Tbet KO (6dpi), 3


title: CUT&RUN, Tle3, effector, Tbet KO (6dpi), 2


title: CUT&RUN, Tle3, effector, WT (6dpi), 4


title: CUT&RUN, Tle3, effector, WT (6dpi), 3


title: CUT&RUN, Tle3, effector, WT (6dpi), 2


title: CUT&RUN, Tle3, effector, WT (6dpi), 1


title: CUT&RUN, Tle3, effector, Tbet/Runx3 dKO (4dpi), 1

value: Tbet/Runx3 dKO


title: CUT&RUN, Tle3, effector, Tbet/Runx3 dKO (4dpi), 2


title: CUT&RUN, Tle3, effector, WT (4dpi), 4


title: CUT&RUN, Tle3, effector, Tbet/Runx3 dKO (4dpi), 3


title: NL_18_iPSC_PCRFree_WGS

value: iPSC


title: CUT&RUN, Tle3, effector, WT (4dpi), 2


title: CUT&RUN, Tle3, effector, WT (4dpi), 1


title: FXS_421_iPSC_PCRFree_WGS


title: ATACseq, Tem, WT tam-treated, 3

data_processing:
ATAC-seq reads were trimmed remaining 100 bp from 5'end using trim_galore (v3.5).
ATAC-seq reads were aligned to the mm10 genome using Bowtie2 version 2.3.4.1.
Sam files were then processed to bam files using samtools (v1.7) and duplication reads were removed using picard MarkDuplicates (v2.21.6).
Bam files were then processed by macs2 (v2.1.1) with qval<0.05, FC>4 to call narrowPeak.
BigWig files were transfered from macs2 output bdg files normalized by reads on peaks.
Assembly: mm10
Supplementary files format and content: narrowPeak

growth_protocol: CD45.2+ WT or CreER+Tle3-floxed P14 TCR transgenic CD8 T cells were adoptively transferred into CD45.1+ B6.SJL recipients, followed by i.p. infection with LCMV-Armstrong. After ≥ 30 days, CD45.2+CD62L-CD8+ Tem cells were sort-purified for downstream analysis

extract_protocol:
CD8 T cell subsets were treated with TN5 transposase to generate tagged DNA fragments.
TN5-tagged DNA fragements were purified, PCR amplified to build ATAC-seq libraries

treatment_protocol: Sorted Tem cells were cultured with 4-OHT for 48 hrs, and then viable cells were sort-purified for downstream analyses.

value: WT Tem cells

value: ex vivo 4-OHT

tag: time

value: 48 hrs


title: ATACseq, Tem, WT tam-treated, 2


title: ATACseq, Tem, Tle3 induced deletion, 1

value: Tle3 induced KO Tem cells


title: ATACseq, Tem, Tle3 induced deletion, 3


title: 4SU, UVA, 0h, rep2

status: Public on Nov 03 2023

city: Würzburg

first: Julian

last: Konig

address: Am Hubland

country: Germany

institute: Würzburg University

data_processing:
Quality control: FastQC (v0.11.9)
Barcode and adapter trimming: Flexbar (v3.5.0) with non-default parameters: --zip-output GZ --threads 4 --stdout-log --adapter-seq AGATCGGAAGAGCGGTTCAG --adapter-min-overlap 1 --min-read-length 15 --length-dist --umi-tags --barcode-unassigned samplebarcodes.fasta (using sample barcodes: 4SU, UVA, 0h, rep1: NNNNNGCCTAANNNN, 4SU, UVA, 0h, rep2: NNNNNTGGTCANNNN)
Mapping: STAR (v2.7.3a) with non-default parameters: --genomeDir Gencode_release31_GRCh38.p12 --sjdbGTFfile gencode.v31.primary_assembly.annotation.gtf --sjdbOverhang 124 --runThreadN 1 --outMultimapperOrder Random --alignEndsType Extend5pOfRead1 --outFilterMismatchNoverReadLmax 0.04 --outFilterMismatchNmax 999 --outFilterMultimapNmax 1 --outSAMattributes All --outReadsUnmapped Fastx --outSJfilterReads Unique --readFilesCommand zcat --outSAMtype BAM SortedByCoordinate (output: SAMPLE.mapped.bam)
Remove reads directly mapped at chromosome ends (their upstream/crosslink position does not exist): Samtools (v1.10), Bedtools (v2.29.2): bedtools bamtobed -i SAMPLE.mapped.bam | sort -k1,1 > SAMPLE.mapped.bed; join -t $'\t' -j1 -e "NA" -a1 SAMPLE.mapped.bed CHROMOLENGTHTABLE > SAMPLE.mapped.len.bed; cat SAMPLE.mapped.len.bed | awk '{if(($2==0) || ($3>=$7)) printf "%s\t%s\t%s\t%s\t%s\t%s\n",$1,$2,$3,$4,$5,$6;}' > SAMPLE.idlist; samtools view -H SAMPLE.mapped.bam > SAMPLE.header; samtools view SAMPLE.mapped.bam > SAMPLE.body; awk 'FNR==NR && NF {a[$4];next} !($1 in a)' SAMPLE.idlist SAMPLE.body > SAMPLE.body.filtered; cat SAMPLE.header SAMPLE.body.filtered | samtools view -b - > SAMPLE.bam
Duplicate removal: UMI-tools (v1.1.2) with non-default parameter: umi_tools dedup --method unique –random-seed=100 (output: SAMPLE.duprm.bam)
BAM to BED shifting one base upstream: bedtools (v2.29.2): bedtools bamtobed -i SAMPLE.duprm.bam | bedtools shift -m 1 -p -1 -i stdin -g CHROMOLENGTHTABLE | sort -k1,1 -k2,2n > SAMPLE.shifted1bp.bed
BED to bedGraph considering only 5' end positions: bedtools (v2.29.2): bedtools genomecov -bg -strand + -5 -i SAMPLE.shifted1bp.bed -g CHROMOLENGTHTABLE > SAMPLE.duprm.plus.bedgraph; bedtools genomecov -bg -strand - -5 -i SAMPLE.shifted1bp.bed -g CHROMOLENGTHTABLE > SAMPLE.duprm.minus.bedgraph
bedGraph to bigWig using bedGraphToBigWig of the UCSC tool suite (v385)
Assembly: GRCh38.p12 (Gencode release 31)
Supplementary files format and content: bigWig (crosslink events per nucleotide)
Library strategy: iCLIP2

source_name: kidney, embryo

extract_protocol:
proteins were crosslinked to RNA through overnight incorporation of 5µM 4sU and UVA irradiation (150 J/cm2); after irradiation cells were harvested in ice-cold PBS and lysed in iCLIP lysis buffer; samples were homogenized by sonication for 10 cycles (30 s ON, 30 s OFF) with Bioruptor® Plus and protein concentration was quantified by BCA assay; lysates were incubated with Turbo DNAse and RNAse I dilution (1/50) for 3 min at 37°C; protein clean-up for 50 µg of protein was done with SP3 beads in a 1:10 ratio for 1 h at 4°C.
iCLIP2 protocol; RNA was dephosphorylated at the 3´end before L3 linker ligation and 5´end radioactive labelling. After western blotting RNA-protein complexes were isolated and digested with proteinase K; reverse transcription of RNA to cDNA; RNA-Hydrolysis before clean-up of cDNA with MyONE Silane beads and adapter ligation; cDNA was amplified and size selected using ProNex® Size-Selective purification system. The library was sequenced on an Illumina NextSeq 500 sequencer with a read length of 150 nt (single-end), an index length of 6nt as well as 5+4-nt unique molecular identifiers (UMIs).

value: kidney, embryo

value: epithelial

value: 4sU + UVA


title: RNA-seq, Tem, Tle3 induced deletion, 3

data_processing:
Sequence reads adapter were removed using trim_galore (v3.5)
Adapter removed sequence reads were mapped to mm10 genome using htseq-count (1.99.2).
Assembly: mm10
Supplementary files format and content: tab-delimited text files include raw count value for each gene

extract_protocol:
CD8 T cell subsets were used for total RNA extraction using standard Qiagen RNeasy columns
RNA libraries were prepared for sequencing using stardard Illumina protocol


title: RNA-seq, Tem, Tle3 induced deletion, 2


title: RNA-seq, Tem, WT tam-treated, 3


title: RNA-seq, Tem, WT tam-treated, 2


title: 4SU, UVA, 0h, rep1


title: RNA-seq, Tem, Tle3 KO, 3

data_processing:
Sequence reads were trimmed for 100bp fixed length using trimmomatic (v0.39)
Trimmed sequence reads were mapped to mm10 genome using STAR-2.7.9a.
Read count extraction were performed using featureCounts (v2.0.1)
Assembly: mm10
Supplementary files format and content: tab-delimited text files include raw count value for each gene

source_name: RNA-seq, CD8, Tem, Tle3 mutant

growth_protocol: CD45.2+ WT or Tle3-deficient P14 TCR transgenic CD8 T cells were adoptively transferred into CD45.1+ B6.SJL recipients, followed by i.p. infection with LCMV-Armstrong. After 8 or ≥ 30 days, CD45.2+CD8+ cells were sort-purified in different subsets for downstream analysis.

treatment_protocol: Ex vivo sorted CD8 T cell subsets were used directly for downstream analyses.

value: Tle3-deficient Tem cells

value: i.p. infection with LCMV-Armstrong

value: >= 30 days

tag: growth protocol

value: CD45.2+ WT or Tle3-deficient P14 TCR transgenic CD8 T cells were adoptively transferred into CD45.1+ B6.SJL recipients, followed by i.p. infection with LCMV-Armstrong. After ≥ 30 days, CD45.2+CD8+ cells were sort-purified in different subsets for downstream analysis.


title: RNA-seq, Tem, Tle3 KO, 2

value: splenocytes


title: RNA-seq, Tem, Tle3 induced deletion, 1


title: RNA-seq, Tem, WT, 3

source_name: RNA-seq, CD8, Tem


title: RNA-seq, Tem, WT, 2


title: CUT&RUN, Tle3, effector, WT (4dpi), 3

value: WT

value: 4 dpi


title: scRNA-seq, CD8, Tcm [Tle3_ko]

description: total RNA pool from barcoded single cells

library_source: transcriptomic single cell

data_processing:
Sequence reads were processed by the instructions described in the Drop-seq Laboratory Protocol v3 using Drop-Seq Tools (v2.4.1)
Processed reads were aligned to mm10 mouse genome using STAR (v.2.7.9a)
The digital gene expression files were generated using Drop-Seq Tools (v2.4.1)
Assembly: mm10
Supplementary files format and content: tab-delimited text files include raw count value for each gene

growth_protocol: CD45.2+ WT or Tle3-deficient P14 TCR transgenic CD8 T cells were adoptively transferred into CD45.1+ B6.SJL recipients, followed by i.p. infection with LCMV-Armstrong. After ≥ 30 days, CD45.2+CD8+ cells were sort-purified (without subset separation) for single cell RNA-seq analysis.

extract_protocol:
Sorted memory CD8+ T cells were used to generate single-cell gel-bead in emulsion (GEM) following standard protocols by 10X Genomics.
The scRNA-seq libraries were constructed with 10X Genomics Chromium Next GEM Single Cell 5’ library kit following the manufacturer's manual.

value: Tle3-deficient memory CD8+ T cells

value: P14 cell transfer and  infection with LCMV-Armstrong

value: ≥ 30 days post-infection


title: RNA-seq, Tem, WT, 1

value: WT Tem cells


title: RNA-seq, Tcm, Tle3 KO, 2

source_name: RNA-seq, CD8, Tcm, Tle3 mutant

value: Tle3-deficient Tcm cells


title: ATACseq, Tem, Tle3 induced deletion, 2

value: ex vivo 4-OHT

value: 48 hrs


title: RNA-seq, Tcm, WT, 3

source_name: RNA-seq, CD8, Tcm

value: WT Tcm cells


title: RNA-seq, Tcm, Tle3 KO, 1


title: RNA-seq, Tcm, WT, 1


title: CUT&RUN, Tle3, Tem (≥30 dpi), 1

data_processing:
Cut&Run reads were trimmed remaining 36 bp from 5'end using Trimmomatic v0.39
Cut&Run reads were aligned to the mm10 genome using Bowtie2 version 2.4.4. Mapping reads with the quality score over 30 were retained.
To create Cut&Run binding plots, the locations of the mapped reads were coverted to the bigWig file format using bamCoverage in deepTools(v3.5.1) with the RPKM normalization.
Assembly: mm10
Supplementary files format and content: bigWig
Library strategy: Cut&Run

value: wild-type

value: CD45.2+ WT P14 TCR transgenic CD8 T cells were adoptively transferred into CD45.1+ B6.SJL recipients, followed by i.p. infection with LCMV-Armstrong. After 8 or ≥ 30 days, CD45.2+CD8+ cells were sort-purified in different subsets for downstream analysis.


title: RNA-seq, Tcm, WT, 2


title: CUT&RUN, Tle3, Tem (≥30 dpi), 2


title: CUT&RUN, Tle3, Tcm (≥30 dpi), 2


title: CUT&RUN, Tle3, effector (8 dpi), 2

value: 8 dpi


title: CUT&RUN, Tle3, Tcm (≥30 dpi), 1


title: CUT&RUN, Tle3, effector (8 dpi), 1


title: CUT&RUN, Tle3, naïve, 2

value: time 0


title: RNA-seq, Tem, WT tam-treated, 1


title: scRNA-seq, CD8, Tcm [Tle3_wt]

value: WT memory CD8+ T cells


title: ATAC_seq, Tem, Tle3KO, 1

data_processing:
ATAC-seq reads were trimmed remaining 36 bp from 5'end using Trimmomatic v0.39
ATAC-seq reads were aligned to the mm10 genome using Bowtie2 version 2.4.4. Mapping reads with the quality score over 30 were retained.
To create ATAC-seq coverage plots, the locations of the mapped reads were coverted to the bigWig file format using bamCoverage in deepTools(v3.5.1) with the RPKM normalization.
Assembly: mm10
Supplementary files format and content: bigWig

value: Tle3-deficient Tem cells

value: i.p. infection with LCMV-Armstrong

value: >= 30 days

value: CD45.2+ WT or Tle3-deficient P14 TCR transgenic CD8 T cells were adoptively transferred into CD45.1+ B6.SJL recipients, followed by i.p. infection with LCMV-Armstrong. After ≥ 30 days, CD45.2+CD8+ cells were sort-purified in different subsets for downstream analysis.


title: ATAC_seq, Tem, Tle3KO, 2

value: splenocytes


title: CUT&RUN, Tle3, naïve, 3


title: RNA-seq, Tem, Tle3 KO, 1


title: ATAC_seq, Tcm, Tle3KO, 3


title: ATAC_seq, Tem, WT, 2


title: ATAC_seq, Tcm, Tle3KO, 1


title: ATAC_seq, Tcm, Tle3KO, 2


title: RNA-seq, Tcm, Tle3 KO, 3


title: ATAC_seq, Tem, WT, 1


title: ATAC_seq, Tcm, WT, 3


title: ATAC_seq, Tcm, WT, 2


title: CONTR 9522-MT-0024

status: Public on Oct 02 2023

city: Nashville

first: Kathleen

middle: E

last: DelGiorno

state: TN

address: 465 21st Ave S

department: Cell and Developmental Biology

institute: Vanderbilt University

data_processing:
Raw sequencing data (FASTQ files) generated on the NovaSeq 6000 were processed through standard quality control pipelines. Base calling was performed using Illumina Real Time Analysis software and NovaSeq Control Software (version 1.8.0). Overall sequencing quality was assessed with MultiQC (version 1.7). Paired-end RNA-sequencing reads (150 bp) were trimmed and quality-filtered using TrimGalore (version 0.6.7). Trimmed reads were aligned to the mm39 mouse reference genome with STAR (version 2.7.9a) using the quantMode GeneCounts option, and gene-level counts were generated using GENCODE comprehensive gene annotations (Release M31).
Assembly: mm39 for 10007-NJ libraries and mm10 for 9522-MT libraries
Supplementary files format and content: Comma separated values file includes raw counts for each sample

source_name: 4838-Intraductal Papillary Mucinous Neoplasms (IPMNs)

growth_protocol: Cells were grown in RPMI media with tet-approved FBS

extract_protocol:
RNA was extracted using the Quick-RNA Miniprep Kit (Zymo)
Library prep was performed using the NEBNext Ultra II RNA Library Prep Kit (E776L) per manufacturer's instructions

treatment_protocol: Cells or organoids were treated with 1-2 ug/mL of doxycyline for 48-72 hours

value: PDAC

value: Vehicle

tag: biological replicates

value: C


title: DOX 9522-MT-0022

value: 4838-Intraductal Papillary Mucinous Neoplasms (IPMNs)

value: Dox


title: CONTR 9522-MT-0020

source_name: C241-Intraductal Papillary Mucinous Neoplasms (IPMNs)


title: DOX 9522-MT-0021


title: CONTR 9522-MT-0023


title: CONTR 9522-MT-0019

value: C241-Intraductal Papillary Mucinous Neoplasms (IPMNs)


title: DOX 9522-MT-0018


title: CONTR 9522-MT-0016

value: B


title: DOX 9522-MT-0017


title: DOX 9522-MT-0014


title: CONTR 9522-MT-0015


title: CUT&RUN, Tle3, naïve, 1

value: wild-type


title: DOX 9522-MT-0013


title: CONTR 9522-MT-0012


title: DOX 9522-MT-0006

value: A


title: DOX 9522-MT-0010


title: DOX 9522-MT-0005


title: DOX 9522-MT-0009


title: CONTR 9522-MT-0004


title: CONTR 9522-MT-0003


title: CONTR 9522-MT-0008


title: CONTR 9522-MT-0007


title: DOX 9522-MT-0001


title: ATAC_seq, Tcm, WT, 1

value: WT Tcm cells


title: DOX 9522-MT-0002


title: genomic DNA from eutopic endometrium Sample_984

status: Public on Sep 12 2023

type: genomic

city: Herston

first: Sally

last: Mortlock

state: QLD

address: School of Public Health

department: School of Public Health

country: Australia

institute: University of Queensland

description:
genomic DNA from eutopic endometrium
Control eutopic endometrium sample

hyb_protocol: All DNA samples were adjusted to the same volume and concentration for sodium bisulfite conversion followed by DNAm analysis on the Illumina Infinium MethylationEPIC Beadchip using standard Illumina protocol

scan_protocol: Standard Illumina scan protocol was performed at the University of Southern California Epigenome Center.

data_processing:
Background correction with dye-bias, signal intensity normalization and Beta value generation performed using the SeSAME R package. Samples with a low overall intensity signal (median unmethylated or methylated signal <9), a detection p-value >0.05 in more than 1% of DNAm sites were removed. Probes with a detection p-value >0.05 in more than 10% of samples and probes not overlapping between batches were removed. Probes were masked based on the SeSAME package. 759,345 DNAm sites for 984 samples remained.
Normalized Beta and Normalized M-value

label: Cy3 and Cy5

source_name: endometrium sample 984

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted and purified from endometrial samples

tag: gender

value: Female

tag: sample type

value: endometrium

tag: disease state

value: Control

tag: cycle phase

value: PE

tag: plate

tag: terminus

tag: batch

tag: euro

value: EUR

tag: recruiment


title: genomic DNA from eutopic endometrium Sample_983

description:
genomic DNA from eutopic endometrium
Endometriosis eutopic endometrium sample

source_name: endometrium sample 983

value: Endometriosis

tag: age


title: genomic DNA from eutopic endometrium Sample_979

source_name: endometrium sample 979

value: ESE


title: genomic DNA from eutopic endometrium Sample_982

source_name: endometrium sample 982

value: MSE


title: genomic DNA from eutopic endometrium Sample_981

source_name: endometrium sample 981


title: genomic DNA from eutopic endometrium Sample_977

source_name: endometrium sample 977


title: genomic DNA from eutopic endometrium Sample_978

source_name: endometrium sample 978


title: genomic DNA from eutopic endometrium Sample_976

source_name: endometrium sample 976


title: genomic DNA from eutopic endometrium Sample_973

source_name: endometrium sample 973


title: genomic DNA from eutopic endometrium Sample_974

source_name: endometrium sample 974


title: genomic DNA from eutopic endometrium Sample_975

source_name: endometrium sample 975


title: genomic DNA from eutopic endometrium Sample_972

source_name: endometrium sample 972


title: genomic DNA from eutopic endometrium Sample_971

source_name: endometrium sample 971


title: genomic DNA from eutopic endometrium Sample_969

source_name: endometrium sample 969


title: CONTR 9522-MT-0011

tag: cell line

tag: cell type

value: PDAC

tag: treatment

value: Vehicle


title: genomic DNA from eutopic endometrium Sample_970

source_name: endometrium sample 970


title: genomic DNA from eutopic endometrium Sample_968

source_name: endometrium sample 968


title: genomic DNA from eutopic endometrium Sample_967

source_name: endometrium sample 967


title: genomic DNA from eutopic endometrium Sample_966

source_name: endometrium sample 966


title: genomic DNA from eutopic endometrium Sample_963

source_name: endometrium sample 963


title: genomic DNA from eutopic endometrium Sample_964

source_name: endometrium sample 964


title: genomic DNA from eutopic endometrium Sample_965

source_name: endometrium sample 965


title: genomic DNA from eutopic endometrium Sample_962

source_name: endometrium sample 962


title: genomic DNA from eutopic endometrium Sample_960

source_name: endometrium sample 960


title: genomic DNA from eutopic endometrium Sample_980

source_name: endometrium sample 980


title: genomic DNA from eutopic endometrium Sample_957

source_name: endometrium sample 957


title: genomic DNA from eutopic endometrium Sample_959

source_name: endometrium sample 959

value: SE


title: genomic DNA from eutopic endometrium Sample_956

source_name: endometrium sample 956


title: genomic DNA from eutopic endometrium Sample_955

source_name: endometrium sample 955


title: genomic DNA from eutopic endometrium Sample_954

source_name: endometrium sample 954


title: genomic DNA from eutopic endometrium Sample_952

source_name: endometrium sample 952


title: genomic DNA from eutopic endometrium Sample_953

source_name: endometrium sample 953


title: genomic DNA from eutopic endometrium Sample_951

source_name: endometrium sample 951


title: genomic DNA from eutopic endometrium Sample_950

source_name: endometrium sample 950


title: genomic DNA from eutopic endometrium Sample_948

source_name: endometrium sample 948


title: genomic DNA from eutopic endometrium Sample_949

source_name: endometrium sample 949


title: genomic DNA from eutopic endometrium Sample_947

source_name: endometrium sample 947

value: Menstrual


title: genomic DNA from eutopic endometrium Sample_938

source_name: endometrium sample 938


title: genomic DNA from eutopic endometrium Sample_944

source_name: endometrium sample 944

value: LSE


title: genomic DNA from eutopic endometrium Sample_941

source_name: endometrium sample 941


title: genomic DNA from eutopic endometrium Sample_942

source_name: endometrium sample 942


title: genomic DNA from eutopic endometrium Sample_943

source_name: endometrium sample 943


title: genomic DNA from eutopic endometrium Sample_945

source_name: endometrium sample 945


title: genomic DNA from eutopic endometrium Sample_946

source_name: endometrium sample 946


title: genomic DNA from eutopic endometrium Sample_939

source_name: endometrium sample 939


title: genomic DNA from eutopic endometrium Sample_961

source_name: endometrium sample 961


title: genomic DNA from eutopic endometrium Sample_937

source_name: endometrium sample 937


title: genomic DNA from eutopic endometrium Sample_936

source_name: endometrium sample 936


title: genomic DNA from eutopic endometrium Sample_934

source_name: endometrium sample 934


title: genomic DNA from eutopic endometrium Sample_933

source_name: endometrium sample 933


title: genomic DNA from eutopic endometrium Sample_935

source_name: endometrium sample 935


title: genomic DNA from eutopic endometrium Sample_958

source_name: endometrium sample 958


title: genomic DNA from eutopic endometrium Sample_931

source_name: endometrium sample 931


title: genomic DNA from eutopic endometrium Sample_932

source_name: endometrium sample 932


title: genomic DNA from eutopic endometrium Sample_930

source_name: endometrium sample 930


title: genomic DNA from eutopic endometrium Sample_929

source_name: endometrium sample 929


title: genomic DNA from eutopic endometrium Sample_928

source_name: endometrium sample 928


title: genomic DNA from eutopic endometrium Sample_927

source_name: endometrium sample 927


title: genomic DNA from eutopic endometrium Sample_923

source_name: endometrium sample 923


title: genomic DNA from eutopic endometrium Sample_925

source_name: endometrium sample 925


title: genomic DNA from eutopic endometrium Sample_922

source_name: endometrium sample 922


title: genomic DNA from eutopic endometrium Sample_924

source_name: endometrium sample 924


title: genomic DNA from eutopic endometrium Sample_921

source_name: endometrium sample 921


title: genomic DNA from eutopic endometrium Sample_920

source_name: endometrium sample 920


title: genomic DNA from eutopic endometrium Sample_940

source_name: endometrium sample 940


title: genomic DNA from eutopic endometrium Sample_919

source_name: endometrium sample 919


title: genomic DNA from eutopic endometrium Sample_917

source_name: endometrium sample 917


title: genomic DNA from eutopic endometrium Sample_915

source_name: endometrium sample 915


title: genomic DNA from eutopic endometrium Sample_914

source_name: endometrium sample 914


title: genomic DNA from eutopic endometrium Sample_918

source_name: endometrium sample 918


title: genomic DNA from eutopic endometrium Sample_913

source_name: endometrium sample 913


title: genomic DNA from eutopic endometrium Sample_909

source_name: endometrium sample 909


title: genomic DNA from eutopic endometrium Sample_916

source_name: endometrium sample 916


title: genomic DNA from eutopic endometrium Sample_911

source_name: endometrium sample 911


title: genomic DNA from eutopic endometrium Sample_904

source_name: endometrium sample 904


title: genomic DNA from eutopic endometrium Sample_910

source_name: endometrium sample 910


title: genomic DNA from eutopic endometrium Sample_906

source_name: endometrium sample 906


title: genomic DNA from eutopic endometrium Sample_907

source_name: endometrium sample 907


title: genomic DNA from eutopic endometrium Sample_905

source_name: endometrium sample 905


title: genomic DNA from eutopic endometrium Sample_903

source_name: endometrium sample 903


title: genomic DNA from eutopic endometrium Sample_912

source_name: endometrium sample 912


title: genomic DNA from eutopic endometrium Sample_902

source_name: endometrium sample 902


title: genomic DNA from eutopic endometrium Sample_908

source_name: endometrium sample 908


title: genomic DNA from eutopic endometrium Sample_900

source_name: endometrium sample 900


title: genomic DNA from eutopic endometrium Sample_901

source_name: endometrium sample 901


title: genomic DNA from eutopic endometrium Sample_898

source_name: endometrium sample 898


title: genomic DNA from eutopic endometrium Sample_899

source_name: endometrium sample 899


title: genomic DNA from eutopic endometrium Sample_926

source_name: endometrium sample 926


title: genomic DNA from eutopic endometrium Sample_896

source_name: endometrium sample 896


title: genomic DNA from eutopic endometrium Sample_897

source_name: endometrium sample 897


title: genomic DNA from eutopic endometrium Sample_894

source_name: endometrium sample 894


title: genomic DNA from eutopic endometrium Sample_895

source_name: endometrium sample 895


title: genomic DNA from eutopic endometrium Sample_892

source_name: endometrium sample 892


title: genomic DNA from eutopic endometrium Sample_891

source_name: endometrium sample 891


title: genomic DNA from eutopic endometrium Sample_890

source_name: endometrium sample 890


title: genomic DNA from eutopic endometrium Sample_889

source_name: endometrium sample 889


title: genomic DNA from eutopic endometrium Sample_885

source_name: endometrium sample 885


title: genomic DNA from eutopic endometrium Sample_888

source_name: endometrium sample 888


title: genomic DNA from eutopic endometrium Sample_883

source_name: endometrium sample 883


title: genomic DNA from eutopic endometrium Sample_884

source_name: endometrium sample 884


title: genomic DNA from eutopic endometrium Sample_880

source_name: endometrium sample 880


title: genomic DNA from eutopic endometrium Sample_881

source_name: endometrium sample 881


title: genomic DNA from eutopic endometrium Sample_879

source_name: endometrium sample 879


title: genomic DNA from eutopic endometrium Sample_876

source_name: endometrium sample 876


title: genomic DNA from eutopic endometrium Sample_875

source_name: endometrium sample 875


title: genomic DNA from eutopic endometrium Sample_878

source_name: endometrium sample 878


title: genomic DNA from eutopic endometrium Sample_874

source_name: endometrium sample 874


title: genomic DNA from eutopic endometrium Sample_870

source_name: endometrium sample 870


title: genomic DNA from eutopic endometrium Sample_877

source_name: endometrium sample 877


title: genomic DNA from eutopic endometrium Sample_867

source_name: endometrium sample 867


title: genomic DNA from eutopic endometrium Sample_872

source_name: endometrium sample 872


title: genomic DNA from eutopic endometrium Sample_865

source_name: endometrium sample 865


title: genomic DNA from eutopic endometrium Sample_893

source_name: endometrium sample 893


title: genomic DNA from eutopic endometrium Sample_871

source_name: endometrium sample 871


title: genomic DNA from eutopic endometrium Sample_868

source_name: endometrium sample 868


title: genomic DNA from eutopic endometrium Sample_873

source_name: endometrium sample 873


title: genomic DNA from eutopic endometrium Sample_866

source_name: endometrium sample 866


title: genomic DNA from eutopic endometrium Sample_861

source_name: endometrium sample 861


title: genomic DNA from eutopic endometrium Sample_862

source_name: endometrium sample 862


title: genomic DNA from eutopic endometrium Sample_887

source_name: endometrium sample 887


title: genomic DNA from eutopic endometrium Sample_886

source_name: endometrium sample 886


title: genomic DNA from eutopic endometrium Sample_882

source_name: endometrium sample 882


title: genomic DNA from eutopic endometrium Sample_860

source_name: endometrium sample 860


title: genomic DNA from eutopic endometrium Sample_858

source_name: endometrium sample 858


title: genomic DNA from eutopic endometrium Sample_859

source_name: endometrium sample 859


title: genomic DNA from eutopic endometrium Sample_856

source_name: endometrium sample 856


title: genomic DNA from eutopic endometrium Sample_857

source_name: endometrium sample 857


title: genomic DNA from eutopic endometrium Sample_852

source_name: endometrium sample 852


title: genomic DNA from eutopic endometrium Sample_854

source_name: endometrium sample 854


title: genomic DNA from eutopic endometrium Sample_855

source_name: endometrium sample 855


title: genomic DNA from eutopic endometrium Sample_869

source_name: endometrium sample 869


title: genomic DNA from eutopic endometrium Sample_853

source_name: endometrium sample 853


title: genomic DNA from eutopic endometrium Sample_864

source_name: endometrium sample 864


title: genomic DNA from eutopic endometrium Sample_851

source_name: endometrium sample 851


title: genomic DNA from eutopic endometrium Sample_848

source_name: endometrium sample 848


title: genomic DNA from eutopic endometrium Sample_847

source_name: endometrium sample 847


title: genomic DNA from eutopic endometrium Sample_850

source_name: endometrium sample 850


title: genomic DNA from eutopic endometrium Sample_863

source_name: endometrium sample 863


title: genomic DNA from eutopic endometrium Sample_849

source_name: endometrium sample 849


title: genomic DNA from eutopic endometrium Sample_841

source_name: endometrium sample 841


title: genomic DNA from eutopic endometrium Sample_844

source_name: endometrium sample 844


title: genomic DNA from eutopic endometrium Sample_840

source_name: endometrium sample 840


title: genomic DNA from eutopic endometrium Sample_843

source_name: endometrium sample 843


title: genomic DNA from eutopic endometrium Sample_838

source_name: endometrium sample 838


title: genomic DNA from eutopic endometrium Sample_839

source_name: endometrium sample 839


title: genomic DNA from eutopic endometrium Sample_837

source_name: endometrium sample 837


title: genomic DNA from eutopic endometrium Sample_836

source_name: endometrium sample 836


title: genomic DNA from eutopic endometrium Sample_835

source_name: endometrium sample 835


title: genomic DNA from eutopic endometrium Sample_834

source_name: endometrium sample 834


title: genomic DNA from eutopic endometrium Sample_832

source_name: endometrium sample 832


title: genomic DNA from eutopic endometrium Sample_831

source_name: endometrium sample 831


title: genomic DNA from eutopic endometrium Sample_833

source_name: endometrium sample 833


title: genomic DNA from eutopic endometrium Sample_830

source_name: endometrium sample 830


title: genomic DNA from eutopic endometrium Sample_828

source_name: endometrium sample 828


title: genomic DNA from eutopic endometrium Sample_827

source_name: endometrium sample 827


title: genomic DNA from eutopic endometrium Sample_845

source_name: endometrium sample 845


title: genomic DNA from eutopic endometrium Sample_826

source_name: endometrium sample 826


title: genomic DNA from eutopic endometrium Sample_825

source_name: endometrium sample 825


title: genomic DNA from eutopic endometrium Sample_823

source_name: endometrium sample 823


title: genomic DNA from eutopic endometrium Sample_829

source_name: endometrium sample 829


title: genomic DNA from eutopic endometrium Sample_824

source_name: endometrium sample 824


title: genomic DNA from eutopic endometrium Sample_820

source_name: endometrium sample 820


title: genomic DNA from eutopic endometrium Sample_842

source_name: endometrium sample 842


title: genomic DNA from eutopic endometrium Sample_846

source_name: endometrium sample 846


title: genomic DNA from eutopic endometrium Sample_818

source_name: endometrium sample 818


title: genomic DNA from eutopic endometrium Sample_821

source_name: endometrium sample 821


title: genomic DNA from eutopic endometrium Sample_816

source_name: endometrium sample 816


title: genomic DNA from eutopic endometrium Sample_822

source_name: endometrium sample 822


title: genomic DNA from eutopic endometrium Sample_814

source_name: endometrium sample 814


title: genomic DNA from eutopic endometrium Sample_813

source_name: endometrium sample 813


title: genomic DNA from eutopic endometrium Sample_815

source_name: endometrium sample 815


title: genomic DNA from eutopic endometrium Sample_812

source_name: endometrium sample 812


title: genomic DNA from eutopic endometrium Sample_819

source_name: endometrium sample 819


title: genomic DNA from eutopic endometrium Sample_811

source_name: endometrium sample 811


title: genomic DNA from eutopic endometrium Sample_809

source_name: endometrium sample 809


title: genomic DNA from eutopic endometrium Sample_810

source_name: endometrium sample 810


title: genomic DNA from eutopic endometrium Sample_808

source_name: endometrium sample 808


title: genomic DNA from eutopic endometrium Sample_807

source_name: endometrium sample 807


title: genomic DNA from eutopic endometrium Sample_806

source_name: endometrium sample 806


title: genomic DNA from eutopic endometrium Sample_804

source_name: endometrium sample 804


title: genomic DNA from eutopic endometrium Sample_803

source_name: endometrium sample 803


title: genomic DNA from eutopic endometrium Sample_802

source_name: endometrium sample 802


title: genomic DNA from eutopic endometrium Sample_801

source_name: endometrium sample 801


title: genomic DNA from eutopic endometrium Sample_799

source_name: endometrium sample 799


title: genomic DNA from eutopic endometrium Sample_797

source_name: endometrium sample 797


title: genomic DNA from eutopic endometrium Sample_796

source_name: endometrium sample 796


title: genomic DNA from eutopic endometrium Sample_798

source_name: endometrium sample 798


title: genomic DNA from eutopic endometrium Sample_800

source_name: endometrium sample 800


title: genomic DNA from eutopic endometrium Sample_817

source_name: endometrium sample 817


title: genomic DNA from eutopic endometrium Sample_795

source_name: endometrium sample 795


title: genomic DNA from eutopic endometrium Sample_792

source_name: endometrium sample 792


title: genomic DNA from eutopic endometrium Sample_794

source_name: endometrium sample 794


title: genomic DNA from eutopic endometrium Sample_791

source_name: endometrium sample 791


title: genomic DNA from eutopic endometrium Sample_789

source_name: endometrium sample 789


title: genomic DNA from eutopic endometrium Sample_793

source_name: endometrium sample 793


title: genomic DNA from eutopic endometrium Sample_787

source_name: endometrium sample 787


title: genomic DNA from eutopic endometrium Sample_790

source_name: endometrium sample 790


title: genomic DNA from eutopic endometrium Sample_786

source_name: endometrium sample 786


title: genomic DNA from eutopic endometrium Sample_785

source_name: endometrium sample 785


title: genomic DNA from eutopic endometrium Sample_782

source_name: endometrium sample 782


title: genomic DNA from eutopic endometrium Sample_783

source_name: endometrium sample 783


title: genomic DNA from eutopic endometrium Sample_788

source_name: endometrium sample 788


title: genomic DNA from eutopic endometrium Sample_781

source_name: endometrium sample 781


title: genomic DNA from eutopic endometrium Sample_779

source_name: endometrium sample 779


title: genomic DNA from eutopic endometrium Sample_780

source_name: endometrium sample 780


title: genomic DNA from eutopic endometrium Sample_805

source_name: endometrium sample 805


title: genomic DNA from eutopic endometrium Sample_778

source_name: endometrium sample 778


title: genomic DNA from eutopic endometrium Sample_777

source_name: endometrium sample 777


title: genomic DNA from eutopic endometrium Sample_776

source_name: endometrium sample 776


title: genomic DNA from eutopic endometrium Sample_775

source_name: endometrium sample 775


title: genomic DNA from eutopic endometrium Sample_774

source_name: endometrium sample 774


title: genomic DNA from eutopic endometrium Sample_772

source_name: endometrium sample 772


title: genomic DNA from eutopic endometrium Sample_773

source_name: endometrium sample 773


title: genomic DNA from eutopic endometrium Sample_770

source_name: endometrium sample 770


title: genomic DNA from eutopic endometrium Sample_769

source_name: endometrium sample 769


title: genomic DNA from eutopic endometrium Sample_768

source_name: endometrium sample 768


title: genomic DNA from eutopic endometrium Sample_767

source_name: endometrium sample 767


title: genomic DNA from eutopic endometrium Sample_764

source_name: endometrium sample 764


title: genomic DNA from eutopic endometrium Sample_763

source_name: endometrium sample 763


title: genomic DNA from eutopic endometrium Sample_766

source_name: endometrium sample 766


title: genomic DNA from eutopic endometrium Sample_771

source_name: endometrium sample 771


title: genomic DNA from eutopic endometrium Sample_760

source_name: endometrium sample 760


title: genomic DNA from eutopic endometrium Sample_765

source_name: endometrium sample 765


title: genomic DNA from eutopic endometrium Sample_761

source_name: endometrium sample 761


title: genomic DNA from eutopic endometrium Sample_762

source_name: endometrium sample 762


title: genomic DNA from eutopic endometrium Sample_758

source_name: endometrium sample 758


title: genomic DNA from eutopic endometrium Sample_757

source_name: endometrium sample 757


title: genomic DNA from eutopic endometrium Sample_759

source_name: endometrium sample 759


title: genomic DNA from eutopic endometrium Sample_754

source_name: endometrium sample 754


title: genomic DNA from eutopic endometrium Sample_755

source_name: endometrium sample 755


title: genomic DNA from eutopic endometrium Sample_784

source_name: endometrium sample 784


title: genomic DNA from eutopic endometrium Sample_753

source_name: endometrium sample 753


title: genomic DNA from eutopic endometrium Sample_756

source_name: endometrium sample 756


title: genomic DNA from eutopic endometrium Sample_749

source_name: endometrium sample 749


title: genomic DNA from eutopic endometrium Sample_751

source_name: endometrium sample 751


title: genomic DNA from eutopic endometrium Sample_752

source_name: endometrium sample 752


title: genomic DNA from eutopic endometrium Sample_748

source_name: endometrium sample 748


title: genomic DNA from eutopic endometrium Sample_750

source_name: endometrium sample 750


title: genomic DNA from eutopic endometrium Sample_744

source_name: endometrium sample 744


title: genomic DNA from eutopic endometrium Sample_742

source_name: endometrium sample 742


title: genomic DNA from eutopic endometrium Sample_745

source_name: endometrium sample 745


title: genomic DNA from eutopic endometrium Sample_743

source_name: endometrium sample 743