title: RNA-seq_dTAG_rep3

data_processing:
Sequenced reads were aligned to the mm10 genome via STAR (v 2.7.2b) (Dobin et al, 2013). Gene counts were obtained from featureCounts of the Rsubread package (R/Bioconductor). Only reads with counts per million > 2 were kept for subsequent analysis. ERCC spike-in reads were counted to ensure similar numbers among samples. After confirming that the number of ERCC counts among samples is highly similar, then the counts mapping to the mm10 genome were normalized using the internal TMM normalization in edgeR (Robinson et al, 2009) and differential expression was performed using the limma (Ritchie et al, 2015) package. Significant genes with an absolute logFC > 1 and adjusted P-value < 0.05 were considered as differentially expressedSequenced reads were aligned to the mm10 genome via STAR (v 2.7.2b) (Dobin et al, 2013). Gene counts were obtained from featureCounts of the Rsubread package (R/Bioconductor). Only reads with counts per million > 2 were kept for subsequent analysis. ERCC spike-in reads were counted to ensure similar numbers among samples. After confirming that the number of ERCC counts among samples is highly similar, then the counts mapping to the mm10 genome were normalized using the internal TMM normalization in edgeR (Robinson et al, 2009) and differential expression was performed using the limma (Ritchie et al, 2015) package. Significant genes with an absolute logFC > 1 and adjusted P-value < 0.05 were considered as differentially expressed
Genome_build: mm10

extract_protocol: RNA was isolated using the RNeasy Plus Mini Kit (QIAGEN, 74136) according to manufacturer’s instructions. ERCC spike-in controls were added to the RNA samples prior to library preparation. Stranded Ribo-depleted selected libraries were prepared using the TruSeq Stranded mRNA Library Prep Kit (Illumina, RS-122-2101) according to manufacturer’s standard protocol. Libraries were subject to 75 bp paired-end end sequencing on an Illumina NextSeq instrument.


title: RNA-seq HP1 KD repl1

status: Public on Apr 03 2021

type: SRA

city: Milano

first: Yinxiu

last: Zhan

address: Via Adamello 16

country: Italy

institute: European Institute for Oncology

description: RNA-seq HP1 KD repl1

library_source: transcriptomic

data_processing:
Reads were mapped to D. melanogaster (build dm6) using STAR [Dobin et al 2013], using the following options: --outSJfilterReads Unique --outFilterType BySJout --outFilterMultimapNmax 1000000 --alignSJoverhangMin 6 --alignSJDBoverhangMin 2 --outFilterMismatchNoverLmax 0.04 --alignIntronMin 20 --alignIntronMax 1000000 --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonicalUnannotated --seedSearchStartLmax 50 --twopassMode basic. Gene expression was quantified using qCount from QuasR package [Gaidatzis et al 2015] using the "TxDb.Dmelanogaster.UCSC.dm6.ensGene" database for gene annotation and UCSC repeatMasker table for repeats annotation
Genome_build: dm6
Supplementary_files_format_and_content: csv file containing the count table

molecule: total RNA

organism: Drosophila melanogaster

source_name: RNA-seq HP1 KD repl1

growth_protocol: The flies were reared under standard conditions (25 C) and transferred to cages to collect the embryos for further experiments.

extract_protocol:
The Trizol solution was defrosted on ice filled up to 500 µl and incubated for 5 min at room temperature.  After the addition of 100 µl chloroform and vigorous mixing, the samples were spun in a table top centrifuge at 4 °C, 12.000 g for 15 min in order to separate the organic and aqueous phase. The aqueous phase was transferred in to 300 µl of chloroform and the step the first step was repeated. Subsequently the aqueous phase was transferred into isopropanol containing 20 µg of glycogen. The RNA was precipitated at -20 °C at least overnight and pelleted by centrifugation (4 °C, 12.000 g for 60 min). The pellet was washed with 80% ethanol and resuspended in DNase-digestion buffer (2 U TurboDNase Ambion, 1x TurboDNase buffer Ambion). After digestion for 30 min at 37 °C the reaction was stopped by adding EDTA to a final concentration of 15 mM and heating the samples to 75 °C for 10 min. The RNA was quantified using Qubit RNA BR Assay kit (ThermoScientific Q10210) and integrity was assessed on agarose gels or the fragmentanalyzer (Agilent).
The Illumina TruSeq Stranded Total RNA protocol was used for library preparation for next generation sequencing.

treatment_protocol: In order to induce RNAi mediated silencing of certain gene products we employed the Gal4-UAS system. By crossing males of a Gal4 driver line (Bloomington #7063) to females of the fly RNAi collection TRiP1 we obtained an F1 generation depleted for HP1 in the female germ line (Bloomington #33400). These females were crossed to siblings and produced embryos that were depleted of HP1 mRNA and protein. Embryos were collected on apple juice agar plates. In order to hand-stage the embryos they were submerged with halocarbon oil 27 (Sigma Aldrich H8773) to allow staging. Embryos of the correct developmental stage were then transferred individually into 50 µl of Trizol (ThermoScientific, 15596026), crashed with a tissue grinder, snap-frozen and stored at -80 °C until RNA extraction.

tag: tissue

value: WT embryo at stage 5

value: embryo

tag: genotype/variation

value: HP1-KD (Bloomington #33400)


title: RNA-seq WT repl3

description: RNA-seq WT repl3

source_name: RNA-seq WT repl3

value: control (Bloomington #36303)


title: RNA-seq WT repl4

description: RNA-seq WT repl4

source_name: RNA-seq WT repl4


title: 41-HNRNP U KD_UN_replicate 2

city: Bryan

first: Kristin

middle: L

last: Patrick

state: Texas

address: 8447 Riverside Pkwy, MREB 3102

department: Microbial Pathogenesis and Immunology

country: USA

institute: Texas A&M University, College of Medicine

data_processing:
2x150 paired-end sequence reads
Illumina software used for basecalling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Ensemble Grcm38 with CLC genomics Workbench
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using CLC Genomics Workbench
Genome_build: Grcm38
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

organism: Mus musculus

source_name: RAW 264.7 Macrophage

extract_protocol:
RNA was harvested using Trizol reagent. Zymo Research Direct-zol kits were used to isolate RNA with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: RAW 264.7 Macrophages seeded in a 12 well dish at 8x10^5 cells/well overnight. The next day cells were ~80% confluent. For baseline (UN) measurements, cells were collected without treatment. For infected (SAL) samples, cells were infected with Salmonella Tyhpimurium (SAL) (MOI = 10) and collected at 4h post-infection.

tag: genotype

value: HNRNP U KD shRNA Knockdown

tag: cell line

tag: treatment

value: no treatment


title: RNA-seq HP1 KD repl2

description: RNA-seq HP1 KD repl2

source_name: RNA-seq HP1 KD repl2


title: RNA-seq_dTAG_rep1

city: Cambridge

first: Laurie

middle: A

last: Boyer

state: MA

address: 77 Massachusetts Avenue

department: Biology

institute: Massachusetts Institute of Technology

growth_protocol: V6.5 murine embryonic stem (mES) cells were grown in 2i + LIF conditions. The media used for 2i + LIF media conditions is as follows: 484 mL DMEM/F12 (GIBCO 11320), 2.5 mL N2 supplement (GIBCO 17502048), 5 mL B27 supplement (GIBCO 17504044), 0.5 mM L-glutamine (GIBCO 25030), 1X non-essential amino acids (GIBCO 11140), 100 U/mL Penicillin-Streptomycin (GIBCO 15140), 0.1 mM β-mercaptoethanol (Sigma), 1 uM PD0325901 (Stemgent 04-0006), 3 uM CHIR99021 (Stemgent 04-0004), and 1000 U/mL recombinant LIF.

tag: cell type

value: Embryonic stem cells


title: RNA-seq_dTAG_rep2


title: 40-HNRNP U KD_UN_replicate 1


title: RNA-seq WT repl2

description: RNA-seq WT repl2

source_name: RNA-seq WT repl2


title: RNA-seq WT repl1

description: RNA-seq WT repl1

source_name: RNA-seq WT repl1


title: 39-HNRNP U KD_SAL_replicate 3

value: Salmonella infection


title: HiC K9M stage 5 repl1

description: HiC K9M stage 5 repl1

library_source: genomic

data_processing:
Hi-C paired end datasets were processed using HiC-Pro (version 2.11.1). HiC-Pro covers the whole analysis from fastq files to the interaction matrix
Genome_build: dm6
Supplementary_files_format_and_content: iced and binned matrix (10kb). The format of the matrix is the standard from HiC-Pro, namely, 3 columns: start end interactions. It's a sparce matrix annotation, no zero values are reported.

molecule: genomic DNA

source_name: HiC K9M stage 5 repl1

extract_protocol:
Embryos were defrosted in ice cold HiC lysis buffer (10 mM Tris-HCl [pH 8], 10 mM NaCl, 0.2% Igepal,   1x Protease Inhibitor Cocktail (Roche, 11836170001)) on ice and immediately crashed with a pestle for 30 sec. The crashing of the embryos was checked under a microscope. The nuclei were pelleted for 5 min at 3000 g (rcf) and 4 °C. After discarding the supernatant the pellet was incubated in 50 µl 0.5% SDS for 10 min at RT. The reaction was quenched by adding 145 µl of water and 25 µl of 10% Triton X100.   To digest the chromatin 25 µl of DpnII buffer were added and 0.7 µl of DpnII (NEB R0543T). The reaction was incubated for 90 min at 37 °C in a thermomixer at 600 rpm and a second instance of 0.7 µl of DpnII was added followed by a second incubation of 90 min.    The nuclei were pelleted for 5 min at 1000 xg (rcf) and RT and resuspended in 135 µl of 1x CutSmart buffer (NEB B7204S). To biotinylate the free chromatin ends, dNTP-mix (NEB) (final 0.15 mM), Biotin-14-dATP (Jena Bioscience, NU-835-BIO14-S) (final 0.05 mM) and 10 U of Klenow (NEB M0210 L) were added to the reaction (final volume 150 µl) and incubated for 60 min at 25 °C. Next the free ends of the chromatin were ligated in a total volume of 1200 µl by adding ligation buffer (NEB B0202S) (1x final), 10% Triton (0.8% final), 120 µg BSA, 2000 U ligase (NEB M0202S). After two hours a second instance of 2000 U ligase was added and incubated for another 2 hours. Following the incubation the nuclei were pelleted at 1000 g for 5 min at RT, the supernatant was discarded and the nuclei resuspended in 200 µl elution buffer (10 mM Tris-HCl [pH 8], 1 mM EDTA, 1% SDS). Proteins were digested upon addition of 400 µg Proteinase K for 30 min at 55 °C. The chromatin was reverse crosslinked in the presence of 0.365 M NaCl at 68 °C overnight.   The next day DNA was purified using the ChIP DNA Clean&Concentrator Kit (Zymo Research D5205) eluted in 50 µl and biotin was removed from unligated fragments by adding NEB buffer 2 (NEB B7002S) (1x final), 12 µg of BSA, dATP and dGTP (0.025 final each), 3 U T4 DNA polymerase (NEB M0203S) in a final volume of 120 µl. The reaction was stopped by adding EDTA to a final concentration of 13 mM.  The DNA was transferred to Covaris microTUBE snap cap (520045) and sheared using the Covaris E220 (with intensifier (50014) and the following parameters duty factor 10%, peak incident power 140, cycle/burst 200, 120 sec. The DNA fragments were in the range of 200-300 bp.  Ligated and biotinylated fragments were enriched through biotin pulldown using Dynabeads MyOne Streptavidin C1 (Invitrogen 65001). The samples were filled up to a total of 400 µl with 2x binding buffer (10 mM Tris-HCl [pH 8], 1 mM EDTA, 2 M NaCl) (1x final) and beads (equilibrated with TWB (5 mM Tris-HCl [pH 8], 0.5 mM EDTA, 1 M NaCl, 0.05% Tween) resuspended in 1x binding buffer were added. The beads were washed twice for 2 min at 55 °C with TWB and twice with EB-buffer (Qiagen). Last the beads were resuspended in 50 µl of EB-buffer and directly used for library preparation using the NEB Ultra II DNA Library Prep Kit for Illumina (E7645S) following the manufacturer’s instructions except that the adapter ligation happened on the biotin beads. The fragments were released from the beads before the PCR reaction (by heating to 98 °C for 10 min) after unligated adapters had been removed. To amplify the libraries 12-13 cycles of PCR were performed.
We used NEB Ultra II DNA Library Prep Kit for Illumina (E7645S) following the manufacturer’s instructions except that the adapter ligation happened on the biotin beads.

treatment_protocol: In order to induce RNAi mediated silencing of certain gene products we employed the Gal4-UAS system. By crossing males of a Gal4 driver line (Bloomington #7063) to females of the fly RNAi collection TRiP1 we obtained an F1 generation depleted for HP1 in the female germ line (Bloomington #33400). These females were crossed to siblings and produced embryos that were depleted of HP1 mRNA and protein. The same driver line and strategy was used to overexpress transgenes in the female germ line and early embryos. To collect precisely time staged embryos the flies were allowed to lay eggs on apple juice agar plates in cages for one hour at 25 °C. In order to synchronize the laying of the flies, plates were changeds for three consecutive times and the embryos were discarded. After three pre-lays, the embryos were collected for one hours and aged for another two hours at 25 °C to reach the stage of zygotic genome activation. The plate with the embryos was removed from the incubator and the embryos were dechorionated with 50% bleach, washed with water and carefully dried. The embryos were transferred in 7 ml of heptane and 5 ml of freshly prepared fixative were added. The fixative consists of  bufferof buffer A (60 mM KCl, 15 mM NaCl, 15 mM HEPES [pH 7.6], 4 mM MgCl2) and 1.8% of formaldehyde. During the formaldehyde fixation the embryos were incubated on an orbital shaker at maximum speed for 15 min. The fixation was stopped by the addition of 225 mM glycine (final concentration). The embryos were incubated for 5 min on a wheel and washed with buffer A + 0.1% Triton. After washing, the embryos were hand sorted on a cooling station under a microscope with transmitted light. The typical clear rim and the cellular membranes that form at zygotic genome activation characterize this developmental stage. The embryos were shock frozen and stored in batches of 50-100 at -80 °C.

value: pUASP::H3.3K9M expression


title: HiC HP1 KD rnai1 S2 cells repl 1

description: HiC HP1 KD rnai1 S2 cells repl 1

source_name: HiC HP1 KD rnai1 S2 cells repl 1

growth_protocol: Cells were seeded in Express Five SFM (Gibco 10486025) supplemented with GlutaMAX (Gibco 35050061) at 1 Mio cells/ml in 6 ml shaking flasks and grown for 4 days to reach a total of approximately 40 Mio cells (6-7 Mio cells/ml).

extract_protocol:
For S2 cells the nuclei were released using the NEXSON protocol. Briefly, the cells were resuspended in 1 ml of ice-cold HiC lysis buffer and subjected to ultrasound in a Covaris sonicator (using the following parameters peak power 75, duty factor 2, cycles/burst 200, 67 sec). The integrity of the nuclei was checked under the microscope.  The nuclei were pelleted for 5 min at 3000 g (rcf) and 4 °C. After discarding the supernatant, the pellet was incubated in 50 µl 0.5% SDS for 10 min at RT. The reaction was quenched by adding 145 µl of water and 25 µl of 10% Triton X100.   To digest the chromatin 25 µl of DpnII buffer were added and 0.7 µl of DpnII (NEB R0543T). The reaction was incubated for 90 min at 37 °C in a thermomixer at 600 rpm and a second instance of 0.7 µl of DpnII was added followed by a second incubation of 90 min.    The nuclei were pelleted for 5 min at 1000 xg (rcf) at RT and resuspended in 135 µl of 1x CutSmart buffer (NEB B7204S). To biotinylate the free chromatin ends, dNTP-mix (NEB) (final 0.15 mM), Biotin-14-dATP (Jena Bioscience, NU-835-BIO14-S) (final 0.05 mM) and 10 U of Klenow (NEB M0210 L) were added to the reaction (final volume 150 µl) and incubated for 60 min at 25 °C. Next the free ends of the chromatin were ligated in a total volume of 1200 µl by adding ligation buffer (NEB B0202S) (1x final), 10% Triton (0.8% final), 120 µg BSA, 2000 U ligase (NEB M0202S). After two hours a second instance of 2000 U ligase was added and incubated for another 2 hours. Following the incubation, the nuclei were pelleted at 1000 g for 5 min at RT, the supernatant was discarded and the nuclei resuspended in 200 µl elution buffer (10 mM Tris-HCl [pH 8], 1 mM EDTA, 1% SDS). Proteins were digested upon addition of 400 µg Proteinase K for 30 min at 55 °C. The chromatin was reverse crosslinked in the presence of 0.365 M NaCl at 68 °C overnight.   The next day DNA was purified using the ChIP DNA Clean&Concentrator Kit (Zymo Research D5205) eluted in 50 µl and biotin was removed from unligated fragments by adding NEB buffer 2 (NEB B7002S) (1x final), 12 µg of BSA, dATP and dGTP (0.025 final each), 3 U T4 DNA polymerase (NEB M0203S) in a final volume of 120 µl. The reaction was stopped by adding EDTA to a final concentration of 13 mM.  The DNA was transferred to Covaris microTUBE snap cap (520045) and sheared using the Covaris E220 (with intensifier (50014) and the following parameters duty factor 10%, peak incident power 140, cycle/burst 200, 120 sec. The DNA fragments were in the range of 200-300 bp.  Ligated and biotinylated fragments were enriched through biotin pulldown using Dynabeads MyOne Streptavidin C1 (Invitrogen 65001). The samples were filled up to a total of 400 µl with 2x binding buffer (10 mM Tris-HCl [pH 8], 1 mM EDTA, 2 M NaCl) (1x final) and beads (equilibrated with TWB (5 mM Tris-HCl [pH 8], 0.5 mM EDTA, 1 M NaCl, 0.05% Tween) resuspended in 1x binding buffer were added. The beads were washed twice for 2 min at 55 °C with TWB and twice with EB-buffer (Qiagen). Last the beads were resuspended in 50 µl of EB-buffer and directly used for library preparation using the NEB Ultra II DNA Library Prep Kit for Illumina (E7645S and E6440 or E7335, E7500, E7710, E7730) following the manufacturer’s instructions except that the adapter ligation happened on the biotin beads. The fragments were released from the beads before the PCR reaction (by heating to 98 °C for 10 min) after unligated adapters had been removed. To amplify the libraries 12-13 cycles of PCR were performed.
We used NEB Ultra II DNA Library Prep Kit for Illumina (E7645S) following the manufacturer’s instructions except that the adapter ligation happened on the biotin beads.

treatment_protocol: In order to deplete HP1 mRNA in S2 cells, oligos were designed (http://www.dkfz.de/signaling/e-rnai3/) that allowed the production of T7 binding sites coupled 150 bp long PCR products including the coding sequence of the third or the fourth exon of the HP1 transcript. Two independent regions were chosen to control for off-target effects. The regions were amplified from cDNA of 0-3 hr embryos. As a control a 300 bp region of GST was amplified from the vector pET41a. The PCR product was gel-purified and 500 ng -1 µg were used for in-vitro transcription using the HiScribe T7 In Vitro Transcription Kit (NEB E2050) running the reaction overnight. The fragments were purified using the MEGAclear transcription clean-up kit (Invitrogen AM1908). The RNA was eluted twice with EB-buffer heated to 95 °C. The RNA was aliquoted and stored at -80 °C.   To treat S2 cells with the dsRNA, cells were seeded in Express Five SFM (Gibco 10486025) supplemented with GlutaMAX (Gibco 35050061) at 1 Mio cells/ml in 6 ml shaking flasks. The dsRNA was thawed on ice and heated to 95 °C for 5 min, then the heating block was switched of the dsRNA was allowed to cool down to 40 °C before it was transferred to a metal rack at RT for 10 min and then transferred to ice. The dsRNA was diluted in 250 µl of Express Five SFM to reach a final amount of 60 µg of dsRNA per sample (10 µg of dsRNA in 1 Mio cells). To increase transfection efficiency 15 µl of Lipofectamine RNAiMAX (Invitrogen 13778100 ) were also diluted in 250 µl of Express Five SFM. Following the Lipofectamine mix and the diluted dsRNA were mixed and incubated for 15 min at RT. The Lipofectamine-dsRNA mix was added to the cells. The cells were grown shaking for 2 days, when a boost of dsRNA (5 µg/1 Mio cells) was added. After 4 days the cells had reached a density of 5-6 Mio cells/ml and knockdown efficiency was assessed by Western Blot and qPCR. To perform HiC the cells were harvested by centrifugation at 1300 xg for 5 min, washed with buffer A (supplemented with 10 mM of sodiumbutyrate) and fixed for 10 min at RT by adding 1 ml of 1% PFA diluted in buffer A (supplemented with 10 mM of sodiumbutyrate). The fixation was stopped by adding 100 µl of 2.5 M glycine and the cells were immediately pelleted 1300 xg for 5 min. The cells were washed again twice with buffer A (supplemented with 10 mM of sodiumbutyrate), shock frozen and stored until further use at -80 °C.

tag: clone

value: WT S2 cell line

value: S2 cell

value: RNAi HP1 dsRNA 1


title: 44-SRSF1 KD_SAL_replicate 2

value: SRSF1 KD shRNA Knockdown


title: RNA-seq_Control_rep3


title: 38-HNRNP U KD_SAL_replicate 2


title: HiC HP1 KD + rescued stage 5 repl 3

description: HiC HP1 KD + rescued  stage 5 repl 3

source_name: HiC HP1 KD + rescued  stage 5 repl 3

value: HP1-KD+pUASP::Flag-HA-HP1 expression


title: HiC HP1 KD + rescued stage 5 repl 2

description: HiC HP1 KD + rescued  stage 5 repl 2

source_name: HiC HP1 KD + rescued  stage 5 repl 2


title: RNA-seq_Control_rep2


title: 37-HNRNP U KD_SAL_replicate 1


title: HiC HP1 KD stage 5 repl 5

description: HiC HP1 KD stage 5 repl 5

source_name: HiC HP1 KD stage 5 repl 5


title: HiC HP1 KD + rescued stage 5 repl 1

description: HiC HP1 KD + rescued  stage 5 repl 1

source_name: HiC HP1 KD + rescued  stage 5 repl 1


title: RNA-seq_Control_rep1


title: HiC HP1 KD stage 5 repl 4

description: HiC HP1 KD stage 5 repl 4

source_name: HiC HP1 KD stage 5 repl 4


title: 36-HNRNP K KD_UN_replicate 3

value: HNRNP K KD shRNA Knockdown


title: 35-HNRNP K KD_UN_replicate 2


title: ChIP-nexus_RNAPII_dTAG_TRI40min_rep2

data_processing:
Fastq files were filtered for the presence of the four mixed barcodes and were deduplicated using Q-Nexus (Hansen et al., 2016).  Bowtie2 (v 2.3.5) was used for alignment to either the mm10 or hg19 genome. Normalization factors were computed for reads mapping uniquely to the human genome using Deseq2 (Love, Huber, & Anders, 2014). All aligned mouse ChIP-nexus BAM files were converted to bigwig (1 bp bin), separated by strand, and normalized to human spike-in controls using deepTools (v 3.0) with an “–offset 1” to record the position of the 5’ end of the sequencing read which corresponds to TF footprint.
Genome_build: mm10

extract_protocol: DNA-protein-complexes were isolated with specific antibodies when still being attached to protein A-dynabeads. DNA was end repaired using NEBNext End repair module (#E6050L). A single 3'-A overhang was added to the blunted ends using NEBNext dA-Tailing module (#E6053L). Adapters with single 3'-T overhangs and 5’ overhangs (barcode composed of 5 random nucleotides) were ligated to the adenylated fragments. Ligated fragments were blunted again by Klenow 3'-5' exo- polymerase to fill in the 5’ overhang first and then by T4 DNA polymerase to trim any possible 3’ overhang. Blunted DNA was subsequently digested by lambda exonuclease first and RecJf afterwards. Digested single strand DNA was then eluted, reverse cross-linked and purified prior to self-circularization by Circligase. An oligonucleotide was mixed with circularized single DNA for subsequent BamHI digestion to linearize the single DNA again. Linearized single strand DNA was then PCR-amplified using adaptor sequences and library was purified on 2% agarose gel to remove adaptor-adaptor ligation products. Following cluster generation on the flowcell surface, the sequencing libraries were sequenced following Illumina's protocol.

value: H2afz-FKBP-V + Dendra2-RNAPII

value: dTAG + Triptolide 40 min

tag: antibody

value: Anti-Dendra2 (OriGene TA180094)


title: HiC HP1 KD stage 5 repl 3

description: HiC HP1 KD stage 5 repl 3

source_name: HiC HP1 KD stage 5 repl 3

value: WT embryo at stage 5

value: embryo


title: HiC WT stage 5 repl7

description: HiC WT stage 5 repl7

source_name: HiC WT stage 5 repl7

value: control (Bloomington #36303)


title: HiC HP1 KD stage 5 repl 1

description: HiC HP1 KD stage 5 repl 1

source_name: HiC HP1 KD stage 5 repl 1

value: HP1-KD (Bloomington #33400)


title: ChIP-nexus_RNAPII_dTAG_TRI40min_rep1


title: HiC WT stage 5 repl6

description: HiC WT stage 5 repl6

source_name: HiC WT stage 5 repl6


title: 34-HNRNP K KD_UN_replicate 1

value: no treatment


title: ChIP-nexus_RNAPII_dTAG_TRI20min_rep2

value: Embryonic stem cells

value: dTAG + Triptolide 20 min


title: HiC WT stage 5 repl5

description: HiC WT stage 5 repl5

source_name: HiC WT stage 5 repl5


title: HiC WT stage 5 repl4

description: HiC WT stage 5 repl4

source_name: HiC WT stage 5 repl4


title: 33-HNRNP K KD_SAL_replicate 3

source_name: RAW 264.7 Macrophage

value: Salmonella infection


title: HiC WT stage 5 repl3

description: HiC WT stage 5 repl3

source_name: HiC WT stage 5 repl3


title: ChIP-nexus_RNAPII_dTAG_TRI20min_rep1


title: HiC WT stage 5 repl2

description: HiC WT stage 5 repl2

source_name: HiC WT stage 5 repl2


title: 32-HNRNP K KD_SAL_replicate 2


title: ChIP Pol2 IP repl2

description: ChIP Pol2 IP repl2

data_processing:
Reads were mapped to D. melanogaster (build dm6) using qAlign from QuasR package [Gaidatzis et al 2015] using the following alignments parameters: -n 2 -l 28 -e 70 -k 1 -X 500. This allows to keep reads mapping to multiple loci to be randomly assigned to one of the multiple locations. ChIP enrichment over input was calculated using bamCompare from deepTools using the following parameters: --scaleFactorsMethod SES --smoothLength 900 --binSize 300. Peaks were called using macs2 [Zhang et al 2008], using a cut-off of 0.05 on the q-value. --broad option was added for the H3K9me3 and HP1 ChIP.
Genome_build: dm6
Supplementary_files_format_and_content: bigwig file containing the enrichment of IP over input

source_name: ChIP Pol2 IP repl2

extract_protocol:
To extract the nuclei the embryos were transferred into Lysis buffer (140 mM NaCl, 15 mM HEPES [pH 7.6], 1 mM EDTA, 0.5 mM EGTA, 1 % TritonX100, 0.5 mM DTT, 0.1 % Sodium Deoxycholate, 10 mM Sodium Butyrate, 0.1% SDS, 0.5% N-Laurosylsarcosine,1X  Protease Inhibitors) and subjected to ultrasound treatment (Covaris E220, 45 sec, peak power 75, duty factor 10, cycles burst 200). The chromatin was sheared using Covaris E220 (900 sec, peak power 140, duty factor 5, cycle burst 200). The quality of the shearing was inspected on a Bioanalyzer 2100 (Agilent).  After sonication and 10 min high-speed centrifugation, fragmented chromatin was recovered in the supernatant. Chromatin was precleared by addition of 50 μl of Protein A-Agarose (PA) suspension (Roche 11134515001) followed by overnight incubation at 4°C. PA was removed by centrifugation, antibodies were added to the supernatant, and samples were incubated for 4 hr at 4°C in a rotating wheel. PA (50 μl) was added, and incubation was continued overnight at 4°C. Antibody-protein complexes were collected by centrifugation at 4,000 rpm for 1 min, and the supernatants were discarded. Samples were washed four times in Lysis buffer (with only 0.05% SDS) and twice in 1 mM EDTA, 10 mM Tris (pH 8) buffer (each wash, 5 min at 4°C). Chromatin was eluted from PA in 150 μl of 10 mM EDTA, 1% SDS, 50 mM Tris (pH 8) at 65°C for 15 min, followed by centrifugation and recovery of the supernatant. The eluate was incubated overnight at 65°C to reverse crosslinks and treated with Proteinase K for 3 hr at 50°C.  The chromatin was purified using ChIP DNA Clean & Concentrator columns (Zymo Research).
libraries were prepared using NEB Ultra II DNA Library Prep Kit for Illumina (E7645S) following the manufacturers instructions

treatment_protocol: To collect precisely time staged embryos the flies were allowed to lay eggs on apple juice agar plates in cages for one hour at 25 °C. In order to synchronize the laying of the flies, plates were changed for three consecutive times and the embryos were discarded. After three pre-lays, the embryos were collected for one hours and aged for another two hours at 25 °C to reach the stage of zygotic genome activation. The plate with the embryos was removed from the incubator and the embryos were dechorionated with 50% bleach, washed with water and carefully dried. The embryos were transferred in 7 ml of heptane and 5 ml of freshly prepared fixative were added. The fixative consists of  bufferof buffer A (60 mM KCl, 15 mM NaCl, 15 mM HEPES [pH 7.6], 4 mM MgCl2) and 1% of formaldehyde. We also used DSG (disuccinimidyl glutarate) for fixation in order to crosslink loosely bound complexes to chromatin and investigate the localization of HP1 more in detail. For DSG fixation the embryos were first incubated for 45 min in heptane and a fixative (buffer A with 2 mM DSG) followed by a second formaldehyde fixation for 15 min. During the formaldehyde fixation the embryos were incubated on an orbital shaker at maximum speed for 15 min. The fixation was stopped by the addition of 225 mM glycine (final concentration). The embryos were incubated for 5 min on a wheel and washed with buffer A + 0.1% Triton. After washing, the embryos were hand sorted on a cooling station under a microscope with transmitted light. The typical clear rim and the cellular membranes that form at zygotic genome activation characterize this developmental stage.  The embryos were shock frozen and stored in batches of 400 at -80 °C.

value: embryo (Bloomington #36303)

value: Carla Margulies, 3 µl


title: HiC WT stage 5 repl1

description: HiC WT stage 5 repl1

source_name: HiC WT stage 5 repl1


title: ChIP-nexus_RNAPII_dTAG_TRI10min_rep2

value: dTAG + Triptolide 10 min


title: ChIP Pol2 IP repl1

description: ChIP Pol2 IP repl1

source_name: ChIP Pol2 IP repl1


title: 31-HNRNP K KD_SAL_replicate 1


title: ChIP-nexus_RNAPII_dTAG_TRI10min_rep1


title: ChIP HP1 input repl1 DSG

description: ChIP HP1 input repl1 DSG

source_name: ChIP HP1 input repl1 DSG

value: WT embryo2-3 hrs


title: 30-HNRNP C KD_UN_replicate 3

value: HNRNP C KD shRNA Knockdown


title: ChIP HP1 IP repl1 DSG

description: ChIP HP1 IP repl1 DSG

source_name: ChIP HP1 IP repl1 DSG

value: HP1, Developmental Studies Hybridoma Bank C1A9, 2 µg


title: ChIP HP1 IP repl1 Flag HA

description: ChIP HP1 IP repl1 Flag HA

source_name: ChIP HP1 IP repl1 Flag HA

value: embryo (pUASP::Flag-HA-HP1)

value: HA, Cell Signaling #3724S, 5 µl


title: ChIP-nexus_RNAPII_dTAG_rep1

value: H2afz-FKBP-V + Dendra2-RNAPII

value: dTAG + no drug

value: Anti-Dendra2 (OriGene TA180094)


title: 29-HNRNP C KD_UN_replicate 2


title: ChIP HP1 IP repl3

description: ChIP HP1 IP repl3

source_name: ChIP HP1 IP repl3


title: ChIP HP1 input repl3

description: ChIP HP1 input repl3

source_name: ChIP HP1 input repl3


title: 27-HNRNP C KD_SAL_replicate 3


title: 26-HNRNP C KD_SAL_replicate 2


title: ChIP HP1 input repl1

description: ChIP HP1 input repl1

source_name: ChIP HP1 input repl1

value: WT embryo at stage 5


title: ChIP HP1 IP repl1

description: ChIP HP1 IP repl1

source_name: ChIP HP1 IP repl1


title: ChIP-nexus_RNAPII_Control_TRI40min_rep2

value: Control + Triptolide 40 min


title: ChIP-nexus_RNAPII_Control_TRI40min_rep1


title: ChIP H3K9me3 IP repl2

description: ChIP H3K9me3 IP repl2

source_name: ChIP H3K9me3 IP repl2

value: H3K9me3, ActiveMotif 39161, 1 µg


title: 25-HNRNP C KD_SAL_replicate 1


title: ChIP-nexus_RNAPII_Control_TRI20min_rep1

value: Embryonic stem cells

value: Control + Triptolide 20 min


title: ChIP H3K9me3 input repl1

description: ChIP H3K9me3 input repl1

source_name: ChIP H3K9me3 input repl1


title: ChIP H3K9me3 IP repl1

description: ChIP H3K9me3 IP repl1

source_name: ChIP H3K9me3 IP repl1


title: ChIP-nexus_RNAPII_Control_TRI10min_rep2

value: Control + Triptolide 10 min


title: ChIP H3K9ac input repl1

description: ChIP H3K9ac input repl1

source_name: ChIP H3K9ac input repl1

value: WT embryo 2-3 hrs

value: embryo (Bloomington #36303)


title: ChIP HP1 input repl1 Flag HA

description: ChIP HP1 input repl1 Flag HA

source_name: ChIP HP1 input repl1 Flag HA


title: ChIP H3K9ac IP repl2

description: ChIP H3K9ac IP repl2

source_name: ChIP H3K9ac IP repl2

value: H3K9ac, ActiveMotif 39586, 1 µg


title: ChIP-nexus_RNAPII_Control_TRI20min_rep2


title: ChIP-nexus_RNAPII_dTAG_rep2


title: 23-HNRNP F KD_UN_replicate 2

source_name: RAW 264.7 Macrophage

value: HNRNP F KD shRNA Knockdown

value: no treatment


title: ChIP-nexus_RNAPII_Control_TRI10min_rep1


title: 28-HNRNP C KD_UN_replicate 1

value: HNRNP C KD shRNA Knockdown


title: ChIP H3K4me3 IP repl2

description: ChIP H3K4me3 IP repl2

source_name: ChIP H3K4me3 IP repl2

value: H3K4me3, Diagenode, C15410003, 1 µg


title: ChIP H3K4me3 IP repl1

description: ChIP H3K4me3 IP repl1

source_name: ChIP H3K4me3 IP repl1


title: 22-HNRNP F KD_UN_replicate 1


title: ChIP HP1 IP repl2

description: ChIP HP1 IP repl2

source_name: ChIP HP1 IP repl2

value: HP1, Developmental Studies Hybridoma Bank C1A9, 2 µg


title: ChIP-nexus_RNAPII_Control_rep2

value: H2afz-FKBP-V + Dendra2-RNAPII

value: Control + no drug


title: 21-HNRNP F KD_SAL_replicate 3

value: Salmonella infection


title: ChIP H3K4me1 IP repl1

description: ChIP H3K4me1 IP repl1

source_name: ChIP H3K4me1 IP repl1

value: WT embryo at stage 5

value: H3K4me1, Diagenode, C15410194 (Lot A1862D), 1 µg


title: ChIP HP1 input repl2

description: ChIP HP1 input repl2

source_name: ChIP HP1 input repl2


title: ChIP H3K9me3 input repl2

description: ChIP H3K9me3 input repl2

source_name: ChIP H3K9me3 input repl2


title: ChIP H3K4me1 input repl2

description: ChIP H3K4me1 input repl2

source_name: ChIP H3K4me1 input repl2


title: 24-HNRNP F KD_UN_replicate 3


title: ChIP H3K4me1 IP repl2

description: ChIP H3K4me1 IP repl2

source_name: ChIP H3K4me1 IP repl2


title: ChIP H3K27me3 and Pol2 input repl2

description: ChIP H3K27me3 and Pol2 input repl2

source_name: ChIP H3K27me3 and Pol2 input repl2


title: 19-HNRNP F KD_SAL_replicate 1


title: 20-HNRNP F KD_SAL_replicate 2


title: ChIP H3K27me3 IP repl2

description: ChIP H3K27me3 IP repl2

source_name: ChIP H3K27me3 IP repl2


title: ChIP H3K9ac IP repl1

description: ChIP H3K9ac IP repl1

source_name: ChIP H3K9ac IP repl1

value: H3K9ac, ActiveMotif 39918, 1 µg


title: ChIP H3K27me3 and Pol2 input repl1

description: ChIP H3K27me3 and Pol2 input repl1

source_name: ChIP H3K27me3 and Pol2 input repl1


title: 18-SCR for hnRNP F_UN_replicate 3

value: SCR shRNA Control


title: ChIP H3K27ac and H3K4me3 input repl2

description: ChIP H3K27ac and H3K4me3 input repl2

source_name: ChIP H3K27ac and H3K4me3 input repl2


title: ChIP H3K27me3 IP repl1

description: ChIP H3K27me3 IP repl1

source_name: ChIP H3K27me3 IP repl1


title: ChIP H3K27ac IP repl2

description: ChIP H3K27ac IP repl2

source_name: ChIP H3K27ac IP repl2


title: ChIP H3K27ac IP repl1

description: ChIP H3K27ac IP repl1

source_name: ChIP H3K27ac IP repl1


title: 16-SCR for hnRNP F_UN_replicate 1

source_name: RAW 264.7 Macrophage


title: 15-SCR for SRSF 1 2 6 7 9_UN_replicate 3


title: H3K27_WntMO_r2

city: Ithaca

first: Marcos

last: Simoes-Costa

state: New York

address: 526 Campus Rd

department: Molecular Biology and Genetics

institute: Cornell University

description: CUT&RUN data for H3K27ac in chick neural crest cells at specification stage (HH9) upon Wnt knockdown

data_processing: Paired-end sequencing reads from the CUT&RUN libraries were trimmed using Cutadapt (Martin, 2011). Reads were filtered for those with a minimum length of 25bp or longer and aligned to the reference chicken Galgal5 assembly using Bowtie2 (Langmead and Salzberg, 2012). Picard MarkDuplicates tool was used to mark duplicate reads and BAM files were filtered with SAMtools to discard unmapped reads (those that were not the primary alignment, reads failing platform/vendor quality checks, and PCR/optical duplicates (-f 2 -F 1804)). Bigwig plots were generated using deeptools v3.1.2 bamCoverage function with the following parameters: --binSize 5 --normalizeUsing RPGC --effectiveGenomeSize 1218492533 --extendReads.

organism: Gallus gallus

source_name: Neural folds

extract_protocol:
Neural folds were dissected from HH9 morphant embryos (n=20 per CUT&RUN experiment). Cells were dissociated in Accumax for 20min at RT under mild agitation. CUT&RUN experiments were carried out as previously described (Rothstein and Simoes-Costa, 2019).
CUT&RUN libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit (New England Biolabs, E7645) and sequenced with paired-end reads on an Illumina NextSeq500 instrument.

tag: developmental stage

tag: condition

value: Wnt knockdown


title: ATAC_WntMO_Treat_r2

description: ATAC-seq on dissected neural folds upon Wnt knockdown

data_processing: Base calling was performed using CASAVA 1.8. Sequenced reads were trimmed for adaptor sequence using cutadapt v1.18, and mapped to the galGal5 genome using Bowtie 2 v2.3.4.3 with parameters --local --very-sensitive-local --no-unal --no-mixed --no-discordant -X 2000. Duplicate reads were marked using MarkDuplicates function of Picard tools v 2.0.4 and reads were filtered using samtools  v1.9 -F 1804 -f 2. Bigwig plots were generated using deeptools v3.1.2 bamCoverage function with the following parameters: --binSize 5 --normalizeUsing RPGC --effectiveGenomeSize 1218492533 --extendReads.

extract_protocol:
HH4 embryos were bilateraly injected with control and target (Wnt) morpholinos. Neural folds from morpholino injected side were dissected from HH9 embryos (n=5 per ATAC assay). Cells were dissociated in Accumax for 20min at RT under mild agitation.
ATAC-seq library preparation was performed as previously described (Buenrostro et al., 2015) and sequenced with paired-end reads on an Illumina NextSeq500 instrument.


title: ChIP-nexus_RNAPII_Control_rep1

value: Embryonic stem cells

value: Anti-Dendra2 (OriGene TA180094)


title: 14-SCR for SRSF 1 2 6 7 9_UN_replicate 2


title: ATAC_WntMO_Treat_r1

extract_protocol:
HH4 embryos were bilateraly injected with control and target (Wnt) morpholinos. Neural folds from morpholino injected  side were dissected from HH9 embryos (n=5 per ATAC assay). Cells were dissociated in Accumax for 20min at RT under mild agitation.
ATAC-seq library preparation was performed as previously described (Buenrostro et al., 2015) and sequenced with paired-end reads on an Illumina NextSeq500 instrument.


title: ATAC_WntMO_Ctrl_r2

description: ATAC-seq on dissected neural folds (Wnt knockdown control side)

extract_protocol:
HH4 embryos were bilateraly injected with control and target (Wnt) morpholinos. Neural folds from control side were dissected from HH9 embryos (n=5 per ATAC assay). Cells were dissociated in Accumax for 20min at RT under mild agitation.
ATAC-seq library preparation was performed as previously described (Buenrostro et al., 2015) and sequenced with paired-end reads on an Illumina NextSeq500 instrument.

value: Control


title: 13-SCR for SRSF 1 2 6 7 9_UN_replicate 1


title: ATAC_WntMO_Ctrl_r1


title: 12-SCR for SRSF 1 2 6 7 9_SAL_replicate 3


title: NF_HiChip_r2

description: H3K27ac-HiChIP data of neural folds

data_processing:
Library strategy: HiChIP
Each HiChIP replicate was initially processed with the HiC-Pro pipeline (Servant et al., 2015). Raw fastq (paired-end reads) were aligned to the chicken reference genome (Galgal5) and default settings used to remove duplicate reads, assign reads to MboI restriction fragments and filter for valid interactions. Preprocessed valid interactions were subsequently submitted to the Hichipper pipeline (Lareau and Aryee, 2018) a platform developed for bias-corrected peak calling, library quality control and DNA loop calling in HiChIP datasets using a standard MACS2 background model for H3K27ac peak calling and loop anchoring.

extract_protocol:
Neural folds were dissected from HH9 embryos (n=120 per replicate) in Ringers solution and dissociated in Accumax (Innovative Cell Technologies, #AM105). Whole HH9 embryos were prepared in parallel as control samples (n=20 per replicate). After dissociation cells were crosslinked, washed in cold PBS and submited to the HiChIP protocol as published by (Mumbach, et al. 2016).
In situ contact libraries were generated according to the HiChIP protocol published by (Mumbach, et al. 2016). DNA digestion was performed with MboI and H3K27ac antibody was used for fragment pulldown. DNA fragments were tagmented and PCR amplified. After size selection, libraries were quantified and sequenced with paired-end 75bp reads on an Illumina NextSeq500 instrument.

value: Wild type


title: NF_HiChip_r1

description: H3K27ac-HiChIP data of neural folds


title: 17-SCR for hnRNP F_UN_replicate 2


title: NF_HiChip_r3

description: H3K27ac-HiChIP data of neural folds


title: ChIP H3K27ac, H3K4me1 and H3K4me3 input repl1

value: embryo (Bloomington #36303)


title: 11-SCR for SRSF 1 2 6 7 9_SAL_replicate 2


title: WE_HiChip_r3

description: H3K27ac-HiChIP data of whole embryos

source_name: Whole embryo


title: H3K27_WntMO_r1

extract_protocol:
Neural folds were dissected from HH9 embryos (n=20 per CUT&RUN experiment). Cells were dissociated in Accumax for 20min at RT under mild agitation. CUT&RUN experiments were carried out as previously described (Rothstein and Simoes-Costa, 2019).
CUT&RUN libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit (New England Biolabs, E7645) and sequenced with paired-end reads on an Illumina NextSeq500 instrument.


title: 10-SCR for SRSF 1 2 6 7 9_SAL_replicate 1


title: NET-seq_4h_dTAG_rep2

data_processing:
Library strategy: NET-seq
All the NET-seq FASTQ files were processed using custom Python scripts (https://github.com/BradnerLab/netseq). The sequencing reads are aligned to the mouse reference genome (mm10) using the STAR (v 2.7.2b) aligner (Dobin et al., 2013). PCR duplicates and reads arising from RT bias are also removed. Reads mapping exactly to the last nucleotide of each intron and exon (splicing intermediates) were further removed from the analysis. The final NET-seq BAM files were converted to bigwig, separated by strand, and normalized to SIRV spike-in controls using deepTools (v 3.0) with an “–offset 1” to record the position of the 5’ end of the sequencing read which corresponds to the 3’ end of the nascent RNA. NET-seq tags sharing the same or opposite orientation with the TSS were assigned as “sense” and “antisense” tags, respectively. Promoter-proximal regions were carefully selected for analysis to ensure that there is minimal contamination from transcription arising from other transcription units. Genes overlapping within a region of 2 kb upstream of the TSS were removed from the analysis.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig

source_name: Embryonic stem cells

extract_protocol: The cell fractionation was performed as described previously (Mayer & Churchman, 2016). 10 million ES cells are washed with 500 ml of pre-cooled 1x PBS, resuspended in 150 ml Cytoplasmic lysis buffer (0.15% (v/v) NP-40, 10 mM Tris-HCl (pH 7.0), 150 mM NaCl, 25 mM a-amanitin (Sigma), 50 U SUPERase.In (Life Technologies), x1 Halt Protease Inhibitor cocktail mix (ThermoFisher 87786) and incubated on ice for 5 min. The cell lysate is layered over 400 ml of Sucrose buffer (10 mM Tris-HCl (pH 7.0), 150 mM NaCl, 25% (w/v) sucrose, 25 mM a-amanitin, 50 U SUPERase.In, x1 Halt Protease Inhibitor cocktail mix) and centrifuged at 16,000 g for 10 min at 4C. The nuclei pellet is resuspended in 500 ml Nuclei wash buffer (0.1% (v/v) Triton X-100, 1 mM EDTA, in 1x PBS, 25 mM a-amanitin, 50 U SUPERase.In, 1x Protease inhibitor mix) and centrifuged at 1,150 g for 1 min at 4C. Washed nuclei are resuspended in 200 ml Glycerol buffer (20 mM Tris-HCl (pH 8.0), 75 mM NaCl, 0.5 mM EDTA, 50% (v/v) glycerol, 0.85 mM DTT, 25 mM a-amanitin, 50 U SUPERase.In, 1x Protease inhibitor mix). Next, 200 ml of Nuclei lysis buffer (1% (v/v) NP-40, 20 mM HEPES pH 7.5, 300 mM NaCl, 1M Urea, 0.2 mM EDTA, 1 mM DTT, 25 mM a-amanitin, 50 U SUPERase.In, 1x Protease inhibitor mix) are added, mixed by pulsed vortexing and incubated on ice for 2 min. The lysate is centrifuged at 18,500 g for 2 min at 4C. The chromatin pellet is resuspended in 50 ml Chromatin resuspension solution (25 mM a-amanitin, 50 Units SUPERase.In, 1x Protease inhibitor mix in 1x PBS) before RNA preparation. Biological replicates were obtained from two independent Control and dTAG-13 treated cells. Prior to library preparation, SIRV spike-in controls (1:10,000 dilution) were added to the extracted RNA to account for loss of RNA during library preparation. RNA preparation and NET-seq library construction was conducted as originally described (Mylonas). More than 90% recovery of ligated RNA and cDNA was achieved from 15% TBE-Urea (Invitrogen) and 10% TBE-Urea (Invitrogen), respectively, by adding RNA recovery buffer (R1070-1-10; Zymo Research) to the excised gel slices and further incubating at 70°C (1,500 rpm) for 15 min. Gel slurry was transferred through a ZymoSpin IV Column (C1007-50; Zymo Research) and further precipitated for subsequent library preparation steps. cDNA containing the 3’ end sequences of a subset of mature and heavily sequenced snRNAs, snoRNAs, and rRNAs were specifically depleted using biotinylated DNA oligos (Mylonas). Oligo-depleted circularized cDNA was amplified by PCR and double-stranded DNA was run on a 3% low melt agarose gel. The final NET-seq library running at ~150 bp was extracted and further purified using the ZymoClean Gel DNA recovery kit (Zymo Research). Sample purity and concentration was assessed in a 2200 TapeStation and further deep sequenced in a HiSeq 2500 Illumina Platform The cell fractionation was performed as described previously (Mayer & Churchman, 2016). 10 million ES cells are washed with 500 ml of pre-cooled 1x PBS, resuspended in 150 ml Cytoplasmic lysis buffer (0.15% (v/v) NP-40, 10 mM Tris-HCl (pH 7.0), 150 mM NaCl, 25 mM a-amanitin (Sigma), 50 U SUPERase.In (Life Technologies), x1 Halt Protease Inhibitor cocktail mix (ThermoFisher 87786) and incubated on ice for 5 min. The cell lysate is layered over 400 ml of Sucrose buffer (10 mM Tris-HCl (pH 7.0), 150 mM NaCl, 25% (w/v) sucrose, 25 mM a-amanitin, 50 U SUPERase.In, x1 Halt Protease Inhibitor cocktail mix) and centrifuged at 16,000 g for 10 min at 4C. The nuclei pellet is resuspended in 500 ml Nuclei wash buffer (0.1% (v/v) Triton X-100, 1 mM EDTA, in 1x PBS, 25 mM a-amanitin, 50 U SUPERase.In, 1x Protease inhibitor mix) and centrifuged at 1,150 g for 1 min at 4C. Washed nuclei are resuspended in 200 ml Glycerol buffer (20 mM Tris-HCl (pH 8.0), 75 mM NaCl, 0.5 mM EDTA, 50% (v/v) glycerol, 0.85 mM DTT, 25 mM a-amanitin, 50 U SUPERase.In, 1x Protease inhibitor mix). Next, 200 ml of Nuclei lysis buffer (1% (v/v) NP-40, 20 mM HEPES pH 7.5, 300 mM NaCl, 1M Urea, 0.2 mM EDTA, 1 mM DTT, 25 mM a-amanitin, 50 U SUPERase.In, 1x Protease inhibitor mix) are added, mixed by pulsed vortexing and incubated on ice for 2 min. The lysate is centrifuged at 18,500 g for 2 min at 4C. The chromatin pellet is resuspended in 50 ml Chromatin resuspension solution (25 mM a-amanitin, 50 Units SUPERase.In, 1x Protease inhibitor mix in 1x PBS) before RNA preparation. Biological replicates were obtained from two independent Control and dTAG-13 treated cells. Prior to library preparation, SIRV spike-in controls (1:10,000 dilution) were added to the extracted RNA to account for loss of RNA during library preparation. RNA preparation and NET-seq library construction was conducted as originally described (Mylonas). More than 90% recovery of ligated RNA and cDNA was achieved from 15% TBE-Urea (Invitrogen) and 10% TBE-Urea (Invitrogen), respectively, by adding RNA recovery buffer (R1070-1-10; Zymo Research) to the excised gel slices and further incubating at 70°C (1,500 rpm) for 15 min. Gel slurry was transferred through a ZymoSpin IV Column (C1007-50; Zymo Research) and further precipitated for subsequent library preparation steps. cDNA containing the 3’ end sequences of a subset of mature and heavily sequenced snRNAs, snoRNAs, and rRNAs were specifically depleted using biotinylated DNA oligos (Mylonas). Oligo-depleted circularized cDNA was amplified by PCR and double-stranded DNA was run on a 3% low melt agarose gel. The final NET-seq library running at ~150 bp was extracted and further purified using the ZymoClean Gel DNA recovery kit (Zymo Research). Sample purity and concentration was assessed in a 2200 TapeStation and further deep sequenced in a HiSeq 2500 Illumina Platform

tag: strain


title: 09-SCR for hnRNP F_SAL_replicate 3


title: WE_HiChip_r1

description: H3K27ac-HiChIP data of whole embryos


title: NET-seq_4h_Control_rep2

value: Control (4h)


title: RNA-seq_WntMo_M3

description: RNA-seq of neural upon Wnt knockdown

data_processing: Reads were trimmed using CutAdapt, and aligned to the galGal5 genome using hisat2 and quantified using featureCounts on genes from ENSEMBL release 93. Gene counts were processed using in R and differentially expressed genes were called using DESeq2. Lowly-expressed genes were removed (less than 5 counts any two samples) and DESeq2 revealed 254 differentially expressed genes (padj < 0.05). Regularized logarithm counts were exported for additional analysis.

source_name: Single neural fold

extract_protocol:
Loss of function assays were performed after bilateral injections with their respective controls. Wnt knockdown was performed by the combined inhibition of Wnt 1 and 4 by morpholinos. For RNA expression levels, paired single neural folds were finely dissected and total RNA isolated with the RNAqueous-Micro Total RNA Isolation Kit (Thermo Fisher Scientific, #AM1931) according to the kit’s protocol.
RNA was poly(A) selected using the NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs, E7490). TruSeq-barcoded RNAseq libraries were generated with the NEBNext Ultra II Directional RNA Library Prep Kit (New England Biolabs, E7760) and sequenced on an Illumina NextSeq500 instrument.


title: NET-seq_4h_dTAG_rep1


title: NET-seq_4h_Control_rep1


title: RNA-seq_WntMo_C3

description: RNA-seq of neural fold (control condition)

value: Ctrl


title: CRD vs 10426T

type: genomic

city: Daejeon

first: Myung Soon

last: Kim

address: Yeusung-gu

department: R&D

country: South Korea

institute: Genomictree

description: methylation profiling in 10426T sample

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, microarrays were washed 1 minute at room temperature with CGH/ChIP-on-chip Wash Buffer 1 (Agilent) and 1 minute with 37°C CGH/ChIP-on-chip Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Scanned on an Agilent G2565AA scanner.

data_processing: The scanned images were analyzed with Feature Extraction Software 9.3.2.1 (Agilent) to obtain background subtracted and spatially detrended Processed Signal intensities.

organism: Homo sapiens

source_name: CRD(common reference DNA)

label_protocol: The enriched DNA fragments was amplified using WGA2 kit (Sigma). 4 µg of amplified enriched DNA was labeled using Bioprime kit as following manufacturer's instructions

growth_protocol: Fresh-frozen primary tumors and paired tumor-adjacent normal tissues of bladder cancer patients

extract_protocol:
Genomic DNA extracted using Qiaquick DNA mini kit following manufacturer's instructions
0.5ug genomic DNA was fragmented with sonication. The fragmented DNA was incubated with MBD2bt protein, and then the enriched methylated DNA fragments was purified using Magnetic bead.

value: pooled DNA of 9 adjacent normal samples

value: enriched methylated DNA of bladder tumor tissue

tag: sample id

tag: Sex

value: male

tag: age

tag: Stage

value: IV


title: WE_HiChip_r2

description: H3K27ac-HiChIP data of whole embryos


title: CRD vs 10354T

description: methylation profiling in 10354T sample

value: II


title: 07-SCR for hnRNP F_SAL_replicate 1

value: Salmonella infection


title: RNA-seq_WntMo_M2

description: RNA-seq of neural upon Wnt knockdown


title: CRD vs 10171T

description: methylation profiling in 10171T sample

value: female

value: III


title: 06-SCR for hnRNP C K U_UN_replicate 3

value: SCR shRNA Control

value: no treatment


title: COVID_5_villi, scRNA-seq

city: West Haven

first: Arun

middle: Rajendra

last: Chavan

state: CT

address: 850 West Campus Drive

department: Ecology and Evolutionary Biology

institute: Yale University

description:
counts.tsv.gz
metadata.tsv.gz

data_processing:
Sequencing results were demultiplexed into FASTQ files using the Cell Ranger (10x Genomics, 3.0.2) mkfastq function.
Samples were aligned to GRCh38 10x genome and the count matrix was generated using the cellranger count function with default settings.
Low quality cells containing <500 or >6000 genes detected were removed, as well cells with >20% of transcripts mapping to mitochondrial genes. Genes that were present in less than 3 cells were excluded from analysis.
Gene expression values were then normalized, log-transformed, and scaled.
Single cell transcriptomes from COVID-19 cases and healthy controls were pooled prior to unsupervised cluster analysis.
Genome_build: GRCh38
Supplementary_files_format_and_content: counts.tsv.gz is a tab-delimited file that contain cell by gene matrix of raw counts
Supplementary_files_format_and_content: metadata.tsv.gz is tab-delimited file that contains cell-level metadata including cell QC metrics and cell type annotations

molecule: polyA RNA

source_name: placental villi

extract_protocol:
Dissected tissues were rinsed thoroughly in PBS and minced with scissors in a tissue digestion buffer of Liberase TM (0.28 WU/ml) and DNase I (30 μg/ml) in HBSS with Ca2+ and Mg2+. Finely minced tissue was enzymatically digested at 37°C for 1 hour with agitation, pipetting, and further mincing every 10 minutes until disaggregated. The suspension was passed through sterile gauze, centrifuged at 1000 x g for 5 minutes at 4°C to pellet cells, and washed with fresh digestion buffer. After centrifugation, the supernatant was aspirated and the cell pellet was resuspended in ACK lysing buffer for 5 minutes. Cells were centrifuged and resuspended in RPMI media before filtering through a 70-μm mesh cell strainer.
scRNA-seq libraries were generated using the 10x Chromium Single Cell 3’ Reagent Kit.
single cell RNA-seq

tag: sars-cov-2 status

value: positive

value: placental villi


title: COVID_5_decidua, scRNA-seq

description:
counts.tsv.gz
metadata.tsv.gz

source_name: decidua

value: decidua


title: 05-SCR for hnRNP C K U_UN_replicate 2


title: RNA-seq_WntMo_C2


title: 08-SCR for hnRNP F_SAL_replicate 2


title: COVID_4_villi, scRNA-seq

description:
counts.tsv.gz
metadata.tsv.gz


title: CRD vs 3770T

description: methylation profiling in 3770T sample

value: I


title: COVID_4_decidua, scRNA-seq

description:
counts.tsv.gz
metadata.tsv.gz


title: RNA-seq_WntMo_C1


title: 03-SCR for hnRNP C K U_SAL_replicate 3


title: CRD vs 4385T

description: methylation profiling in 4385T sample


title: 04-SCR for hnRNP C K U_UN_replicate 1


title: 02-SCR for hnRNP C K U_SAL_replicate 2


title: CRD vs J5BZ10T

description: methylation profiling in J5BZ10T sample


title: RNA-seq_WntMo_M1

description: RNA-seq of neural upon Wnt knockdown

value: Wnt knockdown


title: CRD vs 4415T

description: methylation profiling in 4415T sample


title: CRD vs 10171NT

description: methylation profiling in 10171NT sample

value: enriched methylated DNA of adjacent normal tissue


title: LEF1_WntMO_r2

description: CUT&RUN data for LEF1 in chick neural crest cells at specification stage (HH9) upon Wnt knockdown

data_processing:
Library strategy: CUT&RUN
Paired-end sequencing reads from the CUT&RUN libraries were trimmed using Cutadapt (Martin, 2011). Reads were filtered for those with a minimum length of 25bp or longer and aligned to the reference chicken Galgal5 assembly using Bowtie2 (Langmead and Salzberg, 2012). Picard MarkDuplicates tool was used to mark duplicate reads and BAM files were filtered with SAMtools to discard unmapped reads (those that were not the primary alignment, reads failing platform/vendor quality checks, and PCR/optical duplicates (-f 2 -F 1804)). Bigwig plots were generated using deeptools v3.1.2 bamCoverage function with the following parameters: --binSize 5 --normalizeUsing RPGC --effectiveGenomeSize 1218492533 --extendReads.

extract_protocol:
Neural folds were dissected from HH9 morphant embryos (n=20 per CUT&RUN experiment). Cells were dissociated in Accumax for 20min at RT under mild agitation. CUT&RUN experiments were carried out as previously described (Rothstein and Simoes-Costa, 2019).
CUT&RUN libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit (New England Biolabs, E7645) and sequenced with paired-end 37bp reads on an Illumina NextSeq500 instrument.


title: CRD vs 4205T

description: methylation profiling in 4205T sample


title: CRD vs 10354NT

description: methylation profiling in 10354NT sample


title: CRD vs W10QNT

description: methylation profiling in W10QNT sample


title: CRD vs 4363T

description: methylation profiling in 4363T sample


title: 01-SCR for hnRNP C K U_SAL_replicate 1


title: CNTRL_3_villi, scRNA-seq

description:
counts.tsv.gz
metadata.tsv.gz

value: negative


title: Case3

city: Shanghai

first: Xi

last: Cheng

state: State...

address: Ruijin er lu 197

country: China

institute: Shanghai Institute of Digestive Surgery

data_processing:
We applied the reads filtering towards the raw reads after sequencing to achieve the clean data following the criteria: a)10% base quality <15 b) 13% base quality <20.
Hisat2 mapping to reference genome
count counting
Genome_build: GRCh38
Supplementary_files_format_and_content: TXT file contain counts for each sample

growth_protocol: Growth with RMPI 1640 medium

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Treat with shETV5 lentivirus

value: Human colorectal cancer (CRC)


title: CNTRL_3_decidua, scRNA-seq

description:
counts.tsv.gz
metadata.tsv.gz


title: LEF1_WntMO_r1


title: CRD vs 4415NT

description: methylation profiling in 4415NT sample

value: pooled DNA of 9 adjacent normal samples


title: Case2


title: CRD vs 3770NT

description: methylation profiling in 3770NT sample

value: male


title: Mutz-3_H3K4me1

city: Philadelphia

first: Kathrin

last: Bernt

state: PA

address: 3501 Civic Center Boulevard,

institute: Children's Hospital of philadelphia

data_processing:
BWA Alignment
MACS2 peak calling
samtools convert files
IGV 2.8.0
Genome_build: GRCh37
Supplementary_files_format_and_content: bigwig file

source_name: Mutz-3 cell line

growth_protocol: Mutz-3 were grown in alpha-MEM (with ribo- and deoxyribonucleosides) + 20% heat inactivated FBS, 1% Penicillin/Streptomycin + 20% vol conditioned medium of cell line 5637.

extract_protocol:
Briefly, samples were crosslinked, lysed, sonicated and immunoprecipated with the indicated antibody overnight. After a series of washes they were reverse crosslinked overnight and DNA extracted.
Library prep was performed at Genewiz, Illumina HiSeq, 2x150bp paired-end reads, multiplexed

value: aml

tag: chip antibody


title: CNTRL_1_villi, scRNA-seq

description:
counts.tsv.gz
metadata.tsv.gz

tag: tissue


title: Case1


title: LEF1_r2

description: CUT&RUN data for LEF1 in chick neural crest cells at specification stage (HH9)

extract_protocol:
Neural folds were dissected from HH9 embryos (n=20 per CUT&RUN experiment). Cells were dissociated in Accumax for 20min at RT under mild agitation. CUT&RUN experiments were carried out as previously described (Rothstein and Simoes-Costa, 2019).
CUT&RUN libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit (New England Biolabs, E7645) and sequenced with paired-end 37bp reads on an Illumina NextSeq500 instrument.

value: Wild type


title: CRD vs 4385NT

description: methylation profiling in 4385NT sample


title: CNTRL_1_decidua, scRNA-seq

description:
counts.tsv.gz
metadata.tsv.gz


title: Control3


title: CRD vs 4363NT

description: methylation profiling in 4363NT sample


title: Control2


title: Mutz3_Input


title: Human Islet ChIP-input DNA

city: birmingham

first: ildem

last: akerman

address: BR Tower, 3rd Floor, Room 333, Edgbaston,

department: IMSR

country: United Kingdom

institute: University of Birmingham

data_processing:
CASAVA 1.8.2.
Fastq files were aligned to the human genome (hg19) using bowtie (v2.2.1)
Peak calling using MACS2 (v. 2.1.0) against the input control file with q < 0.05.
Genome_build: hg19
Supplementary_files_format_and_content: peak text files (bed format)

source_name: pancreatic islet

growth_protocol: Human pancreatic islets were isolated from multiorgan donors without a history of glucose intolerance after informed consent from family members using established isolation procedures57, shipped in culture medium and re-cultured at 37°C in a humidified chamber with 5% CO2 in glucose-free RPMI 1640 supplemented with 10% fetal calf serum, 100 U/ml penicillin, 100 U/ml streptomycin and 11mM glucose for three days before analysis.

extract_protocol:
Human islets were fixed with 1% formalydehyde for 10 minutes at RT, sonicated and insoluble material removed.
Illumina Trueseq DNA library preparation kit  following manufacturers instructions by the Imperial College genomics facility (index: TTCAGC)

value: Donor derived human islets

value: no antibody pull down


title: Mutz-3_H3K27ac


title: bCAT_r2

description: CUT&RUN data for CTNNB1 in chick neural crest cells at specification stage (HH9)

value: Abcam, #ab32572


title: LEF1_r1


title: Embryonic anole lung E6, scRNA-Seq

city: Princeton

first: Michael

middle: A.

last: Palmer

state: New Jersey

address: 25 William Street

department: Chemical and Biological Engineering

institute: Princeton University

data_processing:
Basecalls performed using RTA version 1.18.64.0
Concatenated fastq files from both lanes of flowcell
Demultiplexed reads using barcode_splitter 0.18.2 (https://bitbucket.org/princeton_genomics/barcode_splitter)
Single cell analysis (alignment, cell identification, gene counts, etc.) performed by CellRanger count version 3.0
Single cell analysis by Seurat (v3)
Genome_build: Anolis carolinensis reference genome AnoCar2.0
Supplementary_files_format_and_content: 10x Cell Ranger HDF5 formatted matrix files

organism: Anolis sagrei

source_name: E6 lung

extract_protocol:
Lungs were dissected from embryonic anoles in cold PBS. Isolated lungs were placed in dispase, and mechanically dissociated with tungsten needles. After 10 minutes in dispase at room temperature, DMEM without HEPES and supplemented with 5% fetal bovine serum (FBS, Atlanta Biologicals) was added, and cell suspensions were passed through a filter with 40-µm-diameter pores. The resultant cell suspensions were then processed by the Princeton Genomics Core Facility.  Cells were loaded and processed using the Chromium Single Cell 3’ Library and Gel Bead Kit v3 on the Chromium Controller (10X Genomics) following manufacturer protocols. Individual cells were encapsulated in droplets with single gel beads carrying unique barcoded primers and then lysed. Then cDNA fragments were synthesized, barcoded, and amplified by PCR.
Illumina sequencing libraries were prepared from the amplified cDNA from each sample group using the Nextra DNA library prep kit (Illumina). The v3 libraries were sequenced on Illumina HiSeq 2500 Rapid flowcells (Illumina) as paired-end 26 + 50 nucleotide reads following manufacturer protocols.

value: whole lung


title: CTCF

description: CUT&RUN data for CTCF in chick neural crest cells at specification stage (HH9)


title: Embryonic anole lung E5, scRNA-Seq

source_name: E5 lung


title: Human Islet GLIS3 ChIP seq

value: GLIS3-antibody pull down


title: bCAT_r1


title: BSA_ful2

status: Public on Apr 02 2021

city: St. Louis

first: Andrea

last: Eveland

state: Missouri

address: 975 North Warson Road

institute: Donald Danforth Plant Science Center

description: processed data file: Supplemental Data Set 1.xlsx

data_processing:
Paired-end reads were first trimmed for adapter sequences using Cutadapt
Clean reads were mapped to S. viridis transcriptome (Sviridis_311_v2; Phytozome v12.1, (phytozome.jgi.doe.gov)) with Salmon (0.13.0)
DNA-seq reads were mapped to S. viridis genome (Sviridis_500_v2.fa downloaded from Phytozome  (phytozome.jgi.doe.gov)) with bwa  (0.7.12-r1039)
Genome_build: Sviridis_311_v2; Phytozome v12.1, (phytozome.jgi.doe.gov)
Supplementary_files_format_and_content: output of the BSA or WG-seq analysis

organism: Setaria viridis

source_name: young seedling

growth_protocol: S. viridis plants for phenotyping were grown under either SD (12 h light/12 h dark) conditions (31°C/22°C [day/night], 50% relative humidity, and light intensity of 400 µmol/sq.meter/s) in a controlled hight-light growth chamber at the Danforth Center’s growth facility

extract_protocol:
Poly-A+ RNA-seq libraries were generated from pools of hand-dissected inflorescence primordia from wild-type and ful2 mutant seedlings. RNA was extracted (PicoPure RNA isolation kit; Thermo Fisher Scientific)
library preparation was conducted from 500ng of total RNA using the NEBNext Ultra Directional RNA Library Prep Kit (Illumina) and size-selected for 200bp inserts
RNA-seq libraries were processed using an Illumina HiSeq 4000 platform at Novogene with a 150bp paired-end sequencing design.
The sequencing was conducted using two lanes to increase the sequencing depth. Fo the downstram analyis sample from lane1 and lane1 were merged.
DNA was extracted from 30 brl1 mutant individuals was pooled to generate a DNA library. The DNA library was made using the NEBNext Ultra DNA Library Prep Kit for Illumina (NEB), size selected for inserts of 500 to 600 bp, and sequenced with 150bp paired-end using standard Illumina protocols on Illumina Hi-Seq 4000 platform at Novogene. DNA libraries for whole genome sequencing were generated from a single brl1 mutant individual in the M2 generation and sequencing with 100bp single end on Illumina Hi-Seq 2500 platform at University of Illinois, Urbana-Champaign W.M. Keck sequencing facility. Read mapping and SNP calling by GATK (3.5-0-v3.5-0-g36282) were performed as described (Huang et al., 2017).

tag: cultivar

tag: genotype/variation

value: young seedling


title: 17DAS_wt_rep4

data_processing:
Paired-end reads were first trimmed for adapter sequences using Cutadapt
Clean reads were mapped to S. viridis transcriptome (Sviridis_311_v2; Phytozome v12.1, (phytozome.jgi.doe.gov)) with Salmon (0.13.0)
Supplementary_files_format_and_content: Supplemental Data Set 5: this file is the GOMAP file for the Setaria viridis genome generated according the pipeline described at https://dill-picl.org/projects/gomap/
Supplementary_files_format_and_content: salmon output

source_name: inflorescence primordia

extract_protocol:
Poly-A+ RNA-seq libraries were generated from pools of hand-dissected inflorescence primordia from wild-type and ful2 mutant seedlings. RNA was extracted (PicoPure RNA isolation kit; Thermo Fisher Scientific)
library preparation was conducted from 500ng of total RNA using the NEBNext Ultra Directional RNA Library Prep Kit (Illumina) and size-selected for 200bp inserts
RNA-seq libraries were processed using an Illumina HiSeq 4000 platform at Novogene with a 150bp paired-end sequencing design.
The sequencing was conducted using two lanes to increase the sequencing depth. For the downstream analyis sample from lane1 and lane1 were merged.

value: inflorescence primordia

tag: genotype

value: wt


title: 21DAS_ful2_rep1


title: 21DAS_ful2_rep3


title: 21DAS_ful2_rep2


title: 17DAS_wt_rep3


title: Control1

tag: cell line


title: 17DAS_wt_rep2


title: 17DAS_wt_rep1


title: 8-9DAS_wt_rep1

value: 8- 9DAS


title: 15DAS_ful2_rep4


title: 8-9DAS_wt_rep4


title: 10-11DAS_wt_rep3


title: 10-11DAS_wt_rep2


title: 15DAS_ful2_rep1


title: 8-9DAS_wt_rep2


title: 15DAS_ful2_rep3


title: 9-10DAS_ful2_rep4


title: 9-10DAS_ful2_rep3


title: 15DAS_ful2_rep2


title: 8-9DAS_wt_rep3


title: 10-11DAS_wt_rep4


title: 9-10DAS_ful2_rep2


title: CRD vs 4205NT

description: methylation profiling in 4205NT sample

value: I


title: 21DAS_ful2_rep4


title: 9-10DAS_ful2_rep1


title: CRD vs 10426NT

description: methylation profiling in 10426NT sample

value: enriched methylated DNA of adjacent normal tissue

value: IV


title: 10-11DAS_wt_rep1


title: WG-seq_ful2


title: TAL1 G1E-ER4+E2 [436]

city: University Park

first: Ross

last: Hardison

address: 303 Wartik Lab

institute: Pennsylvania State University

data_processing:
Basecalls using bcl2fastq-1.8.4, and parameters --no-eamss --mismatches 1
Mapping to reference genome mm10 canon with Bowtie 1.0.0 using parameters --chunkmbs 1024 -y -n 2 --best -k 1 --maxbts 800 -l 28 -e 80 --sam-nohead --sam
Wiggle and peaks called using MACS with parameters --format BAM --gsize 1870000000 --tsize 36 --bw 120 --mfold 12 --wig --space 1
Filter blacklist regions from peaks, and convert the *peaks.xls file from MACs to broadpeak format (see UCSC Genome Browser for format specs).
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: bigWigs, signal from MACS.
Supplementary_files_format_and_content: broadpeaks, peak calls by MACS.

source_name: G1E-ER4+E2 cells

growth_protocol: G1E-ER4 cells were grown in IMDM media + 15% FBS, kit ligand, and erythropoietin in a standard tissue culture incubator at 37°C with 5% CO2.

extract_protocol:
Lysates were prepared from sonicated nuclei and protein-DNA complexes were isolated with antibody.
ChIP-seq samples were prepared by end repair, 3’ adenylation, and adaptor ligation using Illumina’s TruSeq ChIP-seq Sample Preparation Kit.

treatment_protocol: To induce erythroid maturation, G1E-ER4 cells were treated with 10-8 mol/L β-estradiol for 24 hours (G1E-ER4+E2).

tag: cell type

value: ES-derived erythroid progenitor cells

value: CTCF (Millipore 07-729)

tag: average chromatin size in bp as measured between a 100-500 bp window using the agilent bioanalyzer 7500 chip

tag: subjective quality assessment (pass, low pass, fail)

value: Pass


title: J rep2

city: Beijing

first: Wei

last: Wei

address: Chaoyang District, Beichen West Road, Campus #1, No.2

department: State Key Lab of Plant Genomics

institute: Institute of Genetics and Developmental Biology, Chinese Academy of Sciences

data_processing:
RNA-sequencing was performed using an Illumina instrument of NovaSeq 6000
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Glycine max whole genome using Hisat2
Reads counting was performed using featureCounts software.
Differential expressed genes were analyzed using DESeq2 software.
Genome_build: Gmax_508_Wm82.a4.v1.gene.gtf
Supplementary_files_format_and_content: counts.txt

organism: Glycine max

source_name: soybean

extract_protocol:
TRIzol reagent method (Invitrogen)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Wild type (JACK)

value: seed


title: 3-12 rep1

value: Transgenic soybean (GmZF392)


title: 34 rep3

value: Transgenic soybean (GmZF351)


title: 34 rep1


title: N6 rep3

value: Transgenic soybean (GmNFYA)


title: 3-12 rep2


title: N6 rep1


title: J rep3


title: N6 rep2


title: 34 rep2


title: ENS IR LPS, bio rep3

type: RNA

city: Kiel

first: Francois

last: Cossais

address: Otto-Hahn-Platz 8

department: Institute of Anatomy

country: Germany

institute: Kiel University

hyb_protocol: cRNA were hybridized on mouse Clariom S Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 (fluidics protocol FS450_007).

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

data_processing: The data were analyzed with Transcriptomic Analysis Console Version 4.0.1.36 (TAC 4.0) using Affymetrix default analysis settings and global scaling as normalization method.

label: biotin

source_name: ENS primary culture, LPS treated

label_protocol: cRNA was performed using the GeneChip WT Plus Reagent Kit on 100ng total RNA  (Thermo-fisher Scientific)

growth_protocol: Primary cultures of ENS were derived from gut isolated from e14.5 mouse embryos. Cells were grown in DMEM+10% FCS for 24h, then medium was changed for DMEM-HAMF12 (1/1) supplemented with N2

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Cells were treated with 6-mercaptopurine (50µM) for 16 hours before treatment with LPS (10ng/ml) for 6 hours or left untreated (controls)

value: ENS primary cultures

tag: treatment

value: LPS treated


title: 3-12 rep3


title: ENS IR 6MP+LPS, bio rep3

source_name: ENS primary culture, 6MP and LPS treated

value: 6MP and LPS treated


title: J rep1


title: ENS IR 6MP, bio rep3

source_name: ENS primary culture, 6MP treated

value: 6MP treated


title: ENS IR control, bio rep3

source_name: ENS primary culture, control

value: control condition


title: ENS IR control, bio rep1


title: ENS IR 6MP, bio rep2


title: ENS IR LPS, bio rep2


title: ENS IR 6MP+LPS, bio rep1


title: ENS IR control, bio rep2


title: ENS IR 6MP, bio rep1


title: Patient 11 Adipose Tissue SoluCortef

city: Manchester

first: Adam

last: Stevens

address: Oxford Road

department: Medicine

institute: University of Manchester

hyb_protocol: GeneChip® ST Arrays (GeneChip® Human Gene 2.0 ST Array) were hybridized for 16 hours in a 45°C incubator, rotated at 60 rpm. According to the GeneChip® Expression Wash, Stain and Scan Manual (P/N 702731 Rev. 3, Affymetrix Inc.), the arrays were then washed and stained using the GeneChip™ Fluidics Station 450

scan_protocol: Scanned using the GeneChip® Scanner 3000 7G

data_processing:
Gene level summary of the exon array was performed after RMA data processing using quality control of transcriptomic data within Qlucore Omics Explorer 3.3 Principal component analysis (PCA) with cross validation and data consistency was used to  confirm data consistency. Differential gene expression was determined by a paired t-test comparing the two interventions. Principal component analysis (PCA) was performed to provide further quality control and to define the relationship of variance between samples, allowing structure within the data set to be defined (Qlucore Omics Explorer 3.3, Lund, Sweden).
HuGene-2_0-st.pgf
HuGene-2_0-st-v1.na36.hg19.transcript.csv

source_name: Adipose Tissue

label_protocol: Microarray gene expression analysis in both PBMC and adipose tissue was performed at the Array and Analysis Facility, Science for Life Laboratory at Uppsala Biomedical Center (BMC), Sweden. RNA quality was evaluated using the Agilent 2100 Bioanalyzer system (Agilent Technologies Inc., Palo Alto, CA). Total RNA 150 ng from each PBMC sample and 10 ng from each adipose tissue sample were used to generate amplified and biotinylated sense-strand cDNA from the entire expressed genome according to the GeneChip® WT PLUS Reagent Kit User Manual (P/N 703174 Rev. 1, Affymetrix Inc., Santa Clara, CA).

extract_protocol: Adipose tissue was collected after local injection with lidocaine under the umbilicus on the right side of the abdomen during saline infusion and on the left side during HC infusion. Samples were lysed using QIAzol Lysis Buffer (Qiagen, Hilden, Germany). The lysate was subsequently frozen and stored at –70°C. Samples were eluted in RNAse-free water. RNA concentration was measured spectrophotometrically and the A260/A280 ratio was 1.97 to 2.05.

treatment_protocol: The study was a single-center, single-blind, randomized, two-period/crossover clinical trial.Men and women with Addison’s disease for > 12 months on stable cortisol replacement (with HC 15 to 30 mg/day) for ≥ 3 months were eligible for inclusion. Other inclusion criteria were age 20 to 60 years, body mass index 20 to 30 kg/m2, and ability to comply with the protocol procedures. Exclusion criteria were GC replacement therapy for indication other than Addison’s disease, any treatment with sex hormones including contraceptive drugs, treatment with levothyroxine, renal or hepatic failure, significant and symptomatic cardiovascular disease, diabetes mellitus, current infectious disease with fever, and pregnancy or breastfeeding. HC infusion was prepared by adding 0.4 mL of Solu-Cortef® 50 mg/mL to 999.6 mL 0.9% saline, which resulted in 1 mg HC per 50 mL intravenous infusion. HC infusion was adjusted in accordance with previous observations in healthy males  and interventions in both sexes. The aim was to achieve a near-physiological circadian cortisol curve with early morning rise in serum cortisol that would peak at 7 AM and trough concentrations at midnight. In the GC-withdrawal intervention, 0.9% saline infusion alone was administered using the same volume as during the HC infusion. Thus, a person weighing 75 kg received 2 L of intravenous infusion over 26 hours during each intervention.

tag: gender

value: M

value: SoluCortef


title: ENS IR 6MP+LPS, bio rep2


title: Patient 11 Adipose Tissue placebo

value: placebo


title: ENS IR LPS, bio rep1


title: Patient 10 Adipose Tissue SoluCortef

value: F


title: Patient 9 Adipose Tissue SoluCortef


title: Patient 8 Adipose Tissue SoluCortef


title: Patient 6 Adipose Tissue placebo


title: Patient 10 Adipose Tissue placebo


title: Patient 4 Adipose Tissue SoluCortef


title: Patient 3 Adipose Tissue SoluCortef


title: Patient 10 Peripheral blood mononuclear cells placebo

source_name: Peripheral blood mononuclear cells

extract_protocol: PBMCs were isolated on-site from whole blood using a gradient-based separation procedure and Ficoll-Paque PREMIUM (GE Healthcare). Purified PBMCs were lysed using QIAzol Lysis Buffer (Qiagen, Hilden, Germany) on a QIAshredder column (Qiagen). The lysate was subsequently frozen and stored at –70°C. Samples were eluted in RNAse-free water. RNA concentration was measured spectrophotometrically and the A260/A280 ratio was 1.97 to 2.05.


title: Patient 7 Adipose Tissue SoluCortef


title: Patient 8 Adipose Tissue placebo


title: Patient 6 Adipose Tissue SoluCortef


title: Patient 9 Adipose Tissue placebo


title: Patient 1 Adipose Tissue SoluCortef


title: Patient 3 Adipose Tissue placebo


title: Patient 11 Peripheral blood mononuclear cells placebo


title: Patient 6 Peripheral blood mononuclear cells placebo


title: CNTRL_2_villi, scRNA-seq

description:
counts.tsv.gz
metadata.tsv.gz

value: negative

value: placental villi


title: Patient 10 Peripheral blood mononuclear cells SoluCortef


title: Patient 9 Peripheral blood mononuclear cells placebo


title: Patient 7 Adipose Tissue placebo


title: Patient 2 Adipose Tissue placebo


title: Patient 9 Peripheral blood mononuclear cells SoluCortef


title: Patient 7 Peripheral blood mononuclear cells placebo


title: Patient 1 Adipose Tissue placebo


title: Patient 11 Peripheral blood mononuclear cells SoluCortef


title: Patient 7 Peripheral blood mononuclear cells SoluCortef


title: Patient 4 Adipose Tissue placebo


title: Patient 8 Peripheral blood mononuclear cells SoluCortef


title: Patient 2 Adipose Tissue SoluCortef


title: Patient 4 Peripheral blood mononuclear cells placebo


title: Patient 8 Peripheral blood mononuclear cells placebo


title: Patient 3 Peripheral blood mononuclear cells SoluCortef


title: Patient 6 Peripheral blood mononuclear cells SoluCortef


title: Patient 3 Peripheral blood mononuclear cells placebo


title: Patient 4 Peripheral blood mononuclear cells SoluCortef


title: ESC_Ctrl_Input

city: Copenhagen N

first: Chunarum

last: Choudhary

state: --- Select a state ---

address: Blegdamsvej 3B

department: Novo Nordisk Foundation Center for Protein Research

country: Denmark

institute: University of Copenhagen

description: ESC Control

data_processing:
Read alignment was performed using BWA with default parameters. Low mapping quality read (MAPQ 10) and duplicated reads were removed using samtools. The DAC Blacklisted Regions were also omitted from the bam file using bedtools. Peaks were called using epic with the following parameters: --fragment-size 200 --gaps-allowed 5.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: bigWig

source_name: mouse ES cells

growth_protocol: E14Tg2A Rosa26-Cre Oct4-IRES-Puro mouse ESCs were used for all experiments 11932748. ESCs were cultured in a custom-made N2B27 medium consisting of 1:1 mix of DMEM/F12 and Neurobasal medium, without L-arginine and L-lysine (C.C.Pro GmbH, Oberdorla). The media was supplemented with L-arginine, L-lysine, 1000 units/ml leukemia inhibitory factor (LIF) (Merck Millipore), 1µM PD0325901, 3µM CT-99021 (custom-made by ABCR), 100µM 2-mercaptoethanol, 150µM sodium pyruvate, 0.5x B27 supplement (Thermo Fisher Scientific), as well as with 0.5x N2 supplement (made in house; or from Thermo Fisher Scientific).

extract_protocol:
Cells were cross-linked for 10 min at room temperature with 1% formaldehyde solution with gentle agitation and quenched with 0.125 M glycine. Cross-linked cells were washed once with PBS, added swelling buffer (10 mM Tris-HCl pH8.0, 1.5 mM MgCl2, 10 mM NaCl, 0.5% NP-40) and incubated on ice for 10 minutes. After centrifugation, pellets were suspended with RIPA buffer (10 mM Tris-HCl pH8.0, 1 mM EDTA, 140 mM NaCl, 1% Triton X-100, 0.1% SDS, 0.1% Sodium Deoxycholate) containing proteinase inhibitor cocktail (Roche), and then were sonicated by using a BioRuptor sonicator (Diagenode). After centrifugation, solubilized chromatin was recovered and incubated with 5 µg of antibody bound to protein A/G magnetic beads (Pierce). After overnight incubation at 4ºC, the magnetic beads were washed with RIPA buffer twice, RIPA high salt buffer (10 mM Tris-HCl pH8.0, 1 mM EDTA, 500 mM NaCl, 1% Triton X-100, 0.1% SDS, 0.1% Sodium Deoxycholate), LiCl buffer (10 mM Tris-HCl pH8.0, 1 mM EDTA, 250 mM LiCl, 0.5% NP-40, 0.5% Sodium Deoxycholate) and TE buffer. The bound materials were eluted with elution buffer (10 mM Tris-HCl pH8.0, 5 mM EDTA, 300 mM NaCl, 0.1% SDS) overnight at 65ºC and treated with RNaseA for 30 min for 37°C and further incubation with Proteinase K for 1 hour at 37ºC. Then DNA was purified with a PCR purification kit (Qiagen).
ChIP-seq libraries were prepared by using the NEBNext Ultra II DNA prep kit (NEB E7645) following the manufacturer's instruction and sequenced on a Next-Seq 500 Sequencer (Illumina).

treatment_protocol: A-485 (10uM) or JQ1 (0.5mM) were treated for 60 min if not indicated. For control samples, 0.1% DMSO was added.

value: ES cells

value: DMSO for 60 min


title: fAb-4

city: Boston

first: Yae-Huei

last: Liou

address: 665 Huntington Ave.

department: MET

institute: Harvard School of Public health

description:
Nnah_Liou_GEO_Processed-1.txt
12-FA4

data_processing:
Trimming of Illumina adapters (CLC Genomics Workbench v.10 )
Quality control for individual samples (CLC Genomics Workbench v.10 )
Mapping against the reference genome (CLC Genomics Workbench v.10 )
Calculation of expression values using unique matches (CLC Genomics Workbench v.10)
Normalisation by scaling 10.000.000 reads per sample per transcript (TPM),
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: IMG

growth_protocol: All IMG cell are the same passage

extract_protocol:
RNA was harvested by spin column.
RNA libraries were prepared for sequencing using Illumina’s TruSeq Stranded mRNA Library Preparation Kit based on the Kit’s manual. 2 ug total RNA was used as input.

treatment_protocol: scramble, oAb or fAb treat for 8 hours

tag: strain

value: wild type

value: fAb

value: IMG


title: CTL-3

description:
Nnah_Liou_GEO_Processed-1.txt
Nnah_Liou_GEO_Processed-2.txt
3-C3

value: Scramble


title: fAb-3

description:
Nnah_Liou_GEO_Processed-1.txt
11-FA3


title: CTL-4

description:
Nnah_Liou_GEO_Processed-1.txt
Nnah_Liou_GEO_Processed-2.txt
4-C4


title: oAb-1

description:
Nnah_Liou_GEO_Processed-2.txt
5-OA1

value: oAb


title: oAb-4

description:
Nnah_Liou_GEO_Processed-2.txt
8-OA4


title: CTL-2

description:
Nnah_Liou_GEO_Processed-1.txt
Nnah_Liou_GEO_Processed-2.txt
2-C2


title: Patient 1 Peripheral blood mononuclear cells placebo


title: CTL-1

description:
Nnah_Liou_GEO_Processed-1.txt
Nnah_Liou_GEO_Processed-2.txt
1-C1


title: oAb-2

description:
Nnah_Liou_GEO_Processed-2.txt
6-OA2


title: fAb-1

description:
Nnah_Liou_GEO_Processed-1.txt
9-FA1


title: fAb-2

description:
Nnah_Liou_GEO_Processed-1.txt
10-FA2


title: E14.5 Osr2-KICre;Runx2fl/fl2

city: LA

first: Xia

last: Han

state: CA

address: 2250 Alcazar Street

institute: University of Southern California

description:
mRNA
Partek_xiah_Osr2Runx2_E14_5_Nextseq_Jul2018_Filter_groups_Filtered_counts
gene_list_Osr2-Kicre;Runx2_E14.5
OR_7-12-18_E14_5

data_processing:
Illumina Casava1.8 software used for basecalling.Sequenced reads were trimmed for bases with Phred score<20 from both ends, mapped to mm10 whole genome and transcriptome using STAR 2.6.1d, quantified with Gencode M20 annotation, and normalized using counts per million. Differential expression was carried out using Gene-specific analysis by Partek flow with default settings (Partek Inc., USA).
assembly: mm10

extract_protocol:
The soft palate of E14.5 mice was collected for RNA isolation with an RNeasy Micro Kit (QIAGEN).
The quality of RNA samples was evaluated using an Agilent 2100 Bioanalyzer and all samples used for sequencing had RNA integrity (RIN) numbers >9.0. cDNA library preparation and sequencing were performed by UCLA translational genomics core. Paired-end reads with 75 cycles were performed on NextSeq500 for three pairs of samples.
mRNA-Seq

value: soft palate


title: E14.5 Osr2-KICre;Runx2fl/fl3

description:
mRNA
Partek_xiah_Osr2Runx2_E14_5_Nextseq_Jul2018_Filter_groups_Filtered_counts
gene_list_Osr2-Kicre;Runx2_E14.5
OR_7-9-18_E14_5


title: Ad2_4_S1

description:
genomic DNA
Ad2_4

data_processing:
ATAC-seq reads were aligned to the UCSC mm10 reference genome using BWA-MEM (Li, 2013). ATAC-seq peaks were called by MACS2 (Zhang et al., 2008). Peaks were annotated and known transcription factor binding motifs were analyzed in the ATAC-seq peaks by HOMER (Heinz et al., 2010)).
assembly: mm10

source_name: E13.5-E14.0 soft palate

extract_protocol:
Single cells suspension were prepared from E13.5-E14.0 using trypLE digestion at 37 degree.
ATAC-seq libraries were prepared according to a published protocol (Buenrostro et al., 2015). Sequencing was performed on the NextSeq 500 platform (Illumina, San Diego, CA).
ATAC-Seq

value: soft palate mesenchyme


title: Patient 1 Peripheral blood mononuclear cells SoluCortef


title: E14control3


title: E14control2


title: E14control1


title: E14.5 Osr2-KICre;Runx2fl/fl1


title: oAb-3

description:
Nnah_Liou_GEO_Processed-2.txt
7-OA3


title: HSCs, Young rep2

city: Groningen

first: Leonid

last: Bystrykh

state: Groningen

address: A. Deusinglaan 1

department: European Research Institute for the Biology of Ageing - ERIBA

country: Netherlands

institute: University Medical Center Groningen

description:
Young_ATAC_S2
Tn5 tagmented native DNA

data_processing:
After demultiplexing, run quality was evaluated using FastQC 0.11.9
FASTQ files were merged for each sample
FASTQ files were aligned to the reference genome using BWA mem aligner (0.7.17) with standard arguments
Peak calling was performed with MACS2 (2.1.2). For narrow peaks, --format BAMPE, --nomodel --keep-dup all --call-summits -g 1.87e9 -p 0.01
Peak calling was performed with MACS2 (2.1.2). For broad peaks, --format BAMPE, --nomodel --keep-dup all --broad -g 1.87e9 -p 0.01
Differently open chromatin accessible sites were determined with DiffBind (2.14.0)
Genome_build: GRCm38 M13
Supplementary_files_format_and_content: narrow and broad peak calling files and DBS for young and aged samples

source_name: Hematopoietic Stem Cells

extract_protocol:
25000 LT-HSCs were sorted from young and aged mice in biological replicates.  Cells were immediately lysed and tagmented for 1h at 37C.
Samples were PCR amplified between 11 and 12 cycles. Following, samples were size selected between 150-1000bp. All samples were pooled equimolarly.

value: WT

value: Hematopoietic Stem Cells


title: HSCs, Aged rep2

description:
Aged_ATAC_S2
Tn5 tagmented native DNA


title: RNA_Memory_2

city: Chicago

first: Weiguo

last: Cui

state: IL

address: 303 E Chicago Ave

department: Pathology

institute: Northwestern University

data_processing:
Reads were aligned to the mouse reference genome (mm10) using Tophat (version 2.1.1)
Expression values for each gene were quantified and differential gene expression analysis was carried out using Cuffdiff (Cufflinks version 2.2.2)
Genome_build: mm10
Supplementary_files_format_and_content: genes.read_group_tracking contains the FPKM values for each gene in each replicate

source_name: P14 CD8 T cells

growth_protocol: Naïve CD8 T cells (CD8+ CD62L+ CD44-) were sorted from uninfected female P14 mice. MPECs (CD8+ CD44+ Thy1.1+ IL-7Rhi KLRG1lo) and SLECs (CD8+ CD44+ Thy1.1+ IL-7Rlo KLRG1hi) were sorted from female P14 chimeric mice on day 9 p.i. Memory CD8 T cells (CD8+ CD44+ Thy1.1+ IL-7Rhi KLRG1lo) were sorted from female P14 chimeric mice on day 40+ p.i.

extract_protocol:
Total RNA was purified from sorted cells using RNeasy Plus Mini Kit (QIAGEN).
mRNA isolation and library preparation were completed using NEBNext Poly(A) mRNA Magnetic Isolation Module and NEBNext Ultra RNA Library Prep Kit for Illumina (NEB).

tag: strain background

value: P14 CD8 T cells

tag: cell subset

value: CD8+ CD44+ Thy1.1+ IL-7Rhi KLRG1lo


title: RNA_SLEC_2

value: CD8+ CD44+ Thy1.1+ IL-7Rlo KLRG1hi


title: RNA_Memory_1


title: RNA_SLEC_3


title: HSCs, Young rep1

description:
Young_ATAC_S1
Tn5 tagmented native DNA

tag: age


title: RNA_SLEC_1


title: H3K27Ac_Memory_2

data_processing:
Reads were aligned to mouse reference genome mm10 using Bowtie2 (version 2.3.4.3).
Reads were then filtered using SAMtools (-F1796) (version 1.8).
Duplicates were marked with Picard (version 2.6) and removed.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files were generated using the bamCoverage function of deepTools.

extract_protocol:
DNA was purified using QIAquick PCR Purification Kit (QIAGEN).
Library preparation was completed using the NEBNext Ultra DNA Library Prep Kit for Illumina (NEB).

treatment_protocol: 200,000-400,000 sorted cells were crosslinked in 1% formaldehyde for 10 min, the reaction was quenched with 0.125 M glycine for 5 min, and cell pellets were then stored at -80 °C. Cells were resuspended in ChIP lysis buffer (1% SDS, 10 mM EDTA, 50 mM Tris-HCl, 1x protease inhibitor cocktail) and then sonicated for 20 cycles at 4 °C in a Bioruptor sonicator (Diagenode). Sheared chromatin was then centrifuged to remove debris. The supernatant was then diluted 1:10 in ChIP dilution buffer (0.01% SDS, 1.1% Triton X-100, 1.2 mM EDTA, 16.7 mM Tris-HCl, 167 mM NaCl). 10% of each sample was saved as input control. 2.5 ug anti-histone H3K27Ac antibody (Abcam, ab4729) was added to sheared chromatin and incubated at 4 °C overnight. 1.35 mg Dynabeads Protein G beads were added and incubated at 4 °C for 2 h. The beads were then washed with low salt wash buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl, 150 mM NaCl), high salt wash buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl, 500 mM NaCl), LiCl wash buffer (0.25 M LiCl, 1% NP-40, 1% deoxycholic acid, 1 mM EDTA, 10 mM Tris-HCl), and 1x TE (1 mM EDTA, 10 mM Tris-HCl). DNA was eluted by adding 150 ul elution buffer (1% SDS, 0.1 M NaHCO3) and incubating at room temperature for 15 min twice, and then combining the eluants. Crosslinking was reversed by incubating with 0.2 M NaCl at 65 °C overnight.

tag: antibody


title: RNA_Naive_1


title: RNA_Naive_2


title: RNA_MPEC_2


title: RNA_MPEC_1


title: H3K27Ac_SLEC_2


title: ATAC_Memory_1

data_processing:
Reads were aligned to mouse reference genome mm9 using Bowtie2 (version 2.3.4.3).
Reads were then filtered using SAMtools (-F1804) (version 1.8).
Duplicates were marked with Picard (version 2.6) and removed.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files were generated using the bamCoverage function of deepTools.

extract_protocol: Libraries were prepared using 50,000 cells as described in published protocol (Buenrostro et al., 2015).


title: RNA_Naive_3


title: H3K27Ac_SLEC_1


title: H3K27Ac_MPEC_2


title: H3K27Ac_Input


title: ATAC_SLEC_1


title: H3K27Ac_Naive_1


title: H3K27Ac_MPEC_1


title: ATAC_MPEC_2


title: H3K27Ac_Memory_1


title: H3K27Ac_Naive_2


title: ATAC_Memory_2


title: ATAC_MPEC_1


title: ATAC_Naive_2


title: ATAC_Naive_1


title: RNA_ID2_2

data_processing:
Reads were aligned to the mouse reference genome (mm9) using Tophat (version 2.1.1)
Expression values for each gene were quantified and differential gene expression analysis was carried out using Cuffdiff (Cufflinks version 2.2.2)
Genome_build: mm10
Supplementary_files_format_and_content: genes.read_group_tracking_MIG_E47_ID2 contains the FPKM values for each gene in each replicate

growth_protocol: P14 cells were activated for one day with 100 ng/ml gp33 and 1 ng/ml IL-2. Cells were then spin transduced with 1 ml of either MSCV-IRES-GFP (MIG), MIG-E47, or MIG-ID2 retrovirus, 8 ug/ml polybrene, 10 ng/ml IL-2, and 10 mM HEPES Buffer (Corning) for 90 minutes at 32 ºC at 2,500 rpm. Retrovirus-containing media was then removed and replaced with the original media, followed by an additional one day of activation. P14 cells were then washed with PBS and cultured in 10 ng/ml IL-2 for two days for expansion. CD8+ GFP+ cells were then sorted and prepared for RNA-seq.

extract_protocol:
Total RNA from P14 CD8 T cells transduced with MIG, MIG-E47, or MIG-ID2 was purified from sorted cells using RNeasy Plus Mini Kit (QIAGEN).
mRNA isolation and library preparation were completed using NEBNext Poly(A) mRNA Magnetic Isolation Module and NEBNext Ultra RNA Library Prep Kit for Illumina (NEB).

value: CD8+ GFP +

tag: transduction


title: HSCs, Aged rep1

description:
Aged_ATAC_S1
Tn5 tagmented native DNA


title: RNA_E47_1


title: RNA_E47_2


title: RNA_MIG_2

value: MIG


title: ATAC_SLEC_2


title: ATAC_ID2_2

data_processing:
Reads were aligned to mouse reference genome mm10 using Bowtie2 (version 2.3.4.3).
Reads were then filtered using SAMtools (-F1804) (version 1.8).
Duplicates were marked with Picard (version 2.6) and removed.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files were generated using the bamCoverage function of deepTools.

growth_protocol: P14 cells were activated for one day with 100 ng/ml gp33 and 1 ng/ml IL-2. Cells were then spin transduced with 1 ml of either MSCV-IRES-GFP (MIG), MIG-E47, or MIG-ID2 retrovirus, 8 ug/ml polybrene, 10 ng/ml IL-2, and 10 mM HEPES Buffer (Corning) for 90 minutes at 32 ºC at 2,500 rpm. Retrovirus-containing media was then removed and replaced with the original media, followed by an additional one day of activation. P14 cells were then washed with PBS and cultured in 10 ng/ml IL-2 for two days for expansion. CD8+ GFP+ cells were then sorted and prepared for ATAC-seq.


title: ATAC_MIG_1


title: ATAC_E47_2


title: ATAC_ID2_1


title: ATAC_E47_1


title: ATAC_MIG_2


title: Day_0

data_processing:
Demultiplexing was performed using the mkfastq function in Cell Ranger (version 1.3.1) (10x Genomics)
Alignment and generation of gene-barcode matrix was performed using the count function in Cell Ranger (version 1.3.1) (10x Genomics)
Genome_build: mm10
Supplementary_files_format_and_content: barcodes.tsv, genes.tsv, and matrix.mtx: filtered gene-barcode matrix in MEX format

extract_protocol:
Naïve CD8 T cells (CD8+ CD62L+ CD44-) were sorted from uninfected female P14 mice. Total effector cells and memory cells (CD8+ CD44+ Thy1.1+) were sorted from female P14 chimeric mice on day 9 and day 129 p.i., respectively.
Single cell libraries were prepared according the the 10x Genomics Chromium Single Cell 3' Reagent Kit protocol.

tag: time point

value: day 0 p.i.


title: Day_9

value: day 9 p.i.


title: Neuroblastoma Tau-S199E rep1

city: Beer Sheva

first: Debra

last: Toiber

state: Israel

address: Ben Gurion Road #1, Building 40, room 205

country: Israel

institute: Ben Gurion University of the Negev

data_processing:
Mapping and gene-level read count estimation were performed using STAR (v2.5.3a) and RSEM (v1.2.31), respectively, against the human reference genome (GRCh38).
DeSeq2 R package was used to normalize gene counts and perform differential gene expression
Clustering and visualizations were done using the DeSeq2 RLOG function (Variance Stabilizing Transformation).
number of clusters were assessed using the “eclust” function from the “factoextra” R package.
The “clusterprofiler” R package was used for Gene Ontology enrichment analysis, while gene annotation was retrieved from the ensemble biomart using the biomart R package.
Genome_build: genome (GRCh38).

source_name: Neuroblastoma

extract_protocol:
24 hours after transfections RNA was extracted using NucleoSpin® RNA Plus kit
Libraries were prepared using QuantSeq 3′ mRNA-Seq Library Prep Kit FWD for Illumina (015.96, Lexogen GmbH, Vienna, Austria), 400 ng of RNA were used per library.

treatment_protocol: Neuroblastoma (SHSY5Y) cells were transfected using Tau-WT and Tau mutants

value: cell line derived from metastatic bone tumor

tag: transfected construct


title: Neuroblastoma Tau-K174Q rep1


title: Neuroblastoma Tau-K174Q:S199E rep2


title: Neuroblastoma Tau-K174Q rep3


title: Neuroblastoma Tau-K174Q:S199E rep1


title: Neuroblastoma Tau-K174Q rep2


title: Neuroblastoma Tau-S199E rep2


title: Neuroblastoma Tau-S199E rep3


title: Day_129

value: day 129 p.i.


title: Neuroblastoma Tau-WT rep2

value: Tau-WT


title: Neuroblastoma Tau-K174Q:S199E rep3


title: Neuroblastoma Tau-WT rep1


title: Neuroblastoma Tau-WT rep3