title: Nr5a2_2C_rep2

description: Library name: CUT and Tag Sample 2

value: 2-cell embryo


title: GLC7-3xHA-FRB , KY5319 , Rapa , Rtf1 , Rep2

status: Public on Dec 15 2025

type: SRA

city: Pittsburgh

first: Karen

middle: M.

last: Arndt

state: Pennsylvania

address: 4249 Fifth Avenue

department: Biological Sciences

country: USA

institute: University of Pittsburgh

description:
Library name: GLC7_3xHA_FRB_KY5319_Rapa_Rtf1_Rep2
MATalpha his3∆1 leu2∆0 ura3∆0 tor1-1 fpr1∆ RPL13A-2XFKBP12::TRP1 GLC7-3xHA-FRB

library_source: genomic

data_processing:
Reads were aligned to the hydrid genome of S. cerevisiae and the corresponding spike-in (either S. pombe or K. lactis) with bowtie2 version 2.4.5.
Mapped reads were filtered with Sambamba view and Samtools markdup to remove multi-mapped reads and PCR duplicates, respectively.
The filtered hybrid alignment was split into separate S. cerevisiae and spike-in files. Normalization factors were calculated using S. cerevisiae and spike-in read counts in the input and IP.
Spike-in normalization was applied and bigWig files were generated using bamCoverage.
Assembly: S. cerevisiae SacCer3
Assembly: K. lactis ASM251v1
Assembly: S. pombe ASM294v2
Supplementary files format and content: bigWig, spike-in normalized ChIP-seq signal

molecule: genomic DNA

organism: Saccharomyces cerevisiae

growth_protocol: All yeast cultures, including spike-in cells, were grown to mid-log phase in 250 mL YPD+Trp media at 30ºC.

extract_protocol:
Cells were fixed with 1% formaldehyde for 20 minutes. After quenching and cell lysis, chromatin was sheared using a Bioruptor® (Diagenode B01060010) for 25 cycles with 30 seconds on and 30 seconds off.
ChIP-seq libraries were prepared with the NEB Next II Ultra DNA library kit (NEB, E7645S/L) and multiplex oligos (NEB, E6440S/L) using 0.5-1 ng of DNA input and following manufacturer's protocols. Libraries were purified using AMPure XP beads (Beckman Coulter, A63881) and verified using fragment analyzer (Fragment Analyzer, Advanced Analytics).

treatment_protocol:
For auxin inducible degron, the mid-log culture was treated with 5 µM 5-phenyl-indole-3-acetic acid (5-Ph-IAA) or equivalent amount of vehicle (DMSO) for 45 minutes.
For anchor-away experiments, the mid-log culture was treated with 1 µg/mL rapamycin or equivalent amount of vehicle (DMSO) for 1 hour.

tag: cell line

tag: strain

tag: treatment

value: Rapamycin

tag: time

value: 1 hour

tag: chip antibody

tag: batch


title: RBC-step2-3A-r2

city: Vienna

first: Florian

last: Halbritter

address: Zimmermannplatz 10

country: Austria

institute: St. Anna Children's Cancer Research Institute (CCRI)

description: Library name: RBC-step-2--3A-r2

data_processing:
nfcore/atac-seq
Assembly: GRCh38
Supplementary files format and content: bigWig

organism: Homo sapiens

source_name: differentiating HSPCs

growth_protocol: G-CSF-mobilized human peripheral blood CD34+ cells (Stem Cell Technologies) were differentiated into immature erythroid cells utilizing a three-phase culture protocol. Briefly, cells were thawed and cultured overnight at a density of 104 cells/ml in X-VIVO 10 serum-free haematopoietic cell medium (Lonza) supplemented with 100 ng/mL recombinant human SCF (Biotechne), 100 ng/mL recombinant human TPO and 50 ng/mL recombinant human FLT3 Ligand (PeproTech). The next day, cells were washed and resuspended at a density of 1-2,5 x 104 cells/ml into erythroid differentiation medium 1 (EDM1) consisting of IMDM supplemented with 100 ng/ml hSCF, 330 μg/ml human holo-Transferrin, 10 μg/ml recombinant human insulin, 2 IU/ml heparin, 5% heat-inactivated human serum (Sigma), 3 IU human recombinant EPO (Stem Cell Technologies), 1 μM hydrocortisone (Sigma), recombinant human IL-3 (PeproTech) 1% penicillin/streptomycin. From day 7 to day 11, cells were cultured at a concentration of 105 cells/mL in EDM2 (EDM1 without hIL-3 hydrocortisone). From day 11 to day 14, cells were cultured in EDM3 (EDM2 without hSCF) at a concentration of 0.75-1.5 × 106 cells/ml. Cells were cultured at 37°C and 5% CO2.

extract_protocol:
20,000 to 50,000 cells were washed in cold PBS and resuspended in 50ul Lysis buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% Igepal) and immediately spun at 500 xg for 10 min at 4 C. The supernatant was then discarded and the nuclei resuspended in the transposase reaction mix (25 ul 2x TD Buffer, 2.5 ul Transposase (Illumina), 22,5 ul nuclease-free water) and incubated for 30 min at 37C. Immediately after, DNA is purified using a MinElute Kit (Qiagen).
Tagmented DNA was PCR amplified to amend sequencing barcodes and qPCR was used to estimate the number of PCR cycles for exponential amplification. Libraries were pooled and sequenced at 150bp paired-end at Azenta.

tag: cell type

value: differentiating HSPCs

tag: genotype

value: full

tag: flowcell


title: Nr5a2_Morula_rep2

city: Martinsried

first: Siwat

last: Ruangroengkulrith

state: Bavaria

address: Am Klopferspitz 18

department: Totipotency

country: Germany

institute: Max Planck Institute of Biochemistry

description: Library name: CUT and Tag Sample 8

data_processing:
Low quality reads were trimmed out using TrimGalore (version 0.6.2) (https://github.com/FelixKrueger/TrimGalore) using parameters: --paired --quality 20 --length 20.
Read mapping to mm10 genome was done using Bowtie2 (version 2.3.5.1) using parameters: -t -q -N 1 -L 25 -X 2000 --no-mixed --no-discordant.
Unmapped reads and reads with low mapping quality (Q<30) were removed. PCR duplicated reads were identified and discarded using the MarkDuplicates command from Picard (version 2.18.27) (http://broadinstitute.github.io/picard/) with parameters: VALIDATION_STRINGENCY=LENIENT.
The bigwig files were generated using bamCoverage command from deepTools (version 3.5.4) using parameters: --normalizeUsing RPKM --binSize 1 --ignoreForNormalization chrM. Peak calling for CUT&Tag, ATAC-seq, and ChIP-seq datasets were done using MACS2’s callpeak function (version 2.2.9) with default parameters.
Assembly: mm10
Supplementary files format and content: bigWig
Library strategy: CUT&Tag

organism: Mus musculus

source_name: preimplantation embryo

growth_protocol: Frozen zygotes from B6CBAF1 mouse strain (Janvier-lab) were used for CUT&Tag experiments of NR5A2, KLF5 GATA6, and H3K27ac. Zygotes were thawed according to a manual of kits of frozen zygotes and cultured in potassium-supplemented simplex-optimized medium (KSOM) with Lumox dish (Sarstedt). Two-cell, four-cell, eight-cell, morula were collected after thawing at 22-24 hours (34-36 hpf), 29-31 hours (41-43 hpf), 44-46 hours (56-58 hpf), and 61-61 hours (71-72 hpf), respectively. Zygotes from natural mating were used for siRNA knockdown experiment. Females mice (3-5 weeks old B6129F1 strain) were injected with PMSG (5IU) followed by hCG injection 46-48 hours later for superovulation, before mating with B6CBAF1 male mice. Zygotes were after 19 hours post hCG injection. Embryos were then cultured in KSOM with Lumox dish (Sarstedt).

extract_protocol:
CUT&Tag was performed as described previously with few modifications (Kaya-Okur, H.S., Wu, S.J., Codomo, C.A. et al. CUT&Tag for efficient epigenomic profiling of small samples and single cells. Nat Commun 10, 1930 (2019)). Embryos with intact zona pellucida were incubated with ice-cold extraction buffer (25 mM HEPES-NaOH (pH 7.4), 50 mM NaCl, 3 mM MgCl2, 300 mM sucrose and 0.5% Triton X-100) on ice for 6-7 min and were washed three times through with ice-cold extraction buffer without TritonX-100. Pre-extracted embryos were immediately lightly fixed by Dulbecco’s phosphate- buffered saline (DPBS) with 0.1% formaldehyde for 2 min at room temperature. Embryos were incubated in antibody buffer (20 mM HEPES-NaOH (pH7.5), 150 mM NaCl, 0.5 mM Spermidine, 0.1% BSA, 2 mM EDTA and 1x Protease inhibitor cocktail (Roche) with primary antibody (1:100 dilution) overnight at 4°C on nutator. Embryos were washed three times through antibody buffer and further incubated with secondary antibody (1:100 dilution) for 1.5 hours at room temperature. Cells were washed three times through Wash buffer (20 mM HEPES-NaOH (pH7.5), 150 mM NaCl, 0.5 mM Spermidine and 1x Protease inhibitor cocktail (Roche)) and further incubated with homemade pA-Tn5 or pAG-Tn5 adaptor complex (1:250 dilution) for 1.5 hours at room temperature. Embryos were washed three times through Wash-300 buffer (20 mM HEPES-NaOH (pH7.5), 300 mM NaCl, 0.5 mM Spermidine and 1x Protease inhibitor cocktail (Roche)). Embryos were transferred into 1.5 ml of DNA LoBind Tube (Eppendorf) with 200 µl of Tagmentation buffer (10 mM MgCl2 in Wash-300) and incubated at 37°C for 1 hour. The samples were then deproteinized and reverse-crosslinked. The DNA was purified by phenol-chloroform and followed by ethanol precipitation. The DNA was amplified 50 µl of reaction with 1×Q5 High-Fidelity Master mix (NEB) and 0.25 µM barcoded primers using the following PCR program: 72 °C for 5 min; 98°C for 30 sec; 15 cycles of 98°C for 10 sec and 63°C for 10 sec; final extension at 72 °C for 1 min and hold at 4°C. After PCR reaction, libraries were purified by 1.1×AMPure XP magnetic beads (Beckman Coulter) and were eluted in 20 µl of RNase-free water.
Purified DNA libraries were sequenced on a NextSeq 500 (Illumina), Novaseq 6000 (Illumina), or AVITI (Element Biosciences) with paired-end reads.

treatment_protocol: For siRNA knockdown, isolated zygotes (8-9 hpf) were microinjected with siRNAs against targets Nr5a2 (5 µM), Klf5 (10 µM) or control (15 µM). As a control of successful injection 150 ng/µl H2B-EGFP was co-injected. The siRNA targeting control and Nr5a2 were ordered as Silencer select from Life technologies. Predesigned siRNAs were obtained from following vendors: Klf5 (#160900, Silencer pre-designed siRNA, Life technologies); To test Gata6 KD efficiency, 100 M of siRNA targeting Gata6 (#158651, Silencer pre-designed siRNA, Life technologies) was injected into zygotes. The injected embryos were cultured in KSOM using lumox dishes (35 mm, Sarstedt) under 5% O2, 5% CO2, 90% N2.

tag: tissue

value: preimplantation embryo

value: Morula

value: R&D Systems, PP-H2325-00


title: Nr5a2_2C_rep1

description: Library name: CUT and Tag Sample 1


title: RBC-step2-2H-r2

description: Library name: RBC-step-2--2H-r2


title: RBC-step2-2H-r1

description: Library name: RBC-step-2--2H-r1


title: IGG_2C_Biol_Rep2

city: Munich

first: Clara

last: Hermant

address: Feodor-Lynen-Straße 21

department: Institute of Epigenetics and Stem Cells (IES)

institute: Helmholtz Zentrum Munich

description:
Library name: IGG_2C_Biol_Rep2
2x150bp reads

data_processing:
Cut and Tag sequence reads were trimmed for sequence adaptors and low quality ends using Trimmomatic
Paired-end reads were mapped to mm10 using bowtie2
Only high quality, paired, unique mapping alignments were kept for downstream analysis
Optical and PCR duplicates were removed using picard
Assembly: mm10
Supplementary files format and content: Libraries were normalized to rpm values and visualized as biwigs using bedtools genomecov
Library strategy: CUT&Tag

source_name: Late 2-cell embryo

growth_protocol: Between 50-100 (depending on conditions and replicates) late 2-cell stage embryos (between 46-48h post-hCG) were collected directly from the females and directly processed for Cut&Tag

extract_protocol:
Between 50-100 late 2-cell stage embryos were used for Cut&Tag (see methods of the accompanying paper for more information).
Cut&Tag

treatment_protocol: Wild type 2-cell stage embryos were processed directly for Cut&Tag, using either anti-TBP or IGG control antibody

value: Late 2-cell embryo


title: GLC7-3xHA-FRB , KY5318 , Rapa , Rtf1 , Rep1

description:
Library name: GLC7_3xHA_FRB_KY5318_Rapa_Rtf1_Rep1
MATalpha his3∆1 leu2∆0 ura3∆0 tor1-1 fpr1∆ RPL13A-2XFKBP12::TRP1 GLC7-3xHA-FRB


title: RBC-step2-2G-r1

description: Library name: RBC-step-2--2G-r1


title: RBC-step2-2G-r2

description: Library name: RBC-step-2--2G-r2


title: RBC-step2-2F-r2

description: Library name: RBC-step-2--2F-r2


title: Nr5a2_4C_rep2

description: Library name: CUT and Tag Sample 4

value: 4-cell embryo


title: IGG_2C_Biol_Rep1

description:
Library name: IGG_2C_Biol_Rep1
2x150bp reads


title: TBP_2C_Biol_Rep4

description:
Library name: TBP_2C_Biol_Rep4
2x150bp reads


title: Nr5a2_8C_rep1

description: Library name: CUT and Tag Sample 5

value: 8-cell embryo


title: RBC-step2-2F-r1

description: Library name: RBC-step-2--2F-r1


title: GLC7-3xHA-FRB , KY5318 , DMSO , Rtf1 , Rep1

description:
Library name: GLC7_3xHA_FRB_KY5318_DMSO_Rtf1_Rep1
MATalpha his3∆1 leu2∆0 ura3∆0 tor1-1 fpr1∆ RPL13A-2XFKBP12::TRP1 GLC7-3xHA-FRB

value: DMSO


title: WT , KY5366 , Spt5 , Rep2

description:
Library name: WT_KY5366_Spt5_Rep2
MATalpha lys2-128∂ leu2Δ1 ura3-52 3xHA-GLC7


title: TBP_2C_Biol_Rep3

description:
Library name: TBP_2C_Biol_Rep3
2x150bp reads


title: RBC-step2-2E-r1

description: Library name: RBC-step-2--2E-r1


title: RBC-step2-2E-r2

description: Library name: RBC-step-2--2E-r2


title: RBC-step2-2D-r2

description: Library name: RBC-step-2--2D-r2


title: RBC-step2-3B-r1

description: Library name: RBC-step-2--3B-r1


title: RBC-step2-2C-r2

description: Library name: RBC-step-2--2C-r2


title: RBC-step2-2B-r2

description: Library name: RBC-step-2--2B-r2


title: GLC7-3xHA-FRB , KY5319 , DMSO , Rtf1 , Rep2

description:
Library name: GLC7_3xHA_FRB_KY5319_DMSO_Rtf1_Rep2
MATalpha his3∆1 leu2∆0 ura3∆0 tor1-1 fpr1∆ RPL13A-2XFKBP12::TRP1 GLC7-3xHA-FRB


title: TBP_2C_Biol_Rep2

description:
Library name: TBP_2C_Biol_Rep2
2x150bp reads


title: rtf1del , ref2del , swd2del , KY5334 , Spt5 , Rep2

description:
Library name: rtf1del_ref2del_swd2del_KY5334_Spt5_Rep2
MATalpha lys2-128∂ leu2Δ1 ura3-52 rtf1Δ101::LEU2 swd2∆::hphMX ref2∆::KanMX 3xHA-GLC7


title: WT , KY5366 , Spt5 , Rep1

description:
Library name: WT_KY5366_Spt5_Rep1
MATalpha lys2-128∂ leu2Δ1 ura3-52 3xHA-GLC7


title: RBC-step2-2C-r1

description: Library name: RBC-step-2--2C-r1


title: RBC-step2-2B-r1

description: Library name: RBC-step-2--2B-r1


title: TBP_2C_Biol_Rep1

description:
Library name: TBP_2C_Biol_Rep1
2x150bp reads


title: rtf1del , KY5339 , Spt5 , Rep1

description:
Library name: rtf1del_KY5339_Spt5_Rep1
MATa lys2-128∂ leu2Δ1 ura3-52 rtf1Δ101::LEU2 3xHA-GLC7


title: RBC-step2-1H-r2

description: Library name: RBC-step-2--1H-r2


title: FOXJ3_LOF_Batch2_Embryo9

description:
Library name: FOXJ3_LOF_Batch2_Embryo9
2x150bp reads
23L010672_five_2n-read.cntTable.txt

library_source: transcriptomic

data_processing:
A custom Python Script was used to sort between 5' transcript ends and internal fragment according to their adaptor sequence
Reads were mapped to GRCm38 with STAR (V2.7.11a)
BAM files were modified to keep only the Read2 (in case of 5' analysis) using custom Perl script
TE and genes were quantified using TEcount from TE transcript
Single TE insertion for TBP LOF and CONTROL were quantified using TElocal from TEtranscript
Assembly: GRCm38
Supplementary files format and content: Count table from TECount using the second read of the 5' fragments ("five_2n")
Supplementary files format and content: Count table from TELocal ("local") (only for TBP LOF and CONTROL)

molecule: polyA RNA

growth_protocol: Zygotes were collected at 17-18h post-hCG, microinjected twice and culture in KSOM until 48h post-hCG (late 2-cell stage), and collected for RNA-sequencing

extract_protocol:
Single embryos were lyzed and snap frozen in liquid nitrogen and kept at -80 until further processing.For TBP, embryos were collecteed in 3 biological replicates and processed all at once. For FOXJ3 LOF, embryos were processed in two batches, batch1 and batch2. For more information see methods of the accompanying paper.
An adapted version of Smart-seq2 (called Smart-seq+5') enabling to capture both the 5; trasncript information in addition to internal fragment (see methods of the accompaying paper for more information).

treatment_protocol: Mouse embryos (zygotes) were microinjected with antibodies against TBP (TBP LOF), mouse IGG (CONTROL for TBP LOF), FOXJ3 (FOXJ3 LOF) and rabbit IGG (CONTROL for FOXJ3), cultured for 4h and microinjected with Trim21 mRNA (see methods of the accompanying paper for more information).

value: FOXJ3 AB injected


title: rIGG_CONTROL_Batch2_Embryo6

description:
Library name: rIGG_CONTROL_Batch2_Embryo6
2x150bp reads
23L010671_five_2n-read.cntTable.txt

value: rabbit IGG AB injected


title: rtf1del , ref2del , swd2del , KY5334 , Spt5 , Rep1

description:
Library name: rtf1del_ref2del_swd2del_KY5334_Spt5_Rep1
MATalpha lys2-128∂ leu2Δ1 ura3-52 rtf1Δ101::LEU2 swd2∆::hphMX ref2∆::KanMX 3xHA-GLC7


title: WT , KY5366 , Input_Kl , Rep2

description:
Library name: WT_KY5366_Input_Kl_Rep2
MATalpha lys2-128∂ leu2Δ1 ura3-52 3xHA-GLC7


title: RBC-step2-1G-r1

description: Library name: RBC-step-2--1G-r1


title: RBC-step2-1F-r2

description: Library name: RBC-step-2--1F-r2


title: RBC-step2-1H-r1

description: Library name: RBC-step-2--1H-r1


title: rIGG_CONTROL_Batch2_Embryo7

description:
Library name: rIGG_CONTROL_Batch2_Embryo7
2x150bp reads
23L010670_five_2n-read.cntTable.txt


title: rIGG_CONTROL_Batch2_Embryo5

description:
Library name: rIGG_CONTROL_Batch2_Embryo5
2x150bp reads
23L010669_five_2n-read.cntTable.txt


title: RBC-step2-1F-r1

description: Library name: RBC-step-2--1F-r1


title: RBC-step2-2A-r1

description: Library name: RBC-step-2--2A-r1


title: rtf1del , KY5339 , Input_Kl , Rep2

description:
Library name: rtf1del_KY5339_Input_Kl_Rep2
MATa lys2-128∂ leu2Δ1 ura3-52 rtf1Δ101::LEU2 3xHA-GLC7


title: RBC-step2-2D-r1

description: Library name: RBC-step-2--2D-r1


title: rtf1del , KY5339 , Spt5 , Rep2

description:
Library name: rtf1del_KY5339_Spt5_Rep2
MATa lys2-128∂ leu2Δ1 ura3-52 rtf1Δ101::LEU2 3xHA-GLC7


title: FOXJ3_LOF_Batch2_Embryo7

description:
Library name: FOXJ3_LOF_Batch2_Embryo7
2x150bp reads
23L010668_five_2n-read.cntTable.txt


title: RBC-step2-1E-r1

description: Library name: RBC-step-2--1E-r1


title: RBC-step2-1E-r2

description: Library name: RBC-step-2--1E-r2


title: rtf1del , ref2del , swd2del , KY5334 , Input_Kl , Rep2

description:
Library name: rtf1del_ref2del_swd2del_KY5334_Input_Kl_Rep2
MATalpha lys2-128∂ leu2Δ1 ura3-52 rtf1Δ101::LEU2 swd2∆::hphMX ref2∆::KanMX 3xHA-GLC7


title: WT , KY5366 , Input_Kl , Rep1

description:
Library name: WT_KY5366_Input_Kl_Rep1
MATalpha lys2-128∂ leu2Δ1 ura3-52 3xHA-GLC7


title: RBC-step2-1C-r2

description: Library name: RBC-step-2--1C-r2


title: FOXJ3_LOF_Batch2_Embryo6

description:
Library name: FOXJ3_LOF_Batch2_Embryo6
2x150bp reads
23L010667_five_2n-read.cntTable.txt


title: FOXJ3_LOF_Batch2_Embryo5

description:
Library name: FOXJ3_LOF_Batch2_Embryo5
2x150bp reads
23L010666_five_2n-read.cntTable.txt


title: RBC-step2-1C-r1

description: Library name: RBC-step-2--1C-r1


title: RBC-step2-1D-r1

description: Library name: RBC-step-2--1D-r1


title: RBC-step2-2A-r2

description: Library name: RBC-step-2--2A-r2


title: rtf1del , KY5339 , Input_Kl , Rep1

description:
Library name: rtf1del_KY5339_Input_Kl_Rep1
MATa lys2-128∂ leu2Δ1 ura3-52 rtf1Δ101::LEU2 3xHA-GLC7


title: RBC-step2-1B-r1

description: Library name: RBC-step-2--1B-r1


title: RBC-step2-1A-r1

description: Library name: RBC-step-2--1A-r1


title: rtf1del , ref2del , swd2del , KY5334 , Input_Kl , Rep1

description:
Library name: rtf1del_ref2del_swd2del_KY5334_Input_Kl_Rep1
MATalpha lys2-128∂ leu2Δ1 ura3-52 rtf1Δ101::LEU2 swd2∆::hphMX ref2∆::KanMX 3xHA-GLC7


title: rIGG_CONTROL_Batch2_Embryo3

description:
Library name: rIGG_CONTROL_Batch2_Embryo3
2x150bp reads
23L010665_five_2n-read.cntTable.txt


title: RBC-step1-8-r2

description: Library name: RBC-step-1-8-r2


title: RBC-step1-8-r1

description: Library name: RBC-step-1-8-r1


title: RBC-step1-7-r2

description: Library name: RBC-step-1-7-r2


title: WT , KY5366 , 8WG16 , Rep2

description:
Library name: WT_KY5366_8WG16_Rep2
MATalpha lys2-128∂ leu2Δ1 ura3-52 3xHA-GLC7


title: rIGG_CONTROL_Batch2_Embryo2

description:
Library name: rIGG_CONTROL_Batch2_Embryo2
2x150bp reads
23L010664_five_2n-read.cntTable.txt


title: RBC-step1-7-r1

description: Library name: RBC-step-1-7-r1


title: rtf1del , KY5339 , 8WG16 , Rep2

description:
Library name: rtf1del_KY5339_8WG16_Rep2
MATa lys2-128∂ leu2Δ1 ura3-52 rtf1Δ101::LEU2 3xHA-GLC7


title: rIGG_CONTROL_Batch2_Embryo1

description:
Library name: rIGG_CONTROL_Batch2_Embryo1
2x150bp reads
23L010663_five_2n-read.cntTable.txt


title: FOXJ3_LOF_Batch2_Embryo3

description:
Library name: FOXJ3_LOF_Batch2_Embryo3
2x150bp reads
23L010662_five_2n-read.cntTable.txt


title: RBC-step1-6-r1

description: Library name: RBC-step-1-6-r1


title: RBC-step1-5-r2

description: Library name: RBC-step-1-5-r2


title: rtf1del , ref2del , swd2del , KY5334 , 8WG16 , Rep2

description:
Library name: rtf1del_ref2del_swd2del_KY5334_8WG16_Rep2
MATalpha lys2-128∂ leu2Δ1 ura3-52 rtf1Δ101::LEU2 swd2∆::hphMX ref2∆::KanMX 3xHA-GLC7


title: FOXJ3_LOF_Batch2_Embryo2

description:
Library name: FOXJ3_LOF_Batch2_Embryo2
2x150bp reads
23L010661_five_2n-read.cntTable.txt


title: RBC-step1-6-r2

description: Library name: RBC-step-1-6-r2


title: WT , KY5366 , 8WG16 , Rep1

description:
Library name: WT_KY5366_8WG16_Rep1
MATalpha lys2-128∂ leu2Δ1 ura3-52 3xHA-GLC7


title: RBC-step1-5-r1

description: Library name: RBC-step-1-5-r1


title: RBC-step1-4-r2

description: Library name: RBC-step-1-4-r2


title: FOXJ3_LOF_Batch2_Embryo1

description:
Library name: FOXJ3_LOF_Batch2_Embryo1
2x150bp reads
23L010660_five_2n-read.cntTable.txt


title: rtf1del , KY5339 , 8WG16 , Rep1

description:
Library name: rtf1del_KY5339_8WG16_Rep1
MATa lys2-128∂ leu2Δ1 ura3-52 rtf1Δ101::LEU2 3xHA-GLC7


title: rIGG_CONTROL_Batch1_Embryo7

description:
Library name: rIGG_CONTROL_Batch1_Embryo7
2x150bp reads
22L004936_five_2n-read.cntTable.txt


title: RBC-step1-4-r1

description: Library name: RBC-step-1-4-r1


title: RBC-step1-3-r2

description: Library name: RBC-step-1-3-r2


title: rtf1del , ref2del , swd2del , KY5334 , 8WG16 , Rep1

description:
Library name: rtf1del_ref2del_swd2del_KY5334_8WG16_Rep1
MATalpha lys2-128∂ leu2Δ1 ura3-52 rtf1Δ101::LEU2 swd2∆::hphMX ref2∆::KanMX 3xHA-GLC7


title: RBC-step1-3-r1

description: Library name: RBC-step-1-3-r1


title: RBC-step2-1D-r2

description: Library name: RBC-step-2--1D-r2


title: RBC-step1-2-r2

description: Library name: RBC-step-1-2-r2


title: rIGG_CONTROL_Batch1_Embryo6

description:
Library name: rIGG_CONTROL_Batch1_Embryo6
2x150bp reads
22L004935_five_2n-read.cntTable.txt


title: RBC-step1-2-r1

description: Library name: RBC-step-1-2-r1


title: rIGG_CONTROL_Batch1_Embryo5

description:
Library name: rIGG_CONTROL_Batch1_Embryo5
2x150bp reads
22L004934_five_2n-read.cntTable.txt


title: rtf1del , KY5339 , Input_Sp , Rep2

description:
Library name: rtf1del_KY5339_Input_Sp_Rep2
MATa lys2-128∂ leu2Δ1 ura3-52 rtf1Δ101::LEU2 3xHA-GLC7


title: WT , KY5366 , Input_Sp , Rep2

description:
Library name: WT_KY5366_Input_Sp_Rep2
MATalpha lys2-128∂ leu2Δ1 ura3-52 3xHA-GLC7


title: RBC-step1-8-r2_pilot

description: Library name: RBC-step1-8-r2

value: pilot


title: RBC-step1-1-r1

description: Library name: RBC-step-1-1-r1


title: FOXJ3_LOF_Batch1_Embryo11

description:
Library name: FOXJ3_LOF_Batch1_Embryo11
2x150bp reads
22L004933_five_2n-read.cntTable.txt


title: RBC-step1-8-r1_pilot

description: Library name: RBC-step1-8-r1


title: RBC-step1-7-r2_pilot

description: Library name: RBC-step1-7-r2


title: RBC-step1-7-r1_pilot

description: Library name: RBC-step1-7-r1


title: RBC-step1-6-r2_pilot

description: Library name: RBC-step1-6-r2


title: WT , KY5366 , Input_Sp , Rep1

description:
Library name: WT_KY5366_Input_Sp_Rep1
MATalpha lys2-128∂ leu2Δ1 ura3-52 3xHA-GLC7


title: FOXJ3_LOF_Batch1_Embryo9

description:
Library name: FOXJ3_LOF_Batch1_Embryo9
2x150bp reads
22L004931_five_2n-read.cntTable.txt


title: rtf1del , ref2del , swd2del , KY5334 , Input_Sp , Rep2

description:
Library name: rtf1del_ref2del_swd2del_KY5334_Input_Sp_Rep2
MATalpha lys2-128∂ leu2Δ1 ura3-52 rtf1Δ101::LEU2 swd2∆::hphMX ref2∆::KanMX 3xHA-GLC7


title: RBC-step1-5-r2_pilot

description: Library name: RBC-step1-5-r2


title: rtf1del , KY5339 , Input_Sp , Rep1

description:
Library name: rtf1del_KY5339_Input_Sp_Rep1
MATa lys2-128∂ leu2Δ1 ura3-52 rtf1Δ101::LEU2 3xHA-GLC7


title: rIGG_CONTROL_Batch1_Embryo4

description:
Library name: rIGG_CONTROL_Batch1_Embryo4
2x150bp reads
22L004930_five_2n-read.cntTable.txt


title: rtf1del , ref2del , swd2del , KY5334 , Input_Sp , Rep1

description:
Library name: rtf1del_ref2del_swd2del_KY5334_Input_Sp_Rep1
MATalpha lys2-128∂ leu2Δ1 ura3-52 rtf1Δ101::LEU2 swd2∆::hphMX ref2∆::KanMX 3xHA-GLC7


title: RBC-step1-4-r1_pilot

description: Library name: RBC-step1-4-r1


title: RBC-step1-4-r2_pilot

description: Library name: RBC-step1-4-r2


title: RBC-step1-5-r1_pilot

description: Library name: RBC-step1-5-r1


title: WT , KY5366 , HA , Rep2

description:
Library name: WT_KY5366_HA_Rep2
MATalpha lys2-128∂ leu2Δ1 ura3-52 3xHA-GLC7

value: HA (Santa Cruz, #sc-7392 AC)


title: rIGG_CONTROL_Batch1_Embryo2

description:
Library name: rIGG_CONTROL_Batch1_Embryo2
2x150bp reads
22L004928_five_2n-read.cntTable.txt


title: RBC-step1-1-r2

description: Library name: RBC-step-1-1-r2


title: RBC-step1-3-r2_pilot

description: Library name: RBC-step1-3-r2


title: rtf1del , KY5339 , HA , Rep2

description:
Library name: rtf1del_KY5339_HA_Rep2
MATa lys2-128∂ leu2Δ1 ura3-52 rtf1Δ101::LEU2 3xHA-GLC7


title: RBC-step1-3-r1_pilot

description: Library name: RBC-step1-3-r1


title: rIGG_CONTROL_Batch1_Embryo1

description:
Library name: rIGG_CONTROL_Batch1_Embryo1
2x150bp reads
22L004927_five_2n-read.cntTable.txt


title: FOXJ3_LOF_Batch1_Embryo7

description:
Library name: FOXJ3_LOF_Batch1_Embryo7
2x150bp reads
22L004926_five_2n-read.cntTable.txt


title: FOXJ3_LOF_Batch1_Embryo10

description:
Library name: FOXJ3_LOF_Batch1_Embryo10
2x150bp reads
22L004932_five_2n-read.cntTable.txt


title: RBC-step1-1-r2_pilot

description: Library name: RBC-step1-1-r2


title: RBC-step1-1-r1_pilot

description: Library name: RBC-step1-1-r1


title: WT , KY5366 , HA , Rep1

description:
Library name: WT_KY5366_HA_Rep1
MATalpha lys2-128∂ leu2Δ1 ura3-52 3xHA-GLC7


title: Human fibroblast cell line BJ, treated with GSSG liposome, 48 hour,replicate3

city: Chicago

first: Jiacheng

last: Li

state: IL

address: 900 E 57th Street,

department: Medicine

institute: University of Chicago

description: Library name: G48_3

data_processing:
Reference genome and gene model annotation files were downloaded  from genome website directly. Index of the reference genome was built using  Hisat2 v2.0.5 and paired-end clean 1 reads were aligned to the reference  genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that  Hisat2 can generate a database of splice junctions based on the gene model  annotation file and thus a better mapping result than other non-splice mapping  tools
featureCounts v1.5.0-p3 was used to count the reads numbers mapped  to each gene. And then FPKM of each gene was calculated based on the  length of the gene and reads count mapped to this gene. FPKM, expected  number of Fragments Per Kilobase of transcript sequence per Millions base  pairs sequenced, considers the effect of sequencing depth and gene length for  the reads count at the same time, and is currently the most commonly used  method for estimating gene expression levels
Assembly: hg38
Supplementary files format and content: csv. file with raw gene counts

molecule: total RNA

source_name: Human fibroblast cell line BJ established from skin taken from normal foreskin from a neonatal male

growth_protocol: The base medium for this cell line is ATCC-formulated Eagle's Minimum Essential Medium (ATCC 30-2003). To make the complete growth medium, add the following components to the base medium: fetal bovine serum (ATCC 30-2020) to a final concentration of 10%.

extract_protocol:
RNeasy Mini Kit; Qiagen
Messenger RNA was purified from total RNA using poly-T oligo-attached  magnetic beads. After fragmentation, the first strand cDNA was synthesized  using random hexamer primers, followed by the second strand cDNA  synthesis using either dUTP for directional library or dTTP for non-directional  library.For the non-directional library, it was ready after end repair, A-tailing,  adapter ligation, size selection, amplification, and purification.For the directional library, it was ready after end repair, A-tailing, adapter ligation, size selection, USER enzyme digestion, amplification, andpurification.

treatment_protocol: treat cells with 10% GSSG liposome and Control liposome for 48 hours

value: Human fibroblast cell line BJ

value: Normal, Human fibroblast cell line

value: Wild type

value: treated with GSSG liposome, 48 hour,


title: FOXJ3_LOF_Batch1_Embryo6

description:
Library name: FOXJ3_LOF_Batch1_Embryo6
2x150bp reads
22L004925_five_2n-read.cntTable.txt


title: rtf1del , KY5339 , HA , Rep1

description:
Library name: rtf1del_KY5339_HA_Rep1
MATa lys2-128∂ leu2Δ1 ura3-52 rtf1Δ101::LEU2 3xHA-GLC7


title: RBC-step1-6-r1_pilot

description: Library name: RBC-step1-6-r1

value: differentiating HSPCs


title: Human fibroblast cell line BJ, treated with GSSG liposome, 48 hour,replicate2

description: Library name: G48_2

value: Human fibroblast cell line BJ established from skin taken from normal foreskin from a neonatal male


title: FOXJ3_LOF_Batch1_Embryo5

description:
Library name: FOXJ3_LOF_Batch1_Embryo5
2x150bp reads
22L004924_five_2n-read.cntTable.txt


title: Human fibroblast cell line BJ, treated with Control liposome, 48 hour,replicate3

description: Library name: CON3

value: treated with Control liposome, 48 hour,


title: Human fibroblast cell line BJ, treated with GSSG liposome, 48 hour,replicate1

description: Library name: G48_1


title: rtf1del , ref2del , swd2del , KY5334 , HA , Rep1

description:
Library name: rtf1del_ref2del_swd2del_KY5334_HA_Rep1
MATalpha lys2-128∂ leu2Δ1 ura3-52 rtf1Δ101::LEU2 swd2∆::hphMX ref2∆::KanMX 3xHA-GLC7


title: Human fibroblast cell line BJ, treated with Control liposome, 48 hour,replicate1

description: Library name: CON1


title: spt5delCTR , KY4894 , Rtf1 , Rep2

description:
Library name: spt5_delCTR_KY4894_Rtf1_Rep2
MATalpha lys2-128δ leu2∆1 ura3-52 3xHSV-PAF1 spt5∆CTR::NatMX


title: FOXJ3_LOF_Batch1_Embryo4

description:
Library name: FOXJ3_LOF_Batch1_Embryo4
2x150bp reads
22L004923_five_2n-read.cntTable.txt


title: FOXJ3_LOF_Batch1_Embryo3

description:
Library name: FOXJ3_LOF_Batch1_Embryo3
2x150bp reads
22L004922_five_2n-read.cntTable.txt


title: Human fibroblast cell line BJ, treated with Control liposome, 48 hour,replicate2

description: Library name: CON2


title: RBC-step1-2-r2_pilot

description: Library name: RBC-step1-2-r2


title: FOXJ3_LOF_Batch1_Embryo2

description:
Library name: FOXJ3_LOF_Batch1_Embryo2
2x150bp reads
22L004921_five_2n-read.cntTable.txt


title: RBC-step1-2-r1_pilot

description: Library name: RBC-step1-2-r1


title: rtf1del , ref2del , swd2del , KY5334 , HA , Rep2

description:
Library name: rtf1del_ref2del_swd2del_KY5334_HA_Rep2
MATalpha lys2-128∂ leu2Δ1 ura3-52 rtf1Δ101::LEU2 swd2∆::hphMX ref2∆::KanMX 3xHA-GLC7


title: E-mu-Myc-#506 cells-derived BCL_Vehicle treated

city: Nice

first: Johanna

last: CHICHE

address: 151 Route de Saint Antoine de Ginestière, Batiment Archimed

department: C3M, Inserm U 1065

country: France

institute: INSERM

description: Library name: Sample 13

data_processing:
Raw reads were mapped with STAR_2.4.0 aligner to mm10 using GRCm38.83 release.
Features quantifications were performed using featureCounts (subread-1.5.0-p3-Linux-X86_64) with –primary -g gene_name -p -s 1 -C parameters.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each samples

source_name: B-cell lymphoma (lymph node)

growth_protocol: E-mu-Myc-cells were maintained in DMEM-GlutaMAX medium (31966047, Thermo Fisher Scientific) supplemented with 10% of fetal bovine serum (FBS) (F7524, Sigma), 50 µM of 2-Mercaptoethanol (31350010, Thermo Fisher Scientific), 0.37 mM of L-asparagine (A0884, Sigma), 10 mM of HEPES pH 7.4 (15630056, Thermo Fisher Scientific) and 100 U/ml of Penicillin-Streptomycin (15140122, Thermo Fisher Scientific).

extract_protocol:
Total RNA was extracted from E-mu-Myc-cells or from E-mu-Myc-cells-derived B-cell lymphomas, using the RNeasy mini kit (74104, Qiagen) according to manufacturer’s instructions. 1 µg of total RNA was used for the construction of sequecing libraries.
Libraries were generated using Truseq Stranded mRNA kit (Illumina). Libraries were then quantified with Qubit dsDNA High Sensitivity Assay Kit (Invitrogen) and pooled. 4nM of this pool were loaded on a Nextseq 500 High output Flowcell and sequenced on a NextSeq 500 platform (Illumina) with 2 × 75bp paired-end chemistry.

treatment_protocol: No treatment for samples 1 to 12. Samples 13 and 14 were in vivo treated with Vehicle (NaCl 0.9%) or L-asparaginase (ASNase), respectively.

value: B-cell lymphoma (lymph node)

value: WT

value: Vehicle (NaCl 0.9%) treatment in vivo


title: E-mu-Myc-#801 cells

description: Library name: Sample 12

source_name: E-mu-Myc cells from E-mu-MycTg/+ mouse #801

value: Malignant B cells

value: No treatment


title: E-mu-Myc-#688 cells

description: Library name: Sample 11

source_name: E-mu-Myc cells from E-mu-MycTg/+ mouse #688


title: E-mu-Myc-#506 cells-derived BCL_ASNase treated

description: Library name: Sample 14

value: L-asparaginase (ASNase) treatment in vivo


title: E-mu-Myc-#649 cells

description: Library name: Sample 10

source_name: E-mu-Myc cells from E-mu-MycTg/+ mouse #649


title: spt5-S1-15A , KY4912 , Rtf1 , Rep2

description:
Library name: spt5_S1_15A_KY4912_Rtf1_Rep2
MATa lys2-128δ leu2∆1 ura3-52 3xHSV-PAF1 spt5-S1-15A


title: FOXJ3_LOF_Batch1_Embryo1

description:
Library name: FOXJ3_LOF_Batch1_Embryo1
2x150bp reads
22L004920_five_2n-read.cntTable.txt

value: Late 2-cell embryo

value: FOXJ3 AB injected


title: E-mu-Myc-#524 cells

description: Library name: Sample 8

source_name: E-mu-Myc cells from E-mu-MycTg/+ mouse #524


title: E-mu-Myc-#517 cells

description: Library name: Sample 7

source_name: E-mu-Myc cells from E-mu-MycTg/+ mouse #517


title: mIGG_CONTROL_Embryo10

description:
Library name: mIGG_CONTROL_Embryo10
2x150bp reads
22L004919_five_2n-read.cntTable.txt
22L004919_local.cntTable.txt

value: mouse IGG AB injected


title: E-mu-Myc-#549 cells

description: Library name: Sample 9

source_name: E-mu-Myc cells from E-mu-MycTg/+ mouse #549


title: spt5-S1-15D , KY3594 , Rtf1 , Rep2

description:
Library name: spt5_S1_15D_KY3594_Rtf1_Rep2
MATa lys2-128δ leu2Δ1 ura3-52 3xHSV-PAF1 spt5-S1-15D


title: mIGG_CONTROL_Embryo9

description:
Library name: mIGG_CONTROL_Embryo9
2x150bp reads
22L004918_five_2n-read.cntTable.txt
22L004918_local.cntTable.txt


title: E-mu-Myc-#505 cells

description: Library name: Sample 5

source_name: E-mu-Myc cells from E-mu-MycTg/+ mouse #505


title: E-mu-Myc-#506 cells

description: Library name: Sample 6

source_name: E-mu-Myc cells from E-mu-MycTg/+ mouse #506


title: mAID-SPT5 , KY4793 , IAA , Rtf1 , Rep2

description:
Library name: mAID_SPT5_KY4793_IAA_Rtf1_Rep2
MATa his3∆200::OsTIR-F74G-HIS3 lys2-128δ leu2∆1 ura3-52 3xHSV-PAF1 1xminiAID-SPT5

value: 45 min


title: mIGG_CONTROL_Embryo8

description:
Library name: mIGG_CONTROL_Embryo8
2x150bp reads
22L004917_five_2n-read.cntTable.txt
22L004917_local.cntTable.txt


title: E-mu-Myc-#309 cells

description: Library name: Sample 3

source_name: E-mu-Myc cells from E-mu-MycTg/+ mouse #309


title: E-mu-Myc-#136 cells

description: Library name: Sample 2

source_name: E-mu-Myc cells from E-mu-MycTg/+ mouse #136


title: Tbp_LOF_Embryo11

description:
Library name: Tbp_LOF_Embryo11
2x150bp reads
22L004916_five_2n-read.cntTable.txt
22L004916_local.cntTable.txt

value: TBP AB injected


title: spt5delCTR , KY4894 , Rtf1 , Rep1

description:
Library name: spt5_delCTR_KY4894_Rtf1_Rep1
MATalpha lys2-128δ leu2∆1 ura3-52 3xHSV-PAF1 spt5∆CTR::NatMX


title: WT , KY4803 , Rtf1 , Rep2

description:
Library name: WT_KY4803_Rtf1_Rep2
MATa lys2-128δ leu2∆1 ura3-52 3xHSV-PAF1


title: E-mu-Myc-#115 cells

description: Library name: Sample 1

source_name: E-mu-Myc cells from E-mu-MycTg/+ mouse #115


title: Tbp_LOF_Embryo10

description:
Library name: Tbp_LOF_Embryo10
2x150bp reads
22L004915_five_2n-read.cntTable.txt
22L004915_local.cntTable.txt


title: spt5-S1-15A , KY4912 , Rtf1 , Rep1

description:
Library name: spt5_S1_15A_KY4912_Rtf1_Rep1
MATa lys2-128δ leu2∆1 ura3-52 3xHSV-PAF1 spt5-S1-15A


title: mIGG_CONTROL_Embryo7

description:
Library name: mIGG_CONTROL_Embryo7
2x150bp reads
22L004914_five_2n-read.cntTable.txt
22L004914_local.cntTable.txt


title: T-cells, tumor_met, HTO

city: New York

first: Sneha

last: Mitra

state: NY

address: 1275 York Avenue

institute: Memorial Sloan Kettering Cancer Center

description:
Library name: T_hto
HTO library: read1 contains cell barcode and UMI; read2 contains Hashtag Antibody Derived Tag reads

library_source: other

data_processing:
Multiome files we demultiplexed using cellranger mkfastq
Demultiplexed data was processed using the cellranger multi pipeline
Assembly: mm10
Supplementary files format and content: Cellranger output files:T_filtered_feature_bc_matrix.h5, nonT_filtered_feature_bc_matrix.h5
Library strategy: CITE-seq

molecule: other

source_name: primary tumor, liver metastases, lymph node metastases

extract_protocol:
Immediately following sorting, cells were washed then used for 10X RNA+TCR sequencing following manufacturer protocols.
Libaries construction for both scTCR and scRNA followed manufacturer protocols (10X genomics).

value: T-cell

tag: library type

value: HTO


title: nonT-cells, tumor_met, HTO

description:
Library name: nonT_hto
HTO library: read1 contains cell barcode and UMI; read2 contains Hashtag Antibody Derived Tag reads

value: primary tumor, liver metastases, lymph node metastases

value: nonT immune cell


title: spt5del5 , KY4798 , Rtf1 , Rep2

description:
Library name: spt5_del5_KY4798_Rtf1_Rep2
MATa lys2-128δ leu2∆1 ura3-52 3xHSV-PAF1 spt5∆5::NatMX


title: nonT-cells, tumor_met, GEX

description:
Library name: nonT_mRNA
5' mRNA: read1 contains cell barcode and UMI; read2 contains transcript sequence

library_source: transcriptomic single cell

data_processing:
Multiome files we demultiplexed using cellranger mkfastq
Demultiplexed data was processed using the cellranger multi pipeline
Assembly: mm10
Supplementary files format and content: Cellranger output files:T_filtered_feature_bc_matrix.h5, nonT_filtered_feature_bc_matrix.h5

value: mRNA


title: WT , KY4803 , Rtf1 , Rep1

description:
Library name: WT_KY4803_Rtf1_Rep1
MATa lys2-128δ leu2∆1 ura3-52 3xHSV-PAF1


title: mIGG_CONTROL_Embryo6

description:
Library name: mIGG_CONTROL_Embryo6
2x150bp reads
22L004913_five_2n-read.cntTable.txt
22L004913_local.cntTable.txt


title: T-cells, tumor_met, GEX

description:
Library name: T_mRNA
5' mRNA: read1 contains cell barcode and UMI; read2 contains transcript sequence


title: T-cells, tumor_met, TCR

description:
Library name: T_tcr
VDJ library: read1 contains cell barcode and UMI; read2 contains the VDJ reads

data_processing:
Multiome files we demultiplexed using cellranger mkfastq
Demultiplexed data was processed using the cellranger multi pipeline
Assembly: mm10
Supplementary files format and content: Cellranger output files:T_filtered_feature_bc_matrix.h5, nonT_filtered_feature_bc_matrix.h5
Library strategy: TCR-seq

value: VDJ


title: Mm_Wnt1-Cre-Nedd4fl-fl-Embryo_Mutant_rep3

city: Adelaide

first: John

last: Toubia

address: Frome Rd

country: Australia

institute: Centre for Cancer Biology

description:
Library name: Mut_3
column name in combined_counts.tsv: Mut_3_dedup

data_processing:
Basecalls were performed using bcl2fastq v2.20
Reads were mapped against the mouse reference genome (mm10) using the STAR spliced alignment algorithm (version 2.6.1d with default parameters and --chimSegmentMin 20, --quantMode GeneCounts)
Duplicate reads found in the aligned bam file were marked and subsequently removed using Picard Tools (version 2.16.0)
Assembly: mm10
Supplementary files format and content: tab delimited raw STAR gene counts file for each sample
Supplementary files format and content: tab delimited raw genecounts for each sample combined

source_name: Second heart field region

growth_protocol: Pregnant dams carrying wildtype and Wnt1-Cre; Nedd4fl/fl embryos were housed under standard condidtions, and embryos harvested at embryoic day E9.5.

extract_protocol:
RNA was prepared from tissue by lysing in 4M guanidine isothiocyanate solution (Invitrogen) and precipitating with sodium acetate and ethanol. After 75% ethanol wash, RNA pellet was resuspended in 12ml H2O, with 1ml reserved for Bioanalyser quality control of RNA, and 9.5ml used for subsequent cDNA synthesis.
Isolated RNA samples were submitted to the ACRF Genomics Facility for library preparation and sequencing. Extracted RNA was quantified using the Bioanalyser Pico chip and 9.5ul (containing 5-17ng of RNA) was input into SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Takara Bio) for generation and amplification of double-stranded full-length cDNA (using 9 cycles of LD-PCR). Prior to library preparation, cDNA was sheared to 200-500 bp fragments using the Covaris system. NGS libraries were prepared using the ThruPLEX DNA-seq Kit (Takara Bio) together with the DNA Unique Dual Index Kit (Takara Bio), using 11 cycles of PCR for library amplification.

treatment_protocol: Mouse embryos were fresh-frozen in OCT, cryosectioned and collected on PEN membrane slides. Slides were stained with 1% Cresyl Violet to visualise tissue sections, airdried, and then laser dissection performed promptly (Leica LMD) to specifically capture the central anterior second heart field region (with associated neural crest and pharyngeal endoderm tissue).

value: Second heart field region

value: cardiac progenitors, neural crest, endoderm

value: Mutant


title: spt5del5 , KY4798 , Rtf1 , Rep1

description:
Library name: spt5_del5_KY4798_Rtf1_Rep1
MATa lys2-128δ leu2∆1 ura3-52 3xHSV-PAF1 spt5∆5::NatMX


title: Mm_Wnt1-Cre-Nedd4fl-fl-Embryo_Mutant_rep1

description:
Library name: Mut_1
column name in combined_counts.tsv: Mut_1_dedup


title: Mm_Wnt1-Cre-Nedd4fl-fl-Embryo_Mutant_rep2

description:
Library name: Mut_2
column name in combined_counts.tsv: Mut_2_dedup


title: Mm_Wnt1-Cre-Nedd4fl-fl-Embryo_Wild-Type_rep3

description:
Library name: WT_3
column name in combined_counts.tsv: WT_3_dedup

value: WT


title: spt5-S1-15D , KY3594 , Rtf1 , Rep1

description:
Library name: spt5_S1_15D_KY3594_Rtf1_Rep1
MATa lys2-128δ leu2Δ1 ura3-52 3xHSV-PAF1 spt5-S1-15D


title: Tbp_LOF_Embryo9

description:
Library name: Tbp_LOF_Embryo9
2x150bp reads
22L004912_five_2n-read.cntTable.txt
22L004912_local.cntTable.txt


title: E-mu-Myc-#504 cells

description: Library name: Sample 4

source_name: E-mu-Myc cells from E-mu-MycTg/+ mouse #504

value: Malignant B cells

value: No treatment


title: mAID-SPT5 , KY4793 , DMSO , Rtf1 , Rep2

description:
Library name: mAID_SPT5_KY4793_DMSO_Rtf1_Rep2
MATa his3∆200::OsTIR-F74G-HIS3 lys2-128δ leu2∆1 ura3-52 3xHSV-PAF1 1xminiAID-SPT5

value: DMSO


title: mAID-SPT5 , KY4793 , IAA , Rtf1 , Rep1

description:
Library name: mAID_SPT5_KY4793_IAA_Rtf1_Rep1
MATa his3∆200::OsTIR-F74G-HIS3 lys2-128δ leu2∆1 ura3-52 3xHSV-PAF1 1xminiAID-SPT5


title: Tbp_LOF_Embryo8

description:
Library name: Tbp_LOF_Embryo8
2x150bp reads
22L004911_five_2n-read.cntTable.txt
22L004911_local.cntTable.txt

source_name: Late 2-cell embryo

value: Late 2-cell embryo


title: mAID-SPT5 , KY4793 , DMSO , Rtf1 , Rep1

description:
Library name: mAID_SPT5_KY4793_DMSO_Rtf1_Rep1
MATa his3∆200::OsTIR-F74G-HIS3 lys2-128δ leu2∆1 ura3-52 3xHSV-PAF1 1xminiAID-SPT5


title: Mm_Wnt1-Cre-Nedd4fl-fl-Embryo_Wild-Type_rep1

description:
Library name: WT_1
column name in combined_counts.tsv: WT_1_dedup


title: 5781-MSH2-KO

city: NEW YORK

first: Alexander

last: Tsankov

state: New York

address: 1425 Madison Ave

department: Genetics and Genomic Sciences

institute: Icahn School of Medicine at Mount Sinai

description:
Library name: Sample 11
10x Genomics

data_processing:
We initiated our analysis by aligning the raw fastq files to the customized mouse genome reference mm10, which included the Rfp sequence. This alignment process was executed using CellRanger v5.0.0 by 10X Genomics. Following alignment, we used the CellRanges algorithm to filter count matrices. Cells with less than 400 genes, fewer than 1000 UMI (unique molecular identifier), or over 25% mitochondrial gene expression were excluded. Subsequent data processing and analysis were conducted using the Seurat v4.2.2 R package. The data was normalized using the NormalizeData function, utilizing the normalization.method = 'LogNormalize' parameter. For dimensionality reduction, we focused on the top 2,000 variable features, using functions such as FindVariableFeatures, ScaleData, and RunPCA. Ultimately, we generated UMAPs based on the top 15 principal components (PCs).
To subcluster the immune compartment, we employed the R package Harmony to address batch effects stemming from technical variations across replicates. De novo clustering was carried out using the Louvain algorithm at multiple resolutions (0.2, 0.4, 0.8, 2, 3, 5, 8) within the KNN graph space. For high-level cell type annotation, we iteratively and semi-supervisedly assigned de novo discovered clusters to cell types based on the expression of established marker genes defining each cluster. The annotation of cell subtypes at a lower level followed a similar approach to the high-level annotation, with additional assistance from de novo marker discovery utilizing the Seurat FindMarkers function and Wilcoxon Rank Sum test.
To identify clusters enriched with doublets, we searched for cell clusters that exhibited the expression of canonical markers for two or more distinct cell types and a higher count of genes/UMI. These identified clusters were subsequently excluded from further analysis.
Cell-level proliferation analysis was performed using the Seurat function CellCycleScoring, which utilized a curated list of murine cell cycle genes. Subsequently, cells were categorized as 'cycling' or 'non-cycling' based on whether their S-phase score or G2M-score exceeded a threshold of 0.10 for the tumor compartment and immune compartment.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: brain tumor

extract_protocol:
Tumors were dissected from the brain, minced into pieces < 1 mm3, and digested with an enzymatic mixture that includes papain (0.94 mg/ml, Worthington, LS003120), EDTA (0.18 mg/ml, Sigma, E6758), cysteine (0.18 mg/ml, Sigma, A8199), and DNase I (60 μg/ml, Roche, 11284932001) in 2 ml HBSS (Gibco, 14175-095). Tumor tissues were kept at 37°C for 15 minutes with occasional agitation. The digestion was terminated with the addition of 2 ml Ovomucoid (0.7 mg/ml, Worthington, LS003086). Following digestion, single cells were passed through a 70 μm cell strainer, centrifuged, and resuspended in 30% Percoll (GE Healthcare, 17-0891-01) solution containing 10% FBS (Hyclone SH30396.03). Cells were separated by centrifugation at 800g for 15 minutes at 4°C. The pellet was resuspended in RBC lysis buffer (BioLegend, 420301) for 1 min at 37°C before they were centrifuged at 450g for 5 min. The pellet was resuspended in PBS and immediately delivered for GEM preparation.
Gel-Bead in Emulsions (GEMs) were generated on the sample chip in the Chromium controller. Barcoded cDNA was extracted from the GEMs by Post-GEM RT-cleanup and amplified for 12 cycles. Amplified cDNA was fragmented and subjected to end-repair, poly A-tailing, adapter ligation, and 10X-specific sample indexing following the manufacturer’s protocol. Libraries were quantified using Bioanalyzer (Agilent) and QuBit (ThermoFisher) analyses.

value: brain tumor


title: 5711-MSH2KO-B-p53

description:
Library name: Sample 9
10x Genomics


title: 5742-MSH2KO-B-p53

description:
Library name: Sample 10
10x Genomics


title: spt5delCTR , KY4894 , Spt6 , Rep2

description:
Library name: spt5_delCTR_KY4894_Spt6_Rep2
MATalpha lys2-128δ leu2∆1 ura3-52 3xHSV-PAF1 spt5∆CTR::NatMX


title: Tbp_LOF_Embryo6

description:
Library name: Tbp_LOF_Embryo6
2x150bp reads
22L004909_five_2n-read.cntTable.txt
22L004909_local.cntTable.txt


title: 6283-Msh2het-B

description:
Library name: Sample 8
10x Genomics


title: Tbp_LOF_Embryo5

description:
Library name: Tbp_LOF_Embryo5
2x150bp reads
22L004908_five_2n-read.cntTable.txt
22L004908_local.cntTable.txt


title: 5725-MSH2HET-B-p53

description:
Library name: Sample 6
10x Genomics


title: 6027-MSH2-het

description:
Library name: Sample 7
10x Genomics


title: mIGG_CONTROL_Embryo5

description:
Library name: mIGG_CONTROL_Embryo5
2x150bp reads
22L004907_five_2n-read.cntTable.txt
22L004907_local.cntTable.txt

value: mouse IGG AB injected


title: 5713-MSH2HET-B-p53

description:
Library name: Sample 5
10x Genomics


title: spt5-S1-15A , KY4912 , Spt6 , Rep2

description:
Library name: spt5_S1_15A_KY4912_Spt6_Rep2
MATa lys2-128δ leu2∆1 ura3-52 3xHSV-PAF1 spt5-S1-15A


title: WT , KY4803 , Spt6 , Rep2

description:
Library name: WT_KY4803_Spt6_Rep2
MATa lys2-128δ leu2∆1 ura3-52 3xHSV-PAF1


title: 5783-TVA-B

description:
Library name: Sample 4
10x Genomics


title: mIGG_CONTROL_Embryo4

description:
Library name: mIGG_CONTROL_Embryo4
2x150bp reads
22L004906_five_2n-read.cntTable.txt
22L004906_local.cntTable.txt


title: Mm_Wnt1-Cre-Nedd4fl-fl-Embryo_Wild-Type_rep2

description:
Library name: WT_2
column name in combined_counts.tsv: WT_2_dedup


title: 5709-TVA-B

description:
Library name: Sample 2
10x Genomics


title: spt5del5 , KY4798 , Spt6 , Rep2

description:
Library name: spt5_del5_KY4798_Spt6_Rep2
MATa lys2-128δ leu2∆1 ura3-52 3xHSV-PAF1 spt5∆5::NatMX


title: mIGG_CONTROL_Embryo3

description:
Library name: mIGG_CONTROL_Embryo3
2x150bp reads
22L004905_five_2n-read.cntTable.txt
22L004905_local.cntTable.txt


title: Tbp_LOF_Embryo7

description:
Library name: Tbp_LOF_Embryo7
2x150bp reads
22L004910_five_2n-read.cntTable.txt
22L004910_local.cntTable.txt

value: TBP AB injected


title: 5310-WT-B-p53

description:
Library name: Sample 1
10x Genomics


title: T-cells, tumor, HTO [mm10_tcr_2_4_6_weeks]

description:
Library name: tumor_hto
HTO library: read1 contains cell barcode and UMI; read2 contains Hashtag Antibody Derived Tag reads

data_processing:
Multiome files we demultiplexed using cellranger mkfastq
Demultiplexed data was processed using the cellranger multi pipeline
Assembly: mm10
Supplementary files format and content: Cellranger output files:gut_filtered_feature_bc_matrix.h5, LN_filtered_feature_bc_matrix.h5, tumor_filtered_feature_bc_matrix.h5, gut_airr_rearrangement.tsv, LN_airr_rearrangement.tsv, tumor_airr_rearrangement.tsv
Library strategy: CITE-seq

source_name: tumor

value: tumor

value: T-cell


title: spt5-S1-15D , KY3594 , Spt6 , Rep2

description:
Library name: spt5_S1_15D_KY3594_Spt6_Rep2
MATa lys2-128δ leu2Δ1 ura3-52 3xHSV-PAF1 spt5-S1-15D


title: T-cells, lymph node, HTO [mm10_tcr_2_4_6_weeks]

description:
Library name: lymph_node_hto
HTO library: read1 contains cell barcode and UMI; read2 contains Hashtag Antibody Derived Tag reads

source_name: lymph node

value: lymph node

value: HTO


title: T-cells, tumor, GEX [mm10_tcr_2_4_6_weeks]

description:
Library name: tumor_mRNA
5' mRNA: read1 contains cell barcode and UMI; read2 contains transcript sequence

data_processing:
Multiome files we demultiplexed using cellranger mkfastq
Demultiplexed data was processed using the cellranger multi pipeline
Assembly: mm10
Supplementary files format and content: Cellranger output files:gut_filtered_feature_bc_matrix.h5, LN_filtered_feature_bc_matrix.h5, tumor_filtered_feature_bc_matrix.h5, gut_airr_rearrangement.tsv, LN_airr_rearrangement.tsv, tumor_airr_rearrangement.tsv

value: mRNA


title: mIGG_CONTROL_Embryo2

description:
Library name: mIGG_CONTROL_Embryo2
2x150bp reads
22L004904_five_2n-read.cntTable.txt
22L004904_local.cntTable.txt


title: mAID-SPT5 , KY4793 , IAA , Spt6 , Rep2

description:
Library name: mAID_SPT5_KY4793_IAA_Spt6_Rep2
MATa his3∆200::OsTIR-F74G-HIS3 lys2-128δ leu2∆1 ura3-52 3xHSV-PAF1 1xminiAID-SPT5

value: 45 min


title: T-cells, lymph node, GEX [mm10_tcr_2_4_6_weeks]

description:
Library name: lymph_node_mRNA
5' mRNA: read1 contains cell barcode and UMI; read2 contains transcript sequence


title: Tbp_LOF_Embryo2

description:
Library name: Tbp_LOF_Embryo2
2x150bp reads
22L004902_five_2n-read.cntTable.txt
22L004902_local.cntTable.txt


title: mAID-SPT5 , KY4793 , DMSO , Spt6 , Rep2

description:
Library name: mAID_SPT5_KY4793_DMSO_Spt6_Rep2
MATa his3∆200::OsTIR-F74G-HIS3 lys2-128δ leu2∆1 ura3-52 3xHSV-PAF1 1xminiAID-SPT5


title: mIGG_CONTROL_Embryo1

description:
Library name: mIGG_CONTROL_Embryo1
2x150bp reads
22L004903_five_2n-read.cntTable.txt
22L004903_local.cntTable.txt


title: T-cells, gut, HTO [mm10_tcr_2_4_6_weeks]

description:
Library name: gut_hto
HTO library: read1 contains cell barcode and UMI; read2 contains Hashtag Antibody Derived Tag reads

source_name: cecum

value: cecum


title: spt5delCTR , KY4894 , Spt6 , Rep1

description:
Library name: spt5_delCTR_KY4894_Spt6_Rep1
MATalpha lys2-128δ leu2∆1 ura3-52 3xHSV-PAF1 spt5∆CTR::NatMX


title: Tbp_LOF_Embryo1

description:
Library name: Tbp_LOF_Embryo1
2x150bp reads
22L004901_five_2n-read.cntTable.txt
22L004901_local.cntTable.txt


title: 5726-TVA-B

description:
Library name: Sample 3
10x Genomics


title: T-cells, gut, GEX [mm10_tcr_2_4_6_weeks]

description:
Library name: gut_mRNA
5' mRNA: read1 contains cell barcode and UMI; read2 contains transcript sequence


title: spt5-S1-15A , KY4912 , Spt6 , Rep1

description:
Library name: spt5_S1_15A_KY4912_Spt6_Rep1
MATa lys2-128δ leu2∆1 ura3-52 3xHSV-PAF1 spt5-S1-15A


title: T-cells, lymph node, TCR [mm10_tcr_2_4_6_weeks]

description:
Library name: lymph_node_tcr
VDJ library: read1 contains cell barcode and UMI; read2 contains the VDJ reads

data_processing:
Multiome files we demultiplexed using cellranger mkfastq
Demultiplexed data was processed using the cellranger multi pipeline
Assembly: mm10
Supplementary files format and content: Cellranger output files:gut_filtered_feature_bc_matrix.h5, LN_filtered_feature_bc_matrix.h5, tumor_filtered_feature_bc_matrix.h5, gut_airr_rearrangement.tsv, LN_airr_rearrangement.tsv, tumor_airr_rearrangement.tsv
Library strategy: TCR-seq

value: VDJ


title: Multiome, T-cells, tumor, ATAC

description:
Library name: tumor_ATAC
ATAC: read1 contains cell barcode and UMI; read2 contains ATAC sequences

library_source: genomic single cell

data_processing:
Multiome files we demultiplexed using cellranger-arc-2.0.0 mkfastq
Demultiplexed data was processed using the cellranger-arc count pipeline
Assembly: mm10
Supplementary files format and content: Cellranger output files: tumor_filtered_feature_bc_matrix.h5, gut_filtered_feature_bc_matrix.h5, atac_fragments_gut.tsv.gz, atac_fragments_gut.tsv.gz

extract_protocol:
Immediately following sorting, cells were washed and nuclei were isolated by lysing cell membranes. Nuclei were then used for 10X multi-ome for sc ATAC and sc nuclear RNA following manufacturer protocols.
Libaries construction for both scATAC and snRNA followed manufacturer protocols (10X genomics) for single cell Multi-omic protocols.

value: ATAC


title: DRG_VEH

city: Baltimore

first: Aaron

last: James

state: Maryland

address: 720 Rutland Avenue, Ross Bldg., Room 529

department: Pathology

institute: Johns Hopkins University

description: 10x Genomics

data_processing:
Data were processed using the 10x Genomics Cell Ranger pipeline at default settings
Assembly: mm10-2020-A
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Dorsal Root Ganglia

growth_protocol: Mice were kept under a 12-h light/dark cycle with food and water provided ad libitum. All procedures involving mice were approved by the Institutional Animal Care and Use Committee of The Johns Hopkins University.

extract_protocol:
7 d post injury, lumbar L1-L5 DRG was collected from the injected side. DRG were minced and digested with 25U/mL Papain. Then subjected to three sequential enzymatic digestions with a mixture containing 1 mg/mL collagenase type I (1 mg/ml; Worthington Biochemical Corporation, Lakewood, NJ, USA, LS004197), 1.2 mg/mL dispase II (Sigma, T8003).  The distal femur epiphysis including the surrounding tissue of injured growth plate was carefully dissected and subjected to five sequential enzymatic digestions with collagenase type I/II (1 mg/ml), with each digestion for 10 mins. Then cell fractions (from sequential digestions 1 to 5) were collected and subsequently filtered through 40-μm sterile strainers
for all samples, 10x Genomics Chromium standard protocol

treatment_protocol: intraperitoneal (IP) injections of 1NMPP1 were performed 48 h before, 2 h before surgery using a 5 mM solution at a dosage of 17 ug/g body weight. In all cases, DMSO containing vehicle was used for control treatment. Animals were thereafter maintained on 1NMPP1 containing drinking water (40 uM 1NMPP1 in ddH2O with 1% PBS-Tween 20)

value: Dorsal Root Ganglia

value: Dorsal Root Ganglia cells

value: VEH


title: DRG_1NMPP1

description: 10x Genomics


title: Multiome, T-cells, gut, ATAC

description:
Library name: gut_ATAC
ATAC: read1 contains cell barcode and UMI; read2 contains ATAC sequences


title: GP_1NMPP1

description: 10x Genomics

source_name: Growth Plate

value: Growth Plate

value: Growth Plate cells


title: T-cells, tumor, ADT [mm10_tcr_2_4_6_weeks]

description:
Library name: tumor_adt
VDJ library: read1 contains cell barcode and UMI; read2 contains the VDJ reads


title: nonT-cells, tumor, HTO

description:
Library name: tumor_nonT_hto
HTO library: read1 contains cell barcode and UMI; read2 contains Hashtag Antibody Derived Tag reads

data_processing:
Multiome files we demultiplexed using cellranger mkfastq
Demultiplexed data was processed using the cellranger multi pipeline
Assembly: mm10
Supplementary files format and content: Cellranger output files:cecum_T_filtered_feature_bc_matrix.h5, tumor_T_filtered_feature_bc_matrix.h5, cecum_nonT_filtered_feature_bc_matrix.h5, tumor_nonT_filtered_feature_bc_matrix.h5, cecum_T_airr_rearrangement.tsv, tumor_T_airr_rearrangement.tsv
Library strategy: CITE-seq

value: nonT immune cell


title: nonT-cells, tumor, GEX

description:
Library name: tumor_nonT_mRNA
5' mRNA: read1 contains cell barcode and UMI; read2 contains transcript sequence

data_processing:
Multiome files we demultiplexed using cellranger mkfastq
Demultiplexed data was processed using the cellranger multi pipeline
Assembly: mm10
Supplementary files format and content: Cellranger output files:cecum_T_filtered_feature_bc_matrix.h5, tumor_T_filtered_feature_bc_matrix.h5, cecum_nonT_filtered_feature_bc_matrix.h5, tumor_nonT_filtered_feature_bc_matrix.h5, cecum_T_airr_rearrangement.tsv, tumor_T_airr_rearrangement.tsv


title: spt5-S1-15D , KY3594 , Spt6 , Rep1

description:
Library name: spt5_S1_15D_KY3594_Spt6_Rep1
MATa lys2-128δ leu2Δ1 ura3-52 3xHSV-PAF1 spt5-S1-15D

data_processing:
Reads were aligned to the hydrid genome of S. cerevisiae and the corresponding spike-in (either S. pombe or K. lactis) with bowtie2 version 2.4.5.
Mapped reads were filtered with Sambamba view and Samtools markdup to remove multi-mapped reads and PCR duplicates, respectively.
The filtered hybrid alignment was split into separate S. cerevisiae and spike-in files. Normalization factors were calculated using S. cerevisiae and spike-in read counts in the input and IP.
Spike-in normalization was applied and bigWig files were generated using bamCoverage.
Assembly: S. cerevisiae SacCer3
Assembly: K. lactis ASM251v1
Assembly: S. pombe ASM294v2
Supplementary files format and content: bigWig, spike-in normalized ChIP-seq signal


title: spt5del5 , KY4798 , Spt6 , Rep1

description:
Library name: spt5_del5_KY4798_Spt6_Rep1
MATa lys2-128δ leu2∆1 ura3-52 3xHSV-PAF1 spt5∆5::NatMX


title: mAID-SPT5 , KY4793 , IAA , Spt6 , Rep1

description:
Library name: mAID_SPT5_KY4793_IAA_Spt6_Rep1
MATa his3∆200::OsTIR-F74G-HIS3 lys2-128δ leu2∆1 ura3-52 3xHSV-PAF1 1xminiAID-SPT5


title: GP_VEH

description: 10x Genomics


title: nonT-cells, gut, GEX

description:
Library name: cecum_nonT_mRNA
5' mRNA: read1 contains cell barcode and UMI; read2 contains transcript sequence


title: T-cells, tumor, HTO

description:
Library name: tumor_T_hto
HTO library: read1 contains cell barcode and UMI; read2 contains Hashtag Antibody Derived Tag reads


title: T-cells, gut, TCR [mm10_tcr_2_4_6_weeks]

description:
Library name: gut_tcr
VDJ library: read1 contains cell barcode and UMI; read2 contains the VDJ reads


title: T-cells, tumor, TCR

description:
Library name: tumor_T_tcr
VDJ library: read1 contains cell barcode and UMI; read2 contains the VDJ reads

data_processing:
Multiome files we demultiplexed using cellranger mkfastq
Demultiplexed data was processed using the cellranger multi pipeline
Assembly: mm10
Supplementary files format and content: Cellranger output files:cecum_T_filtered_feature_bc_matrix.h5, tumor_T_filtered_feature_bc_matrix.h5, cecum_nonT_filtered_feature_bc_matrix.h5, tumor_nonT_filtered_feature_bc_matrix.h5, cecum_T_airr_rearrangement.tsv, tumor_T_airr_rearrangement.tsv
Library strategy: TCR-seq


title: 1-month Terc

city: Shanghai

first: Junjie

last: Gao

address: 600 Yishan Road

country: China

institute: Shanghai Sixth People’s Hospital Affiliated to Shanghai Jiao Tong University School of Medicine

data_processing:
Basecalls performed using CASAVA version 1.8
Cellranger was utilized to calculate the raw counts and cell whitelist by default parameter
1. We applied the Seurat [https://satijalab.org/seurat/] package for cell normalization and cell filtering considering the MT percentage, minimum and maximum gene numbers under following criteria:   MT% < 20%;    Cell Gene Number < Median Gene Number * 2;   Cell Gene Number > 200.  PCA and tSNE analysis was used for the single cell to cell relation description. The fastMNN function  (k = 5, d = 50, approximate = TRUE, auto.order = TRUE) from R package scran (v1.10.2) was used to apply mutual nearest neighbor method to correct for batch effect among samples.  Graphcluster was utilized for cell clustering and based on the marker gene achieved some cluster was combined. Wilcox rank sum test was then used for marker gene analysis.
Assembly: mm10
Supplementary files format and content: MTX file and TSV file contain counts for each barcodes and genes

source_name: Bone marrow

extract_protocol:
Bone marrow was flushed and kept in MACS Tissue Storage Solution (Miltenyi Biotec). Samples were sieved through 40µm cell strainers, and centrifuged at 300 g for 5 min. Pelleted cells were suspended in red blood cell lysis buffer (Miltenyi Biotec) for lysing red blood cells.Brain tissues were surgically removed and minced into small pieces (approximately 1mm3) on ice and digested by 200 U/mL Papine (Diamond) and Cysteine-HCL (Sigma). Then samples were sieved through 70 µm cell strainers, centrifuged at 300 g for 10 min, and further cleaned for red blood cells using red blood cell lysis buffer (Miltenyi Biotec).
RNA libraries were generated by 10xGenomics Single Cell 3’ Library Gel Bead Kit V3 and prepared for sequencing using standard Illumina protocols

value: Bone marrow

value: Terc knock-out


title: mAID-SPT5 , KY4793 , DMSO , Spt6 , Rep1

description:
Library name: mAID_SPT5_KY4793_DMSO_Spt6_Rep1
MATa his3∆200::OsTIR-F74G-HIS3 lys2-128δ leu2∆1 ura3-52 3xHSV-PAF1 1xminiAID-SPT5

value: DMSO


title: nonT-cells, gut, HTO

description:
Library name: cecum_nonT_hto
HTO library: read1 contains cell barcode and UMI; read2 contains Hashtag Antibody Derived Tag reads


title: Multiome, T-cells, tumor, GEX

description:
Library name: tumor_RNA
3' mRNA: read1 contains cell barcode and UMI; read2 contains transcript sequence

value: tumor

value: T-cell


title: proximal small intestine scraping 69

city: Wageningen

first: Evert

last: van Schothorst

address: De Elst 1

country: Netherlands

institute: Wageningen University

data_processing:
fastq files were generated and cleaned by BGI
FASTQC was perforemd to ensure quality of the reads
alignment was perforemed using STAR and counts were obtained using Htseq
Assembly: Mus_musculus.GRCm39.108
Supplementary files format and content: Raw counts using HTSeq / .txt
Supplementary files format and content: .txt

source_name: proximal small intestine scraping

growth_protocol: Weaned 21-days-old mice were stratified by body weight and divided into the three isocaloric dietary groups. The galactose group received a diet containing 16 en% in galactose + 16 en% in glucose, the glucose group was fed with a diet containing 32 en% in glucose, the lactose group was fed  a diet containing 32 en% in lactose. The three diets were otherwise identical. The mice were fed for 3 weeks with the intervention diets and sacrificed on day PN42 in the fed state. The RNA used for the analysis was obtained from the scraping of the proximal part of the small intestine; the full small intestines (from pylorus till ileal-ceacal valve) was divided into two equal lenghts and the proximal 2cm of duodenum was cut off. The remaider of the proximal part was used for scrapings. Intestines were cut open, washed, and subsequently scraped to collect mainly the enterocytic intestinal cells. Collected tissue was snap frozen in liquid nitrogen and stored at -80°C until further analysis.

extract_protocol:
Total RNA was isolated with RNeasy columns (Qiagen, Venlo, TheNetherlands). RNA integrity was checked on an Agilent 2200 Tapestation according to the manufacturer's instructions (Agilent Technologies Inc., Santa Clara, CA, USA), and all samples passed the thresholds.
RNA preparation, library construction and sequencing on DNBSEQ platform was performed at Beijing Genomics Institute.

value: proximal small intestine scraping

tag: age

value: 42 days

tag: Sex

value: female

value: lactose


title: spt5delCTR , KY4894 , Spt5 , Rep2

description:
Library name: spt5_delCTR_KY4894_Spt5_Rep2
MATalpha lys2-128δ leu2∆1 ura3-52 3xHSV-PAF1 spt5∆CTR::NatMX


title: proximal small intestine scraping 68

value: glucose


title: T-cells, gut, HTO

description:
Library name: cecum_T_hto
HTO library: read1 contains cell barcode and UMI; read2 contains Hashtag Antibody Derived Tag reads

value: cecum

value: HTO


title: WT , KY4803 , Spt6 , Rep1

description:
Library name: WT_KY4803_Spt6_Rep1
MATa lys2-128δ leu2∆1 ura3-52 3xHSV-PAF1


title: Multiome, T-cells, gut, GEX

description:
Library name: gut_RNA
3' mRNA: read1 contains cell barcode and UMI; read2 contains transcript sequence

value: mRNA


title: T-cells, gut, TCR

description:
Library name: cecum_T_tcr
VDJ library: read1 contains cell barcode and UMI; read2 contains the VDJ reads

value: VDJ


title: ATAC_Morula_rep2

description: Library name: ATAC Sample 8

data_processing:
Low quality reads were trimmed out using TrimGalore (version 0.6.2) (https://github.com/FelixKrueger/TrimGalore) using parameters: --paired --quality 20 --length 20.
Read mapping to mm10 genome was done using Bowtie2 (version 2.3.5.1) using parameters: -t -q -N 1 -L 25 -X 2000 --no-mixed --no-discordant.
Unmapped reads and reads with low mapping quality (Q<30) were removed. PCR duplicated reads were identified and discarded using the MarkDuplicates command from Picard (version 2.18.27) (http://broadinstitute.github.io/picard/) with parameters: VALIDATION_STRINGENCY=LENIENT.
The bigwig files were generated using bamCoverage command from deepTools (version 3.5.4) using parameters: --normalizeUsing RPKM --binSize 1 --ignoreForNormalization chrM. Peak calling for CUT&Tag, ATAC-seq, and ChIP-seq datasets were done using MACS2’s callpeak function (version 2.2.9) with default parameters.
Assembly: mm10
Supplementary files format and content: bigWig

source_name: preimplantation embryo

extract_protocol:
Omni ATAC-seq was performed as described previously (Corces, M., Trevino, A., Hamilton, E. et al. An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues. Nat Methods 14, 959–962 (2017)). Zona pellucida was removed by treatment with acidic Tyrode. Embryos were transferred into 1.5 ml of DNA LoBind Tube (Eppendorf) with 200 μl of PBS and were spun at 500×g at 4°C for 5 min to remove supernatant. 50 μl of ATAC-Resuspension buffer (RSB) (10 mM Tris-HCl (pH 7.4), 10 mM NaCl, 3 mM MgCl2) containing 0.1% NP-40, 0.1% Tween-20 and 0.01% Digitonin was added into tube and incubated for 3 min on ice. After incubation, 200 μl of ATAC-RSB containing 0.1% Tween-20 was further added into the tube to wash out lysis. Nuclei were spun at 500×g at 4°C for 10 min to remove supernatant. Nuclei were incubated with 50 μl of transposition mixture (10 mM Tris-HCl (pH 7.6), 5 mM MgCl2, 10% Dimethyl formamide, 33% PBS, 0.1 % Tween-20, 0.01% Digitonin and 95 nM Tn5-adaptor complex) at 37°C for 30 min with 1000 rpm mixing. The samples were then deproteinized and further purified by phenol-chloroform and followed by ethanol precipitation. The DNA was amplified 50 µl of reaction with 1×NEBNext HF 2×PCR Master mix (NEB) and 0.25 µM barcoded primers using the following PCR program: 72 °C for 5 min; 98°C for 30 sec; 15 cycles of 98°C for 10 sec, 63°C for 30 sec and 72 °C for 1 min; final extension at 72 °C for 5 min and hold at 4°C. After PCR reaction, libraries were purified by 1.1×AMPure XP magnetic beads (Beckman Coulter) and were eluted in 20 μl of RNase-free water.
Purified DNA libraries were sequenced on a NextSeq 500 (Illumina), Novaseq 6000 (Illumina), or AVITI (Element Biosciences) with paired-end reads.

value: preimplantation embryo

value: Morula


title: WT , KY4803 , Spt5 , Rep2

description:
Library name: WT_KY4803_Spt5_Rep2
MATa lys2-128δ leu2∆1 ura3-52 3xHSV-PAF1


title: proximal small intestine scraping 67

value: galactose


title: T-cells, gut, GEX

description:
Library name: cecum_T_mRNA
5' mRNA: read1 contains cell barcode and UMI; read2 contains transcript sequence


title: ATAC_8C_rep2

description: Library name: ATAC Sample 6

value: 8-cell embryo


title: proximal small intestine scraping 65


title: proximal small intestine scraping 66


title: spt5-S1-15A , KY4912 , Spt5 , Rep2

description:
Library name: spt5_S1_15A_KY4912_Spt5_Rep2
MATa lys2-128δ leu2∆1 ura3-52 3xHSV-PAF1 spt5-S1-15A


title: ATAC_8C_rep1

description: Library name: ATAC Sample 5


title: rIGG_CONTROL_Batch1_Embryo3

description:
Library name: rIGG_CONTROL_Batch1_Embryo3
2x150bp reads
22L004929_five_2n-read.cntTable.txt

data_processing:
A custom Python Script was used to sort between 5' transcript ends and internal fragment according to their adaptor sequence
Reads were mapped to GRCm38 with STAR (V2.7.11a)
BAM files were modified to keep only the Read2 (in case of 5' analysis) using custom Perl script
TE and genes were quantified using TEcount from TE transcript
Single TE insertion for TBP LOF and CONTROL were quantified using TElocal from TEtranscript
Assembly: GRCm38
Supplementary files format and content: Count table from TECount using the second read of the 5' fragments ("five_2n")
Supplementary files format and content: Count table from TELocal ("local") (only for TBP LOF and CONTROL)

value: Late 2-cell embryo

value: rabbit IGG AB injected


title: ATAC_4C_rep1

description: Library name: ATAC Sample 3

value: 4-cell embryo


title: ATAC_4C_rep2

description: Library name: ATAC Sample 4


title: T-cells, tumor, GEX

description:
Library name: tumor_T_mRNA
5' mRNA: read1 contains cell barcode and UMI; read2 contains transcript sequence

value: tumor

value: T-cell


title: spt5-S1-15D , KY3594 , Spt5 , Rep2

description:
Library name: spt5_S1_15D_KY3594_Spt5_Rep2
MATa lys2-128δ leu2Δ1 ura3-52 3xHSV-PAF1 spt5-S1-15D


title: proximal small intestine scraping 64

value: proximal small intestine scraping

value: 42 days


title: ATAC_2C_rep2

description: Library name: ATAC Sample 2

value: 2-cell embryo


title: mAID-SPT5 , KY4793 , IAA , Spt5 , Rep2

description:
Library name: mAID_SPT5_KY4793_IAA_Spt5_Rep2
MATa his3∆200::OsTIR-F74G-HIS3 lys2-128δ leu2∆1 ura3-52 3xHSV-PAF1 1xminiAID-SPT5

value: 45 min


title: H3K27ac_morula_rep2

description: Library name: CUT and Tag Sample 25

data_processing:
Low quality reads were trimmed out using TrimGalore (version 0.6.2) (https://github.com/FelixKrueger/TrimGalore) using parameters: --paired --quality 20 --length 20.
Read mapping to mm10 genome was done using Bowtie2 (version 2.3.5.1) using parameters: -t -q -N 1 -L 25 -X 2000 --no-mixed --no-discordant.
Unmapped reads and reads with low mapping quality (Q<30) were removed. PCR duplicated reads were identified and discarded using the MarkDuplicates command from Picard (version 2.18.27) (http://broadinstitute.github.io/picard/) with parameters: VALIDATION_STRINGENCY=LENIENT.
The bigwig files were generated using bamCoverage command from deepTools (version 3.5.4) using parameters: --normalizeUsing RPKM --binSize 1 --ignoreForNormalization chrM. Peak calling for CUT&Tag, ATAC-seq, and ChIP-seq datasets were done using MACS2’s callpeak function (version 2.2.9) with default parameters.
Assembly: mm10
Supplementary files format and content: bigWig
Library strategy: CUT&Tag

value: Active motif, 39133


title: proximal small intestine scraping 63

value: female

value: lactose


title: H3K27ac_morula_rep1

description: Library name: CUT and Tag Sample 24


title: mAID-SPT5 , KY4793 , DMSO , Spt5 , Rep2

description:
Library name: mAID_SPT5_KY4793_DMSO_Spt5_Rep2
MATa his3∆200::OsTIR-F74G-HIS3 lys2-128δ leu2∆1 ura3-52 3xHSV-PAF1 1xminiAID-SPT5

value: DMSO


title: proximal small intestine scraping 62


title: spt5delCTR , KY4894 , Spt5 , Rep1

description:
Library name: spt5_delCTR_KY4894_Spt5_Rep1
MATalpha lys2-128δ leu2∆1 ura3-52 3xHSV-PAF1 spt5∆CTR::NatMX


title: H3K27ac_8C_rep2

description: Library name: CUT and Tag Sample 23

value: preimplantation embryo


title: ATAC_2C_rep1

description: Library name: ATAC Sample 1


title: proximal small intestine scraping 61

value: glucose


title: spt5-S1-15A , KY4912 , Spt5 , Rep1

description:
Library name: spt5_S1_15A_KY4912_Spt5_Rep1
MATa lys2-128δ leu2∆1 ura3-52 3xHSV-PAF1 spt5-S1-15A


title: H3K27ac_8C_rep1

description: Library name: CUT and Tag Sample 22


title: H3K27ac_4C_rep1

description: Library name: CUT and Tag Sample 20


title: H3K27ac_4C_rep2

description: Library name: CUT and Tag Sample 21


title: proximal small intestine scraping 60


title: spt5del5 , KY4798 , Spt5 , Rep2

description:
Library name: spt5_del5_KY4798_Spt5_Rep2
MATa lys2-128δ leu2∆1 ura3-52 3xHSV-PAF1 spt5∆5::NatMX


title: H3K27ac_2C_rep2

description: Library name: CUT and Tag Sample 19


title: proximal small intestine scraping 59


title: H3K27ac_2C_rep1

description: Library name: CUT and Tag Sample 18


title: WT , KY4803 , Spt5 , Rep1

description:
Library name: WT_KY4803_Spt5_Rep1
MATa lys2-128δ leu2∆1 ura3-52 3xHSV-PAF1


title: Klf5_8C_rep1

description: Library name: CUT and Tag Sample 9

value: Proteintech, 21017-1-AP


title: ATAC_Morula_rep1

description: Library name: ATAC Sample 7

value: Morula


title: spt5del5 , KY4798 , Spt5 , Rep1

description:
Library name: spt5_del5_KY4798_Spt5_Rep1
MATa lys2-128δ leu2∆1 ura3-52 3xHSV-PAF1 spt5∆5::NatMX


title: proximal small intestine scraping 58

value: galactose


title: Col1a1 GFP+ Cardiac Fibroblasts 6 days after MI Replicate 3

city: Pamplona

first: Núria

last: Planell

address: Pio XII, 55

country: Spain

institute: CIMA - UNAV

data_processing:
Samples were demultiplexed using Illumina bcl2fastq software (1.2.4) and aligned with the mouse (mm10). Quantification and generation of gene expression matrices were performed with the function featureCounts, implemented in the R package Rsubread.
Additional filtering, data transformation, normalization, and testing for differential expression was performed with DESeq2.
Assembly: mm10
Supplementary files format and content: Files with raw counts after gene level quantification.

source_name: Heart

growth_protocol: Primary cells isolates from reporter mice

extract_protocol:
Mouse cardiac interstitial cells (CIC) from infarcted (1 to 6 days post-infarction) 8-10 week old mice heart were obtained by enzymatic digestion. Erythrocytes were removed using RBC lysis buffer. A positive selection of CIC, enriched in Cardiac fibroblasts, was performed using LS columns and Feeder Removal MicroBeads (Miltenyi) according to the manufacturer’s instructions. For Col1a1-GFP+ reporter mouse, GFP+/CD31-/CD45- cardiac fibroblasts (CF) were FACS-sorted in 1X PBS, 0.05% BSA.
Bulk RNA-seq was performed following a massively parallel RNA single-cell sequencing (MARS-seq) protocol adapted for bulk RNA-seqwith minor modifications. Briefly, poly-A RNA was extracted with Dynabeads Oligo (dT) (Ambion) and reverse-transcribed with AffinityScript Multiple Temperature Reverse Transcriptase (RT) (Agilent) using poly-dT oligo primers (IDT) carrying a 7 bp index. Samples were subjected to linear amplification via IVT using the HiScribe T7 High Yield RNA Synthesis Kit from New England Biolabs (NEB). The resulting antisense RNA was fragmented into 250-350 bps fragments with RNA Fragmentation Reagents (Ambion) and dephosphorylated with 1U FastAP (Thermo Scientific) for 15 min at 37 °C. Partial Illumina adaptor sequences were ligated with T4 RNA Ligase 1 (NEB) followed by a second reverse transcription. Full Illumina adaptor sequences were added during library amplification with KAPA HiFi DNA Polymerase (Kapa Biosystems). Libraries were quantified using a Qubit 3.0 Fluorometer and their size profiles examined in Agilent's 4200 TapeStation System. Sequencing was carried out in an Illumina NextSeq 500 using paired-end, dual-index sequencing (Read1: 68 cycles; Read2: 15 cycles; i7 index: 8 cycles) at a depth of 10 million reads per sample.

value: Heart

value: Col1a1-GFP+ cells

value: myocardial infarction


title: Col1a1 GFP+ Cardiac Fibroblasts 6 days after MI Replicate 1


title: spt5-S1-15D , KY3594 , Spt5 , Rep1

description:
Library name: spt5_S1_15D_KY3594_Spt5_Rep1
MATa lys2-128δ leu2Δ1 ura3-52 3xHSV-PAF1 spt5-S1-15D


title: Col1a1 GFP+ Cardiac Fibroblasts 5 days after MI Replicate 3


title: Col1a1 GFP+ Cardiac Fibroblasts 4 days after MI Replicate 3


title: Col1a1 GFP+ Cardiac Fibroblasts 6 days after MI Replicate 2


title: proximal small intestine scraping 56


title: proximal small intestine scraping 57


title: Col1a1 GFP+ Cardiac Fibroblasts 4 days after MI Replicate 2


title: Col1a1 GFP+ Cardiac Fibroblasts 4 days after MI Replicate 1


title: mAID-SPT5 , KY4793 , DMSO , Spt5 , Rep1

description:
Library name: mAID_SPT5_KY4793_DMSO_Spt5_Rep1
MATa his3∆200::OsTIR-F74G-HIS3 lys2-128δ leu2∆1 ura3-52 3xHSV-PAF1 1xminiAID-SPT5


title: Col1a1 GFP+ Cardiac Fibroblasts 2 days after MI Replicate 3


title: proximal small intestine scraping 55


title: spt5delCTR , KY4894 , Input_Kl , Rep2

description:
Library name: spt5_delCTR_KY4894_Input_Kl_Rep2
MATalpha lys2-128δ leu2∆1 ura3-52 3xHSV-PAF1 spt5∆CTR::NatMX


title: Col1a1 GFP+ Cardiac Fibroblasts 2 days after MI Replicate 2


title: proximal small intestine scraping 54


title: proximal small intestine scraping 53


title: Col1a1 GFP+ Cardiac Fibroblasts 1 days after MI Replicate 2


title: Col1a1 GFP+ Cardiac Fibroblasts 1 days after MI Replicate 1


title: Col1a1 GFP+ Cardiac Fibroblasts 3 days after MI Replicate 4


title: WT , KY4803 , Input_Kl , Rep2

description:
Library name: WT_KY4803_Input_Kl_Rep2
MATa lys2-128δ leu2∆1 ura3-52 3xHSV-PAF1


title: proximal small intestine scraping 52


title: Col1a1 GFP+ Cardiac Fibroblasts 2 days after MI Replicate 1


title: spt5del5 , KY4798 , Input_Kl , Rep2

description:
Library name: spt5_del5_KY4798_Input_Kl_Rep2
MATa lys2-128δ leu2∆1 ura3-52 3xHSV-PAF1 spt5∆5::NatMX


title: Col1a1 GFP+ Cardiac Fibroblasts 3 days after MI Replicate 3


title: proximal small intestine scraping 51


title: Col1a1 GFP+ Cardiac Fibroblasts 3 days after MI Replicate 2


title: mAID-SPT5 , KY4793 , IAA , Spt5 , Rep1

description:
Library name: mAID_SPT5_KY4793_IAA_Spt5_Rep1
MATa his3∆200::OsTIR-F74G-HIS3 lys2-128δ leu2∆1 ura3-52 3xHSV-PAF1 1xminiAID-SPT5


title: spt5-S1-15D , KY3594 , Input_Kl , Rep2

description:
Library name: spt5_S1_15D_KY3594_Input_Kl_Rep2
MATa lys2-128δ leu2Δ1 ura3-52 3xHSV-PAF1 spt5-S1-15D


title: Col1a1 GFP+ Cardiac Fibroblasts 3 days after MI Replicate 1


title: proximal small intestine scraping 50


title: lung immune cells, day 2 naphthalene 3

city: Boston

first: Irene

middle: Gar-Ling

last: Wong

address: 1 Blackfan St.

institute: Boston Children's Hospital

data_processing:
10X Genomics Cell Ranger 3.1.0 Pipeline was used to perform sample demultiplexing, barcode processing, and single cell 3’ gene counting.
Assembly: mm10-1.2.0
Supplementary files format and content: h5 files for each library

source_name: lung

extract_protocol:
Bronchoalveolar lavage fluid (BAL) and lungs were extracted from mice at 2 or 7 days after injection. BAL fluid was set aside while lungs were dissociated into single-cell suspension and immune cells enriched via FACS. BAL cells were then combined at a 1:1 ratio with the sorted immune cells.
10X Genomics 3' Single Cell RNA Sequencing Protocol Version 3.1
3' Single Cell RNA Sequencing

treatment_protocol: Adult mice were given intraperitoneal injections of 200 mg/kg naphthalene in corn oil or corn oil control (of equal volume).

value: lung

value: Immune

value: Wildtype

value: 200 mg/kg naphthalene

tag: timepoint

value: Day 2


title: mAID-SPT5 , KY4793 , IAA , Input_Kl , Rep2

description:
Library name: mAID_SPT5_KY4793_IAA_Input_Kl_Rep2
MATa his3∆200::OsTIR-F74G-HIS3 lys2-128δ leu2∆1 ura3-52 3xHSV-PAF1 1xminiAID-SPT5

extract_protocol:
Cells were fixed with 1% formaldehyde for 20 minutes. After quenching and cell lysis, chromatin was sheared using a Bioruptor® (Diagenode B01060010) for 25 cycles with 30 seconds on and 30 seconds off.
ChIP-seq libraries were prepared with the NEB Next II Ultra DNA library kit (NEB, E7645S/L) and multiplex oligos (NEB, E6440S/L) using 0.5-1 ng of DNA input and following manufacturer's protocols. Libraries were purified using AMPure XP beads (Beckman Coulter, A63881) and verified using fragment analyzer (Fragment Analyzer, Advanced Analytics).

value: 45 min


title: lung immune cells, day 2 naphthalene 2


title: lung immune cells, day 2 naphthalene 1


title: proximal small intestine scraping 49

value: proximal small intestine scraping

value: 42 days

value: female


title: lung immune cells, day 2 corn oil 1

value: Corn oil


title: proximal small intestine scraping 18

value: lactose


title: spt5delCTR , KY4894 , Input_Kl , Rep1

description:
Library name: spt5_delCTR_KY4894_Input_Kl_Rep1
MATalpha lys2-128δ leu2∆1 ura3-52 3xHSV-PAF1 spt5∆CTR::NatMX


title: lung immune cells, day 7 naphthalene 3

value: Day 7


title: spt5-S1-15A , KY4912 , Input_Kl , Rep2

description:
Library name: spt5_S1_15A_KY4912_Input_Kl_Rep2
MATa lys2-128δ leu2∆1 ura3-52 3xHSV-PAF1 spt5-S1-15A


title: proximal small intestine scraping 17

value: glucose


title: Col1a1 GFP+ Cardiac Fibroblasts 1 days after MI Replicate 3


title: spt5-S1-15A , KY4912 , Input_Kl , Rep1

description:
Library name: spt5_S1_15A_KY4912_Input_Kl_Rep1
MATa lys2-128δ leu2∆1 ura3-52 3xHSV-PAF1 spt5-S1-15A


title: lung immune cells, day 7 naphthalene 1


title: lung immune cells, day 7 corn oil 2


title: proximal small intestine scraping 16

value: galactose


title: WT , KY4803 , Input_Kl , Rep1

description:
Library name: WT_KY4803_Input_Kl_Rep1
MATa lys2-128δ leu2∆1 ura3-52 3xHSV-PAF1


title: spt5del5 , KY4798 , Input_Kl , Rep1

description:
Library name: spt5_del5_KY4798_Input_Kl_Rep1
MATa lys2-128δ leu2∆1 ura3-52 3xHSV-PAF1 spt5∆5::NatMX


title: Col1a1 GFP+ Cardiac Fibroblasts 3 days after MI

data_processing:
Demultiplexing, alignment to the mouse (mm10) genome and quantification was performed using 10X Genomics Cell Ranger (v2.0)
Further analysis steps (quality control filtering, normalization, clustering and differential expression) were performed using R package Seurat (v2.3.4)
Assembly: mm10
Supplementary files format and content: HDF5 Feature Barcode Matrix. Gene x Cells UMI count matrix

extract_protocol:
Mouse cardiac interstitial cells (CIC) from healthy or infarcted (7, 14 or 30 days post-infarction) 8-10 week old mice heart were obtained by enzymatic digestion. Erythrocytes were removed using RBC lysis buffer. A positive selection of CIC, enriched in Cardiac fibroblasts, was performed using LS columns and Feeder Removal MicroBeads (Miltenyi) according to the manufacturer’s instructions. For Col1a1-GFP+ reporter mouse, GFP+/CD31-/CD45- cardiac fibroblasts (CF) were FACS-sorted in 1X PBS, 0.05% BSA.
Single cell RNA-seq libraries were constructed using the Chromium System from 10X Genomics. Single Cell 3' Reagent Kits v2 were employed for all the samples

value: Heart


title: proximal small intestine scraping 15


title: CrGPDH_4

city: San Diego

first: Xingxiu

last: Pan

state: California

address: 6868 Nancy Ridge Dr

institute: Scintillon institute

description: Library name: Sample 8

data_processing:
Illumina HiSeq X reads were trimmed and clipped for quality control inTrimmomatic v.0.36.
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality.
Using the STAR aligner v.2.5.2b., the trimmed reads were mapped to the Homo sapiens GRCh38 reference genome available on ENSEMBL.
Unique gene hit counts were calculated by using feature Counts from the Subread package v.1.5.2.
Counts were then processed in R using the DESeq2 package
Assembly: GRCh38
Supplementary files format and content: unique hit counts for each sample: sample.counts.txt
Supplementary files format and content: hit count for all the gene

source_name: Uterus; Cervix

growth_protocol: Hela cells were cultured in DMEM+FBS [Dulbecco's Modified Eagle Medium without pyruvate and glucose supplemented with 25 mM glucose, 10% non-dialyzed FBS and 1% penicillin/streptomycin  at 37C in an atmosphere of 5% CO2

extract_protocol:
Twenty-four hours after addition of doxycycline, cells were harvested, and cell pellets were snapfrozen.Samples were submitted to GENEWIZ for NGS RNA sequencing.
RNA libraries for RNA-seq were prepared using polyA selection.

treatment_protocol: Twenty-four hours later, media was exchanged with 10 mL of DMEM+dFBS ± 300 ng/mL Dox.

value: Uterus; Cervix

value: HeLa

value: epithelial cell

value: CrGPDH

value: 24h doxycycline


title: proximal small intestine scraping 14


title: proximal small intestine scraping 13


title: mAID-SPT5 , KY4793 , DMSO , Input_Kl , Rep2

description:
Library name: mAID_SPT5_KY4793_DMSO_Input_Kl_Rep2
MATa his3∆200::OsTIR-F74G-HIS3 lys2-128δ leu2∆1 ura3-52 3xHSV-PAF1 1xminiAID-SPT5

value: DMSO


title: mAID-SPT5 , KY4793 , IAA , Input_Kl , Rep1

description:
Library name: mAID_SPT5_KY4793_IAA_Input_Kl_Rep1
MATa his3∆200::OsTIR-F74G-HIS3 lys2-128δ leu2∆1 ura3-52 3xHSV-PAF1 1xminiAID-SPT5


title: CrGPDH_1

description: Library name: Sample 5


title: LUC_3

description: Library name: Sample 3

value: Luciferase


title: LUC_2

description: Library name: Sample 2


title: mAID-SPT5 , KY4793 , DMSO , Input_Kl , Rep1

description:
Library name: mAID_SPT5_KY4793_DMSO_Input_Kl_Rep1
MATa his3∆200::OsTIR-F74G-HIS3 lys2-128δ leu2∆1 ura3-52 3xHSV-PAF1 1xminiAID-SPT5

value: 45 min


title: spt5delCTR , KY4894 , HSV , Rep2

description:
Library name: spt5_delCTR_KY4894_HSV_Rep2
MATalpha lys2-128δ leu2∆1 ura3-52 3xHSV-PAF1 spt5∆CTR::NatMX

value: HSV (Sigma-Aldrich, #H6030)


title: proximal small intestine scraping 11

value: proximal small intestine scraping

value: 42 days


title: LUC_1

description: Library name: Sample 1


title: lung immune cells, day 7 corn oil 1

value: lung

value: Immune

value: Wildtype

value: Corn oil


title: CrGPDH_3

description: Library name: Sample 7


title: proximal small intestine scraping 10

value: female

value: glucose


title: proximal small intestine scraping 9


title: Col1a1 GFP+ Cardiac Fibroblasts 5 days after MI

value: Heart

value: Col1a1-GFP+ cells

value: myocardial infarction


title: lung immune cells, day 7 naphthalene 2

value: 200 mg/kg naphthalene

value: Day 7


title: LUC_4

description: Library name: Sample 4

value: Uterus; Cervix

value: HeLa

value: epithelial cell

value: 24h doxycycline


title: spt5-S1-15D , KY3594 , Input_Kl , Rep1

description:
Library name: spt5_S1_15D_KY3594_Input_Kl_Rep1
MATa lys2-128δ leu2Δ1 ura3-52 3xHSV-PAF1 spt5-S1-15D


title: CrGPDH_2

description: Library name: Sample 6

value: CrGPDH


title: spt5-S1-15A , KY4912 , HSV , Rep2

description:
Library name: spt5_S1_15A_KY4912_HSV_Rep2
MATa lys2-128δ leu2∆1 ura3-52 3xHSV-PAF1 spt5-S1-15A

value: HSV (Sigma-Aldrich, #H6030)


title: WT , KY4803 , HSV , Rep2

description:
Library name: WT_KY4803_HSV_Rep2
MATa lys2-128δ leu2∆1 ura3-52 3xHSV-PAF1


title: proximal small intestine scraping 8

value: proximal small intestine scraping

value: 42 days

value: lactose


title: proximal small intestine scraping 12


title: proximal small intestine scraping 7

value: galactose


title: spt5del5 , KY4798 , HSV , Rep2

description:
Library name: spt5_del5_KY4798_HSV_Rep2
MATa lys2-128δ leu2∆1 ura3-52 3xHSV-PAF1 spt5∆5::NatMX


title: spt5-S1-15D , KY3594 , HSV , Rep2

description:
Library name: spt5_S1_15D_KY3594_HSV_Rep2
MATa lys2-128δ leu2Δ1 ura3-52 3xHSV-PAF1 spt5-S1-15D


title: proximal small intestine scraping 6

value: female


title: mAID-SPT5 , KY4793 , IAA , HSV , Rep2

description:
Library name: mAID_SPT5_KY4793_IAA_HSV_Rep2
MATa his3∆200::OsTIR-F74G-HIS3 lys2-128δ leu2∆1 ura3-52 3xHSV-PAF1 1xminiAID-SPT5

value: 45 min


title: WAT_O1

type: RNA

city: Kyoto

first: Masahiro

last: Kameda

state: Kyoto

address: Sakyoku Shougoin Kawaramati 54

department: Geriatric Unit

country: Japan

institute: Kyoto University Hospital

description: Gene expression

hyb_protocol: Following fragmentation, 1.65 ug of cRNA were hybridized to the Agilent expression microarray according to the protocols provided by the manufacturer

scan_protocol: Arrays were scanned using the Agilent Technologies G4900DA SG12494263

data_processing: Array data export processing and analysis was performed using Agilent Feature Extraction v11.0.1.1

label_protocol: labeled cRNA were prepared from 1~5 ug total RNA using the Agilent’s Quick Amp Labeling Kit

extract_protocol: Total RNA was prepared with an RNeasy kit

tag: gender

value: male

value: WAT


title: proximal small intestine scraping 5


title: WAT_Y1

description: Gene expression


title: mAID-SPT5 , KY4793 , DMSO , HSV , Rep2

description:
Library name: mAID_SPT5_KY4793_DMSO_HSV_Rep2
MATa his3∆200::OsTIR-F74G-HIS3 lys2-128δ leu2∆1 ura3-52 3xHSV-PAF1 1xminiAID-SPT5

value: DMSO


title: WAT_O3

description: Gene expression


title: WAT_O2

description: Gene expression


title: WAT_Y3

description: Gene expression


title: Kidney_O3

description: Gene expression

value: Kidney


title: spt5delCTR , KY4894 , HSV , Rep1

description:
Library name: spt5_delCTR_KY4894_HSV_Rep1
MATalpha lys2-128δ leu2∆1 ura3-52 3xHSV-PAF1 spt5∆CTR::NatMX


title: spt5-S1-15A , KY4912 , HSV , Rep1

description:
Library name: spt5_S1_15A_KY4912_HSV_Rep1
MATa lys2-128δ leu2∆1 ura3-52 3xHSV-PAF1 spt5-S1-15A


title: proximal small intestine scraping 4


title: Kidney_O1

description: Gene expression


title: WAT_Y2

description: Gene expression


title: Kidney_Y3

description: Gene expression


title: Kidney_O2

description: Gene expression


title: proximal small intestine scraping 2


title: proximal small intestine scraping 3


title: Kidney_Y1

description: Gene expression


title: proximal small intestine scraping 1

value: glucose


title: Kidney_Y2

description: Gene expression


title: spt5del5 , KY4798 , HSV , Rep1

description:
Library name: spt5_del5_KY4798_HSV_Rep1
MATa lys2-128δ leu2∆1 ura3-52 3xHSV-PAF1 spt5∆5::NatMX


title: Liver_Y2

description: Gene expression

value: Liver


title: Liver_O1

description: Gene expression


title: Liver_O4

description: Gene expression


title: WT , KY4803 , HSV , Rep1

description:
Library name: WT_KY4803_HSV_Rep1
MATa lys2-128δ leu2∆1 ura3-52 3xHSV-PAF1


title: Liver_O2

description: Gene expression


title: spt5-S1-15D , KY3594 , HSV , Rep1

description:
Library name: spt5_S1_15D_KY3594_HSV_Rep1
MATa lys2-128δ leu2Δ1 ura3-52 3xHSV-PAF1 spt5-S1-15D


title: Liver_Y3

description: Gene expression


title: Lung_O3

description: Gene expression

value: Lung


title: mAID-SPT5 , KY4793 , IAA , HSV , Rep1

description:
Library name: mAID_SPT5_KY4793_IAA_HSV_Rep1
MATa his3∆200::OsTIR-F74G-HIS3 lys2-128δ leu2∆1 ura3-52 3xHSV-PAF1 1xminiAID-SPT5


title: lambdaN tethered WAGO-3_rep2

city: Worcester

first: GANGMING

last: ZHANG

state: MA

address: 368 Plantation St, Asc5-2010

institute: RNA Therapeutics Institute, University of Massachusetts Chan Medical School

description: Library name: Sample 24

data_processing:
Sequencing adaptors were trimmed from FASTQ files using cutadapt 4.9.
Total reads with length longer than 16 nts were selected and mapped to the reporter or total reads with length between 21 nts and 23 nts were selected and mapped to the mRNA, pseudogenes and transposons with bowtie 1.3.1. Read counts were normalized to the total number of genome-mapped reads.
Assembly: WBcel235
Supplementary files format and content: merged counts.tsv

organism: Caenorhabditis elegans

source_name: lambdaN tethered strain

extract_protocol:
Worms were lysated and  small-RNAs were later extracted by Trizol.
Purified small-RNAs were pre-treated with PIR-1 and ligated with 3' and 5' linkers. cDNA were generated by reverse transcribed and further amplified by PCR. A size selection procedure on native PAGE were carried out.

value: lambdaN tethered strain

value: untreated

value: small RNAs

value: small-RNA seq


title: mAID-SPT5 , KY4793 , DMSO , HSV , Rep1

city: Pittsburgh

first: Karen

last: Arndt

address: 4249 Fifth Avenue

institute: University of Pittsburgh

description:
Library name: mAID_SPT5_KY4793_DMSO_HSV_Rep1
MATa his3∆200::OsTIR-F74G-HIS3 lys2-128δ leu2∆1 ura3-52 3xHSV-PAF1 1xminiAID-SPT5

value: HSV (Sigma-Aldrich, #H6030)


title: lambdaN tethered strain wild type_rep1

description: Library name: Sample 25


title: lambdaN tethered strain wild type_rep2

description: Library name: Sample 26


title: spt5delCTR , KY4894 , 8WG16 , Rep2

description:
Library name: spt5_delCTR_KY4894_8WG16_Rep2
MATalpha lys2-128δ leu2∆1 ura3-52 3xHSV-PAF1 spt5∆CTR::NatMX


title: lambdaN tethered WAGO-3_rep1

description: Library name: Sample 23


title: spt5-S1-15A , KY4912 , 8WG16 , Rep2

description:
Library name: spt5_S1_15A_KY4912_8WG16_Rep2
MATa lys2-128δ leu2∆1 ura3-52 3xHSV-PAF1 spt5-S1-15A


title: lambdaN tethered WAGO-1_rep2

description: Library name: Sample 22


title: Lung_O2

description: Gene expression


title: Lung_Y3

description: Gene expression


title: WT , KY4803 , 8WG16 , Rep2

description:
Library name: WT_KY4803_8WG16_Rep2
MATa lys2-128δ leu2∆1 ura3-52 3xHSV-PAF1


title: lambdaN tethered PRG-1_rep2

description: Library name: Sample 18


title: lambdaN tethered RDE-1_rep1

description: Library name: Sample 19


title: lambdaN tethered WAGO-1_rep1

description: Library name: Sample 21


title: spt5del5 , KY4798 , 8WG16 , Rep2

description:
Library name: spt5_del5_KY4798_8WG16_Rep2
MATa lys2-128δ leu2∆1 ura3-52 3xHSV-PAF1 spt5∆5::NatMX


title: lambdaN tethered PGL-3_rep1

description: Library name: Sample 15


title: lambdaN tethered RDE-1_rep2

description: Library name: Sample 20


title: lambdaN tethered MUT-16(ex773-1050)_rep2

description: Library name: Sample 14


title: Lung_O1

description: Gene expression


title: lambdaN tethered MUT-16(de773-1050)_rep2

description: Library name: Sample 12


title: Lung_Y2

description: Gene expression


title: lambdaN tethered PRG-1_rep1

description: Library name: Sample 17


title: lambdaN tethered MUT-16(de773-1050)_rep1

description: Library name: Sample 11


title: mAID-SPT5 , KY4793 , DMSO , 8WG16 , Rep2

description:
Library name: mAID_SPT5_KY4793_DMSO_8WG16_Rep2
MATa his3∆200::OsTIR-F74G-HIS3 lys2-128δ leu2∆1 ura3-52 3xHSV-PAF1 1xminiAID-SPT5


title: Liver_Y1

description: Gene expression


title: lambdaN tethered MUT-16_rep1

description: Library name: Sample 9


title: spt5delCTR , KY4894 , 8WG16 , Rep1

description:
Library name: spt5_delCTR_KY4894_8WG16_Rep1
MATalpha lys2-128δ leu2∆1 ura3-52 3xHSV-PAF1 spt5∆CTR::NatMX


title: spt5-S1-15D , KY3594 , 8WG16 , Rep2

description:
Library name: spt5_S1_15D_KY3594_8WG16_Rep2
MATa lys2-128δ leu2Δ1 ura3-52 3xHSV-PAF1 spt5-S1-15D


title: lambdaN tethered MUT-16(ex773-1050)_rep1

description: Library name: Sample 13


title: spt5-S1-15A , KY4912 , 8WG16 , Rep1

description:
Library name: spt5_S1_15A_KY4912_8WG16_Rep1
MATa lys2-128δ leu2∆1 ura3-52 3xHSV-PAF1 spt5-S1-15A


title: Lung_Y1

description: Gene expression


title: rde-3 mut-16(DE6R)_rep2

description: Library name: Sample 6

source_name: rde-3 mut-16(DE6R)

value: rde-3 mut-16(DE6R)


title: JW92_L

city: Milan

first: Loris

last: De Cecco

address: via Venezian 1

country: Italy

institute: IRCSS Istituto Nazionale Tumori

hyb_protocol: Standard Affymetrix hybridization protocol

scan_protocol: Standard Affymetrix scanning protocol

data_processing: Gene-level signal were derived from CEL files using sst-RMA algorithm implemente in Affymetrix Expression Console software

label: biotin

label_protocol: RNA from each sample was labeled according to the manufacturers recommendations (Affymetrix).

extract_protocol: RNA was extracted with miRNeasy FFPE kit (Qiagen) in accordance with the manufacture's protocol.

value: Larynx


title: JW95_OP_HPVneg

value: Oropharynx


title: JW50_L


title: lambdaN tethered MUT-16_rep2

description: Library name: Sample 10


title: JW24_OC

value: Oral Cavity


title: JQ42_OP_HPVpos


title: JQ60_HP

value: Hypopharynx


title: JW30_HP


title: JQ45_OC


title: JJ73_OP_HPVpos


title: JJ77_OP_HPVpos


title: WT_rep2

description: Library name: Sample 2

source_name: wild-type

value: wild-type


title: lambdaN tethered MUT-14_rep1

description: Library name: Sample 7


title: WT , KY4803 , 8WG16 , Rep1

description:
Library name: WT_KY4803_8WG16_Rep1
MATa lys2-128δ leu2∆1 ura3-52 3xHSV-PAF1


title: mut-16(DE6R)_rep2

description: Library name: Sample 4


title: mAID-SPT5 , KY4793 , IAA , 8WG16 , Rep2

description:
Library name: mAID_SPT5_KY4793_IAA_8WG16_Rep2
MATa his3∆200::OsTIR-F74G-HIS3 lys2-128δ leu2∆1 ura3-52 3xHSV-PAF1 1xminiAID-SPT5

value: 45 min


title: mut-16(DE6R)_rep1

description: Library name: Sample 3